334,606 results on '"Biology and life sciences"'
Search Results
2. Highlights in BioScience
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biology and life sciences ,chemical biology ,genetics ,biochemistry ,biophysics ,Biology (General) ,QH301-705.5 ,Biochemistry ,QD415-436 - Published
- 2022
3. Researchers from University of Agriculture Faisalabad Report on Findings in Biology and Life Sciences (Production and Acceptability of Jam Produced from Kiwi Fruit and Cucumber).
- Abstract
Researchers from the University of Agriculture Faisalabad in Pakistan have conducted a study on the production and acceptability of jam made from kiwi fruit and cucumber. The researchers aimed to create a unique and nutritious mixed fruit jam using these two ingredients due to their exceptional nutritional value. Through comprehensive analysis, they found that the jam made with a 50%:50% kiwi ratio stood out in terms of its physicochemical properties and sensory appeal. This kiwi-based jam is not only a healthy option but also a delicious spread that can be enjoyed by individuals of all ages. [Extracted from the article]
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- 2024
4. Research on Biology and Life Sciences Published by Researchers at Central Queensland University (Physicochemical and Nutritional Analysis of Molasses for Rum Fermentation).
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New research conducted at Central Queensland University focuses on the physicochemical and nutritional analysis of molasses for rum fermentation. The study found that the composition of molasses significantly influences the flavor, aroma, and alcohol content of the final rum product. The researchers analyzed molasses samples obtained from three storage wells and found that they contained high sugar concentrations, essential amino acids, vitamins, and various organic acids. However, there were variations in ash content, nitrogen compounds, and minerals between batches, suggesting the need for blending or standardization to minimize variation prior to fermentation. This study provides valuable information for optimizing the utilization of molasses in rum fermentation and other applications. [Extracted from the article]
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- 2024
5. Researchers from San Raffaele Open University Report Recent Findings in Biology and Life Sciences (Promoting Legume Consumption: Strategies for Health, Nutrition, and Culinary Applications).
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Researchers from San Raffaele Open University in Rome have published a report on strategies to promote the consumption of legumes for health, nutrition, and culinary applications. The report highlights innovative methods such as soaking, sprouting, and the use of advanced technologies to reduce anti-nutrients and improve digestibility. Culinary approaches, such as including legumes in salads and hummus, are also recommended to enhance palatability. The research concludes that combining science, culinary techniques, and education can lead to improved diet quality and health benefits through increased legume consumption. [Extracted from the article]
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- 2024
6. Research from University of Peradeniya Reveals New Findings on Biology and Life Sciences [An Assessment of the Bioactive Compounds and the Antioxidant, Anti-Inflammatory, and Antidiabetic Potential of Hydro-Methanolic Extracts Derived from Fresh...].
- Abstract
A recent study conducted by researchers at the University of Peradeniya in Sri Lanka has revealed the potential health benefits of Noni fruit. Noni, also known as Morinda citrifolia L., is a tropical fruit that has gained interest as a bioactive source. The study found that methanolic-extracted fresh Noni fruits have notable antioxidant, anti-inflammatory, and antidiabetic properties. Further exploration of the bioactive compounds in Noni could lead to innovative treatments for conditions related to oxidative stress, inflammation, and diabetes. [Extracted from the article]
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- 2024
7. Study Findings from Reggio Emilia Broaden Understanding of Biology and Life Sciences (Dietary Consumption of Edible Mushrooms for Disease Prevention: A Literature Overview).
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A study conducted in Reggio Emilia, Italy, explored the potential health benefits of consuming edible mushrooms as part of a balanced diet. The researchers reviewed five articles from PubMed and Google Scholar and found that regular mushroom consumption was associated with a reduced risk of neoplasms, particularly breast cancer, as well as improved glucose, lipid, and vitamin D levels. However, the studies did not find consistent effects on cholesterol levels, blood pressure, or body weight. The researchers concluded that including a serving of edible mushrooms in the diet two to three times a week may contribute to reducing the risk of cancer and metabolic diseases. They also suggested that further research should investigate the health effects of different mushroom species and determine the minimum amount needed for significant benefits. [Extracted from the article]
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- 2024
8. New Findings from University of Burgos in the Area of Biology and Life Sciences Described (Effects of a Functional Product Derived from Beet Molasses Vinasse on Blood Pressure and Endothelial Function in Hypertensive Rats).
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BLOOD pressure ,LIFE sciences ,LIFE (Biology) ,VINASSE ,BEETS - Abstract
A recent study conducted at the University of Burgos in Spain investigated the effects of a functional product derived from beet molasses vinasse on blood pressure and endothelial function in hypertensive rats. The researchers identified and quantified fifteen potential bioactive compounds in the product and found that the blood pressure values remained stable in the group of rats that received the product, while it increased in the control group. The ingestion of the vinasse-derived product led to decreased ACE mRNA levels and higher SOD2 and eNOS gene expression, resulting in an increased antioxidant, anti-inflammatory, and vasodilatory response. The study suggests that the intake of vinasse-derived products could potentially mitigate hypertension and associated endothelial dysfunction. [Extracted from the article]
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- 2024
9. Researchers at Instituto de Ciencia y Tecnologia de los Alimentos Have Published New Study Findings on Biology and Life Sciences (Impact of Manufacture and Digestion Process of Foods Enriched with Sesame Flour on the Antioxidant Response of...).
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ENRICHED foods ,LIFE sciences ,LIFE (Biology) ,RESEARCH personnel ,MANUFACTURING processes - Abstract
Researchers at the Instituto de Ciencia y Tecnologia de los Alimentos in Cordoba, Argentina, have conducted a study on the impact of the manufacture and digestion process of foods enriched with sesame flour on the antioxidant response of human hepatocytes. The study found that sesame flour may promote antioxidant response and provide preventive benefits and protective action against oxidative damage. The study also demonstrated that the actions of sesame flour on the redox state vary depending on the food matrix and its degree of digestion. The research highlights the need to improve knowledge of the biological actions of certain metabolites in food and the impact of digestion on their effective role in health. [Extracted from the article]
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- 2024
10. Researchers from Cukurova University Detail Research in Biology and Life Sciences (The Potential Use of Synbiotic Combinations in Bread-A Review).
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LIFE sciences ,RESEARCH personnel ,LIFE (Biology) ,SYNBIOTICS ,UNIVERSITY research - Abstract
A recent study conducted by researchers from Cukurova University in Adana, Turkey, explores the potential use of synbiotic combinations in bread. The study highlights the commonly used probiotics in these combinations, such as Lactobacillaceae and Bifidobacteriaceae, but also suggests the potential use of heat-resistant bacteria like Bacillus coagulans and probiotic yeast like Saccharomyces boulardii. Inulin is identified as the most commonly used prebiotic source in these bread formulations, and co-encapsulations of probiotics with prebiotics could be beneficial. While there are some health benefits for diabetics consuming synbiotic bread, further comprehensive clinical trials are needed. [Extracted from the article]
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- 2024
11. Trial watch: chemotherapy-induced immunogenic cell death in oncology
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Sprooten, Jenny, Laureano, Raquel S., Vanmeerbeek, Isaure, Govaerts, Jannes, Naulaerts, Stefan, Borras, Daniel M., Kinget, Lisa, Fucikova, Jitka, Spisek, Radek, Jelinkova, Lenka Palova, Kepp, Oliver, Kroemer, Guido, Krysko, Dmitri V., Coosemans, An, Vaes, Rianne D.W., De Ruysscher, Dirk, De Vleeschouwer, Steven, Wauters, Els, Smits, Evelien, Tejpar, Sabine, Beuselinck, Benoit, Hatse, Sigrid, Wildiers, Hans, Clement, Paul M., Vandenabeele, Peter, Zitvogel, Laurence, and Garg, Abhishek D.
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dendritic cell ,Immunology ,chemotherapy ,danger signals ,ENDOPLASMIC-RETICULUM STRESS ,immunogenic cell death ,Medicine and Health Sciences ,ANTITUMOR IMMUNITY ,cancer ,antigen-presenting cells ,immune-checkpoint blockers ,DAMPs ,CAR T cells ,CALRETICULIN EXPOSURE ,Science & Technology ,I INTERFERON ,HIGH-MOBILITY GROUP ,Biology and Life Sciences ,ER STRESS ,SOLID TUMORS ,NEGATIVE BREAST-CANCER ,Oncology ,cancer therapy ,Human medicine ,trial watch ,immunotherapy ,Life Sciences & Biomedicine ,MESOTHELIN - Abstract
Immunogenic cell death (ICD) refers to an immunologically distinct process of regulated cell death that activates, rather than suppresses, innate and adaptive immune responses. Such responses culminate into T cell-driven immunity against antigens derived from dying cancer cells. The potency of ICD is dependent on the immunogenicity of dying cells as defined by the antigenicity of these cells and their ability to expose immunostimulatory molecules like damage-associated molecular patterns (DAMPs) and cytokines like type I interferons (IFNs). Moreover, it is crucial that the host's immune system can adequately detect the antigenicity and adjuvanticity of these dying cells. Over the years, several well-known chemotherapies have been validated as potent ICD inducers, including (but not limited to) anthracyclines, paclitaxels, and oxaliplatin. Such ICD-inducing chemotherapeutic drugs can serve as important combinatorial partners for anti-cancer immunotherapies against highly immuno-resistant tumors. In this Trial Watch, we describe current trends in the preclinical and clinical integration of ICD-inducing chemotherapy in the existing immuno-oncological paradigms. ispartof: ONCOIMMUNOLOGY vol:12 issue:1 ispartof: location:United States status: accepted
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- 2023
12. Machine Learning and Gene Editing at the Helm of a Societal Evolution.
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Zakaria S, Marler T, Cabling M, Genc S, Honich A, Virdee M, and Stockwell S
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The integration of artificial intelligence (AI) and biotechnology, whilst in its infancy, presents significant opportunities and risks, and proactive policy is needed to manage these emerging technologies. Whilst AI continues to have significant and broad impact, its relevance and complexity magnify when integrated with other emerging technologies. The confluence of Machine Learning (ML), a subset of AI, with gene editing (GE) in particular can foster substantial benefits as well as daunting risks that range from ethics to national security. These complex technologies have implications for multiple sectors, ranging from agriculture and medicine to economic competition and national security. Consideration of technology advancements and policies in different geographic regions, and involvement of multiple organisations further confound this complexity. As the impact of ML and GE expands, forward looking policy is needed to mitigate risks and leverage opportunities. Thus, this study explores the technological and policy implications of the intersection of ML and GE, with a focus on the United States (US), the United Kingdom (UK), China, and the European Union (EU). Analysis of technical and policy developments over time and an assessment of their current state have informed policy recommendations that can help manage beneficial use of technology advancements and their convergence, which can be applied to other sectors. This study is intended for policymakers to prompt reflection on how to best approach the convergence of the two technologies. Technical practitioners may also find it valuable as a resource to consider the type of information and policy stakeholders engage with., (Copyright © 2024 RAND Corporation.)
