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Research on the impact of and attention given to journal covers is a crucial research topic in academia. This study investigated whether a paper featured on the cover of a journal receives more citations and higher usage than non-cover papers. Unlike previous studies that focused on just a few prestigious journals, we analyzed the citations and usage counts of 3196 cover and 36,652 non-cover papers published in 42 cell biology journals from 2011 to 2015. To address the above question, four new indicators were used to compare descriptive differences in stratified sets, and both linear regression model analysis and robustness testing were applied to further explore the relationships. Our main results showed that being a cover paper has positive and significant relationships both with citations and usage counts. Moreover, additional analyses show that the two relationships are strengthened in top-tier journals, and the main effects remain robust when we consider the influence of author ability. This new exploration of factors relevant for citations and usage counts in this empirical analysis consolidates and broadens the findings of previous studies. [ABSTRACT FROM AUTHOR]

Background: We performed a systematic review that identified at least 9,000 scientific papers on PubMed that include immunofluorescent images of cells from the central nervous system (CNS). These CNS papers contain tens of thousands of immunofluorescent neural images supporting the findings of over 50,000 associated researchers. While many existing reviews discuss different aspects of immunofluorescentmicroscopy, such as image acquisition and staining protocols, few papers discuss immunofluorescent imaging from an image-processing perspective. We analyzed the literature to determine the image processing methods that were commonly published alongside the associated CNS cell, microscopy technique, and animal model, and highlight gaps in image processing documentation and reporting in the CNS research field. Methods: We completed a comprehensive search of PubMed publications using Medical Subject Headings (MeSH) terms and other general search terms for CNS cells and common fluorescent microscopy techniques. Publications were found on PubMed using a combination of column description terms and row description terms. We manually tagged the comma-separated values file (CSV) metadata of each publication with the following categories: animal or cell model, quantified features, threshold techniques, segmentation techniques, and image processing software. Results: Of the almost 9,000 immunofluorescent imaging papers identified in our search, only 856 explicitly include image processing information. Moreover, hundreds of the 856 papers are missing thresholding, segmentation, and morphological feature details necessary for explainable, unbiased, and reproducible results. In our assessment of the literature, we visualized current image processing practices, compiled the image processing options from the top twelve software programs, and designed a road map to enhance image processing. We determined that thresholding and segmentation methods were often left out of publications and underreported or underutilized for quantifying CNS cell research. Discussion: Less than 10% of papers with immunofluorescent images include image processing in their methods. A few authors are implementing advanced methods in image analysis to quantify over 40 different CNS cell features, which can provide quantitative insights in CNS cell features that will advance CNS research. However, our review puts forward that image analysis methods will remain limited in rigor and reproducibility without more rigorous and detailed reporting of image processing methods. Conclusion: Image processing is a critical part of CNS research that must be improved to increase scientific insight, explainability, reproducibility, and rigor. [ABSTRACT FROM AUTHOR]

How plants sense their orientation in relation to gravity and steer their root and shoot growth accordingly is not fully understood. The discovery of key steps needed for this process fills in some of the gaps in our knowledge.LAZY proteins hitchhike when roots reorient relative to gravity. [ABSTRACT FROM AUTHOR]

A challenge in the pandemic era is to implement effective but flexible practical teaching for biological sciences courses. Such teaching needs to deliver conceptual, analytical and practical skills training while having the option to rapidly respond to health and safety issues, local regulations, staff and student concerns. In this paper, we describe a set of cell biology practicals (mini‐project) that meets many of these requirements and provides flexibility in providing skills training both through online and in practical laboratory environments. We have used a human adenocarcinoma cell line A431 stably transfected with a fluorescent cell cycle reporter as a biological model to deliver training through discrete work packages encompassing cell culture, fluorescence microscopy, biochemistry and statistics. How such work packages can be modified to, an online format either partially or completely is also described. Furthermore, the activities can be adapted for teaching both undergraduate and postgraduate level courses to ensure effective skills training which is applicable to a wide range of biological degree programs and levels of study. [ABSTRACT FROM AUTHOR]

From ancient sea species to clues on comets, papers by the country’s talented scientists are regularly making headlines. [ABSTRACT FROM AUTHOR]

