bluuebunny/crossref_metadata_2025 huggingface dataset:
The Role of Heat Shock Proteins in Type 1 Diabetes
Authors: Moin Abu Saleh Md , Nandakumar Manjula , Diane Abdoulaye , Dehbi Mohammed , Butler Alexandra E.
Published: January 2021

Type 1 diabetes (T1D) is a T-cell mediated autoimmune disease characterized by recognition of pancreatic β-cell proteins as self-antigens, called autoantigens (AAgs), followed by loss of pancreatic β-cells. (Pre-)proinsulin ([P]PI), glutamic acid decarboxylase (GAD), tyrosine phosphatase IA-2, and the zinc transporter ZnT8 are key molecules in T1D pathogenesis and are recognized by autoantibodies detected in routine clinical laboratory assays. However, generation of new autoantigens (neoantigens) from β-cells has also been reported, against which the autoreactive T cells show activity. Heat shock proteins (HSPs) were originally described as “cellular stress responders” for their role as chaperones that regulate the conformation and function of a large number of cellular proteins to protect the body from stress. HSPs participate in key cellular functions under both physiological and stressful conditions, including suppression of protein aggregation, assisting folding and stability of nascent and damaged proteins, translocation of proteins into cellular compartments and targeting irreversibly damaged proteins for degradation. Low HSP expression impacts many pathological conditions associated with diabetes and could play a role in diabetic complications. HSPs have beneficial effects in preventing insulin resistance and hyperglycemia in type 2 diabetes (T2D). HSPs are, however, additionally involved in antigen presentation, presenting immunogenic peptides to class I and class II major histocompatibility molecules; thus, an opportunity exists for HSPs to be employed as modulators of immunologic responses in T1D and other autoimmune disorders. In this review, we discuss the multifaceted roles of HSPs in the pathogenesis of T1D and in autoantigen-specific immune protection against T1D development.
Using the Stable Isotopic Composition of Heliconoides inflatus Pteropod Shells to Determine Calcification Depth in the Cariaco Basin
Authors: Oakes Rosie L. , Davis Catherine V. , Sessa Jocelyn A.
Published: January 2021

Pteropods have been hailed as the “canary in the coal mine” for ocean acidification, however, questions remain about their life history, habitat, and the environmental parameters that the isotopic composition of their shells reflect. In order to use pteropods as recorders of ocean chemistry, it is first necessary to understand where they calcify and how this may change through the year, whether this signal is affected by dissolution, and if shells are retained in the subfossil, and eventually fossil, record. Here we create the first annual record of the stable isotopic composition of shells of the pteropodHeliconoides inflatusin the Cariaco Basin, Venezuela utilizing samples and data from the CARIACO time series. Sixty-fourH. inflatusspecimens from 17 sediment trap samples between November 1996 and April 1998, and 22 specimens from the late Holocene-aged CAR2000-MC-2 core were analyzed for shell condition (an assessment of the amount of dissolution that a shell has experienced), size, and carbon and oxygen isotopic composition. Carbon isotopic measurements of juveniles (< 1mm) were more variable than those in adults (>1 mm), suggesting juvenile pteropods likely have a higher growth rate, and therefore different metabolic vital effects, and a more varied diet than adult pteropods.H. inflatuswas found to have an apparent calcification depth of 51.2 ± 34.0 m, suggesting they calcify at the shallowest part of their diurnal migration in the mixed layer (10–35 m in the Cariaco Basin).H. inflatusshell calcification will therefore only be impacted by changes in water chemistry at mixed layer depths. The shell condition did not impact the stable isotopic composition of the shells in either the sediment trap or core sample, suggesting the potential for using the isotopic composition of pteropod shells as oceanographic proxies when they are preserved. Comparisons between sediment trap and core sample show a 0.5°C warming that is marginally significant and a significant 0.45‰ decrease in δ13C between the late Holocene and the late 1990's. These measurements reflect changes in oceanic conditions linked to anthropogenic fossil fuel emissions known as the Suess effect, and lay the groundwork for establishing pteropods as paleoceanographic proxies in the future.
High-Resolution Carbonate System Dynamics of Netarts Bay, OR From 2014 to 2019
Authors: Fairchild William , Hales Burke
Published: January 2021

Netarts Bay is a shallow, temperate, tidal lagoon located on the northern coast of Oregon and the site of the Whiskey Creek Shellfish Hatchery (WCSH). Data collected with an autonomous continuous flow-through system installed at WCSH capable of high-resolution (1 Hz) partial pressure of aqueous CO2 (pCO2) and hourly total dissolved inorganic carbon (TCO2) measurements, with combined measurement uncertainties of < 2.0% and 0.5%, respectively, is analyzed over the 2014–2019 interval. Summer upwelling, wintertime downwelling, and in situ bay biogeochemistry represent significant modes of the observed variability in carbonate system dynamics. Summer upwelling is associated with large amplitude diel pCO2 variability, elevated TCO2 and alkalinity, but weak variability in salinity. Wintertime downwelling is associated with bay freshening by both local and remote sources, a strong tidal signature in salinity, TCO2, and alkalinity, with diel pCO2 variability much less amplified when compared to summer. Further, analysis of alkalinity-salinity relationships suggests multiple water masses inhabiting the bay during 1 year: mixing of end-members associated with direct precipitation, coastal rivers, southward displacement of the Columbia River plume, California Current surface and deep upwelled waters. The importance of in-bay processes such as net community metabolism during intervals of high productivity are apparent. These direct measurements of pCO2 and TCO2 have been useful to local hatchery owners who have monitored intake waters following historic seed-production failures related to high-CO2 conditions exacerbated by ocean acidification.
Long-Term Presence of the Island Mass Effect at Rangiroa Atoll, French Polynesia
Authors: Vollbrecht Carleigh , Moehlenkamp Paula , Gove Jamison M. , Neuheimer Anna B. , McManus Margaret A.
Published: January 2021

