bluuebunny/crossref_metadata_2025 huggingface dataset:
Collating biodiversity occurrence data for conservation
Authors: Spear Dian , van Wilgen Nicola J. , Rebelo Anthony G. , Botha Judith M.
Published: March 2023

Plant and animal checklists, with conservation status information, are fundamental for conservation management. Historical field data, more recent data of digital origin and data-sharing platforms provide useful sources for collating species locality data. However, different biodiversity datasets have different formats and inconsistent naming systems. Additionally, most digital data sources do not provide an easy option for download by protected area. Further, data-entry-ready software is not readily available for conservation organization staff with limited technical skills to collate these heterogeneous data and create distribution maps and checklists for protected areas. The insights presented here are the outcome of conceptualizing a biodiversity information system for South African National Parks. We recognize that a fundamental requirement for achieving better standardization, sharing and use of biodiversity data for conservation is capacity building, internet connectivity, national institutional data management support and collaboration. We focus on some of the issues that need to be considered for capacity building, data standardization and data support. We outline the need for using taxonomic backbones and standardizing biodiversity data and the utility of data from the Global Biodiversity Information Facility and other available sources in this process. Additionally, we make recommendations for the fields needed in relational databases for collating species data that can be used to inform conservation decisions and outline steps that can be taken to enable easier collation of biodiversity data, using South Africa as a case study.
Transcriptome analysis reveals defense-related genes and pathways during dodder (Cuscuta australis) parasitism on white clover (Trifolium repens)
Authors: Zhou Li , Zawaira Alexander , Lu Qiuwei , Yang Beifen , Li Junmin
Published: March 2023

Dodders (Cuscuta australis R. Br.) are holo-parasitic stem angiosperms with an extensive host range that have significant ecological and economic potential impact on the ecosystem and the agricultural system. However, how the host plant responds to this biotic stress remains mostly unexplored. To identify the defense-related genes and the pathways in white clover (Trifolium repens L.) induced by dodder parasitism, we performed a comparative transcriptome analysis of the leaf and root tissues from white clover with and without dodder infection by high throughput sequencing. We identified 1,329 and 3,271 differentially expressed genes (DEGs) in the leaf and root tissues, respectively. Functional enrichment analysis revealed that plant-pathogen interaction, plant hormone signal transduction, and phenylpropanoid biosynthesis pathways were significantly enriched. Eight WRKY, six AP2/ERF, four bHLH, three bZIP, three MYB, and three NAC transcription factors showed a close relationship with lignin synthesis-related genes, which defended white clover against dodder parasitism. Real-time quantitative PCR (RT-qPCR) for nine DEGs, further validated the data obtained from transcriptome sequencing. Our results provide new insights into understanding the complex regulatory network behind these parasite-host plant interactions.
Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut
Authors: Gangurde Sunil S. , Pasupuleti Janila , Parmar Sejal , Variath Murali T. , Bomireddy Deekshitha , Manohar Surendra S. , Varshney Rajeev K. , Singam Prashant , Guo Baozhu , Pandey Manish K.
Published: March 2023

Seed size is not only a yield-related trait but also an important measure to determine the commercial value of groundnut in the international market. For instance, small size is preferred in oil production, whereas large-sized seeds are preferred in confectioneries. In order to identify the genomic regions associated with 100-seed weight (HSW) and shelling percentage (SHP), the recombinant inbred line (RIL) population (Chico × ICGV 02251) of 352 individuals was phenotyped for three seasons and genotyped with an Axiom_Arachis array containing 58K SNPs. A genetic map with 4199 SNP loci was constructed, spanning a map distance of 2708.36 cM. QTL analysis identified six QTLs for SHP, with three consistent QTLs on chromosomes A05, A08, and B10. Similarly, for HSW, seven QTLs located on chromosomes A01, A02, A04, A10, B05, B06, and B09 were identified. BIG SEED locus and spermidine synthase candidate genes associated with seed weight were identified in the QTL region on chromosome B09. Laccase, fibre protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins were identified in the QTL regions associated with shelling percentage. The associated markers for major-effect QTLs for both traits successfully distinguished between the small- and large-seeded RILs. QTLs identified for HSW and SHP can be used for developing potential selectable markers to improve the cultivars with desired seed size and shelling percentage to meet the demands of confectionery industries.
Performance comparisons between clustering models for reconstructing NGS results from technical replicates
Authors: Zhai Yue , Bardel Claire , Vallée Maxime , Iwaz Jean , Roy Pascal
Published: March 2023

To improve the performance of individual DNA sequencing results, researchers often use replicates from the same individual and various statistical clustering models to reconstruct a high-performance callset. Here, three technical replicates of genome NA12878 were considered and five model types were compared (consensus, latent class, Gaussian mixture, Kamila–adapted k-means, and random forest) regarding four performance indicators: sensitivity, precision, accuracy, and F1-score. In comparison with no use of a combination model, i) the consensus model improved precision by 0.1%; ii) the latent class model brought 1% precision improvement (97%–98%) without compromising sensitivity (= 98.9%); iii) the Gaussian mixture model and random forest provided callsets with higher precisions (both >99%) but lower sensitivities; iv) Kamila increased precision (>99%) and kept a high sensitivity (98.8%); it showed the best overall performance. According to precision and F1-score indicators, the compared non-supervised clustering models that combine multiple callsets are able to improve sequencing performance vs. previously used supervised models. Among the models compared, the Gaussian mixture model and Kamila offered non-negligible precision and F1-score improvements. These models may be thus recommended for callset reconstruction (from either biological or technical replicates) for diagnostic or precision medicine purposes.
CAXII inhibitors: Potential sensitizers for immune checkpoint inhibitors in HCC treatment
Authors: Han Rui , Li Jiayin , Hony Jing , Xiao Zhiwei , wang Jinghui , Yao Man , Liang Shufang , Lu Lingeng
Published: March 2023

