bluuebunny/crossref_metadata_2025 huggingface dataset:
Scientific Article Dietary electrolyte balance on serum hematological and biochemical parameters of broilers under heat stress
Authors: Silva e Silva Danilo Rodrigo , de Sousa Moura Francinete Alves , de Sousa Lima Vânia Batista , Miranda Lopes Patrícia , de Fatima Saraiva Cardoso Janaina , do Prado Alan Costa , Machado Luciana Pereira , Átila de Sousa Richard , Biagiotti Daniel , Barros Dourado Leilane Rocha
Published: January 2021

The aim of this study was to evaluate the effect of different dietary electrolyte balance (DEB) levels over the hematological parameters and the biochemical profile of broilers under stress caused by cyclic heat. We used 1050 male broilers from Ross lineage, for two experimental phases: phase 1 (broilers from 1 until 21 days old) and phase 2 (broilers from 22 until 42 days old). The broilers were distributed under a completely randomized design, built for five treatments (110; 175; 240; 305; 370 mEq of DEB/kg of ration) and seven repetitions. For the hematological analyses were used two broilers in each repetition, one to blood count evaluation (Hemogram) and another one to the biochemistry evaluation, collected in the end of each experimental phase. During the phase of 1 - 21 days old, the variable hemoglobin number (Heme), mean corpuscular volume (MCV) and Serum Chloride (Cl) presented a linear effect (p<0,05) DEB levels. There was no effects (p>0,05) over the corpuscular volume (CV), total plasma protein (TPP), leukocytes number (Leu), heterophiles (Het), lymphocytes (Lyn), eosinophils (Eos), basophils (Bas), monocytes (Mon), calcium (Ca), phosphor (P), uric acid (UA) e urea (U). During the phase two of 22 – 42 days old there was effect (p<0,05) quadratic to the variables Leu and Het and linear to the variable P and significative difference (p<0,05) between the variable means UA at the levels of DEB tested.

There was no effect (p>0,05) over the variable CV, Heme, MCV, TPP, Lyn, Eos, Bas, Mon, Cl, Ca and U on the DEB levels tested. The supplementation of the DEB levels 110, 175 e 240, 305 and 370 to the phase from 1 until 21 days old presented great results in the hematological evaluation and biochemical, because it provided possibly a longer useful life to the Hem without promoting a metabolic imbalance. In the phase from 22 until 42 days old the level of 268 to 280 mEq of DEB/kg of ration presented a better answer from the broilers immune systemic.
Utilisation of semiconductor sequencing for the detection of predictive biomarkers in glioblastoma
Authors: Williams Gareth H , Thatcher Robert , Hardisty Keeda-Marie , Loddo Marco
Published: January 2021

The standard treatment for glioblastoma involves a combination of surgery, radiation and chemotherapy but have limited impact on survival. The exponential increase in targeted agents directed at pivotal oncogenic pathways now provide new therapeutic opportunities for this tumour type. However, lack of comprehensive precision oncology testing at diagnosis means such therapeutic opportunities are potentially overlooked.

To investigate the role of semiconductor sequencing for detection of predictive biomarkers in routine glioblastoma samples we have undertaken analysis of test trending data generated by a clinically validated next generation sequencing platform designed to capture 764 of the leading anti-cancer targeted agents/combinations and immunotherapies via analysis of actionable genomic variants distributed across 505 genes. Analysis was performed across a cohort of 55 glioblastoma patients.

Analysis of trending data has revealed a complex and rich actionable mutational landscape in which 166 actionable mutations were detected across 36 genes linked to 17 off label targeted therapy protocols and 111 clinical trials. The majority of patients harboured three or more actionable mutations affecting key cancer related regulatory networks including the PI3K/AKT/MTOR and RAS/RAF/MEK/MAPK signalling pathways, DNA-damage repair pathways and cell cycle checkpoints. Linkage with immunotherapy and PARP inhibitors was identified in 44% of glioblastoma patients as a consequence of alterations in DNA-damage repair genes.

Taken together our data indicates that precision oncology testing utilising semiconductor sequencing can be used to identify a broad therapeutic armamentarium of targeted therapies and immunotherapies that can be potentially employed for the improved clinical management of glioblastoma patients.
MultipleTesting.com: a tool for life science researchers for multiple hypothesis testing correction
Authors: Menyhárt Otília , Weltz Boglárka , Győrffy Balázs
Published: January 2021

Scientists from nearly all disciplines face the problem of simultaneously evaluating many hypotheses. Conducting multiple comparisons increases the likelihood that a non-negligible proportion of associations will be false positives, clouding real discoveries.

Drawing valid conclusions require taking into account the number of performed statistical tests and adjusting the statistical confidence measures. Several strategies exist to overcome the problem of multiple hypothesis testing. We aim to summarize critical statistical concepts and widely used correction approaches while also draw attention to frequently misinterpreted notions of statistical inference.

We provide a step-by-step description of each multiple-testing correction method with clear examples and present an easy-to-follow guide for selecting the most suitable correction technique.