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- 2024
13. Encyclopedia
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biology and life sciences ,earth sciences ,physical sciences ,materials science ,chemistry ,medicine and pharmacology ,Science - Published
- 2021
14. Researchers from University of Barcelona Discuss Findings in Biology and Life Sciences (Mediterranean-like Diet May Modulate Acute Inflammation in Wistar Rats).
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A recent study conducted by researchers from the University of Barcelona explored the impact of a Mediterranean-like diet on acute inflammation in Wistar rats. The Mediterranean diet is known for its rich content of bioactive and immunomodulatory components, some of which have shown protective activity against inflammation. The study involved two groups of rats, one receiving the experimental diet and the other a reference diet. The results indicated that the rats on the Mediterranean-like diet exhibited lower paw volume during an induced inflammatory process. This research provides insights into the potential benefits of a Mediterranean diet in modulating inflammation. [Extracted from the article]
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- 2024
15. I.M. Sechenov First Moscow State Medical University Researchers Provide Details of New Studies and Findings in the Area of Biology and Life Sciences (Precision Neuronutrition: Personalized Approaches for Optimizing Brain Health).
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Researchers from I.M. Sechenov First Moscow State Medical University have conducted a study on precision neuronutrition, which aims to identify personalized nutrient requirements to optimize brain health and prevent neurological disorders. The study highlights the main pathological mechanisms of brain health disruption, including neuroinflammation, oxidative stress, gut-brain disturbances, and nutrient deficiencies. The researchers suggest that precision interventions such as omega-3 fatty acids, vitamin B12, vitamin D, magnesium, coenzyme q10, polyphenols, l-carnitine, prebiotics, and probiotics can help maintain brain health and improve outcomes. Continued research in this field holds great potential for improving brain health outcomes. [Extracted from the article]
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- 2024
16. New Biology and Life Sciences Study Results from European University of Madrid Described [Associations between Vitamin D Receptor (VDR) Polymorphisms and Gut Microbiota in a Spanish Population Sample].
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A study conducted by the European University of Madrid examined the relationship between genetic variations in the Vitamin D Receptor (VDR) gene and the composition of gut microbiota in a Spanish population. The researchers found that the genetic variations were in Hardy-Weinberg equilibrium and that the GG genotype from the VDR polymorphism rs731236 was associated with the opportunistic genus Solobacterium. This suggests that genetic variations may influence the composition of gut microbiota. The study provides valuable insights into the potential role of vitamin D in gut health. [Extracted from the article]
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- 2024
17. Pharmacokinetics and depletion of florfenicol in striped catfish Pangasianodon hypophthalmus after oral administration
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Quang Vinh Pham, Quoc Thinh Nguyen, Mathias Devreese, Siska Croubels, Thi Hoang Oanh Dang, Anders Dalsgaard, Masashi Maita, and Minh Phu Tran
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Florfenicol ,Withdrawal time ,Biology and Life Sciences ,Pharmacokinetic ,Aquatic Science ,Striped catfish - Abstract
Florfenicol is commonly used to treat bacterial diseases in striped catfish Pangasianodon hypophthalmus aquaculture with limited knowledge of pharmacokinetic database, explaining treatment failures experienced by farmers. Striped catfish (100 g) were fed medicated feed (10 mg florfenicol/kg fish) by oral gavage. Plasma, liver, and kidney were collected up to 96.0 h after drug administration and analyzed for florfenicol. A single oral gavage dose of 10 mg florfenicol/kg fish revealed a rapid elimination, demonstrated by an elimination half-life (T-1/2el) of 2.56 h. Florfenicol amine was found in liver and kidney tissue. The calculation of T > MIC (time that the concentration remains above the minimum inhibitory concentration) revealed a potential therapeutic effect on bacillary necrosis, a common disease in striped catfish if the dosing interval is 12 h. The depletion of florfenicol in striped catfish muscle was determined in feeding trials with medicated feed containing florfenicol at 10 mg/kg fish for five consecutive days in tank and pond conditions. The fast elimination of florfenicol resulted in a withdrawal time of two days (or 39 degree days) in proposed tank-rearing conditions and four days (or 112 degree days) in pond-rearing conditions.
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- 2023
18. C-terminal frameshift variant of TDP-43 with pronounced aggregation-propensity causes rimmed vacuole myopathy but not ALS/FTD
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Pedro Ervilha Pereira, Nika Schuermans, Antoon Meylemans, Pontus LeBlanc, Lauren Versluys, Katie E. Copley, Jack D. Rubien, Christopher Altheimer, Myra Peetermans, Elke Debackere, Olivier Vanakker, Sandra Janssens, Jonathan Baets, Kristof Verhoeven, Martin Lammens, Sofie Symoens, Boel De Paepe, Sami J. Barmada, James Shorter, Jan L. De Bleecker, Elke Bogaert, and Bart Dermaut
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Cellular and Molecular Neuroscience ,TDP-43 ,Myopathy ,Medicine and Health Sciences ,Phase separation ,Genetics ,Biology and Life Sciences ,Drosophila ,FTD ,Human medicine ,Neurology (clinical) ,ALS ,Pathology and Forensic Medicine - Abstract
Neuronal TDP-43-positive inclusions are neuropathological hallmark lesions in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Pathogenic missense variants in TARDBP, the gene encoding TDP-43, can cause ALS and cluster in the C-terminal prion-like domain (PrLD), where they modulate the liquid condensation and aggregation properties of the protein. TDP-43-positive inclusions are also found in rimmed vacuole myopathies, including sporadic inclusion body myositis, but myopathy-causing TDP-43 variants have not been reported. Using genome-wide linkage analysis and whole exome sequencing in an extended five-generation family with an autosomal dominant rimmed vacuole myopathy, we identified a conclusively linked frameshift mutation in TDP-43 producing a C-terminally altered PrLD (TDP-43p.Trp385IlefsTer10) (maximum multipoint LOD-score 3.61). Patient-derived muscle biopsies showed TDP-43-positive sarcoplasmic inclusions, accumulation of autophagosomes and transcriptomes with abnormally spliced sarcomeric genes (including TTN and NEB) and increased expression of muscle regeneration genes. In vitro phase separation assays demonstrated that TDP-43Trp385IlefsTer10 does not form liquid-like condensates and readily forms solid-like fibrils indicating increased aggregation propensity compared to wild-type TDP-43. In Drosophila TDP-43p.Trp385IlefsTer10 behaved as a partial loss-of-function allele as it was able to rescue the TBPH (fly ortholog of TARDBP) neurodevelopmental lethal null phenotype while showing strongly reduced toxic gain-of-function properties upon overexpression. Accordingly, TDP-43p.Trp385IlefsTer10 showed reduced toxicity in a primary rat neuron disease model. Together, these genetic, pathological, in vitro and in vivo results demonstrate that TDP-43p.Trp385IlefsTer10 is an aggregation-prone partial loss-of-function variant that causes autosomal dominant vacuolar myopathy but not ALS/FTD. Our study genetically links TDP-43 proteinopathy to myodegeneration, and reveals a tissue-specific role of the PrLD in directing pathology.
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- 2023
19. Intraspecific diversity in the mechanisms underlying abamectin resistance in a cosmopolitan pest
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Ernesto Villacis-Perez, Marilou Vandenhole, Wannes Dermauw, Wenxin Xue, Berdien De Beer, and Thomas Van Leeuwen
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TETRANYCHUS-URTICAE ,glutamate-gated chloride channel ,2-SPOTTED SPIDER-MITE ,Biology and Life Sciences ,abamectin ,insecticide resistance ,Tetranychus urticae ,CROSS-RESISTANCE ,GATED CHLORIDE CHANNEL ,TARGET-SITE RESISTANCE ,acaricide resistance ,bulked segregant analysis ,intraspecific variation ,TRANSPOSABLE ELEMENTS ,Genetics ,URTICAE KOCH ACARI ,experimental evolution ,BIOCHEMICAL-MECHANISMS ,PLUTELLA-XYLOSTELLA ,General Agricultural and Biological Sciences ,Ecology, Evolution, Behavior and Systematics - Abstract
Pesticide resistance relies on a myriad of mechanisms, ranging from single mutations to a complex and polygenic architecture, and it involves mechanisms such as target-site insensitivity, metabolic detoxification, or a combination of these, with either additive or synergistic effects. Several resistance mechanisms against abamectin, a macrocyclic lactone widely used in crop protection, have been reported in the cosmopolitan pestTetranychus urticae. However, it has been shown that a single mechanism cannot account for the high levels of abamectin resistance found across different mite populations. Here, we used experimental evolution combined with bulked segregant analyses to map quantitative trait loci (QTL) associated with abamectin resistance in two genetically unrelated strains ofT. urticae. In these two independent QTL mapping experiments, three and four QTLs were identified, of which three were shared between experiments. Shared QTLs contained genes encoding subunits of the glutamate-gated chloride channel (GluCl) and harboured previously reported mutations, including G314D inGluCl1and G326E inGluCl3, but also novel resistance candidate loci, including DNA helicases and chemosensory receptors. Surprisingly, the fourth QTL, present only in only one of the experiments and thus unique for one parental resistant strain, revealed a non-functional variant ofGluCl2, suggesting gene knock-out as resistance mechanism. Our study uncovers the complex basis of abamectin resistance, and it highlights the intraspecific diversity of genetic mechanisms underlying resistance in a cosmopolitan pest.
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- 2023
20. Engineering strategies for insect viruses and microbes for dsRNA production and delivery to insects for targeted gene silencing
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Qi Xue, Ericmar Avila Dos Santos, Guy Smagghe, Moises João Zotti, and Clauvis Nji Tizi Taning
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Pest control ,VIGS ,Delivery systems ,RNAi ,Insect Science ,Microalgae ,Biology and Life Sciences - Abstract
RNA interference (RNAi)-based pest control is viewed as a safe and effective method for insect pest control. However, the stability and efficient cellular delivery of the double stranded RNA (dsRNA) active molecule remains cru- cial to its success in pest control. Among the different approaches that have been proposed to improve dsRNA delivery in insects, the use of nano-carriers, engineered viruses and engineered microbes have been successfully employed in proof of-concept studies. This review focuses on engineering approaches that have been successfully employed to modify insect viruses and different microbes for dsRNA production and delivery in insects. First, the different viral vector systems based on insect RNA and DNA viruses for dsRNA delivery are discussed. Second, a comprehensive overview of different microbe-based (bacteria, fungi, microalgae) dsRNA production and delivery systems that have been developed till date are presented. Finally, future perspectives on the development of other delivery systems with potential in the context of insect pest control are provided. Overall, this review is expected to stimulate awareness, interest, insight and research into prom- ising sources of biotechnologically interesting viruses and microbes for protecting agriculture and human health against insect pests.
