bluuebunny/crossref_metadata_2025 huggingface dataset:
Patterns ofMustelid gammaherpesvirus 1(MusGHV-1) genital reactivation linked to stressors in adult European badgers (Meles meles)
Authors: Tsai Ming-shan , Francois Sarah , Newman Chris , Macdonald David W. , Buesching Christina D.
Published: January 2021

Herpesvirus infections are common and mostly asymptomatic in vertebrates, but can result in impaired reproduction. It is therefore important to understand infection patterns and associated risk factors, particularly the effects of different stressors. Here we use Mustelid gammaherpesvirus 1 (MusGHV-1) infection in European badgers (Meles meles) as a host-pathogen wildlife model to study the effects of a variety of demographic, social, physiological and environmental stressors on viral reactivation in the genital tract. We collected 251 genital swabs from 151 free-ranging individuals across 3 trapping seasons (spring, summer and autumn). We screened for MusGHV-1 using PCR and explored possible links between genital MusGHV-1 reactivation and stressors, and their interactions, using logistic regression. In adults, reactivation was more likely in males, especially those in poorer body condition during summer. In females, reactivation was more likely when living in social groups comprising a higher percentage of cubs, but counter to our predictions, recent lactation appeared not influential. In relation to age, reactivation was more common in individuals over 8 years old than among prime age adults, and among juveniles (<2 years old), especially females and individuals in better body condition, likely due to early puberty. Environmentally, reactivation was more prevalent in summer when food abundance is typically low. Our results evidence age effects on MusGHV-1 reactivation; in juveniles MusGHV-1 shedding in the genital tract is likely related to primary infection, while in adults, genital MusGHV-1 reactivation from latency was associated with aging, social and/ or environmental stress.

Importance

The immuno-suppressive effects of elevated stress levels facilitate disease development, and can ultimately cause host extinction at the population level, especially where diseases are transmitted sexually. The impacts of stress on host-pathogen dynamics through disease, however, are still poorly understood outside the laboratory or captive environments. Our study provides rare evidence from a free-ranging wild mammal population that the infection dynamics of a common and sexually transmittable gammaherpesvirus are linked to demographic, social, physiological and environmental stress. We propose that the effects of stressors on STIs and viral reactivation are an important factor to be taken into account in conservation efforts when working with vulnerable wildlife populations.
In silicoanalysis and cluster validation of potential breast cancer nsSNPs of serological tumor marker CA27.29
Authors: Lakhani Jyoti , Harwani Dharmesh
Published: January 2021

Background & Objectives

CA27.29 is a breast cancer-associated glycoprotein. Many genetic variations caused by non-synonymous nucleotide polymorphisms (nsSNPs) are known to affect the functionality of the CA27.29 protein.

Methods

In the present manuscript, anin silicoanalysis of the genetic variations in CA27.29 was done to observe functional nsSNPs that possibly alter its stability. Among 2205 SNPs identified from the publically available SNP database (dbSNP), 213 (9.66%) synonymous SNPs, 24 (1.09%) non-synonymous SNPs, and 1351 (61.27%) noncoding intronic SNPs were observed. The function predictability tools SIFT, Provean and Polyphen2 were used to uncover variations in the analyzed nsSNPs and their functionality.

Results

A total of 16, 20 and 10 non-synonymous SNPs (nsSNPs) were predicted to be damaging or deleterious by SIFT, Polyphen, and Provean tools respectively. Intriguingly, 9 nsSNPs were predicted to be damaging by all the three tools used while 4 nsSNPs were predicted to be damaging by SIFT and Polyphen tools. The substitutions C/G->T and G->A/T were observed to be dominant in the analyzed nsSNPs that probably have damaging role to CA27.29 glycoprotein. Moreover, the validation of results using ClinVar tool revealed that all the analyzed possibly, probably and highly damaging nsSNPs are yet to be reported and studied. Besides this, we found Global minor allele frequency (Global MAF) for only 11 nsSNPs, the values of which were observed to be <0.1% that further confirmed the novelty of the analyzed variants.

Interpretation & Conclusions

Among the analyzed nsSNPs, 3 nsSNPs rs145691584, rs148332231 and rs191544901 were found to be located in 3’UTR region of CA27.29 gene that were assumed to have the possible functional roles in altering the protein stability. The present study is useful to gain useful insights into the genetic variations in nsSNPs that may playing a critical role in determining the susceptibility to breast cancer.
Heart Rate Variability in Patients with Cirrhosis: A Systematic Review and Meta-analysis
Authors: Oyelade Tope , Canciani Gabriele , Carbone Gabriele , Alqahtani Jaber , Moore Kevin , Mani Ali R.
Published: January 2021

Background

Cirrhosis is associated with abnormal autonomic function and regulation of cardiac rhythm. Measurement of heart rate variability (HRV) provides an accurate and non-invasive measurement of autonomic function as well as liver disease severity currently calculated using the MELD, UKELD, or ChildPugh scores. This review assesses the methods employed for the measurement of HRV, and evaluates the alteration of HRV indices in cirrhosis, as well as their value in prognosis.

