bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pectobacterium colocasium sp. nov. isolated from taro (Colocasia esculenta)
Authors: Klair Diksha , Arizala Dario , Dobhal Shefali , Boluk Gamze , Alvarez Anne M. , Arif Mohammad 
Published: February 2022

ABSTRACTPectobacterium, agenus comprising gram-negative, pectinolytic phytopathogens, is responsible for economic losses in a wide host range of plants. In this study, the bacterial strains PL152T and PL155 were isolated from taro corms in Hawai’i in 2018, and characterized using genomic and biochemical assays. The Next Generation Sequencing technologies, Oxford Nanopore MinION and Illumina NovaSeq, were used for whole genome sequencing of the PL152T strain. Short and long reads were assembled using the Unicycler tool accessible at the bioinformatic resource center, and PATRIC (PathoSystems Resource Integration Center) was used to generate a more accurate and reliable “hybrid” assembly. The 16S rRNA analysis of PL152T with type strains of other known Pectobacterium species showed a close relationship with P. fontis. Multi-locus sequence analysis using nine housekeeping genes (dnaA, gapA, gyrB, recA, dnaN, rpoS, mdh, rpoA and dnaK) differentiated strain PL152T from other species of Pectobacterium and formed a unique and well-defined clade. The concurrent results of average nucleotide identity (ANI) and digital DNA-DNA hybridization, with calculated values lower than 95 and 70%, respectively, supported the delineation of a novel bacterial species. Here, we proposed Pectobacterium colocasium, strain PL152T (=ICMP 24362T; LMG 32536 T) and PL155 as a novel species in the genus Pectobacterium.1.5RepositoriesCP091064; MZ542535 - MZ542540; OM457660
Evidence for RNA or protein transport from somatic tissues to the male reproductive tract in mouse
Authors: Rinaldi Vera , Messemer Kathleen , Desevin Kathleen , Sun Fengyun , Berry Bethany C. , Kukreja Shweta , Tapper Andrew R. , Wagers Amy J. , Rando Oliver J. 
Published: February 2022

ABSTRACTThe development of tools to manipulate the mouse genome, including knockout and transgenic technology, revolutionized our ability to explore gene function in mammals. Moreover, for genes that are expressed in multiple tissues or at multiple stages of development, the use of tissue-specific expression of the Cre recombinase allows gene function to be perturbed in specific cell types and/or at specific times. However, it is well known that putative tissue-specific promoters often drive unanticipated “off target” expression. In our efforts to explore the biology of the male reproductive tract, we unexpectedly found that expression of Cre in the central nervous system resulted in recombination in the epididymis, a tissue where sperm mature for ~1-2 weeks following the completion of testicular development. Remarkably, we not only observed reporter expression in the epididymis when Cre expression was driven from neuron-specific transgenes, but also when Cre expression in the brain was induced from an AAV vector carrying a Cre expression construct. A surprisingly wide range of Cre drivers – including six different neuronal promoters as well as the adipose-specific AdipoQ Cre promoter – exhibited off target recombination in the epididymis, with a subset of drivers also exhibiting unexpected activity in other tissues such as the reproductive accessory glands. Finally, using a combination of parabiosis and serum transfer experiments, we find evidence supporting the hypothesis that Cre may be trafficked from its cell of origin to the epididymis through the circulatory system. Together, our findings should motivate extreme caution when interpreting conditional alleles, and suggest the exciting possibility of inter-tissue RNA or protein trafficking in modulation of reproductive biology.
Investigating carbohydrate-rich feed supplements and the feeding preferences of European starlings (Sturnus vulgaris)
Authors: Brown Dylan J. 
Published: February 2022

AbstractIn the current ecological and ornithological environment in the continental United States, the European starling (Sturnus vulgaris) is one of the most common exotic bird species. After being introduced on the East Coast of the United States, the species spread rapidly across regions and ecosystems, significantly affecting the greater ecology of the nation and often disturbing local species populations. To better understand the behavior and preferences of this species, a study was devised to test the field responses of a population of European starlings in Lyon County, Kansas over a total period of 144 hours (during 48 individual observation periods) to assess and yield knowledge pertaining to their behavior and feeding patterns within a suburban environment. For this experiment, four feed alternatives (i.e., one control and three experimental) were prepared to test the impact of the utilization of carbohydrate-rich feed supplements on the degree to which the starlings would frequent a feeding location. The different feed offered to the local starlings would consist of either 300g of conventional bird feed, 200g of conventional bird feed and 100g of the supplement, 100g of conventional bird feed and 200g of the supplement, or 300g of the supplement, with the conventional bird seed acting as the control. The data suggest that the differences observed with relation to the feed alternatives were negligible, as demonstrated by the starlings’ preference for the different supplement concentrations (according to their feeding frequency for the four alternatives).
Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin
Authors: Huang Rui , Snedden Wayne A , diCenzo George C 
Published: February 2022

