pinecone/core-2020-05-10-deduplication huggingface dataset:
Microbial gardening in the ocean's twilight zone: Detritivorous metazoans benefit from fragmenting, rather than ingesting, sinking detritus

Sinking organic particles transfer ∼10 gigatonnes of carbon into the deep ocean each year, keeping the atmospheric CO2 concentration significantly lower than would otherwise be the case. The exact size of this effect is strongly influenced by biological activity in the ocean's twilight zone (∼50–1,000 m beneath the surface). Recent work suggests that the resident zooplankton fragment, rather than ingest, the majority of encountered organic particles, thereby stimulating bacterial proliferation and the deep-ocean microbial food web. Here we speculate that this apparently counterintuitive behaviour is an example of ‘microbial gardening’, a strategy that exploits the enzymatic and biosynthetic capabilities of microorganisms to facilitate the ‘gardener's’ access to a suite of otherwise unavailable compounds that are essential for metazoan life. We demonstrate the potential gains that zooplankton stand to make from microbial gardening using a simple steady state model, and we suggest avenues for future research
One-way trip: Influenza virus' adaptation to gallinaceous poultry may limit its pandemic potential

We hypothesise that some influenza virus adaptations to poultry may explain why the barrier for human-to-human transmission is not easily overcome once the virus has crossed from wild birds to chickens. Since the cluster of human infections with H5N1 influenza in Hong Kong in 1997, chickens have been recognized as the major source of avian influenza virus infection in humans. Although often severe, these infections have been limited in their subsequent human-to-human transmission, and the feared H5N1 pandemic has not yet occurred. Here we examine virus adaptations selected for during replication in chickens and other gallinaceous poultry. These include altered receptor binding and increased pH of fusion of the haemagglutinin as well as stalk deletions of the neuraminidase protein. This knowledge could aid the delivery of vaccines and increase our ability to prioritize research efforts on those viruses from the diverse array of avian influenza viruses that have greatest human pandemic potential
The origin and evolution of social insect queen pheromones: novel hypotheses and outstanding problems

Queen pheromones, which signal the presence of a fertile queen and induces daughter workers to remain sterile, are considered to play a key role in regulating the reproductive division of labour of insect societies. Although queen pheromones were long thought to be highly taxon-specific, recent studies have shown that structurally related long-chain hydrocarbons act as conserved queen signals across several independently evolved lineages of social insects. These results imply that social insect queen pheromones are very ancient and likely derived from an ancestral signalling system that was already present in their common solitary ancestors. Based on these new insights, we here speculate on what signal precursors social insect queen pheromones may have evolved from and provide compelling evidence that these pheromones should best be seen as honest signals of fertility as opposed to suppressive agents that chemically sterilize the workers against their own best interests.status: publishe
What is the function of mitochondrial networks? A theoretical assessment of hypotheses and proposal for future research

Mitochondria can change their shape from discrete isolated organelles to a large continuous reticulum. The cellular advantages underlying these fused networks are still incompletely understood. In this paper, we describe and compare hypotheses regarding the function of mitochondrial networks. We use mathematical and physical tools both to investigate existing hypotheses and to generate new ones, and we suggest experimental and modelling strategies. Among the novel insights we underline from this work are the possibilities that (i) selective mitophagy is not required for quality control because selective fusion is sufficient; (ii) increased connectivity may have non-linear effects on the diffusion rate of proteins; and (iii) fused networks can act to dampen biochemical fluctuations. We hope to convey to the reader that quantitative approaches can drive advances in the understanding of the physiological advantage of these morphological changes
Evolutionary analyses of caspase-8 and its paralogs: Deep origins of the apoptotic signaling pathways.

Although Caenorhabditis and Drosophila proved invaluable in unraveling the molecular mechanisms of apoptosis, it is now clear that these animals are of limited value for understanding the evolution of apoptotic systems. Whereas data from these invertebrates led to the assumption that the extrinsic apoptotic pathway is restricted to vertebrates, recent data from cnidarians and sponges indicate that this pathway predates bilaterian origins. Here we review the phylogenetic distribution of caspase-8, the initiator caspase of the extrinsic apoptotic pathway, its paralogs and other components of the network. The ancestral caspase-8 gave rise to four paralogs early in vertebrate evolution, and these have been maintained in many tetrapods. However, eutherians have lost caspase-18 and myomorph rodents have lost caspase-10, these losses suggesting functional redundancy amongst caspase-8 paralogs. The apoptotic network of the eumetazoan ancestor appears to have been complex and vertebrate like, and is only now being revealed by studying simple animals
Assessing the potentially misleading nature of metrics and of those who assess and create them

