bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation of essential microelements in large horned cattle in mother-offspring system as factor in development of immunosuppressive state
Authors:   Don State Agrarian University, Ushakova Tatyana M. , Kapelist Ivan V. ,   Don State Technical University, Zelenkova Galina A. , Derezina Tatyana N. ,   Don State Technical University
Published: December 2020

The nature of the mineral supply of certain biogeochemical provinces and their correlative interactions within biological organisms determine the degree of development of immunosuppressive states in animals. So we studied the level of minerals in the samples of hair and blood in cattle in the «mother-offspring» system and established the nature of the correlation of cobalt, zinc, iron and copper. It has been proven that low levels of cobalt (cows - 429.30 ± 4.05 nmol/l and calves - 430.80 ± 5.60 nmol / L) and zinc (cows - 7.21 ± 0.20 pmol/l and calves - 7.60 ± 0.15 pmol/l) against the threshold values of iron (cows - 17.90 ± 1.30 pmol/l and calves - 18.40 ± 1.80 pmol/l) and copper (cows - 13.90 ± 1.80 pmol/l and calves - 14.08 ± 1.05 pmol/l) in the blood caused hematopoietic function impairment and led to the development of mild hypochromic anemia (erythrocytes: cows - 6.01 ± 0.40x1012/l and calves - 6.36±0.50x1012/l) in animals in the «mother-offspring» system. In addition, metabolic disorders caused by nutritional deficiency of zinc contributed to a decrease in the synthesis of alkaline phosphatase (cows - 87.90 ± 5.10 U/l and calves - 126.80±4.02 U/l), exacerbating the disorder of erythropoietic function of red bone animal brain. A long-term imbalance of copper and zinc in the nutrient substrates of the studied animals was revealed, as evidenced by the results of a mineralogram of hairline samples (copper: cows - 13.910 ± 0.67 mg/kg and calves - 12.609 ± 0.70 mg/kg; zinc: cows - 57.960 ± 0.90 mg/kg and calves 60.315 ± 0.99 mg/kg), which ultimately led to a deficiency of zinc in the body, leading to the development of an immunosuppressive state (Ig M: cows - 0.99 ± 0.15 mg/ml and calves - 1.64 ± 0.05 mg/ml; Ig A: cows - 0.30 ± 0.05 mg/ml and calves - 2.05 ± 0.10 mg/ml).
FUNÇÃO QUADRÁTICA: ANÁLISE DOS FENÔMENOS DE CONGRUÊNCIA E NÃO CONGRUÊNCIA EM ATIVIDADES REALIZADAS POR ESTUDANTES DO 9º ANO DO ENSINO FUNDAMENTAL
Authors: Ferreira Graziele Santos , Pires Rogério Fernando
Published: December 2020

Este artigo relata os resultados de uma pesquisa de caráter qualitativo que teve por objetivo analisar à luz da Teoria dos Registros de Representação Semiótica a manipulação e a coordenação das representações de função quadrática explicitadas por um grupo de estudantes do 9º ano do Ensino Fundamental. O estudo foi realizado com uma turma de vinte e cinco alunos, dividida em sete grupos, de uma escola da rede pública localizada no sudoeste baiano. No decorrer da pesquisa, os estudantesrealizaram duas atividades envolvendo as noções de função quadrática, cujos resultados foram obtidos a partir da análise dos dados à luz da teoria utilizada, mostrando que os estudantes tiveram facilidade em lidar com as situações que envolviam o fenômeno de congruência, porém, quando tiveram quetratar com a representação algébrica do objeto matemático, a dificuldade esteve presente, mesmo quando a conversão era congruente. As atividades em que os estudantes obtiveram êxito e as conversões eram não congruentes, envolveram situações familiares para eles.
РЕКОНСТРУКЦИЯ ФИЗИЧЕСКОГО ТИПА ПОЗДНЕСРЕДНЕВЕКОВЫХ КРЫМСКИХ ТАТАР КЕРЧЕНСКОГО ПОЛУОСТРОВА
Authors: Боруцкая Светлана Борисовна , Сергей Владимирович Васильев
Published: December 2020

В статье приводится комплексный палеоантропологический анализ населения, оставившего некрополь Биели (г. Керчь, Республика Крым). Большой интерес эта серия представляет в связи с изучением этногенеза крымских татар. В работе дается краниологическая характеристика позднесредневековых крымских татар. Приводятся реконструкции лица по черепу по методу М.М. Герасимова. Особое внимание уделено реконструированию физического облика данного населения. Выявлены высокая детская смертность и низкий показатель средней продолжительности жизни населения, что говорит о невысоком благополучии в изучаемой группе.
The article provides a comprehensive paleoanthropological analysis of the population from the Bieli necropolis (Kerch, Republic of Crimea). This sample is of great interest in connection with the study of the Crimean Tatars ethnogenesis. The work features a craniological characteristic of the late medieval Crimean Tatars and reconstructions of the face based on the skull by the method of M.M. Gerasimov. Particular attention is paid to the reconstruction of the physical appearance of a given population. High infant mortality and a low indicator of the average life expectancy of the population were revealed, which reflects general low well-being in the studied group.
Association Between the Morphology of Proximal Tibiofibular Joint and the Presence of Knee OA
Authors: Qi Xin-Zheng , Wang Min , Zhang Bo , Nie Mao-Dan , Ma Xiao-Ying , Wang Hui-Zhi , Wang Xiao-Hong , Cheng Cheng-Kung , Zhang Min
Published: December 2020

Objective: The aim of this study was to evaluate the association between the morphology of the proximal tibiofibular joint (PTFJ) and the presence of knee osteoarthritis (OA).