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- 2023
21. No Effect of Acute Balenine Supplementation on Maximal and Submaximal Exercise Performance in Recreational Cyclists
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Sarah de Jager, Stefaan Van Damme, Siegrid De Baere, Siska Croubels, Ralf Jäger, Martin Purpura, Eline Lievens, Jan G. Bourgois, and Wim Derave
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(sports) nutrition ,Nutrition and Dietetics ,histidine-containing dipeptides ,Medicine and Health Sciences ,cycling time trial ,Biology and Life Sciences ,Medicine (miscellaneous) ,Orthopedics and Sports Medicine ,General Medicine ,Exercise physiology ,balenine ingestion ,ergogenic supplement - Abstract
Carnosine (β-alanyl-L-histidine) and its methylated analogues anserine and balenine are highly concentrated endogenous dipeptides in mammalian skeletal muscle that are implicated in exercise performance. Balenine has a much better bioavailability and stability in human circulation upon acute ingestion, compared to carnosine and anserine. Therefore, ergogenic effects observed with acute carnosine and anserine supplementation may be even more pronounced with balenine. This study investigated whether acute balenine supplementation improves physical performance in four maximal and submaximal exercise modalities. A total of 20 healthy, active volunteers (14 males; six females) performed cycling sprints, maximal isometric contractions, a 4-km TT and 20-km TT following either preexercise placebo or 10 mg/kg of balenine ingestion. Physical, as well as mental performance, along with acid–base balance and glucose concentration were assessed. Balenine was unable to augment peak power (p = .3553), peak torque (p = .3169), time to complete the 4 km (p = .8566), nor 20 km time trial (p = .2660). None of the performances were correlated with plasma balenine or CN1 enzyme activity. In addition, no effect on pH, bicarbonate, and lactate was observed. Also, the supplement did not affect mental performance. In contrast, glucose remained higher during and after the 20 km time trial following balenine ingestion. In conclusion, these results overall indicate that the functionality of balenine does not fully resemble that of carnosine and anserine, since it was unable to elicit performance improvements with similar and even higher plasma concentrations.
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- 2023
22. Atm deficient zebrafish model reveals conservation of the tumour suppressor function and a role in fertility
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Jeroen Vierstraete, Charlotte Fieuws, David Creytens, Jo Van Dorpe, Andy Willaert, Anne Vral, and Kathleen BM Claes
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Medicine and Health Sciences ,Biology and Life Sciences ,Cell Biology ,Molecular Biology ,Biochemistry ,Genetics (clinical) - Published
- 2023
23. Specification and evolution of lateral roots
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Abdellah Lakehal, Asma Dob, and Tom Beeckman
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Biology and Life Sciences ,General Agricultural and Biological Sciences ,General Biochemistry, Genetics and Molecular Biology - Abstract
Plants have evolved a remarkable capacity to develop new organs post-embryonically throughout their lifespan. A prime example of this is root branching. Root branching occurs in two ways: dichotomous and lateral branching. The dichotomous branching is the result of the division of the root apical meristem into two daughter meristems, likely through symmetric cell divisions of the root apical cell, as has recently been illustrated in the extant lycophyte Selaginella moellendorffii (Figure 1). Lateral root branching relies on the de novo specification of a subset of founder cells (hereinafter referred to as lateral root stem cells) located in the internal tissues of an existing root. This step is followed by initiation, in which the specified cells re-enter the cell cycle, and subsequently by primordium formation and emergence. In this primer, we summarize recent advances describing the molecular bases underlying lateral root stem cell specification in angiosperms and highlight the important positional signals that fine tune this process. By delving into the evolutionary origins of root branching, we point out that positional control of lateral root stem cell specification has not been the prevailing mechanism among all plants and discuss the process in ferns (i.e., a sister group of seed plants), where it seems to be under the control of lineage-dependent mechanisms.
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- 2023
24. Charting plant gene functions in the multi-omics and single-cell era
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Thomas Depuydt, Bert De Rybel, and Klaas Vandepoele
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gene function ,machine learning ,networks ,Biology and Life Sciences ,Plant Science ,multi-omics ,single-cell ,data integration - Abstract
Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.
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- 2023
25. <scp>PhenoWell</scp> ®—A novel screening system for soil‐grown plants
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Ji Li, Michael A. C. Mintgen, Sam D'Haeyer, Anne Helfer, Hilde Nelissen, Dirk Inzé, and Stijn Dhondt
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high-throughput screening assays ,phytohormones ,plant leaves ,abiotic stress ,nutrients ,seedlings ,Arabidopsis ,growth and development ,Biology and Life Sciences ,maize ,General Agricultural and Biological Sciences ,soil - Abstract
As agricultural production is reaching its limits regarding outputs and land use, the need to further improve crop yield is greater than ever. The limited translatability from in vitro lab results into more natural growth conditions in soil remains problematic. Although considerable progress has been made in developing soil-growth assays to tackle this bottleneck, the majority of these assays use pots or whole trays, making them not only space- and resource-intensive, but also hampering the individual treatment of plants. Therefore, we developed a flexible and compact screening system named PhenoWell® in which individual seedlings are grown in wells filled with soil allowing single-plant treatments. The system makes use of an automated image-analysis pipeline that extracts multiple growth parameters from individual seedlings over time, including projected rosette area, relative growth rate, compactness, and stockiness. Macronutrient, hormone, salt, osmotic, and drought stress treatments were tested in the PhenoWell® system. The system is also optimized for maize with results that are consistent with Arabidopsis while different in amplitude. We conclude that the PhenoWell® system enables a high-throughput, precise, and uniform application of a small amount of solution to individually soil-grown plants, which increases the replicability and reduces variability and compound usage.
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- 2023
26. 25 years after Dolly: Update on long‐term effects of embryo biotechnologies
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Pascale Chavatte‐Palmer and Catharina De Schauwer
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intra-cytoplasmic ,IN-VITRO CULTURE ,Biology and Life Sciences ,ARTIFICIAL-INSEMINATION ,CELL NUCLEAR TRANSFER ,INTRACYTOPLASMIC SPERM INJECTION ,cryopreservation ,programming ,ASSISTED REPRODUCTIVE TECHNOLOGIES ,TRANSCRIPTOME PROFILE ,in-vitro fertilisation ,LARGE OFFSPRING SYNDROME ,Endocrinology ,ORIGINS ,PICK-UP ,Animal Science and Zoology ,Veterinary Sciences ,animal reproductive technologies ,DEVELOPMENTAL ,periconception ,OVUM ,GENE-EXPRESSION ,sperm injection ,Biotechnology - Abstract
Since the announcement of the birth of Dolly, the world's first mammal produced by cloning, it was demonstrated for the first time that somatic cells could be reprogrammed to produce a whole individual. This represented a considerable change in paradigm in the field of embryo technologies both in humans and animals which led to an intense burst of research on nuclear transfer but also on the establishment of pluripotency and the directed edition of the genome. As such, induced pluripotent cells and gene editing tools, the best known being CRISPR-Cas9, are now available to the scientific community. Nevertheless, cloning was associated with important developmental abnormalities in a variable proportion of pregnancies, raising concern about the long-term effects of embryo technologies at a time when the concept of the developmental origins of health and disease had emerged, together with a better understanding of the underlying epigenetic modifications. The focus of this article is to review current knowledge on long-term effects of artificial reproduction technologies in mammals, leading to globally reassuring information although differences are present and caution remains necessary taking the current increasing number of in vitro-produced ruminant and equine embryos into account and their potential intergenerational consequences.
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- 2023
27. Dynamic GOLVEN-ROOT GROWTH FACTOR 1 INSENSITIVE signaling in the root cap mediates root gravitropism
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Ke Xu, Joris Jourquin, Xiangyu Xu, Ive De Smet, Ana I Fernandez, Tom Beeckman, and Testerink, Christa
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Physiology ,root gravitropism ,auxin transport ,Biology and Life Sciences ,Plant Science ,ARABIDOPSIS ,GENE ,TRANSPORT ,RGF peptides ,LATERAL ROOT ,TRANSDUCTION PATHWAY ,PIN2 ,RGI receptors ,lateral root cap ,AUXIN EFFLUX CARRIER ,GOLVEN peptides ,PEPTIDE-HORMONES ,GRAVITY ,Genetics ,PLANT - Abstract
Throughout the exploration of the soil, roots interact with their environment and adapt to different conditions. Directional root growth is guided by asymmetric molecular patterns but how these become established or are dynamically regulated is poorly understood. Asymmetric gradients of the phytohormone auxin are established during root gravitropism, mainly through directional transport mediated by polarized auxin transporters. Upon gravistimulation, PIN-FORMED2 (PIN2) is differentially distributed and accumulates at the lower root side to facilitate asymmetric auxin transport up to the elongation zone where it inhibits cell elongation. GOLVEN (GLV) peptides function in gravitropism by affecting PIN2 abundance in epidermal cells. In addition, GLV signaling through ROOT GROWTH FACTOR 1 INSENSITIVE (RGI) receptors regulates root apical meristem maintenance. Here, we show that GLV-RGI signaling in these 2 processes in Arabidopsis (Arabidopsis thaliana) can be mapped to different cells in the root tip and that, in the case of gravitropism, it operates mainly in the lateral root cap (LRC) to maintain PIN2 levels at the plasma membrane (PM). Furthermore, we found that GLV signaling upregulates the phosphorylation level of PIN2 in an RGI-dependent manner. In addition, we demonstrated that the RGI5 receptor is asymmetrically distributed in the LRC and accumulates in the lower side of the LRC after gravistimulation. Asymmetric GLV-RGI signaling in the root cap likely accounts for differential PIN2 abundance at the PM to temporarily support auxin transport up to the elongation zone, thereby representing an additional level of control on the asymmetrical auxin flux to mediate differential growth of the root.
