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Dead animal biomass (carrion) is present in all terrestrial ecosystems, and its consumption, decomposition, and dispersal can have measurable effects on vertebrates, invertebrates, microbes, parasites, plants, and soil. But despite the number of studies examining the influence of carrion on food webs, there has been no attempt to identify how general ecological processes around carrion might be used as an ecosystem indicator. We suggest that knowledge of scavenging and decomposition rates, scavenger diversity, abundance, and behavior around carrion, along with assessments of vegetation, soil, microbe, and parasite presence, can be used individually or in combination to understand food web dynamics. Monitoring carrion could also assist comparisons of ecosystem processes among terrestrial landscapes and biomes. Although there is outstanding research needed to fully integrate carrion ecology and monitoring into ecosystem management, we see great potential in using carrion as an ecosystem indicator of an intact and functional food web., We argue that information about the processes and organisms involved with the consumption and decomposition of dead animal matter (carrion) can provide insights into the broader health and integrity of ecosystems.

Individuals infected with the severe acute respiratory syndrome (SARS)‐related coronavirus 2 (SARS‐CoV‐2) develop a critical and even fatal disease, called Coronavirus disease‐19 (COVID‐19), that eventually evolves into acute respiratory distress syndrome. The gravity of the SARS‐CoV‐2 pandemic, the escalating number of confirmed cases around the world, the many unknowns related to the virus mode of action, and the heterogenous outcome of COVID‐19 disease in the population ask for the rapid development of alternative approaches, including repurposing of existing drugs, that may dampen virus infectivity. SARS‐CoV‐2 infects human cells through interaction with sialylated receptors at the surface of epithelial cells, such as angiotensin‐converting enzyme 2 (ACE2). Glycan composition on virus entry receptors has been shown to influence the rate of infection of SARS‐CoV‐2 and spreading of virions has recently been linked to altered lysosomal exocytosis. These processes could concurrently involve the lysosomal system and its glycosidases. We hypothesize that modulating the activity of one of them, the lysosomal sialidase NEU1, could impinge on both the sialylation status of ACE2 and other host receptors as well as the extent of lysosomal exocytosis. Thus NEU1‐controlled pathways may represent therapeutic targets, which could impact on SARS‐CoV‐2 susceptibility, infectivity, and spread.

Negative interspecific mating interactions, known as reproductive interference, can hamper species coexistence in a local patch and promote niche partitioning or geographical segregation of closely related species. Conspecific sperm precedence (CSP), which occurs when females that have mated with both conspecific and heterospecific males preferentially use conspecific sperm for fertilization, might contribute to species coexistence by mitigating the costs of interspecific mating and hybridization. We discussed whether two species exhibiting CSP can coexist in a local environment in the presence of reproductive interference. First, using a behaviorally explicit mathematical model, we demonstrated that two species characterized by negative mating interactions are unlikely to coexist because the costs of reproductive interference, such as loss of mating opportunity with conspecific partners, are inevitably incurred when individuals of both species are present. Second, we experimentally examined differences in mating activity and preference in two Harmonia ladybird species known to exhibit CSP. These behavioral differences may lead to local extinction of H. yedoensis because of reproductive interference by H. axyridis. This prediction is consistent with field observations that H. axyridis uses various food sources and habitats whereas H. yedoensis is confined to a less preferred prey item and a pine tree habitat. Finally, by a comparative approach, we observed that niche partitioning or parapatric distribution, but not sympatric coexistence in the same habitat, is maintained between species with CSP belonging to a wide range of taxa, including vertebrates and invertebrates living in aquatic or terrestrial environments. Taken together, it is possible that reproductive interference may destabilize local coexistence even in closely related species that exhibit CSP., We discussed whether two closely related species exhibiting conspecific sperm precedence can coexist in a local environment in the presence of reproductive interference. We used mathematical models, behavioral experiment, and comparative study. We suggested that conspecific sperm precedence does not reduce the overall cost of reproductive interference sufficiently to allow the interacting species to coexist in the same local environment.

Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome‐scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR‐based Sanger sequencing, following the dawn of the second‐generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained., A significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from the ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples.

Over thirty species of littoral marine Gammaridea occur along the coasts of the North Atlantic. From one to several species can coexist in a single region. There is an evident, inverse relationship between egg incubation time and temperature (from 14 to >120 days) and consequent trends in the size of the animals on reaching maturity (from 5 mm in warmer waters to 30 mm in the coldest ones) and in lifespan (from 5 years). Littoral gammarids are a good example of the shrinking size effect of increasing temperatures and size‐related species diversity. In large species, the annual cohorts of the population (3–5 annual size groups) functionally replace the adults of smaller species. The ongoing warming of the European Arctic seas may extend the distribution limits of boreal species so that more Gammarus species may appear on northern coasts hitherto occupied by just one or at most two species., Warming of the arctic shortens the long life cycles of large local amphipod littoral crustaceans. Faster development and maturity at smaller size opens space for competing small species that were not able to coexist with the large ones.

Pre‐biopsy multiparametric magnetic resonance imaging (mpMRI) has transformed the risk stratification and diagnostic approach for suspected prostate cancer. The majority of clinically significant prostate cancers are visible on pre‐biopsy mpMRI, however, there are a subset of significant tumors that are not detected by mpMRI. The radiobiological mechanisms underpinning mpMRI‐visibility and invisibility of these cancers remain uncertain. Emerging evidence suggests that mpMRI‐visible tumors are enriched with molecular features associated with increased disease aggressivity and poor clinical prognosis, which is supported by short‐term endpoints, such as biochemical recurrence following surgery. Furthermore, at the histopathological level, mpMRI‐visible tumors appear to exhibit increased architectural and vascular density compared to mpMRI‐invisible disease. It seems probable that the genomic, pathological, radiological, and clinical features of mpMRI‐visible and mpMRI‐invisible prostate cancers are interrelated. Here, we propose a novel cross‐disciplinary theory that links genomic and molecular evidence with cellular and histopathological appearances, elucidating both the mpMRI visibility and clinical status of significant prostate cancer.

DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination., Neutral models of mitochondrial evolution predict mitochondrial DNA barcoding cannot work for recently diverged taxa, but mt DNA barcoding accurately delimits species across a wide spectrum of bilaterian animals. I propose that the tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. If selective sweeps play a key role in generating mt DNA barcode gaps, then the most important factor determining whether or not mt DNA sequences diagnose species boundaries within a taxon would be the extent to which the mt chromosomes of individuals within that taxon engage in recombination.

COVID‐19 may cause pneumonia, acute respiratory distress syndrome, cardiovascular alterations, and multiple organ failure, which have been ascribed to a cytokine storm, a systemic inflammatory response, and an attack by the immune system. Moreover, an oxidative stress imbalance has been demonstrated to occur in COVID‐19 patients. N‐ Acetyl‐L‐cysteine (NAC) is a precursor of reduced glutathione (GSH). Due to its tolerability, this pleiotropic drug has been proposed not only as a mucolytic agent, but also as a preventive/therapeutic agent in a variety of disorders involving GSH depletion and oxidative stress. At very high doses, NAC is also used as an antidote against paracetamol intoxication. Thiols block the angiotensin‐converting enzyme 2 thereby hampering penetration of SARS‐CoV‐2 into cells. Based on a broad range of antioxidant and anti‐inflammatory mechanisms, which are herein reviewed, the oral administration of NAC is likely to attenuate the risk of developing COVID‐19, as it was previously demonstrated for influenza and influenza‐like illnesses. Moreover, high‐dose intravenous NAC may be expected to play an adjuvant role in the treatment of severe COVID‐19 cases and in the control of its lethal complications, also including pulmonary and cardiovascular adverse events.

