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Understanding T cell function in vivo is of key importance for basic and translational immunology alike. To study T cells in vivo, we developed a new knock-in mouse line, which expresses a fusion protein of granzyme B, a key component of cytotoxic granules involved in T cell-mediated target cell-killing, and monomeric teal fluorescent protein from the endogenous Gzmb locus. Homozygous knock-ins, which are viable and fertile, have cytotoxic T lymphocytes with endogeneously fluorescent cytotoxic granules but wild-type-like killing capacity. Expression of the fluorescent fusion protein allows quantitative analyses of cytotoxic granule maturation, transport and fusion in vitro with super-resolution imaging techniques, and two-photon microscopy in living knock-ins enables the visualization of tissue rejection through individual target cell-killing events in vivo. Thus, the new mouse line is an ideal tool to study cytotoxic T lymphocyte biology and to optimize personalized immunotherapy in cancer treatment., eLife digest Cytotoxic, or killer, T cells are a key part of the immune system. They carry a lethal mixture of toxic chemicals, stored in packages called cytotoxic granules. Killer T cells inject the contents of these granules into infected, cancerous or otherwise foreign cells, forcing them to safely self-destruct. In test tubes, T cells are highly efficient serial killers, moving from one infected cell to the next at high speed. But, inside the body, their killing rate slows down. Researchers think that this has something to do with how killer T cells interact with other immune cells, but the details remain unclear. To get to grips with how killer T cells work in their natural environment, researchers need a way to follow them inside the body. One approach could be to use genetic engineering to attach a fluorescent tag to a protein found inside killer T cells. That tag then acts as a beacon, lighting the cells up and allowing researchers to track their movements. Tagging a protein inside the cytotoxic granules would allow close monitoring of T cells as they encounter, recognize and kill their targets. But fluorescent tags are bulky, and they can stop certain proteins from working as they should. To find out whether it is possible to track killer T cells with fluorescent tags, Chitirala, Chang et al. developed a new type of genetically modified mouse. The modification added a teal-colored tag to a protein inside the granules of the killer T cells. Chitirala, Chang et al. then used a combination of microscopy techniques inside and outside of the body to find out if the T cells still worked. This analysis showed that, not only were the tagged T cells able to kill diseased cells as normal, the tags made it possible to watch it happening in real time. Super-resolution microscopy outside of the body allowed Chitirala, Chang et al. to watch the killer T cells release their toxic granule content. It was also possible to follow individual T cells as they moved into, and destroyed, foreign tissue that had been transplanted inside the mice. These new mice provide a tool to understand how killer T cells really work. They could allow study not only of the cells themselves, but also their interactions with other immune cells inside the body. This could help to answer open questions in T cell research, such as why T cells seem to be so much more efficient at killing in test tubes than they are inside the body. Understanding this better could support the development of new treatments for viruses and cancer.

Ludwig van Beethoven (1770–1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven’s genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven’s severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven’s patrilineal ancestry. Introduction Results - Authentication of hair samples - Genetic variants associated with somatic disease - Hepatitis B virus DNA recovered from Beethoven’s hair Discussion - Authenticity of Beethoven’s genome - Comparison with living individuals’ genomes - Origins of Beethoven’s diseases - Hepatitis B virus DNA in Beethoven’s hair - Future directions

Objective To identify the patterns of nonprescription psychoactive substance (PAS) use among persons with spinal cord injury (SCI) and the relationships with demographic and injury characteristics. Design Cross-sectional, self-report assessment (SRA). Setting A medical university in the southeastern United States. Participants The participants (N=4670) were identified through a specialty hospital and 2 state-based surveillance registries. Interventions Not applicable. Main Outcome Measures Participants completed SRAs and reported the past 3 months’ use of the following substances for which they did not have a prescription: cannabis, cocaine, amphetamine-type stimulants, inhalants, sedatives/hypnotics and sleeping pills, hallucinogens, and opioids. PAS use was grouped into 4 categories: none, cannabis use only, use of cannabis and other PAS, and use of other PAS only. Results Of the 4577 participants who responded to the PAS use questions, 24.1% reported using at least 1 PAS without a prescription. Cannabis was the most frequently reported substance (16.4%), followed by sedatives or sleeping pills (8.0%). By PAS use group, 12.1% reported use of cannabis use only, followed by use of other PAS only (7.7%) and use of cannabis and other PAS (4.3%). There were significant differences among the groups of use by nearly all personal characteristics. Conclusions The use of nonprescription PASs is prevalent among adults with chronic SCI, and there are clear differences in patterns and characteristics of use.

Sociality is a fundamental organizing principle across taxa, thought to come with a suite of adaptive benefits. However, making causal inferences about these adaptive benefits requires experimental manipulation of the social environment, which is rarely feasible in the field. Here we manipulated the number of conspecifics in Trinidadian guppies (Poecilia reticulata) in the wild, and quantified how this affected a key benefit of sociality, social foraging, by investigating several components of foraging success. As adaptive benefits of social foraging may differ between sexes, we studied males and females separately, expecting females, the more social and risk-averse sex, to benefit more from conspecifics than males. Conducting over 1,600 foraging trials, we found that in both sexes, increasing the number of conspecifics led to faster detection of novel food patches and a higher probability of feeding following detection of the patch, resulting in greater individual resource consumption. The slope of the latter relationship differed between the sexes, with males unexpectedly exhibiting a stronger social benefit. Our study provides rare causal evidence for the adaptive benefits of social foraging in the wild, and highlights that sex differences in sociality do not necessarily imply an unequal ability to profit from the presence of others.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. © 2022, The Author(s). 8028-00005B; IP DKRVO 2019-2023, MK000094862; 220457/Z/20/Z, ERC-2013-StG-337574-UNDEAD, ERC-2019-StG-853272-PALAEOFARM; 075-15-2021-1069; European Molecular Biology Organization, EMBO: 217223/Z/19/Z; Vallee Foundation; Velux Fonden; Wellcome Trust, WT; Francis Crick Institute, FCI: FC001595; Horizon 2020 Framework Programme, H2020: 796877; Medical Research Council, MRC; Natural Environment Research Council, NERC: 210119/Z/18/Z, NE/K003259/1, NE/K005243/1, NE/S00078X/1, NE/S007067/1; Cancer Research UK, CRUK; European Research Council, ERC: 852558; Grantová Agentura České Republiky, GA ČR: 15-06446S; Svenska Forskningsrådet Formas: 2018-01640; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR: 681396, BELSPO B2/191/P2/ICHIE; Russian Science Foundation, RSF: 16-18-10265-RNF, 20-17-00033, 21-18-00457-RNF, 310763; Science for Life Laboratory, SciLifeLab; Narodowa Agencja Wymiany Akademickiej, NAWA: PPN/PPO/2018/1/00037 This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome ( https://computerome.dtu.dk ) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