- Published
- 2023
28. Insights into the Stabilization of Interferon Alpha by Two Surfactants Revealed by STD-NMR Spectroscopy
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Hristo L. Svilenov, Katharina T. Kopp, Alexander P. Golovanov, Gerhard Winter, and Matja Zalar
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Chemistry ,spectroscopy ,Nuclear Magnetic Resonance (NMR) ,Protein(s) ,Drug-excipient interaction(s) ,Protein formulation(s) ,Medicine and Health Sciences ,Biology and Life Sciences ,Pharmaceutical Science ,Surfactant(s) ,Protein aggregation - Abstract
Surfactants are commonly used in biopharmaceutical formulations to stabilize proteins against aggregation. However, the choice of a suitable surfactant for a particular protein is decided mostly empirically, and their mechanism of action on molecular level is largely unknown. Here we show that a straightforward label-free method, saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy, can be used to detect protein-surfactant interactions in formulations of a model protein, interferon alpha. We find that polysorbate 20 binds with its fatty acid to interferon, and that the binding is stronger at pH closer to the isoelectric point of the protein. In contrast, we did not detect interactions between poloxamer 407 and interferon alpha. Neither of the two surfactants affected the tertiary structure and the thermal stability of the protein as evident from circular dichroism and nanoDSF measurements. Interestingly, both surfactants inhibited the formation of subvisible particles during long-term storage, but only polysorbate 20 reduced the amount of small soluble aggregates detected by size-exclusion chromatography. This proof-of-principle study demonstrates how STD-NMR can be employed to quickly assess surfactant-protein interactions and support the choice of surfactant in protein formulation.
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- 2023
29. Small heat shock proteins operate as molecular chaperones in the mitochondrial intermembrane space
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Elias Adriaenssens, Bob Asselbergh, Pablo Rivera-Mejías, Sven Bervoets, Leen Vendredy, Vicky De Winter, Katrien Spaas, Riet de Rycke, Gert van Isterdael, Francis Impens, Thomas Langer, and Vincent Timmerman
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Medicine and Health Sciences ,Biology and Life Sciences ,Human medicine ,Cell Biology ,Biology - Abstract
Adriaenssens et al. provide evidence suggesting that cytosolic small heat shock proteins localize to the mitochondrial intermembrane space, where they operate as molecular chaperones. Mitochondria are complex organelles with different compartments, each harbouring their own protein quality control factors. While chaperones of the mitochondrial matrix are well characterized, it is poorly understood which chaperones protect the mitochondrial intermembrane space. Here we show that cytosolic small heat shock proteins are imported under basal conditions into the mitochondrial intermembrane space, where they operate as molecular chaperones. Protein misfolding in the mitochondrial intermembrane space leads to increased recruitment of small heat shock proteins. Depletion of small heat shock proteins leads to mitochondrial swelling and reduced respiration, while aggregation of aggregation-prone substrates is countered in their presence. Charcot-Marie-Tooth disease-causing mutations disturb the mitochondrial function of HSPB1, potentially linking previously observed mitochondrial dysfunction in Charcot-Marie-Tooth type 2F to its role in the mitochondrial intermembrane space. Our results reveal that small heat shock proteins form a chaperone system that operates in the mitochondrial intermembrane space.
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- 2023
30. The transcription factor AtMYB12 is part of a feedback loop regulating cell division orientation in the root meristem vasculature
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Brecht Wybouw, Helena E Arents, Baojun Yang, Jonah Nolf, Wouter Smet, Michael Vandorpe, Max Minne, Xiaopeng Luo, Inge De Clercq, Daniël Van Damme, Matouš Glanc, Bert De Rybel, and Turner, Simon
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EMS screen ,cytokinin ,Arabidopsis thaliana ,root development ,Physiology ,transcription factors ,Biology and Life Sciences ,Plant Science ,vascular development - Abstract
Transcriptional networks are crucial to integrate various internal and external signals into optimal responses during plant growth and development. In Arabidopsis thaliana, primary root vasculature patterning and proliferation are controlled by a network centred around the basic Helix-Loop-Helix transcription factor complex, formed by TARGET OF MONOPTEROS 5 (TMO5) and LONESOME HIGHWAY (LHW), which control cell proliferation and division orientation by modulating the cytokinin response and other downstream factors. Despite recent progress, many aspects of the TMO5/LHW pathway are not fully understood. In particular, the upstream regulators of TMO5/LHW activity remain unknown. Here, using a forward genetics approach to identify new factors of the TMO5/LHW pathway, we discovered a novel function of the MYB-type transcription factor, MYB12. MYB12 physically interacts with TMO5 and dampens the TMO5/LHW-mediated induction of direct target gene expression, as well as the periclinal/radial cell divisions. The expression of MYB12 is activated by the cytokinin response, downstream of TMO5/LHW, resulting in a novel MYB12-mediated negative feedback loop that restricts TMO5/LHW activity, to ensure optimal cell proliferation rates during root vascular development.
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- 2023
31. In vivo inhibition of epileptiform afterdischarges in rat hippocampus by light‐activated chloride channel, <scp>stGtACR2</scp>
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Anirudh R. Acharya, Lars Emil Larsen, Jean Delbeke, Wytse J. Wadman, Kristl Vonck, Alfred Meurs, Paul Boon, and Robrecht Raedt
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STIMULATION ,INTERNEURONS ,Pharmacology ,chloride ,LEVELS ,hippocampus ,Biology and Life Sciences ,CL-TRANSPORTERS ,MECHANISMS ,afterdischarges ,Psychiatry and Mental health ,Physiology (medical) ,OPTOGENETIC CONTROL ,ANOMALOUS ,Medicine and Health Sciences ,SEIZURE ,GtACR2 ,Pharmacology (medical) ,BRAIN-RESPONSIVE NEUROSTIMULATION ,optogenetics ,EPILEPSY ,THALAMUS ,seizures - Abstract
AimsThe blue light-sensitive chloride-conducting opsin, stGtACR2, provides potent optogenetic silencing of neurons. The present study investigated whether activation of stGtACR2 in granule cells of the dentate gyrus (DG) inhibits epileptic afterdischarges in a rat model. MethodsRats were bilaterally injected with 0.9 mu l of AAV2/7-CaMKII alpha-stGtACR2-fusionred in the DG. Three weeks later, afterdischarges were recorded from the DG by placing an optrode at the injection site and a stimulation electrode in the perforant path (PP). Afterdischarges were evoked every 10 min by unilateral electrical stimulation of the PP (20 Hz, 10 s). During every other afterdischarge, the DG was illuminated for 5 or 30 s, first ipsilaterally and then bilaterally to the PP stimulation. The line length metric of the afterdischarges was compared between illumination conditions. ResultsIpsilateral stGtACR2 activation during afterdischarges decreased the local field potential line length only during illumination and specifically at the illuminated site but did not reduce afterdischarge duration. Bilateral illumination did not terminate the afterdischarges. ConclusionOptogenetic inhibition of excitatory neurons using the blue-light sensitive chloride channel stGtACR2 reduced the amplitude of electrically induced afterdischarges in the DG at the site of illumination, but this local inhibitory effect was insufficient to reduce the duration of the afterdischarge.
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- 2022
32. The endocytic TPLATE complex internalizes ubiquitinated plasma membrane cargo
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Peter Grones, Andreas De Meyer, Roman Pleskot, Evelien Mylle, Michael Kraus, Michael Vandorpe, Klaas Yperman, Dominique Eeckhout, Jonathan Michael Dragwidge, Qihang Jiang, Jonah Nolf, Benjamin Pavie, Geert De Jaeger, Bert De Rybel, and Daniël Van Damme
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POLAR LOCALIZATION ,DEUBIQUITINATING ENZYME AMSH3 ,BORATE TRANSPORTER BOR1 ,BRASSINOSTEROID INSENSITIVE1 ,INTRACELLULAR TRAFFICKING ,Biology and Life Sciences ,RECOGNITION RECEPTOR FLS2 ,SOMATIC CYTOKINESIS ,Plant Science ,DEPENDENT ENDOCYTOSIS ,CLATHRIN-MEDIATED ENDOCYTOSIS ,Article ,CELLULOSE SYNTHASE - Abstract
Endocytosis controls the perception of stimuli by modulating protein abundance at the plasma membrane. In plants, clathrin-mediated endocytosis is the most prominent internalization pathway and relies on two multimeric adaptor complexes, the AP-2 and the TPLATE complex (TPC). Ubiquitination is a well-established modification triggering endocytosis of cargo proteins, but how this modification is recognized to initiate the endocytic event remains elusive. Here, we show that TASH3, one of the large subunits of TPC, recognizes ubiquitinated cargo at the plasma membrane via its SH3 domain-containing appendage. TASH3 lacking this evolutionary specific appendage modification allows TPC formation, but the plants show severely reduced endocytic densities, which correlates with reduced endocytic flux. Moreover, comparative plasma membrane proteomics identified differential accumulation of multiple ubiquitinated cargo proteins for which we confirm altered trafficking. Our findings position TPC as a key player for ubiquitinated cargo internalization, allowing future identification of target proteins under specific stress conditions.
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- 2022
33. Clinical, splicing and functional analysis to classify BRCA2 exon 3 variants
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Thomassen, M., Mesman, R.L.S., Hansen, T.V.O., Menendez, M., Rossing, M., Esteban-Sanchez, A., Tudini, E., Torngren, T., Parsons, M.T., Pedersen, I.S., Teo, S.H., Kruse, T.A., Moller, P., Borg, A., Jensen, U.B., Christensen, L.L., Singer, C.F., Muhr, D., Santamarina, M., Brandao, R., Andresen, B.S., Feng, B.J., Canson, D., Richardson, M.E., Karam, R., Pesaran, T., LaDuca, H., Conner, B.R., Abualkheir, N., Hoang, L., Calleja, F.M.G.R., Andrews, L., James, P.A., Bunyan, D., Hamblett, A., Radice, P., Goldgar, D.E., Walker, L.C., Engel, C., Claes, K.B.M., Machackova, E., Baralle, D., Viel, A., Wappenschmidt, B., Lazaro, C., Vega, A., Vreeswijk, M.P.G., Hoya, M. de la, Spurdle, A.B., ENIGMA Consortium, RS: GROW - R4 - Reproductive and Perinatal Medicine, and Klinische Genetica
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splicing ,AMP classification ,quantitation ,ACMG/AMP classification ,dPCR ,ACMG ,Medicine and Health Sciences ,Genetics ,Biology and Life Sciences ,BRCA2 ,Genetics (clinical) ,functional analysis - Abstract
Skipping of BRCA2 exon 3 (∆E3) is a naturally occurring splice event, complicating clinical classification of variants that may alter ∆E3 expression. This study used multiple evidence types to assess pathogenicity of 85 variants in/near BRCA2 exon 3. Bioinformatically predicted spliceogenic variants underwent mRNA splicing analysis using minigenes and/or patient samples. ∆E3 was measured using quantitative analysis. A mouse embryonic stem cell (mESC) based assay was used to determine the impact of 18 variants on mRNA splicing and protein function. For each variant, population frequency, bioinformatic predictions, clinical data and existing mRNA splicing and functional results were collated. Variant class was assigned using a gene-specific adaptation of ACMG/AMP guidelines, following a recently proposed points-based system. mRNA and mESC analysis combined identified six variants with transcript and/or functional profiles interpreted as loss of function. Cryptic splice site use for acceptor site variants generated a transcript encoding a shorter protein that retains activity. Overall, 69/85 (81%) variants were classified using the point-based approach. Our analysis shows the value of applying gene-specific ACMG/AMP guidelines using a points-based approach and highlights the consideration of cryptic splice site usage to appropriately assign PVS1 code strength. This article is protected by copyright. All rights reserved.
