bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable carbon isotopes of dissolved inorganic carbon in the Western North Pacific Ocean: Proxy for water mixing and dynamics
Authors: Ge Tiantian , Luo Chunle , Ren Peng , Zhang Hongmei , Fan Di , Chen Hongtao , Chen Zhaohui , Zhang Jing , Wang Xuchen
Published: September 2022

The uptake of atmospheric CO2 and the cycle of dissolved inorganic carbon (DIC) in the ocean are the major mechanisms and pathways controlling global climate change and carbon cycling. The stable carbon isotope (δ13C) of DIC, therefore, provides an important tracer for processes such as air-sea exchange, photosynthesis, and water dynamics in the ocean. Here, we present new δ13C-DIC data on water samples collected from a north-south transect (13°N–40°N, 150°E) in the western North Pacific (NP) Ocean in November 2019 and compare the results with those previously reported for similar transects (149.3°E) during WOCE and CLIVAR projects over the past three decades. The values of δ13C-DIC, ranging from -0.83‰ to 0.86‰, were higher in the surface waters and decreased with depth. The high δ13C-DIC values in the surface waters were influenced primarily by isotopic fractionation during air-sea exchange and photosynthesis. With depth, the movement of different water masses and mixing, as well as bathypelagic respiration in the dark water of the ocean, all play important roles in influencing the distribution and isotopic signatures of δ13C-DIC in the western NP Ocean. The δ13C-DIC values of the 0–200 m water layer varied from -0.17‰ to 0.86‰, with lower values at high latitudes, affected by the low δ13C-DIC values carried by the Oyashio Current to the Kuroshio Extension (KE) region. A downward trend was present in the δ13C-DIC signature from north to south in the North Pacific Intermediate Water (NPIW) and Pacific Deep Water (PDW) in the western NP, which reflected the remineralization of organic matter with a horizontal transport of NPIW and PDW. We found a strong 13C Suess Effect in the upper 2,000 m in the western NP Ocean, and δ13C-DIC at the surface (<50 m) has decreased by 0.60‰-0.85‰ since 1993. The mean δ13C-DIC change in the surface ocean was estimated at 0.28‰ per decade between 1993 and 2019. The air-sea exchange and water mixing in the study area may have accelerated the absorption of anthropogenic CO2 in recent years, which likely caused a slightly faster rate of decrease in the δ13C-DIC from 2005–2019 than that observed from 1993–2005.
Risk Factors for Infection, Predictors of Severe Disease, and Antibody Response to COVID-19 in Patients With Inflammatory Rheumatic Diseases in Portugal—A Multicenter, Nationwide Study
Authors: Cruz-Machado Ana Rita , Barreira Sofia C. , Bandeira Matilde , Veldhoen Marc , Gomes Andreia , Serrano Marta , Duarte Catarina , Rato Maria , Miguel Fernandes Bruno , Garcia Salomé , Pinheiro Filipe , Bernardes Miguel , Madeira Nathalie , Miguel Cláudia , Torres Rita , Bento Silva Ana , Pestana Jorge , Almeida Diogo , Mazeda Carolina , Cunha Santos Filipe , Pinto Patrícia , Sousa Marlene , Parente Hugo , Sequeira Graça , Santos Maria José , Fonseca João Eurico , Romão Vasco C.
Published: September 2022

Objective

To identify risk factors for SARS-CoV-2 infection and for severe/critical COVID-19, and to assess the humoral response after COVID-19 in these patients.

Methods

Nationwide study of adult patients with inflammatory RMDs prospectively followed in the Rheumatic Diseases Portuguese Register—Reuma.pt—during the first 6 months of the pandemic. We compared patients with COVID-19 with those who did not develop the disease and patients with mild/moderate disease with those exhibiting severe/critical COVID-19. IgG antibodies against SARS-CoV-2 were measured ≥3 months after infection and results were compared with matched controls.

Results

162 cases of COVID-19 were registered in a total of 6,363 appointments. Patients treated with TNF inhibitors (TNFi; OR = 0.160, 95% CI 0.099–0.260, P < 0.001) and tocilizumab (OR 0.147, 95% CI 0.053–0.408, P < 0.001) had reduced odds of infection. Further, TNFi tended to be protective of severe and critical disease. Older age, major comorbidities, and rituximab were associated with an increased risk of infection and worse prognosis. Most patients with inflammatory RMDs (86.2%) developed a robust antibody response. Seroconversion was associated with symptomatic disease (OR 13.46, 95% CI 2.21–81.85, P = 0.005) and tended to be blunted by TNFi (OR 0.17, 95% CI 0.03–1.05; P = 0.057).

Conclusions

TNFi and tocilizumab reduced the risk of infection by SARS-CoV-2. Treatment with TNFi also tended to reduce rates of severe disease and seroconversion. Older age, general comorbidities and rituximab were associated with increased risk for infection and worse prognosis, in line with previous reports. Most patients with RMDs developed a proper antibody response after COVID-19, particularly if they had symptomatic disease.
Lateral elbow tendinopathy and artificial intelligence: Binary and multilabel findings detection using machine learning algorithms
Authors: Droppelmann Guillermo , Tello Manuel , García Nicolás , Greene Cristóbal , Jorquera Carlos , Feijoo Felipe
Published: September 2022

Background

Ultrasound (US) is a valuable technique to detect degenerative findings and intrasubstance tears in lateral elbow tendinopathy (LET). Machine learning methods allow supporting this radiological diagnosis.

