bluuebunny/crossref_metadata_2025 huggingface dataset:
Study on the spatial variation of China’s territorial ecological space based on the standard deviation ellipse
Authors: Zhang Yang , Jiang Ping , Cui Liye , Yang Yang , Ma Zijun , Wang Yan , Miao Donghui
Published: August 2022

With the rapid development of China’s economy and the acceleration of urbanization, the rapid expansion of urban space has led to a growing demand for land that has resulted in the destruction and expropriation of a large amount of ecological land in China. In the face of the current situation of China’s resource constraints, environmental degradation, and ecosystem destruction, it is necessary to thoroughly study the territorial ecological space of China and its evolution rules. Based on previous studies on the classification of ecological land use, this study proposes the concept of territorial ecological space and distinguishes it from urban space and agricultural space. A matching ecological space classification system has been established, which may help in understanding the ecosystem model and related ecological processes. According to the constructed ecological space classification system, ecological spatial data processing was conducted. The standard deviation ellipse model was used to analyze the pattern of various ecological spaces in China and the migration of their barycenter. The results of the study show the following: 1) China’s territorial ecological space area showed a downward trend from 2000 to 2015. From the aspect of flow, the area of ecological space mainly flows into urban space, followed by agricultural space. According to the division of the first-level ecological space, the main ecological space structure of China is grassland ecological space and woodland ecological space. 2) The spatial distribution characteristics of China’s territorial ecological space are more prominent, and the distribution is very uneven. During the study period, the variation of the standard deviation ellipse angle θ of the ecological space is small, and the migration of the barycenter is not obvious, indicating that China’s territorial ecological space is in a relatively stable state. 3) It is necessary to implement a differentiated policy on the optimization and control of territorial ecological space according to the non-equilibrium of territorial space, and build a unified and coordinated territorial space management and control system. Such a differentiation policy would provide a basis for decision making and a reference for formulating strategies for the sustainable development of the regional ecological environment and optimizing the spatial layout of the territory.
The bio-immobilization of Pb(II) induced by the Chlorella–montmorillonite composite in the Ca(II) environment
Authors: Wang Zhen , Chen Jinhui , Tan Jiaqi , Lu Zijing , Wang Xizhuo , Jianbo Li
Published: August 2022

The clay–microbial consortium is ubiquitous in the soil near the mining area and plays an important role in the transport of heavy metals. In this study, Chlorella sorokiniana FK was separated from lead–zinc mine tailings. The montmorillonite–Chlorella sorokiniana FK system as a typical case was applied to study Pb(II) biomineralization in the presence of usually co-existent Ca(II) and further reduce the migration and transformation of Pb(II) in the Ca(II) environment. Chlorella sorokiniana FK showed good resistance to Pb(II), and the addition of montmorillonite provided a more stable pH environment, which is conducive to the stability of Pb(II)-bearing bio-minerals. Montmorillonite created a low-biotoxicity environment in the overall process, especially less Pb(II) bio-adsorption capacity of individual Chlorella to protect the process of mineralization effectively. Batch experiment results also demonstrated that montmorillonite as the formation site of bio-minerals results in dispersed minerals on the surface of Chlorella and Chlorella–MMT composite, which is beneficial to the survival of Chlorella. Moreover, Pb(II)-bearing phosphate minerals tended to form in the Ca(II) environment rather than without Ca(II). This study demonstrated the mechanism of Pb(II) immobilization induced by Chlorella in the Ca(II) environment, further presenting a green, sustainable, and effective strategy for Pb(II) bio-immobilization combining clay minerals and microorganisms.
Ecological aspiration and the income of farmers aroused by Grain for Green Project
Authors: Chen Shengdong , Duan Pei , Yu Xiaoying
Published: August 2022

For farmers, the more fragile the state of the ecology becomes, the more their awareness of the need for environmental protection grows. China’s Grain for Green Project (G.G.P.) policy of returning farmland to forests and grassland, as an external shock to the environment, has sparked people’s ecological aspirations. Many people have noticed the phenomenon of ecosystem degradation and overlapping poverty. Analyzing the environmental and income changes brought about by the G.G.P., and this study considers farmers’ self-selection problems due to their lack of subjective thinking regarding this initiative. Our study aims to fill this gap by using a forest–grass model to assess the level of farmers’ ecological aspirations in ecologically vulnerable areas of Xinjiang, China. This article is based on aspiration theory and a theoretical model assessing the economic impact of ecological aspiration on the G.G.P. in China. The results show that farmers’ ecological aspirations can increase their enthusiasm to participate in the G.G.P. Under counterfactual conditions, participation in the G.G.P. initially reduces farmers’ total income to a certain extent; however, in the long run, it can significantly increase the total income of farmers. When the intermediary effect is used to analyze the economic effect of ecological aspiration on returning farmland to forest, it is found that farmers’ ecological aspirations affect household income by influencing income expectations. Our findings have essential practical implications and provide an important reference for consolidating poverty alleviation efforts and effectively promoting rural revitalization. In addition, the results suggest a way to achieve the goals of carbon peak and carbon neutrality, and it is necessary for building environmental-friendly regions.
Simultaneously collecting coding and non-coding phylogenomic data using homemade full-length cDNA probes, tested by resolving the high-level relationships of Colubridae
Authors: Li JiaXuan , Liang Dan , Zhang Peng
Published: August 2022