To facilitate multiple-testing corrections, we developed a fully automated solution not requiring programming skills or the use of a command line. Our registration free online tool is available atwww.multipletesting.comand compiles the five most frequently used adjustment tools, including the Bonferroni, the Holm (step-down), the Hochberg (step-up) corrections, allows to calculate False Discovery Rates (FDR) and q-values.

The current summary provides a much needed practical synthesis of basic statistical concepts regarding multiple hypothesis testing in a comprehensible language with well-illustrated examples. The web tool will fill the gap for life science researchers by providing a user-friendly substitute for command-line alternatives.
Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome
Authors: Shirogane Yuta , Rousseau Elsa , Voznica Jakub , Xiao Yinghong , Su Weiheng , Catching Adam , Whitfield Zachary J. , Rouzine Igor M. , Bianco Simone , Andino Raul
Published: January 2021

1

During replication, RNA viruses accumulate genome alterations, such as mutations and deletions. The interactions between individual variants can determine the fitness of the virus population and, thus, the outcome of infection. To investigate the effects of defective interfering genomes (DI) on wild-type (WT) poliovirus replication, we developed an ordinary differential equation model. We experimentally determined virus and DI replication during co-infection, and use these data to infer model parameters. Our model predicts, and our experimental measurements confirm, that DI replication and encapsidation are the most important determinants for the outcome of the competition. WT replication inversely correlates with DI replication. Our model predicts that genome replication and effective DI genome encapsidation are critical to effectively inhibit WT production, but an equilibrium can be established which enables WT to replicate, albeit to reduce levels.
The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages and chelicerate genome architecture
Authors: Gainett Guilherme , González Vanessa L. , Ballesteros Jesús A. , Setton Emily V. W. , Baker Caitlin M. , Gargiulo Leonardo Barolo , Santibáñez-López Carlos E. , Coddington Jonathan A. , Sharma Prashant P.
Published: January 2021

Chelicerates exhibit dynamic evolution of genome architecture, with multiple whole genome duplication events affecting groups like spiders, scorpions, and horseshoe crabs. Yet, genomes remain unavailable for several chelicerate orders, such as Opiliones (harvestmen), which has hindered comparative genomics and developmental genetics across arachnids. We assembled a draft genome of the daddy-long-legsPhalangium opilio,which revealed no signal of whole genome duplication. To test the hypothesis that single-copy Hox genes of the harvestman exhibit broader functions than subfunctionalized spider paralogs, we performed RNA interference againstDeformedinP. opilio.Knockdown ofDeformedincurred homeotic transformation of the two anterior pairs of walking legs into pedipalpal identity; by comparison, knockdown of the spatially restricted paralogDeformed-Ain the spider affects only the first walking leg. To investigate the genetic basis for leg elongation and tarsomere patterning, we identified and interrogated the function of anEpidermal growth factor receptor (Egfr)homolog. Knockdown ofEgfrincurred shortened appendages and the loss of distal leg structures. The overlapping phenotypic spectra ofEgfrknockdown experiments in the harvestman and multiple insect models are striking because tarsomeres have evolved independently in these groups. Our results suggest a conserved role forEgfrin patterning distal leg structures across arthropods, as well as cooption of EGFR signaling in tarsomere patterning in both insects and arachnids. The establishment of genomic resources forP. opilio,together with functional investigations of appendage fate specification and distal patterning mechanisms, are key steps in understanding how daddy-long-legs make their long legs.
Maternal behavior and the neonatal HPA axis in the Wistar Audiogenic Rat (WAR) strain: early life implications for a genetic animal model in epilepsy
Authors: Godoy Lívea Dornela , Garcia-Cairasco Norberto
Published: January 2021

Epileptogenesis is a multistage process and seizure susceptibility can be influenced by stress early in life.Wistar Audiogenic Rat(WAR) strain is an interesting model to study the association between stress and epilepsy, since it is naturally susceptible to seizures and present changes in the hypothalamus-pituitary-adrenal (HPA) axis activity. All these features are related to the pathogenic mechanisms usually associated to psychiatric comorbidities present in epilepsy. Therefore, the current study aimed to evaluate the neonate HPA axis function and maternal care under control and stress conditions in the WAR strain. Maternal behavior and neonate HPA axis were evaluated in Wistar and WAR strains under rest and after the presence of stressors. We observed that WAR pups present higher plasmatic corticosterone concentration as compared to Wistar pups. Although WAR dams do not show significant altered maternal behavior at rest, there is a higher latency to recover the litter in the pup retrieval test, while some did not recover all the litter. WAR dams presented similar behaviors to Wistar dams to a female intruder and maternal care with the pups in the maternal defense test. Taken together, these findings indicate that the WAR strain could show HPA axis disruption early in life and dams present altered maternal behavior under stressful events. Those alterations make the WAR strain an interesting model to evaluate vulnerability to epilepsy and its associated neuropsychiatric comorbidities.
SplitStaphylococcus aureusprime editor for AAV delivery
Authors: Aird Eric J. , Zdechlik Alina C. , Ruis Brian L. , Rogers Colette B. , Lemmex Andrew L. , Nelson Andrew T. , Hendrickson Eric A. , Schmidt Daniel , Gordon Wendy R.
Published: January 2021