The role of central estrogen in cognitive, metabolic, and reproductive health has long fascinated the lay public and scientists alike. In the last two decades, insight into estrogen signaling in the brain and its impact on female physiology is beginning to catch up with the vast information already established for its actions on peripheral tissues. Using newer methods to manipulate estrogen signaling in hormone-sensitive brain regions, neuroscientists are now identifying the molecular pathways and neuronal subtypes required to establish crucial sex differences in energy allocation. However, the immense cellular complexity of these hormone-sensitive brain regions makes it clear that more research is needed to fully appreciate how estrogen modulates neural circuits to regulate physiological and behavioral end points. Such insight is essential for understanding how natural or drug-induced hormone fluctuations across lifespan affect women's health. Expected final online publication date for the Annual Review of Physiology, Volume 84 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Background The global distribution of melioidosis is under considerable scrutiny, with both unmasking of endemic disease in African and Pacific nations and evidence of more recent dispersal in the Americas. Because of the high incidence of disease in tropical northern Australia, The Darwin Prospective Melioidosis Study commenced in October, 1989. We present epidemiology, clinical features, outcomes, and bacterial genomics from this 30-year study, highlighting changes in the past decade. Methods The present study was a prospective analysis of epidemiological, clinical, and laboratory data for all culture-confirmed melioidosis cases from the tropical Northern Territory of Australia from Oct 1, 1989, until Sept 30, 2019. Cases were identified on the basis of culture-confirmed melioidosis, a laboratory-notifiable disease in the Northern Territory of Australia. Patients who were culture-positive were included in the study. Multivariable analysis determined predictors of clinical presentations and outcome. Incidence, survival, and cluster analyses were facilitated by population and rainfall data and genotyping of Burkholderia pseudomallei, including multilocus sequence typing and whole-genome sequencing. Findings There were 1148 individuals with culture-confirmed melioidosis, of whom 133 (12%) died. Median age was 50 years (IQR 38–60), 48 (4%) study participants were children younger than 15 years of age, 721 (63%) were male individuals, and 600 (52%) Indigenous Australians. All but 186 (16%) had clinical risk factors, 513 (45%) had diabetes, and 455 (40%) hazardous alcohol use. Only three (2%) of 133 fatalities had no identified risk. Pneumonia was the most common presentation occurring in 595 (52%) patients. Bacteraemia occurred in 633 (56%) of 1135 patients, septic shock in 240 (21%) patients, and 180 (16%) patients required mechanical ventilation. Cases correlated with rainfall, with 80% of infections occurring during the wet season (November to April). Median annual incidence was 20·5 cases per 100 000 people; the highest annual incidence in Indigenous Australians was 103·6 per 100 000 in 2011–12. Over the 30 years, annual incidences increased, as did the proportion of patients with diabetes, although mortality decreased to 17 (6%) of 278 patients over the past 5 years. Genotyping of B pseudomallei confirmed case clusters linked to environmental sources and defined evolving and new sequence types. Interpretation Melioidosis is an opportunistic infection with a diverse spectrum of clinical presentations and severity. With early diagnosis, specific antimicrobial therapy, and state-of-the-art intensive care, mortality can be reduced to less than 10%. However, mortality remains much higher in the many endemic regions where health resources remain scarce. Genotyping of B pseudomallei informs evolving local and global epidemiology. Funding The Australian National Health and Medical Research Council.

A case of human infection with influenza A(H1N1)pdm09 virus containing a nonstructural gene highly similar to Eurasian avian-like H1Nx swine influenza virus was detected in Denmark in January 2021. We describe the clinical case and report testing results of the genetic and antigenic characterizations of the virus.

BACKGROUND: Recruitment and activation of brown adipose tissue (BAT) results in increased energy expenditure (EE) via thermogenesis and represents an intriguing therapeutic approach to combat obesity and treat associated diseases. Thermogenesis requires an increased and efficient supply of energy substrates and oxygen to the BAT. The hemoprotein myoglobin (MB) is primarily expressed in heart and skeletal muscle fibres, where it facilitates oxygen storage and flux to the mitochondria during exercise. In the last years, further contributions of MB have been assigned to the scavenging of reactive oxygen species (ROS), the regulation of cellular nitric oxide (NO) levels and also lipid binding. There is a substantial expression of MB in BAT, which is induced during brown adipocyte differentiation and BAT activation. This suggests MB as a previously unrecognized player in BAT contributing to thermogenesis. METHODS AND RESULTS: This study analyzed the consequences of MB expression in BAT on mitochondrial function and thermogenesis in vitro and in vivo. Using MB overexpressing, knockdown or knockout adipocytes, we show that expression levels of MB control brown adipocyte mitochondrial respiratory capacity and acute response to adrenergic stimulation, signalling and lipolysis. Overexpression in white adipocytes also increases their metabolic activity. Mutation of lipid interacting residues in MB abolished these beneficial effects of MB. In vivo, whole-body MB knockout resulted in impaired thermoregulation and cold- as well as drug-induced BAT activation in mice. In humans, MB is differentially expressed in subcutaneous (SC) and visceral (VIS) adipose tissue (AT) depots, differentially regulated by the state of obesity and higher expressed in AT samples that exhibit higher thermogenic potential. CONCLUSIONS: These data demonstrate for the first time a functional relevance of MBs lipid binding properties and establish MB as an important regulatory element of thermogenic capacity in brown and likely beige adipocytes.

The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections., Alexander Immel et al. performed genome-wide analyses of 42 individuals from a collective burial in Niedertiefenbach, Germany from the Wartberg Culture. The authors find that this population had a large hunter-gatherer ancestry component and a distinct HLA pool, which indicates immune defenses against viral pathogens.

