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Bioessays 2018 Dec 3:e1800223. Epub 2018 Dec 3.

Lab Histology-Embryology, Medical School, National Kapodistrian University of Athens, 75 Mikras Asias Str., GR-11527 Athens, Greece.

Bioessays 2018 Dec 3:e1800182. Epub 2018 Dec 3.

Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK.

The extreme length of chromosomal DNA requires organizing mechanisms to both promote functional genetic interactions and ensure faithful chromosome segregation when cells divide. Microscopy and genome-wide contact frequency analyses indicate that intra-chromosomal looping of DNA is a primary pathway of chromosomal organization during all stages of the cell cycle. DNA loop extrusion has emerged as a unifying model for how chromosome loops are formed in cis in different genomic contexts and cell cycle stages. Read More

Bioessays 2018 Dec 4:e1800180. Epub 2018 Dec 4.

Academic Medical Center (AMC), University of Amsterdam, Medical Biochemistry, Room K1-257, 1105, AZ Amsterdam, The Netherlands.

Aspects of peroxisome evolution, uncoupling, carnitine shuttles, supercomplex formation, and missing neuronal fatty acid oxidation (FAO) are linked to reactive oxygen species (ROS) formation in respiratory chains. Oxidation of substrates with high FADH /NADH (F/N) ratios (e.g. Read More

Bioessays 2018 Nov 30:e1800215. Epub 2018 Nov 30.

Raymond Purves Bone and Joint Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia.

Bioessays 2018 Nov 30:e1800164. Epub 2018 Nov 30.

Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA.

It is proposed that the multiple enhancer elements associated with locus control regions and super-enhancers recruit RNA polymerase II and efficiently assemble elongation competent transcription complexes that are transferred to target genes by transcription termination and transient looping mechanisms. It is well established that transcription complexes are recruited not only to promoters but also to enhancers, where they generate enhancer RNAs. Transcription at enhancers is unstable and frequently aborted. Read More

Bioessays 2018 Nov 28:e1800166. Epub 2018 Nov 28.

McCaig institute for Bone and Joint Health, University of Calgary, Calgary, Alberta T2N4N1, Canada.

Proteoglycan 4 (PRG4), first identified in synovial fluid, is an extracellular matrix structural protein in the joint implicated in reducing shear at the cartilage surface as well as controlling adhesion-dependent synovial growth and regulating bulk protein deposition onto the cartilage. However, recent evidence suggests that it can bind to and effect downstream signaling of a number of cell surface receptors implicated in regulating the inflammatory response. Therefore, we pose the hypothesis: Does PRG4 regulate the inflammatory response and maintain tissue homeostasis? Based on these novel findings implicating PRG4 as an inflammatory signaling molecule, we will present and discuss several hypotheses regarding potential mechanisms by which PRG4 may be able to regulate inflammation. Read More

Bioessays 2018 Nov 28:e1800206. Epub 2018 Nov 28.

Programa de Pós-graduação em Ciências Fisiológicas, Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande - FURG, Av Itália, Km 8 s/n - Rio Grande, Rio Grande, RS, 96210-900, Brazil.

The overflow of scientific literature stimulates poor reading habits which can aggravate science's reproducibility crisis. Thus, solving the reproducibility crisis demands not only methodological changes, but also changes in our relationship with the scientific literature, especially our reading habits. Importantly, this does not mean reading more, it means reading better. Read More

Bioessays 2018 Nov 28. Epub 2018 Nov 28.

Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, 27599, USA.

Focal adhesions disassemble during mitosis, but surprisingly little is known about how these structures respond to other phases of the cell cycle. Three recent papers reveal unexpected results as they examine adhesions through the cell cycle. A biphasic response is detected where focal adhesions grow during S phase before disassembly begins early in G2. Read More

Bioessays 2018 Dec;40(12):e1800218

Bioessays 2018 Dec;40(12):e1870105

Bioessays 2018 Dec;40(12):e1870124

Bioessays 2018 Nov 15. Epub 2018 Nov 15.