ABSTRACTHost/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts. Notably, transcripts encoding highly-cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were ~2-fold more abundant in M. sativa than in M. officinalis, and ~27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly-cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.
Effects of substrate on shrimp growth, water quality and bacterial community in the biofloc system nursing Penaeus vannamei postlarvae
Authors: Huang Hai-Hong , Li Chao-Yun , Lei Yan-Ju , Kuang Wei-Qi , Zhou Bo-Lan , Zou Wan-Sheng , Yang Pin-Hong 
Published: February 2022

AbstractThis study aimed to investigate the effects of substrate on water quality, shrimp growth and bacterial community in the biofloc system with a salinity of 5‰. Two treatments, biofloc system with (sB) or without (nB) addition of elastic solid packing filler (nylon) as substrate, were set up. Penaeus vannamei postlarvae (PL, ~ stage 15) were stocked at a density of 4000 PL m−3 in each treatment with triplicates for a 28-days culture experiment, taking glucose as carbon source (C:N 15:1). Results showed that the survival rate (96.3±3.6%), FCR (0.76±0.06) and productivity (1.54±0.12 kg m−3) in sB treatment were significantly better than those in nB treatment (81.0±7.1%, 0.98±0.08 and 1.14±0.09 kg m−3, P<0.05). All water parameters were in the recommended ranges. Substrate showed significant effect on TAN, TSS, turbidity, biofloc volume, pH and carbonate alkalinity (P < 0.05). Actinobacteria (4.0-22.7%), Bacteroidetes (10.4-33.5%), Firmicutes (0.2-11.2%), Planctomycetes (4.0-14.9%) and Proteobacteria (29.4-59.0%) were the most dominant phyla for both treatments. However, the bacterial community in sB treatment showed to be significantly different from that in nB treatment (Jaccard distance 0.94±0.01, P=0.001). Substrate showed significant effects on Shannon, Heip, Pielou and Simpson index, as well as relative abundances of Actinobacteria, Bacteroidetes and Planctomycetes (P < 0.05). The results suggested that addition of substrate affected the shrimp growth, water quality and bacterial community in the biofloc system nursing P. vannamei PL with a 5‰ salinity.
The efficacy of commercial decontamination agents differs between standardised test settings and real-world usage for a variety of bacterial species
Authors: Uy Benedict , Read Hannah , van de Pas Shara , Marnane Rebecca , Casu Francesca , Swift Simon , Wiles Siouxsie 
Published: February 2022

AbstractDecontamination of surfaces and items plays an important role in reducing the spread of infectious microorganisms in many settings including hospitals and research institutes. Regardless of the location, appropriate decontamination procedures are required for maintaining biosafety and biosecurity. For example, effective decontamination of microbial cultures is essential to ensure proper biocontainment and safety within microbiological laboratories. To this end, many commercial decontamination agents are available which have been tested to a prescribed standard to substantiate their efficacy. However, these standardised tests are unlikely to accurately reflect all conditions encountered in medical and biomedical research. Despite this, laboratory workers and other users of decontamination agents may assume that all decontamination agents will work in all situations. We tested commonly used commercial decontamination agents against a range of bacterial species to determine their efficacy under real-world laboratory conditions. As each decontamination agent has a different recommended dilution for use, to compare their efficacy we calculated their ‘effective ratio’ which reflects the difference between the manufacturer-recommended dilution and the dilution needed to achieve decontamination under real-world laboratory conditions. Effective ratios above 1 indicate that the agent was active at a dilution more dilute than recommended whereas effective ratios lower than 1 indicate that the agent required a higher concentration than recommended. Our results show that the quaternary ammonium agents TriGene Advance and Chemgene HLD4L were the most active out of the agents tested, with biocidal activity measured at up to 64 times the recommended dilution. In contrast, hypochlorite (bleach) and Prevail™ (stabilised hydrogen peroxide) had the lowest effective ratios amongst the tested agents. In conclusion, our data suggest that not all decontamination agents will work at the recommended dilutions under real-world laboratory conditions. We recommend that the protocols for the use of decontamination agents are verified under the specific conditions required to ensure they are fit for purpose.
A Novel congenic Mouse Model to study Obesity, Diabetes and NAFLD
Authors: Kumar MJ Mahesh , Arindkar Shailendra , Nagarajan Perumal 
Published: February 2022