Resolving intractable phylogenetic relationships often requires simultaneously analyzing a large number of coding and non-coding orthologous loci. To gather both coding and non-coding data, traditional sequence capture methods require custom-designed commercial probes. Here, we present a cost-effective sequence capture method based on homemade probes, to capture thousands of coding and non-coding orthologous loci simultaneously, suitable for all organisms. This approach, called “FLc-Capture,” synthesizes biotinylated full-length cDNAs from mRNA as capture probes, eliminates the need for costly commercial probe design and synthesis. To demonstrate the utility of FLc-Capture, we prepared full-length cDNA probes from mRNA extracted from a common colubrid snake. We performed capture experiments with these homemade cDNA probes and successfully obtained thousands of coding and non-coding genomic loci from 24 Colubridae species and 12 distantly related snake species of other families. The average capture specificity of FLc-Capture across all tested snake species is 35%, similar to the previously published EecSeq method. We constructed two phylogenomic data sets, one including 1,075 coding loci (∼817,000 bp) and the other including 1,948 non-coding loci (∼1,114,000 bp), to study the phylogeny of Colubridae. Both data sets yielded highly similar and well-resolved trees, with 85% of nodes having >95% bootstrap support. Our experimental tests show that FLc-Capture is a flexible, fast, and cost-effective sequence capture approach for simultaneously gathering coding and non-coding phylogenomic data sets to study intractable phylogenetic questions. We hope that this method will serve as a new data collection tool for evolutionary biologists working in the era of phylogenomics.
Experimental and in-host evolution of triazole resistance in human pathogenic fungi
Authors: Handelman Mariana , Osherov Nir
Published: August 2022

The leading fungal pathogens causing systemic infections in humans are Candida spp., Aspergillus fumigatus, and Cryptococcus neoformans. The major class of antifungals used to treat such infections are the triazoles, which target the cytochrome P450 lanosterol 14-α-demethylase, encoded by the ERG11 (yeasts)/cyp51A (molds) genes, catalyzing a key step in the ergosterol biosynthetic pathway. Triazole resistance in clinical fungi is a rising concern worldwide, causing increasing mortality in immunocompromised patients. This review describes the use of serial clinical isolates and in-vitro evolution toward understanding the mechanisms of triazole resistance. We outline, compare, and discuss how these approaches have helped identify the evolutionary pathways taken by pathogenic fungi to acquire triazole resistance. While they all share a core mechanism (mutation and overexpression of ERG11/cyp51A and efflux transporters), their timing and mechanism differs: Candida and Cryptococcus spp. exhibit resistance-conferring aneuploidies and copy number variants not seen in A. fumigatus. Candida spp. have a proclivity to develop resistance by undergoing mutations in transcription factors (TAC1, MRR1, PDR5) that increase the expression of efflux transporters. A. fumigatus is especially prone to accumulate resistance mutations in cyp51A early during the evolution of resistance. Recently, examination of serial clinical isolates and experimental lab-evolved triazole-resistant strains using modern omics and gene editing tools has begun to realize the full potential of these approaches. As a result, triazole-resistance mechanisms can now be analyzed at increasingly finer resolutions. This newfound knowledge will be instrumental in formulating new molecular approaches to fight the rapidly emerging epidemic of antifungal resistant fungi.
Comprehensive analysis of nine m7G-related lncRNAs as prognosis factors in tumor immune microenvironment of hepatocellular carcinoma and experimental validation
Authors: Wang Tao , Zhou Zhijia , Wang Xuan , You Liping , Li Wenxuan , Zheng Chao , Zhang Jinghao , Wang Lingtai , Kong Xiaoni , Gao Yueqiu , Sun Xuehua
Published: August 2022

Background: Hepatocellular carcinoma (HCC) remains the most prevalent gastrointestinal malignancy worldwide, with robust drug resistance to therapy. N7-methylguanosine (m7G) mRNA modification has been significantly related to massive human diseases. Considering the effect of m7G-modified long non-coding RNAs (lncRNAs) in HCC progression is unknown, the study aims at investigating a prognostic signature to improve clinical outcomes for patients with HCC.

Methods: Two independent databases (TCGA and ICGC) were used to analyze RNAseq data of HCC patients. First, co-expression analysis was applied to obtain the m7G-related lncRNAs. Moreover, consensus clustering analysis was employed to divide HCC patients into clusters. Then, using least absolute shrinkage and selection operator-Cox regression analysis, the m7G-related lncRNA prognostic signature (m7G-LPS) was first tested in the training set and then confirmed in both the testing and ICGC sets. The expression levels of the nine lncRNAs were further confirmed via real-time PCR in cell lines, principal component analysis, and receiver operating characteristic curve. The m7G-LPS could divide HCC patients into two different risk groups with the optimal risk score. Then, Kaplan–Meier curves, tumor mutation burden (TMB), therapeutic effects of chemotherapy agents, and expressions of immune checkpoints were performed to further enhance the availability of immunotherapeutic treatments for HCC patients.

Results: A total of 1465 lncRNAs associated with the m7G genes were finally selected from the TCGA database, and through the univariate Cox regression, the expression levels of 22 m7G-related lncRNAs were concerning HCC patients’ overall survival (OS). Then, the whole patients were grouped into two subgroups, and the OS in Cluster 1 was longer than that of patients in Cluster 2. Furthermore, nine prognostic m7G-related lncRNAs were identified to conduct the m7G-LPS, which were further verified. A prognostic nomogram combined age, gender, HCC grade, stage, and m7G-LPS showed strong reliability and accuracy in predicting OS in HCC patients. Finally, immune checkpoint expression, TMB, and several chemotherapy agents were remarkably associated with risk scores. More importantly, the OS of the TMB-high patients was the worst among the four groups.