Method

We undertook a systematic review using Medline, Embase and Pubmed databases in July 2020. Data were extracted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Risk of bias of included studies was assessed by a modified version of the Newcastle Ottawa Scale. The studies descriptive were analysed and the standardized mean differences of HRV indices were pooled.

Results

Of the 247 studies generated from our search, 14 studies were included. One of the 14 studies was excluded from meta-analysis because it reported only median of HRV indices. The studies included have a low risk of bias, and include 583 patients with cirrhosis and 349 healthy controls. The HRV time and frequency domains were significantly lower in cirrhotic patients. Between-studies heterogeneity was high in most of the pooled studies (P<0.05). Further, HRV indices predict survival independent of the severity of liver disease as assessed by MELD.

Conclusion

HRV is decreased in patients with cirrhosis compared with healthy matched controls. HRV correlated with severity of liver disease and independently predicted survival. There was considerable variation in the methods used for HRV analysis, and this impedes interpretation and clinical applicability. Based on the data analysed, SDNN (standard deviation of inter-beat intervals) and cSDNN (i.e. SDNN corrected for basal heart rate) are the most suitable indices for prognosis in patients with cirrhosis.
Histone dynamics mediate DNA unwrapping and sliding in nucleosomes: insights from multi-microsecond molecular dynamics simulations
Authors: Armeev Grigoriy A. , Kniazeva Anastasia S. , Komarova Galina A. , Kirpichnikov Mikhail P. , Shaytan Alexey K.
Published: January 2021

Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ~147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucle-osomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.

We developed a web site for an interactive preview of molecular dynamics trajectories athttps://intbio.github.io/Armeev_et_al_2021.
γδ intraepithelial lymphocytes facilitate pathological epithelial cell shedding via CD103-mediated granzyme release
Authors: Hu Madeleine D. , Golovchenko Natasha B. , Kelly Thomas J. , Agos Jonathan , Zeglinski Matthew R. , Bonder Edward M. , Sandrock Inga , Prinz Immo , Granville David J. , Watson Alastair J.M. , Edelblum Karen L.
Published: January 2021

Excessive shedding of enterocytes into the intestinal lumen is observed in inflammatory bowel disease and is correlated with disease relapse. However, the mechanisms underlying this phenomenon remain unclear. Intraepithelial lymphocytes (IEL) expressing the γδ T-cell receptor (TCR) provide surveillance of the intestinal mucosa at steady-state, which is regulated, in part, by CD103. Intravital microscopy of lipopolysaccharide (LPS)-treated mice revealed that γδ IELs make extended contact with shedding enterocytes. These prolonged interactions require CD103 engagement by E-cadherin, as CD103 blockade significantly reduces LPS-induced shedding. Furthermore, we find that granzymes A and B, but not perforin, are required for cell shedding, and that these granzymes are released by γδ IELs both constitutively and following CD103/E-cadherin ligation. These findings indicate that extracellular granzyme facilitates shedding, likely through cleavage of extracellular matrix proteins. Our results uncover a previously unrecognized role for γδ IELs in facilitating pathological cell shedding in a CD103- and granzyme-dependent manner.
A two-year study on the phenology, host and habitat associations, and pathogens ofHaemaphysalis longicornisin Virginia, U.S.A.
Authors: Thompson Alec T. , White Seth A. , Shaw David , Garrett Kayla B. , Wyckoff Seth T. , Doub Emily E. , Ruder Mark G. , Yabsley Michael J.
Published: January 2021

Understanding the abiotic and biotic variables affecting tick populations is essential for studying the biology and health risks associated with vector species. We conducted a study on the phenology of exoticHaemaphysalis longicornis(Asian longhorned tick) at a site in Albemarle County, Virginia. We assessed the importance of available wildlife hosts, habitats, and microclimate variables such as temperature, relative humidity, and wind speed on this exotic tick’s presence and abundance. In addition, we determined the prevalence of selected tick-borne pathogens potentially transmitted byH. longicornis. We determined that the seasonal activity ofH. longicorniswas slightly different from previous studies in the northeastern United States. We observed nymphal ticks persist year-round but were most active in the spring, followed by a peak in adult activity in the summer and larval activity in the fall seasons. We also observed a lower probability of detectingH. longicornisin field habitats and the summer months. In addition, we detectedH. longicornison several wildlife hosts, including coyote (Canis latrans), eastern cottontail (Sylvilagus floridanus), raccoon (Procyon lotor), Virginia opossum (Didelphis virginiana), white-tailed deer(Odocoileus virginianus), woodchuck (Marmota monax), and aPeromyscussp. This is the first detection of this tick on a rodent host important to the epidemiology of tick-borne pathogens of humans and animals. Finally, we continued to detect the exotic piroplasm parasite,Theileria orientalisIkeda, inH. longicornisas well as other pathogens, includingRickettsia felis, Anaplasma phagocytophilum(AP-1), and aHepatozoonsp. previously characterized inAmblyomma americanum. These represent some of the first detections of arthropod-borne pathogens native to the United States in host-seekingH. longicornis. These data increase our understanding ofH. longicornisbiology in the United States and provide valuable information into the future health risks associated with this tick and pathogens.
RIPK1 activates distinct gasdermins in macrophages and neutrophils upon pathogen blockade of innate immune signalling
Authors: Chen Kaiwen W. , Demarco Benjamin , Heilig Rosalie , Ramos Saray P , Grayczyk James P , Assenmacher Charles-Antoine , Radaelli Enrico , Joannas Leonel D. , Henao-Mejia Jorge , Brodsky Igor E , Broz Petr
Published: January 2021