Enhancement of phytoplankton biomass near island and atoll reef ecosystems—termed the Island Mass Effect (IME)—is an ecologically important phenomenon driving marine ecosystem trophic structure and fisheries in the midst of oligotrophic tropical oceans. This study investigated the occurrence of IME at Rangiroa Atoll in the French Polynesian Tuamotu archipelago, and the physical mechanisms driving IME, through the analysis of satellite and in situ data. Comparison of chlorophyll-a concentration near Rangiroa Atoll with chlorophyll-a concentration in open ocean water 50 km offshore, over a 16-year period, showed phytoplankton enhancement as high as 130% nearshore, over 75.7% of the study period. Our statistical model examining physical drivers showed the magnitude of IME to be significantly enhanced by higher sea surface temperature (SST) and lower photosynthetically active radiation (PAR). Further, in situ measurements of water flowing through Tiputa Channel revealed outflowing lagoon water to be warmer, lower in salinity, and higher in particulate load compared to ocean water. We suggest that water inside Rangiroa’s lagoon is enriched in nutrients and organic material by biological processes and advected as a result of tidal and wave forcing to coastal ocean waters, where it fuels primary production. We suggest that a combination of oceanographic and biological mechanisms is at play driving frequency and magnitude of IME at Rangiroa Atoll. Understanding the underlying processes driving IME at Rangiroa is essential for understanding future changes caused by a warming climate and changing environmental conditions for the marine ecosystem.
Hydroperiod and Salinity Interactions Control Mangrove Root Dynamics in a Karstic Oceanic Island in the Caribbean Sea (San Andres, Colombia)
Authors: Medina-Calderón Jairo Humberto , Mancera-Pineda José Ernesto , Castañeda-Moya Edward , Rivera-Monroy Víctor H.
Published: January 2021

Mangroves sustain high soil accretion and carbon sequestration rates, yet it is still unknown if they can keep pace with increasing sea level rise (SLR) across a wider range of coastal geomorphic settings. Because accretion rates are controlled by mineral sediment inputs and organic matter accumulation, it is paramount to assess the relative contribution of root productivity to soil formation. Here, we evaluated root biomass, production, and turnover in three mangrove ecotypes to evaluate the role of soil nutrient limitation, stressors, and hydroperiod in controlling root dynamics in San Andres Island (SAI), a karstic oceanic island in the Caribbean Sea. Root production was modulated by soil stress conditions and not by nutrient availability as it has been reported for other karstic environments. The lowest root biomass allocation, and both production and turnover of fine roots were measured under low flooding duration, and low salinity (<20 PSU) and sulfide concentrations (0.84 ± 0.4 mM). Yet, when soil stress conditions increased during high flooding duration (6207 h y–1) and low oxygen conditions (Eh), root tissues reached the highest biomass and production values, including a relative fast turnover of fine roots (<2 mm; 0.75 y–1). Our results follow the predictions of the plant root longevity cost-benefit hypothesis where plants maintain roots only until the efficiency of resource acquisition is maximized by water and nutrient acquisition. Because of the importance of groundwater in controlling porewater salinity and mangrove root productivity in karstic oceanic islands such as SAI, water use and coastal development should be regulated in the short term to avoid the loss of mangrove area and concomitant ecosystem services.
Inconsistency Between Socio-Spatial and Genetic Structure in a Coastal Dolphin Population
Authors: Chabanne Delphine B. H. , Allen Simon J. , Sherwin William Bruce , Finn Hugh , Krützen Michael
Published: January 2021

Identifying population structure and boundaries among communities of wildlife exposed to anthropogenic threats is key to successful conservation management. Previous studies on the demography, social and spatial structure of Indo-Pacific bottlenose dolphins (Tursiops aduncus) suggested four nearly discrete behavioral communities in Perth metropolitan waters, Western Australia. We investigated the genetic structure of these four communities using highly polymorphic microsatellite markers and part of the hypervariable segment of the mitochondrial control region. Overall, there was no evidence of spatial genetic structure. We found significant, yet very small genetic differentiation between some communities, most likely due to the presence of highly related individuals within these communities. Our findings of high levels of contemporary migration and highly related individuals among communities point toward a panmictic genetic population with continuous gene flow among each of the communities. In species with slow life histories and fission-fusion dynamics, such asTursiopsspp., genetic and socio-spatial structures may reflect different timescales. Thus, despite genetic similarity, each social community should be considered as a distinct ecological unit to be conserved because they are exposed to different anthropogenic threats and occur in different ecological habitats, social structure being as important as genetic information for immediate conservation management. The estuarine community, in particular, is highly vulnerable and appropriate conservation measures are needed in order to maintain its connectivity with the adjacent, semi-enclosed coastal communities.
DNA Barcoding of Fish in Mischief Reef—Fish Diversity of a Reef Fish Community From Nansha Islands
Authors: Shan Binbin , Liu Yan , Yang Changping , Zhao Yu , Zhang Gongjun , Wu Qiaer , Sun Dianrong
Published: January 2021