Carrion represents an unpredictable and widely distributed primary food source for vultures and other avian scavengers. Avian scavengers in African savanna ecosystems are reported to rely exclusively on visual stimuli to locate carcasses. However, carnivores’ predation of large mammalian herbivores and subsequent competition for access to the carcass can result in considerable noise, often audible over long distances and for prolonged periods. Vultures and other avian scavengers may therefore detect and respond to these auditory cues, as do the mammalian carnivores alongside which vultures have coevolved, but this has not been investigated to date. Working in the Serengeti ecosystem, Tanzania, we used diurnal auditory broadcasts to simulate predation and competitive carnivore feeding interactions. Based on the current understanding of avian scavenger ecology, we hypothesized that avian responses to call‐in stations would be evoked exclusively by visual, rather than auditory, cues. We therefore predicted that (a) the arrival of avian scavengers at call‐in stations should be preceded and facilitated by mammalian carnivores and that (b) the arrival of avian scavengers would be positively correlated with the number of mammalian scavengers present, which would increase detectability. We recorded 482 birds during 122 separate playback events. In 22% of these instances, avian scavengers arrived first, ruling out responses based exclusively on visual observations of mammalian carnivores, thereby contradicting our first prediction. Furthermore, the first avian arrivals at survey sessions were inversely related to the number of hyenas and jackals present, contradicting our second prediction. Since no bait or carcasses were used during the experiments, these responses are indicative of the birds’ ability to detect and respond to audio stimuli. Our findings challenge the current consensus of sensory perception and foraging in these species and provide evidence that avian scavengers have the ability to use sound to locate food resources., Avian scavengers in African savanna ecosystems are reported to rely exclusively on visual stimuli to locate carcasses. Here, we report on the response of vultures and other avian scavengers to auditory cues indicative of foraging opportunities. Based on our findings, we hypothesize that these birds are able to utilize auditory cues while foraging.

Drug repurposing is potentially the fastest available option in the race to identify safe and efficacious drugs that can be used to prevent and/or treat COVID‐19. By describing the life cycle of the newly emergent coronavirus, SARS‐CoV‐2, in light of emerging data on the therapeutic efficacy of various repurposed antimicrobials undergoing testing against the virus, we highlight in this review a possible mechanistic convergence between some of these tested compounds. Specifically, we propose that the lysosomotropic effects of hydroxychloroquine and several other drugs undergoing testing may be responsible for their demonstrated in vitro antiviral activities against COVID‐19. Moreover, we propose that Niemann‐Pick disease type C (NPC), a lysosomal storage disorder, may provide new insights into potential future therapeutic targets for SARS‐CoV‐2, by highlighting key established features of the disorder that together result in an “unfavorable” host cellular environment that may interfere with viral propagation. Our reasoning evolves from previous biochemical and cell biology findings related to NPC, coupled with the rapidly evolving data on COVID‐19. Our overall aim is to suggest that pharmacological interventions targeting lysosomal function in general, and those particularly capable of reversibly inducing transient NPC‐like cellular and biochemical phenotypes, constitute plausible mechanisms that could be used to therapeutically target COVID‐19.

The sudden outbreak of COVID‐19 has led to more than seven thousand deaths. Unfortunately, there are no specific drugs available to cure this disease. Type 2 taste receptors (TAS2Rs) may play an important role in host defense mechanisms. Based on the idea of host‐directed therapy (HDT), we performed a negative co‐expression analysis using big data of 60 000 Affymetrix expression arrays and 5000 TCGA data sets to determine the functions of TAS2R10, which can be activated by numerous bitter substances. Excitingly, we found that the main functions of TAS2R10 involved controlling infectious diseases caused by bacteria, viruses, and parasites, suggesting that TAS2R10 is a key trigger of host defense pathways. To quickly guide the clinical treatment of 2019‐nCoV, we searched currently available drugs that are agonists of TAS2Rs. We identified many cheap, available, and safe medicines, such as diphenidol, quinine, chloroquine, artemisinin, chlorpheniramine, yohimbine, and dextromethorphan, which may target the most common symptoms caused by 2019‐nCoV. We suggest that a cocktail‐like recipe of existing bitter drugs may help doctors to fight this catastrophic disease and that the general public may drink or eat bitter substances, such as coffee, tea, or bitter vegetables, to reduce the risk of infection.

While biological distributions are not static and change/evolve through space and time, nonstationarity of climatic and land‐use conditions is frequently neglected in species distribution models. Even recent techniques accounting for spatiotemporal variation of species occurrence basically consider the environmental predictors as static; specifically, in most studies using species distribution models, predictor values are averaged over a 50‐ or 30‐year time period. This could lead to a strong bias due to monthly/annual variation between the climatic conditions in which species' locations were recorded and those used to develop species distribution models or even a complete mismatch if locations have been recorded more recently. Moreover, the impact of land‐use change has only recently begun to be fully explored in species distribution models, but again without considering year‐specific values. Excluding dynamic climate and land‐use predictors could provide misleading estimation of species distribution. In recent years, however, open‐access spatially explicit databases that provide high‐resolution monthly and annual variation in climate (for the period 1901–2016) and land‐use (for the period 1992–2015) conditions at a global scale have become available. Combining species locations collected in a given month of a given year with the relative climatic and land‐use predictors derived from these datasets would thus lead to the development of true dynamic species distribution models (D‐SDMs), improving predictive accuracy and avoiding mismatch between species locations and predictor variables. Thus, we strongly encourage modelers to develop D‐SDMs using month‐ and year‐specific climatic data as well as year‐specific land‐use data that match the period in which species data were collected., In most studies using species distribution models, predictor variables are averaged over a 50‐ or 30‐year time‐period, leading to a strong bias due to monthly/annual variation between the climatic conditions in which species' locations were recorded and those used to develop species distribution models or even a complete mismatch if locations have been recorded more recently. However, thanks to recent development of open access spatially explicit databases providing monthly and annual variation of climate and land‐use conditions at global scale, it is now possible to develop dynamic species distribution models, matching dates in which species locations were collected and predictor values.

International audience; The regulation of body temperature (thermoregulation) and of water balance (defined here as hydroregulation) are key processes underlying ecological and evolutionary responses to climate fluctuations in wild animal populations. In terrestrial (or semiterrestrial) ectotherms, thermoregulation and hydroregulation closely interact and combined temperature and water constraints should directly influence individual performances. Although comparative physiologists traditionally investigate jointly water and temperature regulation, the ecological and evolutionary implications of these coupled processes have so far mostly been studied independently. Here, we revisit the concept of thermo‐hydroregulation to address the functional integration of body temperature and water balance regulation in terrestrial ectotherms. We demonstrate how thermo‐hydroregulation provides a framework to investigate functional adaptations to joint environmental variation in temperature and water availability, and potential physiological and/or behavioral conflicts between thermoregulation and hydroregulation. We extend the classical cost–benefit model of thermoregulation in ectotherms to highlight the adaptive evolution of optimal thermo‐hydroregulation strategies. Critical gaps in the parameterization of this conceptual optimality model and guidelines for future empirical research are discussed. We show that studies of thermo‐hydroregulation refine our mechanistic understanding of physiological and behavioral plasticity, and of the fundamental niche of the species. This is illustrated with relevant and recent examples of space use and dispersal, resource‐based trade‐offs, and life‐history tactics in insects, amphibians, and nonavian reptiles.