Conclusion: The prognostic model we established was validated by abundant algorithms, which provided a new perspective on HCC tumorigenesis and thus improved individualized treatments for patients.
Investigating circulating miRNA in transition dairy cows: What miRNAomics tells about metabolic adaptation
Authors: Veshkini Arash , Hammon Harald Michael , Lazzari Barbara , Vogel Laura , Gnott Martina , Tröscher Arnulf , Vendramin Vera , Sadri Hassan , Sauerwein Helga , Ceciliani Fabrizio
Published: August 2022

In the current study, we investigated dairy cows’ circulating microRNA (miRNA) expression signature during several key time points around calving, to get insights into different aspects of metabolic adaptation. In a trial with 32 dairy cows, plasma samples were collected on days −21, 1, 28, and 63 relative to calving. Individually extracted total RNA was subjected to RNA sequencing using NovaSeq 6,000 (Illumina, CA) on the respective platform of IGA Technology Services, Udine, Italy. MiRDeep2 was used to identify known and novel miRNA according to the miRbase collection. Differentially expressed miRNA (DEM) were assessed at a threshold of fold-change > 1.5 and false discovery rate < 0.05 using the edgeR package. The MiRWalk database was used to predict DEM targets and their associated KEGG pathways. Among a total of 1,692 identified miRNA, 445 known miRNA were included for statistical analysis, of which 84, 59, and 61 DEM were found between days −21 to 1, 1 to 28, and 28 to 63, respectively. These miRNA were annotated to KEGG pathways targeting the insulin, MAPK, Ras, Wnt, Hippo, sphingolipid, T cell receptor, and mTOR signaling pathways. MiRNA-mRNA network analysis identified miRNA as master regulators of the biological process including miR-138, miR-149-5p, miR-2466-3p, miR-214, miR-504, and miR-6523a. This study provided new insights into the miRNA signatures of transition to the lactation period. Calving emerged as a critical time point when miRNA were most affected, while the following period appeared to be recovering from massive parturition changes. The primarily affected pathways were key signaling pathways related to establishing metabolic and immune adaptations.
Mutational signatures representative transcriptomic perturbations in hepatocellular carcinoma
Authors: Wu Qiong , Wang Lingyi , Tsui Stephen Kwok-Wing
Published: August 2022

Hepatocellular carcinoma (HCC) is a primary malignancy with increasing incidence and poor prognosis. Heterogeneity originating from genomic instability is one of the critical reasons of poor outcomes. However, the studies of underlying mechanisms and pathways affected by mutations are still not intelligible. Currently, integrative molecular-level studies using multiomics approaches enable comprehensive analysis for cancers, which is pivotal for personalized therapy and mortality reduction. In this study, genomic and transcriptomic data of HCC are obtained from The Cancer Genome Atlas (TCGA) to investigate the affected coding and non-coding RNAs, as well as their regulatory network due to certain mutational signatures of HCC. Different types of RNAs have their specific enriched biological functions in mutational signature-specific HCCs, upregulated coding RNAs are predominantly associated with lipid metabolism-related pathways, and downregulated coding RNAs are enriched in axonogenesis for tumor microenvironment generation. Additionally, differentially expressed miRNAs are inclined to concentrate in cancer-related signaling pathways. Some of these RNAs also serve as prognostic factors that help predict the survival outcome of HCCs with certain mutational signatures. Furthermore, deregulation of competing endogenous RNA (ceRNA) regulatory network is identified, which suggests a potential therapy via interference of miRNA activity for mutational signature-specific HCC. This study proposes a projection approach to reduce therapeutic complexity from genomic mutations to transcriptomic alterations. Through this method, we identify genes and pathways critical for mutational signature-specific HCC and further discover a series of prognostic markers indicating patient survival outcome.
mRNAsi-related metabolic risk score model identifies poor prognosis, immunoevasive contexture, and low chemotherapy response in colorectal cancer patients through machine learning
Authors: Weng Meilin , Li Ting , Zhao Jing , Guo Miaomiao , Zhao Wenling , Gu Wenchao , Sun Caihong , Yue Ying , Zhong Ziwen , Nan Ke , Liao Qingwu , Sun Minli , Zhou Di , Miao Changhong
Published: August 2022

Colorectal cancer (CRC) is one of the most fatal cancers of the digestive system. Although cancer stem cells and metabolic reprogramming have an important effect on tumor progression and drug resistance, their combined effect on CRC prognosis remains unclear. Therefore, we generated a 21-gene mRNA stemness index-related metabolic risk score model, which was examined in The Cancer Genome Atlas and Gene Expression Omnibus databases (1323 patients) and validated using the Zhongshan Hospital cohort (200 patients). The high-risk group showed more immune infiltrations; higher levels of immunosuppressive checkpoints, such as CD274, tumor mutation burden, and resistance to chemotherapeutics; potentially better response to immune therapy; worse prognosis; and advanced stage of tumor node metastasis than the low-risk group. The combination of risk score and clinical characteristics was effective in predicting overall survival. Zhongshan cohort validated that high-risk score group correlated with malignant progression, worse prognosis, inferior adjuvant chemotherapy responsiveness of CRC, and shaped an immunoevasive contexture. This tool may provide a more accurate risk stratification in CRC and screening of patients with CRC responsive to immunotherapy.
The impact of pulmonary tuberculosis on immunological and metabolic features of diabetic patients
Authors: Chen Haijun , Su Li , Bao Jinhua , Zhang Kun , Li Yuze , Mao Enuo
Published: August 2022

