bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helicobacter pyloriFlgV forms a flagellar motor ring structure required for optimal motility
Authors: Botting Jack M. , Tachiyama Shoichi , Gibson Katherine H. , Liu Jun , Starai Vincent J. , Hoover Timothy R. 
Published: October 2022

ABSTRACTThe bacteriumHelicobacter pylorihas a large flagellar motor that generates significantly higher torque than the archetypicalEscherichia colimotor. To understand howH. pylorinavigates the viscous environment of the stomach, it is essential to establish how specific motor components contribute to efficient motility. We show here that the protein FlgV, required for motility inCampylobacter jejuni, forms a novel ring associated with the MS and C rings inH. pylori. Deletion offlgVfromH. pyloriB128 or a highly motile variant ofH. pyloriG27 (G27M) resulted in reduced motility in soft agar medium. Based on comparative analyses ofin-situflagellar motor structures ofH. pyloriwild-type and ΔflgVmutants, the reduced motility of the ΔflgVmutants and the location of the FlgV ring suggest it stabilizes interactions between the MS and C rings and/or plays a role in switching the direction of flagellar rotation. Overall, these results identify a novel motor accessory likely adapted to promote flagellar function for bacterial colonization of high-load environments such as the gastric mucosa.
Conventional dendritic cells 2, the targeted antigen-presenting-cell, induces enhanced type 1 immune responses in mice immunized with CVC1302 in oil formulation
Authors: Du Luping , Qiao Xuwen , Zhang Yuanpeng , Hou Liting , Yu Xiaoming , Cheng Haiwei , Chen Jin , Zheng Qisheng , Hou Jibo , Tong Guangzhi 
Published: October 2022

AbstractMultifunctional CD4+T helper 1 (Th1) cells, producing IFN-γ, TNF-α and IL-2, define a correlate of vaccine-mediated protection against intracellular infection. In our previous study, we found that CVC1302 in oil formulation promoted the differentiation of IFN-γ+/TNF-α+/IL-2+Th1 cells. In order to extend the application of CVC1302 in oil formulation, this study aimed to elucidate the mechanism of action in improving the Th1 immune response. Considering the signals required for the differentiation of CD4+T cells to Th1 cells, we detected the distribution of innate immune cells and the model antigen OVA-FITC in lymph node (LN), as well as the quantity of cytokines produced by the innate immune cells. The results of these experiments show that, cDC2 and OVA-FITC localized to inter-follicular region (IFR) of the draining lymph nodes, inflammatory monocytes localized to both IFR and T cell zone, which mainly infiltrate from the blood. In this inflammatory niche within LN, CD4+T cells were attracted into IFR by CXCL10, secreting by inflammatory monocytes, then activated by IL-12-secreting cDC2. Above all, CVC1302 in oil formulation, on the one hand, targeted antigen and inflammatory monocyte into the LN IFN in order to attract CD4+T cells, on the other hand, targeted cDC2 to produce IL-12 in order to promote optimal Th1 differentiation. The new finding will provide a blueprint for application of immunopotentiators in optimal formulations.ImportanceAlong with the development of veterinary immunology, immunopotentiator and delivery system were not simply mixed with antigen, more and more attentions paid on the optimal compatibility in order to induce multifunctional immune responses. As reported, LPS formulated in IFA targeted antigens to the IFR of the LN, and recruited Mo into the IFR, then attracted antigen-specific CD4+T cells, which differentiated into Th1 cells under the IL-12 produced by DC-SIGN+DC(1). Herein, we further found that CVC1302 formulated with Marcol 52 induced enhanced Th1 immunity. Combined with our previous finding that CVC1302 in oil formulation induced improved humoral immunity, we concluded that CVC1302 in oil formulation provided multifunctional immunity, not only higher antibody titers to prevent pathogen infection, but also cellular immunity cytokine to prevent viral shedding.
Within-flock differences in exploratory tendency and flock performance in a highly gregarious bird
Authors: Carere Claudio , Audebrand Celine , Desigaux Florian , Pinxten Rianne , Eens Marcel , Rödel Heiko G. , d’Ettorre Patrizia 
Published: October 2022