Since the 1980s, dengue incidence has increased 30-fold. However, in 2017, there was a noticeable reduction in reported dengue incidence cases within the Americas, including severe and fatal cases. Understanding the mechanism underlying dengue's incidence and decline in the Americas is vital for public health planning. We aimed to provide plausible explanations for the decline in 2017.An expert panel of representatives from scientific and academic institutions, Ministry of Health officials from Latin America and PAHO/WHO staff met in October 2017 to propose hypotheses. The meeting employed six moderated plenary discussions in which participants reviewed epidemiological evidence, suggested explanatory hypotheses, offered their expert opinions on each and developed a consensus.The expert group established that in 2017, there was a generalised decreased incidence, severity and number of deaths due to dengue in the Americas, accompanied by a reduction in reported cases of both Zika and chikungunya virus infections, with no change in distribution among age groups affected. This decline was determined to be unlikely due to changes in epidemiological surveillance systems, as similar designs of surveillance systems exist across the region. Although sudden surveillance disruption is possible at a country or regional level, it is unlikely to occur in all countries simultaneously. Retrospective modelling with epidemiological, immunological and entomological information is needed. Host or immunological factors may have influenced the decline in dengue cases at the population level through immunity; however, herd protection requires additional evidence. Uncertainty remains regarding the effect on the outcome of sequential infections of different dengue virus (DENV) types and Zika virus (ZIKV), and vice versa. Future studies were recommended that examine the epidemiological effect of prior DENV infection on Zika incidence and severity, the epidemiological effect of prior Zika virus infection on dengue incidence and severity, immune correlates based on new-generation ELISA assays, and impact of prior DENV/other arbovirus infection on ZIKV immune response in relation to number of infections and the duration of antibodies in relation to interval of protection. Follow-up studies should also investigate whether increased vector control intensification activities contributed to the decline in transmission of one or more of these arboviruses. Additionally, proposed studies should focus on the potential role of vector competence when simultaneously exposed to various arboviruses, and on entomological surveillance and its impact on circulating vector species, with a goal of applying specific measures that mitigate seasonal occurrence or outbreaks.Multifactorial events may have accounted for the decline in dengue seen in 2017. Differing elements might explain the reduction in dengue including elements of immunity, increased vector control, and even vector and\or viruses changes or adaptations. Most of the results of this expert consensus group meeting are hypothetical and based on limited evidence. Further studies are needed.Depuis les années 1980, l'incidence de la dengue a été multipliée par 30. Cependant, en 2017, il y a eu une réduction notable du nombre de cas d'incidence de dengue rapportés dans les Amériques. Nous voulions fournir des explications plausibles à la baisse en 2017. MÉTHODES: Un groupe d'experts constitué de représentants d'institutions scientifiques et académiques, d'officiels des Ministères de la Santé d'Amérique Latine et de membres du personnel de l’OPS/OMS s'est réuni en octobre 2017 pour proposer et évaluer des hypothèses. RÉSULTATS: En 2017, il y a eu une baisse généralisée de l'incidence, de la sévérité et du nombre de décès dus à la dengue dans les Amériques, accompagnée d'une réduction des cas rapportés d'infections par le virus Zika et par le virus du chikungunya, sans modification dans la répartition entre les groupes d’âge affectés. Il a été déterminé que ce déclin était peu probablement dû aux changements dans les systèmes de surveillance épidémiologique, étant donné que des systèmes de surveillance similaires existaient dans toute la région. Bien que des perturbations soudaines dans la surveillance soient possibles au niveau national ou régional, il est peu probable que cela se produise simultanément dans tous les pays. Une modélisation rétrospective avec des informations épidémiologiques, immunologiques et entomologiques est nécessaire. Des facteurs liés à l'hôte ou immunologiques peuvent avoir influencé le déclin des cas de dengue au niveau de la population par le biais de l'immunité; cependant, l’évidence d'une protection conférée par l'effet du troupeau nécessite des données supplémentaires. Une incertitude subsiste quant à l'effet sur le résultat des infections séquentielles de différents types du virus de la dengue (DENV) et du virus Zika (ZIKV), et vice-versa. Les études à venir devraient examiner (1) l'effet épidémiologique d'une infection antérieure par le DENV sur l'incidence et la sévérité du virus Zika, (2) l'effet épidémiologique d'une infection antérieure par le virus Zika sur l'incidence et la sévérité de la dengue, (3) les corrélats immunitaires basés sur des tests ELISA de nouvelle génération, (4) l’ impact d'une infection antérieure à DENV/autres arbovirus sur la réponse immunitaire au ZIKV en fonction du nombre d'infections et de la durée des anticorps en fonction de l'intervalle de protection, (5) si des activités d'intensification de la lutte antivectorielle ont contribué à la diminution de la transmission d'un ou plusieurs de ces arbovirus, (6) le rôle potentiel de la compétence vectorielle lorsqu'ils sont exposés simultanément à différents arbovirus, (7) la surveillance entomologique et son impact sur la circulation d'espèces de vecteurs, dans le but d'appliquer des mesures spécifiques qui réduisent l'occurrence saisonnière d’épidémies.Des événements multifactoriels pourraient expliquer le déclin observé de la dengue en 2017. La plupart des résultats de cette réunion du groupe de consensus d'experts sont hypothétiques, reposent sur des données limitées et requièrent des investigations supplémentaires.

Theories in soil biology, such as plant–microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below‐ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above‐ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost‐effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature‐based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.

Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource‐partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data., The interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales.

Novel coronary pneumonia (COVID‐19) is a respiratory distress syndrome caused by a new type of coronavirus. Understanding the genetic basis of susceptibility and prognosis to COVID‐19 is of great significance to disease prevention, molecular typing, prognosis, and treatment. However, so far, there have been only two genome‐wide association studies (GWASs) on the susceptibility of COVID‐19. Starting with these reported DNA variants, we found the genes regulated by these variants through cis‐eQTL and cis‐meQTL acting. We further did a series of bioinformatics analysis on these potential risk genes. The analysis shows that the genetic variants on EHF regulate the expression of its neighbor CAT gene via cis‐eQTL. There was significant evidence that CAT and the SARS‐CoV‐2‐related S protein binding protein ACE2 interact with each other. Intracellular localization results showed that CAT and ACE2 proteins both exists in the cell membrane and extracellular area and their interaction could have an impact on the cell invasion ability of S protein. In addition, the expression of these three genes showed a significant positive correlation in the lungs. Based on these results, we propose that CAT plays a crucial intermediary role in binding effectiveness of ACE2, thereby affecting the susceptibility to COVID‐19.