Aim

To assess multilabel classification models using machine learning models to detect degenerative findings and intrasubstance tears in US images with LET diagnosis.

Materials and methods

A retrospective study was performed. US images and medical records from patients with LET diagnosis from January 1st, 2017, to December 30th, 2018, were selected. Datasets were built for training and testing models. For image analysis, features extraction, texture characteristics, intensity distribution, pixel-pixel co-occurrence patterns, and scales granularity were implemented. Six different supervised learning models were implemented for binary and multilabel classification. All models were trained to classify four tendon findings (hypoechogenicity, neovascularity, enthesopathy, and intrasubstance tear). Accuracy indicators and their confidence intervals (CI) were obtained for all models following a K-fold-repeated-cross-validation method. To measure multilabel prediction, multilabel accuracy, sensitivity, specificity, and receiver operating characteristic (ROC) with 95% CI were used.

Results

A total of 30,007 US images (4,324 exams, 2,917 patients) were included in the analysis. The RF model presented the highest mean values in the area under the curve (AUC), sensitivity, and also specificity by each degenerative finding in the binary classification. The AUC and sensitivity showed the best performance in intrasubstance tear with 0.991 [95% CI, 099, 0.99], and 0.775 [95% CI, 0.77, 0.77], respectively. Instead, specificity showed upper values in hypoechogenicity with 0.821 [95% CI, 0.82, −0.82]. In the multilabel classifier, RF also presented the highest performance. The accuracy was 0.772 [95% CI, 0.771, 0.773], a great macro of 0.948 [95% CI, 0.94, 0.94], and a micro of 0.962 [95% CI, 0.96, 0.96] AUC scores were detected. Diagnostic accuracy, sensitivity, and specificity with 95% CI were calculated.

Conclusion

Machine learning algorithms based on US images with LET presented high diagnosis accuracy. Mainly the random forest model shows the best performance in binary and multilabel classifiers, particularly for intrasubstance tears.
Host-directed therapies in pulmonary tuberculosis: Updates on anti-inflammatory drugs
Authors: Cubillos-Angulo Juan M. , Nogueira Betânia M. F. , Arriaga María B. , Barreto-Duarte Beatriz , Araújo-Pereira Mariana , Fernandes Catarina D. , Vinhaes Caian L. , Villalva-Serra Klauss , Nunes Vanessa M. , Miguez-Pinto João P. , Amaral Eduardo P. , Andrade Bruno B.
Published: September 2022

Tuberculosis (TB) is a lethal disease and remains one of the top ten causes of mortality by an infectious disease worldwide. It can also result in significant morbidity related to persistent inflammation and tissue damage. Pulmonary TB treatment depends on the prolonged use of multiple drugs ranging from 6 months for drug-susceptible TB to 6–20 months in cases of multi-drug resistant disease, with limited patient tolerance resulting from side effects. Treatment success rates remain low and thus represent a barrier to TB control. Adjunct host-directed therapy (HDT) is an emerging strategy in TB treatment that aims to target the host immune response to Mycobacterium tuberculosis in addition to antimycobacterial drugs. Combined multi-drug treatment with HDT could potentially result in more effective therapies by shortening treatment duration, improving cure success rates and reducing residual tissue damage. This review explores the rationale and challenges to the development and implementation of HDTs through a succinct report of the medications that have completed or are currently being evaluated in ongoing clinical trials.
Clinical manifestation and treatment of small intestinal lymphangioma: A single center analysis of 15 cases
Authors: Wang Zhen-zhen , Shen Ling-yan , Zhou Jing-jing , Tang Jia-li , Ye Li-ping , Shen Chen-bo , Li Shao-wei , Zhou Xian-bin
Published: September 2022

Background

Small intestinal lymphangioma is a very rare benign lesion. Thus far, the literature on small intestinal lymphangioma has mainly involved case reports. The present study retrospectively examined the clinical features of patients with a pathological diagnosis of small intestinal lymphangioma.

Materials and methods

From January 2010 to January 2021, 15 patients were pathologically diagnosed with small intestinal lymphangioma. The age, gender, clinical manifestation, computed tomography (CT) findings, endoscopic findings, localization of the lesion, treatment method, complications, and follow-up were retrospectively analyzed.

Results

Most of the patients had no symptoms, and those with symptoms had melena or abdominal pain. Lymphangioma was located in the duodenum in nine cases (60.0%), jejunum in two (13.3%), jejunal-ileal junction with mesentery involvement in one (6.7%) and ileum in three (20.0%). Three cases (20.0%) had multiple lesions, and the other 12 (80.0%) had single lesions. The median size of the lesions was 0.8 cm. Thirteen cases were found by endoscopy, and nine cases of them had white-colored spots on the surface. Ten cases (66.7%) underwent endoscopic treatment, three (20.0%) underwent surgical treatment, and two (13.3%) were followed up. Postoperative acute pancreatitis developed in one patient after endoscopic resection of duodenal papillary lymphangioma; postoperative abdominal bleeding occurred in one patient with jejunal lymphangioma who underwent partial small bowel resection.