Background: Petasites japonicus (PJ), also known as Butterbur, has a rich history as a traditional healing remedy across numerous countries. Objectives: This study was designed to evaluate the potential anti-cancer properties of the methanol extract derived from PJ (PJE). Materials and Methods: Cell viability was measured with 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide. Cell cycle analysis, caspase activity assays, western blotting, and reactive oxygen species (ROS) assays were also used to investigate the anticancer effects of PJE on cancer cells. Results: It was shown that PJE inhibited the cell viability of the colon carcinoma cell line Caco-2 (half-maximal inhibitory concentration [IC50]: 268.4 µg/mL), of the hepatocellular carcinoma cell line Hep3B (IC50: 420.2 µg/mL), and of the bladder carcinoma cell line 5637 (IC50: 99.43 µg/mL). Analysis of DNA content indicated an increase in the sub-G1 population of 5637 cells as a result of PJE treatment. Furthermore, PJE caused a reduction in mitochondrial membrane potential and the ratio of Bcl-2 to Bax. Moreover, PJE enhanced the levels of various components involved in the proapoptotic cascade, such as caspase-3, caspase-9, and poly-adenosine diphosphate-ribose polymerase. Moreover, it was observed that PJE modulated mitogen-activated protein kinases (MAPKs) activation and induced an elevation in intracellular production of ROS. Conclusion: These combined results strongly suggest that PJE possesses significant proapoptotic properties as an herbal medicine, acting through ROS-dependent MAPK signaling pathways in bladder cancer cells. [ABSTRACT FROM AUTHOR]

Background: This study aimed to evaluate dentin wear and biological performance of desensitizing materials. Methods: Seventy bovine root dentin blocks were sectioned. Half of the surface of each specimen was untreated (control) and the other half was immersed in EDTA and treated with the following desensitizing materials: placebo varnish (PLA), fluoride varnish (FLU), sodium fluoride (NaF) varnish + sodium trimetaphosphate (TMP), universal adhesive (SBU), S-PRG varnish (SPRG), biosilicate (BIOS), and amelotin solution (AMTN). After application, the specimens were submitted to an erosive-abrasive challenge and the wear analyzed by optical profilometer. Serial dilutions of extracts obtained from the culture medium containing discs impregnated with those desensitizers were applied on fibroblasts and odontoblasts-like cells cultures. Cytotoxicity and production of total protein (TP) by colorimetric assays were determined after 24 h. Data were statistically analyzed using Kruskal-Wallis, Dunn's, One-way ANOVA and Tukey tests (p ≤ 0.05). Results: No dentin wear was observed only for SBU. The lowest dentin wear was observed for AMTN and TMP. Cell viability was significantly reduced after treatment with undiluted extracts of PLA, FLU, TMP and SBU in fibroblasts and TMP and SBU in odontoblast-like cells. SPRG, BIOS and AMTN were cytocompatible at all dilutions tested. Considering TP results, no statistical difference was observed among the groups and high levels for TP were observed after TMP and FLU treatments. Conclusions: Universal adhesive system may protect dentin with opened tubules from wear after challenge. Extracts of adhesive and fluoride varnishes presented cytotoxic mainly on fibroblasts. The enamel protein may be a future alternative to treat dentin with opened tubules because it may cause low wear under erosive-abrasive challenge with low cytotoxic effects. [ABSTRACT FROM AUTHOR]

Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function. [ABSTRACT FROM AUTHOR]

Flow cytometry is a mainstay technique in cell biology research, where it is used for phenotypic analysis of mixed cell populations. Quantitative approaches have unlocked a deeper value of flow cytometry in drug discovery research. As the number of drug modalities and druggable mechanisms increases, there is an increasing drive to identify meaningful biomarkers, evaluate the relationship between pharmacokinetics and pharmacodynamics (PK/PD), and translate these insights into the evaluation of patients enrolled in early clinical trials. In this review, we discuss emerging roles for flow cytometry in the translational setting that supports the transition and evaluation of novel compounds in the clinic. [ABSTRACT FROM AUTHOR]

Base excision repair (BER) is a cellular process that removes damaged bases arising from exogenous and endogenous sources including reactive oxygen species, alkylation agents, and ionizing radiation. BER is mediated by the actions of multiple proteins which work in a highly concerted manner to resolve DNA damage efficiently to prevent toxic repair intermediates. During the initiation of BER, the damaged base is removed by one of 11 mammalian DNA glycosylases, resulting in abasic sites. Many DNA glycosylases are product-inhibited by binding to the abasic site more avidly than the damaged base. Traditionally, apurinic/apyrimidinic endonuclease 1, APE1, was believed to help turn over the glycosylases to undergo multiple rounds of damaged base removal. However, in a series of papers from our laboratory, we have demonstrated that UV-damaged DNA binding protein (UV-DDB) stimulates the glycosylase activities of human 8-oxoguanine glycosylase (OGG1), MUTY DNA glycosylase (MUTYH), alkyladenine glycosylase/N-methylpurine DNA glycosylase (AAG/MPG), and single-strand selective monofunctional glycosylase (SMUG1), between three- and five-fold. Moreover, we have shown that UV-DDB can assist chromatin decompaction, facilitating access of OGG1 to 8-oxoguanine damage in telomeres. This review summarizes the biochemistry, single-molecule, and cell biology approaches that our group used to directly demonstrate the essential role of UV-DDB in BER. [ABSTRACT FROM AUTHOR]