Lymphopenia is commonly observed in SARS and COVID‐19 patients although the lymphocyte count is not always below 0.8 × 109/L in all the patients. It is suggested that lymphopenia serves as a useful predictor for prognosis in the patients. It is also hypothesized that lymphopenia is related to glucocorticoids and apoptosis. However, the ordering between lymphopenia and apoptosis appears different between SARS and COVID‐19 patients, ie, lymphopenia is prior to apoptosis in SARS patients whereas apoptosis is prior to lymphopenia in COVID‐19 patients. This paper attempts to figure out this contradiction through three players, lymphopenia, glucocorticoids, and apoptosis. Although the literature does not provide a solid explanation, the level of glucocorticoids could determine the ordering between lymphopenia and apoptosis because the administration of high doses of glucocorticoids could lead to lymphopenia whereas low doses of glucocorticoids could benefit patients. In the meantime, this paper raises several questions, which need to be answered in order to better understand the whole course of COVID‐19.

Ecosystems worldwide depend on habitat‐forming foundation species that often facilitate themselves with increasing density and patch size, while also engaging in facultative mutualisms. Anthropogenic global change (e.g., climate change, eutrophication, overharvest, land‐use change), however, is causing rapid declines of foundation species‐structured ecosystems, often typified by sudden collapse. Although disruption of obligate mutualisms involving foundation species is known to precipitate collapse (e.g., coral bleaching), how facultative mutualisms (i.e., context‐dependent, nonbinding reciprocal interactions) affect ecosystem resilience is uncertain. Here, we synthesize recent advancements and combine these with model analyses supported by real‐world examples, to propose that facultative mutualisms may pose a double‐edged sword for foundation species. We suggest that by amplifying self‐facilitative feedbacks by foundation species, facultative mutualisms can increase foundation species’ resistance to stress from anthropogenic impact. Simultaneously, however, mutualism dependency can generate or exacerbate bistability, implying a potential for sudden collapse when the mutualism's buffering capacity is exceeded, while recovery requires conditions to improve beyond the initial collapse point (hysteresis). Thus, our work emphasizes the importance of acknowledging facultative mutualisms for conservation and restoration of foundation species‐structured ecosystems, but highlights the potential risk of relying on mutualisms in the face of global change. We argue that significant caveats remain regarding the determination of these feedbacks, and suggest empirical manipulation across stress gradients as a way forward to identify related nonlinear responses., Ecosystems worldwide depend on habitat‐forming foundation species that engage in facultative mutualisms. Global change, however, is causing rapid declines of foundation species‐structured ecosystems, often typified by sudden collapse. Here, we synthesize recent advancements and combine this with model analyses to propose that facultative mutualisms can increase foundation species resistance to global change stressors, but simultaneously increase the risk of sudden collapse by generating or exacerbating bistability.

The novel coronavirus disease, COVID‐19, has grown into a global pandemic and a major public health threat since its breakout in December 2019. To date, no specific therapeutic drug or vaccine for treating COVID‐19 and SARS has been FDA approved. Previous studies suggest that berberine, an isoquinoline alkaloid, has shown various biological activities that may help against COVID‐19 and SARS, including antiviral, anti‐allergy and inflammation, hepatoprotection against drug‐ and infection‐induced liver injury, as well as reducing oxidative stress. In particular, berberine has a wide range of antiviral activities such as anti‐influenza, anti‐hepatitis C, anti‐cytomegalovirus, and anti‐alphavirus. As an ingredient recommended in guidelines issued by the China National Health Commission for COVID‐19 to be combined with other therapy, berberine is a promising orally administered therapeutic candidate against SARS‐CoV and SARS‐CoV‐2. The current study comprehensively evaluates the potential therapeutic mechanisms of berberine in preventing and treating COVID‐19 and SARS using computational modeling, including target mining, gene ontology enrichment, pathway analyses, protein‐protein interaction analysis, and in silico molecular docking. An orally available immunotherapeutic‐berberine nanomedicine, named NIT‐X, has been developed by our group and has shown significantly increased oral bioavailability of berberine, increased IFN‐γ production by CD8+ T cells, and inhibition of mast cell histamine release in vivo, suggesting a protective immune response. We further validated the inhibition of replication of SARS‐CoV‐2 in lung epithelial cells line in vitro (Calu3 cells) by berberine. Moreover, the expression of targets including ACE2, TMPRSS2, IL‐1α, IL‐8, IL‐6, and CCL‐2 in SARS‐CoV‐2 infected Calu3 cells were significantly suppressed by NIT‐X. By supporting protective immunity while inhibiting pro‐inflammatory cytokines; inhibiting viral infection and replication; inducing apoptosis; and protecting against tissue damage, berberine is a promising candidate in preventing and treating COVID‐19 and SARS. Given the high oral bioavailability and safety of berberine nanomedicine, the current study may lead to the development of berberine as an orally, active therapeutic against COVID‐19 and SARS.

Infection rates, severity, and fatalities due to COVID‐19, the pandemic mediated by SARS‐CoV‐2, vary greatly between countries. With few exceptions, these are lower in East and Southeast Asian and Sub‐Saharan African countries compared with other regions. Epidemiological differences may reflect differences in border closures, lockdowns, and social distancing measures taken by each county, and by cultural differences, such as common use of face masks in East and Southeast Asian countries. The plasma serine protease inhibitor alpha‐1 antitrypsin was suggested to protect from COVID‐19 by inhibiting TMPRSS2, a cell surface serine protease essential for the SARS‐CoV‐2 cell entry. Here, we present evidence that population differences in alpha‐1 antitrypsin deficiency allele frequencies may partially explain national differences in the COVID‐19 epidemiology. Our study compared reported national estimates for the major alpha‐1 antitrypsin deficiency alleles PiZ and PiS (SERPINA1 rs28929474 and rs17580, respectively) with the Johns Hopkins University Coronavirus Resource Center dataset. We found a significant positive correlation (R = .54, P = 1.98e−6) between the combined frequencies of the alpha‐1 antitrypsin PiZ and PiS deficiency alleles in 67 countries and their reported COVID‐19 mortality rates. Our observations suggest that alpha‐1 antitrypsin deficiency alleles may contribute to national differences in COVID‐19 infection, severity, and mortality rates. Population‐wide screening for carriers of alpha‐1 antitrypsin deficiency alleles should be considered for prioritizing individuals for stricter social distancing measures and for receiving a SARS‐CoV‐2 vaccine once it becomes available.

The current coronavirus disease 2019 (COVID‐19) pandemic presents a global challenge for managing acutely ill patients and complications from viral infection. Systemic inflammation accompanied by a “cytokine storm,” hemostasis alterations and severe vasculitis have all been reported to occur with COVID‐19, and emerging evidence suggests that dysregulation of lipid transport may contribute to some of these complications. Here, we aim to summarize the current understanding of the potential mechanisms related to COVID‐19 dyslipidemia and propose possible adjunctive type therapeutic approaches that modulate lipids and lipoproteins. Specifically, we hypothesize that changes in the quantity and composition of high‐density lipoprotein (HDL) that occurs with COVID‐19 can significantly decrease the anti‐inflammatory and anti‐oxidative functions of HDL and could contribute to pulmonary inflammation. Furthermore, we propose that lipoproteins with oxidized phospholipids and fatty acids could lead to virus‐associated organ damage via overactivation of innate immune scavenger receptors. Restoring lipoprotein function with ApoA‐I raising agents or blocking relevant scavenger receptors with neutralizing antibodies could, therefore, be of value in the treatment of COVID‐19. Finally, we discuss the role of omega‐3 fatty acids transported by lipoproteins in generating specialized proresolving mediators and how together with anti‐inflammatory drugs, they could decrease inflammation and thrombotic complications associated with COVID‐19.