Conclusion

Small intestinal lymphangioma is extremely rare, and its clinical manifestations are non-specific. Endoscopy is of great value in the diagnosis of small intestinal lymphangioma. Depending on the clinical manifestations, the size, location and scope of the lesions, follow-up, endoscopic treatment and surgery can be selected.
Delayed application of N fertilizer mitigates the carbon emissions of pea/maize intercropping via altering soil microbial diversity
Authors: Xu Ke , Hu Falong , Fan Zhilong , Yin Wen , Niu Yining , Wang Qiming , Chai Qiang
Published: September 2022

Strategies to reduce carbon emissions have been a hotspot in sustainable agriculture production. The delayed N fertilizer application had the potential to reduce carbon emissions in pea (Pisum sativum L.)/maize (Zea mays L.) intercropping, but its microbial mechanism remains unclear. In this study, we investigated the effects of delayed N fertilizer application on CO2 emissions and soil microbial diversity in pea/maize intercropping. The soil respiration (Rs) rates of intercropped pea and intercropped maize were decreased by 24.7% and 25.0% with delayed application of N fertilizer, respectively. The total carbon emissions (TCE) of the pea/maize intercropping system were also decreased by 21.1% compared with that of the traditional N fertilizer. Proteobacteria, Bacteroidota, and Chloroflexi were dominant bacteria in pea and maize strips. Heatmap analysis showed that the soil catalase activity at the pea flowering stage and the soil ΝΗ4+-Ν at the maize silking stage contributed more to the variations of bacterial relative abundances than other soil properties. Network analysis demonstrated that Rs was positively related to the relative abundance of Proteobacteria and Bacteroidota, while negatively related to the relative abundance of Chloroflexi in the pea/maize intercropping system. Overall, our results suggested that the delayed application of N fertilizer combined with the pea/maize intercropping system altered soil bacterial community diversity, thereby providing novel insights into connections between soil microorganisms and agricultural carbon emissions.
Effect of the ratio of dietary metabolizable energy to nitrogen content on production performance, serum metabolites, rumen fermentation parameters, and bacterial diversity in yaks
Authors: Liu Xiaojing , Li Jie , Hao Lizhuang , Degen Allan , Wang Dongyang , Ma Yonggui , Niu Jianzhang , Cheng Yanfen , Liu Shujie
Published: September 2022

This study examined the effect of the ratio of dietary metabolizable energy (MJ) to nitrogen (g) content (ME:N) on average daily gain (ADG), blood biochemical indices, rumen fermentation parameters, and rumen bacterial community in yaks. Thirty-six male yaks, aged 2–3 years, were divided into three groups and received a ME:N ratio of 0.42 (HY), 0.36 (MY,) or 0.32 (LY) MJ/g. Dry matter intake ranged between 3.16 and 3.63 kg/d and was lesser (p < 0.001) in the LY group than the other two groups. ME intake increased (p < 0.001) with an increase in the ME:N ratio, while N intake did not differ among groups. The ADG was 660 g/day for the MY group, which was higher (p < 0.005) than the 430 g/day in the LY group, while the HY group gained 560 g/day and did not differ from the other two groups. Feed intake to ADG ratio ranged between 5.95 and 7.95, and numerically was highest in the LY group and lowest in the MY group. In general, the concentration of ruminal total volatile fatty acids (p < 0.03) and molar proportions of propionate (p < 0.04), increased, while the molar proportion of acetate (p < 0.005) and the acetate:propionate ratio decreased (p < 0.001) with a decrease in the ME:N ratio. The molar proportion of butyrate did not differ among groups (p = 0.112). Group MY had higher ruminal NH3-N content than group HY and had a higher serum glucose content but lower urea content, lactate dehydrogenase, and creatine kinase content than group LY. In ruminal bacteria at the phylum level, the relative abundance of Firmicutes (F) was greater and of Bacteroidetes (B) was lesser, while the F:B ratio was greater in group MY than in groups HY an LY. We concluded that the yaks consuming the diet containing a ME:N ratio of 0.36 MJ/g had the best performance of the three groups.
Detection of Alternaria solani with high accuracy and sensitivity during the latent period of potato early blight
Authors: Niu Zijian , Zheng Lijia , Yang Pan , Wang Jinhui , Tian Mengjun , Pan Yang , Zhao Dongmei , Yang Zhihui , Zhu Jiehua
Published: September 2022

Early blight (EB) disease, caused mainly byAlternaria solani, is an economic threat to potato and tomato production worldwide. Thus, accurate and sensitive detection of the fungal pathogen of this disease in plants at the early infection stage is important for forecasting EB epidemics. In this study, we developed an RNA-based method that enables highly accurate and sensitiveA. solanidetection in a whole potato leaf at a single spore level based on quantitative real-time polymerase chain reaction (qPCR). We discovered jg1677, a highly expressed gene whose full-length coding sequence is very specific forA. solani, by analyzingA. solanitranscripts isolated from enhanced high throughput transcriptome of infected potato leaves byA. solaniand using the National Center for Biotechnology Information’s basic local alignment search tool. The specificity of the primers derived from jg1677 was determined using 22 isolates of common potato pathogens, including sevenAlternariaisolates. Detecting jg1677 transcripts with qPCR is 1,295 times more sensitive than detecting genomic DNA. In addition, the expression pattern of jg1677 at different infection stages was determined by qPCR. What is more, jg1677 was expressed relatively stable between 15 and 35°C in infected leaves, and its expression was virtually unaffected in isolated leaves left at room temperature for 24 h. Our work provides a much more sensitive and accurate method compared to conditional DNA-based ones, permitting a very early diagnosis of EB and lowering the risk of EB epidemics.
Manipulating Bacterial Biofilms Using Materiobiology and Synthetic Biology Approaches
Authors: Shi Yue , Chen Tingli , Shaw Peter , Wang Peng-Yuan
Published: September 2022