AbstractThe genetic background of the mutant mouse strain plays an important role in disease development. We investigated whetherLeprmutation on different genetic background (WSB/EiJ) influences the development of obesity, diabetes and non-alcoholic fatty liver diseases (NAFLD). For this study heterozygote (db/+) mice were backcrossed with WSB/EiJ strain (that is resistant to obesity and NAFLD) for more than 10 generations and intercrossed for five generations havingLeprmutated gene incorporated in WSB/EiJ background. The newly derived congenic strain was assessed and related with the B6.db strain and WSB/EiJ strain for the development of obesity, NAFLD. TheLeprmutated congenic strain on the WSB/EiJ background gained significant body weight and showed other characteristic features of obesity. However, the incidence of diabetes, NAFLD, and other kidney complications were not observed in this strain. The novel congenic mouse strain havingLeprgene on WSB/EiJ background would be a promising model for the study of obesity without NAFLD and will also help to understand the various mechanisms involved in the development of NAFLD.
N-acylethanolamine acid amide hydrolase is a novel target for drugs against SARS-CoV-2 and Zika virus
Authors: Lai Michele , La Rocca Veronica , Amato Rachele , Iacono Elena , Filipponi Carolina , Catelli Elisa , Bogani Lucia , Fonnesu Rossella , Lottini Giulia , De Carli Alessandro , Mengozzi Alessandro , Masi Stefano , Quaranta Paola , Spezia Pietro Giorgio , Freer Giulia , Lenzi Paola , Fornai Francesco , Piomelli Daniele , Pistello Mauro 
Published: February 2022

AbstractSeveral compounds have been tested against SARS-CoV-2; at present, COVID-19 treatments decrease the deleterious inflammatory response and acute lung injury. However, the best therapeutic response would be expected by combining anti-inflammatory properties, while concomitantly blocking viral replication. These combined effects should drastically reduce both infection rate and severe complications induced by novel SARS-CoV-2 variants. Therefore, we explored the antiviral potency of a class of anti-inflammatory compounds that inhibit the N-Acylethanolamine acid amidase (NAAA). This enzyme catalyzes the hydrolysis of palmitoylethanolamide (PEA), a bioactive lipid that mediates anti-inflammatory and analgesic activity through the activation of peroxisome proliferator receptor-α (PPAR-α). Similarly, this pathway is likely to be a significant target to impede viral replication since PPAR-α activation leads to dismantling of lipid droplets, where viral replication of Flaviviruses and Coronaviruses occurs.Here, we show that either genetic or pharmacological inhibition of the NAAA enzyme leads to five-fold reduction in the replication of both SARS-CoV-2 and ZIKV in various cell lines. Once NAAA enzyme is blocked, both ZIKV and SARS CoV-2 replication decrease, which parallels a sudden five-fold decrease in virion release. These effects induced by NAAA inhibition occurs concomitantly with stimulation of autophagy during infection. Remarkably, parallel antiviral and anti-inflammatory effects of NAAA antagonism were confirmed in ex-vivo experiments, within SARS-CoV-2 infected human PBMC cells, in which both viral genomes and TNF-α production drop by ~60%. It is known that macrophages contribute to viral spread, excessive inflammation and macrophage activation syndrome that NAAA inhibitors might prevent, reducing the macrophage-induced acute respiratory distress syndrome and subsequent death of COVID-19 patients.
SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export
Authors: Hall Ross , Guedán Anabel , Yap Melvyn W. , Young George R. , Harvey Ruth , Stoye Jonathan P. , Bishop Kate N. 
Published: February 2022

