bluuebunny/crossref_metadata_2025 huggingface dataset:
Does haplodiploidy help drive the evolution of insect eusociality?
Authors: Joshi Chinmay Hemant , Wiens John J.
Published: March 2023

Understanding the evolution of eusociality in insects has been a long-standing and unsolved challenge in evolutionary biology. For decades, it has been suggested that haplodiploidy plays an important role in the origin of eusociality. However, some researchers have also suggested that eusociality is unrelated to haplodiploidy. Surprisingly, there have been no large-scale phylogenetic tests of this hypothesis (to our knowledge). Here, we test whether haplodiploidy might help explain the origins of eusociality across 874 hexapod families, using three different phylogenetic comparative methods. Two of the methods used support the idea that the evolution of eusociality is significantly associated with haplodiploidy, providing possibly the first phylogenetic support for this decades-old hypothesis across insects. However, some patterns were clearly discordant with this hypothesis, and one phylogenetic test was non-significant. Support for this hypothesis came largely from the repeated origins of eusociality within the haplodiploid hymenopterans (and within thrips). Experimental manipulations of the data show that the non-significant results are primarily explained by the origins of eusociality without haplodiploidy in some groups (i.e., aphids, termites). Overall, our results offer mixed phylogenetic support for the long-standing hypothesis that haplodiploidy helps drive the evolution of eusociality.
Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice
Authors: Illa-Berenguer Eudald , LaFayette Peter R. , Parrott Wayne A.
Published: March 2023

The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
Identification of the cuproptosis-related hub genes and therapeutic agents for sarcopenia
Authors: Zhu Yingqian , Chen Xin , Geng Shasha , Li Qingqing , Li Yang , Yuan Huixiao , Jiang Hua
Published: March 2023

Background: Along with acceleration of population aging, the increasing prevalence of sarcopenia has posed a heavy burden on families as well as society. In this context, it is of great significance to diagnose and intervene sarcopenia as early as possible. Recent evidence has indicated the role of cuproptosis in the development of sarcopenia. In this study, we aimed to seek the key cuproptosis-related genes that can be used for identification and intervention of sarcopenia.

Methods: The GSE111016 dataset was retrieved from GEO. The 31 cuproptosis-related genes (CRGs) were obtained from previous published studies. The differentially expressed genes (DEGs) and Weighed gene co-expression network analysis (WGCNA) were subsequently analyzed. The core hub genes were acquired by the intersection of DEGs, WGCNA and CRGs. Through logistic regression analysis, we established a diagnostic model of sarcopenia based on the selected biomarkers and was validated in muscle samples from GSE111006 and GSE167186. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis were performed on these genes. Furthermore, the gene set enrichment analysis (GSEA), and immune cell infiltration were also conducted on the identified core genes. Finally, we screened the potential drugs targeting the potential biomarkers of sarcopenia.

Results: A total of 902 DEGs and WGCNA containing 1,281 significant genes were preliminarily selected. Intersection of DEGs, WGCNA and CRGs yielded four core genes (PDHA1, DLAT, PDHB, and NDUFC1) as potential biomarkers for the prediction of sarcopenia. The predictive model was established and validated with high AUC values. KEGG pathway and Gene Ontology biological analysis indicated these core genes may play a crucial role in energy metabolism in mitochondria, oxidation process, and aging-related degenerative diseases. In addition, the immune cells may be involved in the development of sarcopenia through mitochondrial metabolism. Finally, metformin was identified as a promising strategy of sarcopenia treatment via targeting NDUFC1.

Conclusion: The four cuproptosis-related genes PDHA1, DLAT, PDHB and NDUFC1 may be the diagnostic biomarkers for sarcopenia, and metformin holds great potential to be developed as a therapy for sarcopenia. These outcomes provide new insights for better understanding of sarcopenia and innovative therapeutic approaches.
Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array
Authors: Xie Xinke , Huang Cong , Huang Yizhong , Zou Xiaoxiao , Zhou Runxin , Ai Huashui , Huang Lusheng , Ma Junwu
Published: March 2023

Introduction: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the “giant panda” (very precious) in the world’s pig species by Chinese animal husbandry.

Methods: Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs.

Results: We found that the average GP value of Erhualian was unusually low (68.09 μmol/g), but the variation was large (10.4–112.7 μmol/g). The SNP-based heritability estimates for the four traits ranged from 0.16–0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including eight for RG, nine for G6P, nine for LAT, five for GP. Of these loci, eight were genome-wide significant (p < 3.8 × 10−7), and six loci were common to two or three traits. Multiple promising candidate genes such as FTO, MINPP1, RIPOR2, SCL8A3, LIFR and SRGAP1 were identified. The genotype combinations of the five GP-associated SNPs also showed significant effect on other meat quality traits.