Bacteria form biofilms on material surfaces within hours. Biofilms are often considered problematic substances in the fields such as biomedical devices and the food industry; however, they are beneficial in other fields such as fermentation, water remediation, and civil engineering. Biofilm properties depend on their genome and the extracellular environment, including pH, shear stress, and matrices topography, stiffness, wettability, and charges during biofilm formation. These surface properties have feedback effects on biofilm formation at different stages. Due to emerging technology such as synthetic biology and genome editing, many studies have focused on functionalizing biofilm for specific applications. Nevertheless, few studies combine these two approaches to produce or modify biofilms. This review summarizes up-to-date materials science and synthetic biology approaches to controlling biofilms. The review proposed a potential research direction in the future that can gain better control of bacteria and biofilms.
Proteomics in Biomarker Discovery for Tuberculosis: Current Status and Future Perspectives
Authors: Guo Jiubiao , Zhang Ximeng , Chen Xinchun , Cai Yi
Published: September 2022

Tuberculosis (TB) continues to threaten many peoples’ health worldwide, regardless of their country of residence or age. The current diagnosis of TB still uses mainly traditional, time-consuming, and/or culture-based techniques. Efforts have focused on discovering new biomarkers with higher efficiency and accuracy for TB diagnosis. Proteomics—the systematic study of protein diversity—is being applied to the discovery of novel protein biomarkers for different types of diseases. Mass spectrometry (MS) technology plays a revolutionary role in proteomics, and its applicability benefits from the development of other technologies, such as matrix-based and immune-based methods. MS and derivative strategies continuously contribute to disease-related discoveries, and some promising proteomic biomarkers for efficient TB diagnosis have been identified, but challenges still exist. For example, there are discrepancies in the biomarkers identified among different reports and the diagnostic accuracy of clinically applied proteomic biomarkers. The present review summarizes the current status and future perspectives of proteomics in the field of TB biomarker discovery and aims to elicit more promising findings for rapid and accurate TB diagnosis.
Heat Stress Weakens the Skin Barrier Function in Sturgeon by Decreasing Mucus Secretion and Disrupting the Mucosal Microbiota
Authors: Yang Shiyong , Xu Wenqiang , Tan Chaolun , Li Minghao , Li Datian , Zhang Chaoyang , Feng Langkun , Chen Qianyu , Jiang Jun , Li Yunkun , Du Zongjun , Luo Wei , Li Caiyi , Gong Quan , Huang Xiaoli , Du Xiaogang , Du Jun , Liu Guangxun , Wu Jiayun
Published: September 2022

Heat stress induced by global warming has damaged the well-being of aquatic animals. The skin tissue plays a crucial role as a defense barrier to protect organism, however, little is known about the effect of heat stress on fish skin, particularly in cold-water fish species. Here, we investigated the effects of mild heat stress (24°C, MS) and high heat stress (28°C, HS) on Siberian sturgeon skin using RNA-seq, histological observation, and microbial diversity analysis. In RNA-seq, 8,819 differentially expressed genes (DEGs) in MS vs. C group and 12,814 DEGs in HS vs. C group were acquired, of which the MS vs. C and HS vs. C groups shared 3,903 DEGs, but only 1,652 DEGs were successfully annotated. The shared DEGs were significantly enriched in pathways associating with mucins synthesis. Histological observation showed that the heat stresses significantly reduced the number of skin mucous cells and induced the damages of epidermis. The microbial diversity analysis elicited that heat stress markedly disrupted the diversity and abundance of skin microbiota by increasing of potential pathogens (Vibrionimonas, Mesorhizobium, and Phyllobacterium) and decreasing of probiotics (Bradyrhizobium and Methylovirgula). In conclusion, this study reveals that heat stress causes adverse effects on sturgeon skin, reflecting in decreasing the mucus secretion and disordering the mucosal microbiota, which may contribute to develop the preventive strategy for heat stress caused by global warming.
The Staphylococcus epidermidis Transcriptional Profile During Carriage
Authors: Teichmann Pascâl , Both Anna , Wolz Christiane , Hornef Mathias W. , Rohde Holger , Yazdi Amir S. , Burian Marc
Published: September 2022