To date, the recently discovered SARS‐CoV‐2 virus has afflicted >6.9 million people worldwide and disrupted the global economy. Development of effective vaccines or treatments for SARS‐CoV‐2 infection will be aided by a molecular‐level understanding of SARS‐CoV‐2 proteins and their interactions with host cell proteins. The SARS‐CoV‐2 nucleocapsid (N) protein is highly homologous to the N protein of SARS‐CoV, which is essential for viral RNA replication and packaging into new virions. Emerging models indicate that nucleocapsid proteins of other viruses can form biomolecular condensates to spatiotemporally regulate N protein localization and function. Our bioinformatic analyses, in combination with pre‐existing experimental evidence, suggest that the SARS‐CoV‐2 N protein is capable of forming or regulating biomolecular condensates in vivo by interaction with RNA and key host cell proteins. We discuss multiple models, whereby the N protein of SARS‐CoV‐2 may harness this activity to regulate viral life cycle and host cell response to viral infection.

The medical, public health, and scientific communities are grappling with monumental imperatives to contain COVID‐19, develop effective vaccines, identify efficacious treatments for the infection and its complications, and find biomarkers that detect patients at risk of severe disease. The focus of this communication is on a potential biomarker, short telomere length (TL), that might serve to identify patients more likely to die from the SARS‐CoV‐2 infection, regardless of age. The common thread linking these patients is lymphopenia, which largely reflects a decline in the numbers of CD4/CD8 T cells but not B cells. These findings are consistent with data that lymphocyte TL dynamics impose a limit on T‐cell proliferation. They suggest that T‐cell lymphopoiesis might stall in individuals with short TL who are infected with SARS‐CoV‐2.

As of April 20, 2020, over time, the COVID‐19 pandemic has resulted in 157 970 deaths out of 2 319 066 confirmed cases, at a Case Fatality Rate of ~6.8%. With the pandemic rapidly spreading, and health delivery systems being overwhelmed, it is imperative that safe and effective pharmacotherapeutic strategies are rapidly explored to improve survival. In this paper, we use established and emerging evidence to propose a testable hypothesis that, a vicious positive feedback loop of des‐Arg(9)‐bradykinin‐ and bradykinin‐mediated inflammation → injury → inflammation, likely precipitates life threatening respiratory complications in COVID‐19. Through our hypothesis, we make the prediction that the FDA‐approved molecule, icatibant, might be able to interrupt this feedback loop and, thereby, improve the clinical outcomes. This hypothesis could lead to basic, translational, and clinical studies aimed at reducing COVID‐19 morbidity and mortality.

International audience; Among all causes of grapevine decline, Grapevine Trunk Diseases (GTDs) are major concerns for grape growers. This paper reviews knowledge and proposes hypotheses on two major GTDs, esca and Botryosphaeria dieback, and assembles a conceptual model. The objective was to collect information into a sequence, from grapevine nursery propagation processes, through foliar symptom expression, to plant death in mature vineyards. Pathogen infection and colonization steps in woody vine tissues, and the hypotheses that have been formulated to explain the outburst of foliar symptoms, are reported and discussed. Factors that could aggravate or repress GTD symptoms and incidence expansion are also addressed. Vine physiology and pathology together could expand understanding of these diseases. Knowledge and hypotheses that need validation are summarized, and a conceptual model is proposed to explain the occurrence of symptoms and the influencing factors. The model could be useful to cope with the complexity of GTDs, and as a starting point for research to unravel knowledge gaps and suggest new disease management strategies.

Animals exhibit an extraordinary diversity of life history strategies. These realised combinations of survival, development, and reproduction are predicted to be constrained by physiological limitations and trade-offs in resource allocation. However, our understanding of these patterns is restricted to a few taxonomic groups. Using demographic data from 121 species, ranging from humans to sponges, we test whether such trade-offs universally shape animal life history strategies. We show that, after accounting for body mass and phylogenetic relatedness, 71% of the variation in animal life history strategies can be explained by life history traits associated with both the fast-slow continuum and by a separate second axis defined by the distribution of age-specific mortality hazards and the spread of reproduction. While we found that life history strategies are associated with metabolic rate and ecological modes-of-life, surprisingly similar life history strategies can be found across the phylogenetic and physiological diversity of animals.The turquoise killifish, Nothobranchius furzeri, can complete its lifecycle in just 14 days1. In contrast, the Greenland shark only becomes sexual mature after 156 years2. Despite their differences, the evolution of both these life histories is underpinned by the same evolutionary principal of maximising fitness through differing rates of survival, development, and reproduction3. As these species demonstrate, different combinations of traits associated with fitness, known as life history traits4, can successfully maintain viable populations over evolutionary time. The range of variation in life history traits and how they combine into life history strategies across the animal Kingdom is vast. Hexactinellid sponges can live for millennia5 while Gastrotrichs can complete their life cycle within days6. Pacific salmon (Oncorhynchus tshawytscha) release thousands of eggs in a single reproductive event7, while Laysan albatross (Phoebastria immutabilis) individuals are known to reproduce continuously for decades8. Understanding how variation in these traits combines into life history strategies, and in turn how these strategies relate to the range of forms, physiologies and ecologies found in the animal kingdom, is key to our understanding of questions ranging from the invasive potential of species9 to the evolution of senescence10. Despite the diversity of life history strategies, not all are possible. Darwinian demons, hypothetical organisms which live forever and reproduce at infinite rates, do not exist due to limitations in resources11. The structure of life history strategies also reflects the environmental and physical constraints they evolve under. For example, to attain larger adult sizes individuals typically allocate resources towards development at the expense of reproductive output4. There are many such trade-offs that shape life history strategies12. The most well-understood of these results is the fast-slow continuum4,13 where the allocation of resources between survival, development, and reproduction results in a continuum of strategies ranging from a combination of fast development, short lifespans, and high reproductive rates, to combinations of slow development, longer lifespans, and low reproductive rates2. Additional axes of variation beyond the fast-slow continuum have also been described13-16. These typically relate to various moments of reproduction such as its annual intensity, duration, and its spread across the life course14.Identifying these major axes of variation provides a framework which can aid in mapping how conservation management strategies17, degrees of invasiveness9 and diversity18 relate to different life history strategies. However, current patterns of animal life history strategies are either based on taxonomically restricted groups, typically Mammalia11 and Aves13,19, or do not account for the potential variation in life history traits that can be attributed to body size16. Hence our current understanding of patterns in life history strategies effectively misses the wider variation in life history traits observed across the animal kingdom. Here, we exploit the recent rapid expansion in taxonomic coverage of animal demographic data20 to incorporate age related measures of mortality and reproduction10, along with other life history traits (Figure 1), into a test of the universality of life history patterns from the level of populations to the scale of the animal evolutionary tree (Figure 2).