California Institute of Technology, JPL/NASA, 4800 Oak Grove Drive, M/S 183-601, Pasadena, California.

Bioessays 2018 Dec 2;40(12):e1800140. Epub 2018 Nov 2.

Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA.

Efforts from diverse disciplines, including evolutionary studies and biomechanical experiments, have yielded new insights into the genetic, signaling, and mechanical control of tooth formation and functions. Evidence from fossils and non-model organisms has revealed that a common set of genes underlie tooth-forming potential of epithelia, and changes in signaling environments subsequently result in specialized dentitions, maintenance of dental stem cells, and other phenotypic adaptations. In addition to chemical signaling, tissue forces generated through epithelial contraction, differential growth, and skeletal constraints act in parallel to shape the tooth throughout development. Read More

Bioessays 2018 Dec 29;40(12):e1800178. Epub 2018 Oct 29.

Department of Philosophy, Macquarie University, Building W6A, North Ryde, New South Wales, Australia 2109.

Microbiome research attributes to whole microbiomes a causal role in the occurrence of different health outcomes. I argue, following some distinctions about causal relationships and explanations made within a philosophical account of causation, the "interventionist account," that such claims need more scrutiny. Read More

Bioessays 2018 Dec 29;40(12):e1800181. Epub 2018 Oct 29.

Department of Microbiology & Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 955 Main Street, Buffalo, NY 14203.

The process of antigenic variation in parasitic African trypanosomes is a remarkable mechanism for outwitting the immune system of the mammalian host, but it requires a delicate balancing act for the monoallelic expression, folding and transport of a single variant surface glycoprotein (VSG). Only one of hundreds of VSG genes is expressed at time, and this from just one of ≈15 dedicated expression sites. By switching expression of VSGs the parasite presents a continuously shifting antigenic facade leading to prolonged chronic infections lasting months to years. Read More

Bioessays 2018 Dec 29;40(12):e1800136. Epub 2018 Oct 29.

N.I. Vavilov Institute of General Genetics of RAS, 119991, Moscow, Russia.

Malignant cells are characterized by an increased content of endogenous formaldehyde formed as a by-product of biosynthetic processes. Accumulation of formaldehyde in cancer cells is combined with activation of the processes of cellular formaldehyde clearance. These mechanisms include increased ALDH and suppressed ADH5/FDH activity, which oncologists consider poor and favorable prognostic markers, respectively. Read More

Bioessays 2018 Dec 29;40(12):e1800085. Epub 2018 Oct 29.

Division of Cell and Developmental Biology, Medical University Vienna, Center for Anatomy and Cell Biology, Schwarzspanierstrasse 17, A-1090, Vienna, Austria.

Membranous organelles allow sub-compartmentalization of biological processes. However, additional subcellular structures create dynamic reaction spaces without the need for membranes. Such membrane-less organelles (MLOs) are physiologically relevant and impact development, gene expression regulation, and cellular stress responses. Read More

Bioessays 2018 Nov;40(11):e1800202

Bioessays 2018 Dec 17;40(12):e1800130. Epub 2018 Oct 17.

Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France.

Amphioxus represents the most basally divergent group in chordates and probably the best extant proxy to the ancestor of all chordates including vertebrates. The amphioxus, or lancelets, are benthic filter feeding marine animals and their interest as a model in research is due to their phylogenetic position and their anatomical and genetic stasis throughout their evolutionary history. From the first works in the 19th century to the present day, enormous progress is made mainly favored by technical development at different levels, from spawning induction and husbandry techniques, through techniques for studies of gene function or of the role of different signalling pathways through embryonic development, to functional genomics techniques. Read More

Bioessays 2018 Dec 12;40(12):e1800173. Epub 2018 Oct 12.

Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.

Irreplicability is framed as crisis, blamed on sloppy science motivated by perverse stimuli in research. Structural changes to the organization of science, targeting sloppy science (e.g. Read More

Bioessays 2018 Dec 12;40(12):e1800053. Epub 2018 Oct 12.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.

