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Bioessays 2020 May 25:e2000005. Epub 2020 May 25.

Division of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo, 113-0033, Japan.

High-molecular-weight hyaluronan acts as a ligand of the tumor-suppressive Hippo signal, whereas degradation of hyaluronan from a high-molecular-weight form to a low-molecular-weight forms by hyaluronidase 2 inhibits Hippo signal activation and thereby activates the pro-oncogenic transcriptional coactivator yes-associated protein (YAP), which creates a cancer-predisposing microenvironment and drives neoplastic transformation of cells through both cell-autonomous and non-cell-autonomous mechanisms. In fact, accumulation of low-molecular-weight hyaluronan in tissue stroma is observed in many types of cancers. Since inhibition of YAP activity suppresses tumor growth in vivo, pharmacological intervention of the Hippo-YAP signal is an attractive approach for future drug development. Read More

Bioessays 2020 Jun;42(6):e2000095

Bioessays 2020 Jun;42(6):e1900226

Complexity Science Hub (CSH) Vienna, Josefstädter Straße 39, Vienna, 1080, Austria.

The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype-phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference-making causes of phenotypes is re-examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. Read More

Bioessays 2020 May 24:e2000090. Epub 2020 May 24.

Depts. Oncology, Biochemistry and Surger, University of Western Ontario, Lawson Health Research Institute, Canada.

Bioessays 2020 Jun 4;42(6):e2000057. Epub 2020 May 4.

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, 08003, Spain.

Bioessays 2020 May 4:e1900221. Epub 2020 May 4.

KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, Solna, 17165, Sweden.

Recent advances in spatially resolved transcriptomics have greatly expanded the knowledge of complex multicellular biological systems. The field has quickly expanded in recent years, and several new technologies have been developed that all aim to combine gene expression data with spatial information. The vast array of methodologies displays fundamental differences in their approach to obtain this information, and thus, demonstrate method-specific advantages and shortcomings. Read More

Bioessays 2020 May 4:e1900246. Epub 2020 May 4.

Department of Molecular Biology, University of Wyoming, 1000 E University Avenue, Laramie, WY, 82071, USA.

The outer membrane (OM) is an essential barrier that guards Gram-negative bacteria from diverse environmental insults. Besides functioning as a chemical gatekeeper, the OM also contributes towards the strength and stiffness of cells and allows them to sustain mechanical stress. Largely influenced by studies of Escherichia coli, the OM is viewed as a rigid barrier where OM proteins and lipopolysaccharides display restricted mobility. Read More

Bioessays 2020 Jun 4;42(6):e2000070. Epub 2020 May 4.

All Souls College, University of Oxford, Oxford, OX1 4AL, UK.

Bioessays 2020 Jun 4;42(6):e1900237. Epub 2020 May 4.

Department of Medical Sciences, Occupational and Environmental Medicine, Uppsala University, Uppsala, 75185, Sweden.

Intentional weight loss can increase health risk in the long-term, despite short-term benefits, because human adipose tissue is widely contaminated with various lipophilic environmental contaminants, especially persistent organic pollutants (POPs). Recently, chronic exposure to low POPs has emerged as a new risk factor for common metabolic diseases and cardiovascular diseases. The amount of POPs released from adipocytes to the circulation increases during weight loss, thereby increasing POPs exposure of other critical organs. Read More

Bioessays 2020 May 4:e2000021. Epub 2020 May 4.

Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, 38010, Spain.

It has been recently demonstrated that yeast cells are able to partially regress chromosome segregation in telophase as a response to DNA double-strand breaks (DSBs), likely to find a donor sequence for homology-directed repair (HDR). This regression challenges the traditional concept that establishes anaphase events as irreversible, hence opening a new field of research in cell biology. Here, the nature of this new behavior in yeast is summarized and the underlying mechanisms are speculated about. Read More

Bioessays 2020 Jun 4;42(6):e2000069. Epub 2020 May 4.

Division of Health Sciences, School of Applied Sciences, Kydd Building, Abertay University, Bell St., Dundee, DD1 1HG, UK.

Bioessays 2020 Jun 29;42(6):e1900229. Epub 2020 Apr 29.

University of Mississippi Medical Center, Department of Cell and Molecular Biology, 2500 North State Street, Jackson, MS, 39216, USA.

