bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia colismall heat shock protein IbpA is an aggregation-sensor that self-regulates its own expression at a translational level
Authors: Miwa Tsukumi , Chadani Yuhei , Taguchi Hideki 
Published: April 2020

AbstractAggregation is an inherent characteristic of proteins. Risk management strategies to reduce aggregation are critical for cells to survive upon stresses that induce aggregation. Cells cope with protein aggregation by utilizing a variety of chaperones, as exemplified by heat-shock proteins (Hsps). The heat stress-induced expression of IbpA and IbpB, small Hsps inEscherichia coli, is regulated by the σ32heat-shock transcriptional regulator and the temperature-dependent translational regulation via mRNA heat fluctuation. We found that, even without heat stress, either the expression of aggregation-prone proteins or theibpAgene deletion profoundly increases the expression of IbpA. Combined with other evidence, we propose novel mechanisms for the regulation of the small Hsp expression. Oligomeric IbpA self-represses theibpA/ibpBexpression at the translational level, but the self-repression is relieved by the sequestration of IbpA into protein aggregates. Thus, the function of IbpA as a chaperone to form co-aggregates is harnessed as an aggregation sensor to tightly regulate the IbpA level. Since the excessive preemptive supply of IbpA in advance of stress is harmful, the prodigious and rapid expression of IbpA/IbpB on demand is necessary for IbpA to function as a first line of defense against acute protein aggregation.Author summaryAll organisms have protein quality control systems against stresses disturbing cellular protein homeostasis (proteostasis). The systems have multiple stages: folding, degradation, and sequestration. Sequestration of denatured proteins is the first step to support other maintenance strategies. Small heat shock proteins (sHsps), which are well-conserved chaperones, are representative “sequestrases” that co-aggregate with denatured proteins. We found that IbpA, anEscherichia colisHsp, is a direct mediator for negative feedback regulation at the translational level. Recruitment of IbpA into the protein aggregates relieves theibpAexpression suppression. This novel mechanism of IbpA as an aggregation-sensor tightly regulates the IbpA level, enabling the sHsp to function as a sequestrase upon aggregation stress.
Genotypic and phenotypic characterization ofStreptococcus mutansisolated from dental caries
Authors: Hossain Md. Shahadat , Alam Sadab , Nibir Yead Morshed , Tusty Tahrima Arman , Bulbul Sayyeed Mahmud , Islam Shahidul , Hossain Mohammad Shahnoor 
Published: April 2020

AbstractStreptococcus mutans, considered as principal causative agent of dental caries, maintains a biofilm lifestyle in the dental plaque. The oral cavity harbors numerousS. mutansstrains, which displayed remarkable genotypic and phenotypic diversity. This study evaluated the genotypic and phenotypic diversity of 209S. mutansstrains isolated from 336 patients with dental caries and compared with the universal reference strain UA159. Our study has revealed a high degree of genotypic and phenotypic variability among the clinical strains. We observed significant differences in colony morphology, generation time, biofilm formation, bacteriocin and acid production while growing in culture medium. All the clinical isolates were able to lower pH while growing in THY broth. In consistent with phenotypic variations, we also observed tremendous level of genotypic variation by AP-PCR and gene specific PCR. AP-PCR analysis suggested that most of the patients with dental caries have distinct type ofS. mutansstrains. Genes related to various two component systems were highly conserved among the strains, however, bacteriocin encoding genes such asnlmAB, nlmCwere absent in half of the clinical isolates. In sum, our study highlights the genotypic and phenotypic diversity ofS. mutansclinical isolates and indicates the presence of diverse mechanism to initiate and establish the biofilm lifestyle which leads to tooth decay.
Efficacy of transoral laser surgery versus linear accelerator radiotherapy for the treatment of T1 glottic carcinoma: a meta-analysis of oncologic outcomes
Authors: Zhu Jiawei , Shen Jing , Zheng Ziye , Lian Xin , Miao Zheng , Hu Ke , Zhang Fuquan 
Published: April 2020