Hepatocellular carcinoma (HCC) is a lethal malignancy with a lack of effective treatments particularly for the disease at an advanced stage. Even though immune checkpoint inhibitors (ICIs) have made great progress in the treatment of HCC, durable and ideal clinical benefits still cannot be achieved in plenty of patients with HCC. Therefore, novel and refined ICI-based combination therapies are still needed to enhance the therapeutic effect. The latest study has reported that the carbonic anhydrase XII inhibitor (CAXIIi), a novel type of anticancer drug, can modify the tumor immunosuppression microenvironment by affecting hypoxic/acidic metabolism and alter the functions of monocytes and macrophages by regulating the expression of C-C motif chemokine ligand 8 (CCL8). These observations shine a light on improving programmed cell death protein 1 (PD-1)/programmed cell death ligand-1 (PD-L1) immunotherapy in combination with CAXIIis. This mini-review aims to ignite enthusiasm to explore the potential application of CAXIIis in combination with immunotherapy for HCC.
A chemokine network of T cell exhaustion and metabolic reprogramming in renal cell carcinoma
Authors: Pichler Renate , Siska Peter J. , Tymoszuk Piotr , Martowicz Agnieszka , Untergasser Gerold , Mayr Roman , Weber Florian , Seeber Andreas , Kocher Florian , Barth Dominik A. , Pichler Martin , Thurnher Martin
Published: March 2023

Renal cell carcinoma (RCC) is frequently infiltrated by immune cells, a process which is governed by chemokines. CD8+ T cells in the RCC tumor microenvironment (TME) may be exhausted which most likely influence therapy response and survival. The aim of this study was to evaluate chemokine-driven T cell recruitment, T cell exhaustion in the RCC TME, as well as metabolic processes leading to their functional anergy in RCC. Eight publicly available bulk RCC transcriptome collectives (n=1819) and a single cell RNAseq dataset (n=12) were analyzed. Immunodeconvolution, semi-supervised clustering, gene set variation analysis and Monte Carlo-based modeling of metabolic reaction activity were employed. Among 28 chemokine genes available,CXCL9/10/11/CXCR3, CXCL13/CXCR5 and XCL1/XCR1mRNA expression were significantly increased in RCC compared to normal kidney tissue and also strongly associated with tumor-infiltrating effector memory and central memory CD8+T cells in all investigated collectives. M1 TAMs, T cells, NK cells as well as tumor cells were identified as the major sources of these chemokines, whereas T cells, B cells and dendritic cells were found to predominantly express the cognate receptors. The cluster of RCCs characterized by high chemokine expression and high CD8+T cell infiltration displayed a strong activation of IFN/JAK/STAT signaling with elevated expression of multiple T cell exhaustion-associated transcripts. ChemokinehighRCCs were characterized by metabolic reprogramming, in particular by downregulated OXPHOS and increased IDO1-mediated tryptophan degradation. None of the investigated chemokine genes was significantly associated with survival or response to immunotherapy. We propose a chemokine network that mediates CD8+T cell recruitment and identify T cell exhaustion, altered energy metabolism and high IDO1 activity as key mechanisms of their suppression. Concomitant targeting of exhaustion pathways and metabolism may pose an effective approach to RCC therapy.
COVID-19 vaccination in psoriasis patients receiving systemic treatment: A prospective single-center study
Authors: Lodde Georg Christian , Krefting Frederik , Placke Jan-Malte , Schneider Lea , Fiedler Melanie , Dittmer Ulf , Becker Jürgen Christian , Hölsken Stefanie , Schadendorf Dirk , Ugurel Selma , Sondermann Wiebke
Published: March 2023

Background

The rate of seroconversion after COVID-19 vaccination in patients with moderate to severe psoriasis requiring systemic treatment is poorly understood.

Objectives

The aim of this prospective single-center cohort study performed between May 2020 and October 2021 was to determine the rate of seroconversion after COVID-19 vaccination in patients under active systemic treatment for moderate to severe psoriasis.

Methods

Inclusion criteria were systemic treatment for moderate to severe psoriasis, known COVID-19 vaccination status, and repetitive anti-SARS-CoV-2-S IgG serum quantification. The primary outcome was the rate of anti-SARS-CoV-2-S IgG seroconversion after complete COVID-19 vaccination.

Results

77 patients with a median age of 55.9 years undergoing systemic treatment for moderate to severe psoriasis were included. The majority of patients received interleukin- (n=50, 64.9%) or tumor necrosis factor (TNF)-α inhibitors (n=16, 20.8%) as systemic treatment for psoriasis; nine patients (11.7%) were treated with methotrexate (MTX) monotherapy, and one patient each received dimethyl fumarate (1.3%), respectively apremilast (1.3%). All included patients completed COVID-19 vaccination with two doses over the course of the study. Serum testing revealed that 74 patients (96.1%) showed an anti-SARS-CoV-2-S IgG seroconversion. While all patients on IL-17A, -12 or -12/23 inhibitors (n=50) achieved seroconversion, three of 16 patients (18.8%) receiving MTX and/or a TNF-α inhibitor as main anti-psoriatic treatment did not. At follow-up, none of the patients had developed symptomatic COVID-19 or died from COVID-19.