Mycobacterium haemophilum is a rare pathogen belonging to the group of slowly growing nontuberculous mycobacteria (NTM) that can cause infections, especially in immunocompromised patients. Detection by culturing is difficult because M. haemophilum only grows under special cultivation conditions. Therefore, it is believed that the pathogen is too rarely identified as a cause of disease overall. In addition to patients with severe immunodeficiency, e.g. due to acquired immunodeficiency syndrome (AIDS), chemotherapy or immunosuppression after transplantation, patients with underlying rheumatic diseases are increasingly described in the literature, who are at risk due to the immunosuppressive treatment regimen. Clinically, ulcerative skin alterations, lymphadenopathy and arthropathy are in the foreground. In immunosuppressed patients with unclear skin lesions, infections due to M. haemophilum should be considered and specific microbiological diagnostics should be initiated.

The antiplasmodium assay-guided investigation of the roots, stem bark, and leaves of Persea americana Mill. led to the isolation of a new fatty alcohol, perseatriol (1), along with six known compounds (2–7). Their structures were elucidated based on the analysis of their NMR and MS data. All crude extracts and fractions exhibited good antiplasmodial activity on Plasmoduim falciparum 3D7 with IC50 values ranging from 0.76 to 10.5 μg/mL; they also displayed cytotoxicity against HeLa cells with low selectivity indexes (SIs). A preliminary Plasmodium lactate dehydrogenase (pLDH) assay was also performed on the isolated compounds. 9,9′-Di-O-feruloyl-5,5′-dimethoxysecoisolariciresinol (4) turned out to be non-toxic and displayed the best activities on P. falciparum with an IC50 value of 0.05 μM, comparable to the reference drug chloroquine with an IC50 value of 0.03 μM. Furthermore, besides compound 4, this work reports the first isolation of lutein (2) and scopoletin (3) from P. americana. The crude extracts of roots, stem bark, and leaves of P. americana, their fractions and compounds completely suppressed the growth of P. falciparum. The observed activity supports the use of P. americana in folk medicine for the treatment of malaria.

Reaction of K8{Ta6O19}·16H2O with [Ni(tren)(H2O)Cl]Cl·H2O in different solvents led to the formation of single crystals of the title compound, [Ni4Ta6O19(C6H18N4)4]·19H2O or {[Ni2(κ4-tren)(μ-κ3-tren)]2Ta6O19}·19H2O (tren is N,N-bis(2-aminoethyl)-1,2-ethanediamine, C6H18N4). In its crystal structure, one Lindqvist-type anion {Ta6O19}8– (point group symmetry \overline{1}) is connected to two NiII cations, with both of them coordinated by one tren ligand into discrete units. Both NiII cations are sixfold coordinated by O atoms of the anion and N atoms of the organic ligand, resulting in slightly distorted [NiON5] octahedra for one and [NiO3N3] octahedra for the other cation. These clusters are linked by intermolecular O—H...O and N—H...O hydrogen bonding involving water molecules into layers parallel to the bc plane. Some of these water molecules are positionally disordered and were refined using a split model. Powder X-ray diffraction revealed that a pure crystalline phase was obtained but that on storage at room-temperature this compound decomposed because of the loss of crystal water molecules.

Plant growth and fertility strongly depend on environmental conditions such as temperature. Remarkably, temperature also influences meiotic recombination and thus, the current climate change will affect the genetic make-up of plants. To better understand the effects of temperature on meiosis, we followed male meiocytes in Arabidopsis thaliana by live cell imaging under three temperature regimes: at 21°C; at heat shock conditions of 30°C and 34°C; after an acclimatization phase of 1 week at 30°C. This work led to a cytological framework of meiotic progression at elevated temperature. We determined that an increase from 21°C to 30°C speeds up meiosis with specific phases being more amenable to heat than others. An acclimatization phase often moderated this effect. A sudden increase to 34°C promoted a faster progression of early prophase compared to 21°C. However, the phase in which cross-overs mature was prolonged at 34°C. Since mutants involved in the recombination pathway largely did not show the extension of this phase at 34°C, we conclude that the delay is recombination-dependent. Further analysis also revealed the involvement of the ATAXIA TELANGIECTASIA MUTATED kinase in this prolongation, indicating the existence of a pachytene checkpoint in plants, yet in a specialized form.

Oestrogen depletion in rodents and humans leads to inactivity, fat accumulation and diabetes1,2, underscoring the conserved metabolic benefits of oestrogen that inevitably decrease with age. In rodents, the preovulatory surge in 17β-oestradiol (E2) temporarily increases energy expenditure to coordinate increased physical activity with peak sexual receptivity. Here we report that a subset of oestrogen-sensitive neurons in the ventrolateral ventromedial hypothalamic nucleus (VMHvl)3–7 projects to arousal centres in the hippocampus and hindbrain, and enables oestrogen to rebalance energy allocation in female mice. Surges in E2 increase melanocortin-4 receptor (MC4R) signalling in these VMHvl neurons by directly recruiting oestrogen receptor-α (ERα) to the Mc4r gene. Sedentary behaviour and obesity in oestrogen-depleted female mice were reversed after chemogenetic stimulation of VMHvl neurons expressing both MC4R and ERα. Similarly, a long-term increase in physical activity is observed after CRISPR-mediated activation of this node. These data extend the effect of MC4R signalling — the most common cause of monogenic human obesity8 — beyond the regulation of food intake and rationalize reported sex differences in melanocortin signalling, including greater disease severity of MC4R insufficiency in women9. This hormone-dependent node illuminates the power of oestrogen during the reproductive cycle in motivating behaviour and maintaining an active lifestyle in women. A subset of oestrogen-sensitive neurons integrate melanocortin and oestrogen signalling to rebalance energy allocation in female mice leading to reduced sedentary behaviour and decreasing obesity in oestrogen-depleted female mice

The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long-standing questions about the evolution of biodiversity largely unexplored. Here, we used whole-genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single-nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high-quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.