Methods: Twenty-eight OA subjects and 30 healthy subjects were enrolled in this study. A 3D model of the lower limb of each subject was constructed from CT scans and used to measure the characteristics of the PTFJ, including the shape of the articular facets, articular surface area, joint inclination, relative articular height, and joint declination. The association between the characteristics of the PTFJ and presence of knee OA was assessed using binomial logistic regression analysis.

Results: There was a significant difference between the OA and healthy groups in terms of the inclination (p = 0.028) and declination (p = 0.020) of the PTFJ and relative articular height (p = 0.011). A greater inclination angle (OR: 1.463, 95% CI: 1.124–1.582, p = 0.021), greater declination angle (OR: 1.832, 95% CI: 1.691–2.187, p = 0.009), and lower relative articular height (OR: 0.951, 95% CI: 0.826–0.992, p = 0.008) were found to be associated with an increased likelihood of knee OA being present.

Conclusion: The results of this study suggest that abnormal PTFJ morphology is associated with the presence of knee OA.
Cognitive Gains of Aerobic Exercise in Patients With Ischemic Cerebrovascular Disorder: A Systematic Review and Meta-Analysis
Authors: Shu Yimei , He Qing , Xie Yi , Zhang Wanrong , Zhai Shuang , Wu Ting
Published: December 2020

Background: Cognitive impairment has become an important problem in ischemic cerebrovascular disorder survivors as disease related deaths have been significantly reduced. Aerobic exercise, the most prevalent mode of physical activity, positively contributes to cognition in both healthy population and people with cognitive impairment. However, studies on its associations with cognitive gains in patients with ischemic cerebrovascular disease showed mixed findings.

Objective: To explore the cognitive effects of aerobic exercise on ischemic cerebrovascular disorder survivors and investigate the possible moderators on exercise benefits.

Method: Randomized controlled trials investigating the effects of sole aerobic exercise on cognitive function in population with ischemic intracranial vascular disorder compared to any control group who did not receive the intervention were enrolled in this systematic review and meta-analysis. Four online database (Pubmed, Cochrane Library, Embase, and Web of Science) were searched.

Results: The initial search returned 1,522 citations and ultimately 11 studies were included in the systematic review. Analysis of seven studies showed the beneficial but not statistically significant impact of aerobic exercise on global cognitive function (0.13; 95% Cl −0.09 to 0.35; p = 0.25). Participants already with cognitive impairment benefited more from this intervention (0.31; 95% Cl 0.07–0.55; p = 0.01) and moderate intensity might be the optimal choice (0.34; 95% Cl −0.01 to 0.69; p = 0.06). The program duration and initiation time after stroke occurrence did not predict better cognitive outcome. Aerobic exercise was not associated with improvement of processing speed and executive function, the two subdomains of cognitive function.

Conclusions: Aerobic exercise may contribute to cognitive gains in survivors of ischemic cerebrovascular disorder, especially for population already with cognitive decline. Our findings suggest that the adoption of moderate intensity aerobic exercise might improve cognition in such population.
Transfection With Plasmid Causing Stable Expression of a Foreign Gene Affects General Proteome Pattern in Giardia lamblia Trophozoites
Authors: Heller Manfred , Braga Sophie , Müller Norbert , Müller Joachim
Published: December 2020

Giardia lamblia is an important causative agent of persistent diarrhea in humans, domestic animals, and cattle. Basic research is usually performed with the strain WBC6 and includes genetic manipulations such as transfections. Here, we investigate how transfection with a plasmid causing stable expression of a foreign gene affects the whole proteome pattern. Using shotgun mass spectrometry, we compare the proteomes of untransfected trophozoites to trophozoites transfected with Escherichia coli glucuronidase A (GusA). Besides GusA, which is detected in the transfected trophozoites only, the proteomes of untransfected and transfected trophozoites differ by 132 differentially expressed proteins. In particular, transfection induces antigenic variation. Since transfection causing stable expression affects the proteome pattern, transfection experiments should take into account this effect. Due to a unique peptide panel, GusA is an example for a suitable internal standard for experiments involving transfected cells. Data are available via ProteomeXchange with identifier PXD022565.
Cross-Situational Word Learning in Two Foreign Languages: Effects of Native Language and Perceptual Difficulty
Authors: Tuninetti Alba , Mulak Karen E. , Escudero Paola
Published: December 2020