Discussion: These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.
Integrated analysis to identify the prognostic and immunotherapeutic roles of coagulation-associated gene signature in clear cell renal cell carcinoma
Authors: Yin Guicao , Tian Tai , Ji Xing , Zheng Shengqi , Zhu Zhenpeng , Li Yifan , Zhang Cuijian
Published: March 2023

The coagulation system is closely related to the physiological status and immune response of the body. Recent years, studies focusing on the association between coagulation system abnormalities and tumor progression have been widely reported. In clear cell renal cell carcinoma (ccRCC), poor prognosis often occurs in patients with venous tumor thrombosis and coagulation system abnormalities, and there is a lack of research in related fields. Significant differences in coagulation function were also demonstrated in our clinical sample of patients with high ccRCC stage or grade. Therefore, in this study, we analyzed the biological functions of coagulation-related genes (CRGs) in ccRCC patients using single-cell sequencing and TCGA data to establish the 5-CRGs based diagnostic signature and predictive signature for ccRCC. Univariate and multivariate Cox analyses suggested that prognostic signature could be an independent risk factor. Meanwhile, we applied CRGs for consistent clustering of ccRCC patients, and the two classes showed significant survival and genotype differences. The differences in individualized treatment between the two different subtypes were revealed by pathway enrichment analysis and immune cell infiltration analysis. In summary, we present the first systematic analysis of the significance of CRGs in the diagnosis, prognosis, and individualized treatment of ccRCC patients.
Epithelioid hemangioendothelioma of the retroperitoneal giant type treated with Toripalimab: A case report
Authors: Bu Yuqing , Peng Lili , Liu Miaomiao , He Liya , Wang Fayan , Li Bingjie , Niu Xueliang , Zhang Hongzhen
Published: March 2023

Epithelioid hemangioendotheliomas (EHEs), low-grade malignant tumors of vascular endothelial cell origin, are characterized by vascular endothelial proliferation. In 2002, the World Health Organization classified EHEs as locally aggressive tumors with the potential to metastasize. Currently, the diagnosis of EHE is based on pathology, histological and immunohistochemical examinations. There are no standard treatment guidelines. We here report a 69-year-old man who presented with left-sided chest and abdominal pain for more than 2 months. Enhanced computed tomography of the thorax and abdomen in another hospital suggested a mass in the left adrenal region that was considered malignant. Positron emission tomography- computed tomography in our hospital suggested a large multi-loculated, hypermetabolic, cystic mass in the left adrenal region that was considered malignant. Accordingly, a puncture biopsy of the mass was performed and the diagnosis of EHE confirmed by pathological examination, including immunohistochemical staining. This patient was treated with the programmed death 1 (PD-1) immune checkpoint inhibitor toripalimab with long-term success. The best response was stable disease (SD) with a progression-free survival (PFS) of more than 13 months. The patient is still alive now. Because the sample size of previous studies was small, further studies are needed to determine the safety and efficacy of toripalimab in the treatment of EHE.
Control of myeloid cell functions by nociceptors
Authors: Hanč Pavel , Messou Marie-Angèle , Wang Yidi , von Andrian Ulrich H.
Published: March 2023

The immune system has evolved to protect the host from infectious agents, parasites, and tumor growth, and to ensure the maintenance of homeostasis. Similarly, the primary function of the somatosensory branch of the peripheral nervous system is to collect and interpret sensory information about the environment, allowing the organism to react to or avoid situations that could otherwise have deleterious effects. Consequently, a teleological argument can be made that it is of advantage for the two systems to cooperate and form an “integrated defense system” that benefits from the unique strengths of both subsystems. Indeed, nociceptors, sensory neurons that detect noxious stimuli and elicit the sensation of pain or itch, exhibit potent immunomodulatory capabilities. Depending on the context and the cellular identity of their communication partners, nociceptors can play both pro- or anti-inflammatory roles, promote tissue repair or aggravate inflammatory damage, improve resistance to pathogens or impair their clearance. In light of such variability, it is not surprising that the full extent of interactions between nociceptors and the immune system remains to be established. Nonetheless, the field of peripheral neuroimmunology is advancing at a rapid pace, and general rules that appear to govern the outcomes of such neuroimmune interactions are beginning to emerge. Thus, in this review, we summarize our current understanding of the interaction between nociceptors and, specifically, the myeloid cells of the innate immune system, while pointing out some of the outstanding questions and unresolved controversies in the field. We focus on such interactions within the densely innervated barrier tissues, which can serve as points of entry for infectious agents and, where known, highlight the molecular mechanisms underlying these interactions.
Type I interferon score is associated with the severity and poor prognosis in anti-MDA5 antibody-positive dermatomyositis patients
Authors: Qian Jinjing , Li Rui , Chen Zhiwei , Cao Zehui , Lu Liangjing , Fu Qiong
Published: March 2023

Objectives

To investigate the clinical significance of the interferon (IFN) score, especially the IFN-I score, in patients with anti-melanoma differentiation-associated gene 5 (MDA5) antibody-positive dermatomyositis (anti-MDA5+ DM).