ABSTRACTHow individual differences translate into group outcomes is a timely and debated issue. Recent studies, especially in social arthropods and fish, focus on diversity of personality traits. These studies suggest that the phenotypic group assortment by personality type of an animal group, including the presence of “keystone” individuals, leads to group-level personality differences and can strongly impact both group and individual outcomes. However, little attention has been given to the variation of a given trait within a group. Theory predicts that phenotypic homogeneity rather than heterogeneity yields the optimal group performance, especially in an anti-predatory context, but the experimental support includes mainly morphological traits, e.g. body size or colouration. Here, we focus on personality and group level differences in a highly gregarious bird, the European starling (Sturnus vulgaris). We investigated how different degrees of within-flock variation in exploration affect flock outcomes in exploratory behaviour and in escape response after a frightening stimulus. First, we established consistent individual differences in exploration. Then, flocks of 4 birds were formed to obtain gradual differences in mean and in variation of exploration scores among flocks. Flocks underwent an exploration test and a perturbation test. More exploratory individuals entered the test arena earlier, tended to start flying more rapidly and also stopped flying sooner upon frightening. Flocks with a more homogeneous distribution with respect to this personality trait were significantly faster to enter the test room, but no effect on the escape response emerged. The mean exploration tendency of the flock or the maximum exploration tendency of purported ‘key’ individuals within groups did not play a notable role in explaining such differences in group performance. Our results indicate that it is not the individual that predicts/drives the flock outcome, but rather a group feature, namely phenotypic variation within the group.
OVGP1 is an oviductal fluid factor essential particularly for early embryonic development in golden hamsters
Authors: Yamatoya Kenji , Kurosawa Masaru , Hirose Michiko , Miura Yoshiki , Taka Hikari , Nakano Tomoyuki , Hasegawa Akiko , Kagami Kyosuke , Yoshitake Hiroshi , Goto Kaoru , Ueno Takashi , Fujiwara Hiroshi , Shinkai Yoichi , Kan Frederick W. K. , Ogura Atsuo , Araki Yoshihiko 
Published: October 2022

AbstractThe mammalian oviductal lumen is a specialized chamber that provides an environment that strictly regulates fertilization an early embryogenesis, the regulatory mechanisms to gametes/zygote are still largely unknown. In this report, we studied the oviductal regulation of early embryonic development usingOvgp1(a gene encoding an oviductal humoral factor, OVGP1)-knockout (KO) hamsters. The experimental results revealed the following: 1) FemaleOvgp1-KO hamsters fail to produce any litters at all; 2) In the oviducts from KO animal, fertilized eggs are sometimes identified, but their morphology shows abnormal features; 3) The number of implantations in the KO females is evidently low; 4) Even if implantations occur, the embryos develop abnormally and eventually become embryonic lethal; and 5)Ovgp1-KO females transferred to wild-type females produce KO egg-derived litters, but the reverse experiment does not. These results suggest that OVGP1-mediated physiological events are crucial for early embryonic developmentin vivo. This animal model shows that the fate of the fertilized egg is not only genetically determined, but that the surrounding oviductal microenvironment plays a pivotal role in normal embryonic development.Summary statementDeficiency an oviductal humoral factor (OVGP1) caused female infertility in the golden hamsters. The presence or absence of OVGP1 has significant physiological effects on early embryonic developmentin vivo.
Territorial aggression in male bower-building cichlidsNyassachromiscf.microcephalusis disrupted by exposure to environmental concentrations of fluoxetine
Authors: Lee Paige , Smith Alan , King Hannah , Gilbert James , Morrell Lesley , Joyce Domino 
Published: October 2022

AbstractSelective serotonin reuptake inhibitors (SSRIs) are commonly prescribed drugs for treating human depression, but the role of serotonin—often called the happy chemical—is complex, associated with the regulation of appetite, anxiety, aggression, and more. With such psychoactive pharmaceuticals being increasingly detected in aquatic environments and their effects on non-target species an uncertainty, this study seeks to investigate how inhibiting the serotonin pathway with the SSRI fluoxetine affects territorial aggression, using the cichlid fishNyassachromiscf.microcephalusas a model. Males of this sand-dwelling Lake Malawi species build bowers to attract females within a lekking system, where male-male competition is intense. Being aggressive in defending against intruders would serve to maximise mating opportunities and reproductive success for the territory holding male. However, after a one-week exposure to fluoxetine at environmentally relevant concentrations, a decline in aggression was observed in the male cichlids. This implies the serotonergic system plays an important role in modulating aggression and therefore sexual selection in cichlid fishes, and that environmental pollution has the potential to disrupt these behaviours.
Natural hybridisation reduces vulnerability to climate change
Authors: Brauer Chris J. , Sandoval-Castillo Jonathan , Gates Katie , Hammer Michael , Unmack Peter J. , Bernatchez Louis , Beheregaray Luciano B. 
Published: October 2022