Conclusions

Anti-SARS-CoV-2-S IgG seroconversion rates following COVID-19 vaccination in psoriasis patients under systemic treatment were high. An impaired serological response, however, was observed in patients receiving MTX and/or TNF-α inhibitors, in particular infliximab.
Isolated anti-Ro52 identifies a severe subset of Sjögren’s syndrome patients
Authors: Lee Adrian Y. S. , Putty Trishni , Lin Ming-Wei , Swaminathan Sanjay , Suan Dan , Chataway Tim , Thurlings Rogier M. , Gordon Tom P. , Wang Jing Jing , Reed Joanne H.
Published: March 2023

Introduction

Serum autoantibodies targeting the SSA/Ro proteins are a key component of the classification criteria for the diagnosis of Sjögren’s syndrome (SS). Most patients' serum reacts with both Ro60 and Ro52 proteins. Here we compare the molecular and clinical characteristics of patients diagnosed with SS with anti-Ro52 in the presence or absence of anti-Ro60/La autoantibodies.

Methods

A cross-sectional study was performed. Patients in the SS biobank at Westmead Hospital (Sydney, Australia) that were positive for anti-Ro52 were included and stratified based on the absence (isolated) or presence (combined) of anti-Ro60/La, measured by line immunoassay. We examined clinical associations and the serological and molecular characteristics of anti-Ro52 using ELISA and mass spectrometry in serological groups.

Results

A total of 123 SS patients were included for study. SS patients with isolated anti-Ro52 (12%) identified a severe serological subset characterised by higher disease activity, vasculitis, pulmonary involvement, rheumatoid factor (RhF) and cryoglobulinaemia. Serum antibodies reacting with Ro52 in the isolated anti-Ro52 subset displayed less isotype switching, less immunoglobulin variable region subfamily usage and a lower degree of somatic hypermutation than the combined anti-Ro52 subset.

Conclusions

In our cohort of SS patients, isolated anti-Ro52 represents a severe subset of SS, and is associated with the presence of cryoglobulinaemia. We therefore provide clinical relevance to the stratification of SS patients by their sero-reactivities. It is possible that the autoantibody patterns may be immunological epiphenomena of the underlying disease process, and further work is required to unearth the mechanisms of the differential clinical phenotypes.
The impact of hepatocyte-specific deletion of hypoxia-inducible factors on the development of polymicrobial sepsis with focus on GR and PPARα function
Authors: Vanderhaeghen Tineke , Timmermans Steven , Eggermont Melanie , Watts Deepika , Vandewalle Jolien , Wallaeys Charlotte , Nuyttens Louise , De Temmerman Joyca , Hochepied Tino , Dewaele Sylviane , Berghe Joke Vanden , Sanders Niek , Wielockx Ben , Beyaert Rudi , Libert Claude
Published: March 2023

Introduction

Polymicrobial sepsis causes acute anorexia (loss of appetite), leading to lipolysis in white adipose tissue and proteolysis in muscle, and thus release of free fatty acids (FFAs), glycerol and gluconeogenic amino acids. Since hepatic peroxisome proliferator-activated receptor alpha (PPARα) and glucocorticoid receptor (GR) quickly lose function in sepsis, these metabolites accumulate (causing toxicity) and fail to yield energy-rich molecules such as ketone bodies (KBs) and glucose. The mechanism of PPARα and GR dysfunction is not known.

Methods & results

We investigated the hypothesis that hypoxia and/or activation of hypoxia inducible factors (HIFs) might play a role in these issues with PPARα and GR. After cecal ligation and puncture (CLP) in mice, leading to lethal polymicrobial sepsis, bulk liver RNA sequencing illustrated the induction of the genes encoding HIF1α and HIF2α, and an enrichment of HIF-dependent gene signatures. Therefore, we generated hepatocyte-specific knock-out mice for HIF1α, HIF2α or both, and a new HRE-luciferase reporter mouse line. After CLP, these HRE-luciferase reporter mice show signals in several tissues, including the liver. Hydrodynamic injection of an HRE-luciferase reporter plasmid also led to (liver-specific) signals in hypoxia and CLP. Despite these encouraging data, however, hepatocyte-specific HIF1α and/or HIF2α knock-out mice suggest that survival after CLP was not dependent on the hepatocyte-specific presence of HIF proteins, which was supported by measuring blood levels of glucose, FFAs, and KBs. The HIF proteins were also irrelevant in the CLP-induced glucocorticoid resistance, but we found indications that the absence of HIF1α in hepatocytes causes less inactivation of PPARα transcriptional function.