Development of effective conservation and management strategies requires assessments of ecosystem biodiversity status, especially in understudied hotspots of global fish diversity. Coral reefs are important habitats for fishes, with biodiversity hotspots known globally. We present the first data on molecular diversity of fishes of Mischief Reef, the largest atoll in the Nansha Islands. Partial sequences (650 bp) of mitochondrial COI gene (Cytochrome c oxidase subunit I) are used to identify 209 individuals, representing 101 species, referable to 62 genera, 27 families, 8 orders, and 1 class. The most abundant orders are the Perciformes (176 specimens, 84.21%), Tetraodontiformes (13 specimens, 6.22%), and Beryciformes (13 specimens, 6.22%). Mean Kimura 2-Parameter genetic distances within genera, families, and orders are 4.51, 13.90, and 17.63%, respectively. We record Monotaxis heterodon from this region for the first time—a species that may previously have been misidentified as M. grandoculis. In addition, we recognized possible cryptic species of Lethrinus olivaceus based on significantly diverging barcode sequences. Barcode data provide new insights into fish diversity of Mischief Reef, important for developing further researches on this fauna, and for its conservation.
Manuka Honey and Zein Coatings Impart Bioactive Glass Bone Tissue Scaffolds Antibacterial Properties and Superior Mechanical Properties
Authors: Arango-Ospina Marcela , Lasch Kristina , Weidinger Julius , Boccaccini Aldo R.
Published: January 2021

The combination of traditional herbal medicine (phytotherapeutic agents) with bioactive glasses is a promising strategy to generate advanced scaffolds for bone tissue engineering (BTE). An old remedy used for wound care since ancient times is honey. The antioxidant, antimicrobial and antibacterial properties of Manuka honey, in particular, make it an attractive substance for application in BTE scaffolds to prevent infections and biofilm formation. In this study 45S5 bioactive glass-based scaffolds produced via the foam replica technique were coated with corn protein zein and Manuka honey with two purposes: to improve the mechanical properties of the brittle scaffolds and to impart antibacterial properties. The morphology and chemical composition of the coated scaffolds were characterized with scanning electron microscopy and Fourier transform infrared spectroscopy, respectively, demonstrating the presence of Manuka honey in the coating. The release of the honey was quantified via ultraviolet-visible spectrophotometry; moreover, the antibacterial activity against Staphylococcus aureus was evaluated via colony-forming units counting, reduction of Alamar blue and turbidity measurements. Our findings suggest the effective combination of Manuka honey and bioactive glass, adding one more system to the novel family of bioactive glass scaffolds functionalized with phytotherapeutic agents.
Hot Stamping of a B-Pillar Reinforced Panel With 7075 Aluminum Alloy and the Feasibility Study of Short-Time Aging
Authors: Liu Yong , Li Jiahao , Wang Liang , Wang Kai , Zhu Bin , Zhang Yisheng
Published: January 2021

The hot stamping of a B-pillar reinforced panel with 7075 aluminum alloy was carried out in an industrial production line. The effect of blank holding force (BHF) on the formability of the B-pillar reinforced panel and the effect of solution heat treatment (SHT) time on the mechanical properties were studied. Additionally, the forming precisions of a formed part before and after standard aging were detected further. Finally, both standard aging and short-time aging processes were carried out to investigate the feasibility of short-time aging for real parts. The stamping results demonstrated that lower BHF or no blank holding should be used during hot stamping to avoid cracking and wrinkling. The detection of forming precisions indicated that the great majority of measured points on the part were within ±1 mm of nominal. The mechanical property testing showed that the strength of the formed parts after a short-time aging was up to more than 90% of the as-received T6 state and more than 93% of the time can be reduced if the 90% of strength can be accepted.
Family Medicine Training in Lesotho: A Strategy of Decentralized Training for Rural Physician Workforce Development
Authors: Bryden Benjamin , Bryden Mariel , Steer-Massaro Jonathan , Malope Sebaka
Published: January 2021

Family medicine is a relatively new but rapidly expanding medical discipline in Sub-Saharan Africa. Specialization in family medicine is an effective means for building and retaining a highly skilled rural physician workforce in low- and middle-income countries. The Lesotho Boston Health Alliance Family Medicine Specialty Training Program is the first and only postgraduate family medicine program and the only accredited postgraduate training program in the Kingdom of Lesotho. Lesotho has unique challenges as a small mountainous enclave of South Africa with one of the lowest physician-to-patient ratios in the world. Most health professionals are based in the capital city, and the kingdom faces challenging health problems such as high human immunodeficiency virus prevalence, high maternal mortality, and malnutrition, as well as increasing burdens of non-communicable diseases such as hypertension, diabetes, and obesity. In response to these health crises and the severe shortage of health professionals, Lesotho Boston Health Alliance partnered with the Lesotho Ministry of Health in 2008 to introduce family medicine as a new specialty in order to recruit home and retain Basotho doctors. Family medicine training in Lesotho uses a unique decentralized, non-university-based model with trainees posted at rural district hospitals throughout the country. While family medicine in Lesotho is still in the early stages of development, this model of decentralized training demonstrates an effective strategy to develop the rural health workforce in Lesotho, has the potential to change the physician workforce and health care system of Lesotho, and can be a model for physician training in similar environments.
Structural Comparison of the SARS CoV 2 Spike Protein Relative to Other Human-Infecting Coronaviruses
Authors: Cueno Marni E. , Imai Kenichi
Published: January 2021