AbstractUnderstanding how species can respond to climate change is a major global challenge. Species unable to track their niche via range shifts are largely reliant on genetic variation to adapt and persist. Genomic vulnerability predictions are used to identify populations that lack the necessary variation, particularly at climate relevant genes. However, hybridization as a source of novel adaptive variation is typically ignored in genomic vulnerability studies. We estimated environmental niche models and genomic vulnerability for closely related species of rainbowfish (Melanotaeniaspp.) across an elevational gradient in the Australian wet tropics. Hybrid populations between a widespread generalist and narrow range endemics exhibited reduced vulnerability to projected climates compared to pure narrow endemics. Overlaps between introgressed and adaptive genomic regions were consistent with a signal of adaptive introgression. Our findings highlight the often-underappreciated conservation value of hybrid populations and indicate that adaptive introgression may contribute to evolutionary rescue of species with narrow environmental ranges.
Contribution of genetics and lifestyle to the risk of major cardiovascular and thromboembolic complications following COVID-19
Authors: Xie Junqing , Feng Yuliang , Newby Danielle , Zheng Bang , Feng Qi , Prats-Uribe Albert , Li Chunxiao , Wareham Nicholas J , Paredes R , Prieto-Alhambra Daniel 
Published: October 2022

AbstractClinical determinants for cardiovascular and thromboembolic (CVE) complications of COVID-19 are well-understood, but the roles of genetics and lifestyle remain unknown. We performed a prospective cohort study using UK Biobank, including 25,335 participants with confirmed SARS-CoV-2 infection between March 1, 2020, and September 3, 2021. Outcomes were hospital-diagnosed atrial fibrillation (AF), coronary artery disease (CAD), ischemic stroke (ISS), and venous thromboembolism (VTE) within 90 days post-infection. Heritable risk was represented by validated polygenic risk scores (PRSs). Lifestyle was defined by a composite of nine variables. We estimated adjusted hazard ratios (aHR) and confidence intervals (CI) using Cox proportional hazards models. In the COVID-19 acute phase, PRSs linearly predicted a higher risk of AF (aHR 1.52 per standard deviation increase, 95% CI 1.39 to 1.67), CAD (1.59, 1.40 to 1.81), and VTE (1.30, 1.11 to 1.53), but not ISS (0.92, 0.64 to 1.33). A healthy lifestyle was associated with a substantially lower risk of post-COVID-19 AF (0.70, 0.53 to 0.92), CAD (0.64, 0.44 to 0.91), and ISS (0.28, 0.12 to0.64), but not VTE (0.82, 0.48 to 1.39), compared with an unhealthy lifestyle. No evidence for interactions between genetics and lifestyle was found. Our results demonstrated that population genetics and lifestyle considerably influence cardiovascular complications following COVID-19, with implications for future personalised thromboprophylaxis and healthy lifestyle campaigns to offset the elevated cardiovascular disease burden imposed by the ongoing pandemic.
3D morphometric analysis of mouse skulls using microcomputed tomography and computer vision
Authors: Gulner Beatrice R. , Navabi Zahra S. , Kodandaramaiah Suhasa B. 
Published: October 2022