Conclusion

We conclude that HIF1α and HIF2α are activated in hepatocytes in sepsis, but their contribution to the mechanisms leading to lethality are minimal.
LAMP3 expression in the liver is involved in T cell activation and adaptive immune regulation in hepatitis B virus infection
Authors: Wang Zilong , Wang Xiaoxiao , Jin Rui , Liu Feng , Rao Huiying , Wei Lai , Chen Hongsong , Feng Bo
Published: March 2023

Background

The disease burden caused by chronic hepatitis B virus (HBV) infection is still heavy, and the current treatment scheme has not achieved a complete cure. Changes in natural and adaptive immunity usually accompany chronic HBV infection. As a marker expressed on dendritic cells (DCs), whether lysosome-associated membrane glycoprotein 3 (LAMP3) participates in chronic HBV infection deserves further analysis.

Methods

We retrieved chronic HBV infection transcriptional information from the Gene Expression Omnibus (GEO) database. The LAMP3 expression in the liver of patients with chronic hepatitis B (CHB) was analyzed in three GEO datasets and confirmed in our validation cohort (27 patients with CHB). Differentially expressed genes were obtained from one CHB cohort by comparing LAMP3high and LAMP3low expression subgroups. These genes underwent Gene Ontology, Kyoto Encyclopedia of Genes and Genomes analysis, and Gene Set Enrichment Analysis to decipher the influence of LAMP3 on the biological process and immunity changes in HBV infection. Furthermore, we investigated the potential relationship between LAMP3 levels, the abundance of infiltrating immune cells, and liver dysfunction.

Results

Compared to healthy controls, LAMP3 expression was upregulated in the transcriptional profiles of the liver in patients with CHB. The high LAMP3 expression was related to T cell activation and the chemokine signaling pathway. The LAMP3 gene was positively linked to marker sets of infiltrating activated regulatory T cells (Treg), T cell exhaustion, monocytes, and DCs. Moreover, CHB patients with high LAMP3 expression had unfavorable liver dysfunction.

Conclusions

LAMP3 is a gene related to HBV infection, which might be involved in HBV infection by regulating T cell activation and adaptive immune response.
The current understanding of the immune landscape relative to radiotherapy across tumor types
Authors: Iliadi Chrysanthi , Verset Laurine , Bouchart Christelle , Martinive Philippe , Van Gestel Dirk , Krayem Mohammad
Published: March 2023

Radiotherapy is part of the standard of care treatment for a great majority of cancer patients. As a result of radiation, both tumor cells and the environment around them are affected directly by radiation, which mainly primes but also might limit the immune response. Multiple immune factors play a role in cancer progression and response to radiotherapy, including the immune tumor microenvironment and systemic immunity referred to as the immune landscape. A heterogeneous tumor microenvironment and the varying patient characteristics complicate the dynamic relationship between radiotherapy and this immune landscape. In this review, we will present the current overview of the immunological landscape in relation to radiotherapy in order to provide insight and encourage research to further improve cancer treatment. An investigation into the impact of radiation therapy on the immune landscape showed in several cancers a common pattern of immunological responses after radiation. Radiation leads to an upsurge in infiltrating T lymphocytes and the expression of programmed death ligand 1 (PD-L1) which can hint at a benefit for the patient when combined with immunotherapy. In spite of this, lymphopenia in the tumor microenvironment of ‘cold’ tumors or caused by radiation is considered to be an important obstacle to the patient’s survival. In several cancers, a rise in the immunosuppressive populations is seen after radiation, mainly pro-tumoral M2 macrophages and myeloid-derived suppressor cells (MDSCs). As a final point, we will highlight how the radiation parameters themselves can influence the immune system and, therefore, be exploited to the advantage of the patient.
A global gridded ocean salinity dataset with 0.5° horizontal resolution since 1960 for the upper 2000 m
Authors: Li Guancheng , Cheng Lijing , Pan Yuying , Wang Gongjie , Liu Hailong , Zhu Jiang , Zhang Bin , Ren Huanping , Wang Xutao
Published: March 2023

A gridded salinity dataset with high resolution is essential for investigating global ocean salinity variability and understanding its role in climate and the ocean ecosystem. In this study, a new version of the Institute of Atmospheric Physics gridded salinity dataset with a higher resolution (0.5° by 0.5°) is provided by using a revised ensemble optimal interpolation scheme with a dynamic ensemble. The performance of this dataset is evaluated using “subsample test” and the high-resolution satellite-based data. Compared with the previous 1° by 1° resolution IAP product, the new dataset is more capable of representing regional salinity changes with the meso-scale and small-scale signals (i.e., in the coastal and boundary currents regions), meanwhile, maintains the large-scale structure and variability. Therefore, the new dataset complements the previous data product. Besides, the new dataset is compared with in situ observations and several international salinity products for the salinity multiscale variabilities and patterns. The comparison shows the smaller magnitude of mean difference and Root-mean-square deviation (RMSD) in basin scale for the new dataset, some differences in strength and fine structure of the “fresh gets fresher, salty gets saltier” surface and subsurface salinity pattern amplification trends from 1980 to 2017, a broad similarity for the salinity changes associated with El Niño-Southern Oscillation (ENSO) and a consistent salinity dipole mode in the tropical Indian Ocean (S-IOD). These results support the future use of gridded salinity data.
Few-shot fine-grained fish species classification via sandwich attention CovaMNet
Authors: Zhai Jiping , Han Lu , Xiao Ying , Yan Mai , Wang Yueyue , Wang Xiaodong
Published: March 2023