Impaired immune responses have been observed in patients with type-2 diabetes mellitus (T2DM), which increases susceptibility to tuberculosis infection. However, the effect of the tuberculosis infection on the immunological and metabolic features of T2DM is largely unknown. To investigate this question, age- and sex-matched patients with pulmonary tuberculosis (PTB), T2DM, or T2DM combined with PTB were recruited from the Infectious Disease Hospital of Heilongjiang Province between January and September 2020. Healthy subjects were used as controls. Cytokines and chemokines in fasting serum samples were determined using the Quantibody Inflammation Array. Compared with T2DM alone, patients with T2DM combined with PTB have higher fasting blood glucose levels and monocyte counts in circulation. Among the four groups, circulating IL-10 levels peaked in patients with T2DM and PTB (p<0.05). Univariate linear analysis showed that serum IL-10 levels were positively associated with myeloid cells but negatively correlated with lymphocyte counts in these patients (p<0.05). Serum IL-6 levels were 1.6-fold higher in patients with T2DM plus PTB than in those with T2DM alone. In conclusion, PTB infection in patients with T2DM had distinct inflammatory profiles and sustained hyperglycaemia compared with PTB or T2DM alone. IL-10 levels and elevated monocyte counts could be hallmarks of patients with T2DM infected with PTB.
Peripheral enthesitis assessed by whole-body MRI in axial spondyloarthritis: Distribution and diagnostic value
Authors: Guo Zikang , Li Boya , Zhang Yimeng , Kong Chunyu , Liu Yang , Qu Jin , Zhan Ying , Shen Zhiwei , Lei Xinwei
Published: August 2022

Objective

To determine the distribution and diagnostic value of peripheral enthesitis detected by whole-body MRI (WBMRI) in axial spondyloarthritis (axSpA) diagnosis, and to determine the value of the peripheral enthesitis score in axSpA assessment.

Methods

Sixty axSpA patients [mean age of 33.2 (24.8–40.6) years] and 50 controls with chronic low back pain (LBP) [mean age of 34.7 (28.3–41.1) years] were enrolled. The gold standard was physician’s comprehensive diagnosis based on current classification criteria and physical examination. All subjects underwent WBMRI, and 47 peripheral entheses were assessed for each patient with scores of 0–188.

Results

WBMRI identified 155 enthesitis sites in 78.3% (n = 47) patients with axSpA. Meanwhile, 23 enthesitis sites were identified in 32% (n = 16) controls. The pelvis had the maximum number of enthesitis sites (52, 33.5%) in axSpA patients. Pelvic and anterior chest wall enthesitis had the highest sensitivity (51.67%) and specificity (100%) in axSpA diagnosis, respectively. There were different manifestations of enthesitis subtypes between axSpA patients and the control group. Osteitis was more present than soft-tissue inflammation in axSpA patients. The AUC for the number of enthesitis sites was 0.819 (95% CI 0.739–0.899), and that for the enthesitis score was 0.833 (95% CI 0.755–0.910), indicating statistically significant differences (P = 0.025). Based on the Youden index and clinical need, three enthesitis sites (sensitivity of 53.33, specificity of 98, and Youden index of 0.51) and enthesitis score (sensitivity of 58.33, specificity of 98, and Youden index of 0.56) may have the greatest value for axSpA diagnosis.

Conclusion

The distribution of peripheral enthesitis can be adequately assessed by whole-body MRI, which could help diagnose axial spondyloarthritis. The enthesitis score may provide a more accurate assessment and diagnostic tool in axSpA compared with enthesitis site counting.
Late Pleistocene to Holocene variations in marine productivity and terrestrial material delivery to the western South Atlantic
Authors: Dauner Ana Lúcia Lindroth , Mollenhauer Gesine , Hefter Jens , Bícego Márcia Caruso , de Mahiques Michel Michaelovitch , Martins César de Castro
Published: August 2022

Despite the increased number of paleoceanographic studies in the SW Atlantic in recent years, the mechanisms controlling marine productivity and terrestrial material delivery to the South Brazil Bight remain unresolved. Because of its wide continental shelf and abrupt change in coastline orientation, this region is under the influence of several environmental forcings, causing the region to have large variability in primary production. This study investigated terrestrial organic matter (OM) sources and marine OM sources in the South Brazil Bight, as well as the main controls on marine productivity and terrestrial OM export. We analyzed OM geochemical (bulk and molecular) proxies in sediment samples from a core (NAP 63-1) retrieved from the SW Atlantic slope (24.8°S, 44.3°W, 840-m water depth). The organic proxies were classified into “terrestrial-source” and “marine-source” groups based on a cluster analysis. The two sources presented different stratigraphical profiles, indicating distinct mechanisms governing their delivery. Bulk proxies indicate the predominance of marine OM, although terrestrial input also affected the total OM deposition. The highest marine productivity, observed between 50 and 39 ka BP, was driven by the combined effects of the South Atlantic Central Water upwelling promoted by Brazil Current eddies and fluvial nutrient inputs from the adjacent coast. After the last deglaciation, decreased phytoplankton productivity and increased archaeal productivity suggest a stronger oligotrophic tropical water presence. The highest terrestrial OM accumulation occurred between 30 and 20 ka BP, with its temporal evolution controlled mainly by continental moisture evolution. Sea level fluctuations affected the distance between the coastline and the sampling site. In contrast, continental moisture affected the phytogeography, changing from lowlands covered by grasses and saltmarshes to a landscape dominated by mangroves and the Atlantic Forest. Our results suggest how the OM cycle in the South Brazil Bight may respond to warmer and dryer climate conditions.
Co-occurrence and diversity patterns of benthonic and planktonic communities in a shallow marine ecosystem
Authors: Ríos-Castro Raquel , Costas-Selas Cecilia , Pallavicini Alberto , Vezzulli Luigi , Novoa Beatriz , Teira Eva , Figueras Antonio
Published: August 2022