Injection of effector proteins to block host innate immune signalling is a common strategy used by many pathogenic organisms to establish an infection. PathogenicYersiniaspecies for example inject the acetyltransferase YopJ into target cells to inhibit NF-κB and MAPK signalling. To counteract this, detection of YopJ activity in myeloid cells promotes the assembly of a RIPK1-caspase-8 death-inducing platform that confers antibacterial defence. While recent studies revealed that caspase-8 cleaves the pore-forming protein, gasdermin D (GSDMD) to trigger pyroptosis in macrophages, whether RIPK1 activates additional substrates downstream of caspase-8 to promote host defence is unclear. Here, we report that the related gasdermin family member gasdermin E (GSDME) is activated upon detection of YopJ activity in a RIPK1 kinase-dependent manner. Specifically, GSDME promotes neutrophil pyroptosis and IL-1β release, which is critical for anti-Yersiniadefence. Duringin vivoinfection, IL-1β neutralisation increases bacterial burden in wild type but notGsdme-deficient mice. Thus, our study establishes GSDME as an important mediator that counteracts pathogen blockade of innate immune signalling.
Inhibition of microglial GBA hampers the microglia-mediated anti-oxidant and protective response in neurons
Authors: Brunialti Electra , Villa Alessandro , Mekhaeil Marianna , Mornata Federica , Vegeto Elisabetta , Maggi Adriana , Di Monte Donato A. , Ciana Paolo
Published: January 2021

Homozygotic mutations in the GBA gene cause Gaucher’s disease, moreover, both patients and heterozygotic carriers have been associated with 20- to 30-fold increased risk of developing Parkinson’s disease. In homozygosis, these mutations impair the activity of β-glucocerebrosidase, the enzyme encoded by GBA, and generate a lysosomal disorder in macrophages, which changes morphology towards an engorged phenotype, considered the hallmark of Gaucher’s disease. In the brain, most of the pathological effects caused by GBA mutations have been attributed to the β-glucocerebrosidase deficit in neurons, while a microglial phenotype for these mutations has never been reported. Here, we applied the bioluminescence imaging technology, immunohistochemical and gene expression analysis to investigate the consequences of microglial β-glucocerebrosidase inhibition in the brain of reporter mice, in primary neuron/microglia co-cultures and in cell lines. Our data demonstrate the existence of a novel mechanism by which microglia sustain the antioxidant/detoxifying response mediated by the nuclear factor erythroid 2-related factor 2 in neurons. The central role played by microglia in this neuronal responsein vivowas proven by pharmacological depletion of the lineage in the brain, while co-cultures experiments provided insight on the nature of this cell-to-cell communication showing that this mechanism requires a direct microglia-to-neuron contact supported by functional actin structures. Pharmacological inhibition of microglial β-glucocerebrosidase was proven to induce morphological changes, turn on an anti-inflammatory/repairing pathway and hinder the microglia ability to activate the anti-oxidant/detoxifying response, thus increasing the neuronal susceptibility to neurotoxins.

Altogether, our data suggest that microglial β-glucocerebrosidase inhibition impairs microglia-to-neuron communication increasing the sensitivity of neurons to oxidative or toxic insults, thus providing a possible mechanism for the increased risk of neurodegeneration observed in carriers of GBA mutations.

Graphical Abstract

In Brief

Microglia, through actin-dependent structures, contact neurons and induce a detoxification response by increasing the NFE2L2 signalling pathway. Inhibition of GCase activity by CBE treatment produces a morpho-functional change in microglia cells hampering the neuroprotective microglia-neuron communication thus inducing a phenotype in dopaminergic neurons characterized by increased susceptibility to oxidative stress or toxic insults.
Unraveling the origin of Glucose mediated disparate proliferation dynamics of Cancer stem cells
Authors: Samanta Tagari , Kar Sandip
Published: January 2021

Cancer stem cells (CSCs) often switch on their self-renewal programming aggressively to cause a relapse of cancer. Intriguingly, glucose differentially triggers the proliferation propensities in CSCs in an origin-dependent manner by controlling the expression of the key transcription factor like Nanog. However, the factors that critically govern this glucose-stimulated proliferation dynamics of CSCs remains elusive. Herein, by proposing a mathematical model of glucose-mediated Nanog regulation in CSCs, we showed that the differential proliferation behavior of CSCs can be explained by considering the experimentally observed varied expression levels of key positive (STAT3) and negative (p53) regulators of Nanog. Our model reconciles various experimental observations and predicts ways to fine-tune the proliferation dynamics of specific CSCs in a context-dependent manner. In future, these modeling insights will be useful in developing improved therapeutic strategies to get rid of harmful CSCs.
Comparative whole-genome analysis of a Thar desert strainStreptomycessp. JB150 provides deep insights into the encoded parvome and adaptations to desert edaphic system
Authors: Harwani Dharmesh , Begani Jyotsna , Lakhani Jyoti
Published: January 2021

