bluuebunny/crossref_metadata_2025 huggingface dataset:
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
Authors: Pearson Richard D , Amato Roberto , Kwiatkowski Dominic P ,   MalariaGEN Plasmodium falciparum Community Project
Published: November 2019

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
Modeling adaptive therapy in non-muscle invasive bladder cancer
Authors: Ferrall-Fairbanks Meghan C. , Kimmel Gregory J. , Black Mik , Bravo Rafael , Deac Oana , Martinez Pierre , Myers Maggie , Nazari Fereshteh , Osojnik Ana , Subramanian Hemachander , Viossat Yannick , Whiting Freddie , Li Roger , Mann Karen M. , Altrock Philipp M.
Published: November 2019

Bladder cancer is the 9th most commonly diagnosed cancer. Nearly half of patients with early stage bladder cancer treated with the immune-stimulating agent BCG have disease recurrence, while 13% progress to invasive bladder cancer. Here we explored the potential of tumor mutational heterogeneity and the role of pro- and anti-inflammatory cytokines to identify different subtypes of bladder cancer that may predict therapeutic response to BCG. Further, we used mathematical modeling of dosing strategies to infer tumor response to varying doses and time schedules f BCG administration. As a proof-of-concept, present adaptive therapy scheduling of BCG as a viable strategy to control tumor size and minimize recurrence.
Microglia control small vessel calcification via TREM2
Authors: Zarb Yvette , Nassiri Sina , Utz Sebastian Guido , Schaffenrath Johanna , Rushing Elisabeth J. , Nilsson K. Peter R. , Delorenzi Mauro , Colonna Marco , Greter Melanie , Keller Annika
Published: November 2019

Microglia participate in CNS development and homeostasis and are often implicated in modulating disease processes in the CNS. However, less is known about the role of microglia in the biology of the neurovascular unit (NVU). In particular, data are scant on whether microglia are involved in CNS vascular pathology. In this study, we use a mouse model of primary familial brain calcification (PFBC) –Pdgfbret/retto investigate the role of microglia in calcification of the NVU. We report that microglia enclosing vessel-calcifications, coined calcification-associated microglia (CAM), display a distinct activation signature. Pharmacological ablation of microglia with the CSF1R inhibitor - PLX5622 leads to aggravated vessel calcification. Additionally, depletion of microglia in wild-type andPdgfbret/retmice causes the development of bone protein (osteocalcin, osteopontin) containing axonal spheroids in the white matter. Mechanistically, we show that microglia require functional TREM2 for controlling vessel-associated calcification. In conclusion, our results demonstrate that microglial activity in the setting of pathological vascular calcification is beneficial. In addition, we identify a new, previously unrecognized function of microglia in halting the expansion of ectopic calcification.
Complete microbial genomes for public health in Australia and Southwest Pacific
Authors: Baines Sarah L. , Gonçalves da Silva Anders , Carter Glen , Jennison Amy V. , Rathnayake Irani , Graham Rikki M. , Sintchenko Vitali , Wang Qinning , Rockett Rebecca J. , Timms Verlaine J. , Martinez Elena , Ballard Susan , Tomita Takehiro , Isles Nicole , Horan Kristy A. , Pitchers William , Stinear Timothy P. , Williamson Deborah A. , Howden Benjamin P. ,   Communicable Diseases Genomics Network (CDGN), Seemann Torsten
Published: November 2019

Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.

Announcement

Whole-genome sequence (WGS) data is increasingly important in public health microbiology (1–4). The data can be used to replicate many of the basic bacterial sub-typing approaches, as well as support epidemiological investigations, such as surveillance and outbreak investigation (5–7). The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens that can provide easily portable data that promotes deeper integration of surveillance and investigation efforts across jurisdictions. This promise is leading to a concerted effort to move microbial public health to a primarily genome-based workflow at numerous jurisdictions (8–10), including Australia (11).
Mechanosensory stimulation viaNanchungexpressing neurons can induce daytime sleep inDrosophila
Authors: Lone Shahnaz Rahman , Potdar Sheetal , Venkataraman Archana , Sheeba Vasu , Sharma Vijay Kumar
Published: November 2019