Marine microorganisms are involved in a variety of biogeochemical cycles and live in diverse ecological communities where they interact with each other and with other organisms to guarantee ecosystem functions. The present study focused on a shallow marine environment located in Ría de Vigo (NW, Spain), where sediment and size-fractionated plankton samples were collected from 2016 to 2018. DNA metabarcoding was used to describe the eukaryote and prokaryote composition and diversity in sediments and plankton and to depict possible associations among the most frequent and abundant organisms by co-occurrence network analysis. High eukaryote and prokaryote diversity indices were obtained in all compartments. Significant differences among eukaryote and prokaryote communities were found between sediment and plankton samples, with a high percentage of exclusive operational taxonomic units (OTUs) associated with each compartment, especially from sediment. Despite these differences, shared taxa between water and sediment were also obtained, suggesting a relatively meaningful exchange of organisms between both environmental compartments. Significant co-occurrences were mainly obtained between prokaryotes (41%), followed by eukaryotes–prokaryotes (32%) and between eukaryotes (27%). The abundant and strong positive correlations between organisms, including representatives from the sediment and the water column, suggested an essential role of biotic interactions as community-structuring factors in shallow waters where beneficial associations likely prevail. This study provides a novel approach for the detailed description of the eukaryote and prokaryote diversity and co-occurrence patterns in a shallow marine area, including both the sediment and different water-size fractions. The high diversity obtained and the detection of predominantly coexisting interactions among organisms from sediment and the overlying water column suggest a movement of species between both habitats and therefore confirm the importance of integratively studying shallow marine ecosystems.
Starch accumulation dynamics and transcriptome analysis of Chlorella sorokiniana during transition of sulfur nutritional status
Authors: Xu Haiqing , Yang Jinzhi , Wang Xu , Peng Qing , Han Yanxia , Liu Xudong , Liu Kexin , Dou Shijuan , Li Liyun , Liu Guozhen , Yang Ming
Published: August 2022

Microalgae can effectively accumulate starch by using nutritional limitation methods in the context of bioalcohol fuel production. However, relatively few studies have focused on starch accumulation in microalgae and its molecular basis, especially under sulfur limitation conditions. In this study, the starch accumulation dynamics and physiological responses ofChlorella sorokinianaunder sulfur starvation (SS) and sulfur replenishment (SR) conditions were investigated, and the genes involved in the transcriptional regulation were explored using RNA-seq. The starch content inC. sorokinianacells significantly increased from 1.6% to 55.0% of dry weight within 24 h under SS conditions, and then, it decreased to 3.4% within 12 h after transition to SR conditions. However, cell growth was inhibited, and pigment content decreased under SS conditions. Using RNA-seq analysis, a total of 9720 differentially expressed genes (DEGs) induced by sulfur status were obtained. These genes were narrowed down to 454 starvation and replenishment cross-validated (SRV)-DEGs, among which 283 SRV-DEGs were significantly up-regulated and 171 SRV-DEGs were down-regulated under SS conditions, and returned to their previous state under SR conditions. The SRV-DEGs enriched in the sulfate metabolism pathway were all up-regulated under SS conditions after 6 h to speed up the sulfur metabolic cycle, and the transcriptional abundance of a sulfate transporter (SULTR4), cysteine synthase[O-acetylserine(thiol)-lyase] (OASTL), serine acetyltransferase (SAT), and methanethiol oxidase (SELENBP1) increased 8.6-fold, 12.6-fold, 8.7-fold, and 12.4-fold, respectively. Protein synthesis was correspondingly inhibited, which resulted in the reallocation of carbon and elevated the starch synthesis pathway, in which the expressions of glycogen branching enzyme (GBE) and starch synthase (SS) were up-regulated 12.0- and 3.0-fold, respectively. The fatty acid desaturase (FAD) and phosphatidic acid phosphatase (PAP) in the lipid synthesis pathway were strongly up-regulated 8.8- and 16.2-fold, respectively, indicating the competitive synthesis of lipids. The down-regulation of SRV-DEGs associated with carbon fixation, such as those in the Calvin cycle, possibly affected cell growth. The time-resolved transcriptional analysis identified the SRV-DEGs, revealing the underlying starch accumulation mechanism, as well as the relationship with cell growth and lipid synthesis.
Gut microbiota and meat quality
Authors: Chen Binlong , Li Diyan , Leng Dong , Kui Hua , Bai Xue , Wang Tao
Published: August 2022