AbstractObjectiveA meta-analysis was conducted to compare oncologic outcomes for patients of T1 glottic carcinoma who were treated with transoral laser surgery (TLS) or linear accelerator radiotherapy (linac RT).MethodsAll related studies published up to September 2019 were acquired by searching Pubmed, EMBASE, and Cochrane, with the index words: glottic, vocal, laryngeal, radiation, radiotherapy, irradiation, laser, surgery, cordectomy, carcinoma and cancer. Relative studies which compared oncologic outcomes between linac RT and TLS were included. Sensitivity analysis were performed to evaluate heterogeneity.ResultsA total of twelve eligible studies were included for the analysis, which contained three prospective studies and nine retrospective studies. Patients who underwent TLS had increased overall survival (OR = 1.40, 95% CI=1.02-1.94,P=0.04) and laryngeal preservation (OR = 5.37, 95% CI = 3.05-9.44,P< 0.00001) versus who underwent linac RT. No statistical difference was observed between TLS group and linac RT group in terms of local control (OR=0.88, 95% CI = 0.62-1.24,P= 0.47), disease-specific survival (OR = 0.61, 95% CI = 0.26-1.43,P= 0.26), and disease-free survival (OR = 1.63, 95% CI = 0.70-3.81,P= 0.14).ConclusionsThe results of this meta-analysis indicate that there were clinical benefits for patients with glottic carcinoma after TLS compared with linac RT with respect to overall survival and laryngeal preservation. However, more multi-center randomized controlled trials would be urgently needed to prove these differences.
Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish genepsen2
Authors: Jiang Haowei , Pederson Stephen Martin , Newman Morgan , Dong Yang , Lardelli Michael 
Published: April 2020

AbstractPRESENILIN 2(PSEN2) is one of the genes mutated in early onset familial Alzheimer’s disease (EOfAD).PSEN2shares significant amino acid sequence identity with another EOfAD-related genePRESENILIN 1(PSEN1), and partial functional redundancy is seen between these two genes. However, the complete range of functions ofPSEN1andPSEN2is not yet understood. In this study, we performed targeted mutagenesis of the zebrafishpsen2gene to generate a premature termination codon close downstream of the translation start with the intention of creating a null mutation. Homozygotes for this mutation,psen2S4Ter, are viable and fertile, and adults do not show any gross pigmentation defects, arguing against significant loss of γ-secretase activity. Also, assessment of the numbers of Dorsal Longitudinal Ascending (DoLA) interneurons that are responsive topsen2but notpsen1activity during embryogenesis did not reveal decreasedpsen2function. Transcripts containing theS4Termutation show no evidence of destabilization by nonsense-mediated decay. Forced expression in zebrafish embryos of fusions ofpsen2S4Ter5’ mRNA sequences with sequence encoding enhanced green fluorescent protein (EGFP) indicated that thepsen2S4Termutation permits utilization of cryptic, novel downstream translation start codons. These likely initiate translation of N-terminally truncated Psen2 proteins that obey the “reading frame preservation rule” ofPRESENILINEOfAD mutations. Transcriptome analysis of entire brains from a 6-month-old family of wild type, heterozygous and homozygouspsen2S4Terfemale siblings revealed profoundly dominant effects on gene expression likely indicating changes in ribosomal, mitochondrial, and anion transport functions.
Anatomy of epithemal hydathodes in four monocotyledon plants of economic and academic relevance
Authors: Jauneau Alain , Cerutti Aude , Auriac Marie-Christine , Noël Laurent D. 
Published: April 2020

AbstractHydathode is a plant organ responsible for guttation in vascular plants, i.e. the release of droplets at leaf margin or surface. Because this organ connects the plant vasculature to the external environment, it is also a known entry site for some vascular pathogens. In this study, we present a detailed microscopic examination of monocot hydathodes for three crops (maize, rice and sugarcane) and the model plantBrachypodium distachyon. Our study highlights both similarities and specificities of those epithemal hydathodes. These observations will serve as a foundation for future studies on the physiology and the immunity of hydathodes in monocots.
An image J plugin for the high throughput image analysis ofin vitroscratch wound healing assays
Authors: Suarez-Arnedo Alejandra , Figueroa Felipe Torres , Clavijo Camila , Arbeláez Pablo , Cruz Juan C. , Muñoz-Camargo Carolina 
Published: April 2020