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. [ABSTRACT FROM AUTHOR]

An unusual form of cell death called ferroptosis can sweep over embryonic tissues in a wave-like manner to ensure proper muscle development — evidence that ferroptosis has a role in normal physiology.Iron-dependent cell death sweeps across tissue to shape embryonic muscle. [ABSTRACT FROM AUTHOR]

A new wave of research is unpicking the relationship between cancer and neurons — and looking for ways to stop the crosstalk. [ABSTRACT FROM AUTHOR]

Virtual laboratory simulations (VLs), particularly in Biology education, are gaining popularity. This study focused on assessing students' and teachers' perceptions of VLs, developed by Labster, in a first-year undergraduate cell biology course. The evaluation involved surveys and interviews with 352 respondents. Findings indicate that over 90% of students found VLs user-friendly and visually engaging. However, around 60% noted the need for significant technical resources, which could limit accessibility. Over 80% of students reported that VLs increased their motivation, autonomy, interest, and confidence. While only 72% viewed them as potential replacements for traditional labs, more than 90% preferred using VLs as preparatory material for practical sessions. Teachers generally agreed with these perceptions, emphasizing the need for technical support for effective use. They suggested that VLs are better as pre-lab activities rather than full replacements. Both students and teachers recognized VLs as beneficial for academic performance and learning attitude but noted limitations in technical support for home use. The consensus was that VLs are most effective as complementary material before in-person lab sessions. [ABSTRACT FROM AUTHOR]

Methylene blue is a versatile substance used for various medical purposes for years. It has shown promise as a diagnostic tool and a potential treatment option for illnesses such as methemoglobinemia, cyanide poisoning, and malaria, but primarily neurodegenerative diseases like Alzheimer's. The present study aimed to investigate the hypothesis that hydrogen peroxide-induced neuronal cell death debris could activate inflammation, leading to endothelial cell death. To test this hypothesis, we employed two innovative transwell models, the distant and adjacent models, to replicate intercellular interactions between endothelial and neuronal cells at varying brain ranges. We also analyzed the expression levels of pro-apoptotic genes BAX and BIK in three conditions. Our findings suggest that the proximity between endothelial and neuron cells is crucial in inducing endothelial cell death. We further found that the methylene blue treatment significantly decreased the percentage of cell death in both distant and adjacent models. Moreover, our analysis of IL-2, IL-8, and TNF-alpha expression levels using RT-PCR suggests that MBS may protect endothelial cells by blocking the inflammation pathway, which is critical in regulating inflammation and cell death pathways. Dysregulation of these cytokines and their downstream signaling pathways can lead to cell death and brain damage, contributing to the pathogenesis of inflammatory diseases. Therefore, methylene blue has potential therapeutic benefits as a treatment option for diseases involving neuronal and endothelial cell death. [ABSTRACT FROM AUTHOR]

Rhabdomyosarcoma (RMS) is the most common type of soft tissue sarcoma in children and adolescents. Fusion-negative RMS (FN-RMS) accounts for more than 80% of all RMS cases. The long-term event-free survival rate for patients with high-grade FN-RMS is below 30%, highlighting the need for improved therapeutic strategies. CD73 is a 5' ectonucleotidase that hydrolyzes AMP to adenosine and regulates the purinergic signaling pathway. We found that CD73 is elevated in FN-RMS tumors that express high levels of TWIST2. While high expression of CD73 contributes to the pathogenesis of multiple cancers, its role in FN-RMS has not been investigated. We found that CD73 knockdown decreased FN-RMS cell growth while up-regulating the myogenic differentiation program. Moreover, mutation of the catalytic residues of CD73 rendered the protein enzymatically inactive and abolished its ability to stimulate FN-RMS growth. Overexpression of wildtype CD73, but not the catalytically inactive mutant, in CD73 knockdown FN-RMS cells restored their growth capacity. Likewise, treatment with an adenosine receptor A2A-B agonist partially rescued FN-RMS cell proliferation and bypassed the CD73 knockdown defective growth phenotype. These results demonstrate that the catalytic activity of CD73 contributes to the pathogenic growth of FN-RMS through the activation of the purinergic signaling pathway. Therefore, targeting CD73 and the purinergic signaling pathway represents a potential therapeutic approach for FN-RMS patients. [ABSTRACT FROM AUTHOR]

