14,290 results
Search Results
2. Nucleic Acid Hybridization with RNA Immobilized on Filter Paper
- Author
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Saxinger, W. C., Ponnamperuma, C., and Gillespie, D.
- Published
- 1972
3. Nanos gigantium humeris insidentes: old papers informing new research into Toxoplasma gondii.
- Author
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Lodoen, Melissa B., Smith, Nicholas C., Soldati-Favre, Dominique, Ferguson, David J.P., and van Dooren, Giel G.
- Subjects
- *
TOXOPLASMA gondii , *PARASITES , *PARASITE life cycles , *CYTOLOGY , *INTRACELLULAR pathogens , *TOXOPLASMA , *SCIENTIFIC community - Abstract
[Display omitted] • Seminal papers in Toxoplasma research are revisited. • We focus on a paper that contributed to uncovering the complete life-cycle of Toxoplasma. • A paper that revealed some of the unique cellular biology of the parasite is examined. • A study that elucidated the nature of the compartment in which Toxoplasma resides is described. • We revisit a seminal paper in understanding the immune responses to Toxoplasma infection. Since Nicolle, Manceaux and Splendore first described Toxoplasma gondii as a parasite of rodents and rabbits in the early 20th century, a diverse and vigorous research community has been built around studying this fascinating intracellular parasite. In addition to its importance as a pathogen of humans, livestock and wildlife, modern researchers are attracted to T. gondii as a facile experimental system to study many aspects of evolutionary biology, cellular biology, host-microbe interactions, and host immunity. For new researchers entering the field, the extensive literature describing the biology of the parasite, and the interactions with its host, can be daunting. In this review, we examine four foundational studies that describe various aspects of T. gondii biology, presenting a 'journal club'-style analysis of each. We have chosen a paper that established the beguiling life cycle of the parasite (Hutchison et al., 1971), a paper that described key features of its cellular biology that the parasite shares with related organisms (Gustafson et al., 1954), a paper that characterised the origin of the unique compartment in which the parasite resides within host cells (Jones and Hirsch, 1972), and a paper that established a key mechanism in the host immune response to parasite infection (Pfefferkorn, 1984). These interesting and far-reaching studies set the stage for subsequent research into numerous facets of parasite biology. As well as providing new researchers with an entry point into the literature surrounding the parasite, revisiting these studies can remind us of the roots of our discipline, how far we have come, and the new directions in which we might head. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
4. De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera).
- Author
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Xianjun, Peng, Linhong, Teng, Xiaoman, Wang, Yucheng, Wang, and Shihua, Shen
- Subjects
- *
GENE expression in plants , *PAPER mulberry , *SEEDLINGS , *PLANT species , *PLANT genetics , *GENETIC transcription in plants - Abstract
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]
- Published
- 2014
- Full Text
- View/download PDF
5. Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology
- Author
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Alicia J. Kowaltowski, Fabio Luis Forti, Roberto Kopke Salinas, S C Farah, Nicolas C. Hoch, Ricardo J. Giordano, Ohara Augusto, Glaucia Mendes Souza, A. M. Da-Silva, P. Di Mascio, Cypreste Oliveira, Walter R. Terra, Sayuri Miyamoto, Claudiana Lameu, M. J. M. Alves, Daniela S. Basseres, Alexandre Bruni-Cardoso, Sandro R. Marana, Hugo A. Armelin, Hernan Chaimovich, João C. Setubal, Deborah Schechtman, Marisa Helena Gennari de Medeiros, Sergio Verjovski-Almeida, Eduardo M. Reis, Maria Teresa Machini, Suely Lopes Gomes, Shirley Schreier, F J Gueiros Filho, Henning Ulrich, Bettina Malnic, Walter Colli, Mari Cleide Sogayar, P. Colepicolo Neto, Carlos Takeshi Hotta, Graziella E. Ronsein, Mauricio S. Baptista, Iolanda M. Cuccovia, Daniela R. Truzzi, Leticia Labriola, Flavia Vischi Winck, Carmen Veríssima Ferreira, Guilherme Menegon Arantes, Flavia Carla Meotti, Bianca Zingales, Regina L. Baldini, Nadja C. de Souza-Pinto, and Etelvino J. H. Bechara
- Subjects
0301 basic medicine ,Physiology ,media_common.quotation_subject ,Immunology ,Biophysics ,MEDLINE ,Ocean Engineering ,Biochemistry ,03 medical and health sciences ,Presentation ,0302 clinical medicine ,Political science ,PRÉ-IMPRESSOS ,Humans ,General Pharmacology, Toxicology and Pharmaceutics ,Composition (language) ,Publication ,lcsh:QH301-705.5 ,Molecular Biology ,media_common ,Publishing ,lcsh:R5-920 ,business.industry ,General Neuroscience ,Research ,Subject (documents) ,Cell Biology ,General Medicine ,Concepts and Comments ,Scientific journals ,Open access ,Molecular biology ,030104 developmental biology ,Scientific editing ,lcsh:Biology (General) ,030220 oncology & carcinogenesis ,Pre-prints ,Position paper ,Periodicals as Topic ,business ,lcsh:Medicine (General) ,Scientific communication ,Brazil - Abstract
The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of Sao Paulo, on this subject.