To monitor infection by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and successful vaccination against coronavirus disease 2019 (COVID‐19), the kinetics of neutralizing or blocking anti‐SARS‐CoV‐2 antibody titers need to be assessed. Here, we report the development of a quick and inexpensive surrogate SARS‐CoV‐2 blocking assay (SUBA) using immobilized recombinant human angiotensin‐converting enzyme 2 (hACE2) and human cells expressing the native form of surface SARS‐CoV‐2 spike protein. Spike protein‐expressing cells bound to hACE2 in the absence or presence of blocking antibodies were quantified by measuring the optical density of cell‐associated crystal violet in a spectrophotometer. The advantages are that SUBA is a fast and inexpensive assay, which does not require biosafety level 2‐ or 3‐approved laboratories. Most importantly, SUBA detects blocking antibodies against the native trimeric cell‐bound SARS‐CoV‐2 spike protein and can be rapidly adjusted to quickly pre‐screen already approved therapeutic antibodies or sera from vaccinated individuals for their ACE2 blocking activities against any emerging SARS‐CoV‐2 variants., A simple, inexpensive surrogate SARS‐CoV‐2 neutralization assay is introduced. Ectopic expression of the SARS‐CoV‐2 spike protein confers binding of Ramos‐Ig ‐ or HEK293 cells to plate‐bound recombinant human angiotensin‐converting‐enzyme‐2. This interaction can be blocked with reconvalescent or immune serum or with anti‐receptor‐binding domain antibodies. Bound spike‐expressing cells are quantitated with crystal violet.

Recent advancements in DNA sequencing technologies and laboratory preparation protocols have rapidly expanded the scope of ancient DNA research over the past decade, both temporally and geographically. Discoveries include interactions between archaic and modern humans as well as modern human population dynamics, including those coinciding with the Last Glacial Maximum and the settlement history of most world regions. This new type of data allows us to examine the deep past of human population dynamics and sharpen the current understanding of our present. The continued development in the ancient DNA field has transformed our understanding of human genetic history and will keep uncovering the further mysteries of our recent evolutionary past.

Stimulus-Specific Adaptation (SSA) to repetitive stimulation is a phenomenon that has been observed across many different species and in several brain sensory areas. It has been proposed as a computational mechanism, responsible for separating behaviorally relevant information from the continuous stream of sensory information. Although SSA can be induced and measured reliably in a wide variety of conditions, the network details and intracellular mechanisms giving rise to SSA still remain unclear. Recent computational studies proposed that SSA could be associated with a fast and synchronous neuronal firing phenomenon called Population Spikes (PS). Here, we test this hypothesis using a mean-field rate model and corroborate it using a neuromorphic hardware. As the neuromorphic circuits used in this study operate in real-time with biologically realistic time constants, they can reproduce the same dynamics observed in biological systems, together with the exploration of different connectivity schemes, with complete control of the system parameter settings. Besides, the hardware permits the iteration of multiple experiments over many trials, for extended amounts of time and without losing the networks and individual neural processes being studied. Following this “neuromorphic engineering” approach, we therefore study the PS hypothesis in a biophysically inspired recurrent networks of spiking neurons and evaluate the role of different linear and non-linear dynamic computational primitives such as spike-frequency adaptation or short-term depression (STD). We compare both the theoretical mean-field model of SSA and PS to previously obtained experimental results in the area of novelty detection and observe its behavior on its neuromorphic physical equivalent model. We show how the approach proposed can be extended to other computational neuroscience modelling efforts for understanding high-level phenomena in mechanistic models., Scientific Reports, 11 (1), ISSN:2045-2322

Conditional overexpression of histone reader Tripartite motif containing protein 24 (TRIM24) in mouse mammary epithelia (Trim24COE) drives spontaneous development of mammary carcinosarcoma tumors, lacking ER, PR and HER2. Human carcinosarcomas or metaplastic breast cancers (MpBC) are a rare, chemorefractory subclass of triple-negative breast cancers (TNBC). Comparison of Trim24COE metaplastic carcinosarcoma morphology, TRIM24 protein levels and a derived Trim24COE gene signature reveals strong correlation with human MpBC tumors and MpBC patient-derived xenograft (PDX) models. Global and single-cell tumor profiling reveal Met as a direct oncogenic target of TRIM24, leading to aberrant PI3K/mTOR activation. Here, we find that pharmacological inhibition of these pathways in primary Trim24COE tumor cells and TRIM24-PROTAC treatment of MpBC TNBC PDX tumorspheres decreased cellular viability, suggesting potential in therapeutically targeting TRIM24 and its regulated pathways in TRIM24-expressing TNBC.

Genomic selection has been implemented in several plant and animal breeding programs and it has proven to improve efficiency and maximize genetic gains. Phenotypic data of grain yield was measured in 147 maize (Zea mays L.) singlecross hybrids at 12 environments. Single-cross hybrids genotypes were inferred based on their parents (inbred lines) via single nucleotide polymorphism (SNP) markers obtained from genotyping-by-sequencing (GBS). Factor analytic multiplicative genomic best linear unbiased prediction (GBLUP) models, in the framework of multienvironment trials, were used to predict grain yield performance of unobserved tropical maize single-cross hybrids. Predictions were performed for two situations: untested hybrids (CV1), and hybrids evaluated in some environments but missing in others (CV2). Models that borrowed information across individuals through genomic relationships and within individuals across environments presented higher predictive accuracy than those models that ignored it. For these models, predictive accuracies were up to 0.4 until eight environments were considered as missing for the validation set, which represents 67% of missing data for a given hybrid. These results highlight the importance of including genotype-by-environment interactions and genomic relationship information for boosting predictions of tropical maize single-cross hybrids for grain yield. Made available in DSpace on 2020-12-22T09:02:13Z (GMT). No. of bitstreams: 1 Boosting-predictive.pdf: 1139997 bytes, checksum: 641636e15f14edc0b42f567b080ea4de (MD5) Previous issue date: 2020