Prime editing brings immense promise to correct a large number of human pathogenic mutations and enact diverse edit types without introducing widespread undesired editing events. Delivery of prime editors in vivo would enable such edits to be introduced in a clinical setting. The coding sequence for prime editor, however, is too large to fit within the size-constrained adeno-associated virus (AAV) genome. Herein, we describe a splitStaphylococcus aureusprime editor capable of being delivered by dual AAVs. We characterize the editing ability of plasmid-based versions of anS. aureusprime editor in vitro at a variety of loci with diverse edit types. We investigate various split prime editor architectures and alternative dimerization domains. Finally, we demonstrate the capacity of prime editor to be co-delivered by dual AAVs in vitro. While editing rates are lower than desired, this approach presents an important step to translate prime editing for in vivo delivery.
Local brainstem circuits contribute to reticulospinal output in the mouse
Authors: Chopek Jeremy W. , Zhang Ying , Brownstone Robert M
Published: January 2021

Glutamatergic reticulospinal neurons in the gigantocellular reticular nucleus (GRN) of the medullary reticular formation can function as command neurons, transmitting motor commands to spinal cord circuits. Recent advances in our understanding of this neuron-dense region have been facilitated by the discovery of expression of the transcriptional regulator, Chx10, in excitatory reticulospinal neurons. Here, we address the capacity of local circuitry in the GRN to contribute to reticulospinal output. We define two sub-populations of Chx10-expressing neurons in this region, based on distinct electrophysiological properties and somata size (small and large), and show that these correspond to local interneurons and reticulospinal neurons, respectively. Using focal release of caged-glutamate combined with patch clamp recordings, we demonstrated that Chx10 neurons form microcircuits in which the Chx10 interneurons project to and facilitate the firing of Chx10 reticulospinal neurons. We discuss the implications of these microcircuits in terms of movement selection.

SIGNIFICANCE STATEMENT

Reticulospinal neurons in the medullary reticular formation play a key role in movement. The transcriptional regulator Chx10 defines a population of glutamatergic neurons in this region, a proportion of which have been shown to be involved in stopping, steering, and modulating locomotion. While it has been shown that these neurons integrate descending inputs, we asked whether local processing also ultimately contributes to reticulospinal outputs. Here, we define Chx10-expressing medullary reticular formation interneurons and reticulospinal neurons, and demonstrate how the former modulate the output of the latter. The results shed light on the internal organization and microcircuit formation of reticular formation neurons.
Neuroepithelial organoid patterning is mediated by Wnt-driven Turing mechanism
Authors: Fattah Abdel Rahman Abdel , Grebenyuk Sergei , Salmon Idris , Ranga Adrian
Published: January 2021

Cell patterning in epithelia is critical for the establishment of tissue function during development. The organization of patterns in these tissues is mediated by the interpretation of signals operating across multiple length scales. How epithelial tissues coordinate changes in cell identity across these length scales to orchestrate cellular rearrangements and fate specification remains poorly understood. Here, we use human neural tube organoids as model systems to interrogate epithelial patterning principles that guide domain specification.In silicomodeling of the patterning process by cellular automata, validated byin vitroexperiments, reveal that the initial positions of floor plate cells, coupled with activator-inhibitor signaling interactions, deterministically dictate the patterning outcome according to a discretized Turing reaction-diffusion mechanism. This model predicts an enhancement of organoid patterning by modulating inhibitor levels. Receptor-ligand interaction analysis of scRNAseq data from multiple organoid domains reveals WNT-pathway ligands as the specific inhibitory agents, thereby allowing for the experimental validation of model predictions. These results demonstrate that neuroepithelia employ reaction-diffusion-based mechanisms during early embryonic human development to organize cellular identities and morphogen sources to achieve patterning. The wider implementation of suchin vitroorganoid models in combination within-silicoagent-based modeling coupled to receptor-ligand analysis of scRNAseq data opens avenues for a broader understanding of dynamic tissue patterning processes.
The Th1 cell regulatory circuitry is largely conserved between human and mouse
Authors: Henderson Stephen , Pullabhatla Venu , Hertweck Arnulf , de Rinaldis Emanuele , Herrero Javier , Lord Graham M. , Jenner Richard G.
Published: January 2021