Methods

We enrolled 262 patients with different autoimmune diseases, including idiopathic inflammatory myopathy, systemic lupus erythematosus, rheumatoid arthritis, adult-onset Still’s disease, and Sjögren’s syndrome, as well as 58 healthy controls. Multiplex quantitative real-time polymerase chain reaction (RT-qPCR) using four TaqMan probes was used to evaluate type I IFN-stimulated genes (IFI44 and MX1), one type II IFN-stimulated gene (IRF1), and one internal control gene (HRPT1), which were used to determine the IFN-I score. The clinical features and disease activity index were compared between the high and low IFN-I score groups in 61 patients with anti-MDA5+ DM. The associations between laboratory findings and the predictive value of the baseline IFN-I score for mortality were analyzed.

Results

The IFN score was significantly higher in patients with anti-MDA5+ DM than in healthy controls. The IFN-I score was positively correlated with the serum IFN-α concentration, ferritin concentration, and Myositis Disease Activity Assessment Visual Analogue Scale (MYOACT) score. Compared with patients with a low IFN-I score, patients with a high IFN-I score showed a higher MYOACT score, C-reactive protein concentration, aspartate transaminase concentration, ferritin concentration, plasma cell percentage, and CD3+ T-cell percentage, as well as lower lymphocyte, natural killer cell, and monocyte counts. The 3-month survival rate was significantly lower in patients with an IFN-I score of >4.9 than in those with an IFN-I score of ≤4.9 (72.9% vs. 100%, respectively; P = 0.044).

Conclusion

The IFN score, especially the IFN-I score, measured by multiplex RT-qPCR is a valuable tool to monitor disease activity and predict mortality in patients with anti-MDA5+ DM.
Prognostic signatures of sphingolipids: Understanding the immune landscape and predictive role in immunotherapy response and outcomes of hepatocellular carcinoma
Authors: Zhang Xin , Zhuge Jinke , Liu Jinhui , Xia Zhijia , Wang Huixiong , Gao Qiang , Jiang Hao , Qu Yanyu , Fan Linlin , Ma Jiali , Tan Chunhua , Luo Wei , Luo Yong
Published: March 2023

Background

Hepatocellular carcinoma (HCC) is a complex disease with a poor outlook for patients in advanced stages. Immune cells play an important role in the progression of HCC. The metabolism of sphingolipids functions in both tumor growth and immune infiltration. However, little research has focused on using sphingolipid factors to predict HCC prognosis. This study aimed to identify the key sphingolipids genes (SPGs) in HCC and develop a reliable prognostic model based on these genes.

Methods

The TCGA, GEO, and ICGC datasets were grouped using SPGs obtained from the InnateDB portal. A prognostic gene signature was created by applying LASSO-Cox analysis and evaluating it with Cox regression. The validity of the signature was verified using ICGC and GEO datasets. The tumor microenvironment (TME) was examined using ESTIMATE and CIBERSORT, and potential therapeutic targets were identified through machine learning. Single-cell sequencing was used to examine the distribution of signature genes in cells within the TME. Cell viability and migration were tested to confirm the role of the key SPGs.

Results

We identified 28 SPGs that have an impact on survival. Using clinicopathological features and 6 genes, we developed a nomogram for HCC. The high- and low-risk groups were found to have distinct immune characteristics and response to drugs. Unlike CD8 T cells, M0 and M2 macrophages were found to be highly infiltrated in the TME of the high-risk subgroup. High levels of SPGs were found to be a good indicator of response to immunotherapy. In cell function experiments, SMPD2 and CSTA were found to enhance survival and migration of Huh7 cells, while silencing these genes increased the sensitivity of Huh7 cells to lapatinib.

Conclusion

The study presents a six-gene signature and a nomogram that can aid clinicians in choosing personalized treatments for HCC patients. Furthermore, it uncovers the connection between sphingolipid-related genes and the immune microenvironment, offering a novel approach for immunotherapy. By focusing on crucial sphingolipid genes like SMPD2 and CSTA, the efficacy of anti-tumor therapy can be increased in HCC cells.
Prognostic value of COL10A1 and its correlation with tumor-infiltrating immune cells in urothelial bladder cancer: A comprehensive study based on bioinformatics and clinical analysis validation
Authors: Wang Xiaoming , Bai Yunjin , Zhang Facai , Li Dengxiong , Chen Kai , Wu Ruicheng , Tang Yin , Wei Xin , Han Ping
Published: March 2023

Introduction

Bladder cancer (BLCA) is one of the most lethal diseases. COL10A1 is secreted small-chain collagen in the extracellular matrix associated with various tumors, including gastric, colon, breast, and lung cancer. However, the role of COL10A1 in BLCA remains unclear. This is the first research focusing on the prognostic value of COL10A1 in BLCA. In this research, we aimed to uncover the association between COL10A1 and the prognosis, as well as other clinicopathological parameters in BLCA.