Early or excessive sexualized behaviors and preoccupations with sexuality (SB) exhibited by juveniles who have sexually offended (JSO) are considered risk factors for sexual recidivism. However, research into SB among JSO is scarce. The present study retrospectively examined prevalence rates and patterns of SB among JSO prior to sexual offending and their relation to psychopathology and sexual recidivism. We systematically assessed information from psychiatric and psychological expert reports in case files of 230 JSO aged 12–18 years (M = 14.46, SD = 1.49) from a population sample of JSO with contact sexual offenses. A total of 93 (40.4%) JSO exhibited SB prior to the index sexual offense. Latent class analysis revealed three SB profiles: (1) “low/no SB” (n = 188), (2) “preoccupied SB” (preoccupation with sexuality, e.g., early pornography consumption, excessive masturbation; n = 29), and (3) “dysregulated SB” (exhibiting inappropriate sexualized behaviors toward others, e.g., sexualized speech, touching others inappropriately; n = 13). The preoccupied SB and the dysregulated SB groups showed higher prevalence of psychiatric disorders than the low/no SB. However, none of the JSO of the preoccupied SB or dysregulated SB groups reoffended sexually within 365 days after conviction for the sexual index offense (low/no SB: 12.8%). Overall, our findings do not support a general notion of the presence of SB as an indicator of high risk for persistent sexual offending among JSO. Instead, JSO with SB appear particularly burdened regarding a range of psychiatric disorders that should be treated accordingly.

Alginate films containing natamycin as the antimicrobial agent were developed and its release from the films to liquid and semi-solid media with different water activities was evaluated. In samples immersed in liquid media, the release rate of natamycin increased with an increase in the water activity of the solutions. Effective diffusivities were estimated by fitting Fick’s second law to the data, obtaining values ranging from 0.52 × 10–12 to 5.30 × 10–12 cm2/s. The amount of natamycin that migrated to the semi-solid media indicated incomplete release, with 85% of the initial mass released in gels and only 33% released in cheese samples. This highlights the importance of evaluating the release behavior in real systems. The films were applied to slices of semi-hard cheese, previously inoculated with Aspergillus niger and Penicillium roqueforti. Colony counts on the surface of cheese samples sandwiched between active films were one log cycle lower than that in uncovered slices. Cheese samples covered with control films (without natamycin) also yielded fewer colonies but were not as effective.

Annual fish species have evolved complex adaptations to survive in temporary wetlands. The main adaptation of these fish is the ability to produce embryos that survive dry periods. Embryo development of this fish can show variation at multiple levels influenced by many environmental factors, such as photoperiod and temperature. Predator cues are another factor that can influence the embryonic stage. One way in which annual fish could adapt to predators is by using risk-spreading strategies (through bet-hedging). Nonetheless, this strategy depends on the coevolutionary history between predators and preys and on the degree of environmental unpredictability, resulting in different responses across different species. This study investigated the influence of predator cues on the embryonic development and hatching of two Austrolebias species that inhabit ponds that present differences in hydroperiod and the risk of predator presence. The results confirmed a differentiated response between the two annual fish species tested, corroborating the modulation of hatching against the risk of predation by native predatory fish. The authors further showed that development times varied between the two annual fish species, regardless of the presence of predators. They highlight that the variation in embryonic development is strongly affected by different levels of hydroperiod unpredictability faced by the two species. To unravel finer-scale local adaptations in the annual fish embryo development, future studies should focus on a region with greater spatial gradient.

Plants use a wide array of secondary metabolites including terpenes as defense against herbivore and pathogen attack, which can be constitutively expressed or induced. Here, we investigated aspects of the chemical and molecular basis of resistance against the exotic rust fungus Austropuccinia psidii in Melaleuca quinquenervia, with a focus on terpenes. Foliar terpenes of resistant and susceptible plants were quantified, and we assessed whether chemotypic variation contributed to resistance to infection by A. psidii. We found that chemotypes did not contribute to the resistance and susceptibility of M. quinquenervia. However, in one of the chemotypes (Chemotype 2), susceptible plants showed higher concentrations of several terpenes including α‐pinene, limonene, 1,8‐cineole, and viridiflorol compared with resistant plants. Transcriptome profiling of these plants showed that several TPS genes were strongly induced in response to infection by A. psidii. Functional characterization of these TPS showed them to be mono‐ and sesquiterpene synthases producing compounds including 1,8‐cineole, β‐caryophyllene, viridiflorol and nerolidol. The expression of these TPS genes correlated with metabolite data in a susceptible plant. These results suggest the complexity of resistance mechanism regulated by M. quinquenervia and that modulation of terpenes may be one of the components that contribute to resistance against A. psidii.

Background Non-syndromic congenital ichthyosis describes a heterogeneous group of hereditary skin disorders associated with erythroderma and scaling at birth. Although both severe and mild courses are known, the prediction of the natural history in clinical practice may be challenging. Objectives To determine clinical course and genotype-phenotype correlations in children affected by non-syndromic congenital ichthyosis in a case series from south-western Germany. Methods We performed a retrospective observational study of 32 children affected by non-syndromic congenital ichthyoses seen in our genodermatosis clinic between 2011 and 2020. Follow-ups included assessment of weight and severity of skin involvement utilizing a modified Ichthyosis Area Severity Index (mIASI). mIASI was calculated as a sum comprising the previously published IASI score and an additional novel score to evaluate palmoplantar involvement. Linear regression was assessed using Pearson correlation, and statistical analysis was performed using the Wilcoxon-Mann-Whitney test. Results This study included 23 patients with autosomal recessive congenital ichthyosis, seven with keratinopathic ichthyosis and two with harlequin ichthyosis. Cutaneous manifestations improved in more than 70% of the children during the follow-up. Especially in patients with mutations in ALOXE3 and ALOX12B, mIASI scores dropped significantly. The most common phenotype observed in this study was designated 'mild fine scaling ichthyosis'. Severe palmoplantar involvement occurred in patients with KRT1 and ABCA12 mutations; most patients demonstrated hyperlinearity as a sign of dryness and scaling. Weight was mainly in the normal range and negatively correlated with the severity of skin involvement. Conclusions Congenital ichthyosis that self-improves and evolves with mild fine scaling ichthyosis was the most common phenotype observed in our patients. This type might be underdiagnosed if the genetic diagnosis is not performed in the first year of life. mIASI is an easy and fast instrument for scoring disease severity and adding additional points for palmoplantar involvement might be valuable.