Gene expression programmes controlled by lineage-determining transcription factors are often conserved between species. However, infectious diseases have exerted profound evolutionary pressure, and therefore the genes regulated by immune-specific transcription factors might be expected to exhibit greater divergence due to exposure to species-specific pathogens. T-bet (Tbx21) is the immune-specific lineage-defining transcription factor for T helper type I (Th1) immunity, which is fundamental for the immune response to intracellular pathogens but also underlies inflammatory diseases. We therefore compared T-bet genomic targets between mouse and human CD4+T cells and correlated T-bet binding patterns with species-specific gene expression. Remarkably, we show that the vast majority of T-bet regulated genes are conserved between mouse and human, either via preservation of a binding site or via an alternative binding site associated with transposon-linked insertion. We also identified genes that are specifically targeted by T-bet in humans or mice and which exhibited species-specific expression. These results provide a genome-wide cross-species comparison of T-bet target gene regulation that will enable more accurate translation of genetic targets and therapeutics from pre-clinical models of inflammatory disease into human clinical trials.
Characterization of a novel variant in the HR1 domain ofMFN2in a patient with ataxia, optic atrophy and sensorineural hearing loss
Authors: Sharma Govinda , Saubouny Rasha , Joel Matthew M , Martens Kristina , Martino Davide , de Koning A.P. Jason , Pfeffer Gerald , Shutt Timothy E.
Published: January 2021

Pathogenic variants inMFN2cause Charcot-Marie-Tooth disease (CMT) type 2A (CMT2A) and are the leading cause of the axonal subtypes of CMT. CMT2A is characterized by predominantly distal motor weakness and muscle atrophy, with highly variable severity and onset age. Notably, someMFN2variants can also lead to other phenotypes such as optic atrophy, hearing loss and lipodystrophy. Despite the clear link betweenMFN2and CMT2A, our mechanistic understanding of how dysfunction of the MFN2 protein causes human disease pathologies remains incomplete. This lack of understanding is due in part to the multiple cellular roles of MFN2. Though initially characterized for its role in mediating mitochondrial fusion, MFN2 also plays important roles in mediating interactions between mitochondria and other organelles, such as the endoplasmic reticulum and lipid droplets. Additionally, MFN2 is also important for mitochondrial transport, mitochondrial autophagy, and has even been implicated in lipid transfer. Though over 100 pathogenicMFN2variants have been described to date, only a few have been characterized functionally, and even then, often only for one or two functions. Here, we describe a novel homozygous MFN2 variant, D414V, in a patient presenting with cerebellar ataxia, deafness, blindness, and diffuse cerebral and cerebellar atrophy. Characterization of patient fibroblasts reveals phenotypes consistent with impaired MFN2 functions and expands the phenotypic presentation ofMFN2variants to include cerebellar ataxia.
The biogeographic history of eelpouts and related fishes: linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group
Authors: Hotaling Scott , Borowiec Marek L. , Lins Luana S.F. , Desvignes Thomas , Kelley Joanna L.
Published: January 2021

Modern genetic data sets present unprecedented opportunities to understand the evolutionary origins of taxonomic groups comprising hundreds to thousands of species. When the timing of key events are known, it is also possible to investigate biogeographic history in the context of major phenomena (e.g., continental drift). In this study, we investigated the biogeographic history of the suborder Zoarcoidei, a globally distributed fish group that includes species inhabiting both poles and multiple taxa that produce antifreeze proteins to survive chronic subfreezing temperatures. We first generated a multi-locus, time-calibrated phylogeny for the group. We then used biogeographic modeling to reconstruct ancestral ranges across the tree and quantify the type and frequency of biogeographic events (e.g., founder, dispersal). With these results, we considered how the cooling of the Southern and Arctic Oceans, which reached their present-day subfreezing temperatures 10-15 million years ago (Mya) and 2-3 Mya, respectively, may have shaped the evolutionary history of Zoarcoidei, with an emphasis on the most speciose and widely distributed family, eelpouts (family Zoarcidae). Our phylogenetic results clarified standing issues in the Zoarcoidei taxonomy and showed that the group began to diversify in the Oligocene ∼31-32 Mya, with the center of origin for all families in north temperate waters. Within-area speciation was the most common biogeographic event in the group’s history (80% of all events) followed by dispersal (20%). Finally, we found mixed evidence for polar ocean cooling underpinning Zoarcoidei diversification, with support limited to eelpout speciation in the Southern Ocean over the last 10 million years.
Increased cortical volume without increased neuron number in heterozygousChd8mutant mouse cortex
Authors: Canales Cesar P. , Frank Samuel , Bennett Jeffrey , Beauregard Paris , Lavenex Pierre , Amaral David G. , Nord Alex. S.
Published: January 2021

De novo mutations in the chromatin-remodeling factorCHD8(Chromodomain-Helicase DNA-binding protein 8) have emerged as a key genetic risk factor for Autism Spectrum Disorder (ASD) and, more generally, neurodevelopmental disorders. Individuals with heterozygous mutations inCHD8typically present hallmarks of ASD with comorbid cognitive disability and macrocephaly. Knockdown or haploinsufficiency ofChd8in animal models has recapitulated phenotypes observed in patients, including increased head circumference and brain size. Here, we aimed to determine whether increased neuron numbers or soma size drives increased cortical volume. We performed design-based stereological analyses of cortical structure in adult male and female heterozygousChd8mice and wild-type littermate controls.Chd8haploinsufficient male mice displayed a ~8-12% increase in cortical volume, no differences in cortical neuron number and comparable neuronal soma size. Our study reproduced previous reports of increased brain size associated withCHD8mutation in humans and mice and are consistent with reported sex-specific impacts ofChd8mutations in mice and increased burden ofCHD8mutations in human males with ASD. These findings suggest that the nature of the cortical enlargement due toChd8haploinsufficiency is complex and appears to be due to a factor other than an increased neuron number or soma size.