- Published
- 2019
6. De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera).
- Author
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Xianjun, Peng, Linhong, Teng, Xiaoman, Wang, Yucheng, Wang, and Shihua, Shen
- Subjects
GENE expression in plants ,PAPER mulberry ,SEEDLINGS ,PLANT species ,PLANT genetics ,GENETIC transcription in plants - Abstract
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]
- Published
- 2014
- Full Text
- View/download PDF
7. Review Paper:current Trends in Biocompatibility Testing.
- Author
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Kirkpatrick, C J, Bittinger, F, Wagner, M, Köhler, H, van Kooten, T G, Klein, C L, and Otto, M
- Subjects
BIOCOMPATIBILITY ,BIOMEDICAL materials ,MOLECULAR biology - Abstract
Biocompatibility remains the central theme for biomaterials applications in medicine. It is generally accepted that this term means not only absence of a cytotoxic effect but also positive effects in the sense of biofunctionality, i.e. promotion of biological processes which further the intended aim of the application of a biomaterial. The national and international standards for testing regimes represent a lowest common denominator for such applications and do not necessarily ensure that optimal function will be achieved. The authors' thesis is that biocompatibility testing has scope for extensive development with respect to biofunctionality. The present paper reviews current trends in the in vitro aspects of biocompatibility testing. As well as a critical appraisal of the recent literature, future trends are also stressed, which the authors regard as essential for a meaningful integration of a modern biological approach into new developments in the material sciences. These include the application of modern techniques of cell and molecular biology, the concepts of tissue remodelling, hybrid organ development and encapsulated cell technology. [ABSTRACT FROM AUTHOR]
- Published
- 1998
- Full Text
- View/download PDF
8. TonB or not TonB: is that the question?This paper is one of a selection of papers published in a Special Issue entitled CSBMCB 53rd Annual Meeting — Membrane Proteins in Health and Disease, and has undergone the Journal’s usual peer review process
- Author
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Karla D. Krewulak and Hans J. Vogel
- Subjects
Biochemistry ,Membrane protein ,bacteria ,Cell Biology ,Computational biology ,Biology ,Molecular Biology - Abstract
Bacteria are able to survive in low-iron environments by sequestering this metal ion from iron-containing proteins and other biomolecules such as transferrin, lactoferrin, heme, hemoglobin, or other heme-containing proteins. In addition, many bacteria secrete specific low molecular weight iron chelators termed siderophores. These iron sources are transported into the Gram-negative bacterial cell through an outer membrane receptor, a periplasmic binding protein (PBP), and an inner membrane ATP-binding cassette (ABC) transporter. In different strains the outer membrane receptors can bind and transport ferric siderophores, heme, or Fe3+as well as vitamin B12, nickel complexes, and carbohydrates. The energy that is required for the active transport of these substrates through the outer membrane receptor is provided by the TonB/ExbB/ExbD complex, which is located in the cytoplasmic membrane. In this minireview, we will briefly examine the three-dimensional structure of TonB and the current models for the mechanism of TonB-dependent energy transduction. Additionally, the role of TonB in colicin transport will be discussed.
- Published
- 2011
9. Heterochromatin and the DNA damage response: the need to relaxThis paper is one of a selection of papers in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process
- Author
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Graham Dellaire and Kendra L. CannK.L. Cann
- Subjects
Genetics ,Heterochromatin ,DNA damage ,DNA repair ,Cell Biology ,Biology ,Biochemistry ,Genealogy ,Chromatin ,Higher Order Chromatin Structure ,Heterochromatin protein 1 ,Molecular Biology ,Selection (genetic algorithm) - Abstract
Higher order chromatin structure has an impact on all nuclear functions, including the DNA damage response. Over the past several years, it has become increasingly clear that heterochromatin and euchromatin represent separate entities with respect to both damage sensitivity and repair. The chromatin compaction present in heterochromatin helps to protect this DNA from damage; however, when lesions do occur, the compaction restricts the ability of DNA damage response proteins to access the site, as evidenced by its ability to block the expansion of H2AX phosphorylation. As such, DNA damage in heterochromatin is refractory to repair, which requires the surrounding chromatin structure to be decondensed. In the case of DNA double-strand breaks, this relaxation is at least partially mediated by the ATM kinase phosphorylating and inhibiting the function of the transcriptional repressor KAP1. This review will focus on the functions of KAP1 and other proteins involved in the maintenance or restriction of heterochromatin, including HP1 and TIP60, in the DNA damage response. As heterochromatin is important for maintaining genomic stability, cells must maintain a delicate balance between allowing repair factors access to these regions and ensuring that these regions retain their organization to prevent increased DNA damage and chromosomal mutations.
- Published
- 2011
10. Evidence that FOXO3a is involved in oocyte apoptosis in the neonatal rat ovaryThis paper is one of a selection of papers published in this special issue entitled 'Second International Symposium on Recent Advances in Basic, Clinical, and Social Medicine' and has undergone the Journal's usual peer review process
- Author
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Jin-Jie XuJ.-J. Xu, Xu-Xia SuiX.-X. Sui, Yu-Cai FuY.-C. Fu, and Li-Li LuoL.-L. Luo
- Subjects
Neonatal rat ,Cell Biology ,Biology ,Bioinformatics ,Oocyte ,Biochemistry ,Sprague dawley ,medicine.anatomical_structure ,Social medicine ,Immunology ,medicine ,Forkhead Box Protein O3 ,Molecular Biology - Abstract
Previous studies have proposed that the forkhead transcription factor FOXO3a is involved in cell cycle arrest and apoptosis and that it may also repress follicular development by inducing cell cycle arrest in ovaries. We have recently demonstrated that FOXO3a induces oocyte apoptosis of neonatal rat ovaries under in vitro conditions. In the present study, we evaluated the role of FOXO3a in oocyte apoptosis under in vivo conditions. Ovaries from rats were obtained from newborns on postnatal day (PD) 1, 2, 3, and 4. TUNEL assay results showed that oocyte apoptosis occurred mainly on PD 1 and 2. Immunohistochemical staining of FOXO3a, Bim, Fas ligand (FasL), p27KIP1, caspase-8, and caspase-3 showed that they were all expressed mainly in naked oocytes on PD 1 and 2. The percentage of positive FOXO3a staining of oocytes reached peak levels in the ovaries of 2-day-old rats, which was consistent with the rate of the apoptotic profiles determined by TUNEL. The percentage between TUNEL-positive and FOXO3a-positive oocytes in the nucleus showed no statistical differences within the 4-day-old rat ovaries. Furthermore, the positive oocyte percentage of the target factors of FOXO3a (Bim, p27KIP1, and FasL) and pro-apoptotic proteins (caspase-3 and caspase-8) also reached peak levels in the ovaries of 2-day-old rats, which was similar to the rate of FOXO3a-positive oocytes. These results suggest that FOXO3a in the oocyte nucleus is involved in oocyte apoptosis; that is, FOXO3a-positive oocytes may be the apoptotic cells. To verify this, rat oocytes were subjected to TUNEL and immunofluorescent double-labeling assays. We found that TUNEL-positive cells were also FOXO3a-, Bim-, or FasL-positive. To identify the downstream target of FOXO3a, double immunofluorescent staining with antibodies to Bim and FasL was performed. We found that FOXO3a-positive cells were also Bim- and FasL-positive. We conclude that the overexpression of FOXO3a in the oocyte nucleus of neonatal rat ovaries may play an important role in the apoptosis of naked oocytes, and that Bim, FasL, and p27KIP1 are the key downstream factors of FOXO3a.