Spray cleaning and disinfection products have been associated with adverse respiratory effects in professional cleaners and among residents doing domestic cleaning. This review combines information about use of spray products from epidemiological and clinical studies, in vivo and in vitro toxicological studies of cleaning chemicals, as well as human and field exposure studies. The most frequent chemicals in spray cleaning and disinfection products were compiled, based on registrations in the Danish Product Registry. The chemicals were divided into acids, bases, disinfectants, fragrances, organic solvents, propellants, and tensides. In addition, an assessment of selected cleaning and disinfectant chemicals in spray products was carried out. Chemicals of concern regarding respiratory effects (e.g. asthma) are corrosive chemicals such as strong acids and bases (including ammonia and hypochlorite) and quaternary ammonium compounds (QACs). However, the evidence for respiratory effects after inhalation of QACs is ambiguous. Common fragrances are generally not considered to be of concern following inhalation. Solvents including glycols and glycol ethers as well as propellants are generally weak airway irritants and not expected to induce sensitization in the airways. Mixing of certain cleaning products can produce corrosive airborne chemicals. We discuss different hypotheses for the mechanisms behind the development of respiratory effects of inhalation of chemicals in cleaning agents. An integrative assessment is needed to understand how these chemicals can cause the various respiratory effects.

Background Metabolic alterations can serve as targets for diagnosis and cancer therapy. Due to the highly complex regulation of cellular metabolism, definite identification of metabolic pathway alterations remains challenging and requires sophisticated experimentation. Methods We applied a comprehensive kinetic model of the central carbon metabolism (CCM) to characterise metabolic reprogramming in murine liver cancer. Results We show that relative differences of protein abundances of metabolic enzymes obtained by mass spectrometry can be used to assess their maximal velocity values. Model simulations predicted tumour-specific alterations of various components of the CCM, a selected number of which were subsequently verified by in vitro and in vivo experiments. Furthermore, we demonstrate the ability of the kinetic model to identify metabolic pathways whose inhibition results in selective tumour cell killing. Conclusions Our systems biology approach establishes that combining cellular experimentation with computer simulations of physiology-based metabolic models enables a comprehensive understanding of deregulated energetics in cancer. We propose that modelling proteomics data from human HCC with our approach will enable an individualised metabolic profiling of tumours and predictions of the efficacy of drug therapies targeting specific metabolic pathways.

All‐female sperm‐dependent species are particular asexual organisms that must coexist with a closely related sexual host for reproduction. However, demographic advantages of asexual over sexual species that have to produce male individuals could lead both to extinction. The unresolved question of their coexistence still challenges and fascinates evolutionary biologists. As an alternative hypothesis, we propose those asexual organisms are afflicted by a demographic cost analogous to the production of males to prevent exclusion of the host. Previously proposed hypotheses stated that asexual individuals relied on a lower fecundity than sexual females to cope with demographic advantage. In contrast, we propose that both sexual and asexual species display the same number of offspring, but half of asexual individuals imitate the cost of sex by occupying ecological niches but producing no offspring. Simulations of population growth in closed systems under different demographic scenarios revealed that only the presence of nonreproductive individuals in asexual females can result in long‐term coexistence. This hypothesis is supported by the fact that half of the females in some sperm‐dependent organisms did not reproduce clonally.

As we all know, methane is a kind of fuel. Previous studies have shown that methanogens in the colon can react with carbon dioxide and hydrogen to produce methane. In a recent study, the anti-inflammatory effects of methane were shown in a dog model of small intestinal ischemia/reperfusion. The mechanism of this anti-inflammatory effect needs further investigation. Recently, studies have shown anti-inflammatory, anti-apoptotic and anti-oxidative effects of methane on different organic injuries. According to the results of these studies, we hypothesize that the initial effects of methane are to react with free radicals and enhance expression of antioxidase through forkhead box transcription factor class O pathway. The anti-inflammatory effect is following the anti-oxidative effect, and the anti-apoptotic effect relies on anti-inflammatory and anti-oxidative effects.

In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439–1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation. They enable the analysis of extracellular nematode DNA. The most crucial and unresolved issue remains the limited availability of suitable primers.

Understanding how the cellular niche controls the stem cell phenotype is often hampered due to the complexity of variegated niche composition, its dynamics, and nonlinear stem cell–niche interactions. Here, we propose a systems biology view that considers stem cell–niche interactions as a many‐body problem amenable to simplification by the concept of mean field approximation. This enables approximation of the niche effect on stem cells as a constant field that induces sustained activation/inhibition of specific stem cell signaling pathways in all stem cells within heterogeneous populations exhibiting the same phenotype (niche determinants). This view offers a new basis for the development of single cell‐based computational approaches for identifying niche determinants, which has potential applications in regenerative medicine and tissue engineering.

Mimicry is one of the oldest concepts in biology, but it still presents many puzzles and continues to be widely debated. Simulation of wasps with a yellow‐black abdominal pattern by other insects (commonly called “wasp mimicry”) is traditionally considered a case of resemblance of unprofitable by profitable prey causing educated predators to avoid models and mimics to the advantage of both (Figure 1a). However, as wasps themselves are predators of insects, wasp mimicry can also be seen as a case of resemblance to one's own potential antagonist. We here propose an additional hypothesis to Batesian and Müllerian mimicry (both typically involving selection by learning vertebrate predators; cf. Table 1) that reflects another possible scenario for the evolution of multifold and in particular very accurate resemblances to wasps: an innate, visual inhibition of aggression among look‐alike wasps, based on their social organization and high abundance. We argue that wasp species resembling each other need not only be Müllerian mutualists and that other insects resembling wasps need not only be Batesian mimics, but an innate ability of wasps to recognize each other during hunting is the driver in the evolution of a distinct kind of masquerade, in which model, mimic, and selecting agent belong to one or several species (Figure 1b). Wasp mimics resemble wasps not (only) to be mistaken by educated predators but rather, or in addition, to escape attack from their wasp models. Within a given ecosystem, there will be selection pressures leading to masquerade driven by wasps and/or to mimicry driven by other predators that have to learn to avoid them. Different pressures by guilds of these two types of selective agents could explain the widely differing fidelity with respect to the models in assemblages of yellow jackets and yellow jacket look‐alikes.

Contemporary humans occupy the widest range of socioeconomic environments in their evolutionary history, and this has revealed unprecedented environmentally-induced plasticity in physical growth. This plasticity also has limits, and identifying those limits can help researchers: (1) parse when population differences arise from environmental inputs or not and (2) determine when it is possible to infer socioeconomic disparities from disparities in body form. To illustrate potential limits to environmental plasticity, we analyze body mass index (BMI) and height data from 1,768,962 women and 207,341 men (20-49 y) living in households exhibiting 1000-fold variation in household wealth (51 countries, 1985-2017, 164 surveys) across four world regions-sub-Saharan Africa, South Asia, Latin America, and North Africa and the Middle East. We find that relationships of environmental inputs with both mean height and BMI bottom out at roughly 100-700 USD per capita household wealth (2011 international units, PPP), but at different basal BMIs and basal heights for different regions. The relationship with resources tops out for BMI at around 20 K-35 K USD for women, with growth potential due to environmental inputs in the range of 6.2-8.4 kg/m2. By contrast, mean BMI for men and mean height for both sexes remains sensitive to environmental inputs even at levels far above the low- and middle-income samples studied here. This suggest that further work integrating comparable data from low- and high-income samples should provide a better picture of the full range of environmental inputs on human height and BMI. We conclude by discussing how neglecting such population-specific limits to human growth can lead to erroneous inferences about population differences.