The task of accurately classifying marine fish species is of great importance to marine ecosystem investigations, but previously used methods were extremely labor-intensive. Computer vision approaches have the advantages of being long-term, non-destructive, non-contact and low-cost, making them ideal for this task. Due to the unique nature of the marine environment, marine fish data is difficult to collect and often of poor quality, and learning how to identify additional categories from a small sample of images is a very difficult task, meanwhile fish classification is also a fine-grained problem. Most of the existing solutions dealing with few-shot classification mainly focus on the improvement of the metric-based approaches. For few-shot classification tasks, the features extracted by CNN are sufficient for the metric-based model to make a decision, while for few-shot fine-grained classification with small inter-class differences, the CNN features might be insufficient and feature enhancement is essential. This paper proposes a novel attention network named Sandwich Attention Covariance Metric Network (SACovaMNet), which adds a new sandwich-shaped attention module to the CovaMNet based on metric learning, strengthening the CNN’s ability to perform feature extraction on few-shot fine-grained fish images in a more detailed and comprehensive manner. This new model can not only capture the classification objects from the global perspective, but also extract the local subtle differences. By solving the problem of feature enhancement, this new model can accurately classify few-shot fine-grained marine fish images. Experiments demonstrate that this method outperforms state-of-the-art solutions on few-shot fine-grained fish species classification.
Serum amyloid A—A potential therapeutic target for hyper-inflammatory syndrome associated with COVID-19
Authors: Almusalami Eman M. , Lockett Anthony , Ferro Albert , Posner John
Published: March 2023

Serum amyloid-A (SAA) is associated with inflammatory disorders such as rheumatoid arthritis, Familial Mediterranean Fever, sarcoidosis, and vasculitis. There is accumulating evidence that SAA is a reliable biomarker for these autoinflammatory and rheumatic diseases and may contribute to their pathophysiology. Hyperinflammatory syndrome associated with COVID-19 is a complex interaction between infection and autoimmunity and elevation of SAA is strongly correlated with severity of the inflammation. In this review we highlight the involvement of SAA in these different inflammatory conditions, consider its potential role and discuss whether it could be a potential target for treatment of the hyperinflammatory state of COVID-19 with many potential advantages and fewer adverse effects. Additional studies linking SAA to the pathophysiology of COVID-19 hyper-inflammation and autoimmunity are needed to establish the causal relationship and the therapeutic potential of inhibitors of SAA activity.
Preeclampsia pathophysiology and adverse outcomes during pregnancy and postpartum
Authors: Bisson Courtney , Dautel Sydney , Patel Easha , Suresh Sunitha , Dauer Patricia , Rana Sarosh
Published: March 2023

Background

Preeclampsia is a disease with far-reaching consequences that extend beyond the immediate postpartum period and have a significant impact later in life. Preeclampsia exerts an effect on most organ systems in the body. These sequelae are mediated in part by the incompletely elucidated pathophysiology of preeclampsia and the associated vascular changes.

Content

Current research focuses on unraveling the pathophysiology of preeclampsia with the goal of implementing accurate screening and treatment modalities based on disease development and progression. Preeclampsia causes significant short- and long-term maternal morbidity and mortality, not only in the cardiovascular system but also in other organ systems throughout the body. This impact persists beyond pregnancy and the immediate postpartum period.

The goal of this review is to discuss the current understanding of the pathophysiology of preeclampsia as it relates to the adverse health consequences in patients impacted by this disease, along with a brief discussion of ways to improve overall outcomes.
Isolation of bacteriophages infecting Xanthomonas oryzae pv. oryzae and genomic characterization of novel phage vB_XooS_NR08 for biocontrol of bacterial leaf blight of rice
Authors: Jain Lata , Kumar Vinay , Jain Sanjay Kumar , Kaushal Pankaj , Ghosh Probir Kumar
Published: March 2023

Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive diseases worldwide in rice-growing regions. The Ineffectiveness of chemicals in disease management has increased the interest in phage therapy. In this study, we isolated 19 bacteriophages, infecting Xoo, from a rice field, which belonged to phage families Siphoviridae, Myoviridae, and Podoviridae on the basis of electron microscopy. Among 19 phages, Phage vB_XooS_NR08, a member of the Siphoviridae family, expressed antibacterial activity against all Xoo strains tested and did not lyse X. campestris and other unrelated bacterial hosts. Phage NR08 showed more than 80% viability at a temperature range of 4°C–40°C, pH range of 5–9, and direct exposure to sunlight for 2 h, whereas UV light and chemical agents were highly detrimental. In a one-step growth curve, NR08 has a 40-min latent period, followed by a 30-min burst period with a burst size of 250 particle/bacterium. The genome of NR08 is double-stranded DNA, linear having a size of 98,812 bp with a G + C content of 52.9%. Annotation of the whole-genome sequence indicated that NR08 encodes 142 putative open reading frames (ORFs), including one ORF for tRNA, namely, trna1-GlnTTG. Comparative genome analysis of NR08 showed that it shares maximum similarity with Pseudomonas phage PaMx42 (40% query coverage, 95.39% identity, and acc. Length 43,225) and Xanthomonas phage Samson (40% query coverage, 96.68% identity, and acc. Length 43,314). The average alignment percentage (AP) of NR08 with other Xoophages was only 0.32 to 1.25 since the genome of NR08 (98.8 kb) is almost double of most of the previously reported Xoophages (43–47 kb), thus indicating NR08 a novel Xoophage. In in vitro bacterial challenge assay, NR08 showed bacteriostasis up to 24 h and a 99.95% reduction in bacterial growth in 48 h. In rice pot efficacy trials, single-dose treatment of NR08 showed a significant reduction in disease up to 90.23% and 79.27% on 7 and 21 dpi, respectively. However, treatment using 2% skim milk-supplemented phage preparation was significantly less effective as compared to the neat phage preparation. In summary, this study characterized a novel Xoophage having the potential as a biocontrol agent in the mitigation of BLB in rice.
Production of copropophyrin III, biliverdin and bilirubin by the rufomycin producer, Streptomyces atratus
Authors: Perez-Ortiz Gustavo , Sidda John D. , Peate Jessica , Ciccarelli Davide , Ding Yaoyu , Barry Sarah M.
Published: March 2023