AbstractSARS-CoV-2 is a betacoronavirus and the etiological agent of COVID-19, a devastating infectious disease. Due to its far-reaching effect on human health, there is an urgent and growing need to understand the viral molecular biology of SARS-CoV-2 and its interaction with the host cell. SARS-CoV-2 encodes 9 predicted accessory proteins, which are presumed to be dispensable for in vitro replication, most likely having a role in modulating the host cell environment to aid viral replication. Here we show that the ORF6 accessory protein interacts with cellular Rae1 to inhibit cellular protein production by blocking mRNA export. We utilised cell fractionation coupled with mRNAseq to explore which cellular mRNA species are affected by ORF6 expression and show that ORF6 can inhibit the export of many mRNA including those encoding antiviral factors such as IRF1 and RIG-I. We also show that export of these mRNA is blocked in the context of SARS-CoV-2 infection. Together, our studies identify a novel mechanism by which SARS-CoV-2 can manipulate the host cell environment to supress antiviral responses, providing further understanding to the replication strategies of a virus that has caused an unprecedented global health crisis.Author SummarySARS-CoV-2 is the virus responsible for the current COVID-19 pandemic. Coronaviruses, like SARS-CoV-2, replicate their genome in the cytoplasm of the host cell by hijacking the cellular machinery. In addition to structural proteins and viral enzymes, SARS-CoV-2 encodes 9 accessory proteins. Although these are not required for in vitro replication, they are thought to modulate the host cell environment to favour viral replication. In this work, we show that the ORF6 accessory protein can supress cellular protein production by blocking mRNA nuclear export through interacting with the cellular protein Rae1, a known mRNA export factor. We also investigated which cellular mRNAs were retained in the nucleus when ORF6 was overexpressed. Interestingly, we found that ORF6 inhibited the export of many different mRNAs, including those encoding antiviral factors, like IRF1 and RIG-I, even in the absence of stimulation by interferon. Importantly, we found that the export of these mRNAs was similarly affected in the context of SARS-CoV-2 infection. Therefore, we believe we have identified a novel mechanism that SARS-CoV-2 uses to suppress antiviral responses in order to make the cell more permissive to infection.
Increasing viral transmission paradoxically reduces progression rates to severe COVID-19 during endemic transition
Authors: Hong Hyukpyo , Noh Ji Yun , Lee Hyojung , Choi Sunhwa , Choi Boseung , Kim Jae Kyoung , Shin Eui-Cheol 
Published: February 2022

AbstractNatural infection with SARS-CoV-2 or vaccination induces virus-specific immunity protecting hosts from infection and severe disease. While the infection-preventing immunity gradually declines, the severity-reducing immunity is relatively well preserved. Here, based on the different longevity of these distinct immunities, we develop a mathematical model to estimate courses of endemic transition of COVID-19. Our analysis demonstrates that high viral transmission unexpectedly reduces the rates of progression to severe COVID-19 during the course of endemic transition despite increased numbers of infection cases. Our study also shows that high viral transmission amongst populations with high vaccination coverages paradoxically accelerates the endemic transition of COVID-19 with reduced numbers of severe cases. These results provide critical insights for driving public health policies in the era of ‘living with COVID-19’.
Does 2×2 airplane passenger contact tracing for infectious respiratory pathogens work? A systematic review of the evidence
Authors: Rafferty Anna C , Bofkin Kelly , Hughes Whitney , Souter Sara , Hosegood Ian , Hall Robyn N , Furuya-Kanamori Luis , Liu Bette , Drane Michael , Regan Toby , Halder Molly , Kelaher Catherine , Kirk Martyn D 
Published: February 2022

AbstractWe critically appraise the literature regarding in-flight transmission of a range of respiratory infections to provide an evidence base for public health policies for contact tracing passengers, given the limited pathogen-specific data for SARS-CoV-2 currently available. Using PubMed, Web of Science, and other databases including preprints, we systematically reviewed evidence of in-flight transmission of infectious respiratory illnesses. A meta-analysis was conducted where total numbers of persons on board a specific flight was known, to calculate a pooled Attack Rate (AR) for a range of pathogens. The quality of the evidence provided was assessed using a bias assessment tool developed for in-flight transmission investigations. We identified 103 publications detailing 165 flight investigations. Overall, 43.7% (72/165) of investigations provided evidence for in-flight transmission. H1N1 influenza A virus had the highest reported pooled attack rate per 100 persons (AR= 1.17), followed by SARS-CoV-2 (AR=0.54) and SARS-CoV (AR = 0.32), Mycobacterium tuberculosis (AR= 0.25), and measles virus (AR= 0.09). There was high heterogeneity in estimates between studies, except for TB. Of the 72 investigations that provided evidence for in-flight transmission, 27 investigations were assessed as having a high level of evidence, 23 as medium, and 22 as low. One third of the investigations that reported on proximity of cases showed transmission occurring beyond the 2×2 seating area. We suggest that for emerging pathogens, in the absence of pathogen-specific evidence, the 2×2 system should not be used for contact tracing. Instead, alternate contact tracing protocols and close contact definitions for enclosed areas, such as the same cabin on an aircraft or other forms of transport, should be considered as part of a whole of journey approach.