Laboratory trials conducted over the past decade at U.S. Geological Survey National Wildlife Health Center indicate that wild populations of prairie dogs (Cynomys spp.) display different degrees of susceptibility to experimental challenge with fully virulent Yersinia pestis, the causative agent of plague. We evaluated patterns in prairie dog susceptibility to plague to determine whether the historical occurrence of plague at location of capture was related to survival times of prairie dogs challenged with Y. pestis. We found that black‐tailed prairie dogs (Cynomys ludovicianus) from South Dakota (captured prior to the detection of plague in the state), Gunnison's prairie dogs (Cynomys gunnisoni) from Colorado, and Utah prairie dogs (Cynomys parvidens) from Utah were most susceptible to plague. Though the susceptibility of black‐tailed prairie dogs in South Dakota compared with western locations supports our hypothesis regarding historical exposure, both Colorado and Utah prairie dogs have a long history of exposure to plague. It is possible that for these populations, genetic isolation/bottle necks have made them more susceptible to plague outbreaks., We conduct meta‐analyses of the responses of prairie dogs (Cynomys spp.) from different populations across the western United States to plague challenge. We hypothesized that historical exposure to plague would affect the susceptibility of prairie dog populations to plague. We conclude that though historical exposure may play a role that connectivity of populations is also likely to affect a population's response to plague.

Glaciation accompanied our human ancestors in Africa throughout the Pleistocene. Regrettably, equatorial glaciers and snow are disappearing rapidly, and we are likely the last generation who will get to know these peculiar places. Despite the permanently harsh conditions of glacier/snow habitats, they support a remarkable diversity of life ranging from bacteria to animals. Numerous papers have been devoted to microbial communities and unique animals on polar glaciers and high mountains, but only two reports relate to glacial biodiversity in equatorial regions, which are destined to melt completely within the next few decades. Equatorial glaciers constitute “cold islands” in tropics, and discovering their diversity might shed light on the biogeography, dispersal, and history of psychrophiles. Thus, an opportunity to protect biota of equatorial glaciers hinges on ex situ conservation. It is timely and crucial that we should investigate the glacial biodiversity of the few remaining equatorial glaciers.

In clinical infertility practice, one intractable problem is low (or absent) ovarian reserve which in turn reflects the natural oocyte depletion associated with advancing maternal age. The number of available eggs has been generally thought to be finite and strictly limited, an entrenched and largely unchallenged tenet dating back more than 50 years. In the past decade, it has been suggested that renewable ovarian germline stem cells (GSCs) exist in adults, and that such cells may be utilized as an oocyte source for women seeking to extend fertility. Currently, the issue of whether mammalian females possess such a population of renewable GSCs remains unsettled. The topic is complex and even agreement on a definitive approach to verify the process of ‘ovarian rescue’ or ‘re-potentiation’ has been elusive. Similarities have been noted between wound healing and ovarian tissue repair following capsule rupture at ovulation. In addition, molecular signaling events which might be necessary to reverse the effects of reproductive ageing seem congruent with changes occurring in tissue injury responses elsewhere. Recently, clinical experience with such a technique based on autologous activated platelet-rich plasma (PRP) treatment of the adult human ovary has been reported. This review summarizes the present state of understanding of the interaction of platelet-derived growth factors with adult ovarian tissue, and the outcome of human reproductive potential following PRP treatment.

Purpose: To determine if aqueous humour (AH) concentrations of Retinal Pigment Epithelium (RPE)’s biomarkers are modified after subthreshold micropulse laser (SMPL) treatment of diabetic macular edema (DME). Methods: Naïve DME and healthy subjects were enrolled. All DME patients received SMPL treatments (577-nm yellow light, 5% duty cycle of 0.2 s, power 250 mW), according to study protocol. AH of DME eyes was sampled at baseline and periodically after first SMPL treatment. Control eyes were sampled before cataract surgery. Pigment Epithelium Derived Factor (PEDF) and Erythropoietin (EPO) were quantified with glass-chip protein array. Results: Eighteen DME patients (central retinal thickness ≤ 400 μm on Spectral Domain Optical Coherence Tomography (SD-OCT)) and ten controls were enrolled. The main exclusion criteria were high refractive error, proliferative diabetic retinopathy, glaucoma and neurodegenerative disorders. PEDF concentration was decreased in DME patients at baseline versus controls (P=0.012), while EPO was increased (P=0.029). Both molecules’ concentrations remained stable during follow-up after treatments, compared with DME-baseline. Conclusions: The AH concentrations of RPE biomarkers were significantly different in DME treatment-naïve eyes versus controls. The expression of PEDF and EPO remained unchanged after treatments with SMPL in DME eyes. These data are relevant for future research and applications of SMPL.

Coffee leaf rust (CLR), caused by the fungal pathogen Hemileia vastatrix, has plagued coffee production worldwide for over 150 years. Hemileia vastatrix produces urediniospores, teliospores, and the sexual basidiospores. Infection of coffee by basidiospores of H. vastatrix has never been reported and thus far, no alternate host, capable of supporting an aecial stage in the disease cycle, has been found. Due to this, some argue that an alternate host of H. vastatrix does not exist. Yet, to date, the plant pathology community has been puzzled by the ability of H. vastatrix to overcome resistance in coffee cultivars despite the apparent lack of sexual reproduction and an aecidial stage. The purpose of this study was to introduce a new method to search for the alternate host(s) of H. vastatrix. To do this, we present the novel hypothetical alternate host ranking (HAHR) method and an automated text mining (ATM) procedure, utilizing comprehensive biogeographical botanical data from the designated sites of interests (Ethiopia, Kenya and Sri Lanka) and plant pathology insights. With the HAHR/ATM methods, we produced prioritized lists of potential alternate hosts plant of coffee leaf rust. This is a first attempt to seek out an alternate plant host of a pathogenic fungus in this manner. The HAHR method showed the highest‐ranking probable alternate host as Psychotria mahonii, Rubus apetalus, and Rhamnus prinoides. The cross‐referenced results by the two methods suggest that plant genera of interest are Croton, Euphorbia, and Rubus. The HAHR and ATM methods may also be applied to other plant–rust interactions that include an unknown alternate host or any other biological system, which rely on data mining of published data., This hypothesis piece probes a 150‐year‐old question… “is there an alternate host of the fungal pathogen Hemileia vastatrix?” We use comprehensive geographical botanical data and automated text mining to narrow down the possibilities. Credit: Carvalho et al. [CC BY 2.5 (https://creativecommons.org/licenses/by/2.5)]

Research background: The analysis of the problem was carried out according to the standard scheme: collection of information - description of the received data - generalization of data - recommendations. All the information available on this subject was obtained by questioning teachers, administrative staff and students. Purpose of the article: This case study is aimed at studying social objects and relationships in the process of transition from traditional to remote education methods to obtain new information and identify relevant patterns that depend on gender and position at the university. Methods: An online survey was conducted among 1792 people from March 15 to April 15, 2020 through an electronic questionnaire. The sample included academic and administrative staff, and UNEC’s students. Using the SPSS statistical software package, the Chi Square test is calculated. Findings & Value added: The advantage of this study is the creation of a model that can be used not only to interpret the results of a sociological survey in real time, but also to make decisions and develop strategies for future developments.

