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Bioessays 2019 Apr 18:e1900035. Epub 2019 Apr 18.

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

This paper discusses how our bad reading habits are starting to influence how we write. This short abstract and the picture next to it summarize the arguments in this paper. Just kidding, they do not. Read More

Bioessays 2019 Apr 10:e1800234. Epub 2019 Apr 10.

Clem Jones Centre for Regenerative Medicine, Bond University, Gold Coast, QLD, 4229, Australia.

Bone marrow is the main site for hematopoiesis in adults. It acts as a niche for hematopoietic stem cells (HSCs) and contains non-hematopoietic cells that contribute to stem cell dormancy, quiescence, self-renewal, and differentiation. HSC also exist in resting spleen of several species, although their contribution to hematopoiesis under steady-state conditions is unknown. Read More

Bioessays 2019 Apr 10:e1800251. Epub 2019 Apr 10.

College for Life Sciences, Wissenschaftskolleg zu Berlin (Institute for Advanced Study, Berlin), Germany.

Recent results from engineered and natural samples show that the starkly different lipids of archaea and bacteria can form stable hybrid membranes. But if the two types can mix, why don't they? That is, why do most bacteria and all eukaryotes have only typically bacterial lipids, and archaea archaeal lipids? It is suggested here that the reason may lie on the other main component of cellular membranes: membrane proteins, and their close adaptation to the lipids. Archaeal lipids in modern bacteria could suggest that the last universal common ancestor (LUCA) had both lipid types. Read More

Bioessays 2019 Apr 10:e1800237. Epub 2019 Apr 10.

Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.

The proteasome family of proteases comprises oligomeric assemblies of very different symmetry. In different sizes, it features ring-like oligomers with dihedral symmetry that allow the stacking of further rings of regulatory subunits as observed in the modular proteasome system, but also less symmetric helical assemblies. Comprehensive sequence and structural analyses of proteasome homologs reveal a parsimonious scenario of how symmetry may have emerged from a monomeric ancestral precursor and how it may have evolved throughout the proteasome family. Read More

Bioessays 2019 Apr 10:e1900017. Epub 2019 Apr 10.

CIBIR (Center for Biomedical Research of La Rioja), C/ Piqueras 98, Logrono, 26006, La Rioja, Spain.

The culture of chefs from the world's best restaurants is substituted by new trends paradigmatically epitomized by the TV program Masterchef. The authors feel that a similar transformation affects modern research. Recent scientific policies constrict the design of research grants with the aim of short-term maximization of the monetary value generated by the researcher. Read More

Bioessays 2019 Apr 10:e1800260. Epub 2019 Apr 10.

Department of Physiological Sciences, Stellenbosch University, 7602, Stellenbosch, South Africa.

Inflammatory mediators have an established role in inducing insulin resistance and promoting hyperglycemia. In turn, hyperglycemia has been argued to drive immune cell dysfunction as a result of mitochondrial dysfunction. Here, the authors review the evidence challenging this view. Read More

Bioessays 2019 Apr;41(4):e1800235

Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.

Diploid germ cells produce haploid gametes through meiosis, a unique type of cell division. Independent reassortment of parental chromosomes and their recombination leads to ample genetic variability among the gametes. Importantly, new mutations also occur during meiosis, at frequencies much higher than during the mitotic cell cycles. Read More

Bioessays 2019 Apr;41(4):e1900042

Bioessays 2019 Apr;41(4):e1800169

Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.

Short ("seed") or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post-transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA-regulated processes are reported. Read More

Bioessays 2019 Apr;41(4):e1800201

Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece.

Transcription is a potential threat to genome integrity, and transcription-associated DNA damage must be repaired for proper messenger RNA (mRNA) synthesis and for cells to transmit their genome intact into progeny. For a wide range of structurally diverse DNA lesions, cells employ the highly conserved nucleotide excision repair (NER) pathway to restore their genome back to its native form. Recent evidence suggests that NER factors function, in addition to the canonical DNA repair mechanism, in processes that facilitate mRNA synthesis or shape the 3D chromatin architecture. Read More

Bioessays 2019 Apr;41(4):e1800199

School of Medicine and Surgery, NeuroMI-Milan Center for Neuroscience, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy.

No cure yet exists for devastating Alzheimer's disease (AD), despite many years and humongous efforts to find efficacious pharmacological treatments. So far, neither designing drugs to disaggregate amyloid plaques nor tackling solely inflammation turned out to be decisive. Mesenchymal stem cells (MSCs) and, in particular, extracellular vesicles (EVs) originating from them could be proposed as an alternative, strategic approach to attack the pathology. Read More

Bioessays 2019 Apr 27;41(4):e1800247. Epub 2019 Mar 27.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, UK.