This self-published note makes a formal critique of a paper published in Wiley’s Bioessays as an invited paper: Gutierrez, F.R.S., Beall, J., Forero, D.A. (2015) Spurious alternative impact factors: The scale of the problem from an academic perspective. Bioessays 37: 474-476. DOI: 10.1002/bies.201500011. I am of the opinion that several incorrect and even misleading statements have been made in that paper. The refusal by the authors to respond to these concerns publicly, as well as the excuse by the publisher to not consider this critique on the basis of “journal space limitations” further accentuates the concerns. This model of publishing also serves as a viable way of exposing ideas and criticisms that lie beyond the manipulated hand of the self-serving interests of publishers
Mouse models of colorectal cancer as preclinical models

In this review, we discuss the application of mouse models to the identification and pre-clinical validation of novel therapeutic targets in colorectal cancer, and to the search for early disease biomarkers. Large-scale genomic, transcriptomic and epigenomic profiling of colorectal carcinomas has led to the identification of many candidate genes whose direct contribution to tumourigenesis is yet to be defined; we discuss the utility of cross-species comparative ‘omics-based approaches to this problem. We highlight recent progress in modelling late-stage disease using mice, and discuss ways in which mouse models could better recapitulate the complexity of human cancers to tackle the problem of therapeutic resistance and recurrence after surgical resection.REM, SJAB, MJA and DJA are funded by Cancer Research UK.This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/bies.20150003
Retroviral integration: Site matters: Mechanisms and consequences of retroviral integration site selection

Here, we review genomic target site selection during retroviral integration as a multistep process in which specific biases are introduced at each level. The first asymmetries are introduced when the virus takes a specific route into the nucleus. Next, by co-opting distinct host cofactors, the integration machinery is guided to particular chromatin contexts. As the viral integrase captures a local target nucleosome, specific contacts introduce fine-grained biases in the integration site distribution. In vivo, the established population of proviruses is subject to both positive and negative selection, thereby continuously reshaping the integration site distribution. By affecting stochastic proviral expression as well as the mutagenic potential of the virus, integration site choice may be an inherent part of the evolutionary strategies used by different retroviruses to maximise reproductive success.status: publishe
Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: Dispelling the darkness

Integration of knowledge concerning circadian rhythms, metabolic networks, and sleep-wake cycles is imperative for unraveling the mysteries of biological cycles and their underlying mechanisms. During the last decade, enormous progress in circadian biology research has provided a plethora of new insights into the molecular architecture of circadian clocks. However, the recent identification of autonomous redox oscillations in cells has expanded our view of the clockwork beyond conventional transcription/translation feedback loop models, which have been dominant since the first circadian period mutants were identified in fruit fly. Consequently, non-transcriptional timekeeping mechanisms have been proposed, and the antioxidant peroxiredoxin proteins have been identified as conserved markers for 24-hour rhythms. Here, we review recent advances in our understanding of interdependencies amongst circadian rhythms, sleep homeostasis, redox cycles, and other cellular metabolic networks. We speculate that systems-level investigations implementing integrated multi-omics approaches could provide novel mechanistic insights into the connectivity between daily cycles and metabolic systems.ABR is a Wellcome Trust Senior Clinical Fellow and receives funding from the Wellcome Trust (Grant No. 100333/Z/12/Z), the European Research Council (ERC Starting Grant No. 281348, MetaCLOCK), the European Molecular Biology Organization (EMBO) Young Investigators Programme, and the Lister Institute of Preventative Medicine. SR is supported by the Wellcome Trust.This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1002/bies.20150005
Lipids under stress - a lipidomic approach for the study of mood disorders

The emerging field of lipidomics has identified lipids as key players in disease physiology. Their physicochemical diversity allows precise control of cell structure and signaling events through modulation of membrane prop- erties and trafficking of proteins. As such, lipids are important regulators of brain function and have been implicated in neurodegenerative and mood disorders. Importantly, environmental chronic stress has been associated with anxiety and depression and its exposure in rodents has been extensively used as a model to study these diseases. With the accessibility to modern mass- spectrometry lipidomic platforms, it is now possible to snapshot the extensively interconnected lipid network. Here, we review the fundamentals of lipid biology and outline a framework for the interpretation of lipidomic studies as a new approach to study brain pathophysiology. Thus, lipid profiling provides an exciting avenue for the identification of disease signatures with important implications for diagnosis and treatment of mood disorders.We would like to thank Nuno Sousa for critical reading of the manuscript. André Miranda is funded by Fundação para a Ciência e Tecnologia (PD/BD/105915/2014). Tiago Gil Oliveira is funded by Fundação para a Ciência e Tecnologia (PTDC/ SAU-NMC/118971/2010)
Spontaneous cell polarization: Feedback control of Cdc42 GTPase breaks cellular symmetry.