Why do cells age? Recent advances show that the cytoplasm is organized into many membrane-less compartments via a process known as phase separation, which ensures spatiotemporal control over diffusion-limited biochemical reactions. Although phase separation is a powerful mechanism to organize biochemical reactions, it comes with the trade-off that it is extremely sensitive to changes in physical-chemical parameters, such as protein concentration, pH, or cellular energy levels. Here, we highlight recent findings showing that age-related neurodegenerative diseases are linked to aberrant phase transitions in neurons. We discuss how these aberrant phase transitions could be tied to a failure to maintain physiological physical-chemical conditions. We generalize this idea to suggest that the process of cellular aging involves a progressive loss of the organization of phase-separated compartments in the cytoplasm.

Transcription factors (TFs) have to find their binding sites, which are distributed throughout the genome. Facilitated diffusion is currently the most widely accepted model for this search process. Based on this model the TF alternates between one-dimensional sliding along the DNA, and three-dimensional bulk diffusion. In this view, the non-specific associations between the proteins and the DNA play a major role in the search dynamics. However, little is known about how the DNA properties around the motif contribute to the search. Accumulating evidence showing that TF binding sites are embedded within a unique environment, specific to each TF, leads to the hypothesis that the search process is facilitated by favorable DNA features that help to improve the search efficiency. Here, we review the field and present the hypothesis that TF-DNA recognition is dictated not only by the motif, but is also influenced by the environment in which the motif resides.

Aging is an increase in mortality risk with age due to a decline in vital functions. Research on aging has entered an exciting phase. Advances in biogerontology have demonstrated that proximate mechanisms of aging and interventions to modify lifespan are shared among species. In nature, aging patterns have proven more diverse than previously assumed. The paradigm that extrinsic mortality ultimately determines evolution of aging rates has been questioned and there appears to be a mismatch between intra‐ and inter‐specific patterns. The major challenges emerging in evolutionary ecology of aging are a lack of understanding of the complexity in functional senescence under natural conditions and unavailability of estimates of aging rates for matched populations exposed to natural and laboratory conditions. I argue that we need to reconcile laboratory and field‐based approaches to better understand (1) how aging rates (baseline mortality and the rate of increase in mortality with age) vary across populations within a species, (2) how genetic and environmental variation interact to modulate individual expression of aging rates, and (3) how much intraspecific variation in lifespan is attributable to an intrinsic (i.e., nonenvironmental) component. I suggest integration of laboratory and field assays using multiple matched populations of the same species, along with measures of functional declines.

The main selective force driving floral evolution and diversity is plant–pollinator interactions. Pollinators use floral signals and indirect cues to assess flower reward, and the ensuing flower choice has major implications for plant fitness. While many pollinator behaviors have been described, the impact of parasites on pollinator foraging decisions and plant–pollinator interactions have been largely overlooked. Growing evidence of the transmission of parasites through the shared‐use of flowers by pollinators demonstrate the importance of behavioral immunity (altered behaviors that enhance parasite resistance) to pollinator health. During foraging bouts, pollinators can protect themselves against parasites through self‐medication, disease avoidance, and grooming. Recent studies have documented immune behaviors in foraging pollinators, as well as the impacts of such behaviors on flower visitation. Because pollinator parasites can affect flower choice and pollen dispersal, they may ultimately impact flower fitness. Here, we discuss how pollinator immune behaviors and floral traits may affect the presence and transmission of pollinator parasites, as well as how pollinator parasites, through these immune behaviors, can impact plant–pollinator interactions. We further discuss how pollinator immune behaviors can impact plant fitness, and how floral traits may adapt to optimize plant fitness in response to pollinator parasites. We propose future research directions to assess the role of pollinator parasites in plant–pollinator interactions and evolution, and we propose better integration of the role of pollinator parasites into research related to pollinator optimal foraging theory, floral diversity and agricultural practices.

Understanding how transcription factor (TF) binding is related to gene regulation is a moving target. We recently uncovered genome-wide evidence for a "Hit-and-Run" model of transcription. In this model, a master TF "hits" a target promoter to initiate a rapid response to a signal. As the "hit" is transient, the model invokes recruitment of partner TFs to sustain transcription over time. Following the "run", the master TF "hits" other targets to propagate the response genome-wide. As such, a TF may act as a "catalyst" to mount a broad and acute response in cells that first sense the signal, while the recruited TF partners promote long-term adaptive behavior in the whole organism. This "Hit-and-Run" model likely has broad relevance, as TF perturbation studies across eukaryotes show small overlaps between TF-regulated and TF-bound genes, implicating transient TF-target binding. Here, we explore this "Hit-and-Run" model to suggest molecular mechanisms and its biological relevance.

A major quest in network and community ecology has been centered on understanding the importance of structural patterns in species interaction networks—the synthesis of who interacts with whom in a given location and time. In the past decades, much effort has been devoted to infer the importance of a particular structure by its capacity to tolerate an external perturbation on its structure or dynamics. Here we demonstrate that such a perspective leads to inconsistent conclusions. That is, the importance of a network structure changes as a function of the external perturbations acting on a community at any given point in time. Thus, we discuss a research agenda to investigate the relative importance of the structure of ecological networks under an environment-dependent framework. We hypothesize that only by studying systematically the link between network structure and community dynamics under an environment-dependent framework, we can uncover the limits at which communities can tolerate environmental changes.“Variation stands out as the only meaningful reality”Stephen J. Gould.

The crucial interplay between metabolic remodeling and the epigenetics could contribute to promote cancer progression. A remarkable association within interaction, LKB1 has been reported, suggesting that the expression of key enzymes involving de novo serine synthesis and DNA methyltransferases like DNMT1 and DNMT3A increase LKB1-deficiency cells. However, the complex interactional link between metabolic remodeling and the epigenetics is still unclear. Hence, we focus on the relationship between YAP/TAZ and serine metabolism to control methylation of DNA or histone in breast cancer with LKB1 deficiency. We hypothesize that YAP/TAZ may have the function to activate key enzymes involving serine metabolism like PSPH and up-regulate the amino acid transporters to supply sources of serine synthesis through activation of C-MYC with TEAD1. Further, we speculate that YAP/TAZ in dependent of FOS may promote DNMT1 and subsequently mediate DNMT1–G9A complex involving serine metabolism and the methylation of DNA and histone. We hope that our study will stimulate further studies and a new targeted therapy and early medical intervention for YAP/TAZ could be a useful option for breast cancer cases complicated with LKB1 deficiency.

RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene level. We propose stageR, a two-stage testing paradigm that leverages the increased power of aggregated gene-level tests and allows post hoc assessment for significant genes. This method provides gene-level FDR control and boosts power for testing interaction effects. In transcript-level analysis, it provides a framework that performs powerful gene-level tests while maintaining biological interpretation at transcript-level resolution. The procedure is applicable whenever individual hypotheses can be aggregated, providing a unified framework for complex high-throughput experiments. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1277-0) contains supplementary material, which is available to authorized users.