Sustainable meat production is important to providing safe and quality protein sources for humans worldwide. Intensive artificial selection and high energy input into the diet of many commercial animals for the last decade has significantly increased the daily gain of body weight and shortened the raising period, but unexpectedly decreased the meat quality. The gastrointestinal tract of animals harbors a diverse and complex microbial community that plays a vital role in the digestion and absorption of nutrients, immune system development, pathogen exclusion, and meat quality. Fatty acid composition and oxidative stress in adipose and muscle tissue influences meat quality in livestock and poultry. Recent studies showed that nutraceuticals are receiving increased attention, which could alter the intestinal microbiota and regulate the fat deposition and immunity of hosts to improve their meat quality. Understanding the microbiota composition, the functions of key bacteria, and the host-microbiota interaction is crucial for the development of knowledge-based strategies to improve both animal meat quality and host health. This paper reviews the microorganisms that affect the meat quality of livestock and poultry. A greater understanding of microbial changes that accompany beneficial dietary changes will lead to novel strategies to improve livestock and poultry meat product quality.
Detection of emerging genotypes in Trichophyton mentagrophytes species complex: A proposal for handling biodiversity in dermatophytes
Authors: Tang Chao , Ahmed Sarah A. , Deng Shuwen , Zhang Lu , Zoll Jan , Al-Hatmi Abdullah M. S. , Meis Jacques F. , Thakur Rameshwari , Kang Yingqian , de Hoog G. Sybren
Published: August 2022

A resistant and hypervirulent dermatophyte from India has been described as a taxonomic novelty, Trichophyton indotineae, a species of the Trichophyton mentagrophytes complex. Rapid detection and correct identification of closely similar dermatophytes with different predilections are essential for efficient clinical management. We evaluated the efficacy of rapid diagnostic methods clinical and environmental strains in the T. mentagrophytes complex. The methods included Real-time-PCR, DermaGenius, LAMP, and MALDI-ToF MS, using rDNA ITS sequences as taxonomic standard. The results show that only MALDI-ToF MS can distinguish 96.97% T. indotineae from other closely related species. The complex comprises numerous clones which may differ in anonymous markers but with similar evolutionary behavior. Therefore, we recommend to distinguish species only when they show an appreciable degree of adaptation and thus are clinically significant. The distinction of remaining clonal diversity is an epidemiological query and can be solved by haplotype numbering.
Classification and molecular characteristics of tet(X)-carrying plasmids in Acinetobacter species
Authors: Chen Chong , Huang Ping-Yu , Cui Chao-Yue , He Qian , Sun Jian , Liu Ya-Hong , Huang Jin-Lin
Published: August 2022

The rapid dissemination of plasmid-mediated tet(X) genes in Acinetobacter species has compromised the clinical effectiveness of tigecycline, one of the last-resort antibiotics. However, the classification strategy and homology group of tet(X)-positive Acinetobacter spp. plasmids remain largely unknown. In this study, we classified them by genome-based replicon typing, followed by analyses of structural characteristics, transferability and in vivo effect. A total of 34 plasmids distributed in at least nine Acinetobacter species were collected, including three tet(X3)-positive plasmids and one tet(X6)-positive plasmid from our genome sequencing results. Among them, there were 28 plasmids carrying Rep_3 superfamily replicase genes and classified into six homology groups, consisting of GR31 (82.1%), GR26 (3.6%), GR41 (3.6%), GR59 (3.6%), and novel groups GR60 (3.6%) and GR61 (3.6%). Our tet(X3)-positive plasmids pYH16040-1, pYH16056-1, and pYH12068-1 belonged to the dominant GR31 group, whereas the tet(X6)-positive plasmid pYH12068-2 was unclassified. Structurally, all tet(X)-positive GR31 plasmids shared similar plasmid replication (repB), stability (parA and parB) and accessory modules [tet(X) and sul2], and 97.6% of plasmid-mediated tet(X) genes in Acinetobacter species were adjacent to ISCR2. Conjugation and susceptibility testing revealed pYH16040-1, pYH16056-1, and pYH12068-2, carrying plasmid transfer modules, were able to mediate the mobilization of multiple antibiotic resistance. Under the treatment of tigecycline, the mortality rate of Galleria mellonella infected by pYH16040-1-mediated tet(X3)-positive Acinetobacter spp. isolate significantly increased when compared with its plasmid-cured strain (p < 0.0001). The spread of such plasmids is of great clinical concern, more effects are needed and will facilitate the future analysis of tet(X)-positive Acinetobacter spp. plasmids.
Antifungal activity of non-conventional yeasts against Botrytis cinerea and non-Botrytis grape bunch rot fungi
Authors: Maluleke Evelyn , Jolly Neil Paul , Patterton Hugh George , Setati Mathabatha Evodia
Published: August 2022

Grapes harbour a plethora of non-conventional yeast species. Over the past two decades, several of the species have been extensively characterised and their contribution to wine quality is better understood. Beyond fermentation, some of the species have been investigated for their potential as alternative biological tools to reduce grape and wine spoilage. However, such studies remain limited to a few genera. This work aimed to evaluate the antagonistic activity of grape must-derived non-conventional yeasts against Botrytis cinerea and non-Botrytis bunch-rotting moulds and to further elucidate mechanisms conferring antifungal activity. A total of 31 yeast strains representing 21 species were screened on different agar media using a dual culture technique and liquid mixed cultures, respectively. Pichia kudriavzevii was the most potent with a minimum inhibitory concentration of 102 cells/mL against B. cinerea but it had a narrow activity spectrum. Twelve of the yeast strains displayed broad antagonistic activity, inhibiting three strains of B. cinerea (B05. 10, IWBT FF1 and IWBT FF2), a strain of Aspergillus niger and Alternaria alternata. Production of chitinases and glucanases in the presence of B. cinerea was a common feature in most of the antagonists. Volatile and non-volatile compounds produced by antagonistic yeast strains in the presence of B. cinerea were analysed and identified using gas and liquid chromatography mass spectrometry, respectively. The volatile compounds identified belonged mainly to higher alcohols, esters, organosulfur compounds and monoterpenes while the non-volatile compounds were cyclic peptides and diketopiperazine. To our knowledge, this is the first report to demonstrate inhibitory effect of the non-volatile compounds produced by various yeast species.
The prophylactic effects of monoclonal antibodies targeting the cell wall Pmt4 protein epitopes of Candida albicans in a murine model of invasive candidiasis
Authors: Wang Xiaojuan , Liu Peng , Jiang Yuanying , Han Bing , Yan Lan
Published: August 2022