Methods

We obtained gene expression profiles of BLCA and normal tissues from the TCGA, GEO, and ArrayExpress databases. Immunohistochemistry staining was performed to investigate the protein expression and prognostic value of COL10A1 in BLCA patients. GO and KEGG enrichment along with GSEA analyses were performed to reveal the biological functions and potential regulatory mechanisms of COL10A1 based on the gene co-expression network. We used the “maftools” R package to display the mutation profiles between the high and low COL10A1 groups. GIPIA2, TIMER, and CIBERSORT algorithms were utilized to explore the effect of COL10A1 on the tumor immune microenvironment.

Results

We found that COL10A1 was upregulated in the BLCA samples, and increased COL10A1 expression was related to poor overall survival. Functional annotation of 200 co-expressed genes positively correlated with COL10A1 expression, including GO, KEGG, and GSEA enrichment analyses, indicated that COL10A1 was basically involved in the extracellular matrix, protein modification, molecular binding, ECM-receptor interaction, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling pathway. The most commonly mutated genes of BLCA were different between high and low COL10A1 groups. Tumor immune infiltrating analyses showed that COL10A1 might have an essential role in recruiting infiltrating immune cells and regulating immunity in BLCA, thus affecting prognosis. Finally, external datasets and biospecimens were used, and the results further validated the aberrant expression of COL10A1 in BLCA samples.

Conclusions

In conclusion, our study demonstrates that COL10A1 is an underlying prognostic and predictive biomarker in BLCA.
Biomineralization of struvite induced by indigenous marine bacteria of the genus Alteromonas
Authors: He Wei , Xue Hua-Peng , Liu Chuang , Zhang Ai Hua , Huang Jian-Ke , Zhang Dao-Feng
Published: March 2023

Biomineralization is a universal phenomenon in the ocean that plays an important role in marine geochemical circulation. The genus Alteromonas is an indigenous taxon with a wide distribution and various ecological roles in the ocean, but biomineralization by this genus has not been reported. In this study, five Alteromonas spp. were found to induce mineral crystal formation of different shapes and sizes in agar media. Further studies on deep-sea strains A. alteriprofundi HHU 13199T and A. alterisediminis N102T showed that they could produce mineral crystals with similar morphology when grown in agar or broth media with different concentrations of sea salts (i.e., 2%, 4%, 6%, and 8%), and that their growth was dependent on Ca2+ and/or Mg2+ ion concentrations. Genomic analysis showed that the genus Alteromonas universally possessed the ammonification metabolism pathway and that, during the culture of these bacteria, the production of mineral crystals was accompanied by an increase in ammonia concentration and pH value and a decrease in nitrate nitrogen concentration. The addition of ammonia to broth media (≈ 572.7 mg/L) simulated the ammonia content in media on days 5 and 6 of bacterial growth and also induced mineral crystals to form. Through the analysis using scanning electron microscope–energy-dispersive spectrometry (SEM-EDS), X-ray diffraction (XRD), Fourier-transform infrared microscopy (FTIR), thermogravimetric (TG) analysis, and differential thermal gravity and differential scanning calorimetry (DTG–DSC), mineral crystals induced by bacterial strains and the non-strain (ammonia-added sample) were all identified as struvite mineral. In addition, the characteristics of the struvite mineral induced by bacterial strains were different from the characteristics of the struvite synthesized by non-strain and of a struvite mineral standard. Thus, this study deduces that Alteromonas spp. possess the ability to induce struvite formation. The mechanism mainly lies in the presence of an ammonification metabolism pathway to produce ammonia, which should be recognized as biologically induced mineralization (BIM). This study provides insight into a new ecological role of indigenous marine taxa of the genus Alteromonas.
Hippocampus guttulatus diet based on DNA metabarcoding
Authors: Tamara Lazic , Fosso Bruno , Bachir Balech , Giuseppe Corriero , Michele Gristina , Marinella Marzano , Graziano Pesole , Monica Santamaria , Pierri Cataldo
Published: March 2023

Seahorses are small sedentary fish considered flagship species of the conservation efforts. They are particularly vulnerable to human pressures because inhabiting threatened coastal ecosystems. Indeed, the worldwide decline of local populations in the last decades led to the inclusion of all seahorse species on the IUCN Red List, where most species, including Hippocampus guttulatus, were classified as ‘‘Data Deficient’’ on a global level due to the lack of relative data on several biological and ecological traits. Because of such sensitive conservation status, improvement of the current knowledge on the diet composition of wild animals and its differences among habitats could be of great importance as it could help understanding the way the environment is exploited. In the present study, we used a non-invasive DNA metabarcoding technique to further elucidate long-snouted seahorse diet and expand our understanding of prey choice among different habitats. We identified 24 families, 22 genera and 26 species, and according to the results, most of the seahorse samples contained taxa such as Amphipoda, Decapoda, Isopoda, and Mysida. Several non-native species were discovered in the diet, suggesting their dietary incorporation that could mirror high anthropogenic impacts and habitat modifications. We found significant differences in the diet composition among investigated habitats, thus indicating trophic flexibility of H. guttulatus among diverse habitats, a characteristic that may be essential for the resilience of this iconic yet sensitive species.
Carbonic anhydrase IX-related tumoral hypoxia predicts worse prognosis in breast cancer: A systematic review and meta-analysis
Authors: Numprasit Warapan , Yangngam Supaporn , Prasopsiri Jaturawitt , Quinn Jean A. , Edwards Joanne , Thuwajit Chanitra
Published: March 2023