Lay Summary

We measured the size and neuron number in the neocortex in mice with heterozygousChd8mutation, a model relevant to Autism Spectrum Disorder. We found an increased cortical volume in male mutants, which was not accompanied by increased neuron number or soma size. Our results indicate that the enlarged brain inChd8mutant mice is complex, more evident here in males, and is due to factors other than increased neuron number.
Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens
Authors: Khan Taushif , Rahman Mahbuba , Ahmed Ikhlak , Ali Fatima Al , Jithesh Puthen , Marr Nico
Published: January 2021

Allelic diversity of HLA class II genes may help maintain humoral immunity against infectious diseases. We investigated the relative contribution of specific HLA class II alleles, haplotypes and genotypes on the variation of antibody responses to a variety of common pathogens in a cohort of 800 adults representing the general Arab population. We found that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles play a synergistic role in shaping the antibody repertoire. Interestingly, associations of HLA-DRB1 genotypes with specific antigens were identified. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.
Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale
Authors: Reiter Taylor , Montpetit Rachel , Byer Shelby , Frias Isadora , Leon Esmeralda , Viano Robert , Mcloughlin Michael , Halligan Thomas , Hernandez Desmon , Runnebaum Ron , Montpetit Ben
Published: January 2021

During a wine fermentation,Saccharomyces cerevisiaetransforms grape must through metabolic activities that generate ethanol and other compounds. Thousands of genes change expression over the course of a wine fermentation to allowS. cerevisiaeto adapt to and dominate the fermentation environment. Investigations into these gene expression patterns have previously revealed genes that underlie cellular adaptation to the grape must and wine environment involving metabolic specialization and ethanol tolerance. However, the vast majority of studies detailing gene expression patterns have occurred in controlled environments that do not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, we present an analysis of theS. cerevisiaeRC212 gene expression program across 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. We observe a core gene expression program across all fermentations irrespective of vintage similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomycesmicroorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight intoSaccharomyces cerevisiaebiology critical to fermentation outcomes at industry-relevant scales.

Importance

This study characterizedSaccharomyces cerevisiaeRC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using production-relevant conditions. The reported gene expression patterns of RC212 is generally similar to that observed in laboratory fermentation conditions, but also contains gene expression signatures related to yeast-environment interactions found in a production setting (e.g., presence of non-Saccharomycesmicroorganisms). Key genes and pathways highlighted by this work remain under-characterized, raising the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.
Identification ofNocardiaspecies using Autof MS 1000 and Bruker MALDI-TOF MS systems: A comparison
Authors: Ma Bing , Tian Yunqi , Han Yungang , Ban Lifang , Yang Junwen , Qi Xinkun , Guo Changcheng , Wang Baoya , Yan Wenjuan , Ma Qiong , Wang Shanmei , Yuan Youhua , Li Yi
Published: January 2021

Nocardiais an important cause of clinically invasive disease, but for most clinical laboratories, identification of these isolates to the species level is challenging. Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used for identification of most bacterial and fungal isolates. In this multicenter study, we evaluated the identification ofNocardiaisolates using Autof MS1000 and Bruker Biotyper. A total of 86 non-duplicateNocardiaisolates from 7 hospital laboratories were evaluated. Further, we carried out sequence analysis of 16S rRNA,gyrB, secA1, hsp65, andrpoBgenes as a reference method forNocardiaspecies identification. The 86 isolates were directly spotted on the target plate and plate protein extraction was performed. Data were analyzed by SPSS 19.0. In total, 72 (83.7%) strains (score ≥ 9.0) and 70 (81.4%) strains (score ≥ 2.0) were correctly identified by the Autof MS1000 and Bruker Biotyper systems, respectively, at the species level. There was no significant difference (P > 0.05) between the two systems using the same protein extraction method. In conclusion, the Autof MS 1000 and Bruker MALDI-TOF systems showed no difference in identification ofNocardia spp. to the species level and could meet the most important clinical requirement for species identification.
The duration of antibiotic treatment is associated with carriage of toxigenic and atoxigenic strains ofClostridioides difficilein dogs
Authors: Albuquerque C. , Pagnossin D. , Landsgaard K , Simpson J. , Brown D. , Irvine J.J. , Candlish D. , Ridyard. A.E. , Douce G , Millins C
Published: January 2021