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- 2022
34. Laryngoscopy mediated stress response induces opposite effects on cerebral and paraspinal oxygen saturation
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Vanpeteghem, Caroline, De Hert, Stefan, and Moerman, Anneliese
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Anesthesiology and Pain Medicine ,near -infrared spectroscopy ,Medicine and Health Sciences ,Biology and Life Sciences ,General Medicine ,Adrenergic receptor ,sympathomimetic agents ,laryngoscopy ,ephedrine - Abstract
Background: Intraoperative sympathetic stimulation induces a cascade of metabolic and hormonal changes. It increases perfusion of vital organs, but also causes vasoconstriction of blood vessels supplying less vital organs, potentially leading to organ injury. To date, it is unknown how an endogenous stress reaction affects the spinal cord blood supply. Near-infrared spectroscopy (NIRS) can be applied paravertebrally to monitor the oxygenation of the collateral network, which contributes to the spinal cord blood supply. It has already been demonstrated that regional cerebral oxygen saturation (rScO2) increases following sympathetic stimulation. Objectives: We hypothesized that laryngoscopy would cause an increase in cerebral and paraspinal regional tissue saturations (rScO2 and rSpsO2, respectively). Design: Retrospective analysis of a previous conducted randomized trial. Setting: Laryngoscopy in the operating room. Methods: Data of 28 patients, scheduled for arterial dilation of the lower limb, were retrospectively analyzed. Before induction of anesthesia, standard monitoring, BIS and 8 NIRS sensors were applied (two on the forehead, six bilaterally on the back at T3-T4, T9-T10 and L1-L2). Sympathetic stimulation was induced by laryngoscopy. Main outcome measures: Changes in rStO2 following sympathetic stimulation induced by laryngoscopy. Results: Following laryngoscopy, rScO2 significantly increased and rSpsO2 significantly decreased at T9-T10 and L1-L2. The relative changes (regional tissue oxygen saturation (rStO2) after intubation-rStO2 before intubation)/ rStO2 before intubation), at cerebral level, T9-T10 and L1-L2 were 9%, -5% and -3%, respectively (p < 0.01). rSpsO2 at T3-T4 did not change significantly. Changes (Δ) in mean arterial pressure following laryngoscopy were weakly correlated with ΔrScO2 and moderately correlated with ΔrSpsO2 at T9-T10 and L1-L2. Conclusions: Intraoperative sympathetic stimulation may decrease the oxygen supply to the spinal cord. Trial registration: The trial was registered at ClinicalTrials.gov (NCT 03767296).
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- 2022
35. Noncoding Aberrations in Mismatch Repair Genes Underlie a Substantial Part of the Missing Heritability in Lynch Syndrome
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Iris B.A.W. Te Paske, Arjen R. Mensenkamp, Kornelia Neveling, Nicoline Hoogerbrugge, Marjolijn J.L. Ligtenberg, Richarda M. De Voer, Stéphanie Baert-Desurmont, Kathleen B.M. Claes, Kim de Leeneer, Lisa Elze, Simone van den Heuvel, Rachel S. van der Post, Yvonne van Twuijver, Tjakko J. van Ham, Anja Wagner, Mirjam M. de Jong, Edward M. Leter, Maartje Nielsen, MUMC+: DA KG Polikliniek (9), and RS: FHML non-thematic output
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Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,Hereditary Nonpolyposis/diagnosis ,Hepatology ,Gastroenterology ,Biology and Life Sciences ,DNA Mismatch Repair/genetics ,DNA Mismatch Repair ,Colorectal Neoplasms, Hereditary Nonpolyposis ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Medicine and Health Sciences ,Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis ,Humans ,Colorectal Neoplasms - Abstract
Contains fulltext : 288219.pdf (Publisher’s version ) (Open Access)
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- 2022
36. Predicting Protein Stability with Machine Learning
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Protein stability is a property of high importance and is of interest in a variety of fields. It determines if a protein has its native fold and can be of influence in certain diseases such as Parkinson's and Alzheimer's disease. It can also be of interest in an industrial setting to optimise the stability of enzymes in certain physicochemical environments. Recent developments in machine learning have yielded novel methods able to predict protein characteristics with surprising accuracy solely from sequence information. However, few such models have been proposed for predicting protein stability. The aim of this project was to create a model able to predict protein stability from sequence information, by utilising a multiple sequence alignment based protein language model. Different models were developed to predict two quantities relating to protein stability, Gibbs free energy of unfolding and the heat denaturation temperature. Due to limited training data the performance of the models predicting Gibbs free energy was poor. One of the models predicting heat denaturation temperature, proved more promising, with higher performance than a previously published model trained on similar data. However its ability to predict conventionally obtained heat denaturation temperatures was poor., Can computers find better proteins? Finding more efficient enzymes is critical for chemical industry to become sustainable. In order to efficiently find better enzymes new tools are needed that reliably predict protein properties. The chemical industry is on a search for new green technology that can replace catalysts that are often toxic and made of scarce minerals. A promising alternative is catalytic proteins, so called enzymes, that can be produced renewably and pose no toxic threat. However, in order to be a viable alternative, the enzymes must become more effective and be able to withstand harsher conditions. To design enhanced or entirely new enzymes accurate and fast predictions regarding the protein’s properties are needed. One such highly sought after property is protein stability at high temperatures since it usually speeds up chemical reactions. A promising approach for developing predictive models are machine learning techniques, which have proved powerful in numerous fields. At the department of Biophysical Chemistry at Lund University it was tested if such a model, that predicts the thermal stability of proteins, could be created. The study concluded that the tested models could detect some features of proteins, however for the models to be more useful, they must be trained on more data of high quality. The limiting factor during development was therefore the amount of relevant and available data. This is a common problem in the machine learning field, where the models are created by training on data, the computer is taught how to make predictions by learning from a dataset. The rule of thumb is that the more data it is trained on, the better performance. But what would be the benefit of using computers over good old laboratory work? While resulting in reliable values, laboratory work is usually costly and time-consuming and requires well trained personnel. If a relatively accurate predictive model can be constructed an estimate of a protein’s stabili
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- 2023
37. Autophagy and senescence in primary human bronchial epithelial cells in the context of COPD
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Chronic obstructive pulmonary disease (COPD) is the third largest cause of death worldwide, with its most prominent risk factor being inhalation of smoke and pollutants. In this project, we studied two processes that are involved in COPD: autophagy and cellular senescence. Using primary human bronchial epithelial cells (HBECs) from healthy and COPD donors, we aimed to show that cigarette smoke extract (CSE) gives rise to an impaired autophagy flux as well as increased senescence. With multiple CSE incubation times and CSE concentrations, our data shows an impaired autophagy flux at the early time points 5h and 24h. However, the senescence data is inconclusive. Further optimization of the study design could enable the development of an appropriate in vitro assay. In the end, could continued research of this kind contribute to increased knowledge and understanding of the disease, as well as enable development of medical targets in the mission of disease treatment., Rökextrakt och dess negativa påverkan på återvinningsprocesser i lungceller från KOL-patienter Kroniskt obstruktiv lungsjukdom (KOL) är en global folksjukdom och den tredje största dödsorsaken i världen. Den kan kopplas till en mängd andra sjukdomar och tillstånd som också ofta ökar risken för att utveckla KOL, t ex hög ålder, kardiovaskulära och neurosjukdomar. Men den största och mest välkända riskorsaken för KOL är rökning och exponering för föroreningar. Vi har studerat celler från KOL-patienters andningsvägar och fokuserat på två processer som är viktiga för cellens hälsa: autofagi och cellulär senescence. Vi kan utifrån våra resultat, och i likhet med tidigare publiserad forskning, konstatera att rökningen påverkar dessa processer och ger upphov till en sjuk och skadad cell. Autofagi är ett typ av återvinningssystem i cellen, där proteiner och andra cellkomponenter bryts ned och återvinns. Det är en process som alltid pågår, men som vid cellulär skada och/eller näringsbrist aktiveras ytterligare. Detta med syfte att regenerera komponenter så som aminosyror samt ta hand om de skadade celldelarna. Cellulär senescence å andra sidan, är en process som kan liknas vid cellulärt åldrande. När en cell blir tillräckligt gammal och/eller skadad finns det olika slutdestinationer. Antingen så genomgår cellen programmerad celldöd (apoptos) eller så blir den senescent. Det är ett mer eller mindre permanent tillstånd som innebär att cellen är levande men har slutat celldela sig. Processen är viktig för att hålla vävnad frisk och för att förhindra att skadade celler utvecklas till t ex cancerceller. Samtidigt har förhöjda nivåer av senescence kunnat kopplas ihop med olika sjukdomar, bland annat KOL. Vi studerade nivåerna av autofagi och cellulär senescence i celler från friska och KOL- patienters bronchier, närmare bestämt celler från det yttersta lagret av vävnaden – epitelet. Det är dessa celler som röken kommer i direktkontakt med. Genom att utsätta cellerna för rökextrakt
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- 2023
38. Novel tools for high-throughput genetic engineering, selection, and screening for improved Biotin production in E. coli cell factories