We sequenced the genome ofStreptomycessp. JB150, isolated from a unique site of the Thar desert in India. Genome mining of the JB150 genome revealed the presence of many interesting secondary metabolic biosynthetic gene clusters (BGCs). The encoded parvome of JB150 includes non-ribosomal peptides, polyketides including β-lactone, butyrolactone, ectoine, lantipeptides, lasso peptides, melanin, resorcinol, siderophores, terpenoids, thiopeptides, and other types of hybrid compounds. Among them, ~30% BGCs displayed a high degree of novelty. The genome of JB150 was enriched for a large assortment of specialized genes coding for the production of many interesting biomolecules comprising compatible solutes, multiple stress-response regulators, transport proteins, protein secretion systems, signaling molecules, chaperones and storage reserves, etc. The presence of diverse members of CAZymes enzyme families, high numbers of riboflavin, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), trehalose and aromatic compounds synthesis genes, putative orthologues to several of the classical fatty acid synthesis components, prototrophy for many essential amino acids exhibit metabolic versatility of JB150 to inhabit in the extreme desert environment. Besides, the genome of JB150 was observed to specifically encode thiazole-oxazole-modified thiazolemicrocin (TOMM) and ectoine. The comparison of the complete genomes ofStreptomycessp. JB150 and seven other actinomycete strains belonging to different desert ecosystems unveiled the presence of many previously undetected, distinctive, biological, and genomic signatures. We propose that these genetic traits endowed by these strains are essential for their adaptation in the highly underprivileged, extreme ecosystem of the Thar desert to cope with multiple abiotic stressors, oligotrophic nutrient conditions and to produce a huge repertoire of diverse secondary metabolites.
CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks
Authors: Nagai James S. , Leimkühler Nils B. , Schaub Michael T. , Schneider Rebekka K. , Costa Ivan G.
Published: January 2021

Motivation

Ligand-receptor (LR) network analysis allows the characterization of cellular crosstalk based on single cell RNA-seq data. However, current methods typically provide a list of inferred LR interactions and do not allow the researcher to focus on specific cell types, ligands or receptors. In addition, most of these methods cannot quantify changes in crosstalk between two biological phenotypes.

Results

CrossTalkeR is a framework for network analysis and visualisation of LR interactions. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological phenotypes, i.e. disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterisation of changes in cellular crosstalk in disease.

Availability and Implementation

CrosstalkeR is an R package available athttps://github.com/CostaLab/CrossTalkeR.
Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos
Authors: Ichikawa Masako , Kato Norio , Toda Erika , Kashihara Masakazu , Ishida Yuji , Hiei Yukoh , Isobe Sachiko N. , Shirasawa Kenta , Hirakawa Hideki , Okamoto Takashi , Komari Toshihiko
Published: January 2021

Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativaL., ‘Nipponbare’) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The ratio of single nucleotide variants among the variants was 74.3%, and the natural mutation rate calculated using the variants in the seed-propagated plants was 1.2 × 10−8. The percentage and the mutation rate were consistent with the values reported previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.
Transcriptome Analysis of Chloride Intracellular Channel Knockdown inDrosophilaIdentifies Oxidation-Reduction Function as Possible Mechanism of Altered Sensitivity to Ethanol Sedation
Authors: Weston Rory M. , Schmitt Rebecca E. , Grotewiel Mike , Miles Michael F.
Published: January 2021

Chloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the soleDrosophila melanogasterortholog,Clic, was targeted for RNAi knockdown to identify genes and biological processes associated withClicexpression.Clicknockdown had a substantial impact on global transcription, altering expression of over 9% of transcribedDrosophilagenes. Overrepresentation analysis of differentially expressed genes identified enrichment of 23 Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. DrosophilaClicand vertebrate orthologClic4have previously been tied to ethanol sensitivity and ethanol-regulated expression.Clicknockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity inDrosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity byClicmay be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation inClicknockdown flies. Consistent with previous findings,Clicknockdown reduced acute ethanol sedation sensitivity in flies housed under nomoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests thatDrosophila Clichas a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.
Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation
Authors: Hong Jiayin , Hua Bo , Springer Michael
Published: January 2021