Cross-situational word learning (CSWL) paradigms have gained traction in recent years as a way to examine word learning in ambiguous scenarios in infancy, childhood, and adulthood. However, no study thus far has examined how CSWL paradigms may provide viable learning pathways for second language (L2) word learning. Here, we used a CSWL paradigm to examine how native Australian English (AusE) speakers learned novel Dutch (Experiment 1) and Brazilian Portuguese (Experiment 2) word-object pairings. During each learning phase trial, two words and objects were presented without indication as to which auditory word belonged to which visual referent. The two auditory words formed a non-minimal or vowel minimal pair. Minimal pairs were classified as “perceptually easy” or “perceptually difficult” based on the acoustic-phonetic relationship between AusE and each L2. At test, participants again saw two visual referents but heard one auditory label and were asked to select the corresponding referent. We predicted that accuracy would be highest for non-minimal pair trials (in which the auditory words associated with the target and distractor object formed a non-minimal pair), followed by perceptually easy minimal pairs, with lowest accuracy for perceptually difficult minimal pair trials. Our results support these hypotheses: While accuracy was above chance for all pair types, in both experiments accuracy was highest for non-minimal pair trials, followed by perceptually easy and then perceptually difficult minimal pair trials. These results are the first to demonstrate the effectiveness of CSWL in adult L2 word learning. Furthermore, the difference between perceptually easy and perceptually difficult minimal pairs in both language groups suggests that the acoustic-phonetic relationship between the L1-L2 is an important factor in novel L2 word learning in ambiguous learning scenarios. We discuss the implications of our findings for L2 acquisition, cross-situational learning and encoding of phonetic detail in a foreign language.
Sampling Plants and Malacofauna in 87Sr/86Sr Bioavailability Studies: Implications for Isoscape Mapping and Reconstructing of Past Mobility Patterns
Authors: Britton Kate , Le Corre Mael , Willmes Malte , Moffat Ian , Grün Rainer , Mannino Marcello A. , Woodward Stephen , Jaouen Klervia
Published: December 2020

Establishing strontium isotope (87Sr/86Sr) geographical variability is a key component of any study that seeks to utilize strontium isotopes as tracers of provenance or mobility. Although lithological maps can provide a guideline, estimations of bioavailable87Sr/86Sr are often necessary, both in qualitative estimates of local strontium isotope “catchments” and for informing/refining isoscape models. Local soils, plants and/or animal remains are commonly included in bioavailability studies, although consensus on what (and how extensively) to sample is lacking. In this study, 96 biological samples (plants and snails) were collected at 17 locations spanning 6 lithological units, within a region of south-west France and an area with a high concentration of Paleolithic archaeological sites. Sampling sites aligned with those from a previous study on soil bioavailable strontium, and comparison with these values, and the influence of environmental and anthropogenic variables, was explored. Data confirm a broad correspondence of plant and snail87Sr/86Sr values with lithological unit/soil values, although the correlation between expected87Sr/86Sr values from lithology and bioavailable87Sr/86Sr ratios from biological samples was higher for plants than for snails. Grass, shrub and tree87Sr/86Sr values were similar but grasses had a stronger relationship with topsoil values than trees, reflecting differences in root architecture. Variability in87Sr/86Sr ratios from all plant samples was lower for sites located on homogeneous geological substrates than for those on heterogeneous substrates, such as granite. Among environmental and anthropogenic variables, only an effect of proximity to water was detected, with increased87Sr/86Sr values in plants from sites close to rivers originating from radiogenic bedrock. The results highlight the importance of analyzing biological samples to complement, inform and refine strontium isoscape models. The sampling of plants rather than snails is recommended, including plants of varying root depth, and (if sample size is a limitation) to collect a greater number of samples from areas with heterogeneous geological substrates to improve the characterizations of those regions. Finally, we call for new experimental studies on the mineralized tissues of grazers, browsers, frugivores and/or tree leaf feeders to explore the influence of87Sr/86Sr variability with soil profile/root architecture on87Sr/86Sr values of locally-feeding fauna.
Case Report: The Role of Molecular Analysis of the MUTYH Gene in Asymptomatic Individuals
Authors: Fabišíková Katarína , Hamidová Olívia , Behulová Regína Lohajová , Závodná Katarína , Priščáková Petra , Repiská Vanda
Published: December 2020

MUTYH-associated polyposis (MAP) is a rare hereditary condition caused by the biallelic mutation in the MUTYH gene encoding MUTYH glycosylase. This enzyme is a key member of the base excision repair (BER) pathway responsible for the repair of DNA lesions formed by reactive oxygen species (ROS). We report two cases of MAP. In case 1, a 67-year-old woman who presented with a personal history of colorectal and endometrial cancer and a family history of cancer syndromes underwent multigene panel testing that revealed a germline homozygous (biallelic) pathogenic variant c.1187G > A (p.Gly396Asp) in the MUTYH gene. Subsequent sequencing analysis performed in the offspring of the proband identified all three asymptomatic offspring as carriers of this pathogenic variant. In case 2, a 40-year-old woman with a strong family history of colorectal cancer [the proband’s sister was a carrier of the pathogenic variant c.536A > G (p.Tyr179Cys) of the MUTYH gene] and renal cancer underwent sequencing analysis of the MUTYH gene. The pathogenic heterozygous (monoallelic) variant c.536A > G (p.Tyr179Cys) of the MUTYH gene was identified in the proband. We found another pathogenic variant of the MUTYH gene—heterozygous (monoallelic) mutation c.1187G > A (p.Gly396Asp) in the genome of the proband’s husband. Molecular analysis of their offspring revealed that they are compound heterozygotes for MUTYH pathogenic variants c.536A > G (p.Tyr179Cys)/c.1187G > A (p.Gly396Asp). This paper shows the importance of genetic testing of asymptomatic relatives of the proband to ensure an early surveillance and management of individuals positive for pathogenic variant (s) in the MUTYH gene.
The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution
Authors: Liang Qing , Hu Yudi , Zhang Meina , Lin Chunjie , Zhang Wei , Li Ying , Zhu Ping , Xue Pengxin , Chen Yujie , Li Qiyuan , Wang Kejia
Published: December 2020