Background

Tumoral hypoxia is associated with aggressiveness in many cancers including breast cancer. However, measuring hypoxia is complicated. Carbonic anhydrase IX (CAIX) is a reliable endogenous marker of hypoxia under the control of the master regulator hypoxia-inducible factor-1α (HIF-1α). The expression of CAIX is associated with poor prognosis in many solid malignancies; however, its role in breast cancer remains controversial.

Methods

The present study performed a meta-analysis to evaluate the correlation between CAIX expression and disease-free survival (DFS) and overall survival (OS) in breast cancer.

Results

A total of 2,120 publications from EMBASE, PubMed, Cochrane, and Scopus were screened. Of these 2,120 publications, 272 full texts were reviewed, and 27 articles were included in the meta-analysis. High CAIX was significantly associated with poor DFS (HR = 1.70, 95% CI = 1.39–2.07, p < 0.00001) and OS (HR = 2.02, 95% CI 1.40–2.91, p = 0.0002) in patients with breast cancer. When stratified by subtype, the high CAIX group was clearly associated with shorter DFS (HR = 2.09, 95% CI =1.11–3.92, p = 0.02) and OS (HR = 2.50, 95% CI =1.53–4.07, p = 0.0002) in TNBC and shorter DFS in ER+ breast cancer (HR = 1.81 95% CI =1.38–2.36, p < 0.0001).

Conclusion

High CAIX expression is a negative prognostic marker of breast cancer regardless of the subtypes.
Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line
Authors: Krüger Gabriel I. , Pardo-Esté Coral , Zepeda Phillippi , Olivares-Pacheco Jorge , Galleguillos Nicolas , Suarez Marcia , Castro-Severyn Juan , Alvarez-Thon Luis , Tello Mario , Valdes Jorge H. , Saavedra Claudia P.
Published: March 2023

The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.
Nationwide analysis of antimicrobial resistance in pathogenic Escherichia coli strains isolated from diseased swine over 29 years in Japan
Authors: Kusumoto Masahiro , Tamamura-Andoh Yukino , Hikoda-Kogiku Yuna , Magome Asami , Okuhama Erina , Sato Keisuke , Mizuno Yoshino , Arai Nobuo , Watanabe-Yanai Ayako , Iwata Taketoshi , Ogura Yoshitoshi , Gotoh Yasuhiro , Nakamura Keiji , Hayashi Tetsuya , Akiba Masato
Published: March 2023

Pathogenic Escherichia coli strains are important causes of several swine diseases that result in significant economic losses worldwide. In Japan, the use of antimicrobials in swine is much higher than that in other farm animals every year. Antimicrobial resistance in pathogenic E. coli strains also heavily impacts the swine industry due to the limited treatment options and an increase in the potential risk of the One Health crisis. In 2016, we investigated 684 Japanese isolates of swine pathogenic E. coli belonging to four major serogroups and reported the emergence and increase in the highly multidrug-resistant serogroups O116 and OSB9 and the appearance of colistin-resistant strains. In the present study, by expanding our previous analysis, we determined the serotypes and antimicrobial resistance of 1,708 E. coli strains isolated from diseased swine between 1991 and 2019 in Japan and found recent increases in the prevalences of multidrug-resistant strains and minor serogroup strains. Among the antimicrobials examined in this study that have been approved for animal use, a third-generation cephalosporin was found to be effective against the most isolates (resistance rate: 1.2%) but not against highly multidrug-resistant strains. We also analyzed the susceptibilities of the 1,708 isolates to apramycin and bicozamycin, both which are available for treating swine in Japan, and found that the rates of resistance to apramycin and bicozamycin were low (6.7% and 5.8%, respectively), and both antimicrobials are more effective (resistance rates: 2.7% and 5.4%, respectively) than third-generation cephalosporins (resistance rate: 16.2%) against highly multidrug-resistant strains.
Evaluation of the contribution of gut microbiome dysbiosis to cardiac surgery-associated acute kidney injury by comparative metagenome analysis
Authors: Li Ying , Jiang Xinyi , Chen Jingchun , Hu Yali , Bai Yunpeng , Xu Wang , He Linling , Wang Yirong , Chen Chunbo , Chen Jimei
Published: March 2023

Introduction

Cardiac surgery-associated acute kidney injury (CSA-AKI) is a common hospital-acquired AKI that carries a grave disease burden. Recently, gut-kidney crosstalk has greatly changed our understanding of the pathogenesis of kidney diseases. However, the relationship between gut microbial dysbiosis and CSA-AKI remains unclear. The purpose of this study was to investigate the possible contributions of gut microbiota alterations in CSA-AKI patients.