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Biotin is an essential co-factor in various metabolic processes and is crucial for the growth and maintenance of living organisms. The market need for biotin is multifaceted and driven by its importance in human health, beauty and cosmetics applications, pharmaceuticals, animal nutrition, and other industries. Current methods of industrial biotin production are unsustainable and generate environmentally hazardous waste, fueling the demand for new, greener strategies. The production of biotin through microbial fermentation has thus become an attractive alternative. Biotin biosynthesis is a complex and energy-intensive process that requires several enzymatic reactions, and biotin titers in microbial production have not reached economically viable levels. Biotin Synthase (BioB), the enzyme that catalyzes the last step of this process in E. coli, the conversion of dethiobiotin to biotin, has been identified as the bottleneck for this pathway. Overexpression of the enzyme generates oxidative stress and inhibits growth, though the exact mechanism has not yet been elucidated. This thesis employed a multiplexed engineering approach via high-throughput genetic engineering, selection, and screening methods to explore whether creating E. coli strains more resistant to oxidative stress would lead to higher biotin production capabilities. Using the expression of a DNA methylase to introduce controlled genetic mutations in Biosyntia's proprietary biotin-producing E. coli strains and selecting strains with improved resistance to oxidative stress yielded a selection of strains with increased resistance, which were screened for their biotin production. The improved resistance to oxidative stress and BioB induction in the strains did not lead to higher biotin production levels., The global need for biotin in the food, feed, and cosmetics industries is increasing steadily. Because current production methods use petrochemicals as precursors for synthesis, they are unsustainable and generate environmental waste. This has fueled the demand for alternative, more sustainable strategies. Biotin production via microbial fermentation could be a greener alternative but has not reached economically viable levels and cannot compete with current production methods. E. coli can naturally produce biotin but does so in minute amounts. This thesis aims to improve biotin production levels in biotin-producing E. coli strains to contribute towards a greener, more sustainable process. A bottleneck in the biosynthetic pathway, which has limited production levels, has been identified in previous research: the enzyme BioB, which catalyzes the last step of biotin synthesis. This enzyme creates oxidative stress in the cells and thereby inhibits cell growth. It was hypothesized that creating strains more resistant to oxidative stress and higher levels of intracellular BioB could lead to higher biotin production capabilities. By generating a controlled level of genetic diversity or introducing new genes into the strains and then selecting those with higher oxidative stress resistance, this thesis aims to find a strain that can produce higher levels of biotin. By nature, the randomness of the mutagenesis process generates a high number of strains that need to be tested for their biotin production. In this thesis, the number of strains that need to be tested is systematically reduced by selecting strains with a higher oxidative stress resistance by exposing them to various stressor concentrations. Only the fittest, most resistant strains survive this and are subsequently tested for their biotin-production capabilities. The work revealed that strains with higher resistance to oxidative stress and BioB production did not produce higher levels of biotin, indicating other l
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- 2023
39. Pseudomonas aeruginosa gene expression analysis using pangenome and PAO1 reference genomes
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Development in sequencing technologies has made the analyses of genetic material much more accessible. Processing sequenced data for an accurate analysis comes with its challenges, especially with the studies in microbial in clinical in vivo samples where difficulties in the collection of these samples for sequencing could lower the quality and contamination from the human host which might affect the accuracy of downstream analysis. In this project, we use RNA-seq and different reference genomes to look at the differential gene expression of Pseudomonas aeruginosa (PA), one of the most prevalent species of bacterial pathogens in the progression of chronic pulmonary diseases such as cystic fibrosis, due to its resistance to antimicrobial treatment. In this project, we created a pangenome from 21 strains of PA and explored the use of this, its subsets (core and soft-core gene sets) and a commonly used PA genome (PAO1) as reference genomes. We compared some of the differences and similarities in the results using the four gene sets, including mapping transcripts while developing a feasible pipeline to process raw sample reads from human sputum samples for differential expression and gene ontology enrichment analysis. From the analyses, we have found that differentially expressed genes upregulated in in vivo samples were related to biofilm, which plays a role in the difficulties in the treatment of PA infections, across most of the various genome reference-based results., How a “pan-genome” can help discover which genes that bacteria use to survive inside the human body Have you ever wondered about the microscopic world that exists in our bodies? Would they attack us at our moment of weakness? For people who are affected by cystic fibrosis, a disease that affects the lungs by causing a buildup of fluids, this can become a lifetime warfare against microbes such as Pseudomonas aeruginosa (PA). This tricky species of bacteria can change its growth form, making it difficult to treat patients who are infected. Thanks to a large set of genes in its chromosome, PA can change its growth mode from free-living cells in a liquid to forming a thick layer of cells known as a biofilm, by switching on or off various genetic materials. Since different strains of PA have different sets of genes, it is difficult to study common traits between strains and the importance of each gene. Hence, we want to use a more inclusive approach to explore their gene expression. Here we create a pan-genome, a complete set of genes of different strains to use as a reference when studying how different PA strains use their particular set of genes. We used this to explore what kind of genes are more expressed in human samples from people with PA in their lungs, compared to PA grown in a lab. Improvement in sequencing technology has made the analyses of genetic material more accessible and the use of software tools has become essential in processing these data. We created a pan-genome from 21 strains of PA. From this, we identified a gene set that was shared among all these strains, i.e., the core gene set. While exploring the pan-genome, we found most genes that support their survival are found more commonly in their core gene set. To highlight the importance of which gene set that is used as a reference, we examined how the results from the analysis changed depending on which gene set we used as a reference. We did this by comparing sequenced RNA from the samples by ps
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- 2023
40. Assessing tree modeling algorithm from terrestrial laser scanning in Rumperöd mixed forest
- Abstract
Recent technological advancements have revolutionized tree inventory methods for the forest industry. The development of terrestrial laser scanning (TSL) and automatized tree recognition software to estimate crucial tree parameters such as diameter at breast height (DBH) has made the inventory work faster and more reliable. Forest managers can quickly acquire large amounts of data to safely estimate timber yield and effectively use the resources of the forest. This study assesses the Hough transform algorithms (TreeLS) performance to acquire DBH and tree height in the Rumperöd mixed forest in Scania, Sweden, with continuous cover forestry management. Few studies have been made evaluating the Hough transform script under these challenging conditions with uneven terrain and irregular spatial tree density and dense understory vegetation. The result showed large difficulties for the Hough transform algorithm to correctly identify the trees in the plot due to stones, boulders, and uneven terrain. Only 25% of the trees in the plot were identified correctly. The algorithm also returned artefacts that further impaired the results of the TLS measurements to traditional field measurements. The mean difference in DBH between TLS measurement and field measurement in the plot was 115 mm and for tree height, the mean difference was 7.35 m. This difference in DBH and tree height would have overestimated the timber yield and made this algorithm unsuitable for the forest industry in the conditions present in the Rumperöd mixed forest.
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- 2023
41. Effects of soil factors on pioneer bryophyte species composition
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Bryophytes play a significant role in various ecological processes, including soil succession and colonization after disturbances. Although they are commonly believed to take up nutrients from soil solutions rather than the soil itself, the influence of soil on their growth and distribution is evident from previous studies. In order to examine the impact of soil conditions on bryophyte species composition and abundance, samples of soil and vegetation were collected from industrially disturbed sitesin Skåne. pH and phosphate concentrations were measured and compared with the identified bryophyte species and their coverage. Both pH and phosphate were found to be important factors influencing bryophyte diversity. Most species were associated with high pH and low phosphate conditions. Moreover, total species richness exhibited a decline with rising phosphate levels. Certain species were restricted to very specific conditions. The results indicate the potential benefits of maintaining neutral to high pH and low phosphate levels to aid bryophyte conservation efforts., Moss Matters: The First Step in Reclaiming Disturbed Soils Although frequently escaping the spotlight, bryophytes, consisting of mosses, liverworts, and hornworts, are the second largest group of land plants with a vital role in various ecological processes, such as soil formation, carbon storage and nutrient cycling. As smaller plants, they efficiently take advantage of nutrient-poor soils and recolonize soils following disturbance, thus improving the habitat, and paving the way for the eventual arrival of vascular plants. The main characteristics setting bryophytes apart from vascular plants is how they acquire nutrients. Lacking a traditional root system, they absorb water and minerals across their entire surface, allowing them to grow on various substrates beyond just soil. Despite this strategy, evidence suggests that soil chemistry has a substantial effect on their abundance and diversity. To investigate the relationship between the soil and bryophytes, a study was conducted on industrially disturbed sites of Skåne, a region in southern Sweden. By analyzing the pH and phosphate levels of the soil, as well as identifying the species composition of the populations, the research aimed to gain a deeper insight into how these soil conditions shape bryophyte vegetation. The findings have shed some light on the intricate interactions between soil and bryophytes. The majority of the species showed a clear preference for high pH and low phosphate. This affinity for phosphate-poor environments is likely an adaptive strategy. Given that most vascular plants struggle to establish under such circumstances, this provides bryophytes with a competitive advantage. Moreover, a collaborative effect was observed – when certain species deviated from their usual pH preferences (e.g. a species with a documented preference for alkaline soil was found on acidic soil), they compensated by favoring higher phosphate concentrations. Additionally, several species were confined to very spec