Aberrant immune cell infiltrates and microcircumstances represent characteristic features of liver fibrosis. In this study, we profiled the transcriptomes of intrahepatic CD45+ immune cells, from mice, using single-cell RNA sequencing (scRNA-seq) technology to understand the landscape of intrahepatic immune cells during the pathogenesis of fibrosis. Analysis of approximately 10,000 single-cell transcriptomes revealed an increase in dendritic cells (DCs), macrophages, and neutrophils and a decrease in T and natural killer T (NKT) cells. In addition, we report changes in the transcriptomes of diverse immune cell types, implying a deteriorating intrahepatic immune microcircumstance. Furthermore, we uncovered a novel fibrosis-associated CD8 T (Ccl5+, Ccl4+) and CD4 T (mt-Co1+) cell subpopulation, which infiltrates fibrotic liver and is characterized by abnormal activation or inactivation as well as a TCR decline. The results from scRNA-seq and bulk immune repertoire sequencing (IR-seq) revealed an obvious decline in T cell receptor (TCR) clonotypes combined with shrinking VJ and VDJ segment usage, as well as lower complementarity-determining region 3 (CDR3) amino acid (AA) diversity from fibrotic liver. Interestingly, a deficiency of TCR IR (TcrbKO mice) led to a deterioration of liver fibrosis, coupled with activation of hepatic stellate cells (HSCs) induced by the upregulation of macrophage and γδ T cell distribution in fibrotic TcrbKO livers. Our findings reveal the landscape and dynamics of single immune cells in liver fibrosis, and clarify the protective role of TCR IR in response to chronic liver injury.
Perspective: The Lung, Particles, Fibers, Nanomaterials, and Autoimmunity
Authors: Pollard K. Michael
Published: December 2020

Studies have shown that a wide range of factors including drugs, chemicals, microbes, and other environmental agents can induce pre-clinical autoimmunity. However, only a few have been confidently linked to autoimmune diseases. Among these are exposures to inhaled particulates that are known to be associated with autoimmune diseases such as lupus and rheumatoid arthritis. In this article, the potential of particle, fiber, and nanomaterial exposures to induce autoimmunity is discussed. It is hypothesized that inhalation of particulate material known to be associated with human autoimmune diseases, such as cigarette smoke and crystalline silica, results in a complex interplay of a number of pathological processes, including, toxicity, oxidative stress, cell and tissue damage, chronic inflammation, post-translational modification of self-antigens, and the formation of lymphoid follicles that provide a milieu for the accumulation of autoreactive B and T cells necessary for the development and persistence of autoimmune responses, leading to disease. Although experimental studies show nanomaterials are capable of inducing several of the above features, there is no evidence that this matures to autoimmune disease. The procession of events hypothesized here provides a foundation from which to pursue experimental studies to determine the potential of other environmental exposures to induce autoimmunity and autoimmune disease.
Rapid Evolution of HERC6 and Duplication of a Chimeric HERC5/6 Gene in Rodents and Bats Suggest an Overlooked Role of HERCs in Mammalian Immunity
Authors: Jacquet Stéphanie , Pontier Dominique , Etienne Lucie
Published: December 2020

Studying the evolutionary diversification of mammalian antiviral defenses is of main importance to better understand our innate immune repertoire. The small HERC proteins are part of a multigene family, including HERC5 and HERC6, which have probably diversified through complex evolutionary history in mammals. Here, we performed mammalian-wide phylogenetic and genomic analyses of HERC5 and HERC6, using 83 orthologous sequences from bats, rodents, primates, artiodactyls, and carnivores—the top five representative groups of mammalian evolution. We found that HERC5 has been under weak and differential positive selection in mammals, with only primate HERC5 showing evidences of pathogen-driven selection. In contrast, HERC6 has been under strong and recurrent adaptive evolution in mammals, suggesting past and widespread genetic arms-races with viral pathogens. Importantly, the rapid evolution of mammalian HERC6 spacer domain suggests that it might be a host-pathogen interface, targeting viral proteins and/or being the target of virus antagonists. Finally, we identified a HERC5/6 chimeric gene that arose from independent duplication in rodent and bat lineages and encodes for a conserved HERC5 N-terminal domain and divergent HERC6 spacer and HECT domains. This duplicated chimeric gene highlights adaptations that potentially contribute to rodent and bat immunity. Our findings open new research avenues on the functions of HERC6 and HERC5/6 in mammals, and on their implication in antiviral innate immunity.
Do Antibodies to Malaria Surface Antigens Play a Role in Protecting Mothers From Maternal Anemia?
Authors: Wiebe Madeleine C. , Yanow Stephanie K.
Published: December 2020

Pregnancy-associated malaria (PAM) caused byPlasmodium falciparumcan result in detrimental outcomes for both mother and infant, including low infant birth weight, preterm birth, maternal anemia, spontaneous abortion, and maternal and/or infant mortality. Maternal anemia is a particularly complex outcome, as the body must both maintain erythropoiesis and tolerance of the growing fetus, while directing a Th1 response against the parasite. Underlying the pathogenesis of PAM is the expression of variant surface antigens (VSAPAM) on the surface of infected red blood cells (iRBC) that mediate sequestration of the iRBC in the placenta. Naturally acquired antibodies to VSAPAMcan block sequestration and activate opsonic phagocytosis, both associated with improved pregnancy outcomes. In this review, we ask whether VSAPAMantibodies can also protect mothers against malarial anemia. Studies were identified where VSAPAMantibody titres and/or function were associated with higher maternal hemoglobin levels, thus supporting additional protective mechanisms for these antibodies against PAM. Yet these associations were not widely observed, and many studies reported no association between protection from maternal anemia and VSAPAMantibodies. We discuss the epidemiological, biological and technical factors that may explain some of the variability among these studies. We appraise the current evidence of these complex interactions between PAM-specific immunity and maternal anemia, propose potential mechanisms, and discuss knowledge gaps.
No Population Genetic Structure of Skipjack Tuna (Katsuwonus pelamis) in the Tropical Western and Central Pacific Assessed Using Single Nucleotide Polymorphisms
Authors: Anderson Giulia , Lal Monal , Stockwell Brian , Hampton John , Smith Neville , Nicol Simon , Rico Ciro
Published: December 2020