The neurogenetic bases of sleep, a phenomenon considered crucial for well-being of organisms has recently been under investigation using the model organismDrosophila melanogaster. Although sleep is a state where sensory threshold for arousal is enhanced, it is known that certain kinds of repetitive sensory stimuli such as rocking, can in fact promote sleep in humans. Here we report that orbital motion aided mechanosensory stimulation promotes sleep inDrosophila, independent of the circadian clock, but controlled by the homeostatic system. Mechanosensory receptornanchung(Nan) expressing neurons in the chordotonal organs mediate this sleep induction - flies where these neurons are either silenced or ablated display significantly reduced sleep induction upon mechanosensory stimulation. Transient activation of theNan-expressing neurons also enhances sleep levels confirming the role of these neurons in sleep induction. Thus, we show for the first time that mechanosensory stimulation promotes sleep even in fliesD. melanogasterand that it is mediated by proprioceptors.
Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures
Authors: Begik Oguzhan , Lucas Morghan C. , Liu Huanle , Ramirez Jose Miguel , Mattick John S. , Novoa Eva Maria
Published: November 2019

Background

RNA modifications play central roles in cellular fate and differentiation. These features have placed the epitranscriptome in the forefront of developmental biology and cancer research. However, the machinery responsible for placing, removing and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification–related proteins (RMPs) may be dysregulated in each cancer type.

Results

Here we have performed a comprehensive annotation and evolutionary analysis of human RMPs as well as an integrative analysis of their expression patterns across 32 tissues, 10 species and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. Moreover, through the analysis of paired tumor-normal human samples we uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO, are not significantly up-regulated in most cancer types, once the sample is properly scaled and normalized to the full dataset, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers.

Conclusions

Our analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues, and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviours that are orchestrated by RNA modifications.
Recovering rearranged cancer chromosomes from karyotype graphs
Authors: Aganezov Sergey , Zban Ilya , Aksenov Vitaly , Alexeev Nikita , Schatz Michael C.
Published: November 2019

Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.

Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithmCCRcapable of solving CCCP in polynomial time.

We applyCCRon a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.CCRcan recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.
Natural cryptic variation in epigenetic modulation of an embryonic gene regulatory network
Authors: Ewe Chee Kiang , Cleuren Yamila N. Torres , Flowers Sagen E. , Alok Geneva , Snell Russell G. , Rothman Joel H.
Published: November 2019

Gene regulatory networks (GRNs) that direct animal embryogenesis must respond to varying environmental and physiological conditions to ensure robust construction of organ systems. While GRNs are evolutionarily modified by natural genomic variation, the roles of epigenetic processes in shaping plasticity of GRN architecture are not well-understood. The endoderm GRN inC. elegansis initiated by the maternally supplied SKN-1/Nrf2 bZIP transcription factor; however, the requirement for SKN-1 in endoderm specification varies widely among distinctC. eleganswild isotypes owing to rapid developmental system drift driven by accumulation of cryptic genetic variants. We report here that heritable epigenetic factors that are stimulated by transient developmental diapause also underlie cryptic variation in the requirement for SKN-1 in endoderm development. This epigenetic memory is inherited from the maternal germline, apparently through a nuclear, rather than cytoplasmic, signal, resulting in a parent-of-origin effect (POE), in which the phenotype of the progeny resembles that of the maternal founder. The occurrence and persistence of POE varies between different parental pairs, perduring for at least ten generations in one pair. This long-perduring POE requires piwi-piRNA function and the germline nuclear RNAi pathway, as well as MET-2 and SET-32, which direct histone H3K9 trimethylation and drive heritable epigenetic modification. Such non-genetic cryptic variation may provide a resource of additional phenotypic diversity through which adaptation may facilitate evolutionary changes and shape developmental regulatory systems.
Skeletal and Dental Development Preserve Evidence of Energetic Stress in the Moose of Isle Royale
Authors: Brown C. , Rinaldi C.E. , Ripple W. J. , Van Valkenburgh B.
Published: November 2019

Food shortages can leave diagnostic, and in the case of the dentition, irreversible changes in mineralized tissue that persist into historical and fossil records. Consequently, developmental defects of tooth enamel might be used to track ungulate population irruption but dental tissue’s capacity for preserving historical population density changes has yet to be investigated in wild populations. We test the ability of enamel defects, mandible and metapodial lengths to track changes in the well-known fluctuating moose population of Isle Royale National Park. Our study demonstrates that 1) a moose density threshold exists on the island above which there is a significant decrease in mandible and metatarsus length and a concomitant increase in enamel hypoplasias, 2) food limitation has a more pronounced effect on male than female skeletal growth, and 3) combined data from tooth enamel hypoplasias and bone lengths reflect the relative density of this ungulate population, and should be broadly applicable to other ungulate osteological samples. Developmental defects in dental enamel were among the highest recorded in a wild population, and even during low-density intervals the population density of Isle Royale moose has been high enough to negatively impact skeletal and dental growth, indicating the comparatively poor health of this century-old ecosystem
Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems
Authors: McGonigle Julia M. , Lang Susan Q. , Brazelton William J.
Published: November 2019