The virulence factors of the opportunistic human pathogen Staphylococcus epidermidis have been a main subject of research. In contrast, limited information is available on the mechanisms that allow the bacterium to accommodate to the conditions during carriage, a prerequisite for pathogenicity. Here, we tested the hypothesis that the adaptation of S. epidermidis at different anatomical sites is reflected by differential gene regulation. We used qPCR to profile S. epidermidis gene expression in vivo in nose and skin swabs of 11 healthy individuals. Despite some heterogeneity between individuals, significant site-specific differences were detected. For example, expression of the S. epidermidis regulator sarA was found similarly in the nose and on the skin of all individuals. Also, genes encoding colonization and immune evasion factors (sdrG, capC, and dltA), as well as the sphingomyelinase encoding gene sph, were expressed at both anatomical sites. In contrast, expression of the global regulator agr was almost inactive in the nose but readily present on the skin. A similar site-specific expression profile was also identified for the putative chitinase-encoding SE0760. In contrast, expression of the autolysine-encoding gene sceD and the wall teichoic acid (WTA) biosynthesis gene tagB were more pronounced in the nose as compared to the skin. In summary, our analysis identifies site-specific gene expression patterns of S. epidermidis during colonization. In addition, the observed expression signature was significantly different from growth in vitro. Interestingly, the strong transcription of sphingomyelinase together with the low expression of genes encoding the tricarboxylic acid cycle (TCA) suggests very good nutrient supply in both anatomical niches, even on the skin where one might have suspected a rather lower nutrient supply compared to the nose.
Insights into the microbial life in silica-rich subterranean environments: microbial communities and ecological interactions in an orthoquartzite cave (Imawarì Yeuta, Auyan Tepui, Venezuela)
Authors: Ghezzi Daniele , Foschi Lisa , Firrincieli Andrea , Hong Pei-Ying , Vergara Freddy , De Waele Jo , Sauro Francesco , Cappelletti Martina
Published: September 2022

Microbial communities inhabiting caves in quartz-rich rocks are still underexplored, despite their possible role in the silica cycle. The world’s longest orthoquartzite cave, Imawarì Yeuta, represents a perfect arena for the investigation of the interactions between microorganisms and silica in non-thermal environments due to the presence of extraordinary amounts of amorphous silica speleothems of different kinds. In this work, the microbial diversity of Imawarì Yeuta was dissected by analyzing nineteen samples collected from different locations representative of different silica amorphization phases and types of samples. Specifically, we investigated the major ecological patterns in cave biodiversity, specific taxa enrichment, and the main ecological clusters through co-occurrence network analysis. Water content greatly contributed to the microbial communities’ composition and structures in the cave leading to the sample clustering into three groups DRY, WET, and WATER. Each of these groups was enriched in members of Actinobacteriota, Acidobacteriota, and Gammaproteobacteria, respectively. Alpha diversity analysis showed the highest value of diversity and richness for the WET samples, while the DRY group had the lowest. This was accompanied by the presence of correlation patterns including either orders belonging to various phyla from WET samples or orders belonging to the Actinobacteriota and Firmicutes phyla from DRY group samples. The phylogenetic analysis of the dominant species in WET and DRY samples showed that Acidobacteriota and Actinobacteriota strains were affiliated with uncultured bacteria retrieved from various oligotrophic and silica/quartz-rich environments, not only associated with subterranean sites. Our results suggest that the water content greatly contributes to shaping the microbial diversity within a subterranean quartzite environment. Further, the phylogenetic affiliation between Imawarì Yeuta dominant microbes and reference strains retrieved from both surface and subsurface silica- and/or CO2/CO-rich environments, underlines the selective pressure applied by quartz as rock substrate. Oligotrophy probably in association with the geochemistry of silica/quartz low pH buffering activity and alternative energy sources led to the colonization of specific silica-associated microorganisms. This study provides clues for a better comprehension of the poorly known microbial life in subsurface and surface quartz-dominated environments.
Breaking down the cell wall: Still an attractive antibacterial strategy
Authors: Zhou Jingxuan , Cai Yi , Liu Ying , An Haoyue , Deng Kaihong , Ashraf Muhammad Awais , Zou Lili , Wang Jun
Published: September 2022

Since the advent of penicillin, humans have known about and explored the phenomenon of bacterial inhibition via antibiotics. However, with changes in the global environment and the abuse of antibiotics, resistance mechanisms have been selected in bacteria, presenting huge threats and challenges to the global medical and health system. Thus, the study and development of new antimicrobials is of unprecedented urgency and difficulty. Bacteria surround themselves with a cell wall to maintain cell rigidity and protect against environmental insults. Humans have taken advantage of antibiotics to target the bacterial cell wall, yielding some of the most widely used antibiotics to date. The cell wall is essential for bacterial growth and virulence but is absent from humans, remaining a high-priority target for antibiotic screening throughout the antibiotic era. Here, we review the extensively studied targets, i.e., MurA, MurB, MurC, MurD, MurE, MurF, Alr, Ddl, MurI, MurG, lipid A, and BamA in the cell wall, starting from the very beginning to the latest developments to elucidate antimicrobial screening. Furthermore, recent advances, including MraY and MsbA in peptidoglycan and lipopolysaccharide, and tagO, LtaS, LspA, Lgt, Lnt, Tol-Pal, MntC, and OspA in teichoic acid and lipoprotein, have also been profoundly discussed. The review further highlights that the application of new methods such as macromolecular labeling, compound libraries construction, and structure-based drug design will inspire researchers to screen ideal antibiotics.
Responses of microbial necromass carbon and microbial community structure to straw- and straw-derived biochar in brown earth soil of Northeast China
Authors: Sun Qiang , Yang Xu , Bao Zhengrong , Gao Jian , Meng Jun , Han Xiaori , Lan Yu , Liu Zunqi , Chen Wenfu
Published: September 2022