- Published
- 2010
11. Molecular simulations of protein disorderThis paper is one of a selection of papers published in this special issue entitled 'Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases' and has undergone the Journal's usual peer review process
- Author
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Régis Pomès and Sarah Rauscher
- Subjects
Selection (linguistics) ,Engineering ethics ,Molecular simulation ,Protein folding ,Cell Biology ,Biology ,Intrinsically disordered proteins ,Bioinformatics ,Molecular Biology ,Biochemistry - Abstract
Protein disorder is abundant in proteomes throughout all kingdoms of life and serves many biologically important roles. Disordered states of proteins are challenging to study experimentally due to their structural heterogeneity and tendency to aggregate. Computer simulations, which are not impeded by these properties, have recently emerged as a useful tool to characterize the conformational ensembles of intrinsically disordered proteins. In this review, we provide a survey of computational studies of protein disorder with an emphasis on the interdisciplinary nature of these studies. The application of simulation techniques to the study of disordered states is described in the context of experimental and bioinformatics approaches. Experimental data can be incorporated into simulations, and simulations can provide predictions for experiment. In this way, simulations have been integrated into the existing methodologies for the study of disordered state ensembles. We provide recent examples of simulations of disordered states from the literature and our own work. Throughout the review, we emphasize important predictions and biophysical understanding made possible through the use of simulations. This review is intended as both an overview and a guide for structural biologists and theoretical biophysicists seeking accurate, atomic-level descriptions of disordered state ensembles.
- Published
- 2010
12. Partial unfolding and oligomerization of stromal interaction molecules as an initiation mechanism of store operated calcium entryThis paper is one of a selection of papers published in this special issue entitled 'Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases' and has undergone the Journal's usual peer review process
- Author
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Peter B. Stathopulos and Mitsuhiko Ikura
- Subjects
Biochemistry ,Chemistry ,Stromal Interaction Molecules ,Mechanism (biology) ,Protein folding ,Cell Biology ,Molecular Biology ,Store-operated calcium entry - Abstract
Spatiotemporally discrete cytoplasmic Ca2+ fluctuations are fundamental eukaryotic signals in myriad physiological and pathophysiological functions. Store-operated Ca2+ entry is the process whereby a decrease in endoplasmic reticulum (ER) luminal Ca2+ levels activates Ca2+ release activated calcium (CRAC) channels on the plasma membrane (PM), providing a sustained Ca2+ elevation to the cytoplasm and ultimately replenishing the ER lumen Ca2+ supply. Stromal interaction molecules (STIMs) are the Ca2+ sensors of the ER lumen, which macromolecularly couple depleted ER Ca2+ to the assembly and opening of PM CRAC channels. The considerable stability difference caused by Ca2+ loading and depletion within the luminal portion of STIMs modulates intramolecular cytoplasmic domain interactions essential to the assembly of PM CRAC channels. Thus, the action of the entire complex is tightly regulated through the Ca2+ sensitivity of luminal STIM domains. Recent structural and biochemical studies suggest that partial unfolding – coupled oligomerization of STIMs is a crucial step in CRAC channel activation. Based on these and other published data, this minireview discusses what is currently known about the molecular mechanism of ER Ca2+ sensing by STIMs.
- Published
- 2010
13. Structural disorder and dynamics of elastinThis paper is one of a selection of papers published in this special issue entitled 'Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases' and has undergone the Journal's usual peer review process
- Author
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Fred W. Keeley, Lisa D. MuiznieksL.D. Muiznieks, and Anthony S. WeissA.S. Weiss
- Subjects
Cognitive science ,Structural organization ,biology ,Mechanism (biology) ,Nanotechnology ,Cell Biology ,Biochemistry ,Structure and function ,Tissue elasticity ,Selection (linguistics) ,biology.protein ,Protein folding ,Psychology ,Molecular Biology ,Elastin - Abstract
Elastin is a self-assembling, extracellular-matrix protein that is the major provider of tissue elasticity. Here we review structural studies of elastin from over four decades, and draw together evidence for solution flexibility and conformational disorder that is inherent in all levels of structural organization. The characterization of disorder is consistent with an entropy-driven mechanism of elastic recoil. We conclude that conformational disorder is a constitutive feature of elastin structure and function.
- Published
- 2010
14. Mutational investigation of protein folding transition states by Φ-value analysis and beyond: lessons from SH3 domain foldingThis paper is one of a selection of papers published in this special issue entitled 'Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases' and has undergone the Journal's usual peer review process
- Author
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Sung Lun LinS.L. Lin, Philipp Neudecker, and Arash Zarrine-Afsar
- Subjects
Folding (chemistry) ,Selection (linguistics) ,Protein folding ,Cell Biology ,Sociology ,Bioinformatics ,Molecular Biology ,Biochemistry ,Value (mathematics) ,SH3 domain ,Epistemology - Abstract
Understanding how proteins adopt their unique native structures requires a complete structural characterization of the rate-limiting transition state(s) along the folding pathway. By definition, transition states are not significantly populated and are only accessible via folding kinetics studies. In this respect, interpreting the kinetic effects of amino acid substitutions (especially to Ala) via Φ-value analysis is the most common method to probe the structure of these transient, yet important states. A critical review of the key assumptions required for rigorous interpretation of Φ values reveals that a multiple substitution strategy in which a position of interest is mutated to a variety of amino acids, and not exclusively to Ala, provides the best means to characterize folding transition states. This approach has proven useful in revealing non-native interactions and (or) conformations in folding transition states. Moreover, by simultaneously examining the folding kinetics of multiple substitutions made at a single surface-exposed position using the Brønsted analysis the backbone conformation in a folding transition state can be investigated. For folding equilibria with exchange rates on the order of milliseconds, the kinetic parameters for Φ-value analysis can be obtained from NMR relaxation dispersion experiments, under fully native conditions, along with a wealth of high-resolution structural information about the states in exchange (native, denatured, and intermediate states that populate the pathway). This additional structural information, which is not readily obtained through stopped-flow based methods, can significantly facilitate the interpretation of Φ values because it often reports on the validity of the assumptions required for a rigorous interpretation of Φ values.