Skipjack tuna (Katsuwonus pelamis) has historically been considered panmictic at the ocean basin scale because of the species’ life history and substantial absolute population size. However, recent advances in population genomics have enabled scientists to demonstrate population structure in other species that were likewise traditionally assumed to be panmictic. Accordingly, we used DArTseq, a proprietary platform of reduced-representation genome sequencing developed by Diversity Arrays Technology (DArTech) to genotype 222 skipjack tuna from 9 sample groups collected across 6 exclusive economic zones (EEZs) and over 6 years in the tropical Western and Central Pacific Ocean. This is one of the most fine-scale population genetics assessments of skipjack tuna to date. We found several statistically significant pairwise FST comparisons using purportedly neutral loci, but very little indication of structure based on observed and expected heterozygosity, effective population size, a Mantel test, AMOVA, numerous genetic clustering and population assignment tests, and exploration of correlation with oceanographic features. Significant pairwise FST values were often shallow and resulted in uncertainty about their biological significance. Furthermore, a test of the hypothesis that the geographic and temporal distribution of the potentially adaptive genetic diversity may depict cryptic fine scale structure using two different outlier detection methods, could not reject panmixia based on estimates of fixation indices and two clustering software. Our results support the presence of a single population of skipjack tuna in the tropical Western and Central Pacific Ocean, but highly recommend the expansion of the study area, in latitude, longitude, and seasonality, before drawing any global conclusions.
Application of Spectroscopic and Hyperspectral Imaging Techniques for Rapid and Nondestructive Investigation of Jewish Ritual Parchment
Authors: Cortea Ioana Maria , Ghervase Luminiţa , Ratoiu Lucian , Rădvan Roxana
Published: December 2020

The article presents a multi-analytic investigation of a severely degraded Jewish ritual parchment coming from a private collection. The main aim of the study was to obtain key information on the parchment manufacturing technique and original materials used, information that could help understand the historical context of the object. To this aim, a series of noninvasive investigations were carried out by means of multi- and hyperspectral imaging, Fourier transform infrared (FTIR) spectroscopy and X-ray fluorescence (XRF) spectroscopy. Specific degradations and mapping of previous conservation treatments could be highlighted via multispectral imaging. Short-wave infrared images indicated the use of both iron gall and carbon black ink, probably one related to the original writing and the other to a later intervention. To improve the imaging of degraded or partially lost text, a linear spectral unmixing classification of the HSI dataset was proposed that showed promising results, allowing it to be applied to similar objects. XRF analysis offered an in-depth view of the chemical fingerprint of the original iron gall ink and critical findings on the existence of other inorganic compounds originating from the parchment manufacture. Registered FTIR data indicated denaturation of the collagen fibers and the presence of fungal-derived calcium oxalates and zinc carboxylates. In accordance with ancient Jewish parchment preparation techniques, the use of calcium sulfate, vegetable tannins, and oils was also inferred from the registered infrared spectra. The corroborated results offer valuable information on the origin, production technology, and overall degradation state of the parchment manuscript. Not least, the findings could be of great interest for conservators and restorers in the field.
Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Authors: Yang Weifeng , Wei Qing , Tong Qian , Cui Kaiyu , He Gaiying , Lin Longfei , Ma Lvyan Z. , Cornelis Pierre , Wang Yi
Published: December 2020

Pseudomonas aeruginosa is an opportunistic pathogen that can infect a wide variety of hosts including humans, plants, and animals. The production of virulence factors is the determinant of the infection paradigm and is under orchestrated regulation via cell-to-cell communication process called quorum sensing (QS). To disable QS circuits and prevent bacterial infections, a large battery of anti-QS agents, particularly from traditional Chinese medicine have been developed. Here, we used P. aeruginosa as a model microorganism to investigate the effect of traditional Chinese medicine Tanreqing (TRQ) formula on bacterial pathogenicity. Phenotypic analysis showed that TRQ treatment could completely inhibit the production of phenazine pyocyanin and moderately inhibit the production of virulence factors such as rhamnolipids, elastase, and alkaline protease. Further transcriptomic analyses revealed that TRQ treatment could significantly attenuate the expression of QS-regulated genes in P. aeruginosa and TRQ-treated P. aeruginosa regulon shared a large overlap with QS regulon. Component contribution to QS inhibition shed light on the indispensable role of all five components in TRQ formula. Further genetic analysis indicated that upstream regulators of QS systems, including two-component systems GacS/GacA and PprA/PprB, were both inhibited by TRQ treatment. Finally, our TRQ formula could efficiently protect Caenorhabditis elegans from killing by P. aeruginosa. Altogether, we have proved TRQ formula as an effective and specific agent to attenuate bacterial virulence and combat bacterial infections.
Extensive Microbial Processing of Polysaccharides in the South Pacific Gyre via Selfish Uptake and Extracellular Hydrolysis
Authors: Reintjes Greta , Fuchs Bernhard M. , Amann Rudolf , Arnosti Carol
Published: December 2020