Quantitative traits such as human height are measurable phenotypes that show continuous variation over a wide phenotypic range. Enormous effort has recently been put into determining the genetic influences on a variety of quantitative traits, including human genetic diseases, with mixed success. We identified a quantitative trait in a tractable model system, the GAL pathway in yeast, which controls the uptake and metabolism of the sugar galactose. GAL pathway activation depends both on galactose concentration and on the concentrations of competing, preferred sugars such as glucose. Natural yeast isolates show substantial variation in the behavior of the pathway. All studied yeast strains exhibit bimodal responses relative to external galactose concentration, i.e. a set of galactose concentrations existed at which both GAL-induced and GAL-repressed subpopulations were observed. However, these concentrations differed in different strains. We built a mechanistic model of the GAL pathway and identified parameters that are plausible candidates for capturing the phenotypic features of a set of strains including standard lab strains, natural variants, and mutants.In silicoperturbation of these parameters identified variation in the intracellular galactose sensor, Gal3p, the negative feedback node within the GAL regulatory network, Gal80p, and the hexose transporters, HXT, as the main sources of the bimodal range variation. We were able to switch the phenotype of individual yeast strainsin silicoby tuning parameters related to these three elements. Determining the basis for these behavioral differences may give insight into how the GAL pathway processes information, and into the evolution of nutrient metabolism preferences in different strains. More generally, our method of identifying the key parameters that explain phenotypic variation in this system should be generally applicable to other quantitative traits.

Author summary

Microbes adopt elaborate strategies for the preferred uptake and use of nutrients to cope with complex and fluctuating environments. As a result, yeast strains originating from different ecological niches show significant variation in the way they induce genes in the galactose metabolism (GAL) pathway in response to nutrient signals. To identify the mechanistic sources of this variation, we built a mathematical model to simulate the dynamics of the galactose metabolic regulation network, and studied how parameters with different biological implications contributed to the natural variation. We found that variations in the behavior of the galactose sensor Gal3p, the negative feedback node Gal80p, and the hexose transporters HXT were critical elements in the GAL pathway response. Tuning single parametersin silicowas sufficient to achieve phenotype switching between different yeast strains. Our computational approach should be generally useful to help pinpoint the genetic and molecular bases of natural variation in other systems.
Is Vaccination a Viable Method to Control Johne’s Disease Caused byMycobacterium aviumsubsp.paratuberculosis? Data from 12 Million Ovine Vaccinations and 7.6 Million Carcass Examinations in New South Wales, Australia from 1999-2009
Authors: Links Ian J. , Denholm Laurence J. , Evers Marilyn , Kingham Lloyd J. , Greenstein Robert J.
Published: January 2021

Background

Mycobacterium aviumsubsp.paratuberculosis(MAP) causes Johne’s disease (or paratuberculosis), a chronic wasting disease of ruminants and other animals resulting from granulomatous enteritis. There are increasing concerns that MAP is zoonotic. The prevalence of Johne’s disease is increasing worldwide. In an attempt to control an epidemic of ovine Johne’s disease (OJD) in New South Wales (NSW), a government/industry sponsored voluntary vaccination/on-farm management program commenced in 2000. We report herein an observational study of changes in disease prevalence as vaccination progressed, based on abattoir surveillance data for OJD from 1999 to 2009. We also discuss the epidemiological, policy, regulatory, research, economic and sociological elements that contributed to the development of a mature control program, whose aim was to halt the epidemic spread of OJD in a naïve sheep population.

Methods

NSW was divided into areas of “High” (HPA), “Medium” (MPA) and “Low” (LPA) OJD prevalence. A killed whole cell vaccine (Gudair®) was administered to sheep from 2000 to 2009. Trained examiners evaluated the viscera of adult sheep carcasses at slaughter for gross evidence of OJD. MAP infection was confirmed by histopathology.

Principal findings

From 2000-2009, 12 million vaccine doses were administered in NSW (91%; 10.9 million in the HPA). Many of the vaccinated flocks were suffering > 5% annual mortality in adult sheep, with some individual flocks with 10-15% losses attributable to OJD. A total of 7.6 million carcasses were examined (38%; 2.9 million from the HPA). Overall, 16% of slaughter consignments (sheep consigned to the abattoir from a single vendor) were positive for OJD, of which 94% were from the HPA. In the HPA, the percentage of animals with lesions attributable to OJD at slaughter fell progressively from 2.4% (10,406/432,860) at commencement of vaccination in 2000 to 0.8% (1,573/189,564) by 2009. Herd immunity from vaccination in the HPA was estimated at 70% by 2009. This coincided with a progressive decrease in reports of clinical disease and mortalities in vaccinated flocks.

Significance

We show a decrease in the prevalence of lesions attributable to OJD in NSW concomitant with initiation of voluntary vaccination, on-farm management plans, abattoir monitoring and feedback of animal prevalence data to sheep producers. We conclude that a target of ≤ 1% regional prevalence of OJD affected sheep at slaughter is achievable using these interventions.
Stress and corticotropin releasing factor (CRF) promote necrotizing enterocolitis in a formula-fed neonatal rat model
Authors: Bell Robert L. , Withers Ginger S. , Kuypers Frans A. , Stehr Wolfgang , Bhargava Aditi
Published: January 2021