All organisms live in close association with microbes. However, not all such associations are meaningful in an evolutionary context. Current debate concerns whether hosts and microbes are best described as communities of individuals or as holobionts (selective units of hosts plus their microbes). Read More

Bioessays 2018 Nov 9;40(11):e1800177. Epub 2018 Oct 9.

Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.

Bioessays 2018 Nov 8;40(11):e1800189. Epub 2018 Oct 8.

Institut Pasteur, 25 Rue du Dr Roux, 75015 Paris, France.

Bioessays 2018 Nov 5;40(11):e1800046. Epub 2018 Oct 5.

Laboratory of Immunology, National Eye Institute, Bethesda, MD 20892, USA.

Until recently, the ocular surface is thought by many to be sterile and devoid of living microbes. It is now becoming clear that this may not be the case. Recent and sophisticated PCR analyses have shown that microbial DNA-based "signatures" are present within various ethnic, geographic, and contact lens wearing communities. Read More

Bioessays 2018 Nov 28;40(11):e1800133. Epub 2018 Sep 28.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA.

DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl-DNA glycosylases AlkC and AlkD adopt a unique structure based on α-helical HEAT repeats. Both enzymes identify and excise their substrates without a base-flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double-helix. Read More

Bioessays 2018 Nov 28;40(11):e1800117. Epub 2018 Sep 28.

Boston University, MA, USA - Center for Philosophy and History of Science, 745 Commonwealth Avenue, Boston, MA, 02215, USA.

Bioessays 2018 Nov 28;40(11):e1800044. Epub 2018 Sep 28.

Department of Genetics, Harvard Medical School, 77 Ave Louis Pasteur, NRB 339, Boston, MA 02115, USA.

The Transforming growth factor beta (TGF-β) family of secreted proteins regulates a variety of key events in normal development and physiology. In mammals, this family, represented by 33 ligands, including TGF-β, activins, nodal, bone morphogenetic proteins (BMPs), and growth and differentiation factors (GDFs), regulate biological processes as diverse as cell proliferation, differentiation, apoptosis, metabolism, homeostasis, immune response, wound repair, and endocrine functions. In Drosophila, only 7 members of this family are present, with 4 TGF-β/BMP and 3 TGF-β/activin ligands. Read More

Bioessays 2018 Nov 28;40(11):e1800119. Epub 2018 Sep 28.

Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, Davis, CA, 95616, USA.

We recently discovered a novel subset of beta cells that resemble immature beta cells during pancreas development. We named these "virgin" beta cells as they do not stem from existing mature beta cells. Virgin beta cells are found exclusively at the islet periphery in areas that we therefore designated as the "neogenic niche. Read More

Bioessays 2018 Oct;40(10):e1800170

Bioessays 2018 Nov 24;40(11):e1800148. Epub 2018 Sep 24.

University of Geneva, Geneva 1211, Switzerland.

Concepts have a central and important place in science, therefore, it is important that their meanings are always made clear. However, such clarity does not always exist, even in the case of such fundamental biological concepts as "gene" and "adaptation." A quick look at textbooks reveals that different meanings may be attributed to the same concept, even within the same textbook, without explicitly discussing the differences of those meanings. Read More

Bioessays 2018 Nov 19;40(11):e1800147. Epub 2018 Sep 19.

Department of Physics and Section of Molecular Biology, Division of Biology, University of California San Diego, La Jolla, CA, 92093, USA.

Bioessays 2018 Oct 14;40(10):e1800150. Epub 2018 Sep 14.

Department of Molecular Physiology and Biophysics, Vanderbilt University, 2215 Garland Ave, Nashville, TN 37212, USA.

Bioessays 2018 Nov 14;40(11):e1800149. Epub 2018 Sep 14.

Retired, formerly SRI International, 149 Walter Hays Dr Palo Alto, Menlo Park, 94025, California, USA.

Bioessays 2018 Nov 9;40(11):e1800091. Epub 2018 Sep 9.

Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark.