Mountain ecosystems are considered to be sensitive to global change and human disturbance. Our retrospective analysis of archival aerial imagery showed dynamics of arctic-alpine tundra vegetation in the Krkonose Mountains, Czech Republic; image classification revealed a change in land cover classes in 44% of the study area over the past eighty years. This particular ecosystem holds many rare features, such as high numbers of endemic, glacial relict and rare species as well as relict geomorphological components such as sorted patterned ground. Our study revealed an accelerating expansion of the native and planted shrub, Pinus mugo, from 30.6% of the study area in 1936 to 48.6% in 2018, mostly at the expense of grasslands that decreased from 59.3% in 1936 to 44.2% in 2018. Shrub expansion represents a threat to relict periglacial landforms, covering 8% of the sorted patterned ground in 1936 and 26.5% in 2018. Shrub encroachment was shown to be due to artificial planting of the pine in the past as well as the cessation of former farming (mowing and cattle grazing) and, most probably, also by global change. Both dwarf pine stands and tundra grasslands hold high conservation value (Natura 2000 habitats); a balance between different nature protection interests must, therefore, be ensured. Detailed spatio-temporally, explicit outputs of the remote sensing analysis can serve as a baseline for nature conservation in order to prepare corresponding management plans.

Background Mitochondria play a key role in immune defense pathways, particularly for macrophages. We and others have previously demonstrated that cystic fibrosis (CF) macrophages exhibit weak autophagy activity and exacerbated inflammatory responses. Previous studies have revealed that mitochondria are defective in CF epithelial cells, but to date, the connection between defective mitochondrial function and CF macrophage immune dysregulation has not been fully elucidated. Here, we present a characterization of mitochondrial dysfunction in CF macrophages. Methods Mitochondrial function in wild-type (WT) and CF F508del/F508del murine macrophages was measured using the Seahorse Extracellular Flux analyzer. Mitochondrial morphology was investigated using transmission electron and confocal microscopy. Mitochondrial membrane potential (MMP) as well as mitochondrial reactive oxygen species (mROS) were measured using TMRM and MitoSOX Red fluorescent dyes, respectively. All assays were performed at baseline and following infection by Burkholderia cenocepacia, a multi-drug resistant bacterium that causes detrimental infections in CF patients. Results We have identified impaired oxygen consumption in CF macrophages without and with B. cenocepacia infection. We also observed increased mitochondrial fragmentation in CF macrophages following infection. Lastly, we observed increased MMP and impaired mROS production in CF macrophages following infection with B. cenocepacia. Conclusions The mitochondrial defects identified are key components of the macrophage response to infection. Their presence suggests that mitochondrial dysfunction contributes to impaired bacterial killing in CF macrophages. Our current study will enhance our understanding of the pathobiology of CF and lead to the identification of novel mitochondrial therapeutic targets for CF.

The D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.

Purpose Pathogenic variants in SCN2A cause a wide range of neurodevelopmental phenotypes. Reports of genotype–phenotype correlations are often anecdotal, and the available phenotypic data have not been systematically analyzed. Methods We extracted phenotypic information from primary descriptions of SCN2A-related disorders in the literature between 2001 and 2019, which we coded in Human Phenotype Ontology (HPO) terms. With higher-level phenotype terms inferred by the HPO structure, we assessed the frequencies of clinical features and investigated the association of these features with variant classes and locations within the NaV1.2 protein. Results We identified 413 unrelated individuals and derived a total of 10,860 HPO terms with 562 unique terms. Protein-truncating variants were associated with autism and behavioral abnormalities. Missense variants were associated with neonatal onset, epileptic spasms, and seizures, regardless of type. Phenotypic similarity was identified in 8/62 recurrent SCN2A variants. Three independent principal components accounted for 33% of the phenotypic variance, allowing for separation of gain-of-function versus loss-of-function variants with good performance. Conclusion Our work shows that translating clinical features into a computable format using a standardized language allows for quantitative phenotype analysis, mapping the phenotypic landscape of SCN2A-related disorders in unprecedented detail and revealing genotype–phenotype correlations along a multidimensional spectrum.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) targets the respiratory and gastric epithelium, causing coronavirus disease 2019 (COVID-19). Tissue antigen expression variations influence host susceptibility to many infections. This study aimed to investigate the closely linked Lewis (FUT3) and ABO histo-blood types, including secretor (FUT2) status, to infections with SARS-CoV-2 and the corresponding severity of COVID-19. Study design and methods Patients (Caucasians, n = 338) were genotyped for ABO, FUT3, and FUT2, and compared to a reference population of blood donors (n = 250,298). The association between blood types and severity of COVID-19 was addressed by dividing patients into four categories: hospitalized individuals in general wards, patients admitted to the intensive care unit with and without intubation, and deceased patients. Comorbidities were considered in subsequent analyses. Results Patients with blood type Lewis (a-b-) or O were significantly less likely to be hospitalized (odds ratio [OR] 0.669, confidence interval [CI] 0.446-0.971, OR 0.710, CI 0.556-0.900, respectively), while type AB was significantly more prevalent in the patient cohort (OR 1.519, CI 1.014-2.203). The proportions of secretors/nonsecretors, and Lewis a+ or Lewis b+ types were consistent between patients and controls. The analyzed blood groups were not associated with the clinical outcome as defined. Discussion Blood types Lewis (a-b-) and O were found to be protective factors, whereas the group AB is suggested to be a risk factor for COVID-19. The antigens investigated may not be prognostic for disease severity, but a role for ABO isoagglutinins in SARS-CoV-2 infections is strongly suggested.

Rock-wallabies occupy outcrops, escarpments and cliffs that incorporate structurally complex refuges; because of this, local populations present methodological challenges for monitoring purposes. We describe the development and adaptive modification of a survey technique intended to measure changes in rock-wallaby activity on a site-by-site basis. Twenty spatially independent field sites were collectively sampled across two geological strata using transects consisting of regularly spaced sampling points, with concentric series of fixed-radius circular plots at each sampling point used to count numbers of fresh/recent and/or older rock-wallaby scats. The presence/absence of fresh and/or recently deposited scats was identified as likely to be the more sensitive measure of changing use. Indexes of Activity (IoA) at each field site were subsequently obtained by transect-based sampling at 10 m intervals using 2 m fixed-radius circular plots and recording the presence/absence of fresh/recent scats therein. Derived rock-wallaby IoA ranged between 0.13 and 0.94 across the 20 sites and were approximately normally distributed. Central tendency measures associated with the IoA metrics imply some potential to develop management-themed activity thresholds. Further refinement and potential applications of the approach are discussed.