Fluorescent labels that have greater resistance to bleaching could help researchers to get more from biological imaging. [ABSTRACT FROM AUTHOR]

When chromosomes are lost or gained, massive changes in gene expression disrupt the delicate balance of proteins in a cell. Yeasts with incorrect chromosome numbers counteract this by degrading excess proteins.Aneuploid cells boost protein degradation to rebalance proteome. [ABSTRACT FROM AUTHOR]

Organelles called mitochondria are transferred to blood-vessel-forming cells by support cells. Unexpectedly, these mitochondria are degraded, kick-starting the production of new ones and boosting vessel formation.Mitochondrial transfer enhances endothelial-cell grafts. [ABSTRACT FROM AUTHOR]

Low-level laser therapy (LLLT) has become an important part of the therapeutic process in various diseases. However, despite the broad use of LLLT in everyday clinical practice, the full impact of LLLT on cell life processes has not been fully understood. This paper presents the current state of knowledge concerning the mechanisms of action of LLLT on cells. A better understanding of the molecular processes occurring within the cell after laser irradiation may result in introducing numerous novel clinical applications of LLLT and potentially increases the safety profile of this therapy. [ABSTRACT FROM AUTHOR]

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This paper examines the model of network genomics pioneered in the late 1980s and adopted in the European Commission-led Yeast Genome Sequencing Project (YGSP). It contrasted with the burgeoning large-scale center model being developed in the United States to sequence the yeast genome, chiefly as a pilot for tackling the human genome. We investigate the operation and connections of the two models by exploring a coauthorship network that captures different types of sequencing practices. In our network analysis, we focus on institutions that bridge both the European and American yeast whole-genome sequencing projects, and such concerted projects with non-concerted sequencing of yeast DNA. The institutions include two German biotechnology companies and Biozentrum, a research institute at Universität Basel that adopted yeast as a model to investigate cell biochemistry and molecular biology. Through assessing these bridging institutions, we formulate two analytical distinctions: between proximate and distal, and directed and undirected sequencing. Proximate and distal refer to the extent that intended users of DNA sequence data are connected to the generators of that data. Directed and undirected capture the extent to which sequencing was part of a specific research program. The networked European model, as mobilized in the YGSP, enabled the coexistence and cooperation of institutions exhibiting different combinations of these characteristics in contrast with the more uniformly distal and undirected large-scale centers. This contributes to broadening the historical boundaries of genomics and presenting a thicker historiography, one that inextricably meshes genomics with the trajectories of biotechnology and cell biology. This essay is part of a special issue entitled The Sequences and the Sequencers: A New Approach to Investigating the Emergence of Yeast, Human, and Pig Genomics, edited by Miguel Garcı'a-Sancho and James Lowe. [ABSTRACT FROM AUTHOR]

Simple Summary: The Earth's magnetic field is vital for life to exist. If the field becomes weaker, it's known as hypomagnetic conditions. Studying the impact of hypomagnetic conditions on living beings is significant for multiple reasons. Firstly, it helps us comprehend the biological consequences and learn more about how the magnetic field interacts with living organisms. Secondly, understanding the impact of hypomagnetic conditions on human health is important for preparing for extended space missions. This report outlines the influence of hypomagnetic conditions on various objects such as animals, humans, plants, bacteria, and individual molecules. It explains the effects at both a cellular and organismal level, and lists and characterizes the most likely mechanisms that account for biological responses to magnetic fields. Over the past century, scientists have gathered extensive data on the impacts of hypomagnetic conditions. We aimed to investigate the effect of experimental methods and type of exposure on the observed effects. Our findings indicate that hypomagnetic conditions primarily affect cellular processes such as gene expression and protein synthesis, as well as the functioning of the nervous system including neuron development and behavioral reactions. The geomagnetic field plays an important role in the existence of life on Earth. The study of the biological effects of (hypomagnetic conditions) HMC is an important task in magnetobiology. The fundamental importance is expanding and clarifying knowledge about the mechanisms of magnetic field interaction with living systems. The applied significance is improving the training of astronauts for long-term space expeditions. This review describes the effects of HMC on animals and plants, manifested at the cellular and organismal levels. General information is given about the probable mechanisms of HMC and geomagnetic field action on living systems. The main experimental approaches are described. We attempted to systematize quantitative data from various studies and identify general dependencies of the magnetobiology effects' value on HMC characteristics (induction, exposure duration) and the biological parameter under study. The most pronounced effects were found at the cellular level compared to the organismal level. Gene expression and protein activity appeared to be the most sensitive to HMC among the molecular cellular processes. The nervous system was found to be the most sensitive in the case of the organism level. The review may be of interest to biologists, physicians, physicists, and specialists in interdisciplinary fields. [ABSTRACT FROM AUTHOR]