Bacteria have evolved advanced strategies for surviving during nutritional stress, including expression of specialized enzyme systems that allow them to grow on unusual nutrient sources. Inorganic phosphate (P ) is limiting in most ecosystems, hence organisms have developed a sophisticated, enzymatic machinery known as carbon-phosphorus (C-P) lyase, allowing them to extract phosphate from a wide range of phosphonate compounds. These are characterized by a stable covalent bond between carbon and phosphorus making them very hard to break down. Read More

Bioessays 2018 Nov 6;40(11):e1800079. Epub 2018 Sep 6.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, 117997, Moscow, Russia.

During tumor evolution, cancer cells use the tumor-stroma crosstalk to reorganize the microenvironment for maximum robustness of the tumor. The success of immune checkpoint therapy foretells a new cancer therapy paradigm: an effective cancer treatment should not aim to influence the individual components of super complex intracellular interactomes (molecular targeting), but try to disrupt the intercellular interactions between cancer and stromal cells, thus breaking the tumor as a whole. Arguments are provided in favor of a hypothesis that such interactions include formation of synapse-like structures (interfaces) where the interacting cells are located at a distance of ∼10-15 nm. Read More

Bioessays 2018 Nov 3;40(11):e800068. Epub 2018 Sep 3.

Programa de Pós-graduação em Ciências Fisiológicas, Universidade Federal do Rio Grande-FURG, Rio Grande, Rio Grande do Sul, Brazil.

In recent years there has been a wealth of studies investigating how memories are allocated in the hippocampus. Some of those studies showed that it is possible to manipulate the identity of neurons recruited to represent a given memory without affecting the memory's behavioral expression. Those findings raised questions about how the hippocampus represents memories, with some researchers arguing that hippocampal neurons do not represent fixed stimuli. Read More

Bioessays 2018 Oct 31;40(10):e1800144. Epub 2018 Aug 31.

Laboratório de Comunicação Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21045-900, Brazil.

Bioessays 2018 Nov 30;40(11):e1800069. Epub 2018 Aug 30.

Animal Physiology and Biochemistry, University of Greifswald, Felix Hausdorff-Strasse 1, D-17489 Greifswald, Germany.

Hyperplasia and hypertrophy are elements of phenotypic plasticity adjusting organ size and function. Because they are costly, we assume that they are beneficial. In this review, the authors discuss examples of tissue and organ systems that respond with plastic changes to osmotic stress to raise awareness that we do not always have sufficient experimental evidence to conclude that such processes provide fitness advantages. Read More

Bioessays 2018 Nov 29;40(11):e1800063. Epub 2018 Aug 29.

Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

The vertebrate adaptive immune system has well defined functions in maintaining tolerance to self-tissues. Suppression of autoreactive T cells is dependent on the regulatory cytokine transforming growth factor-β (TGF-β) and regulatory T (Treg) cells, a distinct T cell lineage specified by the transcription factor Foxp3. Although TGF-β promotes thymic Treg (tTreg) cell development by repressing T cell clonal deletion and peripheral Treg cell differentiation by inducing Foxp3 expression, a recent study shows that TGF-β suppresses autoreactive T cells independent of Foxp3 Treg cells. Read More

Bioessays 2018 Oct 28;40(10):e1800118. Epub 2018 Aug 28.

PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.

Fluorescence imaging has become an indispensable tool in cell and molecular biology. GFP-like fluorescent proteins have revolutionized fluorescence microscopy, giving experimenters exquisite control over the localization and specificity of tagged constructs. However, these systems present certain drawbacks and as such, alternative systems based on a fluorogenic interaction between a chromophore and a protein have been developed. Read More

Bioessays 2018 Oct 27;40(10):e1800092. Epub 2018 Aug 27.

Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6.

The North American wood frog, Rana sylvatica, endures seasonal whole-body freezing during the winter and thawing during the spring without sustaining any apparent damage from ice or oxidative stress. Strategies from these frogs may solve the shortage of human donor organs, which is a multidisciplinary problem that can be alleviated by eliminating geographical boundaries. Rana sylvatica deploys an array of molecular and physiological responses, such as glucose production and microRNA regulation, to help it survive the cold. Read More

Bioessays 2018 Oct 27;40(10):e1800107. Epub 2018 Aug 27.