Primary productivity occurs throughout the deep euphotic zone of the oligotrophic South Pacific Gyre (SPG), fueled largely by the regeneration of nutrients and thus recycling of organic matter. We investigated the heterotrophic capabilities of the SPG’s bacterial communities by examining their ability to process polysaccharides, an important component of marine organic matter. We focused on the initial step of organic matter degradation by measuring the activities of extracellular enzymes that hydrolyze six different polysaccharides to smaller sizes. This process can occur by two distinct mechanisms: “selfish uptake,” in which initial hydrolysis is coupled to transport of large polysaccharide fragments into the periplasmic space of bacteria, with little to no loss of hydrolysis products to the external environment, and “external hydrolysis,” in which low molecular weight (LMW) hydrolysis products are produced in the external environment. Given the oligotrophic nature of the SPG, we did not expect high enzymatic activity; however, we found that all six polysaccharides were hydrolyzed externally and taken up selfishly in the central SPG, observations that may be linked to a comparatively high abundance of diatoms at the depth and location sampled (75 m). At the edge of the gyre and close to the center of the gyre, four of six polysaccharides were externally hydrolyzed, and a lower fraction of the bacterial community showed selfish uptake. One polysaccharide (fucoidan) was selfishly taken up without measurable external hydrolysis at two stations. Additional incubations of central gyre water from depths of 1,250 and 2,800 m with laminarin (an abundant polysaccharide in the ocean) led to extreme growth of opportunistic bacteria (Alteromonas), as tracked by cell counts and next generation sequencing of the bacterial communities. These Alteromonas appear to concurrently selfishly take up laminarin and release LMW hydrolysis products. Overall, extracellular enzyme activities in the SPG were similar to activities in non-oligotrophic regions, and a considerable fraction of the community was capable of selfish uptake at all three stations. A diverse set of bacteria responded to and are potentially important for the recycling of organic matter in the SPG.
Application of a Medical Diode Laser (810 nm) for Disinfecting Small Microbiologically Contaminated Spots on Degraded Collagenous Materials for Improved Biosafety in Objects of Exceptional Historical Value From the Auschwitz-Birkenau State Museum and Protection of Human Health
Authors: Rybitwa Dorota , Wawrzyk Anna , Rahnama Mansur
Published: December 2020

The research aim was to optimize the operating parameters of a diode laser irradiation for the effective disinfection of degraded collagenous materials. Historical leather shoes stored at the Auschwitz-Birkenau State Museum in Oświęcim (Poland) were the main study objects. Surfaces of contaminated small spots occurring on the degraded materials were sampled with moistened swabs and microbiologically examined using the molecular techniques MALDI-TOF MS, 16S rRNA, and NGS sequencing. The surfaces were colonized by bacteria with 106CFU/100 cm2and 104CFU/100 cm2by fungi, on average. Microorganisms of the generaBacillusandPenicilliumwere predominant. The effectiveness of the laser treatment was assessed for the new and degraded collagenous materials against isolated environmental strains using four variants of exposure time and number of repetitions. 0.3 W/CW 2 × 2 min variant was the most effective and also did not noticeably change the color of the treated samples. The variant caused a reduction in the numbers of microorganisms by 96–100%. After 1 month, four types of leather were subjected to comprehensive physico-chemical analyses. SEM and FTIR techniques confirmed that laser irradiation in the selected optimal variant did not affect the surface morphology and collagen structure, while XPS technique enabled detection of subtle changes in non-historical protective coatings on the surfaces of tested degraded historical materials.
Propionate Production by Bioelectrochemically-Assisted Lactate Fermentation and Simultaneous CO2 Recycling
Authors: Isipato Marco , Dessì Paolo , Sánchez Carlos , Mills Simon , Ijaz Umer Z. , Asunis Fabiano , Spiga Daniela , De Gioannis Giorgia , Mascia Michele , Collins Gavin , Muntoni Aldo , Lens Piet N. L.
Published: December 2020

Production of volatile fatty acids (VFAs), fundamental building blocks for the chemical industry, depends on fossil fuels but organic waste is an emerging alternative substrate. Lactate produced from sugar-containing waste streams can be further processed to VFAs. In this study, electrofermentation (EF) in a two-chamber cell is proposed to enhance propionate production via lactate fermentation. At an initial pH of 5, an applied potential of −1 V vs. Ag/AgCl favored propionate production over butyrate from 20 mM lactate (with respect to non-electrochemical control incubations), due to the pH buffering effect of the cathode electrode, with production rates up to 5.9 mM d–1 (0.44 g L–1 d–1). Microbial community analysis confirmed the enrichment of propionate-producing microorganisms, such as Tyzzerella sp. and Propionibacterium sp. Organisms commonly found in microbial electrosynthesis reactors, such as Desulfovibrio sp. and Acetobacterium sp., were also abundant at the cathode, indicating their involvement in recycling CO2 produced by lactate fermentation into acetate, as confirmed by stoichiometric calculations. Propionate was the main product of lactate fermentation at substrate concentrations up to 150 mM, with a highest production rate of 12.9 mM d–1 (0.96 g L–1 d–1) and a yield of 0.48 mol mol–1 lactate consumed. Furthermore, as high as 81% of the lactate consumed (in terms of carbon) was recovered as soluble product, highlighting the potential for EF application with high-carbon waste streams, such as cheese whey or other food wastes. In summary, EF can be applied to control lactate fermentation toward propionate production and to recycle the resulting CO2 into acetate, increasing the VFA yield and avoiding carbon emissions and addition of chemicals for pH control.
Fast and Easy Phage-Tagging and Live/Dead Analysis for the Rapid Monitoring of Bacteriophage Infection
Authors: Low Hui Zhi , Böhnlein Christina , Sprotte Sabrina , Wagner Natalia , Fiedler Gregor , Kabisch Jan , Franz Charles M. A. P.
Published: December 2020