ABSTRACTMorphometric studies have provided crucial insights into the skull anatomy of commonly used wildtype (WT) laboratory mice strains such as the C57BL/6. With the increasing use of transgenic (TG) animals in neuroscience research, it is important to determine whether the results from morphometric studies performed on WT strains can be extended to TG strains derived from these WT strains. We report a new computer vision-based analysis pipeline for surveying mouse skull morphology using microcomputed tomography (μCT) scans. We applied this pipeline to study and compare eight cohorts of adult mice from two strains, including both male and female mice at two age points. We found that the overall skull morphology was generally conserved between cohorts, with only 13% of landmark distance differences reaching statistical significance. In addition, we surveyed the dorsal skull bone thickness differences between cohorts. We observed significantly thicker dorsal, parietal, and/or interparietal bones in WT, male, or older mice for 53% of thickness comparisons. This knowledge of dorsal skull bone thickness has potential implications for surgical planning through skull imaging and has applications in automating cranial microsurgeries on mice.
The protist ubiquitin ligase effector PbE3-2 targets RD21A to impede plant immunity
Authors: Li Chao , Luo Shaofeng , Feng Lu , Wang Qianqian , Cheng Jiasen , Xie Jiatao , Lin Yang , Fu Yanping , Jiang Daohong , Chen Tao 
Published: October 2022

AbstractClubroot caused by the soil-borne protist pathogenPlasmodiophora brassicaeis one of the most devastating diseases of Brassica oil and vegetable crops worldwide. Understanding the pathogen infection strategy is crucial for the development of disease control. However, the molecular mechanism by which this pathogen promotes infection remains largely unknown. Here, we identified aP. brassicae-secreted effector PbE3-2 that impedes plant immunity by ubiquitinating the immune regulator RD21A for degradation. Overexpression ofPbE3-2inArabidopsis thalianaresulted in higher susceptibility toP. brassicaeand decreases in chitin-triggered reactive oxygen species burst and expression of marker genes in salicylic acid signaling. PbE3-2 interacted with and ubiquitinated RD21Ain vitroandin vivo. Mutant plants deficient inRD21Aexhibited similar susceptibility and compromsied immune responses as inPbE3-2overexpression plants. These results suggest thatP. brassicaepromotes clubroot disease through RD21A degradation mediated by the effector PbE3-2. As PbE3-2 is widely conserved across differentP. brassicaepathotypes, the degradation of RD21A by PbE3-2 might be a prevalent infection strategy in this pathogen.
Interactome analysis identifies MSMEI_3879 as a substrate ofMycolicibacterium smegmatisClpC1
Authors: Ogbonna Emmanuel , Bheemreddy Priyanka , Schmitz Karl R. 
Published: October 2022

ABSTRACTThe prevalence of drug resistantMycobacterium tuberculosisinfections has prompted extensive efforts to exploit new mycobacterial drug targets. ClpC1, the unfoldase component of the essential ClpC1P1P2 protease, has emerged as one particularly promising antibacterial target. However, efforts to identify and characterize ClpC1-targeting compounds are constrained by our limited knowledge of Clp protease function and regulation. To expand our understanding of ClpC1 physiology, we employed a co-immunoprecipitation and mass spectrometry workflow to identify proteins that interact with ClpC1 inMycolicibacterium smegmatis, a relative ofM. tuberculosis.We identify a diverse panel of interaction partners, many of which make co-immunoprecipitate with both the regulatory N-terminal domain and the ATPase core of ClpC1. Notably, our interactome analysis identifies MSMEI_3879, a truncated gene product unique toM. smegmatis, as a novel proteolytic substrate. Degradation of MSMEI_3879 by ClpC1P1P2in vitrorequires an exposed N-terminal sequence, reinforcing the idea that ClpC1 selectively recognizes disordered motifs. Fluorescent substrates incorporating MSMEI_3879 may be useful in screening for novel ClpC1-targeting antibiotics, to help address the challenge ofM. tuberculosisdrug resistance.
NanoBlot: A Simple Tool for Visualization of RNA Isoform Usage From Third Generation RNA-sequencing Data
Authors: DeMario Samuel , Xu Kevin , He Kevin , Chanfreau Guillaume 
Published: October 2022

AbstractRT-PCR and Northern blots have long been used to study RNA isoforms usage for single genes. Recently, advancements in long read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues we have developed NanoBlot, a simple, open-source, command line tool, which generates Northern blot and RT-PCR-like images from third generation sequencing data. NanoBlot accepts processed bam files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlots include: designing probes to visualize isoforms which would be impossible with traditional RT-PCR or Northern blots, excluding reads from the Nanoblots based on the presence or absence of a specified region and, multiplexing plots with multiple colors. We present examples of NanoBlots compared to actual northern blot data. In addition to traditional gel-like images, NanoBlot also outputs other visualizations such as violin plots. The use of Nanoblot should provide a simple answer to the challenge of visualization of long-read RNA sequencing data.
Sensitivity to direction and velocity of fast frequency chirps in the inferior colliculus of awake rabbit
Authors: Mitchell Paul W. , Henry Kenneth S. , Carney Laurel H. 
Published: October 2022