CNRS, Station Biologique de Roscoff, 29680 Roscoff, France.

The acoel worm Symsagittifera roscoffensis, an early offshoot of the Bilateria and the only well-studied marine acoel that lives in a photosymbiotic relationship, exhibits a centralized nervous system, brain regeneration, and a wide repertoire of complex behaviors such as circatidal rhythmicity, photo/geotaxis, and social interactions. While this animal can be collected by the thousands and is studied historically, significant progress is made over the last decade to develop it as an emerging marine model. The authors here present the feasibility of culturing it in the laboratory and describe the progress made on different areas, including genomic and tissue architectures, highlighting the associated challenges. Read More

Bioessays 2018 Oct 24;40(10):e1800078. Epub 2018 Aug 24.

Department of Medical Biology, The University of Melbourne, 1G Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia.

Histone acetylation has been recognized as an important post-translational modification of core nucleosomal histones that changes access to the chromatin to allow gene transcription, DNA replication, and repair. Histone acetyltransferases were initially identified as co-activators that link DNA-binding transcription factors to the general transcriptional machinery. Over the years, more chromatin-binding modes have been discovered suggesting direct interaction of histone acetyltransferases and their protein complex partners with histone proteins. Read More

Bioessays 2018 Oct 23;40(10):e1800131. Epub 2018 Aug 23.

Molecular Group of Companies, Puthuvype, Ernakulam, Kerala, 682508, India.

Bioessays 2018 Sep;40(9):e1800137

Bioessays 2018 Oct 22;40(10):e1800098. Epub 2018 Aug 22.

School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia.

Despite promising early work into the role of immune cells such as eosinophils in adipose tissue (AT) homeostasis, recent findings revealed that elevating the number of eosinophils in AT alone is insufficient for improving metabolic impairments in obese mice. Eosinophils are primarily recognized for their role in allergic immunity and defence against parasitic worms. They have also been detected in AT and appear to contribute to adipose homeostasis and drive energy expenditure, but the underlying mechanisms remain elusive. Read More

Bioessays 2018 Oct 16;40(10):e1800086. Epub 2018 Aug 16.

Division of Pulmonary and Critical Care, Department of Internal Medicine, Washington University School of Medicine, St. Louis 63110, Missouri.

Recent findings regarding the cellular biology and immunology of BST-2 (also known as tetherin) indicate that its function could be exploited as a universal replication inhibitor of enveloped respiratory viruses (e.g., influenza, respiratory syncytial virus, etc. Read More

Bioessays 2018 Oct 14;40(10):e1800109. Epub 2018 Aug 14.

Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain.

Cohesion is established in S-phase through the action of key replisome factors as replication forks engage cohesin molecules. By holding sister chromatids together, cohesion critically assists both an equal segregation of the duplicated genetic material and an efficient repair of DNA breaks. Nonetheless, the molecular events leading the entrapment of nascent chromatids by cohesin during replication are only beginning to be understood. Read More

Bioessays 2018 Oct 12;40(10):e1800057. Epub 2018 Aug 12.

Beth Israel Deaconess Medical Center - Medicine, 330 Brookline Avenue, Boston, MA, 02215, USA.

Major problems in cancer chemotherapy are toxicity, resistance, and cancer heterogeneity. A new theranostic paradigm has been proposed by the authors. Many million small molecules (SM) are bound to the proteins extracted from a patient's cancer. Read More

Bioessays 2018 Oct 9;40(10):e1800045. Epub 2018 Aug 9.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

Transcription is a fundamental cellular process and the first step in gene regulation. Although RNA polymerase (RNAP) is highly processive, in growing cells the progression of transcription can be hindered by obstacles on the DNA template, such as damaged DNA. The authors recent findings highlight a trade-off between transcription fidelity and DNA break repair. Read More