- Published
- 2010
15. Structural factors underlying the species barrier and susceptibility to infection in prion diseaseThis paper is one of a selection of papers published in this special issue entitled 'Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases' and has undergone the Journal's usual peer review process
- Author
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M. Qasim Khan, A. ChakrabarttyA. Chakrabartty, E. F. PaiE. Pai, and B. SweetingB. Sweeting
- Subjects
Genetics ,animal diseases ,Cell Biology ,Disease ,Biology ,Biochemistry ,Virology ,nervous system diseases ,Species barrier ,Protein folding ,Symptom onset ,Prion Proteins ,Molecular Biology ,Disease transmission ,Peptide sequence - Abstract
The term prion disease describes a group of fatal neurodegenerative diseases that are believed to be caused by the pathogenic misfolding of a host cell protein, PrP. Susceptibility to prion disease differs between species and incubation periods before symptom onset can change dramatically when infectious prion strains are transmitted between species. This effect is referred to as the species or transmission barrier. Prion strains represent different structures of PrPScand the conformational selection model proposes that the source of theses barriers is the preferential incorporation of PrP from a given species into only a subset of PrPScstructures of another species. The basis of this preferential incorporation is predicted to reside in subtle structural differences in PrP from varying species. The overall fold of PrP is highly conserved among species, but small differences in the amino acid sequence give rise to structural variability. In particular, the loop between the second β-strand and the second α-helix has shown structural variability between species, with loop mobility correlating with resistance to prion disease. Single amino acid polymorphisms in PrP within a species can also affect prion susceptibility, but do not appear to drastically alter the biophysical properties of the native form. These polymorphisms affect the propensity of self-association, in recombinant PrP, to form β-sheet enriched, oligomeric, and amyloid-like forms. These results indicate that the major factor in determining susceptibility to prion disease is the ability of PrP to adopt these misfolded forms by promoting conformational change and self association.
- Published
- 2010
16. A spectrum of gene regulatory phenomena at mammalian β-globin gene lociThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process
- Author
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George FrommG. Fromm and Michael Bulger
- Subjects
Genetics ,β globin gene ,Model system ,Cell Biology ,Biology ,Biochemistry ,Chromatin ,Evolutionary biology ,Gene cluster ,Molecular Biology ,Gene ,Selection (genetic algorithm) ,ChIA-PET - Abstract
The β-globin gene cluster in mammals, consisting of a set of erythroid-specific, developmentally activated, and (or) silenced genes, has long presented a model system for the investigation of gene regulation. As the number and complexity of models of gene activation and repression have expanded, so too has the complexity of phenomena associated with the regulation of the β-globin genes. Models for expression from within the locus must account for local (promoter-proximal), distal (enhancer-mediated), and domain-wide components of the regulatory pathways that proceed through mammalian development and erythroid differentiation. In this review, we provide an overview of transcriptional activation, silencing, chromatin structure, and the function of distal regulatory elements involved in the normal developmental regulation of β-globin gene expression.
- Published
- 2009
17. Getting to the center of X-chromosome inactivation: the role of transgenesThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process
- Author
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Jakub Minks and Carolyn J. Brown
- Subjects
Genetics ,XIST ,Cell Biology ,Epigenetics ,Biology ,Molecular Biology ,Biochemistry ,Genealogy ,Selection (genetic algorithm) ,X-inactivation ,Chromatin - Abstract
X-chromosome inactivation is a fascinating epigenetic phenomenon that is initiated by expression of a noncoding (nc)RNA, XIST, and results in transcriptional silencing of 1 female X. The process requires a series of events that begins even before XIST expression, and culminates in an active and a silent X within the same nucleus. We will focus on the role that transgenic systems have served in the current understanding of the process of X-chromosome inactivation, both in the initial delineation of an active and inactive X, and in the function of the XIST RNA. X inactivation is strictly cis-limited; recent studies have revealed elements within the X-inactivation center, the region required for inactivation, that are critical for the initial regulation of Xist expression and chromosome pairing. It has been revealed that the X-inactivation center contains a remarkable compendium of cis-regulatory elements, ncRNAs, and trans-acting pairing regions. We review the functional componentry of the X-inactivation center and discuss experiments that helped to dissect the XIST/Xist RNA and its involvement in the establishment of facultative heterochromatin.