Spontaneous polarization without spatial cues, or symmetry breaking, is a fundamental problem of spatial organization in biological systems. This question has been extensively studied using yeast models, which revealed the central role of the small GTPase switch Cdc42. Active Cdc42-GTP forms a coherent patch at the cell cortex, thought to result from amplification of a small initial stochastic inhomogeneity through positive feedback mechanisms, which induces cell polarization. Here, I review and discuss the mechanisms of Cdc42 activity self-amplification and dynamic turnover. A robust Cdc42 patch is formed through the combined effects of Cdc42 activity promoting its own activation and active Cdc42-GTP displaying reduced membrane detachment and lateral diffusion compared to inactive Cdc42-GDP. I argue the role of the actin cytoskeleton in symmetry breaking is not primarily to transport Cdc42 to the active site. Finally, negative feedback and competition mechanisms serve to control the number of polarization sites
Position-effect variegation revisited: HUSHing up heterochromatin in human cells

Much of what we understand about heterochromatin formation in mammals has been extrapolated from forward genetic screens for modifiers of position-effect variegation (PEV) in the fruit fly Drosophila melanogaster. The recent identification of the HUSH (Human Silencing Hub) complex suggests that more recent evolutionary developments contribute to the mechanisms underlying PEV in human cells. Although HUSH-mediated repression also involves heterochromatin spreading through the reading and writing of the repressive H3K9me3 histone modification, clear orthologues of HUSH subunits are not found in Drosophila but are conserved in vertebrates. Here we compare the insights into the mechanisms of PEV derived from genetic screens in the fly, the mouse and in human cells, review what is currently known about the HUSH complex, and discuss the implications of HUSH-mediated silencing for viral latency. Future studies will provide mechanistic insight into HUSH complex function and reveal the relationship between HUSH and other epigenetic silencing complexes.This work was funded by a Wellcome Trust Principal Research Fellowship to P.J.L. (084957/Z/08/Z) and a Wellcome Trust PhD studentship to I.A.T. The Cambridge Institute for Medical Research is in receipt of a Wellcome Trust Strategic Award.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/bies.20150018
Germline development in amniotes : a paradigm shift in primordial germ cell specification

In the field of germline development in amniote vertebrates, primordial germ cell (PGC) specification in birds and reptiles remains controversial. Avians are believed to adopt a predetermination or maternal specification mode of PGC formation, contrary to an inductive mode employed by mammals and, supposedly, reptiles. Here, we revisit and review some key aspects of PGC development that channelled the current subdivision, and challenge the position of birds and reptiles as well as the binary' evolutionary model of PGC development in vertebrates. We propose an alternative view on PGC specification where germ plasm plays a role in laying the foundation for the formation of PGC precursors (pPGC), but not necessarily of PGCs. Moreover, inductive mechanisms may be necessary for the transition from pPGCs to PGCs. Within this framework, the implementation of data from birds and reptiles could provide new insights on the evolution of PGC specification in amniotes
MicroRNA annotation of plant genomes − Do it right or not at all.

MicroRNAs are non-coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts decisively to improve the accuracy of miRNAome annotations. We encourage genome annotation teams to do it right or not at all
tRNA biology in the omics era: Stress signalling dynamics and cancer progression.

Recent years have seen a burst in the number of studies investigating tRNA biology. With the transition from a gene-centred to a genome-centred perspective, tRNAs and other RNA polymerase III transcripts surfaced as active regulators of normal cell physiology and disease. Novel strategies removing some of the hurdles that prevent quantitative tRNA profiling revealed that the differential exploitation of the tRNA pool critically affects the ability of the cell to balance protein homeostasis during normal and stress conditions. Furthermore, growing evidence indicates that the adaptation of tRNA synthesis to cellular dynamics can influence translation and mRNA stability to drive carcinogenesis and other pathological disorders. This review explores the contribution given by genomics, transcriptomics and epitranscriptomics to the discovery of emerging tRNA functions, and gives insights into some of the technical challenges that still limit our understanding of the RNA polymerase III transcriptional machinery
DNA demethylation pathways: Additional players and regulators.