Teeth are one of the most fascinating innovations of vertebrates. Their diversity of shape, size, location, and number in vertebrates is astonishing. If the molecular mechanisms underlying the morphogenesis of individual teeth are now relatively well understood, thanks to the detailed experimental work that has been performed in model organisms (mainly mouse and zebrafish), the mechanisms that control the organization of the dentition are still a mystery. Read More

Bioessays 2020 Jun 28;42(6):e1900145. Epub 2020 Apr 28.

Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8002, USA.

The examination of the complex cell biology of the human malaria parasite Plasmodium falciparum usually relies on the time-consuming generation of transgenic parasites. Here, metabolic labeling and click chemistry are employed as a fast transfection-independent method for the microscopic examination of protein S-palmitoylation, an important post-translational modification during the asexual intraerythrocytic replication of P. falciparum. Read More

Bioessays 2020 Jun 27;42(6):e1900202. Epub 2020 Apr 27.

Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA.

Schizophrenia (SCZ) is a severe neurodevelopmental disorder affecting 1% of populations worldwide with a grave disability and socioeconomic burden. Current antipsychotic medications are effective treatments for positive symptoms, but poorly address negative symptoms and cognitive symptoms, warranting the development of better treatment options. Further understanding of SCZ pathogenesis is critical in these endeavors. Read More

Bioessays 2020 Jun 27;42(6):e1900243. Epub 2020 Apr 27.

Université de Lyon, Université Claude Bernard Lyon1, École Normale Supérieure de Lyon, CNRS, UMR5276, LGL-TPE, Villeurbanne, 69622, France.

It is hypothesized that iron from biological tissues, liberated during decay, may have played a role in inhibiting loss of anatomical information during fossilization of extinct organisms. Most tissues in the animal kingdom contain iron in different forms. A widely distributed iron-bearing molecule is ferritin, a globular protein that contains iron crystallites in the form of ferrihydrite minerals. Read More

Bioessays 2020 Jun 27;42(6):e2000061. Epub 2020 Apr 27.

Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, Wrocław, 50-383, Poland.

Bioessays 2020 Apr 22:e1900250. Epub 2020 Apr 22.

Department of Translational Science in Psychiatry, Munich, Max Planck Institute of Psychiatry, Munich, 80804, Germany.

Peptidylprolyl-isomerases (PPIases) comprise of the protein families of FK506 binding proteins (FKBPs), cyclophilins, and parvulins. Their common feature is their ability to expedite the transition of peptidylprolyl bonds between the cis and the trans conformation. Thus, it seemed highly plausible that PPIase enzymatic activity is crucial for protein folding. Read More

Bioessays 2020 Jun 22;42(6):e2000045. Epub 2020 Apr 22.

Department of Paleontology, University of Vienna, Geozentrum, Vienna, 1090, Austria.

Bioessays 2020 Apr 22:e1900254. Epub 2020 Apr 22.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.

Our view of heredity can potentially be distorted by the ease of introducing heritable changes in the replicating gene sequences but not in the cycling assembly of regulators around gene sequences. Here, key experiments that have informed the understanding of heredity are reinterpreted to highlight this distortion and the possible variety of heritable changes are considered. Unlike heritable genetic changes, which are always associated with mutations in gene sequence, heritable epigenetic changes can be associated with physical or chemical changes in molecules or only changes in the system. Read More

Bioessays 2020 Jun 20;42(6):e2000006. Epub 2020 Apr 20.

Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48104, USA.

An abundance of information about lung development in animal models exists; however, comparatively little is known about lung development in humans. Recent advances using primary human lung tissue combined with the use of human in vitro model systems, such as human pluripotent stem cell-derived tissue, have led to a growing understanding of the mechanisms governing human lung development. They have illuminated key differences between animal models and humans, underscoring the need for continued advancements in modeling human lung development and utilizing human tissue. Read More

Bioessays 2020 Apr 20:e1900255. Epub 2020 Apr 20.

University of Bordeaux and CNRS - ImmunoConcept, UMR5164, 146 rue Léo Saignat, Bordeaux, 33076, France.