Coronaviruses (CoV) are enveloped positive-stranded RNA viruses and, historically, there are seven known human-infecting CoVs with varying degrees of virulence. CoV attachment to the host is the first step of viral pathogenesis and mainly relies on the spike glycoprotein located on the viral surface. Among the human-infecting CoVs, only the infection of SARS CoV 2 (SARS2) among humans resulted to a pandemic which would suggest that the protein structural conformation of SARS2 spike protein is distinct as compared to other human-infecting CoVs. Surprisingly, the possible differences and similarities in the protein structural conformation between the various human-infecting CoV spike proteins have not been fully elucidated. In this study, we utilized a computational approach to generate models and analyze the seven human-infecting CoV spike proteins, namely: HCoV 229E, HCoV OC43, HCoV NL63, HCoV HKU1, SARS CoV, MERS CoV, and SARS2. Model quality assessment of all CoV models generated, structural superimposition of the whole protein model and selected S1 domains (S1-CTD and S1-NTD), and structural comparison based on RMSD values, Tm scores, and contact mapping were all performed. We found that the structural orientation of S1-CTD is a potential structural feature associated to both the CoV phylogenetic cluster and lineage. Moreover, we observed that spike models in the same phylogenetic cluster or lineage could potentially have similar protein structure. Additionally, we established that there are potentially three distinct S1-CTD orientation (Pattern I, Pattern II, Pattern III) among the human-infecting CoVs. Furthermore, we postulate that human-infecting CoVs in the same phylogenetic cluster may have similar S1-CTD and S1-NTD structural orientation. Taken together, we propose that the SARS2 spike S1-CTD follows a Pattern III orientation which has a higher degree of similarity with SARS1 and some degree of similarity with both OC43 and HKU1 which coincidentally are in the same phylogenetic cluster and lineage, whereas, the SARS2 spike S1-NTD has some degree of similarity among human-infecting CoVs that are either in the same phylogenetic cluster or lineage.
The Comorbid Relationship Between Migraine and Asthma: A Systematic Review and Meta-Analysis of Population-Based Studies
Authors: Wang Long , Deng Zi-Ru , Zu Mei-Dan , Zhang Juan , Wang Yu
Published: January 2021

Objective: Recent studies have indicated a pathophysiologic link between migraine and asthma. This meta-analysis aimed to comprehensively estimate the risk ratio for migraine in asthma as well as that of asthma in migraine based on available evidence.

Method: We systematically searched the electronic databases including PubMed, Web of Science, and SCOPUS for population-based studies that measured either the odds or the risk of asthma in subjects with migraine as well as that of migraine in subjects with asthma. The titles and abstracts were screened by two independent reviewers to identify eligible studies, and this was followed by full-text review of the included studies. Newcastle–Ottawa Scale (NOS) was used to assess the risk of bias of included literature. A meta-analysis was conducted with Review Manager 5.3 Software to calculate the odds ratio (OR) for case-control and cross-sectional studies and either relative ratio (RR) or hazard ratio (HR) for cohort studies, and the source of heterogeneity was assessed. Subgroup and sensitivity analyses were conducted, and the I2 test were used to assess the source of heterogeneity. The funnel plot, Galbraith plot, and Egger's test were used to evaluate publication bias.

Results: Fifteen published studies covering a total of 1,188,780 individuals were identified. Pooled analysis indicated that migraine was associated with increased odds (OR = 1.54; 95% CI: 1.34~1.77) and risk for asthma (HR = 1.42; 95% CI: 1.26~1.60), and asthma associated with increased odds (OR = 1.45; 95% CI: 1.22~1.72) and risk for migraine (HR = 1.47; 95% CI: 1.41~1.52).

Conclusion: Migraine is a potential risk indicator for asthma, and vice versa, asthma is a potential risk indicator for migraine. However, future prospective cohort studies are warranted to provide more evidence concerning the detailed association between migraine and asthma.
Dermoscopic Patterns in Juvenile Xanthogranuloma Based on the Histological Classification
Authors: Xu Jiaosheng , Ma Lin
Published: January 2021

Background: Several dermoscopic features of juvenile xanthogranuloma (JXG) have been previously described in single cases or small case series and need to be further verified in a large sample.

Objective: We aimed to investigate the dermoscopic patterns of JXG in a large case series and the correlations of these with clinical features of different histopathological subtypes of JXG.

Methods: Patients who underwent dermoscopic evaluation and had a histopathological diagnosis of JXG were recruited. Histological findings, including stage and Ki67 proliferative index and the dermoscopic features of each lesion were recorded.