Candida albicans (C. albicans) is the most prevalent opportunistic human pathogen, accounting for approximately half of all clinical cases of candidemia. Resistance to the existing antifungal drugs is a major challenge in clinical therapy, necessitating the development and identification of novel therapeutic agents and potential treatment strategies. Monoclonal antibody-based immunotherapy represents a promising therapeutic strategy against disseminated candidiasis. Protein mannosyltransferase (Pmt4) encodes mannosyltransferases initiating O-mannosylation of secretory proteins and is essential for cell wall composition and virulence of C. albicans. Therefore, the Pmt4 protein of C. albicans is an attractive target for the discovery of alternative antibody agents against invasive C. albicans infections. In the present study, we found that monoclonal antibodies (mAbs) C12 and C346 specifically targeted the recombinant protein mannosyltransferase 4 (rPmt4p) of C. albicans. These mAbs were produced and secreted by hybridoma cells isolated from the spleen of mice that were initially immunized with the purified rPmt4p to generate IgG antibodies. The mAbs C12 and C346 exhibited high affinity to C. albicans whole cells. Remarkably, these mAbs reduced the fungal burden, alleviated inflammation in the kidneys, and prolonged the survival rate significantly in the murine model of systemic candidiasis. Moreover, they could activate macrophage opsonophagocytic killing and neutrophil killing of C. albicans strain in vitro. These results suggested that anti-rPmt4p mAbs may provide immunotherapeutic interventions against disseminated candidiasis via opsonophagocytosis and opsonic killing activity. Our findings provide evidence for mAbs as a therapeutic option for the treatment of invasive candidiasis.
Trichodimerol inhibits inflammation through suppression of the nuclear transcription factor-kappaB/NOD-like receptor thermal protein domain associated protein 3 signaling pathway
Authors: Huo Xue-Yan , Lei Li-Rong , Guo Wen-Xiu , Hu Yun-Jie , Kuang Qi-Xuan , Liu Meng-Dan , Peng Wan , Dai Yi-Fei , Wang Dong , Gu Yu-Cheng , Guo Da-Le , Deng Yun
Published: August 2022

Excessive inflammation causes chronic diseases and tissue damage. Although there has been drug treatment, its side effects are relatively large. Searching for effective anti-inflammatory drugs from natural products has become the focus of attention. First isolated from Trichoderma longibraciatum, trichodimerol is a natural product with TNF inhibition. In this study, lipopolysaccharide (LPS)-induced RAW264.7 macrophages were used as a model to investigate the anti-inflammatory activity of trichodimerol. The results of nitric oxide (NO) detection, enzyme-linked immunosorbent assay (ELISA), and reactive oxygen species (ROS) showed that trichodimerol could reduce the production of NO, ROS, and the proinflammatory cytokines interleukin (IL)-6 and tumor necrosis factor (TNF)-α. Western blotting results showed that trichodimerol could inhibit the production of inflammatory mediators such as cyclooxygenase (COX)-2 and inducible nitric oxide synthase (iNOS) and the protein expression of nuclear transcription factor-kappaB (NF-κB), p-IKK, p-IκB, Toll-like receptor 4 (TLR4), NOD-like receptor thermal protein domain associated protein 3 (NLRP3), cysteinyl aspartate specific proteinase (Caspase)-1, and ASC, which indicated that trichodimerol may inhibit inflammation through the NF-κB and NLRP3 pathways. At the same time, molecular docking showed that trichodimerol can directly combine with the TLR4-MD2 complex. Hence, trichodimerol inhibits inflammation by obstructing the interaction between LPS and the TLR4-MD2 heterodimer and suppressing the downstream NF-κB and NLRP3 pathways.
Geometric deep learning reveals a structuro-temporal understanding of healthy and pathologic brain aging
Authors: Besson Pierre , Rogalski Emily , Gill Nathan P. , Zhang Hui , Martersteck Adam , Bandt S. Kathleen
Published: August 2022

Background

Brain age has historically been investigated primarily at the whole brain level. The ability to deconstruct the brain into its composite parts and explore brain age at the sub-structure level offers unique advantages. These include the exploration of dynamic and interconnected relationships between different brain structures in healthy and pathologic aging. To achieve this, individual brain structures can be rendered as surface representations on which morphologic analysis is carried out. Combining the advantages of deep learning with the strengths of surface analysis, we investigate the aging process at the individual structure level with the hypothesis being that pathologic aging does not uniformly affect the aging process of individual structures.