Clostridioides difficileis a leading cause of human antibiotic-associated diarrhoeal disease globally. Zoonotic reservoirs of infection are increasingly suspected to play a role in the emergence of this disease in the community and dogs are considered as one potential source. Here we use a canine case-control study at a referral veterinary hospital in Scotland to assess: i) the risk factors associated with carriage ofC. difficileby dogs, ii) whether carriage ofC. difficileis associated with clinical disease in dogs and iii) the similarity of strains isolated from dogs with local human clinical surveillance. The overall prevalence ofC. difficilecarriage in dogs was 18.7% (95% CI 14.8-23.2%, n=61/327) of which 36% (n=22/61) were toxigenic strains. We found risk factors related to prior antibiotic treatment were significantly associated withC. difficilecarriage by dogs. However, the presence of toxigenic strains ofC. difficilein a canine faecal sample was not associated with diarrhoeal disease in dogs. Active toxin was infrequently detected in canine faecal samples carrying toxigenic strains (2/11 samples). Both dogs in which active toxin was detected had no clinical evidence of gastrointestinal disease. Among the ten toxigenic ribotypes ofC. difficiledetected in dogs in this study, six of these (012, 014, 020, 026, 078, 106) were ribotypes commonly associated with human clinical disease in Scotland, while atoxigenic isolates largely belonged to 010 and 039 ribotypes. WhilstC. difficiledoes not appear commonly associated with diarrhoeal disease in dogs, antibiotic treatment increases carriage of this bacteria including toxigenic strains commonly found in human clinical disease.
Modifying TIMER, a slow-folding DsRed derivative, for optimal use in quickly-dividing bacteria
Authors: Patel Pavan , O’Hara Brendan J. , Aunins Emily , Davis Kimberly M.
Published: January 2021

It is now well appreciated that members of pathogenic bacterial populations exhibit heterogeneity in growth rates and metabolic activity, and it is known this can impact the ability to eliminate all members of the bacterial population during antibiotic treatment. It remains unclear which pathways promote slowed bacterial growth within host tissues, primarily because it has been difficult to identify and isolate slow growing bacteria from host tissues for downstream analyses. To overcome this limitation, we have developed a novel variant of TIMER, a slow-folding fluorescent protein, to identify subsets of slowly dividing bacteria within host tissues. The original TIMER folds too slowly for fluorescence accumulation in quickly replicating bacterial species (Escherichia coli, Yersinia pseudotuberculosis), however this TIMER42variant accumulates signal in late stationary phase cultures ofE. coliandY. pseudotuberculosis. We show TIMER42signal also accumulates during exposure to sources of nitric oxide (NO), suggesting TIMER42signal detects growth-arrested bacterial cells. In a mouse model ofY. pseudotuberculosisdeep tissue infection, TIMER42signal is clearly detected, and primarily accumulates in bacteria expressing markers of stationary phase growth. There was not significant overlap between TIMER42signal and NO-exposed subpopulations of bacteria within host tissues, suggesting NO stress was transient, allowing bacteria to recover from this stress and resume replication. This novel TIMER42variant represents a new faster folding TIMER that will enable additional studies of slow-growing subpopulations of bacteria, specifically within bacterial species that quickly divide.

Author Summary

We have generated a variant of TIMER that can be used to mark slow-growing subsets ofYersinia pseudotuberculosis, which has a relatively short division time, similar toE. coli. We used a combination of site-directed and random mutagenesis to generate the TIMER42variant, which has red fluorescent signal accumulation in post-exponential or stationary phase cells. We found that nitric oxide (NO) stress is sufficient to promote TIMER42signal accumulation in culture, however within host tissues, TIMER42signal correlates with a stationary phase reporter (dps). These results suggest NO may cause an immediate arrest in bacterial cell division, but during growth in host tissues exposure to NO is transient, allowing bacteria to recover from this stress and resume cell division. Thus instead of indicating a response to host stressors, TIMER42signal accumulation within host tissues appears to identify slow-growing cells that are experiencing nutrient limitation.
Cell cycle exit and stem cell differentiation are coupled through regulation of mitochondrial activity in the Drosophila testis
Authors: de la Maza Diego Sainz , Hof-Michel Silvana , Phillimore Lee , Bökel Christian , Amoyel Marc
Published: January 2021

Stem cells maintain tissue homeostasis by proliferating to replace cells lost to damage or natural turnover. Whereas stem and progenitor cells proliferate, fully differentiated cells exit the cell cycle. How cell identity and cell cycle state are coordinated during this process is still poorly understood. The Drosophila testis niche supports germline stem cells and somatic cyst stem cells (CySCs), which are the only proliferating somatic cells in the testis. CySCs give rise to post-mitotic cyst cells and therefore provide a tractable model to ask how stem cell identity is linked to proliferation. We show that the G1/S cyclin, Cyclin E, is required for CySC self-renewal; however, its canonical transcriptional regulator, a complex of the E2f1 and Dp transcription factors is dispensable for self-renewal and cell cycle progression. Nevertheless, we demonstrate that E2f1/Dp activity must be silenced to allow CySCs to differentiate. We show that E2f1/Dp activity inhibits the expression of genes important for mitochondrial activity. Furthermore, promoting mitochondrial activity or biogenesis is sufficient to rescue the differentiation of CySCs with ectopic E2f1/Dp activity but not their exit from the cell cycle. Our findings together indicate that E2f1/Dp coordinates cell cycle progression with stem cell identity by regulating the metabolic state of CySCs.
Why do some primate mothers carry their infant’s corpse? A cross-species comparative study
Authors: Fernández-Fueyo Elisa , Sugiyama Yukimaru , Matsui Takeshi , Carter Alecia J.
Published: January 2021