The etiology of necrotizing enterocolitis (NEC) is not known. Alterations in gut microbiome, mucosal barrier function, immune cell activation, and blood flow are characterized events in its development, with stress as a contributing factor. The hormone corticotropin-releasing factor (CRF) is a key mediator of stress responses and influences these aforementioned processes. CRF signaling is modulated by NEC’s main risk factors of prematurity and formula feeding. Using an established neonatal rat model of NEC, we tested hypotheses that: (i) increased CRF levels—as seen during stress—promote NEC in formula-fed newborn rats, and (ii) antagonism of CRF action ameliorates NEC. Newborn pups were formula-fed to initiate gut inflammation and randomized to: no stress, no stress with subcutaneous CRF administration, stress (acute hypoxia followed by cold exposure—NEC model), or stress after pretreatment with the CRF peptide antagonist Astressin. Dam-fed unstressed and stressed littermates served as controls. NEC incidence and severity in the terminal ileum were determined using a histologic scoring system. Changes in CRF, CRF receptor (CRFRs), and toll-like receptor 4 (TLR4) expression levels were determined by immunofluorescence and immunoblotting, respectively. Stress exposure in FF neonates resulted in 40.0% NEC incidence, whereas exogenous CRF administration resulted in 51.7% NEC incidence compared to 8.7% in FF non-stressed neonates (p<0.001). Astressin prevented development of NEC in FF-stressed neonates (7.7% vs. 40.0%; p=0.003). CRF and CRFR immunoreactivity increased in the ileum of neonates with NEC compared to dam-fed controls or FF unstressed pups. Immunoblotting confirmed increased TLR4 protein levels in FF stressed (NEC model) animals vs. controls, and Astressin treatment restored TLR4 to control levels. Peripheral CRF may serve as specific pharmacologic target for the prevention and treatment of NEC.
Ribosomal DNA revealed an extensive role of allopolyploidy in the radiation ofUlexL
Authors: Fonseca João P. , Pereira Ana , Robalo Joana I. , Neto Carlos , Costa José C.
Published: January 2021

We studied the phylogeny ofUlexL., a genus of spiny legumes, which its center of diversity in the Iberian Peninsula, using ribosomal DNA markers (rDNA), namely ETS, 5.8S and ITS (45S), and 5S intergenic spacer regions. One of the main findings was the presence of very different haplotypes in 5S-IGS genes and, to a less extent, in ETS and ITS, in seven polyploidtaxa.We interpreted these results as an indication of hybrid origins and proposed allopolyploidy forU. argenteusssp.subsericeus, U. australis ssp. australis, U. australisssp. welwitschianus, U. densus, U. europaeusssp.europaeus, U. europaeusssp.latebracteatus,andU. jussiaei.These results reinforce an early hypothesis which stated that the radiation ofUlexoccurred mainly by polyplodization.

Phylograms showed two main clades, one grouping the hydrophilicU. gallii,U. breoganiiandU. minor, and the other grouping the southern, xerophytic,taxa. The putative allopolyploids showed haplotypes, which grouped in both clades, indicating that allopolyploidy, occurred through hybridization from these hydrophilic and xerophytic lineages.

The phylogenetic position ofU. micranthusis not certain and it is discussed. The 5S-IGS showed to retain more polymorphisms than ETS gene or ITS markers. This result is compatible with the hypothesis that 5S rDNA region is less vulnerable to inter-loci concerted evolution than 45S, providing a more suitable marker for reconstructing histories of allopolyploid species. We discuss the taxonomic consequences of these results.
Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques
Authors: Pereira-Flores Emiliano , Medema Marnix , Buttigieg Pier Luigi , Meinicke Peter , Glöckner Frank Oliver , Fernández-Guerra Antonio
Published: January 2021

Microorganisms produce an immense variety of natural products through the expression of Biosynthetic Gene Clusters (BGCs): physically clustered genes that encode the enzymes of a specialized metabolic pathway. These natural products cover a wide range of chemical classes (e.g., aminoglycosides, lantibiotics, nonribosomal peptides, oligosaccharides, polyketides, terpenes) that are highly valuable for industrial and medical applications1. Metagenomics, as a culture-independent approach, has greatly enhanced our ability to survey the functional potential of microorganisms and is growing in popularity for the mining of BGCs. However, to effectively exploit metagenomic data to this end, it will be crucial to more efficiently identify these genomic elements in highly complex and ever-increasing volumes of data2. Here, we address this challenge by developing the ultrafast Biosynthetic Gene cluster MEtagenomic eXploration toolbox (BiG-MEx). BiG-MEx rapidly identifies a broad range of BGC protein domains, assess their diversity and novelty, and predicts the abundance profile of natural product BGC classes in metagenomic data. We show the advantages of BiG-MEx compared to standard BGC-mining approaches, and use it to explore the BGC domain and class composition of samples in the TARA Oceans3and Human Microbiome Project datasets4. In these analyses, we demonstrate BiG-MEx’s applicability to study the distribution, diversity, and ecological roles of BGCs in metagenomic data, and guide the exploration of natural products with clinical applications.
Ecological outcomes of hybridization vary extensively inCatostomusfishes
Authors: Mandeville Elizabeth G. , Hall Robert O. , Buerkle C. Alex
Published: January 2021