Use of bacteriophages, which are viruses that kill bacteria, for biocontrol of pathogens and antimicrobial resistant bacteria has become increasingly important in recent years. As traditional culture-based methods are laborious and time-consuming, practicable use of bacteriophages will hinge on development of rapid and high throughput methods to analyze, characterize and screen large bacteriophage libraries. We thus established a novel method to fluorescently tag bacteriophages for virus screening and interaction studies, without the need for complicated and laborious purification procedures or genetic engineering of viruses to express fluorescent proteins. Bacteriophage PMBT14 was tagged using DNA dye Syto 13. Simply by using a membrane filter, tagged bacteriophages can be separated from non-sequestered excess dye rapidly, effortlessly, and cheaply. The procedure takes less than 30 min and makes use of simple laboratory consumables that are already commonly used for bacteriophage preparations. As proof of concept, we present here flow cytometric methods to analyze bacteriophage binding, infection and killing that are very accessible for high throughput analysis. We show that the resulting fluorescently tagged bacteriophage can be used to specifically stain its host bacterium Pseudomonas fluorescens DSM 50090. Individual fluorescent bacteriophages, their binding to and initial infection of bacteria could also be observed using confocal microscopy. The infection process was halted by the metabolic inhibitor sodium azide, suggesting a requirement of host metabolic processes for penetration by PMBT14. Flow cytometric live/dead assays was used as a complementary method to determine bacteriophage infection of its host. We made preliminary efforts to adapt the tagging method to two other bacteriophages and discuss potential pitfalls and solutions in the use of tagged phages. Fluorescent phage tagging has previously been demonstrated to facilitate analysis of bacteriophage–host interactions. The method adopted in this study makes it fast, easy as well as cost effective.
Change of Endoglucanase Activity and Rumen Microbial Community During Biodegradation of Cellulose Using Rumen Microbiota
Authors: Takizawa Shuhei , Asano Ryoki , Fukuda Yasuhiro , Feng Mengjia , Baba Yasunori , Abe Kenichi , Tada Chika , Nakai Yutaka
Published: December 2020

Treatment with rumen microorganisms improves the methane fermentation of undegradable lignocellulosic biomass; however, the role of endoglucanase in lignocellulose digestion remains unclear. This study was conducted to investigate endoglucanases contributing to cellulose degradation during treatment with rumen microorganisms, using carboxymethyl cellulose (CMC) as a substrate. The rate of CMC degradation increased for the first 24 h of treatment. Zymogram analysis revealed that endoglucanases of 52 and 53 kDa exhibited high enzyme activity for the first 12 h, whereas endoglucanases of 42, 50, and 101 kDa exhibited high enzyme activities from 12 to 24 h. This indicates that the activities of these five endoglucanases shifted and contributed to efficient CMC degradation. Metagenomic analysis revealed that the relative abundances ofSelenomonas,Eudiplodinium, andMetadiniumdecreased after 12 h, which was positively correlated with the 52- and 53-kDa endoglucanases. Additionally, the relative abundances ofPorphyromonas,Didinium, unclassified Bacteroidetes,Clostridialesfamily XI,LachnospiraceaeandSphingobacteriaceaeincreased for the first 24 h, which was positively correlated with endoglucanases of 42, 50, and 101 kDa. This study suggests that uncharacterized and non-dominant microorganisms produce and/or contribute to activity of 40, 50, 52, 53, and 101 kDa endoglucanases, enhancing CMC degradation during treatment with rumen microorganisms.
The V617I Substitution in Avian Coronavirus IBV Spike Protein Plays a Crucial Role in Adaptation to Primary Chicken Kidney Cells
Authors: Jiang Yi , Gao Mingyan , Cheng Xu , Yu Yan , Shen Xinyue , Li Jianmei , Zhou Sheng
Published: December 2020

The naturally isolated avian coronavirus infectious bronchitis virus (IBV) generally cannot replicate in chicken kidney (CK) cells. To explore the molecular mechanism of IBV adapting to CK cells, a series of recombinant viruses were constructed by chimerizing the S genes of CK cell-adapted strain H120 and non-adapted strain IBYZ. The results showed that the S2 subunit determines the difference in cell tropism of the two strains. After comparing the amino acid sequences of S protein of CK cell-adapted strain YZ120, with its parental strain IBYZ, three amino acid substitutions, A138V, L581F, and V617I, were identified. Using YZ120 as the backbone, one or more of the above-mentioned substitutions were eliminated to verify the correlation between these sites and CK cell tropism. The results showed that the CK cell tropism of the YZ120 strain depends on the V617I substitution, the change of L581F promoted the adaptation in CK cells, and the change at 138 position was not directly related to the CK cell tropism. Further validation experiments also showed that V617I had a decisive role in the adaptation of IBV to CK cells, but other areas of the virus genome also affected the replication efficiency of the virus in CK cells.
Tomato Domestication Attenuated Responsiveness to a Beneficial Soil Microbe for Plant Growth Promotion and Induction of Systemic Resistance to Foliar Pathogens
Authors: Jaiswal Amit K. , Mengiste Tesfaye D. , Myers James R. , Egel Daniel S. , Hoagland Lori A.
Published: December 2020