Methods

MRI data, age at scan time and diagnosis of dementia were collected from seven publicly available data repositories. The data from 17,440 unique subjects were collected, representing a total of 26,276 T1-weighted MRI accounting for longitudinal acquisitions. Surfaces were extracted for the cortex and seven subcortical structures. Deep learning networks were trained to estimate a subject’s age either using several structures together or a single structure. We conducted a cross-sectional analysis to assess the difference between the predicted and actual ages for all structures between healthy subjects, individuals with mild cognitive impairment (MCI) or Alzheimer’s disease dementia (ADD). We then performed a longitudinal analysis to assess the difference in the aging pace for each structure between stable healthy controls and healthy controls converting to either MCI or ADD.

Findings

Using an independent cohort of healthy subjects, age was well estimated for all structures. Cross-sectional analysis identified significantly larger predicted age for all structures in patients with either MCI and ADD compared to healthy subjects. Longitudinal analysis revealed varying degrees of involvement of individual subcortical structures for both age difference across groups and aging pace across time. These findings were most notable in the whole brain, cortex, hippocampus and amygdala.

Conclusion

Although similar patterns of abnormal aging were found related to MCI and ADD, the involvement of individual subcortical structures varied greatly and was consistently more pronounced in ADD patients compared to MCI patients.
Blood neuroexosomal excitatory amino acid transporter-2 is associated with cognitive decline in Parkinson’s disease with RBD
Authors: Leng Bing , Sun Hairong , Li Mengfan , Zhao Junwu , Liu Xiaoxiao , Yao Ran , Shen Tengqun , Li Zhenguang , Zhang Jinbiao
Published: August 2022

Background

Rapid eye movement (REM) sleep behavior disorder (RBD) predicts cognitive decline in Parkinson’s disease (PD) patients without dementia. However, underlying mechanisms remain unknown. Accumulating studies suggest glutamatergic system dysregulation is associated.

Objective

To examine the effect of RBD on the rate of cognitive decline in PD patients and investigate whether plasma levels of the neuroexosomal vesicular glutamate transporter-1 (VGLUT-1) and excitatory amino acid transporter-2 (EAAT-2) are altered in PD patients with RBD.

Methods

This study included 157 newly diagnosed cognitive normal PD patients and 70 healthy controls (HCs). Based on one-night polysomnography recordings, the PD subjects were divided into PD with and without RBD (PD-RBD and PD-nRBD) groups. All participants received a complete clinical and neuropsychological evaluation at baseline. Plasma levels of neuroexosomal VGLUT-1 and EAAT-2 were measured by ELISA kits. After a 3-year follow-up, we evaluated baseline plasma levels of neuroexosomal glutamate transporters in each group as a predictor of cognitive decline using MoCA score changes over 3 years in regression models.

Results

Plasma levels of neuron-derived exosomal EAAT-2 and VGLUT-1 were significantly lower in PD patients than in HCs. Plasma levels of neuroexosomal EAAT-2 were significantly lower in PD-RBD than PD-nRBD group at baseline. At the 3-year follow-up, PD-RBD patients presented greater cognitive decline. Lower baseline blood neuroexosomal EAAT-2 predicted cognitive decline over 3 years in PD-RBD patients (β = 0.064, P = 0.003).

Conclusion

These findings indicate that blood neuroexosomal EAAT-2 is associated with cognitive decline in PD with RBD.
Are superficial neuromasts proprioceptors underlying fast copulatory behavior?
Authors: Martinez-Rivera Noraida , Serrano-Velez Jose L. , Torres-Vazquez Irma I. , Langerhans R. Brian , Rosa-Molinar Eduardo
Published: August 2022

In male Poeciliid fishes, the modified anal fin (i.e., gonopodium) and its axial and appendicular support are repositioned within the axial skeleton, creating a novel sexually dimorphic ano-urogenital region. During copulation, the relative location of the gonopodium is crucial for successful insemination. Therefore, the repositioning of these structures and organ relied on the reorganization of the efferent circuitry that controls spinal motor neurons innervating appendicular muscles critical for the movement of the gonopodium, including the fast and synchronous torque-trust motion during insemination attempts. Copulation occurs when a male positions himself largely outside a female’s field of view, circumducts his gonopodium, and performs a rapid, complex maneuver to properly contact the female urogenital sinus with the distal tip of the gonopodium and transfers sperm. Although understanding of the efferent circuitry has significantly increased in the last 24 years, nothing is known about the cutaneous receptors involved in gonopodium movement, or how the afferent signals are processed to determine the location of this organ during copulation. Using Western mosquitofish, Gambusia affinis, as our model, we attempt to fill this gap in knowledge. Preliminary data showed cutaneous nerves and sensory neurons innervating superficial neuromasts surrounding the base of adult male gonopodium; those cutaneous nerves projected ventrally from the spinal cord through the 14th dorsal root ganglion and its corresponding ventral root towards the base and fin rays of the gonopodium. We asked what role the cutaneous superficial neuromasts play in controlling the positioning and timing of the gonopodium’s fast and synchronous movements for effective sperm transfer. First, we found a greater number of superficial neuromasts surrounding the base of the male’s gonopodium compared to the base of the female’s anal fin. Second, we systemically removed superficial neuromasts surrounding the gonopodium base and observed significant impairment of the positioning and timing of gonopodial movements. Our findings provide a first step to supporting the following hypothesis: during radical reorganization of the Poeciliid body plan, superficial neuromasts have been partially co-opted as proprioceptors that allow the gonopodium to control precise positioning and timing during copulatory attempts.