Visualizing Viral RNA Packaging Signals in Action.

Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5' two-thirds of the gRNA of Satellite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate formation of its T = 1 virus-like particle (VLP). These contacts explain why natural virions only package their positive-sense genomes. Asymmetric cryo-EM reconstructions of these VLPs suggest that interactions occur between amino acid residues in the N-terminal ends of the CP subunits and the gRNA PS loop sequences.

Response of diademed sifaka () to fosa () predation in the Betampona Strict Nature Reserve, Madagascar.

Large-bodied mammals living in fragmented habitats are at higher risk of extinction, and such risk can be influenced by ecological factors such as predator-prey system dynamics. These dynamics can be particularly complex for conservation management when one endangered species preys on another endangered species in an isolated or poor-quality habitat. Here we describe predation events observed over 19 months that involved two threatened species: the largest carnivore in Madagascar, the fosa (), and three groups of diademed sifaka () in the Betampona Strict Nature Reserve.

Reproductive inequality among males in the genus .

Reproductive inequality, or reproductive skew, drives natural selection, but has been difficult to assess, particularly for males in species with promiscuous mating and slow life histories, such as bonobos () and chimpanzees (). Although bonobos are often portrayed as more egalitarian than chimpanzees, genetic studies have found high male reproductive skew in bonobos. Here, we discuss mechanisms likely to affect male reproductive skew in , then re-examine skew patterns using paternity data from published work and new data from the Kokolopori Bonobo Reserve, Democratic Republic of Congo and Gombe National Park, Tanzania.

Barriers to chimpanzee gene flow at the south-east edge of their distribution.

Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability.

Wild origins and mitochondrial genetic diversity of Angolan Colobus monkeys (Colobus angolensis) in AZA-accredited zoos and its implications for ex situ population management.

Across zoo's accredited by the Association of Zoos and Aquariums (AZA), species are typically managed as a single population to retain 90% of the founding members' gene diversity. Often, little is known about the specific geographic origins of the founders or how representative the ex situ population's genetic diversity is of the wild population. This study uses mitochondrial DNA (mtDNA) sequencing to investigate haplotype diversity and geographic female founder origin of the AZA-managed Angolan colobus (Colobus angolensis) monkey population.

Malaria-driven adaptation of MHC class I in wild bonobo populations.

The malaria parasite Plasmodium falciparum causes substantial human mortality, primarily in equatorial Africa. Enriched in affected African populations, the B*53 variant of HLA-B, a cell surface protein that presents peptide antigens to cytotoxic lymphocytes, confers protection against severe malaria. Gorilla, chimpanzee, and bonobo are humans' closest living relatives.

The Influence of Hydrodynamic Conditions in a Laboratory-Scale Bioreactor on Metabolite Production.

Hydrodynamic conditions are critical in bioprocessing because they influence oxygen availability for cultured cells. Processes in typical laboratory bioreactors need optimization of these conditions using mixing and aeration control to obtain high production of the desired bioproduct. It could be done by experiments supported by computational fluid dynamics (CFD) modeling.

Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection.

Many single-stranded, positive-sense RNA viruses regulate assembly of their infectious virions by forming multiple, cognate coat protein (CP)-genome contacts at sites termed Packaging Signals (PSs). We have determined the secondary structures of the bacteriophage MS2 ssRNA genome (gRNA) frozen in defined states using constraints from X-ray synchrotron footprinting (XRF). Comparison of the footprints from phage and transcript confirms the presence of multiple PSs in contact with CP dimers in the former.

Mitochondrial genetic diversity and divergence dating of Angolan colobus monkeys (Colobus angolensis) in the eastern forests of Kenya and Tanzania: Implications for subspeciation and reconstructing historical biogeography.

Whether the Colobus angolensis that reside in the fragmented forests in eastern Kenya and Tanzania represent one subspecies or two has been debated for 50 years. Morphological and more recent genetic and ecological studies suggest that these populations represent two subspecies, C. a.

Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein.

Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme that lacks affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding messenger RNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid that is impermeable to nucleases, and emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity.

Faecal parasites increase with age but not reproductive effort in wild female chimpanzees.

Energy investment in reproduction is predicted to trade off against other necessary physiological functions like immunity, but it is unclear to what extent this impacts fitness in long-lived species. Among mammals, female primates, and especially apes, exhibit extensive periods of investment in each offspring. During this time, energy diverted to gestation and lactation is hypothesized to incur short and long-term deficits in maternal immunity and lead to accelerated ageing.

Sexual dimorphism in chimpanzee (Pan troglodytes schweinfurthii) and human age-specific fertility.