Results: Forty-one patients with JXG were included. The male to female ratio was 1.28: 1 and the median age of onset was 11 months (range: 0–95 months). Fourteen lesions were histologically categorized in the early stage, 17 in the developed stage, and 10 in the late stage. The “setting sun” pattern was observed in 35 lesions (85.4%) and “clouds” of paler yellow areas in 26 lesions (63.4%). The frequency of the “setting sun” pattern was higher in the early and developed stages (30/31) than in the late stage (5/10) (P = 0.002), while that of “clouds” of paler yellow areas was not significantly different between each stage. Branched linear vessels were detected in the early (11/14) and developed stage (6/17), but not in the late stage. The mean Ki67 index of the lesions with linear vessels was 11.8% (range: 2–40%), which was higher than that of lesions without linear vessels (mean index: 5%, range: 1–30%) (P = 0.005). The pigment network and whitish areas were only detected in 6 and 5 lesions in the late stage, respectively. The whitish areas presented either as streak or stellate shape. The pigment network exhibited either in a centric or a peripheral pattern.

Conclusions: The “setting sun” pattern is the characteristic dermoscopic features of JXG in the early and developed stages, while whitish areas and pigment network are the characteristic patterns in the late stage. Linear vessels present as branched patterns and mostly occur in the early stage with a high proliferative index, indicating rapid growth. The whitish areas and pigment network may present in various patterns. Dermoscopy is a useful adjunctive tool in the diagnosis and staging of JXG.
Effects of Mosquito Microbiota on the Survival Cost and Development Success of Avian Plasmodium
Authors: Martínez-de la Puente Josué , Gutiérrez-López Rafael , Díez-Fernández Alazne , Soriguer Ramón C. , Moreno-Indias Isabel , Figuerola Jordi
Published: January 2021

Both intrinsic and extrinsic factors affect the capacity of mosquitoes for the transmission of vector-borne pathogens. Among them, mosquito microbiota may play a key role determining the development of pathogens in mosquitoes and the cost of infections. Here, we used a wild avian malaria-mosquito assemblage model to experimentally test the role of vector microbiota on the cost of infection and their consequences for parasite development. To do so, a cohort of Culex pipiens mosquitoes were treated with antibiotics, including gentamicin sulfate and penicillin-streptomycin, to alter their microbiota, and other cohort was treated with sterilized water as controls. Subsequently, both cohorts were allowed to feed on Plasmodium infected or uninfected house sparrows (Passer domesticus). The antibiotic treatment significantly increased the survival rate of mosquitoes fed on infected birds while this was not the case of mosquitoes fed on uninfected birds. Additionally, a higher prevalence of Plasmodium in the saliva of mosquitoes was found in antibiotic treated mosquitoes than in mosquitoes of the control group at 20 days post exposure (dpe). Analyses of the microbiota of a subsample of mosquitoes at 20 dpe suggest that although the microbiota diversity did not differ between individuals of the two treatments, microbiota in control mosquitoes had a higher number of unique features and enriched in biochemical pathways related to the immune system than antibiotic treated ones. In sum, this study provides support for the role of mosquito microbiota on mosquito survival and the presence of parasite DNA in their saliva.
A Thermostable, Modified Cathelicidin-Derived Peptide With Enhanced Membrane-Active Activity Against Salmonella enterica serovar Typhimurium
Authors: Klubthawee Natthaporn , Aunpad Ratchaneewan
Published: January 2021

Foodborne illness caused by consumption of food contaminated with Salmonella is one of the most common causes of diarrheal disease and affects millions of people worldwide. The rising emergence and spread of antimicrobial resistance, especially in some serotypes of Salmonella, has raised a great awareness of public health issues worldwide. To ensure safety of the food processing chain, the development of new food preservatives must be expedited. Recently, thermal- and pH-stable antimicrobial peptides have received much attention for use in food production, and represent safe alternatives to chemical preservatives. A 12-mer cathelicidin-derived, α-helical cationic peptide, P7, displayed rapid killing activity, against strains of drug-resistant foodborne Salmonella enterica serovar Typhimurium and its monophasic variant (S. enterica serovar 4,5,12:i:-) and had minimal toxicity against mouse fibroblast cells. P7 tended to form helical structure in the membrane-mimic environments as evaluated by circular dichroism (CD) spectroscopy. The action mode of P7 at the membrane-level was affirmed by the results of flow cytometry, and confocal, scanning and transmission electron microscopy. P7 killed bacteria through binding to bacterial membranes, penetration and the subsequent accumulation in S. enterica serovar Typhimurium cytoplasm. This induced membrane depolarization, permeabilization, and sequential leakage of intracellular substances and cell death. Except for sensitivity to proteolytic digestive enzymes, P7 maintained its inhibitory activity against S. enterica serovar Typhimurium in the presence of different conditions [various salts, extreme pHs and heat (even at 100°C)]. Moreover, the peptide is unlikely to induce bacterial resistance in vitro. Taken together, this study demonstrated that the membrane-permeabilizing P7 peptide has much potential as a new antimicrobial agent for use in food processing and preservation.
The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria
Authors: Esquivel-Elizondo Sofia , Bağcı Caner , Temovska Monika , Jeon Byoung Seung , Bessarab Irina , Williams Rohan B. H. , Huson Daniel H. , Angenent Largus T.
Published: January 2021