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- 2023
42. Production of natural pigments from A. platensis grown on wastewater from local treatment facility.
- Abstract
Although microalgae have been considered for the biological treatment of wastewater since the 1950’s, their potential to efficiently remove pollutants from various streams remains largely untapped and is yet to be utilized at large scale. The production of algal biomass and extraction of high-value compounds has, however, become increasingly popular with large scale farms and biorefineries around the world producing many promising alternatives to petroleum-based products and processes. While microalgae systems rival traditional production in terms of environmental sustainability and health benefits, the economic viability remains a challenge. This study aimed to investigate the potential of a biorefinery concept using wastewater as growth medium for the production of natural pigments by cyanobacterium, Arthrospira platensis. Using effluent streams as a growth media drastically cuts costs of production and with this circular approach, we are able to address challenges facing the wastewater treatment industry while providing a sustainable alternative to petroleum-based products. During phase one, the growth of A. platensis was monitored on different amounts of wastewater supplemented with standard growth media. Biomass productivity and growth rate ranged from 233,12 – 2000 mg.L-1.d-1 and 0,19 – 0,37 d-1, with 50% FWW supplemented with 50% Zarrouk media resulting in the highest values and thus proving to be the preferred growth media. However, cultures grown on 75% FWW supplemented with 25% Zarrouk media resulted in the highest PC content and thus was chosen as the growth media for further investigation. Phase two investigated the effect of different photoperiods (14h:10h and 16h:8h) on the production of PC, while assessing the scale-up potential of the system and monitoring nutrient removal. Photoperiod had no significant effect on PC content, however, a decrease in total PC production was seen between phases, suggesting further optimization for scale-up to be viable., Harnessing Microalgae: Transforming Wastewater into Valuable Pigments Innovative solutions are constantly sought to address the challenges of wastewater treatment and the increasing demand for sustainable products. One promising approach involves utilizing microalgae in a biorefinery system that not only cleans wastewater but also extracts valuable pigments from the biomass. This concept presents an intriguing solution that combines environmental remediation with the production of high-value products. Microalgae are microscopic organisms that harness the power of photosynthesis to convert sunlight and carbon dioxide into organic matter. They are incredibly efficient at this process, exhibiting high growth rates and accumulating various valuable compounds, including pigments. Their ability to thrive in diverse environments, including wastewater, makes them an ideal candidate for treatment and resource recovery. Traditional wastewater treatment processes consume large amounts of energy and are environmentally taxing. However, by integrating microalgae cultivation with wastewater treatment systems, we create a symbiotic relationship where the nutrients and organic matter present in the wastewater are used as a nutrient source for growth, effectively purifying the water in the process. One particularly exciting aspect is the extraction of valuable pigments from the microalgae biomass. These pigments not only provide color to the microalgae but also possess significant commercial value in various industries such as food, cosmetics, and pharmaceuticals. This study aims to investigate the potential of this biorefinery concept on local wastewater sources from the treatment facility RecoLab located in Helsingborg, Sweden. By establishing growth of a popular microalgae, Arthrospira platensis, on a food wastewater stream which is high in nutrients, we can optimize the biomass growth and assess the pigment content produced throughout cultivation. Additionally, we investigate th
- Published
- 2023
43. The Examination of Alternative Methods for Sperm Cell Lysis and Purification of Sexual Assault Samples
- Abstract
Forensic sexual assault samples typically contain a mixture of a small quantity of sperm cells and a high quantity of epithelial cells. This relationship complicates the generation of a DNA profile, which prompts the need for differential lysis and extraction of the DNA. Differential extraction is a lengthy method that includes multiple tube transfers and requires a purification step. Amicon Ultra centrifugal filters are employed to purify samples; however, these filters are costly and susceptible to potential breaks in the supply chain. The objective of this project was to examine alternative methods utilizing “off-the-shelf” reagents for sperm cell lysis or sample purification, with the goal of streamlining the current differential extraction protocol. Three methods for sperm cell lysis were studied: alkaline lysis, lysis with the nonionic detergent NP-40, and lysis with a natural decondensation assay. Isopropanol precipitation was examined as an alternative purification method. Additionally, reducing the number of washing steps in the differential extraction protocol was investigated. The results showed that optimized alkaline lysis (25 µL NaOH (0.2 M), 25 µL Tris-HCl (0.2 M) and TE buffer) was comparable to the differential extraction protocol in terms of DNA recovery. Alkaline lysis was also comparable to the differential extraction when performed on mock sexual assault samples. Isopropanol precipitation likewise showed equal DNA yields, complete DNA profiles and peak heights compared to Amicon filtration. Lastly, it was shown that reducing the number of washing steps of the reference protocol produced comparable DNA profiles. In conclusion, the findings suggest that the differential extraction protocol can be modified by using alkaline lysis for sperm cell lysis or isopropanol for purification, as well as by performing only one washing step., Sperm cells are usually the most interesting biological material to analyze in forensic sexual assault samples. However, today’s method for extracting DNA from sperm is both time-consuming and requires purification with expensive filters. It is therefore relevant to investigate alternative protocols that can help streamline the process. The term “sexual offense” it the Swedish legal umbrella term for crimes of a sexual nature, with major crimes including sexual assault. Typically, the biological material of highest interest in sexual assault samples is sperm cells, as DNA can be extracted and potentially linked to a suspect. However, due to the nature of most sexual assault samples, where sperm cells are present in lower quantities in comparison to other cell types (e.g. epithelial cells), successful extraction and analysis of sperm cell DNA is difficult. Because of this, a method called differential extraction is typically performed, where the sperm cells and other cells in the mixture are treated separately. Differential extraction is a lengthy protocol that requires multiple transfers of material between tubes, which can lead to loss of DNA and contamination. On top of this, it uses the strong reagent dithiothreitol (DTT) to successfully break open the sperm cells and release the DNA. DTT interferes with downstream analysis and DNA profiling, for which reason the samples must be purified. At the National Forensic Centre (NFC), purification of samples is done with centrifugal filters called Amicon filters. As there is only one supplier of these filters, the process is susceptible to disruptions in the supply chain, which occurred during the Covid-19 pandemic. Furthermore, Amicon filters are expensive. Therefore, it was relevant to examine alternative methods for sperm cell disruption (lysis) and sample purification that could simplify the current method, preferably while using easily accessible reagents. This project examined three alternative methods for sperm ce
- Published
- 2023
44. Production of natural pigments from A. platensis grown on wastewater from local treatment facility.
- Abstract
Although microalgae have been considered for the biological treatment of wastewater since the 1950’s, their potential to efficiently remove pollutants from various streams remains largely untapped and is yet to be utilized at large scale. The production of algal biomass and extraction of high-value compounds has, however, become increasingly popular with large scale farms and biorefineries around the world producing many promising alternatives to petroleum-based products and processes. While microalgae systems rival traditional production in terms of environmental sustainability and health benefits, the economic viability remains a challenge. This study aimed to investigate the potential of a biorefinery concept using wastewater as growth medium for the production of natural pigments by cyanobacterium, Arthrospira platensis. Using effluent streams as a growth media drastically cuts costs of production and with this circular approach, we are able to address challenges facing the wastewater treatment industry while providing a sustainable alternative to petroleum-based products. During phase one, the growth of A. platensis was monitored on different amounts of wastewater supplemented with standard growth media. Biomass productivity and growth rate ranged from 233,12 – 2000 mg.L-1.d-1 and 0,19 – 0,37 d-1, with 50% FWW supplemented with 50% Zarrouk media resulting in the highest values and thus proving to be the preferred growth media. However, cultures grown on 75% FWW supplemented with 25% Zarrouk media resulted in the highest PC content and thus was chosen as the growth media for further investigation. Phase two investigated the effect of different photoperiods (14h:10h and 16h:8h) on the production of PC, while assessing the scale-up potential of the system and monitoring nutrient removal. Photoperiod had no significant effect on PC content, however, a decrease in total PC production was seen between phases, suggesting further optimization for scale-up to be viable., Harnessing Microalgae: Transforming Wastewater into Valuable Pigments Innovative solutions are constantly sought to address the challenges of wastewater treatment and the increasing demand for sustainable products. One promising approach involves utilizing microalgae in a biorefinery system that not only cleans wastewater but also extracts valuable pigments from the biomass. This concept presents an intriguing solution that combines environmental remediation with the production of high-value products. Microalgae are microscopic organisms that harness the power of photosynthesis to convert sunlight and carbon dioxide into organic matter. They are incredibly efficient at this process, exhibiting high growth rates and accumulating various valuable compounds, including pigments. Their ability to thrive in diverse environments, including wastewater, makes them an ideal candidate for treatment and resource recovery. Traditional wastewater treatment processes consume large amounts of energy and are environmentally taxing. However, by integrating microalgae cultivation with wastewater treatment systems, we create a symbiotic relationship where the nutrients and organic matter present in the wastewater are used as a nutrient source for growth, effectively purifying the water in the process. One particularly exciting aspect is the extraction of valuable pigments from the microalgae biomass. These pigments not only provide color to the microalgae but also possess significant commercial value in various industries such as food, cosmetics, and pharmaceuticals. This study aims to investigate the potential of this biorefinery concept on local wastewater sources from the treatment facility RecoLab located in Helsingborg, Sweden. By establishing growth of a popular microalgae, Arthrospira platensis, on a food wastewater stream which is high in nutrients, we can optimize the biomass growth and assess the pigment content produced throughout cultivation. Additionally, we investigate th
- Published
- 2023
45. How do rainfall patterns change microbial induced carbon dynamics in soil?
- Abstract
Climate change is changing the precipitation patterns around the globe, leading to more extreme weather events like severe drought and heavy rainfalls. These events are intrinsically related to soil moisture fluctuations, which strongly modulates carbon fluxes in terrestrial ecosystems. Studying the behavior of microbial communities present in agriculture soils during drying and rewetting events can help understand soil dynamics under climate change scenarios and help the knowledge gap of how perennial crops can be useful in reducing climate change consequences. In this project, I compared perennial and annual crop systems in depth, down to 90 cm, by characterizing the soils and measuring their microbial responses to a drying and rewetting event. From this study, it was possible to conclude that both soils present a sensitive response to such event, with both lag and recovery times increasing with depth. Moreover, soils exposed to perennial crops generally showed shorter lag and recovery times than those from annual crops, which suggests that perennial crops might have a higher capacity to withstand the negative effects of droughts. Based on the results obtained and the intrinsic limitations of the experiment, it is clear that further investigation is needed, namely in the form of respiration studies, more replicates and statistical analysis., Climate change is causing extreme weather events worldwide, like severe droughts and heavy rainfall, by changing precipitation patterns. These events affect water levels and have a major impact on carbon movement in soils. To understand how soil behaves under changing climate conditions, I studied how microbes in agricultural soils behave after drying and rewetting events, by comparing perennial and annual crops soils to explore their potential in mitigating climate change effects. I characterized soils from perennial and annual croplands from Skåne, Sweden and conducted drying and rewetting experiments to evaluate the microbial responses. The results showed that both soil types were sensitive to drought, with microbes taking longer to recover in deeper soils. Surprisingly, soils from perennial crops showed to be better adapted to drought conditions, with the potential to help fight climate change. Future studies should include more replicates, analyze respiration and the microbial communities by sequencing DNA, and apply statistical techniques to support the validity of the conclusions.
- Published
- 2023
46. Changes in Gishwati-Mukura Forest and effects on biodiversity, floods, and landslides - recommendations for sustainable forest management
- Abstract
Rainforests are of great importance for biodiversity and several ecosystem services. In Rwanda, a considerable decline in rainforest covers have been observed during the last decades. The Gishwati-Mukura Forest is one of the rainforests in Rwanda that has experienced a substantial reduction in forest cover, 99.4 %. The aim of this research has been to investigate what the changes in forest cover of Gishwati-Mukura have been, what impacts they had on local livelihoods, biodiversity and occurrence of floods and landslides, and what the reasons for the deforestation have been. The method used to reach the aim has been a combination between field observations and interviews with local inhabitants in Rwanda, a review of literature, and analysis of changes in forest cover, land use, and hydrological data. The main reasons for the deforestation are found to be an increase of local population, expanded agricultural land use, use of wood as primary source for energy production and mining activities. The deforestation in Gishwati-Mukura has had negative impacts on biodiversity, ecosystem services and resilience of the ecosystems, as the habitats for the species have been fragmented and reduced. A correlation between the decreased forest cover and higher flow rates in Sebeya river has been found, indicating that the loss of forests is a potential cause for more frequent floods and landslides., Allmänt känt är att världens regnskogar bidrar till flertalet ekosystemtjänster som hjälper till att upprätthålla förutsättningarna för liv på jorden och som vi människor kan dra nytta av. Den höga och välutvecklade biologiska mångfald som dessa skogar inrymmer är att tacka för detta. Rwanda, ett litet land beläget i den östra delen av Afrikas tropiska zon, har under det senaste seklet varit objekt för omfattande avskogning som påverkat nationens regnskogars funktionalitet. Under samma period har landet förlorat stora delar av sin ursprungliga biologiska mångfald och årligen utsatts för naturkatastrofer i form av översvämningar och jordskred. Denna masters uppsats ämnar utforska hur avskogningen i västra Rwanda, mer specifikt i nationalparken Gishwati-Mukura, har påverkat skogens biologiska mångfald och riskerna för översvämningar och jordskred i området från år 1960 till idag. Metoderna som använts för att uppnå detta syfte är en kombination av en litteratursammanställning, datainsamling och analys av satellitbilder över området och av flödesförändringar i en av de närliggande floderna, Sebeya. Dessutom har fältstudier på plats i Rwanda genomförts och innefattat observationer från några av de avskogade områdena och intervjuer med lokalbefolkning, forskare och anställda vid statliga institutioner. Resultaten från arbetet fastslår att det totala skogstäcket av naturlig skog minskat med 89 % mellan 1960 och 2019 och att denna minskning gett upphov till förluster av den biologiska mångfalden. Något som inte påvisats är dock till vilken omfattning biodiversiteten påverkats. Studien visar därutöver på ökade flödeshastigheter i Sebeya vilket insinuerar att ökad erosion och således ökad risk för översvämningar och jordskred förekommer. Förordat är att mer forskning om de naturliga skogarnas effekter på och betydelse för biologisk mångfald och förekomst av översvämningar och jordskred genomförs.