Non-human primates respond to the death of a conspecific in diverse ways, some which may present phylogenetic continuity with human thanatological behaviours. Of these responses, infant corpse carrying by mothers (ICC) is the most-frequently reported. Despite its prevalence, quantitative analyses of this behaviour are scarce and inconclusive. We compiled a database of 409 published cases across 50 different primate species of mothers’ responses to their infants’ deaths to test hypotheses proposed to explain between- and within-species variation in corpse carrying. Using Bayesian phylogenetic regressions, we preliminarily identified three factors as possible predictors of ICC occurrence. However, using an information-theoretic approach, no combination of these predictors performed better than the null model, offering no support for any of the hypotheses we tested. In contrast, for those cases where infants’ corpses were carried, infant age affected ICC duration, with longer ICC observed for younger infants. This result may provide support for hypotheses that suggest that ICC is a by-product of a strong mother-infant bond. The results are discussed in the context of the evolution of emotion and their implications for evolutionary thanatology are considered.
Host preference and invasiveness of commensals in theLotusandArabidopsisroot microbiota
Authors: Wippel Kathrin , Tao Ke , Niu Yulong , Zgadzaj Rafal , Guan Rui , Dahms Eik , Zhang Pengfan , Jensen Dorthe B. , Logemann Elke , Radutoiu Simona , Schulze-Lefert Paul , Garrido-Oter Ruben
Published: January 2021

Healthy plants are colonized by microorganisms from the surrounding environment, which form stable communities and provide beneficial services to the host. Culture-independent profiling of the bacterial root microbiota shows that different plant species are colonized by distinct bacterial communities, even if they share the same habitat. It is, however, not known to what extent the host actively selects these communities and whether commensal bacteria are adapted to a specific plant species. Here, we report a sequence-indexed culture collection from roots and nodules of the model legumeLotus japonicusthat contains representatives from the majority of species found in culture-independent profiles. Using taxonomically paired synthetic communities fromL. japonicusand the cruciferArabidopsis thalianain a multi-species gnotobiotic system, we detect clear signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation of either host reveals strong priority effects during the assembly of the root microbiota, where established communities are resilient to invasion by late-comers. However, we found that host preference by commensal bacteria confers a competitive advantage in their native host. We reveal that host preference is prevalent in commensal bacteria from diverse taxonomic groups and that this trait is directly linked to their invasiveness into standing root-associated communities.
Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea
Authors: Castelle Cindy J. , Méheust Raphaël , Jaffe Alexander L. , Seitz Kiley , Gong Xianzhe , Baker Brett J. , Banfield Jillian F.
Published: January 2021

DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 569 newly reconstructed genomes. Protein family content clearly separates DPANN from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.
A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats
Authors: Winans Shelby , Goff Stephen P.
Published: January 2021

Retroviruses utilize the viral integrase (IN) protein to integrate a DNA copy of their genome into the host chromosomal DNA. HIV-1 integration sites are highly biased towards actively transcribed genes, likely mediated by binding of the IN protein to specific host factors, particularly LEDGF, located at these gene regions. We here report a dramatic redirection of integration site distribution induced by a single point mutation in HIV-1 IN. Viruses carrying the K258R IN mutation exhibit more than a 25-fold increase in integrations into centromeric alpha satellite repeat sequences, as assessed by both deep sequencing and qPCR assays. Immunoprecipitation studies identified host factors that uniquely bind to the mutant IN protein and thus may account for the novel bias for integration into centromeres. Centromeric integration events are known to be enriched in the latent reservoir of infected memory T cells, as well as in patients who control viral replication without intervention (so-called elite controllers). The K258R point mutation in HIV-1 IN reported in this study has also been found in databases of latent proviruses found in patients. The altered integration site preference induced by this mutation has uncovered a hidden feature of the establishment of viral latency and control of viral replication.
Expression of a fungal lectin in Arabidopsis enhances plant growth and resistance towards microbial pathogens and plant-parasitic nematode
Authors: Moradi Aboubakr , El-Shetehy Mohamed , Gamir Jordi , Austerlitz Tina , Dahlin Paul , Wieczorek Krzysztof , Künzler Markus , Mauch Felix
Published: January 2021

