Effects of dietary l-carnosine supplementation on the growth, intestinal microbiota, and serum metabolome of fattening lambs by Yaxuan Meng, Yaxuan Meng, Yaxuan Meng, Tingting Xian, Tingting Xian, Guolei Kang, Hongna Wang, Tao Feng, Tao Feng, Tao Feng

“…The fecal microbiota was analyzed using 16S rRNA sequencing, and serum metabolites were analyzed using liquid chromatography–tandem mass spectrometry. …”
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Spatial and single-cell transcriptomics reveal cellular heterogeneity and a novel cancer-promoting Treg cell subset in human clear-cell renal cell carcinoma by Lijuan Wang, Qian He, Weijun Qin, Xiyu Song, Yumeng Zhu, Wenwen Geng, Jianhua Jiao, Hongjiao Liu, Ruo Chen, Xiuxuan Sun, Jiejie Geng, Zhinan Chen

“…However, the spatial and functional heterogeneity of immunosuppressive cells and the mechanisms by which their interactions promote immunosuppression in the ccRCC have not been thoroughly investigated.Methods To further investigate the cellular and regional heterogeneity of ccRCC, we analyzed single-cell and spatial transcriptome RNA sequencing data from four patients, which were obtained from samples from multiple regions, including the tumor core, tumor-normal interface, and distal normal tissue. …”
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High-fat diet-induced liver injury in Channa argus through lipid metabolism, anti-oxidative status, apoptosis, and inflammation by Jiaxin Tian, Ying Li, Jiwu Wan, Zhinan Yang, Guiqin Wang

“…At 90 days, the L22 group exhibited a significant upregulation of mRNA expression levels for liver inflammatory factors, including interleukin-1β (IL-1β), IL-8, IL-10, and tumor necrosis factor-α (TNF-α). …”
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Genetic and audiological determinants of hearing loss in high-risk neonates by Yanan Shi, Naiyao Zhang, Na Du, Tongxi Zheng, Ying Yu, Youjin Li

“…Genetic screening of 33 neonates who failed the diagnostic tests revealed that 7 (21.21%) carried at least one pathogenic variant, with identified 1 homozygotes and 3 heterozygotes in the GJB2, 1 homozygotes and 1 heterozygotes in the SLC26A4 gene, and 1 homoplasmic variant in the MT-RNR (12SrRNA). In the larger hearing screening cohort, 497 (3.34%) were genetically positive for deafness mutations, among whom 29 had the diagnostic hearing tests and 7 eventually diagnosed with hearing loss. …”
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Endoplasmic reticulum stress in the salivary glands of patients with primary and associated Sjögren’s disease, and non-Sjögren’s sicca syndrome: a comparative analysis and the infl... by Graziela Vieira Cavalcanti, Fabiola Reis de Oliveira, Rafael Ferraz Bannitz, Natalia Aparecida de Paula, Ana Carolina Fragoso Motta, Eduardo Melani Rocha, John Chiorini, Hilton Marcos Alves Ricz, Denny Marcos Garcia, Maria Cristina Foss-Freitas, Luiz Carlos Conti de Freitas

“…Histopathological analysis and mRNA expression analysis of genes associated with ERS and UPR (PERK, XBP1, ATF-6, ATF-4, CANX, CALR, CHOP, and BIP) were performed on the samples. …”
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The compensatory enrichment of sphingosine-1-phosphate on HDL in FSGS enhances the protective function of glomerular endothelial cells compared to MCD by Yunfeng Xiong, Qiuping Ye, Lifang Liu, Wanjun Lin, Yonggen Liao, Ruiyu Gao, Jiaming Xu, Xinyu Zhang, Ruoyan Chen, Sihui Chen, Qiaoling Chen, Lixin Wei

“…Knockdown of S1PR1 using siRNA reduced the expression of p-eNOS and NO release. …”
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Identifying health risk determinants and molecular targets in patients with idiopathic pulmonary fibrosis via combined differential and weighted gene co-expression analysis by Abu Tayab Moin, Md. Asad Ullah, Jannatul Ferdous Nipa, Mohammad Sheikh Farider Rahman, Afsana Emran, Md. Minhazul Islam, Swapnil Das, Tawsif Al Arian, Mohammad Mahfuz Enam Elahi, Mukta Akter, Umme Sadea Rahman, Arnab Halder, Shoaib Saikat, Mohammad Jakir Hosen