Soil microbial organisms are conducive to SOC sequestration. However, little attention has been given to the contributions of living MBC and microbial necromass carbon to the SOC pool under biochar and straw amendments. The aims of the study were to explore (1) the effects of maize straw and biochar on MBC, POC, MAOC, DOC and microbial necromass carbon; (2) the contribution of MBC and microbial necromass carbon to the SOC pool; and (3) the relationships among the soil microbial community structure, microbial necromass carbon and other SOC fractions under maize straw and biochar application for nine consecutive years. Three treatments were studied: CK (applied chemical fertilizer only), BC (biochar applied annually at a rate of 2.625 t ha−1 combined with chemical fertilizer), and SR (straw applied annually at a rate of 7.5 t ha−1). Both biochar and straw increased the SOC contents after nine successive maize plant seasons; the DOC and MAOC contents were also increased by biochar and straw amendments. Biochar had advantages in increasing POC contents compared to straw. Biochar and straw increased MBC contents by 48.54% and 60.83% compared to CK, respectively. Straw significantly increased the Galn, GluN, MurA, ManN and total amino contents (P < 0.05); however, biochar significantly increased the Galn and GluN contents (P < 0.05) but had no impact on the MurA contents and decreased the ManN contents. Biochar mainly increased the fungal-derived necromass carbon contents but had no effect on the bacterial-derived necromass carbon, and straw increased both the bacterial- and fungal-derived necromass carbon contents. Straw had no influence on the ratios of microbial necromass carbon accounting for SOC and MAOC, but biochar decreased the ratios in the current study. Similarly, biochar mainly increased the fungal PLFA and total PLFA contents compared to CK, but straw increased bacterial PLFAs, fungal PLFAs and Actinomycetes PLFAs. Maize yield were increased by 7.44 and 9.16% by biochar and straw application, respectively. These results indicate that biochar stimulates fungal activities and turnover to contribute to the stable soil carbon pool and that biochar also improves POC contents to improve the soil organic carbon sink.
Diet drives the gut microbiome composition and assembly processes in winter migratory birds in the Poyang Lake wetland, China
Authors: Wang Binhua , Zhong Hui , Liu Yajun , Ruan Luzhang , Kong Zhaoyu , Mou Xiaozhen , Wu Lan
Published: September 2022

The complex gut bacterial communities may facilitate the function, distribution, and diversity of birds. For migratory birds, long-distance traveling poses selection pressures on their gut microbiota, ultimately affecting the birds’ health, fitness, ecology, and evolution. However, our understanding of mechanisms that underlie the assembly of the gut microbiome of migratory birds is limited. In this study, the gut microbiota of winter migratory birds in the Poyang Lake wetland was characterized using MiSeq sequencing of 16S rRNA genes. The sampled bird included herbivorous, carnivorous, and omnivorous birds from a total of 17 species of 8 families. Our results showed that the gut microbiota of migratory birds was dominated by four major bacterial phyla: Firmicutes (47.8%), Proteobacteria (18.2%), Fusobacteria (12.6%), and Bacteroidetes (9.1%). Dietary specialization outweighed the phylogeny of birds as an important factor governing the gut microbiome, mainly through regulating the deterministic processes of homogeneous selection and stochastic processes of homogeneous dispersal balance. Moreover, the omnivorous had more bacterial diversity than the herbivorous and carnivorous. Microbial networks for the gut microbiome of the herbivorous and carnivorous were less integrated, i.e., had lower average node degree and greater decreased network stability upon node attack removal than those of the omnivorous birds. Our findings advance the understanding of host-microbiota interactions and the evolution of migratory bird dietary flexibility and diversification.
The detection of urinary viruses is associated with aggravated symptoms and altered bacteriome in female with overactive bladder
Authors: Sun Qi , Li Leqian , Zhou Hao , Wu Ying , Gao Yubo , Wu Bingyi , Qiu Yifeng , Zhou Zhipeng , Song Qixiang , Zhao Jie , Wu Peng
Published: September 2022

Although it is known that changes in bacterial components of the urinary microbiome are associated with overactive bladder (OAB), the specific role of viruses is still insufficiently investigated. The aim of the present study is to evaluate the role of urinary viruses in woman with OAB, and analyze the potential relationship between viruses, bacteria and disease. Catheterized urine samples were collected from 55 women with OAB and 18 control individuals. OAB patients fulfilling the following criteria were considered eligible for this study: female, 18 years of age or older; presented with classic OAB symptoms defined by the International Continence Society; and OAB Symptom Score (OABSS) total score ≥ 3 points and question 3 (urgency) score ≥ 2 points. Based on results of metagenomic next-generation sequencing (mNGS), all participants were divided into virus-infected and virus-uninfected groups for analysis. The results of mNGS showed that the diversity of the OAB group was lower than that of the control group when focused on bacterial sequences, which was consistent with our previous study. According to the questionnaire filled out by the patients, OABSS and 8-item OAB questionnaire, female OAB patients who had viruses detected in their urine had more severe symptoms. In parallel, John Cunningham virus (mainly subtype 7 and subtype 2) was the most frequently detected virus in urine. Correlation analysis indicated that risk factors for virus infection in OAB patients include age, habit of holding urine and pelvic surgery history. Given our preliminary data, viral infection can aggravate OAB severity and affect the composition of bacterial. Further research is required to explain how viral infections can aggravate OAB patient symptoms and cause bacterial changes.
Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane
Authors: Benito Merino David , Zehnle Hanna , Teske Andreas , Wegener Gunter
Published: September 2022