A distinction between different notions of "structure" and "function" is suggested for interpreting the overwhelming amount of data on microbiome structure and function. Sequence data, biochemical agents, interaction networks, taxonomic communities, and their dynamics can be linked to potential or actual biochemical activities, causal roles, and selected effects, respectively. This conceptual clarification has important methodological consequences for how to interpret existing data and approach open questions in contemporary microbiome research practice. Read More

Bioessays 2020 Jun 20;42(6):e1900252. Epub 2020 Apr 20.

School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.

CRISPR (clustered regularly interspaced short palindromic repeats) activation (CRISPRa) in bacteria is an attractive method for programmable gene activation. Recently, a eukaryote-like, σ -dependent CRISPRa system has been reported. It exhibits high dynamic ranges and permits flexible target site selection. Read More

Bioessays 2020 Apr 19:e2000016. Epub 2020 Apr 19.

The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

Fusion genes formed by chromosomal rearrangements are common drivers of cancer. Recent innovations in the field of next-generation sequencing (NGS) have seen a dynamic shift from traditional fusion detection approaches, such as visual characterization by fluorescence, to more precise multiplexed methods. There are many different NGS-based approaches to fusion gene detection and deciding on the most appropriate method can be difficult. Read More

Bioessays 2020 Jun 19;42(6):e1900183. Epub 2020 Apr 19.

School of Earth Sciences, The University of Western Australia, Nedlands, WA, 6009, Australia.

A growing awareness of a subsurface fossil record of mostly hyphal fungi organisms stretching back through the Phanerozoic to ≈400 megaannum (Ma) and possibly earlier, provides an alternative view on hyphal development. Parallel with the emergence of hyphal fungi during Ordovician-Devonian times when plants colonized the land, which is the traditional notion of hyphal evolution, hyphae-based fungi existed in the deep biosphere. New insights suggest that the fundamental functions of hyphae may have evolved in response to an ancient subsurface endolithic life style and might have been in place before the colonization of land. Read More

Bioessays 2020 Apr 17:e1900238. Epub 2020 Apr 17.

Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, building A29, 625 00, Brno, Czech Republic.

The terms "eustress" and "distress" are widely used throughout the scientific literature. As of February 2020, 203 items in the Web of Science show up in a search for "eustress," however, there are almost 16 400 items found in a search for the term "distress." Based on the reasoning in this article, however, it is believed there is no such thing as eustress or distress. Read More

Bioessays 2020 May;42(5):e2000064

Bioessays 2020 May;42(5):e1900220

Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, 2192, South Africa.

Indoleamine 2,3-dioxygenase (IDO) is the rate-limiting enzyme in conversion of tryptophan to kynurenines, feeding de novo nicotinamide synthesis. IDO orchestrates materno-foetal tolerance, increasing human reproductive fitness. IDO mediates immune suppression through depletion of tryptophan required by T lymphocytes and other mechanisms. Read More

Bioessays 2020 Jun 17;42(6):e2000042. Epub 2020 Apr 17.

Department of Cell Engineering, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, 141973317, Iran.

Bioessays 2020 May 6;42(5):e1900244. Epub 2020 Apr 6.

Institute of Cell Biology, Medical Faculty, University of Münster, Münster, 48149, Germany.

During morphogenesis, tissues undergo extensive remodeling to get their final shape. Such precise sculpting requires the application of forces generated within cells by the cytoskeleton and transmission of these forces through adhesion molecules within and between neighboring cells. Within individual cells, microtubules together with actomyosin filaments and intermediate filaments form the composite cytoskeleton that controls cell mechanics during tissue rearrangements. Read More

Bioessays 2020 Jun 1;42(6):e1900231. Epub 2020 Apr 1.

Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, 33458, USA.

Ras homolog enriched in the striatum (Rhes) is a striatal enriched protein that promotes the formation of thin membranous tubes resembling tunneling nanotubes (TNT)-"Rhes tunnels"-that connect neighboring cell and transport cargoes: vesicles and proteins between the neuronal cells. Here the literature on TNT-like structures is reviewed, and the implications of Rhes-mediated TNT, the mechanisms of its formation, and its potential in novel cell-to-cell communication in regulating striatal biology and disease are emphasized. Thought-provoking ideas regarding how Rhes-mediated TNT, if it exists, in vivo, would radically change the way neurons communicate in the brain are discussed. Read More

Bioessays 2020 Jun 1;42(6):e1900177. Epub 2020 Apr 1.

Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08827, Korea.

DNA damage repair within telomeres are suppressed to maintain the integrity of linear chromosomes, but the accidental activation of repairs can lead to genome instability. This review develops the concept that mechanisms to repair DNA damage in telomeres contribute to genetic variability and karyotype evolution, rather than catastrophe. Spontaneous breaks in telomeres can be repaired by telomerase, but in some cases DNA repair pathways are activated, and can cause chromosomal rearrangements or fusions. Read More

Bioessays 2020 Jun 1;42(6):e2000030. Epub 2020 Apr 1.

Institut des Sciences de l'Évolution, Université de Montpellier, CC 065, Montpellier 05, 34095, France.

Much contemporary behavioral science stops short of considering the ethical implications of its own findings. This generates a contradiction between methods and discoveries, and hinders translation between updated scientific evidence for animal sentience and corresponding political and legal changes. A recent and particularly illustrative example in rodents is described here. Read More

Bioessays 2020 Mar 30:e2000063. Epub 2020 Mar 30.

Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Rd, Singapore, S487372, Singapore.

Bioessays 2020 Jun 29;42(6):e2000012. Epub 2020 Mar 29.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden.

Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present-day genomes, so-called ghost introgression. Read More

Bioessays 2020 Jun 29;42(6):e1900201. Epub 2020 Mar 29.

Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, F-38700, France.

The rational design of theoretical minimal RNA rings predetermines AUG as the universal start codon. This design maximizes coded amino acid diversity over minimal sequence length, defining in silico theoretical minimal RNA rings, candidate ancestral genes. RNA rings code for 21 amino acids and a stop codon after three consecutive translation rounds, and form a degradation-delaying stem-loop hairpin. Read More

Bioessays 2020 May 20;42(5):e1900192. Epub 2020 Mar 20.

Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, 10029, USA.

Polycomb group proteins are evolutionary conserved chromatin-modifying complexes, essential for the regulation of developmental and cell-identity genes. Polycomb-mediated transcriptional regulation is provided by two multi-protein complexes known as Polycomb repressive complex 1 (PRC1) and 2 (PRC2). Recent studies positioned PRC1 as a foremost executer of Polycomb-mediated transcriptional control. Read More

Bioessays 2020 Jun 20;42(6):e2000040. Epub 2020 Mar 20.

Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, Amsterdam, AZ, 1105, The Netherlands.

Intelligent-design websites misquote to subvert belief in Darwinian evolution. Nowadays, such sites pose as "objective" sources of information. Speaking more generally, spreading misinformation can be linked to climate science denial, vaccination avoidance, and a resurgence of pseudo-scientific racism. Read More

Bioessays 2020 Apr;42(4):e1900163

Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany.

X-chromosome inactivation ensures dosage compensation between the sexes in mammals by randomly choosing one out of the two X chromosomes in females for inactivation. This process imposes a plethora of questions: How do cells count their X chromosome number and ensure that exactly one stays active? How do they randomly choose one of two identical X chromosomes for inactivation? And how do they stably maintain this state of monoallelic expression? Here, different regulatory concepts and their plausibility are evaluated in the context of theoretical studies that have investigated threshold behavior, ultrasensitivity, and bistability through mathematical modeling. It is discussed how a twofold difference between a single and a double dose of X-linked genes might be converted to an all-or-nothing response and how mutually exclusive expression can be initiated and maintained. Read More

Bioessays 2020 Apr;42(4):e2000048

Bioessays 2020 May 17;42(5):e1900205. Epub 2020 Mar 17.

Institut Curie, PSL Research University, CNRS, UMR3664, Paris, F-75005, France.

Specificities associated with chromosomal linearity are not restricted to telomeres. Here, recent results obtained on fission and budding yeast are summarized and an attempt is made to define subtelomeres using chromatin features extending beyond the heterochromatin emanating from telomeres. Subtelomeres, the chromosome domains adjacent to telomeres, differ from the rest of the genome by their gene content, rapid evolution, and chromatin features that together contribute to organism adaptation. Read More

Bioessays 2020 May 16;42(5):e1900160. Epub 2020 Mar 16.

Louis Calder Center, Fordham University, Armonk, NY, 10504, USA.