The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by low-abundance Chloroflexi species. Additionally, we present evidence that metabolically diverse, formate-utilizing Sulfurovum species are living in the transition zone between the interior and exterior of the chimneys.

IMPORTANCE

Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also extraterrestrial ecosystems that might support life. The microscopic life covering towering chimney structures at the Lost City has been well characterized, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.
Magnetic Polymer Models for Epigenetics-Driven Chromosome Folding
Authors: Coli Davide , Michieletto Davide , Marenduzzo Davide , Orlandini Enzo
Published: November 2019

Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control and rewire gene regulatory networks remains an open challenge. In this work we study the effects of epigenetic modifications on the spatial folding of chromosomes -- and hence on the expression of the underlying genes -- by mapping the problem to a class of models known as magnetic polymers. In this work we show that a first order phase transition underlies the simultaneous spreading of certain epigenetic marks and the conformational collapse of a chromosome. Further, we describe Brownian Dynamics simulations of the model in which the topology of the polymer and thermal fluctuations are fully taken into account and that confirm our mean field predictions. Extending our models to allow for non-equilibrium terms yields new stable phases which qualitatively agrees with observations in vivo. Our results show that statistical mechanics techniques applied to models of magnetic polymers can be successfully exploited to rationalize the outcomes of experiments designed to probe the interplay between a dynamic epigenetic landscape and chromatin organization.
High throughput, error corrected Nanopore single cell transcriptome sequencing
Authors: Lebrigand Kevin , Magnone Virginie , Barbry Pascal , Waldmann Rainer
Published: November 2019

Droplet-based high throughput single cell isolation techniques tremendously boosted the throughput of single cell transcriptome profiling experiments. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. We introduce an approach that combines Oxford Nanopore sequencing with unique molecular identifiers to obtain error corrected full length sequence information with the 10×Genomics single cell isolation system. This allows to examine differential RNA splicing and RNA editing at a single cell level.
The human α-defensin-derived peptide HD5(1-9) inhibits cellular attachment and entry of human cytomegalovirus
Authors: Böffert Rebecca , Businger Ramona , Preiß Hannes , Ehmann Dirk , Truffault Vincent , Simon Claudia , Ruetalo Natalia , Hamprecht Klaus , Müller Patrick , Wehkamp Jan , Schindler Michael
Published: November 2019

Human cytomegalovirus (HCMV) infection causes severe illness in newborns and immunocompromised patients. Since treatment options are limited there is an unmet need for new therapeutic approaches. Defensins are cationic peptides, produced by various human tissues, which serve as antimicrobial effectors of the immune system. Furthermore, some defensins are proteolytically cleaved, resulting in the generation of smaller fragments with increased activity. Together, this led us to hypothesize that defensin-derived peptides are natural human inhibitors of virus infection with low toxicity. We screened several human defensin HNP4- and HD5-derived peptides and found HD5(1-9) to be antiviral without toxicity at high concentrations. HD5(1-9) inhibited HCMV cellular attachment and thereby entry and was active against primary as well as a multiresistant HCMV isolate. Moreover, cysteine and arginine residues were identified to mediate the antiviral activity of HD5(1-9). Altogether, defensin-derived peptides, in particular HD5(1-9), qualify as promising candidates for further development as a novel class of HCMV entry inhibitors.