Hybridization has been studied extensively to learn about speciation and mechanisms of reproductive isolation, but increasingly we recognize that hybridization outcomes vary geo-graphically and can depend on the environment. At the same time, hybridization can reshape biotic interactions in an ecosystem, leading to ecological shifts where hybridization occurs. Identifying how hybrid individuals function ecologically would link evolutionary outcomes of hybridization to ecological consequences, but relatively few studies have focused on ecological traits of hybrids. We described the feeding ecology of severalCatostomusfish species and their hybrids by using stable isotopes (δ13C andδ15N) as a proxy for diet and habitat use, and compared two native species, an introduced species, and three interspecific hybrid crosses. We replicated this comparison spatially, including hybrids and parental species from seven rivers in the Upper Colorado River basin where parental species co-occur and the opportunity for hybridization exists. Although relationships between native species in isotopic space varied, individual native species did not fully overlap in isotopic space in any river sampled, suggesting little overlap of resource use between these historically sympatric species. The introduced species overlapped with one or both native species in every river, suggesting similar resource use and potential for competition. Hybrids occupied intermediate, matching, or more extreme (transgressive) isotopic space relative to parental species, and were isotopically variable within and among rivers. We suggest that ecological outcomes of hybridization, like genomic outcomes of hybridization, are likely to vary across locations where a pair of species hybridizes. This variation implies that hybridization might have large unpredictable, idiosyncratic ecological effects on fish assemblages where hybrids occur. Although we found little evidence that hybrids are at a disadvantage ecologically—there were no significant declines in body condition relative to parental species—it is nevertheless possible that abiotic or biotic attributes of a river might constrain the range of interspecific hybrids that are successful, thus contributing to variation in hybridization outcomes across rivers.
Regeneration of spinal motor axons: Negative regulation by Celsr2 implicating Cdc42/Rac1 and JNK/c-Jun signaling
Authors: Wen Quan , Weng Huandi , Liu Tao , Yu Lingtai , Zhao Tainyun , Qin Jingwen , Fadel Tissir , Qu Yibo , Zhou Libing
Published: January 2021

During development, cadherins Celsr2 and Celsr3 control axon navigation. Unlike Celsr3, Celsr2 remains expressed in the adult, suggesting unexplored roles in maintenance and repair. Here we show thatCelsr2knockdown promotes motor axon regeneration in mouse and human spinal cord explants and cultured motor neurons.Celsr2downregulation is accompanied by increased levels of GTP-bound Rac1 and Cdc42, and of JNK and c-Jun proteins. Using a branchial plexus injury model, we show that forelimb functional recovery is improved inCelsr2mutant versus control mice. Compared to controls, in mutant mice, reinnervated biceps muscles are less atrophic, contain more newly formed neuromuscular junctions, and generate larger electromyographic potentials, while motor neuron survival and axon regeneration are improved. GTP-bound Rac1 and Cdc42, JNK and c-Jun are upregulated in injured mutant versus control spinal cord. In conclusion, Celsr2 negatively regulates motor axon regeneration via Cdc42/Rac1/JNK/c-Jun signaling and is a target for neural repair.
Two contrasting mediodorsal thalamic circuits target the medial prefrontal cortex
Authors: Lyuboslavsky Polina , Kizimenko Alena , Brumback Audrey C.
Published: January 2021

At the heart of the prefrontal executive and limbic networks is the mediodorsal thalamus (MD). Despite the importance of MD in a broad range of behaviors and neuropsychiatric disorders, virtually nothing is known about the physiology of neurons in MD. Here, we injected the retrograde tracer cholera toxin subunit B (CTB) into the medial prefrontal cortex (mPFC) of adult (8 – 12 week old) male and female wildtype mice. We prepared acute brain slices and used current clamp electrophysiology to measure and compare the intrinsic properties of the neurons in MD that project to mPFC (MD→mPFC neurons). MD→mPFC neurons are located predominantly in the medial (MD-M) and lateral (MD-L) subnuclei of MD. We found that that MD-M→mPFC neurons have longer membrane time constants, higher membrane resistance, less Hyperpolarization and Cyclic Nucleotide gated (HCN) channel activity, and more readily generate action potentials compared to MD-L→mPFC neurons. Additionally, MD-M→mPFC neurons have larger and more complex dendritic arbors compared to MD-L→mPFC neurons. These data demonstrating that the two populations of MD→mPFC neurons have distinct physiologies and morphologies suggests a differential role in thalamocortical information processing and potentially behavior.
Low photorespiratory capacity is sufficient to block the induction of photosynthetic capacity in high light
Authors: Baker Christopher R. , Cocurrun Jean Christophe , Alonso Ana Paula , Niyogi Krishna K.
Published: January 2021