DNA demethylation can occur passively by "dilution" of methylation marks by DNA replication, or actively and independently of DNA replication. Direct conversion of 5-methylcytosine (5mC) to cytosine (C), as originally proposed, does not occur. Instead, active DNA methylation involves oxidation of the methylated base by ten-eleven translocations (TETs), or deamination of the methylated or a nearby base by activation induced deaminase (AID). The modified nucleotide, possibly together with surrounding nucleotides, is then replaced by the BER pathway. Recent data clarify the roles and the regulation of well-known enzymes in this process. They identify base excision repair (BER) glycosylases that may cooperate with or replace thymine DNA glycosylase (TDG) in the base excision step, and suggest possible involvement of DNA damage repair pathways other than BER in active DNA demethylation. Here, we review these new developments
Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices

Host-pathogen arms race is a universal, central aspect of the evolution of life. Most organisms evolved several distinct yet interacting strategies of anti-pathogen defense including resistance to parasite invasion, innate and adaptive immunity, and programmed cell death (PCD). The PCD is the means of last resort, a suicidal response to infection that is activated when resistance and immunity fail. An infected cell faces a decision between active defense and altruistic  suicide or dormancy induction, depending on whether immunity is “deemed” capable of preventing parasite reproduction and consequent infection of other cells. In bacteria and archaea, immunity genes typically colocalize with PCD modules, such as toxins-antitoxins, suggestive of immunity-PCD coupling, likely mediated by shared proteins that sense damage and “predict” the outcome of infections. In type VI CRISPR-Cas systems, the same enzyme that inactivates the target RNA might execute cell suicide, in a case of ultimate integration of immunity and PCD
Untranslated parts of genes interpreted: making heads or tails of high-throughput transcriptomic data via computational methods

The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by where transcription starts and ends on a genomic locus. The extent of alternative transcription start and alternative poly-adenylation has been revealed by sequencing methods focused on the ends of transcripts, but the application of these methods is not yet widely adopted by the community. In this review we highlight the importance of defining the untranslated parts of transcripts and suggest that computational methods applied to standard high-throughput technologies are a useful alternative to the expertise-demanding 5’ and 3’ sequencing. We present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events, focusing on technical challenges and arguing for the need to include better normalization of the data and more appropriate statistical models of the expected variation in the signal
Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity

Epigenetic and transcriptional variability contribute to the vast diversity of cellular and organismal phenotypes and are key in human health and disease. In this review, we describe different types, sources, and determinants of epigenetic and transcriptional variability, enabling cells and organisms to adapt and evolve to a changing environment. We highlight the latest research and hypotheses on how chromatin structure and the epigenome influence gene expression variability. Further, we provide an overview of challenges in the analysis of biological variability. An improved understanding of the molecular mechanisms underlying epigenetic and transcriptional variability, at both the intra- and inter-individual level, provides great opportunity for disease prevention, better therapeutic approaches, and personalized medicine.SE and SBare funded by the UK National Institute for Health Research UCLH\ud
Biomedical Research Center (BRC84/CN/SB/5984) and the H2020 Project\ud
MultipleMS (733161). VP and AV are funded by the Joint BSC-IRB-CRG\ud
Program in Computational Biology and Severo Ochoa Award (SEV 2015–\ud
0493).TheMRC/BHF Cardiovascular EpidemiologyUnit is supportedby the\ud
UK Medical Research Council (MR/L003120/1), British Heart Foundation\ud
(RG/13/13/30194), andNIHR Cambridge Biomedical Research Centre. We\ud
thank Allan Orozco for providing critical comments on the manuscript, and\ud
Laura Phipps for proofreading the text.Peer ReviewedPostprint (published version
Gutsy moves: The amygdala as a critical node in microbiota to brain signaling

The amygdala is a key brain area regulating responses to stress and emotional stimuli, so improving our understanding of how it is regulated could offer novel strategies for treating disturbances in emotion regulation. As we review here, a growing body of evidence indicates that the gut microbiota may contribute to a range of amygdala-dependent brain functions from pain sensitivity to social behavior, emotion regulation, and therefore, psychiatric health. In addition, it appears that the microbiota is necessary for normal development of the amygdala at both the structural and functional levels. While further investigations are needed to elucidate the exact mechanisms of microbiota-to-amygdala communication, ultimately, this work raises the intriguing possibility that the gut microbiota may become a viable treatment target in disorders associated with amygdala dysregulation, including visceral pain, post-traumatic stress disorder, and beyond
Three Distinct Types of Microautophagy Based on Membrane Dynamics and Molecular Machineries

Microautophagy is originally defined as lysosomal (vacuolar) membrane dynamics to directly enwrap and transport cytosolic components into the lumen of the lytic organelle. Molecular details of microautophagy had remained unknown until genetic studies in yeast identified a set of proteins required for the process. Subsequent studies with other experimental model organisms resulted in a series of discoveries that accompanied an expansion of the definition of microautophagy to also encompass endosomal membrane dynamics. These findings, however, still impose puzzling, non‐integrated images as to the molecular mechanism of microautophagy. By reviewing recent studies on microautophagy in various experimental systems, we propose the classification of microautophagy into three types, as the basis for developing a comprehensive view of the process