AUTHOR SUMMARY

Defensins are peptides produced by various human organs which take part in the natural defense against pathogens. Recently, it has been shown that defensins are further cleaved to smaller peptides that have high intrinsic anti-microbial activity. We here challenged the hypothesis that these peptides might have antiviral activity, and due to their presumably natural occurrence, low toxicity. Indeed, we found one peptide fragment that turned out to block the attachment of the human cytomegalovirus (HCMV) to cells. Furthermore, this peptide did not show toxicity in various cellular assays or impede the embryonic development of zebrafish at the concentrations used to block HCMV. This is important, since HCMV is one of the most important viral congenital infections. Altogether, our results hold promise for the development of a new class of antivirals against HCMV.
Immunoglobulin J chain as a non-invasive indicator of pregnancy in the cheetah (Acinonyx jubatus)
Authors: Byron Michael J. , Koester Diana C. , Edwards Katie L. , Mozdziak Paul E. , Farin Charlotte E. , Crosier Adrienne E.
Published: November 2019

The North American cheetah population serves as a reservoir for the species, and acts as a research population to help understand the unique biology of the species. Little is known about the intrauterine physiology of the cheetah, including embryo differentiation, implantation, and the development of the placenta. After mating, cheetah females frequently experience (30-65% of matings) a non-pregnant luteal phase where progestogen metabolite levels match those found in pregnant females for the first ~55 days of gestation, but parturition does not occur. Immunoglobulin J chain (IgJ) is a molecule that is involved in the activation of the secretory immune response and has been found to be indicative of pregnancy in the cheetah using fecal monitoring. In this study, western blotting was employed to track IgJ abundance in pooled weekly fecal samples following natural breeding or exogenous stimulation to ovulate, and IgJ levels were compared between individuals undergoing a pregnant (n = 12) and non-pregnant (n = 19) luteal phase. It was revealed that IgJ abundance was increased in pregnant females compared to non-pregnant females at week 4 and week 8 post-breeding, indicating the potential modulation of maternal immunity in response to sensitive events such as implantation and the increased secretory activity of the placenta. IgJ levels also tended to be higher early after breeding in females that were bred naturally with intact males compared to exogenously stimulated females with no exposure to seminal plasma, indicating the promotion of maternal tolerance to seminal antigens present upon embryonic implantation. Monitoring fecal IgJ may be a potential method to determine gestational status in the cheetah and will aid future conservation efforts of the species.
Function of ex vivo stimulated Natural killer T cells from patients with chronic HIV-1 infection
Authors: Thapa Prakash , Nehete Pramod , He Hong , Nehete Bharti , Buchl Stephanie J. , Bull Lara M. , Lu Hongzhou , Arduino Roberto C. , Sastry K. Jagannadha , Zhou Dapeng
Published: November 2019

Natural killer T (NKT) cells are innate immune cells that are responsible for the first line of antiviral defense, through crosstalk with downstream antigen-presenting cells, natural killer cells, and adaptive immune cells. Previous studies have indicated that NKT cell function is severely impaired in patients with chronic HIV-1 infection. It was reported that alpha-galactosylceramide, a potent agonist antigen for NKT cells, failed to trigger the expansion of NKT cells, or the production of anti-viral cytokines by NKT cells from HIV-1 infected patients in an in vitro assay, in which peripheral blood mononuclear cells (PBMCs) were cultured in the presence of alpha-galactosylceramide. In this study, we stimulated banked peripheral blood mononuclear cells from HIV-1-infected patients with dendritic cells (DC) generated ex vivo and loaded with alpha-galactosylceramide. The results showed that NKT cells were expanded in HIV infected subjects except in patients with advanced AIDS. Expanded NKT cells were capable of producing antiviral cytokines. Our results indicate that NKT cells in HIV infected individuals are potential targets for therapeutic intervention.
Genomic landscape of reproductive isolation inLucaniakillifish: The role of sex chromosomes and salinity
Authors: Berdan Emma L. , Fuller Rebecca C. , Kozak Genevieve M.
Published: November 2019