Bulk production of medium-chain carboxylates (MCCs) with 6–12 carbon atoms is of great interest to biotechnology. Open cultures (e.g., reactor microbiomes) have been utilized to generate MCCs in bioreactors. When in-line MCC extraction and prevention of product inhibition is required, the bioreactors have been operated at mildly acidic pH (5.0–5.5). However, model chain-elongating bacteria grow optimally at neutral pH values. Here, we isolated a chain-elongating bacterium (strain 7D4C2) that grows at mildly acidic pH. We studied its metabolism and compared its whole genome and the reverse β-oxidation (rBOX) genes to other bacteria. Strain 7D4C2 produces lactate, acetate, n-butyrate, n-caproate, biomass, and H2/CO2 from hexoses. With only fructose as substrate (pH 5.5), the maximum n-caproate specificity (i.e., products per other carboxylates produced) was 60.9 ± 1.5%. However, this was considerably higher at 83.1 ± 0.44% when both fructose and n-butyrate (electron acceptor) were combined as a substrate. A comparison of 7D4C2 cultures with fructose and n-butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing n-caproate specificity from ∼92% at mildly acidic pH (pH 4.5-5.0) to ∼24% at alkaline pH (pH 9.0). Moreover, when carboxylates were extracted from the broth (undissociated n-caproic acid was ∼0.3 mM), the n-caproate selectivity (i.e., product per substrate fed) was 42.6 ± 19.0% higher compared to 7D4C2 cultures without extraction. Based on the 16S rRNA gene sequence, strain 7D4C2 is most closely related to the isolates Caproicibacter fermentans (99.5%) and Caproiciproducens galactitolivorans (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, C. fermentans, and C. galactitolivorans belong to the same genus of Caproiciproducens. Their rBOX genes are conserved and located next to each other, forming a gene cluster, which is different than for other chain-elongating bacteria such as Megasphaera spp. In conclusion, Caproiciproducens spp., comprising strain 7D4C2, C. fermentans, C. galactitolivorans, and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. Caproiciproducens sp. 7D4C2 (DSM 110548) was studied here to understand n-caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into n-caproate.
Characterization of the First Virulent Phage Infecting Oenococcus oeni, the Queen of the Cellars
Authors: Philippe Cécile , Chaïb Amel , Jaomanjaka Fety , Claisse Olivier , Lucas Patrick M. , Samot Johan , Cambillau Christian , Le Marrec Claire
Published: January 2021

There has been little exploration of how phages contribute to the diversity of the bacterial community associated with winemaking and may impact fermentations and product quality. Prophages of Oenococcus oeni, the most common species of lactic acid bacteria (LAB) associated with malolactic fermentation of wine, have been described, but no data is available regarding phages of O. oeni with true virulent lifestyles. The current study reports on the incidence and characterization of the first group of virulent oenophages named Vinitor, isolated from the enological environment. Vinitor phages are morphologically very similar to siphoviruses infecting other LAB. Although widespread during winemaking, they are more abundant in musts than temperate oenophages. We obtained the complete genomic sequences of phages Vinitor162 and Vinitor27, isolated from white and red wines, respectively. The assembled genomes shared 97.6% nucleotide identity and belong to the same species. Coupled with phylogenetic analysis, our study revealed that the genomes of Vinitor phages are architecturally mosaics and represent unique combinations of modules amongst LAB infecting-phages. Our data also provide some clues to possible evolutionary connections between Vinitor and (pro)phages associated to epiphytic and insect-related bacteria.
Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce
Authors: Windisch Saskia , Sommermann Loreen , Babin Doreen , Chowdhury Soumitra Paul , Grosch Rita , Moradtalab Narges , Walker Frank , Höglinger Birgit , El-Hasan Abbas , Armbruster Wolfgang , Nesme Joseph , Sørensen Søren Johannes , Schellenberg Ingo , Geistlinger Jörg , Smalla Kornelia , Rothballer Michael , Ludewig Uwe , Neumann Günter
Published: January 2021

Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76–90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87–97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61–74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.
Integrative Analysis of Whole Genome Sequencing and Phenotypic Resistance Toward Prediction of Trimethoprim-Sulfamethoxazole Resistance in Staphylococcus aureus
Authors: Nurjadi Dennis , Zizmann Elfi , Chanthalangsy Quan , Heeg Klaus , Boutin Sébastien
Published: January 2021