Phylogeography and zooarchaeology are largely separate disciplines, yet each interrogates relationships between humans and commensal species. Knowledge gained about human history from studies of four commensal rats (Rattus rattus, R. tanezumi, R. Read More

Bioessays 2020 May 12;42(5):e1900161. Epub 2020 Mar 12.

Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan.

How vertebrates evolved different traits for acid excretion to maintain body fluid pH homeostasis is largely unknown. The evolution of Na /H  exchanger (NHE)-mediated NH excretion in fishes is reported, and the coevolution with increased ammoniagenesis and accompanying gluconeogenesis is speculated to benefit vertebrates in terms of both internal homeostasis and energy metabolism response to acidic stress. The findings provide new insights into our understanding of the possible adaptation of fishes to progressing global environmental acidification. Read More

Bioessays 2020 May 12;42(5):e2000029. Epub 2020 Mar 12.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.

Bioessays 2020 May 10;42(5):e1900153. Epub 2020 Mar 10.

Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, Amsterdam, AZ, 1105, Netherlands.

Eukaryotic origins are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry. However, the nature of the "host" cell and the mode of entry are subject to heavy debate. It is becoming clear that the mutual adaptation of a relatively simple, archaeal host and the endosymbiont has been the defining influence at the beginning of the eukaryotic lineage; however, many still resist such symbiogenic models. Read More

Bioessays 2020 Apr 6;42(4):e1900188. Epub 2020 Mar 6.

Fakultät für Biologie, Ludwig-Maximilians Universität München, Biozentrum, 82152, Planegg-Martinsried, Germany.

Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differences between active enhancers and their different inactive counterparts: the closed silenced state and the accessible primed and repressed states. Read More

Bioessays 2020 Apr 4;42(4):e1800261. Epub 2020 Mar 4.

Department of Psychology, Arizona State University, 950 S. McAllister Ave, Tempe, AZ, 85287, USA.

Smartphone use changes the landscape of social interactions, including introducing new social dilemmas to daily life. The challenge of putting down one's smartphone is an example of a classic coordination problem from game theory: the stag hunt game. In a stag hunt game, there are two possible coordination points, one that involves big payoffs for both partners (e. Read More

Bioessays 2020 May 4;42(5):e1900162. Epub 2020 Mar 4.

EMBL Australia, John Curtin School of Medical Research, The Australian National University, 131 Garran Rd, Acton 2602, Canberra, ACT, Australia.

The transcriptional co-activators YAP (or YAP1) and TAZ (or WWTR1) are frequently activated during the growth and progression of many solid tumors, including lung, colorectal, breast, pancreatic, and liver carcinomas as well as melanoma and glioma. YAP/TAZ bind to TEAD-family co-activators to drive cancer cell survival, proliferation, invasive migration, and metastasis. YAP/TAZ activation may also confer resistance to chemotherapy, radiotherapy, or immunotherapy. Read More

Bioessays 2020 Apr 4;42(4):e1900122. Epub 2020 Mar 4.

Department of Research , Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. A. Amadeo, 42, I-20133, Milan, Italy.

Thousands of candidate cancer biomarkers have been proposed, but so far, few are used in cancer screening. Failure to implement these biomarkers is attributed to technical and design flaws in the discovery and validation phases, but a major obstacle stems from cancer biology itself. Oncogenomics has revealed broad genetic heterogeneity among tumors of the same histology and same tissue (or organ) from different patients, while tumors of different tissue origins also share common genetic mutations. Read More

Bioessays 2020 May 1;42(5):e1900204. Epub 2020 Mar 1.

Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain.

During replication, the topology of DNA changes continuously in response to well-known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow-down and even stall at precise sites. The way these changes in the rate of replisome progression affect DNA topology is not yet well understood. Read More

Bioessays 2020 May 1;42(5):e1900158. Epub 2020 Mar 1.

Institute of Neurobiology, University of Lübeck, Lübeck, 23562, Germany.

In mammals, a network of cellular circadian clocks organizes physiology and behavior along the 24-h day cycle. The traditional hierarchical model of circadian clock organization with a central pacemaker and peripheral slave oscillators has recently been challenged by studies combining tissue-specific mouse mutants with transcriptome analyses. First, a surprisingly small number of tissue rhythms are lost when only local clocks are ablated and, second, transcriptional circadian rhythms appear to be regulated by a complex mix of local and systemic factors. Read More