- Published
- 2023
47. Optimization of two high-performance size-exclusion chromatography methods with diode-array detection for protein quantification and purity assessment
- Abstract
Background: There is a need to develop methods of determining concentration and purity for two new affinity ligands, protein T and protein H, in order to ensure the quality of an industrial production of said proteins. Aims: To develop a High Performance Size Exclusion Chromatography, HPSEC, method to determine concentration and purity of protein T and to improve an existing HPSEC method for concentration and purity determination of protein H that show selectivity, display linearity between peak area and injection amount and give repeatable results. Methods: For protein T, Xbridge Premier Protein and Superdex Increase columns were used of the lengths 15 and 30 cm together with 50mM and 0.3M Sodium phosphate buffers and PBS and mobile phases. For protein H, only a 15 cm Superdex Increase column was used with 0.3M Sodium phosphate buffer. Different reducing conditions during sample preparation were tested. The linearity and measuring ranges were determined by injecting different volumes of reference standard and evaluating . Repeatability was tested with three triplicates of reference standards across three occasions with the same equipment and running conditions. Results: For protein T the 15 cm Xbridge column with 50mM Sodium Phosphate buffer was selected. Little difference between reduction conditions with exception of reduction at high temperature which resulted in degradation or aggregation for both proteins. Acceptable selectivity and separation between main peak and impurities was demonstrated for both methods. Both methods were linear and gave repeatable results in the measuring ranges 2.43 – 16.98µg, 4.85 – 16.98µg and 2.56 – 15.37µg for purity determination of protein T, concentration determination of protein T and both purity and concentration determination protein H, respectively. Conclusion: Two methods, one for protein T and one for protein H, were developed which met qualification criteria use in quality control., An important part of pharmaceutical production is the purification of the active ingredient which can be done, in part, using proteins called affinity ligands which selectively bind specific targets. Just like the active ingredients in drugs, companies must be sure that these affinity ligands don’t contain harmful impurities and fulfil product specifications in order to protect patient safety. A common efficient method for determining protein concentration and purity is called high performance size exclusion chromatography, HPSEC. HPSEC is a method where a solution flows through a tube filled with porous particles called a column, which separates compounds according to how fast they travel through the column. How fast something travels depends on the size of the compound. Different affinity ligands have different properties which may impact how they interact with the column which may distort results. Therefore suitable parameter conditions must be determined for each affinity ligand to be measured. The aim of this study is to develop to methods by finding suitable HPSEC parameter conditions for determining purity and concentration of two affinity ligands, here called protein T and protein H. Both methods should be separate the affinity ligands well from impurities and be linear and repeatable. To this end, four columns were tried; two different sizes for the porous particles, and two different tube lengths. Solutions with different salt concentrations were used to pass through the column as well as different times and temperatures of preparing the samples were tried so that the ligands were in their active states. Once suitable parameters had been selected, different protein amounts were used to see for what sample concentrations the method would be linear. The concentration and purity of a sample were determined on three different days using the final selected parameters to test if the method was repeatable. The results showed the column with smaller particles were
- Published
- 2023
48. Mussel farming along the south-Swedish coasts - a possible solution to eutrophication?
- Abstract
The concept of mussel farming as a mitigator to nutrient pollution is steadily spreading. The southernmost part of Sweden borders the Baltic Sea where the water quality differs between the costs, however, all are affected by eutrophication. The study presents a suitability analysis using GIS to find potential locations for blue-mussel farm establishment, and the outcome was produced as maps. A multi-criteria analysis (MCA) was done based on the environmental conditions needed for mussel growth (chlorophyll a, salinity, dissolved oxygen, temperature, currents, and water depth), possible disturbances (pipelines, cables, shipping, and nature reserves) and a short discussion on the spatial availability considering potential variations of eutrophication levels in the water based on adjacent land cover. The difference in salinity had a great effect on the location suitability, and adjustments showed that with lower salinity, the area availability increased, marginally along the west coast but to a pronounced degree along the east coast.
- Published
- 2023
49. Legacy effects of temperature alterations on microbial resistance and resilience to drying and rewetting
- Abstract
With warming in soils due to climate change, a series of secondary factors arise, which have multifaceted effects on soil microbial communities. Of these, alterations to soil moisture are among the most crucial to understanding how microbial functions will change in the face of climate change. As living organisms, microbes must adapt to their environment, and their adaptations are reflected in their response to contemporary events. How they respond can determine the fate of soil organic matter and have relevant feedback to climate systems. In this thesis, I address how the legacy effects of a soil microbial community affect its response to a drying and rewetting event in terms of resilience and resistance, as well as how these strategies can affect carbon dynamics in subarctic ecosystems. I achieved this by taking soil samples from study sites that have undergone two-year warming in Abisko, Sweden. I then subjected them to a drying and rewetting cycle, assessing the samples as they dried down and subsequently responded to being rewet. During this time, I measured bacterial and fungal growth via stable isotope probing as well as respiration via gas chromatography. I found that while moisture was affected, microbial resistance was unaffected by warming treatments. However, resilience was affected by warming treatments. Responses also differed primarily based on NDVI, possibly indicating the importance of plant inputs of carbon to the microbial response. Possible conceptual frameworks are then used to explain the observations, notably the YAS framework. Implications for carbon budgeting and models are inferred from these findings. I conclude that interactions between microbes and moisture and plant inputs impact microbial response to moisture stress in warming experiments and that future experiments may want to examine the vegetation relationship with more focus., Alterations to the carbon cycle have caused climate change to warm the planet. The arctic is warming at nearly triple the rate as the rest of the globe. Most of the world’s biologically relevant carbon is below ground in the arctic and subarctic. This is a result of the cold climate reducing decomposition below annual production, for policy to adapt to upcoming climate changes which may affect the stability of this carbon. In this study, I examined how temperature alterations to soil microbial communities alter their response to moisture alterations such as drought and drying then rewetting. I used warmed sites near the Abisko research station in the subarctic birch forest that had five treatments of warming. The treatments consisted of a control plot, a summer warming plot, a winter warming plot, a chronic (year-round) warming plot and an extreme warming plot. I sampled soil and took field measurements of these treatments. I then dried the soil down, and then rewet it. During these alterations, I used isotopic methods to measure the growth of microbes. I also measured their respiration during this time. I found that microbial communities did not stay active during the drought period and that treatments had no effect on this. However, microbial communities that had a higher amount of photosynthesis had a more robust response, while microbial communities that had experienced dryer conditions had a more efficient response. I associate this response with the microbes adapting to both the stress of the moisture deficit as well as potential stress of carbon availability. I theorized that this might be because of microbes have to shift their activities in plots without plants. Plants provide carbon which microbes can use as an energy source and without it, there is a possibility that the ability to respond to stress may have been impaired. The carbon dynamics described in this study could be used in models and carbon budgeting for future warming. Additionally, understandi
- Published
- 2023
50. Influence of Peristaltic Pump Tubes on Protein Particles Formation for Lipase Enzyme Therapeutic Protein
- Abstract
Introduction: In Bio-pharmaceutical production, peristaltic pump tubing is considered one of the factors that influence protein aggregation. Background: Protein particles present challenges for the control and analysis of various manufacturing processes in the biopharmaceutical industry for their significant effects on safety and quality. Aim(s): This research aims to study the effect of different peristaltic pump tubing on particle formation as well as the Characterization of the particles and investigate the effect of surfactants on particle formation. Methods: The study was conducted using a dynamic image analysis instrument (QICPIC) to characterize particles formed by Lipase protein samples while pumping through Silicone and PVC tubing using a peristaltic pump. Lipase samples concentration of 1mg/ml were investigated with and without polysorbate 20, Poloxamer 188, and SDS surfactants, while Lipase 10 mg/ml samples were investigated without using the surfactants. Results: Pumped of all Lipase protein samples resulted in particle formation with varying degrees between Silicone and PVC tubing. The presence of Poloxamer 188 and Sodium Dodecyl Sulfate (SDS) surfactants reduced pumping-induced particles except for Polysorbate 20. Conclusion: Silicone and PVC tubing generate particles even in the presence of surfactants and a great level of reduction the particle formation was achieved with Poloxamer 188 and SDS surfactants., Protein aggregation is a high molecular weight protein content cluster. Their presence in finished therapeutic protein products is considered risky for their significant effects on the quality of the medicine and the safety and health of the patient as it can induce adverse effects. Therefore, it is critical to identify the process that contributes to its formation and address the presence of particles in the development of therapeutic proteins. From a formulation perspective, having profound knowledge of particle development mechanisms and identifying the causes and factors affecting particle formation is important. Knowing the factors that influence particle formation is advantageous to adopt control measures to mitigate risks associated with particles beginning from the initial production steps, through storage life duration. This project was done to investigate the effect of pump tubing, Silicone, and PVC tubing, used for transporting protein during the production process, tubing of a peristaltic pump, on protein particle formation for lipase protein using Silicone and PVC tubing, and characterize the particle formed. Moreover, investigate the effect of using different surfactants on the formation of the particles. The surfactants, a commonly used compound in bio-pharmaceutical formulations to prevent aggregation, used were Polysorbate 20, Poloxamer 188, and Sodium Dodecyl Sulfate (SDS) surfactant. This was done by using a QICPIC instrument for particle analysis and Silicone and PVC tubing for pumped Lipase. The lipase samples with or without surfactant were pumped in through the tubing for thirty minutes and measurements were taken every minute. Particles were characterized using ferret diameter and Sphericity. The results were compared to see the effect of tubing type and surfactants. The results obtained from this investigation showed that peristaltic pumps can induce protein aggregation which depends on the tubing type and the presence of the surfactant. It
- Published
- 2023
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