As whole genome sequencing is becoming more accessible and affordable for clinical microbiological diagnostics, the reliability of genotypic antimicrobial resistance (AMR) prediction from sequencing data is an important issue to address. Computational AMR prediction can be performed at multiple levels. The first-level approach, such as simple AMR search relies heavily on the quality of the information fed into the database. However, AMR due to mutations are often undetected, since this is not included in the database or poorly documented. Using co-trimoxazole (trimethoprim-sulfamethoxazole) resistance in Staphylococcus aureus, we compared single-level and multi-level analysis to investigate the strengths and weaknesses of both approaches. The results revealed that a single mutation in the AMR gene on the nucleotide level may produce false positive results, which could have been detected if protein sequence analysis would have been performed. For AMR predictions based on chromosomal mutations, such as the folP gene of S. aureus, natural genetic variations should be taken into account to differentiate between variants linked to genetic lineage (MLST) and not over-estimate the potential resistant variants. Our study showed that careful analysis of the whole genome data and additional criterion such as lineage-independent mutations may be useful for identification of mutations leading to phenotypic resistance. Furthermore, the creation of reliable database for point mutations is needed to fully automatized AMR prediction.
Novel Naturally Occurring Mutations of Enterovirus 71 Associated With Disease Severity
Authors: Chang Chih-Shin , Liao Chun-Che , Liou An-Ting , Chou Yi-Chun , Yu Ya-Yen , Lin Chi-Yung , Lin Jen-Shiou , Suen Ching-Shu , Hwang Ming-Jing , Shih Chiaho
Published: January 2021

Infection with the re-emerging enterovirus 71 (EV-A71) is associated with a wide range of disease severity, including herpangina, encephalitis, and cardiopulmonary failure. At present, there is no FDA-approved therapeutics for EV-A71. Early diagnosis for the high-risk children is the key to successful patient care. We examined viral genome sequences at the 5′ untranslated region (UTR) and the capsid protein VP1 from 36 mild and 27 severe cases. We identified five EV-A71 mutations associated with severe diseases, including (1) the 5′ UTR mutations C580U, A707G, C709U; (2) a VP1 alanine-to-threonine mutation at position 280 (280T), and (3) a VP1 glutamic acid-to-(non-glutamic acid) at position 145 [145(non-E)]. SCARB2 is a known entry receptor for EV-A71. Based on a recent cryoEM structure of the EV-A71-SCARB2 binding complex, VP1-280T is near the binding interface between the VP1-VP2 complex and its entry receptor SCARB2. Ade novocreated hydrogen bonding between the mutant VP1-280T and the VP2-139T, could help strengthen a web-like interaction structure of the VP1-VP2 complex. A stabilized loop turn of VP2, once in contact with SCARB2, can enhance interaction with the host SCARB2 receptor for viral entry. Our findings here could facilitate early detection of severe cases infected with EV-A71 in clinical medicine. In addition, it opens up the opportunity of functional studies via infectious cDNA cloning, site-directed mutagenesis, and animal models in the future.
Within-Host Microevolution of Pseudomonas aeruginosa Urinary Isolates: A Seven-Patient Longitudinal Genomic and Phenotypic Study
Authors: Cottalorda Agnès , Leoz Marie , Dahyot Sandrine , Gravey François , Grand Maxime , Froidure Thomas , Aujoulat Fabien , Le Hello Simon , Jumas-Bilak Estelle , Pestel-Caron Martine
Published: January 2021

Background

Pseudomonas aeruginosa is responsible for up to 10% of healthcare associated urinary tract infections (UTI), which can be difficult to treat and can lead to bacterial persistence. While numerous whole genome sequencing (WGS) analyses have explored within-host genomic adaptation and microevolution of P. aeruginosa during cystic fibrosis (CF) infections, little is known about P. aeruginosa adaptation to the urinary tract.

Results

Whole genome sequencing was performed on 108 P. aeruginosa urinary isolates, representing up to five isolates collected from 2 to 5 successive urine samples from seven patients hospitalized in a French hospital over 48–488 days. Clone type single nucleotide polymorphisms (ctSNPs) analysis revealed that each patient was colonized by a single clone type (<6000 SNPs between two isolates) at a given time and over time. However, 0–126 SNPs/genome/year were detected over time. Furthermore, large genomic deletions (1–5% of the genome) were identified in late isolates from three patients. For 2 of them, a convergent deletion of 70 genes was observed. Genomic adaptation (SNPs and deletion) occurred preferentially in genes encoding transcriptional regulators, two-component systems, and carbon compound catabolism. This genomic adaptation was significantly associated with a reduced fitness, particularly in artificial urine medium, but no strict correlation was identified between genomic adaptation and biofilm formation.

Conclusion

This study provides the first insight into P. aeruginosa within-host evolution in the urinary tract. It was driven by mutational mechanisms and genomic deletions and could lead to phenotypic changes in terms of fitness and biofilm production. Further metabolomic and phenotypic analyses are needed to describe in-depth genotype-phenotype associations in this complex and dynamic host-environment.
Glucose Oxidation to Pyruvate Is Not Essential for Brucella suis Biovar 5 Virulence in the Mouse Model
Authors: Lázaro-Antón Leticia , de Miguel María Jesús , Barbier Thibault , Conde-Álvarez Raquel , Muñoz Pilar M. , Letesson Jean Jacques , Iriarte Maite , Moriyón Ignacio , Zúñiga-Ripa Amaia
Published: January 2021