The induction of high photosynthetic capacity in high light (HL) is a common response among many herbaceous dicot plants, however, the signals that control this response remain largely unknown. Here, multiple independent lines of evidence are presented in support of the conclusion that low photorespiratory capacity acts a negative signal to limit photosynthetic capacity acclimation in HL inArabidopsis thaliana. Using a panel of natural accessions, primary nitrogen (N) assimilation and photorespiration rates early after a shift to growth in HL, as well as activities for key enzymes in these pathways, were shown to positively correlate with the magnitude of the subsequent induction of photosynthetic capacity, which occurred several days later. Time-resolved metabolomic data during acclimation to HL were collected using a strongly acclimating ecotype and a weakly acclimating ecotype, revealing in greater detail the differences in N assimilation, photorespiration, and triose-phosphate utilization pathways underlying efficient photosynthetic capacity acclimation. When shifted into HL growth conditions under non-photorespiratory conditions, weakly acclimating ecotypes and even photorespiratory mutants gained the ability to strongly induce high photosynthetic capacity in HL. Thus, a negative, photorespiration-dependent signal early in the HL shift appears to block photosynthetic capacity acclimation in accessions with low photorespiratory capacity, whereas accessions with high photorespiratory capacity are licensed to increase photosynthetic capacity.
Osa-miR820 regulatory node primes rice plants to tolerate salt stress in an agronomically advantageous manner
Authors: Sharma Neha , Kumar Sudhir , Sanan-Mishra Neeti
Published: January 2021

Plant microRNAs (miRs) play an important role in regulating gene expression under normal and stressful environments. Here we report the functional implications on the role of Osa-miR820, which can be grouped as a young, rice-specific miR. It is a member of the class II transposon-derived small RNA family and is processed as 21-nt and 24-nt length variants, respectively. Size of the miR820 family varies from 1 to 16 across the Oryza AA genomes. The 21–nt Osa-miR820 negatively regulates ade novomethylase, OsDRM2 (domains rearranged methyl transferase) that prevents methylation of the CACTA transposon loci in the rice genome. In an earlier report we have detailed the expression profiles of Osa-miR820 and its target in abiotic stress responses using rice varieties exhibiting varying response to salt stress. In this study, artificial miR based approach was employed to specifically overexpress 21-nt Osa-miR820 in rice plants (OX-820). These plants exhibited enhanced vigour, ~25-30% increase in the number of spikelets per panicle and increased grain filling, under normal and salt stress conditions. The OX-820 lines showed a better water use efficiency and higher proline accumulation under salt stress. These plants can serve as a useful source for dissecting the molecular machinery governed by Osa-miR820:DRM2 node to prime tolerance to salt stress in an agronomically advantageous manner.
Targeted sensors for glutamatergic neurotransmission
Authors: Hao Yuchen , Toulmé Estelle , König Benjamin , Rosenmund Christian , Plested Andrew J.R.
Published: January 2021

Optical report of neurotransmitter release allows visualization of excitatory synaptic transmission. Sensitive genetically-encoded glutamate reporters operating with a range of affinities and emission wavelengths are available. However, without targeting to synapses, the specificity of the fluorescent signal is uncertain, compared to sensors directed at vesicles or other synaptic markers. We fused the state-of-the-art reporter iGluSnFR to glutamate receptor auxiliary proteins in order to target it to postsynaptic sites. Chimeras of Stargazin and gamma-8 that we named SnFR-γ2 and SnFR-γ8, retained function and reported spontaneous glutamate release in hippocampal cells, with apparently diffraction-limited spatial precision. In autaptic neurons on micro island cultures, evoked release could be quantitatively detected at tens of synapses in a field of view whilst evoked currents were recorded simultaneously. These experiments revealed a specific postsynaptic deficit from Stargazin overexpression, resulting in synapses with normal release but without postsynaptic responses. This defect was reverted by delaying overexpression. By working at different calcium concentrations, we determined that SnFR-γ2 is a linear reporter of the global quantal parameters and short term synaptic plasticity, whereas iGluSnFR is not. On average, half of iGluSnFR regions of interest showing evoked fluorescence changes had intense rundown, whereas less than 5% of SnFR-γ2 ROIs did. We provide an open-source analysis suite for extracting quantal parameters including release probability from fluorescence time series of individual and grouped synaptic responses. Taken together, postsynaptic targeting improves several properties of iGluSnFR and further demonstrates the importance of subcellular targeting for optogenetic actuators and reporters.
Gradual opening of Smc arms in prokaryotic condensin
Authors: Nunez Roberto Vazquez , Polyhach Yevhen , Soh Young-Min , Jeschke Gunnar , Gruber Stephan
Published: January 2021

Multi-subunit SMC ATPases control chromosome superstructure apparently by catalyzing a DNA-loop-extrusion reaction. SMC proteins harbor an ABC-type ATPase ‘head’ and a ‘hinge’ dimerization domain connected by a coiled coil ‘arm’. Two arms in a SMC dimer can co-align, thereby forming a rod-shaped particle. Upon ATP binding, SMC heads engage, and arms are thought to separate. Here, we studied the shape ofB. subtilisSmc-ScpAB by electron-spin resonance spectroscopy. Arm separation was readily detected proximal to the heads in the absence of ligands, while separation near the hinge largely depended on ATP and DNA. Artificial blockage of arm opening eliminated DNA stimulation of ATP hydrolysis, but did not prevent basal ATPase activity. We identified an arm-to-arm contact as being important for controlling the molecular transformations. Point mutations at this arm interface eliminate Smc function. We propose that partially open, intermediary conformations provide directionality to SMC DNA translocation by binding suitable DNA substrates.