- Published
- 2009
18. Influences of orally administered lactoferrin on IFN-γ and IL-10 production by intestinal intraepithelial lymphocytes and mesenteric lymph-node cellsThis paper is one of a selection of papers published in this Special Issue, entitled 7th International Conference on Lactoferrin: Structure, Function, and Applications, and has undergone the Journal's usual peer review process
- Author
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Natsuko Takakura, Mitsunori Takase, Hiroyuki Wakabayashi, and Koji Yamauchi
- Subjects
biology ,Lactoferrin ,business.industry ,medicine.medical_treatment ,Cell Biology ,digestive system ,Biochemistry ,Interleukin 10 ,Cytokine ,Immune system ,medicine.anatomical_structure ,Immunology ,biology.protein ,medicine ,Intraepithelial lymphocyte ,Interferon gamma ,business ,Molecular Biology ,Lymph node ,medicine.drug - Abstract
Intestinal mucosal immunity plays an important role in mucosal and systemic immune responses. We investigated the influences of orally administered bovine lactoferrin (LF) on cytokine production by intestinal intraepithelial lymphocytes (IEL) and mesenteric lymph-node (MLN) cells, especially T cells. Bovine LF or bovine serum albumin (control) was administered to mice once daily for 3 d. After 24 h from the last administration, IEL of the jejunum and ileum and MLN cells were isolated. These cells were cultured with and without the anti-T-cell-receptor antibody, and then the culture supernatants were assayed for cytokines with ELISA. Oral LF did not affect the ratio of T-cell subpopulations in IEL and MLN; however, LF enhanced both interferon (IFN)-γ and interleukin (IL)-10 production by unstimulated IEL and by IEL stimulated with the αβ T-cell receptor but not with the γδ T-cell receptor. LF also enhanced both IFN-γ and IL-10 production by stimulated and unstimulated MLN cells. The production level of IFN-γ by MLN cells was correlated with that of IL-10. These results suggest that oral LF enhances the production of both Th1-type and Th2/Tr-type cytokines in the small intestine of healthy animals.
- Published
- 2006
19. Crystal structure of the N-lobe of lactoferrin binding protein B from Moraxella bovis1 1This paper is an invited article as a result of a presentation at the International Lactoferrin Conference held in Mazatlan, Mexico (May 2011), and has undergone the Journal’s usual peer review process
- Author
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BeddekAmanda, ArutyunovaElena, B SchryversAnthony, W MakMichelle, LemieuxM. Joanne, and L BrooksCory
- Subjects
biology ,Lactoferrin ,Binding protein ,Moraxellaceae ,Cell Biology ,biology.organism_classification ,Biochemistry ,Microbiology ,Immunology ,biology.protein ,Neisseriaceae ,Molecular Biology ,Moraxella - Abstract
Lactoferrin (Lf) is a bi-lobed, iron-binding protein found on mucosal surfaces and at sites of inflammation. Gram-negative pathogens from the Neisseriaceae and Moraxellaceae families are capable of using Lf as a source of iron for growth through a process mediated by a bacterial surface receptor that directly binds host Lf. This receptor consists of an integral outer membrane protein, lactoferrin binding protein A (LbpA), and a surface lipoprotein, lactoferrin binding protein B (LbpB). The N-lobe of the homologous transferrin binding protein B, TbpB, has been shown to facilitate transferrin binding in the process of iron acquisition. Currently there is little known about the role of LbpB in iron acquisition or how Lf interacts with the bacterial receptor proteins. No structural information on any LbpB or domain is available. In this study, we express and purify from Escherichia coli the full-length LbpB and the N-lobe of LbpB from the bovine pathogen Moraxella bovis for crystallization trials. We demonstrate that M. bovis LbpB binds to bovine but not human Lf. We also report the crystal structure of the N-terminal lobe of LbpB from M. bovis and compare it with the published structures of TbpB to speculate on the process of Lf mediated iron acquisition.
- Published
- 2012
20. Prevalence and practices of immunofluorescent cell image processing: a systematic review.
- Author
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Helmbrecht, Hawley, Teng-Jui Lin, Janakiraman, Sanjana, Decker, Kaleb, and Nance, Elizabeth
- Subjects
IMAGE processing ,CELL imaging ,MEDICAL subject headings ,THRESHOLDING algorithms ,IMAGE processing software ,IMAGE analysis - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
21. How we do business (or, Why does it take other journals so long to review your paper?)
- Author
-
Daniel J. Klionsky
- Subjects
business.industry ,Conflict of Interest ,Commerce ,Cell Biology ,Suspect ,Biology ,Public relations ,Periodicals as Topic ,business ,Molecular Biology - Abstract
Have you ever wondered why it takes so long to get comments back from reviewers at some journals? After all, how long should it take to review a paper? I suspect most of us have asked this question at one time or another. While recently contemplating this, I thought it was time to tell you a little about how we run Autophagy, and at the same time compare it to the practices at some other journals where I have, on occasion (notably before the start of Autophagy), sent my own papers.
- Published
- 2008
22. Peer review of scientific papers—A never-ending conundrum
- Author
-
Errol C. Friedberg
- Subjects
Medicine ,Engineering ethics ,Cell Biology ,Periodicals as Topic ,Biology ,Molecular Biology ,Biochemistry - Published
- 2010
23. Effect of Cellulases and Xylanases on Refining Process and Kraft Pulp Properties.
- Author
-
Przybysz Buzała, Kamila, Przybysz, Piotr, Kalinowska, Halina, and Derkowska, Małgorzata
- Subjects
PINE ,CELLULASE ,XYLANASES ,SULFATE pulping process ,MULTIENZYME complexes ,HYDROLYSIS ,XYLANS - Abstract
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]
- Published
- 2016
- Full Text
- View/download PDF
24. White paper on plasma for medicine and hygiene: Future in plasma health sciences.
- Author
-
Bekeschus, Sander, Favia, Pietro, Robert, Eric, and von Woedtke, Thomas
- Subjects
- *
PLASMA materials processing , *MEDICINE , *HYGIENE , *BIOMATERIALS , *WOUND healing , *ONCOLOGY - Abstract
Plasma Science and Technology offer their valuable contribution to human health since more than 50 years, after decades of experiences in the field of biomaterials; and more than a decade in using plasmas for therapeutic uses in medicine. Current knowledge as well as key challenges and opportunities for the human health have been intensely discussed during the Future in Plasma Science II (FIPS II) workshop in February 2016 in Greifswald, Germany. This contribution summarizes the major outcomes of the meeting and the current literature and consensus with an emphasis on major challenges in the fields of Plasma Science and Technology for improving human health. Present and upcoming avenues in 'Plasma Health Science' concluded from the second 'Future in Plasma Science' workshop are summarized. Topics include plasma biomedical surfaces, decontamination, biology, wound healing, and oncology. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
25. Growth-Dependent Alterations in Oligomannosyl Cores of Glycopeptides
- Author
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Ceccarini, Costante, Muramatsu, Takashi, Tsang, Joyce, and Atkinson, Paul H.