Methods

Patients undergoing cardiac surgery were enrolled and divided into acute kidney injury (AKI) and Non_AKI groups. Faecal samples were collected before the operation. Shotgun metagenomic sequencing was performed to identify the taxonomic composition of the intestinal microbiome. All groups were statistically compared with alpha- and beta-diversity analysis, and linear discriminant analysis effect size (LEfSe) analysis was performed.

Results

A total of 70 individuals comprising 35 AKI and 35 Non_AKI were enrolled in the study. There was no significant difference between the AKI and Non_AKI groups with respect to the alpha-and beta-diversity of the Shannon index, Simpson or Chao1 index values except with respect to functional pathways (p < 0.05). However, the relative abundance of top 10 gut microbiota in CSA-AKI was different from the Non_AKI group. Interestingly, both LEfSe and multivariate analysis confirmed that the species Escherichia coli, Rothia mucilaginosa, and Clostridium innocuum were associated with CSA-AKI. Moreover, correlation heat map indicated that altered pathways and disrupted function could be attributed to disturbances of gut microbiota involving Escherichia coli.

Conclusion

Dysbiosis of the intestinal microbiota in preoperative stool affects susceptibility to CSA-AKI, indicating the crucial role of key microbial players in the development of CSA-AKI. This work provides valuable knowledge for further study of the contribution of gut microbiota in CSA-AKI.
Evasion strategies of porcine reproductive and respiratory syndrome virus
Authors: Chen Xin-xin , Qiao Songlin , Li Rui , Wang Jing , Li Xuewu , Zhang Gaiping
Published: March 2023

During the co-evolution of viruses and their hosts, viruses have developed various strategies for overcoming host immunological defenses so that they can proliferate efficiently. Porcine reproductive and respiratory syndrome virus (PRRSV), a significant virus to the swine industry across the world, typically establishes prolonged infection via diverse and complicated mechanisms, which is one of the biggest obstacles for controlling the associated disease, porcine reproductive and respiratory syndrome (PRRS). In this review, we summarize the latest research on how PRRSV circumvents host antiviral responses from both the innate and adaptive immune systems and how this virus utilizes other evasion mechanisms, such as the manipulation of host apoptosis and microRNA. A thorough understanding of the exact mechanisms of PRRSV immune evasion will help with the development of novel antiviral strategies against PRRSV.
Conjugative plasmids inhibit extracellular electron transfer in Geobacter sulfurreducens
Authors: Fessler Mathias , Madsen Jonas Stenløkke , Zhang Yifeng
Published: March 2023

Geobacter sulfurreducens is part of a specialized group of microbes with the unique ability to exchange electrons with insoluble materials, such as iron oxides and electrodes. Therefore, G. sulfurreducens plays an essential role in the biogeochemical iron cycle and microbial electrochemical systems. In G. sulfurreducens this ability is primarily dependent on electrically conductive nanowires that link internal electron flow from metabolism to solid electron acceptors in the extracellular environment. Here we show that when carrying conjugative plasmids, which are self-transmissible plasmids that are ubiquitous in environmental bacteria, G. sulfurreducens reduces insoluble iron oxides at much slower rates. This was the case for all three conjugative plasmids tested (pKJK5, RP4 and pB10). Growth with electron acceptors that do not require expression of nanowires was, on the other hand, unaffected. Furthermore, iron oxide reduction was also inhibited in Geobacter chapellei, but not in Shewanella oneidensis where electron export is nanowire-independent. As determined by transcriptomics, presence of pKJK5 reduces transcription of several genes that have been shown to be implicated in extracellular electron transfer in G. sulfurreducens, including pilA and omcE. These results suggest that conjugative plasmids can in fact be very disadvantageous for the bacterial host by imposing specific phenotypic changes, and that these plasmids may contribute to shaping the microbial composition in electrode-respiring biofilms in microbial electrochemical reactors.
Glis1 and oxaloacetate in nucleus pulposus stromal cell somatic reprogramming and survival
Authors: Lufkin Leon , Samanta Ankita , Baker DeVaun , Lufkin Sina , Schulze JesslynHope , Ellis Benjamin , Rose Jillian , Lufkin Thomas , Kraus Petra
Published: March 2023