Heme is best known for its role as a versatile prosthetic group in prokaryotic and eukaryotic proteins with diverse biological functions including gas and electron transport, as well as a wide array of redox chemistry. However, free heme and related tetrapyrroles also have important roles in the cell. In several bacterial strains, heme biosynthetic precursors and degradation products have been proposed to function as signaling molecules, ion chelators, antioxidants and photoprotectants. While the uptake and degradation of heme by bacterial pathogens is well studied, less is understood about the physiological role of these processes and their products in non-pathogenic bacteria. Streptomyces are slow growing soil bacteria known for their extraordinary capacity to produce complex secondary metabolites, particularly many clinically used antibiotics. Here we report the unambiguous identification of three tetrapyrrole metabolites from heme metabolism, coproporphyrin III, biliverdin and bilirubin, in culture extracts of the rufomycin antibiotic producing Streptomyces atratus DSM41673. We propose that biliverdin and bilirubin may combat oxidative stress induced by nitric oxide production during rufomycin biosynthesis, and indicate the genes involved in their production. This is, to our knowledge, the first report of the production of all three of these tetrapyrroles by a Streptomycete.
Co-infection of TYLCV and ToCV increases cathepsin B and promotes ToCV transmission by Bemisia tabaci MED
Authors: Lu Ding-Yi-Hui , Liao Jin-Yu , Fajar Anugerah , Chen Jian-Bin , Wei Yan , Zhang Zhan-Hong , Zhang Zhuo , Zheng Li-Min , Tan Xin-Qiu , Zhou Xu-Guo , Shi Xiao-Bin , Liu Yong , Zhang De-Yong
Published: March 2023

Tomato disease is an important disease affecting agricultural production, and the combined infection of tomato chlorosis virus (ToCV) and tomato yellow leaf curl virus (TYLCV) has gradually expanded in recent years, but no effective control method has been developed to date. Both viruses are transmitted by Bemisia tabaci Mediteranean (MED). Previously, we found that after B. tabaci MED was fed on ToCV-and TYLCV-infected plants, the transmission efficiency of ToCV was significantly higher than that on plants infected only with ToCV. Therefore, we hypothesize that co-infection could enhance the transmission rates of the virus. In this study, transcriptome sequencing was performed to compare the changes of related transcription factors in B. tabaci MED co-infected with ToCV and TYLCV and infected only with ToCV. Hence, transmission experiments were carried out using B. tabaci MED to clarify the role of cathepsin in virus transmission. The gene expression level and enzyme activity of cathepsin B (Cath B) in B. tabaci MED co-infected with ToCV and TYLCV increased compared with those under ToCV infection alone. After the decrease in cathepsin activity in B. tabaci MED or cathepsin B was silenced, its ability to acquire and transmit ToCV was significantly reduced. We verified the hypothesis that the relative expression of cathepsin B was reduced, which helped reduce ToCV transmission by B. tabaci MED. Therefore, it was speculated that cathepsin has profound research significance in the control of B. tabaci MED and the spread of viral diseases.
Evaluation of the immunogenicity of vaccine candidates developed using a baculovirus surface display system for Crimean-Congo hemorrhagic fever virus in mice
Authors: Zhang Gang , Wang Pu , Jiang Lingling , Wang Sheng , Zhang Sinong , Li Yong
Published: March 2023

Crimean-Congo hemorrhagic fever (CCHF), which has a fatality rate of 20–30%, is widely prevalent in several regions in Asia, Europe, and Africa and has spread to a wider range of areas in recent years. At present, there is a lack of safe and effective vaccines for the prevention of CCHF. In this study, we prepared three vaccine candidates, rvAc-Gn, rvAc-Np, and rvAc-Gn-Np, that encoded the CCHF virus (CCHFV) glycoprotein Gn and the nucleocapsid protein (Np) on the surface of baculovirus using an insect baculovirus vector expression system (BVES) and evaluated their immunogenicity in BALB/c mice. The experimental results showed that both CCHFV Gn and Np were expressed by the respective recombinant baculoviruses and anchored to the viral envelope. BALB/c mice were immunized, and all three recombinant baculoviruses showed significant humoral immunity. At the cellular level, the level of immunity in the rvAc-Gn group was significantly higher than that in the rvAc-Np and rvAc-Gn-Np groups, and the rvAc-Gn-Np coexpression group exhibited the lowest level of cellular immunity. In conclusion, the strategy of coexpressing Gn and Np in the baculovirus surface display system did not result in improvements in immunogenicity, whereas the recombinant baculovirus displaying Gn alone could induce significant humoral and cellular immunity in mice, indicating that rvAc-Gn has potential as a CCHF vaccine candidate. This study thus provides new ideas for the development of a CCHF baculovirus vaccine.
The relationship between gut microbiota and neonatal pathologic jaundice: A pilot case-control study
Authors: You Jia Jia , Qiu Jun , Li Gui Nan , Peng Xiao Ming , Ma Ye , Zhou Chang Ci , Fang Si Wei , Huang Rui Wen , Xiao Zheng Hui
Published: March 2023