- Published
- 1975
26. Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties.
- Author
-
Badalato, Nelly, Guillot, Alain, Sabarly, Victor, Dubois, Marc, Pourette, Nina, Pontoire, Bruno, Robert, Paul, Bridier, Arnaud, Monnet, Véronique, Sousa, Diana Z., Durand, Sylvie, Mazéas, Laurent, Buléon, Alain, Bouchez, Théodore, Mortha, Gérard, and Bize, Ariane
- Subjects
PROTEOMICS ,CELLULOSE ,SOLID waste ,ANAEROBIC digestion ,CELLULOLYTIC bacteria - Abstract
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]
- Published
- 2017
- Full Text
- View/download PDF
27. Pterin-6-aldehyde, a Cancer Cell Catabolite: Identification and Application in Diagnosis and Treatment of Human Cancer
- Author
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Halpern, R., Halpern, B. C., Stea, B., Dunlap, A., Conklin, K., Clark, B., Ashe, H., Sperling, L., Halpern, J. A., Hardy, D., and Smith, R. A.
- Published
- 1977
28. Differentiation between Intracellular and Cell Surface Glycosyl Transferases: Galactosyl Transferase Activity in Intact Cells and in Cell Homogenate
- Author
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Deppert, Wolfgang, Werchau, Hermann, and Walter, Gernot
- Published
- 1974
29. Growth of Hybridoma Cells in Serum-Free Medium: Ethanolamine is an Essential Component
- Author
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Murakami, Hiroki, Masui, Hideo, Sato, Gordon H., Sueoka, Noboru, Chow, Theresa P., and Kano-Sueoka, Tamiko
- Published
- 1982
30. Caveat Pre-Emptor: Contextualising peer review and publication.
- Author
-
null, null
- Subjects
CAVEAT emptor doctrine ,PROFESSIONAL peer review ,EDITORS ,BIOENGINEERING - Abstract
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]
- Published
- 2019
- Full Text
- View/download PDF
31. How China is capturing attention with landmark research.
- Author
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Conroy, Gemma, Pawar, Pratik, and Powell, Sian
- Abstract
From ancient sea species to clues on comets, papers by the country’s talented scientists are regularly making headlines. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
32. A research‐led flexible cell biology practical for biological sciences undergraduate and postgraduate degree courses.
- Author
-
Divan, Aysha, Alzahrani, Areej, Shaik, Faheem, Mitchell, Joanna, Harrison, Michael A., Odell, Adam, and Ponnambalam, Sreenivasan
- Subjects
LIFE sciences ,CYTOLOGY ,COLLEGE curriculum ,CELL culture ,CELL cycle ,ANALYTICAL skills - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
33. Truth in Science Publishing: A Personal Perspective.
- Author
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Südhof, Thomas C.
- Subjects
PROFESSIONAL peer review ,REPRODUCIBLE research ,RESEARCH ,FALSIFICATION of data ,ACADEMIC fraud ,RESEARCH grants ,SCIENCE publishing - Abstract
Scientists, public servants, and patient advocates alike increasingly question the validity of published scientific results, endangering the public’s acceptance of science. Here, I argue that emerging flaws in the integrity of the peer review system are largely responsible. Distortions in peer review are driven by economic forces and enabled by a lack of accountability of journals, editors, and authors. One approach to restoring trust in the validity of published results may be to establish basic rules that render peer review more transparent, such as publishing the reviews (a practice already embraced by some journals) and monitoring not only the track records of authors but also of editors and journals. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
34. Associations between body size, nutrition and socioeconomic position in early life and the epigenome: A systematic review.
- Author
-
Maddock, Jane, Wulaningsih, Wahyu, Kuh, Diana, Hardy, Rebecca, Fernandez, Juan Castillo, Bell, Jordana, Ploubidis, George B., and Goodman, Alissa
- Subjects
BODY size ,NUTRITION ,SOCIOECONOMICS ,DNA methylation ,REGULATION of growth ,GENETICS - Abstract
Background: Body size, nutrition and socioeconomic position (SEP) in early life have been associated with a wide range of long-term health effects. Epigenetics is one possible mechanism through which these early life exposures can impact later life health. We conducted a systematic review examining the observational evidence for the impact of body size, nutrition and SEP in early life on the epigenome in humans. Methods: This systematic review is registered with the PROSPERO database (registration number: CRD42016050193). Three datasets were simultaneously searched using Ovid and the resulting studies were evaluated by at least two independent reviewers. Studies measuring epigenetic markers either at the same time as, or after, the early life exposure and have a measure of body size, nutrition or SEP in early life (up to 12 years), written in English and from a community-dwelling participants were included. Results: We identified 90 eligible studies. Seventeen of these papers examined more than one early life exposure of interest. Fifty six papers examined body size, 37 nutrition and 17 SEP. All of the included papers examined DNA methylation (DNAm) as the epigenetic marker. Overall there was no strong evidence for a consistent association between these early life variables in DNAm which may be due to the heterogeneous study designs, data collection methods and statistical analyses. Conclusions: Despite these inconclusive results, the hypothesis that the early life environment can impact DNAm, potentially persisting into adult life, was supported by some studies and warrants further investigation. We provide recommendations for future studies. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