With the world at their feet, these prolific young researchers are making their mark. [ABSTRACT FROM AUTHOR]

Structures of the machinery for importing proteins into chloroplast organelles of algae, determined using cryo-electron microscopy, have opened a new chapter in efforts to understand how chloroplasts are built. Structure of the TOC-TIC supercomplex from algae. [ABSTRACT FROM AUTHOR]

Trove of health data from space tourists and astronauts reveals the effects of microgravity, radiation and more. [ABSTRACT FROM AUTHOR]

This Editorial describes PLOS Biology's experiment with contextualised publication, whereby potentially controversial studies are published with an Editor’s Note and an accompanying Primer in which the Academic Editor guides the reader, dissects the study, and lays out the thinking behind the decision to publish. [ABSTRACT FROM AUTHOR]

This paper reports on a study which designed and developed a multi-fingered haptic interface in conjunction with a three-dimensional (3D) virtual model of a section of the cell membrane in order to enable students to work collaboratively to learn cell biology. Furthermore, the study investigated whether the addition of haptic feedback to the 3D virtual reality (VR) simulation affected learning of key concepts in nanoscale cell biology for students aged 12 to 13. The haptic interface was designed so that the haptic feedback could be turned on or switched off. Students (N = 64), in two secondary schools, worked in pairs, on activities designed to support learning of specific difficult concepts. Findings from observation of the activities and interviews revealed that students believed that being immersed in the 3D VR environment and being able to feel structures and movements within the model and work collaboratively assisted their learning. More specifically, the pilot/co-pilot model that we developed was successful for enabling collaborative learning and reducing the isolating effects of immersion with a 3D headset. Results of pre and post-tests of conceptual knowledge showed significant knowledge gains but addition of haptic feedback did not affect the knowledge gains significantly. The study enabled identification of important issues to consider when designing and using haptic-enabled 3D VR environments for collaborative learning. [ABSTRACT FROM AUTHOR]

Samples of bleached kraft pine cellulosic pulp, either treated with an enzyme preparation (a Thermomyces lanuginosus xylanase, an Aspergillus sp. cellulase, and a multienzyme preparation NS-22086 containing both these activities) or untreated, were refined in a laboratory PFI mill. The treatment with cellulases contained in the last two preparations significantly improved the pulp’s susceptibility to refining (the target freeness value of 30°SR was achieved in a significantly shorter time), increased water retention value (WRV) and fines contents while the weighted average fiber length was significantly reduced. These changes of pulp parameters caused deterioration of paper strength properties. The treatment with the xylanase, which partially hydrolyzed xylan, small amounts of which are associated with cellulose fibers, only slightly loosened the structure of fibers. These subtle changes positively affected the susceptibility of the pulp to refining (refining energy was significantly reduced) and improved the static strength properties of paper. Thus, the treatment of kraft pulps with xylanases may lead to substantial savings of refining energy without negative effects on paper characteristics. [ABSTRACT FROM AUTHOR]

A burgeoning technique called time-resolved cryo-EM is granting insights into the tiny motors and devices that power life. [ABSTRACT FROM AUTHOR]

Direct interactions between cells in tissue are incompletely understood because the advanced technologies required to examine them are still in their infancy. A new method can decipher cell–cell interactions on a large scale.Tagging method offers versatile way to track interactions between cells. [ABSTRACT FROM AUTHOR]

Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the “xyl-doc” cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics. [ABSTRACT FROM AUTHOR]

The protein NINJ1 drives membrane rupture associated with certain types of cell death. Investigation of NINJ1 reveals mechanistic details of how it functions, raising the possibility of developing new therapeutics.Insights into a mechanism that ruptures the plasma membrane. [ABSTRACT FROM AUTHOR]