AbstractIn vitroscratch wound healing assay, a simple and low-cost technique that works along with other image analysis tools, is one of the most widely used 2D methods to determine the cellular migration and proliferation in processes such as regeneration and disease. There are open-source programs such as imageJ to analyze images ofin vitroscratch wound healing assays, but these tools require manual tuning of various parameters, which is time-consuming and limits image throughput. For that reason, we developed an optimized plugin for imageJ to automatically recognize the wound healing size, correct the average wound width by considering its inclination, and quantify other important parameters such as: area, wound area fraction, average wound width, and width deviation of the wound images obtained from a scratch/ wound healing assay. Our plugin is easy to install and can be used with different operating systems. It can be adapted to analyze both individual images and stacks. Additionally, it allows the analysis of images obtained from bright field, phase contrast, and fluorescence microscopes. In conclusion, this new imageJ plugin is a robust tool to automatically standardize and facilitate quantification of differentin vitrowound parameters with high accuracy compared with other tools and manual identification.
An immunohistochemical prostate cell identification key indicates that aging shifts procollagen 1A1 production from myofibroblasts to fibroblasts in dogs prone to prostate-related urinary dysfunction
Authors: Ruetten Hannah , Cole Clara , Wehber Marlyse , Wegner Kyle A. , Girardi Nicholas M. , Peterson Nelson T. , Scharpf Brandon R. , Romero Michael F. , Wood Michael W. , Colopy Sara A. , Bjorling Dale E. , Vezina Chad M. 
Published: April 2020

AbstractBackgroundThe identity and spatial distribution of prostatic cell types has been determined in humans but not in dogs, even though aging- and prostate-related voiding disorders are common in both species and mechanistic factors, such as prostatic collagen accumulation, appear to be shared between species. In this publication we characterize the regional distribution of prostatic cell types in the young intact dog to enable comparisons with human and mice and we examine how the cellular source of procollagen 1A1 changes with age in intact male dogs.MethodsA multichotomous decision tree involving sequential immunohistochemical stains was validated for use in dog and used to identify specific prostatic cell types and determine their distribution in the capsule, peripheral, periurethral and urethral regions of the young intact canine prostate. Prostatic cells identified using this technique include perivascular smooth muscle cells, pericytes, endothelial cells, luminal, intermediate, and basal epithelial cells, neuroendocrine cells, myofibroblasts, fibroblasts, fibrocytes, and other hematolymphoid cells. Corresponding images were made freely accessible through the GUDMAP database athttps://doi.org/10.25548/16-WMM4.ResultsThe prostatic peripheral region harbors the largest proportion of epithelial cells. Aging does not change the density of hematolymphoid cells, fibroblasts, and myofibroblasts in the peripheral region or in the fibromuscular capsule, regions where we previously observed aging- and androgen-mediated increases in prostatic collagen abundance Instead, we observed aging-related changes the procollagen 1A1 positive prostatic cell identity from a myofibroblast to a fibroblast.ConclusionsHematolymphoid cells and myofibroblasts are often identified as sources of collagen in tissues prone to aging-related fibrosis. We show that these are not the likely sources of pathological collagen synthesis in older intact male dogs. Instead, we identify an aging-related shift in the prostatic cell type producing procollagen 1A1 that will help direct development of cell type and prostate appropriate therapeutics for collagen accumulation.
Motor and non-motor sequence prediction is equally affected in children with Developmental Coordination Disorder
Authors: Opitz Bertram , Brady Daniel , Leonard Hayley C. 
Published: April 2020