Regenerative medicine aims to repair degenerate tissue through cell refurbishment with minimally invasive procedures. Adipose tissue (FAT)-derived stem or stromal cells are a convenient autologous choice for many regenerative cell therapy approaches. The intervertebral disc (IVD) is a suitable target. Comprised of an inner nucleus pulposus (NP) and an outer annulus fibrosus (AF), the degeneration of the IVD through trauma or aging presents a substantial socio-economic burden worldwide. The avascular nature of the mature NP forces cells to reside in a unique environment with increased lactate levels, conditions that pose a challenge to cell-based therapies. We assessed adipose and IVD tissue-derived stromal cells through in vitro transcriptome analysis in 2D and 3D culture and suggested that the transcription factor Glis1 and metabolite oxaloacetic acid (OAA) could provide NP cells with survival tools for the harsh niche conditions in the IVD.
Clinical implications of lncRNA LINC-PINT in cancer
Authors: Bukhari Ihtisham , Khan Muhammad Riaz , Li Fazhan , Swiatczak Bartlomiej , Thorne Rick Francis , Zheng Pengyuan , Mi Yang
Published: March 2023

Long noncoding RNAs (lncRNAs) possess the potential for therapeutic targeting to treat many disorders, including cancers. Several RNA-based therapeutics (ASOs and small interfering RNAs) have gained FDA approval over the past decade. And with their potent effects, lncRNA-based therapeutics are of emerging significance. One important lncRNA target is LINC-PINT, with its universalized functions and relationship with the famous tumor suppressor gene TP53. Establishing clinical relevance, much like p53, the tumor suppressor activity of LINC-PINT is implicated in cancer progression. Moreover, several molecular targets of LINC-PINT are directly or indirectly used in routine clinical practice. We further associate LINC-PINT with immune responses in colon adenocarcinoma, proposing the potential utility of LINC-PINT as a novel biomarker of immune checkpoint inhibitors. Collectively, current evidence suggests LINC-PINT can be considered for use as a diagnostic/prognostic marker for cancer and several other diseases.
Imaging blood–brain barrier disruption in neuroinflammation and Alzheimer’s disease
Authors: Lee Rae-Ling , Funk Kristen E.
Published: March 2023

The blood–brain barrier (BBB) is the neurovascular structure that regulates the passage of cells and molecules to and from the central nervous system (CNS). Alzheimer’s disease (AD) is a neurodegenerative disorder that is associated with gradual breakdown of the BBB, permitting entry of plasma-derived neurotoxins, inflammatory cells, and microbial pathogens into the CNS. BBB permeability can be visualized directly in AD patients using imaging technologies including dynamic contrast-enhanced and arterial spin labeling magnetic resonance imaging, and recent studies employing these techniques have shown that subtle changes in BBB stability occur prior to deposition of the pathological hallmarks of AD, senile plaques, and neurofibrillary tangles. These studies suggest that BBB disruption may be useful as an early diagnostic marker; however, AD is also accompanied by neuroinflammation, which can complicate these analyses. This review will outline the structural and functional changes to the BBB that occur during AD pathogenesis and highlight current imaging technologies that can detect these subtle changes. Advancing these technologies will improve both the diagnosis and treatment of AD and other neurodegenerative diseases.
Causes of nephrotic syndrome in Sweden: The relevance of clinical presentation and demographics
Authors: Jönsson Anneli , Hellmark Thomas , Segelmark Mårten , Forsberg Anna , Dreja Karl
Published: March 2023

Background

Many pathological processes can disrupt the integrity of the glomerular capillary wall and cause a massive leakage of protein, resulting in nephrotic syndrome (NS). Clinical parameters such as age, sex, renal function, presence of diabetes, and how NS is defined influence the spectrum of underlying diseases. In this study, we examine how these parameters interact.

Methods

Age, sex, hematuria, proteinuria, plasma creatinine plasma albumin levels, and final diagnosis were retrieved for all adult patients with NS as an indication for biopsy and/or massive albuminuria in conjunction with low plasma albumin from the biopsy module of the Swedish Renal Registry (SRR) between 2014 and 2019. A basic calculator was developed to demonstrate the importance of clinical presentation in relation to the likelihood of having a specific diagnosis.

Results

A total of 913 unique patients were included in the study. Diabetic nephropathy (DN) and membranous nephropathy (MN) (both found in 17% of patients) were the most common diagnoses. With a stringent definition of NS, MN and minimal change nephropathy (MCN) increased in proportion. Among the cohort as a whole, MCN was the most frequent diagnosis in women and those < 50 years of age (found in 21% and 17%, respectively). In the case of patients aged between 50 and 70 years, those with chronic kidney disease stage 4, and those with negative dipstick tests for hematuria, the most common underlying disease was DN (in 23%, 30%, and 21% of cases, respectively). Among those with high-grade hematuria (dipstick grade 3 or 4), membranoproliferative glomerulonephritis was the most common diagnosis (14%), closely followed by IgA nephropathy (13%). Focal segmental glomerulosclerosis (9.7%) was less common than in many comparable studies.