35. The structural balance analysis of complex dynamical networks based on nodes' dynamical couplings.
- Author
-
Gao, Zilin and Wang, Yinhe
- Subjects
MATHEMATICAL models ,DYNAMICS ,NEURAL circuitry ,COMPUTER networks ,COMPUTATIONAL complexity ,SOCIAL networks ,SYNAPSES - Abstract
The nodes and their connection relationships are the two main bodies for dynamic complex networks. In existing theoretical researches, the phenomena of stabilization and synchronization for complex dynamical networks are generally regarded as the dynamic characteristic behaviors of the nodes, which are mainly caused by coupling effect of connection relationships between nodes. However, the connection relationships between nodes are also one main body of a time-varying dynamic complex network, and thus they may evolve with time and maybe show certain characteristic phenomena. For example, the structural balance in the social networks and the synaptic facilitation in the biological neural networks. Therefore, it is important to investigate theoretically the reasons in dynamics for the occurrence. Especially, from the angle of large-scale systems, how the dynamic behaviors of nodes (such as the individuals, neurons) contribute to the connection relationships is one of worthy research directions. In this paper, according to the structural balance theory of triad proposed by F. Heider, we mainly focus on the connection relationships body, which is regarded as one of the two subsystems (another is the nodes body), and try to find the dynamic mechanism of the structural balance with the internal state behaviors of the nodes. By using the Riccati linear matrix differential equation as the dynamic model of connection relationships subsystem, it is proved under some mathematic conditions that the connection relationships subsystem is asymptotical structural balance via the effects of the coupling roles with the internal state of nodes. Finally, the simulation example is given to show the validity of the method in this paper. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
36. UV-DDB as a General Sensor of DNA Damage in Chromatin: Multifaceted Approaches to Assess Its Direct Role in Base Excision Repair.
- Author
-
Raja, Sripriya J. and Van Houten, Bennett
- Subjects
DNA-binding proteins ,DNA damage ,DNA glycosylases ,ENDONUCLEASES ,CHROMATIN ,REACTIVE oxygen species - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
37. Things fall into place: how plants sense and respond to gravity.
- Author
-
Roychoudhry, Suruchi and Kepinski, Stefan
- Abstract
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]
- Published
- 2024
- Full Text
- View/download PDF
38. Stakeholders’ views and experiences of care and interventions for addressing frailty and pre-frailty: A meta-synthesis of qualitative evidence.
- Author
-
D'avanzo, Barbara, Shaw, Rachel, Riva, Silvia, Apostolo, Joao, Bobrowicz-Campos, Elzbieta, Kurpas, Donata, Bujnowska, Maria, and Holland, Carol
- Subjects
FRAGILITY (Psychology) ,DISEASES in older people ,PUBLIC health ,META-synthesis ,MEDICAL care ,MANAGEMENT - Abstract
Frailty is a common condition in older age and is a public health concern which requires integrated care and involves different stakeholders. This meta-synthesis focuses on experiences, understanding, and attitudes towards screening, care, intervention and prevention for frailty across frail and healthy older persons, caregivers, health and social care practitioners. Studies published since 2001 were identified through search of electronic databases; 81 eligible papers were identified and read in full, and 45 papers were finally included and synthesized. The synthesis was conducted with a meta-ethnographic approach. We identified four key themes: Uncertainty about malleability of frailty; Strategies to prevent or to respond to frailty; Capacity to care and person and family-centred service provision; Power and choice. A bottom-up approach which emphasises and works in synchrony with frail older people's and their families' values, goals, resources and optimisation strategies is necessary. A greater employment of psychological skills, enhancing communication abilities and tools to overcome disempowering attitudes should inform care organisation, resulting in more efficient and satisfactory use of services. Public health communication about prevention and management of frailty should be founded on a paradigm of resilience, balanced acceptance, and coping. Addressing stakeholders’ views about the preventability of frailty was seen as a salient need. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
39. Double helix of the journal Cytology and Genetics: 50 years later.
- Author
-
Blume, Ya.
- Abstract
This survey paper contains a brief analysis of publications included in the current issue of the scientific journal Cytology and Genetics dedicated to its 50th anniversary. These papers reflect scientific achievements of their authors in the field of genetics and cell biology and underline the potential of these two biological disciplines, forming the double helix of the journal. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
40. Detection of preterm birth in electrohysterogram signals based on wavelet transform and stacked sparse autoencoder.
- Author
-
Chen, Lili, Hao, Yaru, and Hu, Xue
- Subjects
PREMATURE labor ,WAVELET transforms ,SUPPORT vector machines ,TIME series analysis ,MACHINE learning - Abstract
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]
- Published
- 2019
- Full Text
- View/download PDF
41. Statistical models discriminating between complex samples measured with microfluidic receptor-cell arrays.
- Author
-
Wehrens, Ron, Roelse, Margriet, Henquet, Maurice, van Lenthe, Marco, Goedhart, Paul W., and Jongsma, Maarten A.
- Subjects
STATISTICAL models ,G protein coupled receptors ,FLUORESCENCE resonance energy transfer ,PHYSICAL sciences ,SOCIAL sciences - Abstract
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]
- Published
- 2019
- Full Text
- View/download PDF
42. Selfish genetic elements.
- Author
-
Ågren, J. Arvid and Clark, Andrew G.
- Subjects
SELFISH genetic elements ,GENOME size ,GENETIC transformation ,BIOLOGICAL evolution ,GENOMICS - Abstract
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]
- Published
- 2018
- Full Text
- View/download PDF
43. Cellulose-binding activity of a 21-kDa endo-ß-1,4-glucanase lacking cellulose-binding domain and its synergy with other cellulases in the digestive fluid of Aplysia kurodai.
- Author
-
Tsuji, Akihiko, Yuasa, Keizo, and Asada, Chikako
- Subjects
CELLULOSE ,APLYSIA ,ENZYME activation ,GLUCANASES ,HYDROLYSIS - Abstract
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]