In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate–methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.
Genome-wide analysis reveals the emergence of multidrug resistant Stenotrophomonas acidaminiphila strain SINDOREI isolated from a patient with sepsis
Authors: Zhang Ying , Li Danhua , Yan Qun , Xu Ping , Chen Wei , Xin Hongya , Wu Dengshu , Zhou Mingxiang , Xu Yajing , Zhang Ao , Wei Wenjia , Jiang Zhiping
Published: September 2022

Stenotrophomonas acidaminiphila, the most recent reported species in genus Stenotrophomonas, is a relatively rare bacteria and is an aerobic, glucose non-fermentative, Gram-negative bacterium. However, little information of S. acidaminiphila is known to cause human infections. In this research, we firstly reported a multidrug-resistant strain S. acidaminiphila SINDOREI isolated from the blood of a patient with sepsis, who was dead of infection eventually. The whole genome of strain SINDOREI was sequenced, and genome comparisons were performed among six closely related S. acidaminiphila strains. The core genes (2,506 genes) and strain-specific genes were identified, respectively, to know about the strain-level diversity in six S. acidaminiphila stains. The presence of a unique gene (narG) and essential genes involved in biofilm formation in strain SINDOREI are important for the pathogenesis of infections. Strain SINDOREI was resistant to trimethoprim/sulfamethoxazole, ciprofloxacin, ofloxacin, cefepime, ceftazidime, and aztreonam. Several common and specific antibiotic resistance genes were identified in strain SINDOREI. The presence of two sul genes and exclusive determinants GES-1, aadA3, qacL, and cmlA5 is responsible for the resistance to multidrug. The virulence factors and resistance determinants can show the relationship between the phenotype and genotype and afford potential therapeutic strategies for infections.
3-Phenyllactic acid generated in medicinal plant extracts fermented with plant-derived lactic acid bacteria inhibits the biofilm synthesis of Aggregatibacter actinomycetemcomitans
Authors: Shakya Shrijana , Danshiitsoodol Narandalai , Noda Masafumi , Inoue Yusuke , Sugiyama Masanori
Published: September 2022

In the present study, the effect of PLA on a periodontic pathogen, Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans), the biofilm, and virulence-related genes was investigated. We confirmed that two lactic acid bacteria (LAB) strains isolated from plant sources, Lactiplantibacillus plantarum MSC-C2 and Pediococcus pentosaceus K40, secrete PLA into the de Man, Rogosa & Sharpe (MRS) broth when supplemented with phenyl pyruvic acid (PPA) as a precursor to PLA. Moreover, PLA was generated in the fermentation broths of two medicinal plant extracts, Paeonia lactiflora Pall (PR) and Carthamus tinctorius (CT), when used by each LAB strain and each extract supplemented with PPA. We determined that the minimum inhibitory concentration (MIC) of PLA against A. actinomycetemcomitans was 20 mM. PLA significantly decreased biofilm formation and suppressed the transcription of pgA, ltxA, and cdtB genes, which encode the poly-N-acetylglucosamine (PGA) polysaccharide of biofilm matrix and exotoxins leukotoxin and cytolethal distending toxin (CDT), respectively. The PLA produced by the MSC-C2 and K40 strains was increased several times by the addition of PPA to the MRS broth. The anti-biofilm effect of the extracts from the fermentation broth was proportional to the increasing PLA concentration, while a cumulatively higher effect than that of PLA alone suggested a combinational effect of PLA and the other metabolites, such as lactic acid (LA). Among the two medicinal plants, PLA, produced after the addition of PPA, was higher in PR extract in case of both the LAB strains. PLA production by the MSC-C2 strain in the PR extract reached 4.8 ± 0.23 mM, which was obviously higher than that in the MRS broth (3.88 ± 0.12 mM) supplemented with 1 mg/ml PPA. The activity to inhibit biofilm formation in the fermented PR extract was clearly high. PLA formed in the fermented PR extract downregulated the dispersin B encoding the dspB gene together with pgA, ltxA, and cdtB. In conclusion, this study shows a promising activity of PLA against the A. actinomycetemcomitans biofilm and virulence genes. In addition, the combinational effect of PLA and the medicinal plant extract can be achieved by fermentation with a specific plant-derived LAB strain.
Soil bacteria are more sensitive than fungi in response to nitrogen and phosphorus enrichment
Authors: Chen Youchao , Yin Shuwei , Shao Yun , Zhang Kerong
Published: September 2022