Made available in DSpace on 2022-05-01T05:29:35Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-10-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Parsley is a biannual herbaceous plant, frequently used as a condiment in Brazilian gastronomy, also having medicinal properties. This work reports the molecular identification, partial host range, and complete genome sequencing of an apium virus Y (Potyvirus) isolate (ApVY-Br) infecting parsley in Brazil. Complete genome sequencing revealed a 9913nt long virus with high identity with previously reported ApVY isolates. The isolate was capable of infecting parsley, coriander, Chenopodium amaranticolor, and Chenopodium quinoa plants. Bayesian phylogenetic analyses based on the complete genome and coat protein sequences clustered the ApVY isolates based on sampling locations. Departamento de Proteção de Plantas Universidade do Estado de São Paulo (UNESP) Departamento de Proteção de Plantas Universidade do Estado de São Paulo (UNESP) CAPES: 001 CNPq: 140130/2019-5

More than 30 years have passed since endothelial nitric oxide synthesis was described using the umbilical artery and vein endothelium. That seminal report set the cornerstone for unveiling the molecular aspects of endothelial function. In parallel, the understanding of placental physiology has gained growing interest, due to its crucial role in intrauterine development, with considerable long-term health consequences. This review discusses the evidence for nitric oxide (NO) as a critical player of placental development and function, with a special focus on endothelial nitric oxide synthase (eNOS) vascular effects. Also, the regulation of eNOS-dependent vascular responses in normal pregnancy and pregnancy-related diseases and their impact on prenatal and postnatal vascular health are discussed. Recent and compelling evidence has reinforced that eNOS regulation results from a complex network of processes, with novel data concerning mechanisms such as mechano-sensing, epigenetic, posttranslational modifications, and the expression of NO- and l-arginine-related pathways. In this regard, most of these mechanisms are expressed in an arterial-venous-specific manner and reflect traits of the fetal systemic circulation. Several studies using umbilical endothelial cells are not aimed to understand placental function but general endothelial function, reinforcing the influence of the placenta on general knowledge in physiology.

A growing body of literature links resources of hosts to their risk of infectious disease. Yet most hosts encounter multiple pathogens, and projections of disease risk based on resource availability could be fundamentally wrong if they do not account for interactions among pathogens within hosts. Here, we measured infection risk of grass hosts (Avena sativa) exposed to three naturally co‐occurring viruses either singly or jointly (barley and cereal yellow dwarf viruses [B/CYDVs]: CYDV‐RPV, BYDV‐PAV, and BYDV‐SGV) along experimental gradients of nitrogen and phosphorus supply. We asked whether disease risk (i.e., infection prevalence) differed in single versus co‐inoculations, and whether these differences varied with rates and ratios of nitrogen and phosphorus supply. In single inoculations, the viruses did not respond strongly to nitrogen or phosphorus. However, in co‐inoculations, we detected illustrative cases of 1) resource‐dependent antagonism (lower prevalence of RPV with increasing N; possibly due to competition), 2) resource‐dependent facilitation (higher prevalence of SGV with decreasing N:P; possibly due to immunosuppression), and 3) weak or no interactions within hosts (for PAV). Together, these within‐host interactions created emergent patterns for co‐inoculated hosts, with both infection prevalence and viral richness increasing with the combination of low nitrogen and high phosphorus supply. We demonstrate that knowledge of multiple pathogens is essential for predicting disease risk from host resources and that projections of risk that fail to acknowledge resource‐dependent interactions within hosts could be qualitatively wrong. Expansions of theory from community ecology theory may help anticipate such relationships by linking host resources to diverse pathogen communities., When hosts encounter multiple pathogens, their risk of infection can depend on the nutrients available to the host. We experimentally show that interactions among pathogens fundamentally transform relationships between host resources and disease. Emergent patterns of infection risk arise from both resource‐dependent antagonism and resource‐dependent facilitation within hosts.

Made available in DSpace on 2022-04-28T19:40:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-06-01 Pepper cultivation in Israel has been constrained by two sympatric poleroviruses, Pepper vein yellows virus-2 (PeVYV-2) and Pepper whitefly-borne vein yellows virus (PeWBVYV), which are transmitted specifically by aphids and whiteflies, respectively. This study investigated the interaction between PeVYV-2 and PeWBVYV inside the host plant and the insect vectors. Our results show that PeVYV-2 and PeWBVYV compete against each other inside the host plant and also inside aphids. PeWBVYV was the weaker competitor inside the host plant, with diminished transmission rates when inoculated simultaneously or successively after PeVYV-2 and could only be transmitted efficiently when inoculated first and then challenged by PeVYV-2. Successive inoculations of plants with viruliferous whiteflies with PeWBVYV followed by viruliferous aphids with PeVYV-2 led to a coinfection rate of 60%, but with severely reduced titers of PeWBVYV in the coinfected plants compared with singly infected plants. In contrast, PeVYV-2 was the weaker competitor inside the insect vector, with reduced quantities of the acquired virus and a reduced transmission rate by aphids when given prior acquisition on PeWBVYV. However, we also show that the transmission efficiency of PeVYV-2 and PeWBVYV from coinfected plants by whiteflies and aphids remained comparable to that from singly infected plants. This is likely attributable to the reduced titers of PeWBVYV inside coinfected plants causing lesser impact on transmission of PeVYV-2 by aphids and the stronger competitiveness of PeWBVYV inside the whitefly. Competitive interactions between PeVYV-2 and PeWBVYV inside the host plant and insect vector can thus be beneficial for their coexistence. Department of Entomology Volcani Center Faculdade de Ci^encias Agron^omicas São Paulo State University (UNESP) Faculdade de Ci^encias Agron^omicas São Paulo State University (UNESP)

EBioMedicine 72, 103588 (2021). doi:10.1016/j.ebiom.2021.103588, Published by Elsevier, Amsterdam [u.a.]