AbstractChildren with Developmental Coordination Disorder (DCD) are diagnosed based on motor difficulties. However, they also exhibit difficulties in several other cognitive domains, including visuospatial processing, executive functioning and attention. One account of the difficulties seen in DCD proposes an impairment in internal forward modelling, i.e., the ability to (i) detect regularities of a repetitive perceptual or motor pattern, (ii) predict future outcomes of motor actions, and (iii) adapt behaviour accordingly. Using electroencephalographic recordings, the present study aimed to delineate these different aspects of internal forward modelling across several domains. To this end, 24 children with DCD and 23 typically-developing children (aged 7-10 years) completed a serial prediction task in the visual, temporal, spatial and motor domains. This task required them to learn short sequences and to indicate whether a sequence was disrupted towards its end. Analyses revealed that, across all domains, children with DCD showed poorer discrimination between intact and disrupted sequences, accompanied by a delayed late parietal positivity elicited by disrupted sequences. These results indicate an impairment in explicit sequence discrimination in DCD across motor and cognitive domains. However, there is no evidence for an impairment in implicit performance on the motor task in DCD. These results suggest an impairment of the updating of an internal forward model in DCD resulting in a blurred representation of that model and consequently in a reduced ability to detect regularities in the environment (e.g., sequences). Such a detailed understanding of internal forward modelling in DCD could help to explain the wide range of co-occurring difficulties experienced by those with a diagnosis of DCD.
Abortion and various associated risk factors in dairy cow and sheep in Ili, China
Authors: Deng Xiaoyu , Zhang Huan , Shao Zhiran , Zhao Xiaoli , Yang Qin , Song Shengnan , Wang Zhen , Wang Yong , Wang Yuanzhi , Sheng Jinliang , Chen Chuangfu 
Published: April 2020

AbstractWe studied livestock abortion and various associated risk factors in the Ili region of northwest China. Livestock abortion prevalence was estimated and correlated with infections (Brucellosis, Salmonellosis,MycoplasmaandChlamydiaseropositivity) and management (farming type and contact with other herds/flocks) risk factors. The prevalence of cow and sheep abortion induced byBrucellawas 76.8% (P<0.0001) and 84.1% (P<0.0001), andMycoplasmacaused an estimated 15.5% (P=0.025) and 17.6% (P<0.001) abortions, respectively. Abortion-related risk factors included mixed farming (cowP=0.001, sheepP<0.001), contact with other flocks (cowP=0.007, sheepP=0.003), brucellosis positivity (cowP<0.001, sheepP<0.001) andMycoplasmapositivity (cowP=0.031, sheepP<0.001). A total of 2996 serum samples (1402 cow, 1594 sheep) were identified by RBPT (Rose Bengal Plate Test), and they showed the seroprevalence of brucellosis in X county was cow 7.1%, sheep 9.1%; in H county was cow 11.7%, sheep 10.7%; and in Q county was cow 4.2%, sheep 9.1%. The seroprevalence ofMycoplasmain X county was cow 3.4%, sheep 7.9%; in H county was cow 5.3%, sheep 9.9%; and in Q county was cow 2.1%, sheep 4.3%. A total of 54 samples, including aborted cow (22), sheep (30) fetuses and milk samples (2), were identified asBrucella melitensis(B. melitensis) positive. A total of 38Brucellawere isolated from 16 aborted cow, 20 sheep fetuses and 2 milk samples. All of these isolates were identified, and confirmed, asB. melitensis. A phylogenetic tree showed that theBrucellaisolates closely matched theB. melitensisbiovar 3 isolated in Inner Mongolia, China, andB. melitensisisolated from Norway and India. These results suggest thatB. melitensisbiovar 3 is the main pathogen responsible for cow and sheep abortion and also pose a human health risk. Additionally, livestock reproduction can also be influenced byMycoplasmainfection and managerial factors (farming type and contact with other herds/flocks), especially in remote areas.
Ligand Sensing Enhances Bacterial Flagellar Motor Output via Stator Recruitment
Authors: Naaz Farha , Agrawal Megha , Chakraborty Soumyadeep , Tirumkudulu Mahesh S. , Venkatesh K.V. 
Published: April 2020

AbstractThe phenomenon of chemotaxis in bacteria, where the cells migrate towards or away from chemicals, has been extensively studied in the past. For flagellated bacteria such asEscherichia coli, a change in chemical concentration in its environment is sensed by a chemoreceptor and communicated via a well-characterised signalling pathway to the flagellar motor. It has been widely accepted that the signals change the rotation bias of the motor without influencing the motor speed. Here, we present results to the contrary and show that the bacteria is also capable of modulating motor speed on merely sensing a ligand. Step changes in concentration of non-metabolisable ligand cause temporary recruitment of stators leading to a momentary increase in motor speeds. For metabolisable ligand, the combined effect of sensing and metabolism leads to higher motor speeds for longer durations. Swimming speeds measured at the population level corroborate the observations. Experiments performed with mutant strains delineate the role of metabolism and sensing in the modulation of motor speed and show how speed changes along with changes in bias can significantly enhance bacteria’s response to changes in its environment.
Antibiotic-resistantSalmonella speciesandEscherichia coliin broiler chickens from farms, abattoirs and open markets in selected districts of Zambia
Authors: Phiri Nelson , Mainda Geoffrey , Mukuma Mercy , Sinyangwe Ntazana N. , Banda Luke John , Kwenda Geoffrey , Muligisa-Muonga Elizabeth , Flavien Bumbangi Nsoni , Mwansa Mwaba , Yamba Kaunda , Munyeme Musso , Muma John Bwalya 
Published: April 2020