Understanding how speciation occurs and how reproductive barriers contribute to population structure at a genomic scale requires elucidating the genetic architecture of reproductive isolating barriers. In particular, it is crucial to determine if loci underlying reproductive isolation are genetically linked or if they are located on sex chromosomes, which have unique inheritance and population genetic properties. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are closely related species that have diverged across a salinity gradient and are reproductively isolated by assortative mating, hybrid male infertility, viability of hybrid offspring at high salinities, as well as reduced overall fitness of F2 offspring and backcrosses toL. goodei. We conducted QTL mapping in backcrosses betweenL. parvaandL. goodeito determine the genetic architecture of sex determination, mate attractiveness, fertility, and salinity tolerance. We find that the sex locus appears to be male determining and located on a chromosome that has undergone a Robertsonian fusion inL. parvarelative toL. goodei. We find that the sex locus on the fused chromosome is involved in several genomic incompatibilities, which affect the survival of backcrossed offspring. Among the backcrossed offspring that survived to adulthood, we find that one QTL for male attractiveness toL. goodeifemales is closely linked to this sex locus on chromosome 1. Males homozygous forL. goodeialleles at the sex locus laid more eggs withL. goodeifemales. QTL associated with salinity tolerance were spread across the genome but did not tend to co-localize with reproductive isolation. Thus, speciation in this system appears to be driven by reinforcement and indirect selection against hybrids rather than direct natural selection for salinity tolerance. Our work adds to growing evidence that sex chromosome evolution may contribute to speciation.
EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen
Authors: Marković Vedrana , Cvrčková Fatima , Potocký Martin , Pejchar Přemysl , Kollárová Eva , Kulich Ivan , Synek Lukáš , Žárský Viktor
Published: November 2019

Pollen development, pollen grain germination and pollen tube elongation are crucial biological processes in angiosperm plants that need precise regulation to deliver sperm cells to fertilize ovules. Pollen grains undergo two major developmental switches: dehydration characterized by metabolic quiescent state, and rehydration upon pollination that leads to extraordinary metabolic and membrane trafficking activity, resulting in germination and rapid tip growth of pollen tubes. To sustain these processes, many plant housekeeping genes evolved their pollen-specific paralogs. Highly polarized secretion at a growing pollen tube tip requires the exocyst tethering complex responsible for specific targeting of secretory vesicles to the plasma membrane. Here, we describe that EXO70A2 (At5g52340) is the main exocyst EXO70 isoform in Arabidopsis pollen, which governs the conventional secretory function of the exocyst, analogically to EXO70A1 (At5g03540) in the sporophyte. Our analysis of a CRISPR-generated exo70a2 mutant revealed that EXO70A2 is essential for efficient pollen maturation, pollen grain germination and pollen tube growth. GFP:EXO70A2 was localized similarly to other exocyst subunits to the apical domain in growing pollen tube tips characterized by intensive exocytosis. Moreover, EXO70A2 could substitute for the EXO70A1 function in the sporophyte, indicating functional redundancy of these two closely related isoforms. Phylogenetic analysis revealed that the ancient duplication of EXO70A to two (or more) paralogs, one of which is highly expressed in pollen, occurred independently in monocots and dicots. In summary, EXO70A2 is a crucial component of the exocyst complex in the Arabidopsis pollen required for efficient plant sexual reproduction.
Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia
Authors: Shanmuganandam Somasundhari , Hu Yiheng , Strive Tanja , Schwessinger Benjamin , Hall Robyn N.
Published: November 2019

European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of the gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors. We analysed the faecal microbiome of wild hares and rabbits from a sympatric environment, additionally comparing Illumina and Nanopore sequencing platforms. The faecal microbiomes varied significantly between hares and rabbits, despite both species occupying a similar habitat. Moreover, we identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria, and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the faecal microbiota between hares and rabbits in Australia may be associated with differences in diet, and potentially behaviour, of the host species in their non-native range, which may influence the environmental impacts that these species have in Australia.
The role of hippocampus during observational learning
Authors: Fuentealba Yerko , Valdés José L
Published: November 2019

Observational learning is a fundamental cognitive ability present in several species, where a naïve animal imitates a goal-directed behavior from the observation of a congener which acts as a demonstrator. Recent evidence in bat and rats suggests that hippocampal place cells of an observer may generate a spatial representation of the locations visited by a demonstrator, during spatial navigation. However, it is still unclear whether this hippocampal neural activity is critical for the process of observational learning or if the patterns of activity during observation differ from those emerging from the execution of a spatial memory task previously observed. To test this idea, we assess the role of the hippocampus by pharmacological reversible inactivation during the observation of a spatial learning task, demonstrating a critical role for this structure in observational learning. Then we recorded the neuronal activity of principal pyramidal cells of the same animal when it was observing or solving the memory task, and two different representation of the space emerged after observation or navigation. This evidences demonstrated that the hippocampus is necessary for observational learning and indicated that the observed and executed hippocampal representation are different, confirming the idea that the hippocampus could represent the position of others in the space, and use this information to improve his behavioral performance.
Neuronal Proteostasis is mediated by the switch-like expression of Heme-regulated Kinase 1, acting as both a sensor and effector
Authors: Alvarez-Castelao Beatriz , tom Dieck Susanne , Fusco Claudia M. , Donlin-Asp Paul G. , Perez Julio D. , Schuman Erin M.
Published: November 2019