Brucella species cause brucellosis, a worldwide extended zoonosis. The brucellae are related to free-living and plant-associated α2-Proteobacteria and, since they multiply within host cells, their metabolism probably reflects this adaptation. To investigate this, we used the rodent-associated Brucella suis biovar 5, which in contrast to the ruminant-associated Brucella abortus and Brucella melitensis and other B. suis biovars, is fast-growing and conserves the ancestral Entner-Doudoroff pathway (EDP) present in the plant-associated relatives. We constructed mutants in Edd (glucose-6-phosphate dehydratase; first EDP step), PpdK (pyruvate phosphate dikinase; phosphoenolpyruvate ⇌ pyruvate), and Pyk (pyruvate kinase; phosphoenolpyruvate → pyruvate). In a chemically defined medium with glucose as the only C source, the Edd mutant showed reduced growth rates and the triple Edd-PpdK-Pyk mutant did not grow. Moreover, the triple mutant was also unable to grow on ribose or xylose. Therefore, B. suis biovar 5 sugar catabolism proceeds through both the Pentose Phosphate shunt and EDP, and EDP absence and exclusive use of the shunt could explain at least in part the comparatively reduced growth rates of B. melitensis and B. abortus. The triple Edd-PpdK-Pyk mutant was not attenuated in mice. Thus, although an anabolic use is likely, this suggests that hexose/pentose catabolism to pyruvate is not essential for B. suis biovar 5 multiplication within host cells, a hypothesis consistent with the lack of classical glycolysis in all Brucella species and of EDP in B. melitensis and B. abortus. These results and those of previous works suggest that within cells, the brucellae use mostly 3 and 4 C substrates fed into anaplerotic pathways and only a limited supply of 5 and 6 C sugars, thus favoring the EDP loss observed in some species.
Antivirulence Strategies for the Treatment of Staphylococcus aureus Infections: A Mini Review
Authors: Ford Caleb A. , Hurford Ian M. , Cassat James E.
Published: January 2021

Staphylococcus aureusis a Gram-positive bacterium capable of infecting nearly all host tissues, causing severe morbidity and mortality. Widespread antimicrobial resistance has emerged amongS. aureusclinical isolates, which are now the most frequent causes of nosocomial infection among drug-resistant pathogens.S. aureusproduces an array of virulence factors that enhancein vivofitness by liberating nutrients from the host or evading host immune responses. Staphylococcal virulence factors have been identified as viable therapeutic targets for treatment, as they contribute to disease pathogenesis, tissue injury, and treatment failure. Antivirulence strategies, or treatments targeting virulence without direct toxicity to the inciting pathogen, show promise as an adjunctive therapy to traditional antimicrobials. This Mini Review examines recent research onS. aureusantivirulence strategies, with an emphasis on translational studies. While many different virulence factors have been investigated as therapeutic targets, this review focuses on strategies targeting three virulence categories: pore-forming toxins, immune evasion mechanisms, and theS. aureusquorum sensing system. These major areas ofS. aureusantivirulence research demonstrate broad principles that may apply to other human pathogens. Finally, challenges of antivirulence research are outlined including the potential for resistance, the need to investigate multiple infection models, and the importance of studying antivirulence in conjunction with traditional antimicrobial treatments.
Heat Shock-Induced Dephosphorylation of Eukaryotic Elongation Factor 1BδL by Protein Phosphatase 1
Authors: Kaitsuka Taku , Tomizawa Kazuhito , Matsushita Masayuki
Published: January 2021

Several variant proteins are produced from EEF1D, including two representative proteins produced via alternative splicing machinery. One protein is the canonical translation eukaryotic elongation factor eEF1Bδ1, and the other is the heat shock-responsive transcription factor eEF1BδL. eEF1Bδ1 is phosphorylated by cyclin-dependent kinase 1 (CDK1), but the machinery controlling eEF1BδL phosphorylation and dephosphorylation has not been clarified. In this study, we found that both proteins were dephosphorylated under heat shock and proteotoxic stress, and this dephosphorylation was inhibited by okadaic acid. Using proteins with mutations at putative phosphorylated residues, we revealed that eEF1Bδ1 and eEF1BδL are phosphorylated at S133 and S499, respectively, and these residues are both CDK1 phosphorylation sites. The eEF1BδL S499A mutant more strongly activated HSPA6 promoter-driven reporter than the wild-type protein and S499D mutant. Furthermore, protein phosphatase 1 (PP1) was co-immunoprecipitated with eEF1Bδ1 and eEF1BδL, and PP1 dephosphorylated both proteins in vitro. Thus, this study clarified the role of phosphorylation/dephosphorylation in the functional regulation of eEF1BδL during heat shock.
Regulator of Chromosome Condensation 2 Modulates Cell Cycle Progression, Tumorigenesis, and Therapeutic Resistance
Authors: Guo Kun , Zhao Cheng , Lang Bin , Wang Huiqin , Zheng Hang , Zhang Feng
Published: January 2021

Accurate regulation of cell cycle is important for normal tissue development and homeostasis. RCC2 (Regulator of Chromosome Condensation 2) play a role as chromosomal passenger complex (CPC) implicated in all cell cycle phases. RCC2 was initially identified as Ran guanine exchange factor (GEF) for small G proteins. Therefore, RCC2 plays a key role in oncogenesis of most cancers. RCC2 is implicated in Colorectal Cancer (CRC), Lung Adenocarcinoma (LUAD), breast cancer, and ovarian cancer. Expression level of RCC2 protein determines regulation of tumor cell proliferation, invasion, metastasis, and radio-chemotherapeutic resistance. In this review, we explored proteins that interact with RCC2 to modulate tumor development and cancer therapeutic resistance by regulation of cell cycle process through various signaling pathways.