AbstractSalmonellaspecies andEscherichia coliare major bacterial enteropathogens of global public health importance that cause foodborne diseases, thereby contributing to increased human morbidity and mortality. Both pathogens have also been found to contribute towards the spread of antimicrobial resistance through the food chain, especially in poultry. The aim of this study was to determine the occurrence of antibiotic-resistantSalmonella sp. andE. coliin broiler chickens at farm level, abattoirs and open markets in selected districts of Zambia. A cross-sectional study was undertaken in seven districts of Zambia to determine the resistance profiles ofSalmonella sp. andE. coliobtained from broiler chickens at farms, abattoirs and open markets. A total of 470 samples were collected, including litter, cloacal swabs and carcass swabs. Samples were inoculated into buffered peptone water, sub-cultured onto MacConkey and Xylose Lysine Deoxycholate agar plates. Identification ofSalmonella sp. and E. coliwas done using the API-20E kit and confirmation by 16S rDNA sequencing. Confirmed isolates were tested against a panel of 10 antibiotics using the Kirby-Bauer disc-diffusion method and interpreted according to the Clinical Laboratory Standards Institute guidelines. Analysis of the antibiotic susceptibility test results was done using WHONET 2018 software. Overall, 4Salmonella spp. and 280E. coliwere isolated. One of theSalmonella sp. was resistant to ampicillin (25%), amoxicillin/clavulanic acid (25%) and cefotaxime (25%).E. coliantibiotic resistance was highest to tetracycline (81.4%) and lowest to imipenem (0.7%). The antibiotic susceptibility profile revealed 55% (154/280) multidrug resistantE. coli, with the highest multidrug resistance profile (20.7%) in the ampicillin-tetracycline-trimethoprim/sulfamethoxazole drug combination. Furthermore, 4.3% (12/280) of the isolates showed Extensive Drug resistance. The levels of antimicrobial resistance toE. coliandSalmonellaobserved in market-ready chickens is of public health concern.
Agonist-induced Functional Analysis and Cell Sorting, a novel tool to select and analyze neurons: Fragile X as a proof of concept
Authors: Castagnola Sara , Cazareth Julie , Lebrigand Kevin , Jarjat Marielle , Magnone Virginie , Delhaye Sebastien , Brau Frederic , Bardoni Barbara , Maurin Thomas 
Published: April 2020

ABSTRACTTo get a better insight into the dynamic interaction between cells and their environment, we developed the agonist-induced Functional Analysis and Cell Sorting (aiFACS) technique, which allows the simultaneous recording and sorting of cells in real-time according to their immediate and individual response to a stimulus. By modulating the aiFACS selection parameters, testing different developmental times, using various stimuli and multiplying the analysis of readouts, it is possible to analyze cell populations of any tissue, including tumors. The association of aiFACS to single-cell transcriptomic allows to build a tissue cartography based on specific functional response/s of cells.As proof of concept, we used aiFACS on the dissociated mouse brain, a highly heterogenous tissue, enriching it in interneurons upon stimulation with an agonist of the glutamate receptors and upon sorting based on calcium levels. Further single-cell RNA-seq of these aiFACS-selected interneurons resulted in a nine-cluster classification. Furthermore, we used aiFACS on interneurons derived from the brain of theFmr1-KO mouse, a rodent model of Fragile X syndrome. We show here that these interneurons manifest a generalized defective pharmacological response compared to wild type, affecting all the analyzed cell clusters at one specific post-natal developmental time.