- Published
- 2018
- Full Text
- View/download PDF
44. Nonequilibrium Enhances Adaptation Efficiency of Stochastic Biochemical Systems.
- Author
-
Jia, Chen and Qian, Minping
- Subjects
BIOLOGICAL adaptation ,STOCHASTIC systems ,SENSE organs ,CHEMOTAXIS ,MARKOV processes - Abstract
Adaptation is a crucial biological function possessed by many sensory systems. Early work has shown that some influential equilibrium models can achieve accurate adaptation. However, recent studies indicate that there are close relationships between adaptation and nonequilibrium. In this paper, we provide an explanation of these two seemingly contradictory results based on Markov models with relatively simple networks. We show that as the nonequilibrium driving becomes stronger, the system under consideration will undergo a phase transition along a fixed direction: from non-adaptation to simple adaptation then to oscillatory adaptation, while the transition in the opposite direction is forbidden. This indicates that although adaptation may be observed in equilibrium systems, it tends to occur in systems far away from equilibrium. In addition, we find that nonequilibrium will improve the performance of adaptation by enhancing the adaptation efficiency. All these results provide a deeper insight into the connection between adaptation and nonequilibrium. Finally, we use a more complicated network model of bacterial chemotaxis to validate the main results of this paper. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
45. Pattern dynamics of the reaction-diffusion immune system.
- Author
-
Zheng, Qianqian, Shen, Jianwei, and Wang, Zhijie
- Subjects
IMMUNE system ,DIFFUSION ,CONTROL theory (Engineering) ,DYNAMICS ,MATHEMATICAL models ,EQUILIBRIUM ,MATHEMATICAL analysis - Abstract
In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
46. Globally fixed-time synchronization of coupled neutral-type neural network with mixed time-varying delays.
- Author
-
Zheng, Mingwen, Li, Lixiang, Peng, Haipeng, Xiao, Jinghua, Yang, Yixian, Zhang, Yanping, and Zhao, Hui
- Subjects
ARTIFICIAL neural networks ,LYAPUNOV functions ,COMPUTER simulation ,FEEDBACK control systems ,TIME-varying systems - Abstract
This paper mainly studies the globally fixed-time synchronization of a class of coupled neutral-type neural networks with mixed time-varying delays via discontinuous feedback controllers. Compared with the traditional neutral-type neural network model, the model in this paper is more general. A class of general discontinuous feedback controllers are designed. With the help of the definition of fixed-time synchronization, the upper right-hand derivative and a defined simple Lyapunov function, some easily verifiable and extensible synchronization criteria are derived to guarantee the fixed-time synchronization between the drive and response systems. Finally, two numerical simulations are given to verify the correctness of the results. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
47. A modeling study of budding yeast colony formation and its relationship to budding pattern and aging.
- Author
-
Wang, Yanli, Lo, Wing-Cheong, and Chou, Ching-Shan
- Subjects
YEAST fungi genetics ,BUDDING (Zoology) ,ELECTRIC properties of cells ,HAPLOIDY ,DIPLOIDY - Abstract
Budding yeast, which undergoes polarized growth during budding and mating, has been a useful model system to study cell polarization. Bud sites are selected differently in haploid and diploid yeast cells: haploid cells bud in an axial manner, while diploid cells bud in a bipolar manner. While previous studies have been focused on the molecular details of the bud site selection and polarity establishment, not much is known about how different budding patterns give rise to different functions at the population level. In this paper, we develop a two-dimensional agent-based model to study budding yeast colonies with cell-type specific biological processes, such as budding, mating, mating type switch, consumption of nutrients, and cell death. The model demonstrates that the axial budding pattern enhances mating probability at an early stage and the bipolar budding pattern improves colony development under nutrient limitation. Our results suggest that the frequency of mating type switch might control the trade-off between diploidization and inbreeding. The effect of cellular aging is also studied through our model. Based on the simulations, colonies initiated by an aged haploid cell show declined mating probability at an early stage and recover as the rejuvenated offsprings become the majority. Colonies initiated with aged diploid cells do not show disadvantage in colony expansion possibly due to the fact that young cells contribute the most to colony expansion. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
48. Optimizing a desirable fare structure for a bus-subway corridor.
- Author
-
Liu, Bing-Zheng, Ge, Ying-En, Cao, Kai, Jiang, Xi, Meng, Lingyun, Liu, Ding, and Gao, Yunfeng
- Subjects
BUS fares ,TRANSPORTATION corridors ,PUBLIC welfare ,TRANSPORTATION ,PASSENGERS - Abstract
This paper aims to optimize a desirable fare structure for the public transit service along a bus-subway corridor with the consideration of those factors related to equity in trip, including travel distance and comfort level. The travel distance factor is represented by the distance-based fare strategy, which is an existing differential strategy. The comfort level one is considered in the area-based fare strategy which is a new differential strategy defined in this paper. Both factors are referred to by the combined fare strategy which is composed of distance-based and area-based fare strategies. The flat fare strategy is applied to determine a reference level of social welfare and obtain the general passenger flow along transit lines, which is used to divide areas or zones along the corridor. This problem is formulated as a bi-level program, of which the upper level maximizes the social welfare and the lower level capturing traveler choice behavior is a variable-demand stochastic user equilibrium assignment model. A genetic algorithm is applied to solve the bi-level program while the method of successive averages is adopted to solve the lower-level model. A series of numerical experiments are carried out to illustrate the performance of the models and solution methods. Numerical results indicate that all three differential fare strategies play a better role in enhancing the social welfare than the flat fare strategy and that the fare structure under the combined fare strategy generates the highest social welfare and the largest resulting passenger demand, which implies that the more equity factors a differential fare strategy involves the more desirable fare structure the strategy has. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
49. Changes in Cell Biology under the Influence of Low-Level Laser Therapy.
- Author
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Rola, Piotr, Włodarczak, Szymon, Lesiak, Maciej, Doroszko, Adrian, and Włodarczak, Adrian
- Subjects
PHOTOBIOMODULATION therapy ,LASER therapy ,CYTOLOGY - Abstract
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]
- Published
- 2022
- Full Text
- View/download PDF
50. Análisis de biología celular clases desde la historia y la filosofía de la ciencia.
- Author
-
de Souza Rosa, Marllon Moreti, Antunes Maciel, Eloísa, and Bologna Soares de Andrade, Mariana Aparecida
- Subjects
PHILOSOPHY of science ,HISTORY of biology ,CYTOLOGY ,STUDENT speech ,ACADEMIC motivation - Abstract
Copyright of Bio-grafía. Escritos Sobre la Biología y su Enseñanza is the property of Universidad Pedaggica Nacional and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2022
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