DNA methylation functions as a repressive epigenetic mark that can be reversed by the Ten-eleven translocation (TET) family of DNA dioxygenases that sequentially oxidize 5-methylcytosine into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Both 5fC and 5caC can be excised by DNA base-excision repair factors leading to unmodified cytosines. TET enzymes were recently implicated as potential risk factors for inflammatory bowel disease (IBD), but the contribution of TET-mediated DNA oxidation to intestinal homeostasis and response to environmental stressors are unknown. Here, we show prominent roles of TET3 in regulating mouse intestinal epithelial differentiation and response to luminal stressors. Compared with wild-type littermates, mice with intestinal epithelial cell-specific ablation of Tet3 (Tet3?IEC) demonstrated a decreased transcriptome involved in innate immune response, Paneth cell differentiation, and epithelial regeneration. Tet3IEC mice exhibited an elevated susceptibility to enteric pathogen infection that is correlated with a decreased epithelial 5hmC abundance. Infection of human enterocytes or mice with the pathogenic bacteria acutely increased 5hmC abundance. Genome-wide 5hmC profiling revealed a shift of genomic enrichment of 5hmC toward genes involved in activating Notch, Wnt, and autophagy pathways. Furthermore, chemical stressor dextran sulfate sodium (DSS) represses epithelial 5hmC abundance in a temporal fashion, and Tet3IEC mice exhibited increased susceptibility to DSS experimental colitis with reduced regenerative capacity. TET3 is a critical regulator of gut epithelial DNA methylome and transcriptome, especially in response to luminal stressors, for the maintenance of tissue homeostasis. [ABSTRACT FROM AUTHOR]

Human plasma kallikrein (PKa) is obtained by activating its precursor, prekallikrein (PK), historically named the Fletcher factor. Human PKa and tissue kallikreins are serine proteases from the same family, having high- and low-molecular weight kininogens (HKs and LKs) as substrates, releasing bradykinin (Bk) and Lys-bradykinin (Lys-Bk), respectively. This review presents a brief history of human PKa with details and recent observations of its evolution among the vertebrate coagulation proteins, including the relations with Factor XI. We explored the role of Factor XII in activating the plasma kallikrein-kinin system (KKS), the mechanism of activity and control in the KKS, and the function of HK on contact activation proteins on cell membranes. The role of human PKa in cell biology regarding the contact system and KSS, particularly the endothelial cells, and neutrophils, in inflammatory processes and infectious diseases, was also approached. We examined the natural plasma protein inhibitors, including a detailed survey of human PKa inhibitors' development and their potential market. [ABSTRACT FROM AUTHOR]

Public participation in research, also known as citizen science, is being increasingly adopted for the analysis of biological volumetric data. Researchers working in this domain are applying online citizen science as a scalable distributed data analysis approach, with recent research demonstrating that non-experts can productively contribute to tasks such as the segmentation of organelles in volume electron microscopy data. This, alongside the growing challenge to rapidly process the large amounts of biological volumetric data now routinely produced, means there is increasing interest within the research community to apply online citizen science for the analysis of data in this context. Here, we synthesise core methodological principles and practices for applying citizen science for analysis of biological volumetric data. We collate and share the knowledge and experience of multiple research teams who have applied online citizen science for the analysis of volumetric biological data using the Zooniverse platform (www.zooniverse.org). We hope this provides inspiration and practical guidance regarding how contributor effort via online citizen science may be usefully applied in this domain. [ABSTRACT FROM AUTHOR]

The sea urchin larva has been used by biologists for more than a century to study the development and evolution of animals. Surprisingly, very little information has been generated regarding the physiology of this small planktonic organism. However, in the context of anthropogenic CO2-driven ocean acidification (OA), the membrane transport physiology and energetics of this marine model organism have received considerable attention in the past decade. This has led to the discovery of new, exciting physiological systems, including a highly alkaline digestive tract and the calcifying primary mesenchyme cells that generate the larval skeleton. These physiological systems directly relate to the energetics of the organisms when challenged by OA. Here we review the latest membrane transport physiology and energetics in the sea urchin larva, we identify emerging questions, and we point to important future directions in the field of marine physiology in times of rapid climate change. [ABSTRACT FROM AUTHOR]