For decades, myxobacteria have been spotlighted as exemplars of social "wolf-pack" predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little relevance to predation in a natural setting. Read More

Bioessays 2019 Apr;41(4):e1800241

Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain.

The fate of cellular RNAs is largely dependent on their structural conformation, which determines the assembly of ribonucleoprotein (RNP) complexes. Consequently, RNA-binding proteins (RBPs) play a pivotal role in the lifespan of RNAs. The advent of highly sensitive in cellulo approaches for studying RNPs reveals the presence of unprecedented RNA-binding domains (RBDs). Read More

Bioessays 2019 Apr;41(4):e1800188

Department of Philosophy, University of Minnesota, Minneapolis, MN, 55455, USA.

Understanding the evolutionary role of environmentally induced phenotypic variation (i.e., plasticity) is an important issue in developmental evolution. Read More

Bioessays 2019 Apr;41(4):e1900029

Department of English and Linguistics, Obama Institute of Transnational American Studies, Johannes Gutenberg University Mainz, Welderweg 18, Mainz, 55118, Germany.

One hundred and fifty years ago, a hopeful young researcher reported a recent discovery he had made. Working in the bowels of a medieval castle in the German city of Tübingen, he had isolated a then entirely new type of molecule. This was the birth of a field that would fundamentally change the course of biology, medicine, and beyond. Read More

Bioessays 2019 Mar;41(3):e1900026

Editor-in-Chief.

Bioessays 2019 Mar;41(3):e1800198

Dr. A. F. Siekmann, Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, 19104, Pennsylvania.

A tree-like hierarchical branching structure is present in many biological systems, such as the kidney, lung, mammary gland, and blood vessels. Most of these organs form through branching morphogenesis, where outward growth results in smaller and smaller branches. However, the blood vasculature is unique in that it exists as two trees (arterial and venous) connected at their tips. Read More

Bioessays 2019 Mar 25;41(3):e1800152. Epub 2019 Feb 25.

School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, 99164.

Somatic mutations arising in human skin cancers are heterogeneously distributed across the genome, meaning that certain genomic regions (e.g., heterochromatin or transcription factor binding sites) have much higher mutation densities than others. Read More

Bioessays 2019 Mar 22;41(3):e1800222. Epub 2019 Feb 22.

Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France.

Targeted transitions in chromatin states at thousands of genes are essential drivers of eukaryotic development. Therefore, understanding the in vivo dynamics of epigenetic regulators is crucial for deciphering the mechanisms underpinning cell fate decisions. This review illustrates how, in addition to its cell memory function, the Polycomb group of transcriptional regulators orchestrates temporal, cell and tissue-specific expression of master genes during development. Read More

Bioessays 2019 Mar 21;41(3):e1800162. Epub 2019 Feb 21.

Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia.

The complexity of the physiological phenotype currently prevents us from identifying an integrative measure to assess how the internal state and environmental conditions modify life-history strategies. In this article, it is proposed that shorter telomeres should lead to a faster pace-of-life where investment in self-maintenance is decreased as a means of saving energy for reproduction, but at the cost of somatic durability. Inversely, longer telomeres would favor an increased investment in soma maintenance and thus a longer reproductive lifespan (i. Read More

Bioessays 2019 Feb 8;41(2):e1970014. Epub 2019 Feb 8.

Bioessays 2019 Feb;41(2):e1700238

Dr. J. A. Watson, Dr. G. S. Watson, School of Science and Engineering, University of the Sunshine Coast, Fraser Coast, Hervey Bay, QL, 4655, Australia.

Living organisms are the ultimate survivalists, having evolved phenotypes with unprecedented adaptability, ingenuity, resourcefulness, and versatility compared to human technology. To harness these properties, functional descriptions and design principles from all sources of biodiversity information must be collated - including the hundreds of thousands of possible survival features manifest in natural history museum collections, which represent 12% of total global biodiversity. This requires a consortium of expert biologists from a range of disciplines to convert the observations, data, and hypotheses into the language of engineering. Read More

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 Mar 7;41(3):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 Mar 7;41(3):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 Mar 4;41(3):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 Mar 1;41(3):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 Mar 1;41(3):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 01;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 01;41(1):e1800242

Bioessays 2019 01 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 01 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 01 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 01 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 01 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 01 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 01 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 01 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 01 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 01 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 01 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 12;40(12):e1800218

Bioessays 2018 12;40(12):e1870105

Bioessays 2019 01 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 12 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 12 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