Background and objective

Neonatal jaundice is a common clinical disease in neonates. Pathologic jaundice is more harmful to neonates. There are a few studies on the biomarkers of pathologic jaundice and the correlation between gut microbiota and clinical indices. Therefore, we aimed to reveal the characteristics of gut microbiota in pathologic jaundice, provide potential biomarkers for the diagnosis of pathologic jaundice, and find the correlation between gut microbiota and clinical indices.

Methods

Fourteen neonates with physiologic jaundice were recruited into a control group (Group A). Additionally, 14 neonates with pathologic jaundice were recruited into a case group (Group B). The microbial communities were analyzed using 16S rDNA sequencing. LEfSe and the differences in the relative abundance of gut microbiota were used to identify different bacteria among the two groups. The ROC curve was used to assess effective biomarkers for pathologic jaundice. Spearman’s rank-sum correlation coefficient was used to evaluate the correlation between gut microbiota and clinical indices.

Results

There were no differences in the total richness or diversity of gut microbiota between the two groups. At the phylum and genus levels, compared with the control group, Bacteroidetes (p = 0.002) and Braydrhizobium (p = 0.01) were significantly higher, while Actinobacteria (p = 0.003) and Bidfldobacterium (p = 0.016) were significantly lower in the case group. Bacteroidetes were valuable in differentiating pathologic jaundice from physiologic jaundice by the ROC curve, and the area under the ROC curve (AUC) value was 0.839 [95%CI (0.648–0.995)]. In the case group, Bacteroidetes were negatively associated with total bilirubin (TBIL) (p < 0.05). In the control group, Bacteroidetes were positively associated with TBIL (p < 0.05).

Conclusion

Bacteroidetes could be used as biomarkers to identify pathologic jaundice and Bacteroidetes are positively associated with bilirubin levels.
Bacillus subtilis DSM29784 attenuates Clostridium perfringens-induced intestinal damage of broilers by modulating intestinal microbiota and the metabolome
Authors: Wang Yuanyuan , Xu Yibin , Cao Guangtian , Zhou Xihong , Wang Qian , Fu Aikun , Zhan Xiuan
Published: March 2023

Necrotic enteritis (NE), especially subclinical NE (SNE), without clinical symptoms, in chicks has become one of the most threatening problems to the poultry industry. Therefore, increasing attention has been focused on the research and application of effective probiotic strains as an alternative to antibiotics to prevent SNE in broilers. In the present study, we evaluated the effects of Bacillus subtilis DSM29784 (BS) on the prevention of subclinical necrotic enteritis (SNE) in broilers. A total of 480 1-day-old broiler chickens were randomly assigned to four dietary treatments, each with six replicates pens of twenty birds for 63 d. The negative (Ctr group) and positive (SNE group) groups were only fed a basal diet, while the two treatment groups received basal diets supplemented with BS (1 × 109 colony-forming units BS/kg) (BS group) and 10mg/kg enramycin (ER group), respectively. On days 15, birds except those in the Ctr group were challenged with 20-fold dose coccidiosis vaccine, and then with 1 ml of C. perfringens (2 × 108) at days 18 to 21 for SNE induction. BS, similar to ER, effectively attenuated CP-induced poor growth performance. Moreover, BS pretreatment increased villi height, claudin-1 expression, maltase activity, and immunoglobulin abundance, while decreasing lesional scores, as well as mucosal IFN-γ and TNF-α concentrations. In addition, BS pretreatment increased the relative abundance of beneficial bacteria and decreased that of pathogenic species; many lipid metabolites were enriched in the cecum of treated chickens. These results suggest that BS potentially provides active ingredients that may serve as an antibiotic substitute, effectively preventing SNE-induced growth decline by enhancing intestinal health in broilers.
The impact of environmental factors on the transport and survival of pathogens in agricultural soils from karst areas of Yunnan province, China: Laboratory column simulated leaching experiments
Authors: Ning Zhuo , Wang Shuaiwei , Guo Caijuan , Zhang Min
Published: March 2023

Introduction

Groundwater is considered the best candidate for drinking water supply in the karst area. The groundwater water resources, however, are vulnerable to pathogenic microorganism contamination because of the typically thin soil layers overlying aquifers and the high permeability of the aquifer host rock, resulting in short residence times and low natural attenuation capacities. Until now, little attention has been paid to the critical environmental factors affecting the pathogenic microorganism contamination in soil-groundwater systems in the karst area.

Methods

In the study, orthogonality column experiments with controlling ambient temperatures, pH values of inlet water, and soil porosities were carried out to investigate the transport and lifespan of pathogenic microorganisms in the leachate of agricultural soils in the karst area of Yunnan province, China. The pathogenic indicators, i.e., total bacteria count (TBC) and total coliforms count (TCC), and hydrochemical parameters, i.e., pH and permanganate index (CODMn) in the leaching water, were systematically monitored.