Simple Summary: Parathyroid-hormone-related protein (PTHrP) is a protein hormone of 139, 141, or 173 amino acids, which may be cleaved into smaller bioactive forms, comprising amino terminus, mid-region, and carboxy terminus peptides, active as key controllers of viability, proliferation, and differentiation in diverse normal and pathological cell and tissue model systems via the reprogramming of gene expression and intracellular signalization. Within the large number of data available in the literature on this matter, the objective of this review is to review selected studies that report the detection of molecular markers of exposure to PTHrP, either as full-length protein or as discrete peptides, in peculiar normal or non-neoplastic biological contexts. In particular, the data presented relate to adipose, bone, dental, cartilaginous, and skin tissues, as well as intestinal, renal, hepatic, pulmonary, and pancreatic epithelia, with a focus on hepatic fibrosis-, pancreatitis-, and diabetes-related changes, as demonstrated by molecular profiling, briefly recapitulating the biological implications of the specific gene and/or pathway activation or inactivation. Parathyroid-hormone-related protein (PTHrP) is encoded by the PTHLH gene which, via alternative promoter usage and splicing mechanisms, can give rise to at least three isoforms of 139, 141, and 173 amino acids with distinct C-terminals. PTHrP is subjected to different post-translational processing that generates smaller bioactive forms, comprising amino terminus, mid-region (containing a nuclear/nucleolar targeting signal), and carboxy terminus peptides. Both the full-length protein and the discrete peptides are key controllers of viability, proliferation, differentiation, and apoptosis in diverse normal and pathological biological systems via the reprogramming of gene expression and remodulation of PKA or PKC-mediated signalization mechanisms. The aim of this review is to pick up selected studies on PTHrP-associated signatures as revealed by molecular profiling assays, focusing on the available data about exemplary differentiating, differentiated, or nontumoral cell and tissue models. In particular, the data presented relate to adipose, bone, dental, cartilaginous, and skin tissues, as well as intestinal, renal, hepatic, pulmonary, and pancreatic epithelia, with a focus on hepatic fibrosis-, pancreatitis-, and diabetes-related changes as diseased states. When reported, the biochemical and/or physiological aspects associated with the specific molecular modulation of gene expression and signal transduction pathways in the target model systems under examination are also briefly described. [ABSTRACT FROM AUTHOR]

How do mitochondrial organelles remove damaged parts of inner membrane for recycling in the cytoplasm? The discovery of an exit route that flips inner membrane outside the organelle provides some answers. Pathway selectively removes inner membrane from mitochondrial organelles. [ABSTRACT FROM AUTHOR]

Cells that form tissue barriers rely on cell–cell contacts called tight junctions. These structures assemble from protein condensates that spread along the cell membrane like a water droplet spreading over glass.Step-by-step formation of tight junctions between epithelial cells. [ABSTRACT FROM AUTHOR]

The discovery that an evolutionarily conserved molecule used to make cholesterol also acts as a defence against a cell-death mechanism called ferroptosis might lead to new ways to treat cancer and other clinical conditions.Molecule used to make cholesterol also protects against cell death. [ABSTRACT FROM AUTHOR]

The hundreds of receptors that give us our sense of smell have been found to have important roles in other parts of the body, and the prospect of targeting them with drugs is growing. [ABSTRACT FROM AUTHOR]

Based on electrohysterogram, this paper designed a new method using wavelet-based nonlinear features and stacked sparse autoencoder for preterm birth detection. For each sample, three level wavelet decomposition of a time series was performed. Approximation coefficients at level 3 and detail coefficients at levels 1, 2 and 3 were extracted. Sample entropy of the detail coefficients at levels 1, 2, 3 and approximation coefficients at level 3 were computed as features. The classifier was constructed based on stacked sparse autoencoder. In addition, stacked sparse autoencoder was further compared with extreme learning machine and support vector machine in relation to their classification performance of electrohysterogram. The experiment results reveal that classifier based on stacked sparse autoencoder showed better performance than the other two classifiers with an accuracy of 90%, a sensitivity of 92%, a specificity of 88%. The results indicate that the method proposed in this paper could be effective for detecting preterm birth in electrohysterogram and the framework designed in this work presents higher discriminability than other techniques. [ABSTRACT FROM AUTHOR]

Data analysis for flow-based in-vitro receptomics array, like a tongue-on-a-chip, is complicated by the relatively large variability within and between arrays, transfected DNA types, spots, and cells within spots. Simply averaging responses of spots of the same type would lead to high variances and low statistical power. This paper presents an approach based on linear mixed models, allowing a quantitative and robust comparison of complex samples and indicating which receptors are responsible for any differences. These models are easily extended to take into account additional effects such as the build-up of cell stress and to combine data from replicated experiments. The increased analytical power this brings to receptomics research is discussed. [ABSTRACT FROM AUTHOR]