Coprinopsis cinerealectin 2 (CCL2) is a fucoside-binding lectin from the basidiomyceteC. cinereathat is toxic to the bacterivorous nematodeCaenorhabditis elegansas well as animal-parasitic and fungivorous nematodes. We expressed CCL2 in Arabidopsis to assess its protective potential towards plant-parasitic nematodes. Our results demonstrate that expression of CCL2 enhances host resistance against the cyst nematodeHeterodera schachtii. Surprisingly, CCL2-expressing plants were also more resistant to fungal pathogens includingBotrytis cinerea, and the phytopathogenic bacteriumPseudomonas syringae. In addition, CCL2 expression positively affected plant growth indicating that CCL2 has the potential to improve two important agricultural parameters namely biomass production and general disease resistance. The mechanism of the CCL2-mediated enhancement of plant disease resistance depended on fucoside-binding by CCL2 as transgenic plants expressing a mutant version of CCL2 (Y92A), compromised in fucoside-binding, exhibited wild type disease susceptibility. The protective effect of CCL2 did not seem to be direct as the lectin showed no growth-inhibition towardsB. cinereainin vitroassays. We detected, however, a significantly enhanced transcriptional induction of plant defense genes in CCL2- but not CCL2-Y92A-expressing lines in response to infection withB. cinereacompared to wild type plants. This study demonstrates a potential of fungal defense lectins in plant protection beyond their use as toxins.
Hypoxia-inducible factor 1α (HIF1α) Suppresses Virus Replication in Human Cytomegalovirus Infection by Limiting Kynurenine Synthesis
Authors: Wise Lisa M. , Xi Yuecheng , Purdy John G.
Published: January 2021

Human cytomegalovirus (HCMV) replication depends on the activities of several host regulators of metabolism. Hypoxia-inducible factor 1α (HIF1α) was previously proposed to support virus replication through its metabolic regulatory function. HIF1α protein levels rise in response to HCMV infection in non-hypoxic conditions, but its effect on HCMV replication was not investigated. We addressed the role of HIF1α in HCMV replication by generating primary human cells with HIF1α knocked out using CRISPR/Cas9. When HIF1α was absent, we found that HCMV replication was enhanced, showing that HIF1α suppresses viral replication. We used untargeted metabolomics to determine if HIF1α regulates metabolite concentrations in HCMV infected cells. We discovered that in HCMV-infected cells, HIF1α suppresses intracellular and extracellular concentrations of kynurenine. HIF1α also suppressed the expression of the indoleamine 2,3-dioxygenase 1 (IDO1) rate-limiting enzyme in kynurenine synthesis. In addition to its role in tryptophan metabolism, kynurenine acts as a signaling messenger by activating aryl hydrocarbon receptor (AhR). Inhibiting AhR reduces HCMV replication while activating AhR with an exogenous ligand increases HCMV replication. Moreover, we found that feeding kynurenine to cells promotes HCMV replication. Overall, our findings indicate that HIF1α reduces HCMV replication by regulating metabolism and metabolite signaling.

Importance

Viruses, like human cytomegalovirus (HCMV), reprogram cellular metabolism using host metabolic regulators to support virus replication. Alternatively, in response to infection, the host can use metabolism to limit virus replication. Here, our findings show that the host uses hypoxia-inducible factor 1α (HIF1α) as a metabolic regulator to reduce HCMV replication. Further, we found that HIF1α suppresses kynurenine synthesis, a metabolite that can promote HCMV replication by signaling through the aryl hydrocarbon receptor (AhR). In infected cells, the rate-limiting enzyme in kynurenine synthesis, indoleamine 2,3-dioxygenase 1 (IDO1), is suppressed by a HIF1α-dependent mechanism. Our findings describe a functional connection between HIF1α, IDO1, and AhR that allows HIF1α to limit HCMV replication through metabolic regulation, advancing our understanding of virus-host interactions.
Convergent extension requires adhesion-dependent biomechanical integration of cell crawling and junction contraction
Authors: Weng Shinuo , Huebner Robert J. , Wallingford John B.
Published: January 2021

Convergent extension is an evolutionarily conserved collective cell movement that elongates the body axis of almost all animals and is required for the morphogenesis of several organ systems. Decades of study have revealed two distinct mechanisms of cell movement during CE, one based on cell crawling and the other on junction contraction. How these two behaviors collaborate during CE is not understood. Here, using quantitative live cell imaging we show that these two modes act both independently and in concert during CE, but that cell movement is more effective when the two modes are integrated via mechano-reciprocity. Based on these findings, we developed a novel computational model that for the first time treats crawling and contraction independently. This model not only confirmed the biomechanical efficacy of integrating the two modes, but also revealed for the first time how the two modes -and their integration- are influenced by cell adhesion. Finally, we use these new insights to further understand the complex CE phenotype resulting from loss of the C-cadherin interacting catenin Arvcf. These data are significant for providing new biomechanical and cell biological insights into a fundamental morphogenetic process that is implicated in human neural tube defects and skeletal dysplasias.