All cells, including neurons, have regulatory feedback mechanisms that couple protein synthesis and degradation to maintain and optimize protein concentrations in the face of intra- and extracellular perturbations. We examined the feedback between the major protein degradation pathway, the ubiquitin-proteasome system (UPS), and protein synthesis in neurons. When protein degradation by the UPS was inhibited we observed a coordinate dramatic reduction in nascent protein synthesis in both neuronal cell bodies and dendrites. The mechanism for translation inhibition involved the phosphorylation of eIF2a, surprisingly mediated by eIF2a kinase 1, or heme-regulated kinase inhibitor (HRI), known for its sensitivity to heme levels in erythrocyte precursors (Han et al., 2001). Under basal conditions, neuronal expression of HRI is barely detectable. Following proteasome inhibition, HRI protein levels increase owing to stabilization of the short-lived HRI protein and enhanced translation via the increased availability of tRNAs for rare codons. Once expressed, HRI is constitutively active in neurons because endogenous heme levels are so low; HRI activity results in eIF2a phosphorylation and the resulting inhibition of translation. These data demonstrate a novel role for HRI in neurons, acting as an “immediate early protein” that senses and responds to compromised function of the proteasome to restore proteostasis.

One sentence summary

Proteasome inhibition leads to a compensatory reduction in neuronal protein synthesis via the stabilization and enhanced translation of short-lived HRI kinase, which is constitutively active upon expression owing to low neuronal heme levels.
Structure of the cell-binding component of theClostridium difficilebinary toxin reveals a novel macromolecular assembly
Authors: Xu Xingjian , Godoy-Ruiz Raquel , Adipietro Kaylin A. , Peralta Christopher , Ben-Hail Danya , Varney Kristen M. , Cook Mary E. , Roth Braden M. , Wilder Paul T. , Cleveland Thomas , Grishaev Alexander , Neu Heather M. , Michel Sarah , Yu Wenbo , Beckett Dorothy , Rustandi Richard R. , Lancaster Catherine , Loughney John W. , Kristopeit Adam , Christanti Sianny , Olson Jessica W. , MacKerell Alex D. , Georges Amedee des , Pozharski Edwin , Weber David J.
Published: November 2019

TargetingClostridium difficileinfection (CDI) is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent CDI often has a binary toxin termed theC. difficiletoxin (CDT), in addition to the enterotoxins TsdA and TsdB. CDT has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single particle cryoEM, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, two novel di-heptamer structures foractivated CDTb (aCDTb; 1.0 MDa) were solved at atomic resolution including a symmetric (SymCDTb; 3.14 Å) and an asymmetric form (AsymCDTb; 2.84 Å). Roles played by two receptor-binding domains of aCDTb were of particular interest since RBD1 lacks sequence homology to any other known toxin, and the RBD2 domain is completely absent in other well-studied heptameric toxins (i.e. anthrax). ForAsymCDTb, a novel Ca2+binding site was discovered in RBD1 that is important for its stability, and RBD2 was found to be critical for host cell toxicity and the novel di-heptamer fold for both forms of aCDTb. Together, these studies represent a starting point for structure-based drug-discovery strategies to targeting CDT in the most severe strains of CDI.

SIGNIFICANCE STATEMENT

There is a high burden fromC. difficileinfection (CDI) throughout the world, and the Center for Disease Control (CDC) reports more than 500,000 cases annually in the United States, resulting in an estimated 15,000 deaths. In addition to the large clostridial toxins, TcdA/TcdB, a thirdC. difficilebinary toxin (CDT) is associated with the most serious outbreaks of drug resistant CDI in the 21stcentury. Here, structural biology and biophysical approaches were used to characterize the cell binding component of CDT, termed CDTb, at atomic resolution. Surprisingly, two novel structures were solved from a single sample that help to explain the molecular underpinnings ofC. difficiletoxicity. These structures will also be important for targeting this human pathogen via structure-based therapeutic design methods.
Transcriptional changes are regulated by metabolic pathway dynamics but decoupled from protein levels
Authors: Feltham Jack E. , Xi Shidong , Murray Struan C. , Wouters Meredith , Urdiain-Arraiza Julian , Heilig Raphael , George Charlotte , Townley Anna F. , Roberts Emile , Kessler Benedikt M. , Liberatori Sabrina , Charles Philip D. , Angel Andrew , Fischer Roman , Mellor Jane
Published: November 2019