Selfish genetic elements (historically also referred to as selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA, genomic outlaws) are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no or a negative effect on organismal fitness. [–] Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are . Early observations of selfish genetic elements were made almost a century ago, but the topic did not get widespread attention until several decades later. Inspired by the popularized by [] and ,[] two papers were published back-to-back in Nature in 1980—by and [] and and Carmen Sapienza[] respectively—introducing the concept of selfish genetic elements (at the time called “selfish DNA”) to the wider scientific community. Both papers emphasized that genes can spread in a population regardless of their effect on organismal fitness as long as they have a transmission advantage. Selfish genetic elements have now been described in most groups of organisms, and they demonstrate a remarkable diversity in the ways by which they promote their own transmission.[] Though long dismissed as genetic curiosities, with little relevance for evolution, they are now recognized to affect a wide swath of biological processes, ranging from genome size and architecture to speciation.[] [ABSTRACT FROM AUTHOR]

Endo-ß-1,4-glucanase AkEG21 belonging to glycosyl hydrolase family 45 (GHF45) is the most abundant cellulase in the digestive fluid of sea hare (Aplysia kurodai). The specific activity of this 21-kDa enzyme is considerably lower than those of other endo ß-1,4-glucanases in the digestive fluid of A. kurodai, therefore its role in whole cellulose hydrolysis by sea hare is still uncertain. Although AkEG21 has a catalytic domain without a cellulose binding domain, it demonstrated stable binding to cellulose fibers, similar to that of fungal cellobiohydrolase (CBH) 1 and CBH 2, which is strongly inhibited by cellohexaose, suggesting the involvement of the catalytic site in cellulose binding. Cellulose-bound AkEG21 hydrolyzed cellulose to cellobiose, cellotriose and cellotetraose, but could not digest an external substrate, azo-carboxymethyl cellulose. Cellulose hydrolysis was considerably stimulated by the synergistic action of cellulose-bound AkEG21 and AkEG45, another ß-1,4-endoglucanase present in the digestive fluid of sea hare; however no synergy in carboxymethylcellulose hydrolysis was observed. When AkEG21 was removed from the digestive fluid by immunoprecipitation, the cellulose hydrolyzing activity of the fluid was significantly reduced, indicating a critical role of AkEG21 in cellulose hydrolysis by A. kurodai. These findings suggest that AkEG21 is a processive endoglucanase functionally equivalent to the CBH, which provides a CBH-independent mechanism for the mollusk to digest seaweed cellulose to glucose. [ABSTRACT FROM AUTHOR]

The tumor suppressor p53 (also known as TP53) plays a central role in cellular stress responses by regulating transcription of multiple target genes. The temporal dynamics of p53 are thought to be important for its function; these encode input information and are decoded to induce distinct cellular phenotypes. However, it remains unclear to what extent the temporal dynamics of p53 reflect the activity of p53-induced gene expression. In this study, we report a multiplexed reporter system that allows us to visualize the transcriptional activity of p53 at the single-cell level. Our reporter system features simple and sensitive observation of the transcriptional activity of endogenous p53 to the response elements of various target genes. Using this system, we show that the transcriptional activation of p53 exhibits strong cell-to-cell heterogeneity. The transcriptional activation of p53 after etoposide treatment is highly dependent on the cell cycle but this is not seen after UV exposure. Finally, we show that our reporter system allows simultaneous visualization of the transcriptional activity of p53 and cell cycle. Our reporter system can thus be a useful tool for studying biological processes involving the p53 signaling pathway. [ABSTRACT FROM AUTHOR]

Forces generated by actin assembly assist membrane invagination during clathrin-mediated endocytosis (CME). The sequential recruitment of core endocytic proteins and regulatory proteins, and assembly of the actin network, are well documented in live cells and are highly conserved from yeasts to humans. However, understanding of CME protein self-organization, as well as the biochemical and mechanical principles that underlie actin's role in CME, is lacking. Here, we show that supported lipid bilayers coated with purified yeast Wiskott Aldrich Syndrome Protein (WASP), an endocytic actin assembly regulator, and incubated in cytoplasmic yeast extracts, recruit downstream endocytic proteins and assemble actin networks. Time-lapse imaging of WASP-coated bilayers revealed sequential recruitment of proteins from different endocytic modules, faithfully replicating in vivo behavior. Reconstituted actin networks assemble in a WASP-dependent manner and deform lipid bilayers, as seen by electron microscopy. Time-lapse imaging revealed that vesicles are released from the lipid bilayers with a burst of actin assembly. Actin networks pushing on membranes have previously been reconstituted; here, we have reconstituted a biologically important variation of these actin networks that self-organize on bilayers and produce pulling forces sufficient to bud off membrane vesicles. We propose that actin-driven vesicle generation may represent an ancient evolutionary precursor to diverse vesicle forming processes adapted for a wide array of cellular environments and applications. [ABSTRACT FROM AUTHOR]