Anthropogenic activities have dramatically increased nitrogen (N) and phosphorous (P) enrichments in terrestrial ecosystems. However, it is still unclear on how bacterial and fungal communities would respond to the simultaneously increased N and P enrichment. In this study, we used a field experiment to simulate N and P input, and examined the effects of N and P additions on the abundance, alpha-diversity, and community composition of soil bacteria and fungi in a riparian forest. Six nutrient-addition treatments, including low N (30 kg N ha–1 year–1), high N (150 kg N ha –1 year–1), low P (30 kg P2O5 ha–1 year–1), high P (150 kg P2O5 ha –1 year–1), low N+P, high N+P, and a control (CK) treatment were set up. We found that the N and P additions significantly affected bacterial abundance, community composition, but not the alpha diversity. Specifically, 16S, nirK, and nirS gene copy numbers were significantly reduced after N and P additions, which were correlated with decreases in soil pH and NO-3-N, respectively; Co-additions of N and P showed significantly antagonistic interactions on bacterial gene copies; Nutrient additions significantly increased the relative abundance of Proteobacteria while reduced the relative abundance of Chloroflexi. Mantel’s test showed that the alteration in bacterial composition was associated with the changes in soil pH and NO-3-N. The nutrient additions did not show significant effects on fungal gene copy numbers, alpha diversity, and community composition, which could be due to non-significant alterations in soil C/N and total P concentration. In conclusion, our results suggest that soil bacteria are more sensitive than fungi in response to N and P enrichment; the alterations in soil pH and NO-3-N explain the effects of N and P enrichment on bacterial communities, respectively; and the co-addition of N and P reduces the negative effects of these two nutrients addition in alone. These findings improve our understanding of microbial response to N and P addition, especially in the context of simultaneous enrichment of anthropogenic nutrient inputs.
Role of ARRB1 in prognosis and immunotherapy: A Pan-Cancer analysis
Authors: Ye Yingquan , Jiang Haili , Wu Yue , Wang Gaoxiang , Huang Yi , Sun Weijie , Zhang Mei
Published: September 2022

Background: β-arrestin1 (ARRB1), was originally identified as a multifunctional adaptor protein. Although ARRB1 has recently been shown to also play an important role in tumor growth, metastasis, inflammation, and immunity, its relationship with distinct tumor types and the tumor immune microenvironment remains unclear.

Methods: We analyzed the ARRB1 expression profile and clinical characteristics in 33 cancer types using datasets from The Cancer Genome Atlas (TCGA) database. Clinical parameters such as patient survival, tumor stage, age, and gender were used to assess the prognostic value of ARRB1. The Human Protein Atlas (HPA) database was used to explore ARRB1 protein expression data. ESTIMATE and CIBERSORT algorithms were performed to assess immune infiltration. Furthermore, putative correlations between ARRB1 and tumor-infiltrating immune cells, the signatures of T-cell subtypes, immunomodulators, the tumor mutation burden (TMB), Programmed cell death ligand 1 (PD-L1), and microsatellite instability (MSI) were also explored. Gene functional enrichment was determined using GSEA. GSE40435 and GSE13213 cohorts were used to validate the correlation of ARRB1 with KIRC and LUAD clinicopathological parameters. Finally, the relationship between ARRB1 and immunotherapeutic responses was assessed using three independent immunotherapy cohorts, namely, GSE67501, GSE168204, and IMvigor210.

Results: We found that ARRB1 expression levels were lower in 17 tumor tissues than in the corresponding normal tissues. We further found that ARRB1 expression was significantly correlated with tumor stage in BRCA, ESCA, KIRC, TGCT, and THCA, while in some tumors, particularly KIRC and LUAD, ARRB1 expression was associated with better prognosis. ARRB1 expression was also positively correlated with the stromal score or the immune score in some tumors. Regarding immune cell infiltration, ARRB1 expression in DLBC was positively correlated with M1 macrophage content and negatively correlated with B-cell infiltration. Additionally, there was a broad correlation between ARRB1 expression and three classes of immunomodulators. Furthermore, high ARRB1 expression levels were significantly correlated with some tumor immune-related pathways. Finally, ARRB1 expression was significantly associated with MSI, PD-L1, and TMB in some tumors and with the efficacy of immune checkpoint inhibitors (ICIs) in melanoma.

Conclusion: ARRB1 has prognostic value in malignant tumors, especially in KIRC and LUAD. At the same time, ARRB1 was closely correlated with the tumor immune microenvironment and indicators of immunotherapy efficacy, indicating its great potential as a reliable marker for predicting the efficacy of immunotherapy.
25 years of neurocognitive aging theories: What have we learned?
Authors: McDonough Ian M. , Nolin Sara A. , Visscher Kristina M.
Published: September 2022

The past 25 years have provided a rich discovery of at least four fundamental patterns that represent structural and functional brain aging across multiple cognitive domains. Of the many potential patterns of brain aging, few are ever examined simultaneously in a given study, leading one to question their mutual exclusivity. Moreover, more studies are emerging that note failures to replicate some brain aging patterns, thereby questioning the universality and prevalence of these patterns. Although some attempts have been made to create unifying theories incorporating many of these age-related brain patterns, we propose that the field’s understanding of the aging brain has been hindered due to a large number of influential models with little crosstalk between them. We briefly review these brain patterns, the influential domain-general theories of neurocognitive aging that attempt to explain them, and provide examples of recent challenges to these theories. Lastly, we elaborate on improvements that can be made to lead the field to more comprehensive and robust models of neurocognitive aging.