Results and Discussion

The results showed that bacteria including coliforms can survive for prolonged periods of time in karst soils. The soils overlying the karst rocks were unable to impede the bacteria from seeping into the groundwater. The soils, in turn, likely served as both reservoirs and incubators for pathogenic bacteria. The ambient temperature was the most predominant influential factor affecting both TBC and TCC. The bacteria concentrations were proportional to the temperature in the leachate. Therefore, more attention should be paid to temperature variations in protecting the water supply, particularly in the high-temperature period, such as during the summer months.
Matured compost amendment improves compost nutrient content by changing the bacterial community during the composting of Chinese herb residues
Authors: Song Xiuchao , Lu Chao , Luo Jia , Gong Xin , Guo Dejie , Ma Yan
Published: March 2023

Composting is a sustainable strategy to deal with organic waste. Our research aimed to study the influence of an amendment of 10% matured compost (MC) during Chinese herb residue (CHR) compost. Here, a 60-day CHR compost was performed, and MC application was able to reduce the nitrogen loss and enhance the humic acid accumulation during the composting as compared with the non-inoculated control (NC), by 25 and 19%, respectively. Furthermore, the matured compost amendment improved the diversity of the bacterial community, increased the complexity of the co-occurrence network, and changed the keystone and module hub bacteria during composting. The increased abundance levels of Thermopolyspora, Thermobispora, and Thermosporomyces, which were significantly higher in MC than in NC, may contribute to the degradation of cellulose and the formation of humic acid. Overall, this study extends our understanding of the effects of matured compost reflux on compost quality and the bacterial community.
In vivo adaptive antimicrobial resistance in Klebsiella pneumoniae during antibiotic therapy
Authors: Li Shuangshuang , Feng Xudong , Li Min , Shen Zhen
Published: March 2023

Klebsiella pneumoniae is one of the leading pathogens contributing to antimicrobial resistance. The emergence of carbapenem-resistant K. pneumoniae (CRKP) has put the use of clinical antimicrobial agents in a dilemma. In particular, CRKP exhibiting resistance to ceftazidime/avibactam, tigecycline and colistin have raised great clinical concern, as these are the last-resort antibiotics for the treatment of CRKP infections. Within-host evolution is a survival strategy closely related to the emergence of antimicrobial resistance, while little attention has been paid to the in vivo genetic process of conversion from antibiotic-susceptible to resistant K. pneumoniae. Here we have a literature review regarding the in vivo evolution of resistance to carbapenems, ceftazidime/avibactam, tigecycline, and colistin in K. pneumoniae during antibacterial therapy, and summarized the detailed resistance mechanisms. In general, acquiring blaKPC and blaNDM harboring-plasmid, specific mutations in blaKPC, and porin genes, such as ompK35 and ompK36, upregulation of blaKPC, contribute to the development of carbapenem and ceftazidime/avibactam resistance in vivo. Overexpression of efflux pumps, acquiring plasmid-carrying tet (A) variants, and ribosomal protein change can lead to the adaptive evolution of tigecycline resistance. Specific mutations in chromosomes result in the cationic substitution of the phosphate groups of lipid A, thus contributing to colistin resistance. The resistant plasmid might be acquired from the co-infecting or co-colonizing strains, and the internal environment and antibiotic selection pressure contribute to the emergence of resistant mutants. The internal environment within the human host could serve as an important source of resistant K. pneumoniae strains.
Evolution of Indian Influenza A (H1N1) Hemagglutinin Strains: A Comparative Analysis of the Pandemic Californian HA Strain
Authors: Pushan Shilpa Sri , Samantaray Mahesh , Rajagopalan Muthukumaran , Ramaswamy Amutha
Published: March 2023

The need for a vaccine/inhibitor design has become inevitable concerning the emerging epidemic and pandemic viral infections, and the recent outbreak of the influenza A (H1N1) virus is one such example. From 2009 to 2018, India faced severe fatalities due to the outbreak of the influenza A (H1N1) virus. In this study, the potential features of reported Indian H1N1 strains are analyzed in comparison with their evolutionarily closest pandemic strain, A/California/04/2009. The focus is laid on one of its surface proteins, hemagglutinin (HA), which imparts a significant role in attacking the host cell surface and its entry. The extensive analysis performed, in comparison with the A/California/04/2009 strain, revealed significant point mutations in all Indian strains reported from 2009 to 2018. Due to these mutations, all Indian strains disclosed altered features at the sequence and structural levels, which are further presumed to be associated with their functional diversity as well. The mutations observed with the 2018 HA sequence such as S91R, S181T, S200P, I312V, K319T, I419M, and E523D might improve the fitness of the virus in a new host and environment. The higher fitness and decreased sequence similarity of mutated strains may compromise therapeutic efficacy. In particular, the mutations observed commonly, such as serine-to-threonine, alanine-to-threonine, and lysine-to-glutamine at various regions, alter the physico-chemical features of receptor-binding domains, N-glycosylation, and epitope-binding sites when compared with the reference strain. Such mutations render diversity among all Indian strains, and the structural and functional characterization of these strains becomes inevitable. In this study, we observed that mutational drift results in the alteration of the receptor-binding domain, the generation of new variant N-glycosylation along with novel epitope-binding sites, and modifications at the structural level. Eventually, the pressing need to develop potentially distinct next-generation therapeutic inhibitors against the HA strains of the Indian influenza A (H1N1) virus is also highlighted here.