Across vertebrates, species with intense male mating competition and high levels of sexual dimorphism in body size generally exhibit dimorphism in age-specific fertility. Compared with females, males show later ages at first reproduction and earlier reproductive senescence because they take longer to attain adult body size and musculature, and maintain peak condition for a limited time. This normally yields a shorter male duration of effective breeding, but this reduction might be attenuated in species that frequently use coalitionary aggression.

Endoscopic management of leaks and fistulas after bariatric surgery: a systematic review and meta-analysis.

Background: Endoscopic techniques have become the first-line therapy in bariatric surgery-related complications such as leaks and fistulas. We performed a systematic review and meta-analysis on the effectiveness of self-expandable stents, clipping, and tissue sealants in closing of post-bariatric surgery leak/fistula.

Methods: A systematic literature search of the Medline/Scopus databases was performed to identify full-text articles published up to February 2019 on the use of self-expandable stents, clipping, or tissue sealants as primary endoscopic strategies used for leak/fistula closure.

Correction to: Nomenclature report 2019: major histocompatibility complex genes and alleles of great and small ape and old and new world monkey species.

The original version of this article contained a spelling error in the Acknowledgments regarding the name of the funding organisation supporting GM and JAH. UKRI-BBSCR should have been UKRI-BBSRC, as is now indicated correctly below.

Nomenclature report 2019: major histocompatibility complex genes and alleles of Great and Small Ape and Old and New World monkey species.

The major histocompatibility complex (MHC) is central to the innate and adaptive immune responses of jawed vertebrates. Characteristic of the MHC are high gene density, gene copy number variation, and allelic polymorphism. Because apes and monkeys are the closest living relatives of humans, the MHCs of these non-human primates (NHP) are studied in depth in the context of evolution, biomedicine, and conservation biology.

Laboratory evidence for hypercoagulability in cirrhotic patients with history of variceal bleeding.

Aim: We aimed to assess the relationship between procoagulant imbalance and the occurrence of variceal bleeding in patients with liver cirrhosis.

Methods: We compared the results of chromogenic assay for the functional evaluation of the Protein C anticoagulant pathway (ThromboPath®), thromboelastometry and the levels of factor VII, VIII, and antithrombin in two groups of cirrhotic patients: Group 1 (n = 25) - patients with moderate or large esophageal or gastric varices, who had never experienced acute gastrointestinal bleeding and Group 2 (n = 24) - patients with a history of variceal bleeding.

Results: Despite the differences in MELD score and the results of basic laboratory tests indicating more severe cirrhosis and suggesting a greater risk of bleeding in Group 2, the results of thromboelastometry did not differ significantly between groups.

Blood platelet function abnormalities in cirrhotic patients with esophageal varices in relation to the variceal bleeding history.

The study aimed at assessing the effect of thrombocytopenia and platelet function abnormalities on the occurrence of variceal bleeding in patients with cirrhosis. The results of impedance aggregometry, von Willebrand factor antigen level and thromboelastometry (TEM) with and without the addition of a platelet inhibitor (FIBTEM, EXTEM test, respectively) were compared in two patient groups: Group 1 ( = 32) - patients with moderate or large esophageal or gastric varices, who had never had symptoms of acute gastrointestinal bleeding and Group 2 ( = 26) - patients with history of variceal bleeding. Standard clotting test indicated more hypocoagulable profile in Group 2 compared to Group 1.

CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.

Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise.

Esophageal pH and impedance reflux parameters in relation to body mass index, obesity-related hormones, and bariatric procedures.

Introduction Obese patients have a higher risk of gastroesophageal reflux disease (GERD), but obesity‑related hormonal changes associated with GERD and the effects of bariatric therapy on reflux are unclear. Objectives The aim of the study was to assess reflux parameters in relation to bariatric therapy and hormonal changes in obese patients. Patients and methods This prospective observational study with a 1‑year follow‑up included 53 obese patients undergoing bariatric therapies.

Rewriting nature's assembly manual for a ssRNA virus.

Satellite tobacco necrosis virus (STNV) is one of the smallest viruses known. Its genome encodes only its coat protein (CP) subunit, relying on the polymerase of its helper virus TNV for replication. The genome has been shown to contain a cryptic set of dispersed assembly signals in the form of stem-loops that each present a minimal CP-binding motif AXXA in the loops.

Sequences of 95 human haplotypes reveal extreme coding variation in genes other than highly polymorphic and .

The most polymorphic part of the human genome, the encodes over 160 proteins of diverse function. Half of them, including the and genes, are directly involved in immune responses. Consequently, the region strongly associates with numerous diseases and clinical therapies.

Bonobos Maintain Immune System Diversity with Three Functional Types of MHC-B.

Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all , their study gives unique perspectives on the human condition. We defined polymorphism of , the bonobo ortholog of , for six wild bonobo populations.