Transcription is necessary for the synthesis of new proteins, often leading to the assumption that changes in transcript levels lead to changes in protein levels which directly impact a cell’s phenotype. Using a synchronized biological rhythm, we show that despite genome-wide partitioning of transcription, transcripts and translation levels into two phase-shifted expression clusters related to metabolism, detectable protein levels remain constant over time. This disconnect between cycling translation and constant protein levels can be explained by slow protein turnover rates, with overall protein levels maintained by low level pulses of new protein synthesis. Instead, rhythmic post-translational regulation of the activities of different proteins, influenced by the metabolic state of the cells, appears to be key to coordinating the physiology of the biological rhythm with cycling transcription. Thus, transcriptional and translational cycling reflects, rather than drives, metabolic and biosynthetic changes during biological rhythms. We propose that transcriptional changes are often the consequence, rather than the cause, of changes in cellular physiology and that caution is needed when inferring the activity of biological processes from transcript data.

Changes in protein levels do not explain the changing states of a biological rhythm

Slow protein turnover rates decouple proteins levels from a rhythmic transcriptome

Metabolites determine protein activity via rhythmic post-translational modifications

Cycling protein activity explains rhythmic transcription and ribosome biogenesis

A cycling transcriptome is a consequence, not a cause, of physiological changes
Structural similarities between some common fluorophores used in biology and marketed drugs, endogenous metabolites, and natural products
Authors: O’Hagan Steve , Kell Douglas B.
Published: November 2019

Background

It is known that at least some fluorophores can act as ‘surrogate’ substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the ‘natural’ substrates of ‘orphan’ transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly ‘drug-like’, and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores.

Results

The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the “quantitative estimate of drug likeness” technique. It is concluded that this set of fluorophores does overlap a significant part of both drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities.
A comparative study of the capacity of mesenchymal stromal cell lines to form spheroids
Authors: Deynoux Margaux , Sunter Nicola , Ducrocq Elfi , Dakik Hassan , Guibon Roseline , Burlaud-Gaillard Julien , Brisson Lucie , le Nail Louis-Romée , Hérault Olivier , Domenech Jorge , Roingeard Philippe , Fromont Gaëlle , Mazurier Frédéric
Published: November 2019

Mesenchymal stem cells (MSCs)-derived spheroid models favor maintenance of stemness, ex vivo expansion and transplantation efficacy. Spheroids may also be considered as useful surrogate models of the hematopoietic niche. However, accessibility to primary cells, from bone marrow (BM) or adipose tissues, may limit their experimental use and the lack of consistency in methods to form spheroids may affect data interpretation. In this study, we aimed to create a simple model by examining the ability of cell lines, from human (HS-27a and HS-5) and murine (MS-5) BM origins, to form spheroids, compared to primary human MSCs (hMSCs). Our protocol efficiently allowed the spheroid formation from all cell types within 24 hours. Whilst hMSCs-derived spheroids began to shrink after twenty-four hours, the size of spheroids derived from cell lines remained constant during three weeks. The difference was partially explained by the balance between proliferation and cell death, which could be triggered by hypoxia and induced oxidative stress. Our results demonstrate that, unlike hMSCs, MSC cell lines make reproductible spheroids that are easily handled. Thus, this model could help in understanding mechanisms involved in MSC functions and may provide a simple model by which to study cell interactions in the BM niche.
Micronutrient composition and microbial community analysis across diverse landraces of the Ethiopian orphan crop enset
Authors: Tamrat Solomon , Borrell James S. , Biswas Manosh K. , Gashu Dawd , Wondimu Tigist , Vásquez-Londoño Carlos A. , Heslop-Harrison Pat J.S. , Demissew Sebsebe , Wilkin Paul , Howes Melanie-Jayne R.
Published: November 2019