Conclusion

Clinical parameters have a profound impact on the likelihood of different diagnoses in adult patients with NS. Differences in clinical practice and study inclusion criteria may be more important than genetic background and environmental factors when explaining differences between studies in different parts of the world.
Exploring high-order correlations with deep-broad learning for autism spectrum disorder diagnosis
Authors: Hao Xiaoke , An Qijin , Li Jiayang , Min Hongjie , Guo Yingchun , Yu Ming , Qin Jing
Published: March 2023

Recently, a lot of research has been conducted on diagnosing neurological disorders, such as autism spectrum disorder (ASD). Functional magnetic resonance imaging (fMRI) is the commonly used technique to assist in the diagnosis of ASD. In the past years, some conventional methods have been proposed to extract the low-order functional connectivity network features for ASD diagnosis, which ignore the complexity and global features of the brain network. Most deep learning-based methods generally have a large number of parameters that need to be adjusted during the learning process. To overcome the limitations mentioned above, we propose a novel deep-broad learning method for learning the higher-order brain functional connectivity network features to assist in ASD diagnosis. Specifically, we first construct the high-order functional connectivity network that describes global correlations of the brain regions based on hypergraph, and then we use the deep-broad learning method to extract the high-dimensional feature representations for brain networks sequentially. The evaluation of the proposed method is conducted on Autism Brain Imaging Data Exchange (ABIDE) dataset. The results show that our proposed method can achieve 71.8% accuracy on the multi-center dataset and 70.6% average accuracy on 17 single-center datasets, which are the best results compared with the state-of-the-art methods. Experimental results demonstrate that our method can describe the global features of the brain regions and get rich discriminative information for the classification task.
Neural mechanisms of brand love relationship dynamics: Is the development of brand love relationships the same as that of interpersonal romantic love relationships?
Authors: Watanuki Shinya
Published: March 2023

Brand love is a relationship between brands and consumers. Managing the relationship is an important issue for marketing strategy since it changes according to temporal flow. Brand love theories, including their dynamics, have been developed based on interpersonal romantic love theories. Although many brand love studies have provided useful findings, the neural mechanism of brand love remains unclear. Especially, its dynamics have not been considered from a neuroscience perspective. The present study addressed the commonalities and differentiations of activated brain regions between brand love and interpersonal romantic love relationships using a quantitative neuroimaging meta-analytic approach, from the view of brain connectivity. Regarding the mental processes of each love relationship related to these activated brain regions, decoding analysis was conducted using the NeuroQuery platform to prevent reverse inference. The results revealed that different neural mechanisms and mental processes were distinctively involved in the dynamics of each love relationship, although the anterior insula overlapped across all stages and the reinforcement learning system was driven between both love relationships in the early stage. Remarkably, regarding the distinctive mental processes, although prosocial aspects were involved in the mental processes of interpersonal romantic love relationships across all stages, they were not involved in the mental processes of brand love relationships. Conclusively, although common brain regions and mental processes between both love relationships were observed, neural mechanisms and mental processes in brand love relationship dynamics might be innately different from those in the interpersonal romantic love relationship dynamics. As this finding indicates essential distinctiveness between both these relationships, theories concerning interpersonal romantic love should be applied cautiously when investigating brand love relationship dynamics.
Association between fatty acids intake and bone mineral density in adults aged 20–59: NHANES 2011–2018
Authors: Fang Ze-Bin , Wang Gao-Xiang , Cai Gui-Zhang , Zhang Peng-Xiang , Liu De-Liang , Chu Shu-Fang , Li Hui-Lin , Zhao Hing-Xia
Published: March 2023

Background

Previous studies have investigated the link between fatty acid intake and bone mineral density (BMD), but the results are controversial. This study aims to examine the relationship between fatty acid intake and BMD in adults aged 20–59.

Methods

The association between fatty acid consumption and BMD was analyzed using a weighted multiple linear regression model with National Health and Nutrition Examination Survey data from 2011 to 2018. The linearity relationship and saturation value of the connection between fatty acid consumption and BMD were assessed by fitting a smooth curve and a saturation effect analysis model.

Results

The study included 8,942 subjects. We found a significant positive correlation between the consumption of saturated fatty acids, monounsaturated fatty acids (MUFAs), and polyunsaturated fatty acids and BMD. In subgroup analyses that were stratified by gender and race, this association was still shown to be significant. Based on the smooth curve and saturation effect analysis, we found no saturation effect for the three fatty acids and total BMD. However, there was a turning point (20.52 g/d) between MUFAs intake and BMD, and only MUFAs intake >20.52 g/d showed a positive correlation between MUFAs and BMD.

Conclusion

We found that fatty acid intake is beneficial for bone density in adults. Therefore, according to our findings, it is recommended that adults consume moderate amounts of fatty acids to ensure adequate bone mass but not metabolic diseases.