AbstractNeurons in the mammalian inferior colliculus (IC) are sensitive to the velocity (speed and direction) of fast frequency chirps contained in Schroeder-phase harmonic complexes (SCHR). However, IC neurons are also sensitive to stimulus periodicity, a prominent feature of SCHR stimuli. Here, to disentangle velocity sensitivity from periodicity tuning, we introduced a novel stimulus consisting of aperiodic random chirps. Extracellular, single-unit recordings were made in the IC of Dutch-belted rabbits in response to both SCHR and aperiodic chirps. Rate-velocity functions were constructed from aperiodic-chirp responses and compared to SCHR rate profiles, revealing interactions between stimulus periodicity and neural velocity sensitivity. A generalized linear model analysis demonstrated that periodicity tuning influences SCHR response rates more strongly than velocity sensitivity. Principal component analysis of rate-velocity functions revealed that neurons were more often sensitive to the direction of lower-velocity chirps and were less often sensitive to the direction of higher-velocity chirps. Overall, these results demonstrate that sensitivity to chirp velocity is common in the IC. Harmonic sounds with complex phase spectra, such as speech and music, contain chirps, and velocity sensitivity would shape IC responses to these sounds.HighlightsIC neurons had diverse sensitivity to chirp velocity (speed and direction) of periodic and aperiodic-chirp stimuli.Both velocity and periodicity sensitivity were necessary to predict neural responses to Schroeder-phase harmonic complexes.Neurons were more commonly sensitive to the direction of chirps at lower-speeds (e.g., < 2 kHz/ms) than higher-speeds (e.g., > 2 kHz/ms) in the tested range.The chirp speeds for which IC neurons were most sensitive are present in common harmonic sounds with realistic phase spectra, such as speech and music.
Performance evaluation of new fluorescent-based lateral flow immunoassay for quantification of HbA1c in diabetic patients
Authors: Younes Nadin , Al Ghwairi Mahmoud M. , Majdalawieh Amin F. , Al-Dweik Nader , Nasrallah Gheyath K. 
Published: October 2022

AbstractBackgroundRapid and constant HbA1c level monitoring is essential in slowing the progression of Type 2 diabetes. This need becomes challenging in low resources countries where the social burden of the disease is overwhelming. Recently, fluorescent-based lateral flow immunoassays (LFIAs) gained wide attention for small or non-laboratory settings and population surveillance.AimThis study aim to evaluate the performance of novel fluorescence-based LFIA Finecare™ HbA1c Rapid Quantitative Test for quantitative measurement of HbA1c along with its reader (Model No. FS-113).MethodsWe conducted a retrospective study using 147 samples (fingerstick and venepuncture whole blood samples) analysed by Finecare™ HbA1c Rapid Quantitative Test. For validating Finecare™ measurements, results were compared with results of the reference assay: Roche Cobas Pro c 503.ResultsFinecare™ showed 92.7% sensitivity and 94.7% specificity compared to the Roche Cobas Pro c 503 using fingerstick whole blood samples. On the other hand, Finecare™ showed 98.7% sensitivity and 100% specificity compared to the Roche Cobas Pro c 503 using venepuncture blood samples. Cohen’s Kappa statistic denoted excellent agreement with Roche Cobas Pro c 503, with values being 0.84 (95% CI: 0.72-0.97) and 0.97 (95% CI: 0.92-1.00) using fingerstick whole blood samples and venous blood, respectively. In addition, a strong correlation was observed between Finecare™/Roche Cobas Pro c 503 (r>0.9,p<0.0001) with fingerstick and venous blood samples. Most importantly, Finecare™ showed a significant difference between the normal, pre-diabetic, and diabetic samples (p<0.001).ConclusionFinecare™ is a reliable assay and can be easily implemented for long-term monitoring of HbA1c in diabetic patients, particularly in none or small laboratory settings.