Crop domestication events followed by targeted breeding practices have been pivotal for improvement of desirable traits and to adapt cultivars to local environments. Domestication also resulted in a strong reduction in genetic diversity among modern cultivars compared to their wild relatives, though the effect this could have on tripartite relationships between plants, belowground beneficial microbes and aboveground pathogens remains undetermined. We quantified plant growth performance, basal resistance and induced systemic resistance (ISR) by Trichoderma harzianum, a beneficial soil microbe against Botrytis cinerea, a necrotrophic fungus and Phytophthora infestans, a hemi-biotrophic oomycete, in 25 diverse tomato genotypes. Wild tomato related species, tomato landraces and modern commercial cultivars that were conventionally or organically bred, together, representing a domestication gradient were evaluated. Relationships between basal and ISR, plant physiological status and phenolic compounds were quantified to identify potential mechanisms. Trichoderma enhanced shoot and root biomass and ISR to both pathogens in a genotype specific manner. Moreover, improvements in plant performance in response to Trichoderma gradually decreased along the domestication gradient. Wild relatives and landraces were more responsive to Trichoderma, resulting in greater suppression of foliar pathogens than modern cultivars. Photosynthetic rate and stomatal conductance of some tomato genotypes were improved by Trichoderma treatment whereas leaf nitrogen status of the majority of tomato genotypes were not altered. There was a negative relationship between basal resistance and induced resistance for both diseases, and a positive correlation between Trichoderma-ISR to B. cinerea and enhanced total flavonoid contents. These findings suggest that domestication and breeding practices have altered plant responsiveness to beneficial soil microbes. Further studies are needed to decipher the molecular mechanisms underlying the differential promotion of plant growth and resistance among genotypes, and identify molecular markers to integrate selection for responsiveness into future breeding programs.
Signal Recognition Particle RNA Contributes to Oxidative Stress Response in Deinococcus radiodurans by Modulating Catalase Localization
Authors: Han Runhua , Fang Jaden , Jiang Jessie , Gaidamakova Elena K. , Tkavc Rok , Daly Michael J. , Contreras Lydia M.
Published: December 2020

The proper functioning of many proteins requires their transport to the correct cellular compartment or their secretion. Signal recognition particle (SRP) is a major protein transport pathway responsible for the co-translational movement of integral membrane proteins as well as periplasmic proteins.Deinococcus radioduransis a ubiquitous bacterium that expresses a complex phenotype of extreme oxidative stress resistance, which depends on proteins involved in DNA repair, metabolism, gene regulation, and antioxidant defense. These proteins are located extracellularly or subcellularly, but the molecular mechanism of protein localization inD. radioduransto manage oxidative stress response remains unexplored. In this study, we characterized the SRP complex inD. radioduransR1 and showed that the knockdown (KD) of the SRP RNA (Qpr6) reduced bacterial survival under hydrogen peroxide and growth under chronic ionizing radiation. Through LC-mass spectrometry (MS/MS) analysis, we detected 162 proteins in the periplasm of wild-typeD. radiodurans, of which the transport of 65 of these proteins to the periplasm was significantly reduced in the Qpr6 KD strain. Through Western blotting, we further demonstrated the localization of the catalases inD. radiodurans, DR_1998 (KatE1) and DR_A0259 (KatE2), in both the cytoplasm and periplasm, respectively, and showed that the accumulation of KatE1 and KatE2 in the periplasm was reduced in the SRP-defective strains. Collectively, this study establishes the importance of the SRP pathway in the survival and the transport of antioxidant proteins inD. radioduransunder oxidative stress.
A Novel Mobile Element ICERspD18B in Rheinheimera sp. D18 Contributes to Antibiotic and Arsenic Resistance
Authors: Fu Jiafang , Zhong Chuanqing , Zhang Peipei , Gao Qingxia , Zong Gongli , Zhou Yingping , Cao Guangxiang
Published: December 2020

Antibiotics and organoarsenical compounds are frequently used as feed additives in many countries. However, these compounds can cause serious antibiotic and arsenic (As) pollution in the environment, and the spread of antibiotic and As resistance genes from the environment. In this report, we characterized the 28.5 kb genomic island (GI), named as ICERspD18B, as a novel chromosomal integrative and conjugative element (ICE) in multidrug-resistant Rheinheimera sp. D18. Notably, ICERspD18B contains six antibiotic resistance genes (ARGs) and an arsenic tolerance operon, as well as genes encoding conjugative transfer proteins of a type IV secretion system, relaxase, site-specific integrase, and DNA replication or partitioning proteins. The transconjugant strain 25D18-B4 was generated using Escherichia coli 25DN as the recipient strain. ICERspD18B was inserted into 3'-end of the guaA gene in 25D18-B4. In addition, 25D18-B4 had markedly higher minimum inhibitory concentrations for arsenic compounds and antibiotics when compared to the parental E. coli strain. These findings demonstrated that the integrative and conjugative element ICERspD18B could mediate both antibiotic and arsenic resistance in Rheinheimera sp. D18 and the transconjugant 25D18-B4.