Made available in DSpace on 2021-06-25T11:15:57Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Since the detection of Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) species in Brazil in the early 1990s, this whitefly has been the predominant species and the main viral vector in the country. In this work, whiteflies were collected from commercial soybean fields near and far from greenhouses where Mediterranean (MED) species had previously been detected infesting vegetable crops. Results indicated that MEAM1 was the predominant whitefly species in soybean in most sampling sites, while MED was found colonizing soybean plants in open field conditions alone and/or with MEAM1 in several places. Among the tested insects, MED species was mostly detected harbouring the facultative endosymbiont Hamiltonella. We also detected cowpea mild mottle virus (CPMMV) infecting soybean plants. Transmission assays demonstrated that MED species was more efficient transmitting CPMMV from beans to beans and from soybean to soybean plants than MEAM1, while MEAM1 was more efficient in transmitting the virus from soybean to bean than MED. Performance assays indicated that adult emergence of both species on CPMMV-infected soybean plants was higher when compared with the emergence on healthy plants. Moreover, nonviruliferous MED and MEAM1 adults preferred to settle more often on healthy plants, while viruliferous adults settled more often on CPMMV-infected soybean plants. As MED has already been found in soybean open fields in São Paulo and Paraná States, Brazil, and it is a good vector of CPMMV, we anticipate problems related to whitefly management and to increase in the incidence of the virus in soybean. UNESP – Faculdade de Ciências Agronômicas Corteva Agriscience Instituto Federal Catarinense – Campus Gulf Coast Research and Education Center University of Florida Instituto Agronômico The Volcani Center Institute of Plant Protection UNESP – Faculdade de Ciências Agronômicas

Whole genome sequencing datasets present the opportunity to not only study evolution in the target organism, but also the associated holobiont. The capacity to study epi-endobiotic kelp associations is improving substantially with the increased availability of high-throughput sequencing datasets. The goal of this study was to determine if shotgun sequencing libraries could be used to document epi- and endophyte/faunal species colonizing Alaria kelp sporophytes from Kamchatka (Russia), the Bay of Fundy (Atlantic Canada) and Nuuk (Greenland). Mitochondrial coxI and plastid rbcL reads were extracted and assembled from six Alaria whole genome sequencing datasets. In total, contigs representing 11 epi-endobiotic species were assembled, of which Chordariacean diversity dominated. Given the presence of a newly discovered phaeophycean coxI sequence lacking an rbcL counterpart, we secondarily tested our hypothesis that the coxI sequence belonged to a phaeophycean parasite. The entire read dataset was assembled for the Alaria specimen hosting the putative parasite, the mitochondrial genome was retrieved, and plastid scaffolds were annotated and screened for phylogenetic placement matching the coxI sequence. The mitochondrial genome of the candidate parasite displayed numerous atypical features, including duplicated genes and rearrangements, and clear signs of relaxed selection, in line with the notion this organism may have a deviant lifestyle. The plastid genome was recovered as several fragments and lacked genes for photosystem and cytochrome complexes and chlorophyll biosynthesis, confirming our hypothesis that the unknown phaeophycean represented a parasitic species. Furthermore, classification to order remained unclear for the phaeophycean parasite, suggesting this species could represent a newly discovered higher-level lineage. Our study showcases the utility of whole-genome sequencing datasets in revealing surprising aspects of the eukaryotic diversity inhabiting kelp holobionts.

Background & Aims Altered gut microbiota composition and function have been associated with inflammatory bowel diseases, including ulcerative colitis (UC), but the causality and mechanisms remain unknown. Methods We applied 16S ribosomal RNA gene sequencing, shotgun metagenomic sequencing, in vitro functional assays, and gnotobiotic colonizations to define the microbial composition and function in fecal samples obtained from a cohort of healthy individuals at risk for inflammatory bowel diseases (pre-UC) who later developed UC (post-UC) and matched healthy control individuals (HCs). Results Microbiota composition of post-UC samples was different from HC and pre-UC samples; however, functional analysis showed increased fecal proteolytic and elastase activity before UC onset. Metagenomics identified more than 22,000 gene families that were significantly different between HC, pre-UC, and post-UC samples. Of these, 237 related to proteases and peptidases, suggesting a bacterial component to the pre-UC proteolytic signature. Elastase activity inversely correlated with the relative abundance of Adlercreutzia and other potentially beneficial taxa and directly correlated with known proteolytic taxa, such as Bacteroides vulgatus. High elastase activity was confirmed in Bacteroides isolates from fecal samples. The bacterial contribution and functional significance of the proteolytic signature were investigated in germ-free adult mice and in dams colonized with HC, pre-UC, or post-UC microbiota. Mice colonized with or born from pre-UC–colonized dams developed higher fecal proteolytic activity and an inflammatory immune tone compared with HC-colonized mice. Conclusions We have identified increased fecal proteolytic activity that precedes the clinical diagnosis of UC and associates with gut microbiota changes. This proteolytic signature may constitute a noninvasive biomarker of inflammation to monitor at-risk populations that can be targeted therapeutically with antiproteases.

Objectives:(1) To investigate if gut microbiota can be a predictor of remission in geriatric depression and to identify features of the gut microbiota that is associated with remission. (2) To determine if changes in gut microbiota occur with remission in geriatric depression.Design:Secondary analysis of a parent randomized placebo-controlled trial (NCT02466958).Setting:Los Angeles, CA, USA (2016-2018)Participants:Seventeen subjects with major depressive disorder, over 60 years of age, 41.2% female.Intervention:Levomilacipran (LVM) or placebo.Measurements:Remission was defined by Hamilton Depression Rating Scale score of 6 or less at 12 weeks. 16S-ribosomal RNA sequencing based fecal microbiota composition and diversity were measured at baseline and 12 weeks. Differences in fecal microbiota were evaluated between remitters and non-remitters as well as between baseline and post-treatment samples. LVM and placebo groups were combined in all the analyses.Results:Baseline microbiota showed no community level α-diversity or β-diversity differences between remitters and non-remitters. At the individual taxa level, a random forest classifier created with nine genera from the baseline microbiota was highly accurate in predicting remission (AUC = .857). Of these, baseline enrichment of Faecalibacterium, Agathobacter and Roseburia relative to a reference frame was associated with treatment outcome of remission. Differential abundance analysis revealed significant genus level changes from baseline to post-treatment in remitters, but not in non-remitters.Conclusions:This is the first study demonstrating fecal microbiota as a potential predictor of treatment response in geriatric depression. Our findings need to be confirmed in larger prospective studies.