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Bioessays 2019 Feb 8;41(2):e1800263. Epub 2019 Feb 8.

Laboratory of Cellular and Structural Biology, The Rockefeller University, NY, 10065, USA.

Bioessays 2019 Feb 8;41(2):e1800042. Epub 2019 Feb 8.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.

While mass spectrometry (MS)-based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. Read More

Bioessays 2019 Feb 7:e1800194. Epub 2019 Feb 7.

Department of Cell and Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA.

Microtubules form a highly dynamic filament network in all eukaryotic cells. Individual microtubules grow by tubulin dimer subunit addition and frequently switch between phases of growth and shortening. These unique dynamics are powered by GTP hydrolysis and drive microtubule network remodeling, which is central to eukaryotic cell biology and morphogenesis. Read More

Bioessays 2019 Feb 7:e1800217. Epub 2019 Feb 7.

Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium.

Timers and sensors are common devices that make our daily life safer, more convenient, and more efficient. In a cellular context, they arguably play an even more crucial role as they ensure the survival of cells in the presence of various extrinsic and intrinsic stresses. Biological timers and sensors generate distinct signaling profiles, enabling them to produce different types of cellular responses. Read More

Bioessays 2019 Feb 4:e1800229. Epub 2019 Feb 4.

Department of Psychology, University of British Columbia, Vancouver, Canada.

A reductionistic, bottom-up, cellular-based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. Read More

Bioessays 2019 Feb 1:e1800183. Epub 2019 Feb 1.

Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada.

Ribosome biogenesis includes the making and processing of ribosomal RNAs, the biosynthesis of ribosomal proteins from their mRNAs in the cytosol and their transport to the nucleolus to assemble pre-ribosomal particles. Several stresses including cellular senescence reduce nucleolar rRNA synthesis and maturation increasing the availability of ribosome-free ribosomal proteins. Several ribosomal proteins can activate the p53 tumor suppressor pathway but cells without p53 can still arrest their proliferation in response to an imbalance between ribosomal proteins and mature rRNA production. Read More

Bioessays 2019 Feb 1:e1800146. Epub 2019 Feb 1.

University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrookes Hospital, CB2 0XY, UK.

It has long been believed that membrane proteins present in degradative compartments such as endolysosomes or vacuoles would be destined for destruction. Now however, it appears that mechanisms and machinery exist in simple eukaryotes such as yeast and more complex organisms such as mammals that can rescue potentially "doomed" membrane proteins by retrieving them from these "late" compartments and recycling them back to the Golgi complex. In yeast, a sorting nexin dimer containing Snx4p can recognize and retrieve the Atg27p membrane protein while in mammals, the AP5 complex (with SPG11 and SPG15) directs the recycling of Golgi-localized proteins along with the cation-independent mannose 6-phosphate receptor (CIMPR). Read More

Bioessays 2019 Feb 1;41(2):e1800132. Epub 2019 Feb 1.

Dr. J. Attig, Prof. J. Ule, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.

Retrotransposon-derived elements (RDEs) can disrupt gene expression, but are nevertheless widespread in metazoan genomes. This review presents a hypothesis that repressive RNA-binding proteins (RBPs) facilitate the large-scale accumulation of RDEs. Many RBPs bind RDEs in pre-mRNAs to repress the effects of RDEs on RNA processing, or the formation of inverted repeat RNA structures. Read More

Bioessays 2019 Feb 7;41(2):e1800258. Epub 2019 Jan 7.

D. Speijer, Academic Medical Center (AMC), University of Amsterdam, Medical Biochemistry, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.

Bioessays 2019 Feb 7;41(2):e1800197. Epub 2019 Jan 7.

Center for Brain and Cognition, UC San Diego, Mandler Hall, 9500 Gilman Drive, La Jolla CA, 92093, US.

It is hypothesized that repeated, non-invasive stimulation of the vestibular (balance) system, via a small electrical current to the skin behind the ears, will cause the brain centers that control energy homeostasis to shift the body toward a leaner physique. This is because these centers integrate multiple inputs to, in effect, fix a set-point for body fat, which though difficult to alter is not immutable. They will interpret repeated stimulation of the parts of the vestibular system that detect acceleration as a state of chronic activity. Read More

Bioessays 2019 Jan;41(1):e1800141

Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA.

In this essay, I propose that DNA-binding anti-cancer drugs work more via chromatin disruption than DNA damage. Success of long-awaited drugs targeting cancer-specific drivers is limited by the heterogeneity of tumors. Therefore, chemotherapy acting via universal targets (e. Read More

Bioessays 2019 Jan;41(1):e1800242

Bioessays 2019 Jan 7;41(1):e1800225. Epub 2018 Dec 7.

Institut für Biochemie und Zellbiologie, Otto-von-Guericke-Universität Magdeburg, Leipziger Str. 44, D-39120 Magdeburg, Germany.

Bioessays 2019 Jan 11;41(1):e1800075. Epub 2018 Dec 11.

Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA.

The Liver kinase B1 with its downstream target AMP activated protein kinase (LKB1-AMPK), and the key nutrient sensor mammalian target of rapamycin complex 1 (mTORC1) form two signaling systems that coordinate metabolic and cellular activity with changes in the environment in order to preserve homeostasis. For example, nutritional fluctuations rapidly feed back on these signaling systems and thereby affect cell-specific functions. Recent studies have started to reveal important roles of these strategic metabolic regulators in Schwann cells for the trophic support and myelination of axons. Read More

Bioessays 2019 Jan 10;41(1):e1800128. Epub 2018 Dec 10.

Laboratory of Integrative Immunology, National Institute of Respiratory Diseases (INER), Calzada de Tlalpan 4502, 14080 Mexico City, Mexico.

Despite abundant evidence associating CD38 overexpression and CD4 T cell depletion in HIV infection, no causal relation has been investigated. To address this issue, a series of mechanisms are proposed, supported by evidence from different fields, by which CD38 overexpression can facilitate CD4 T cell depletion in HIV infection. According to this model, increased catalytic activity of CD38 may reduce CD4 T cells' cytoplasmic nicotin-amide adenine dinucleotide (NAD), leading to a chronic Warburg effect. Read More

Bioessays 2019 Jan 3;41(1):e1800223. Epub 2018 Dec 3.

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

Bioessays 2019 Jan 3;41(1):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 2019 Jan 4;41(1):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 2019 Jan 30;41(1):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 2019 Jan 30;41(1):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 2019 Jan 28;41(1):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 2019 Jan 28;41(1):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 2019 Jan 28;41(1):e1800165. 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 2019 Jan 15;41(1):e1800208. 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