Enset (Ensete ventricosum) is a major starch staple and food security crop for 20 million people. Despite substantial diversity in morphology, genetics, agronomy and utilization across its range, nutritional characteristics have only been reported in relatively few landraces. Here, we survey nutritional composition in 22 landraces from three enset growing regions. We present mineral characterization of enset corm tissue, free amino acid characterization of raw and processed (fermented) tissues and genomic analysis of the microbial community associated with fermentation. We show that compared to regionally important tubers and cereals, enset is high in calcium, iron, potassium and zinc and low in sodium. We report changes in free amino acid composition due to processing, and establish that the bacteria generaAcetobacter,LactobacillusandBifidobacterium, predominate during fermentation. Nutritional and microbial variation presents opportunities to select for improved composition, quality or safety with potentially significant impacts in food security and public health.
Optimising risk-based surveillance for early detection of invasive plant pathogens
Authors: Mastin Alexander J. , Gottwald Timothy R. , van den Bosch Frank , Cunniffe Nik J. , Parnell Stephen R.
Published: November 2019

Emerging infectious diseases of plants continue to devastate ecosystems and livelihoods worldwide. Effective management requires surveillance to detect epidemics at an early stage. However, despite the increasing use of risk-based surveillance programs in plant health, it remains unclear how best to target surveillance resources to achieve this. We combine a spatially explicit model of pathogen entry and spread with a statistical model of detection and use a stochastic optimisation routine to identify which arrangement of surveillance sites maximises the probability of detecting an invading epidemic. Our approach reveals that it is not always optimal to target the highest risk sites, and that the optimal strategy differs depending on, not only patterns of pathogen entry and spread, but also the choice of detection method. We use the example of the economically important arboreal disease huanglongbing to demonstrate how our approach outperforms conventional methods of targeted surveillance.
Polymorphs of 2,4,6-tris(4-pyridyl)-1,3,5-triazine and their mechanical properties
Authors: Yuan Liangqian , Xing Mengyao , Pan Fangfang
Published: November 2019

The second polymorph of the compound 2,4,6-tris(4-pyridyl)-1,3,5-triazine (TPT) is reported, TPT-II, which crystallizes in space groupI2/a. Its higher density and more efficient space filling indicate the lower entropy of TPT-II, while its slightly lower melting point indicates its weaker intermolecular interactions. The conditions of the crystallization experiments for TPT-I and TPT-II are the dominant factors that determine the final crystalline products. The crystals of TPT-II are long needles. They exhibit bending behaviour along the crystallographicbdirection when a mechanical force is imposed perpendicular to it, and regain their original shape after the external stress is removed. The elasticity of the single crystals is interpreted in terms of intermolecular interactions and an energy framework analysis.
How hard metal becomes soft: crystallographic analysis on the mechanical behavior of ultra-coarse cemented carbide
Authors: Hu Huaxin , Liu Xuemei , Hou Chao , Wang Haibin , Tang Fawei , Song Xiaoyan
Published: November 2019

Investigation into the temperature dependence of the mechanical behavior of ultra-coarse grained cemented carbide materials is highly demanded due to its service conditions of concurrent applied stress and high temperature. In the present study, based on the designed experiments and microstructural characterization combined with crystallographic analysis, the evolution of slip systems, motion and interaction of dislocations with temperature are quantified for the WC hard phase. Mechanisms are proposed for the formation of the sessile dislocations in the main slip systems at the room temperature and the glissile dislocations in the new slip systems activated at high temperatures. Furthermore, the correlation of the plastic strain and fracture toughness with the temperature-dependent slip activation, dislocation reaction and transformation is explained quantitatively. Enlightened by the present findings, potential approach to enhance the high-temperature strength of ultra-coarse cemented carbides based on WC strengthening was suggested.
Crystal structure of a high-pressure phase of magnesium chloride hexahydrate determined byin-situX-ray and neutron diffraction methods
Authors: Yamashita Keishiro , Komatsu Kazuki , Hattori Takanori , Machida Shinichi , Kagi Hiroyuki
Published: November 2019

A high-pressure phase of magnesium chloride hexahydrate (MgCl2·6H2O-II) and its deuterated counterpart (MgCl2·6D2O-II) have been identified for the first time byin-situsingle-crystal X-ray and powder neutron diffraction. The crystal structure was analyzed by the Rietveld method for the neutron diffraction pattern based on the initial structure determined by single-crystal X-ray diffraction. This high-pressure phase has a similar framework to that in the known ambient-pressure phase, but exhibits some structural changes with symmetry reduction caused by a subtle modification in the hydrogen-bond network around the Mg(H2O)6octahedra. These structural features reflect the strain in the high-pressure phases of MgCl2hydrates.