“…Regulatory signatures, including transcription factor and microRNA interactions, were also explored, alongside the identification of potential drug targets.ResultsA total of 275 and 167 DEGs were identified across two datasets, with 67 DEGs common to both. …”
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Use of approved cefazolin based intramammary dry goat treatment and its effects on the milk microbiota by Delower Hossain, Filippo Biscarini, Valentina Monistero, Paola Cremonesi, Bianca Castiglioni, Anoar Jamai Masroure, Alessandro Marinoni, Sara Fusar Poli, Matteo Mezzetti, Maria Filippa Addis, Valerio Bronzo, Erminio Trevisi, Paolo Moroni

“…Pooled milk samples were collected at dry-off (T1; 52 samples), colostrum (T2; 46 samples), and 5–10 days in milk (T3; 55 samples) for bacteriological analysis, somatic cell count (SCC), and 16 S rRNA gene sequencing. SCC levels were initially high in both groups at T1 (TG: 1,588,000 cells/mL; CG: 1,629,000 cells/mL), which significantly decreased at T3 (TG: 148,000 cells/mL; CG: 153,000 cells/mL). …”
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PGC-1α辅助激活人PEPCK基因转录

“…【目的】构建人磷酸烯醇式丙酮酸羧激酶(PEPCK)基因启动子荧光素酶报告质粒PGL3-hPCK-luc，并探讨过氧化物酶体增殖物活化受体γ辅助激活因子1α(PGC-1α)在转录因子肝细胞核因子4α(HNF4α)介导下对人PEPCK基因启动子活性的影响【方法】从人全血基因组DNA中克隆PEPCK启动子基因片段，并重组进荧光素酶报告载体PGL3-basic，将pcDNA3.1-PGC-1αpcDNA3.0-HNF4α表达质粒与PGL3-hPCK-luc按不同组合共转染进人肝癌细胞株HepG2细胞或正常人肝细胞株LO2细胞,培养48 h后检测细胞裂解液中荧光素酶活性【结果】通过酶切鉴定及测序证明扩增的人PEPCK启动子片段成功插入载体质粒中转染后人PEPCK启动子基因荧光素酶活性较空白对照组增加60倍(P < 0.05)；共转染质粒进HepG2细胞或LO2细胞后，HNF4α均可以增强人PEPCK启动子基因荧光素酶活性，在HepG2细胞，荧光素酶活性是对照组的2.69倍(P < 0.05)，而在LO2细胞中，荧光素酶活性是对照组的3.64倍(P < 0.05)；PGC-1α可以明显增强HNF4α对人PEPCK启动子的激活作用，在HepG2细胞，荧光素酶活性是PGL3-HPCK-luc+HNF4α组的2.01倍(P < 0.05)，而在LO2细胞中,荧光素酶活性是PGL3-HPCK-luc+HNF4α组的2.82倍(P < 0.05)而与单一转染组相比，共转染pcDNA3.1-PGC-1α与pcDNA3.0-HNF4α显著增加了PEPCK的mRNA和蛋白表达水平(P < 0.05)【结论】人PEPCK启动子基因报告质粒成功构建，且转录因子HNF4α可以激活人PEPCK启动子活性，辅助激活因子PGC-1α可以进一步加强HNF4α的作用…”
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Intratumoral BO-112 in combination with radiotherapy synergizes to achieve CD8 T-cell-mediated local tumor control by Helena Escuin-Ordinas, Ignacio Melero, Marisol Quintero, Jose Luis Perez-Gracia, Maite Alvarez, Maria E Rodriguez-Ruiz, Miguel F Sanmamed, Paloma Sanchez-Mateos, Inmaculada Rodríguez López, Irantzu Serrano-Mendioroz, Celia Barrio-Alonso, Eneko Garate-Soraluze, Victor Diaz Pascual, Leire Arbea Moreno

“…BO-112 is a viral mimetic based on nanoplexed double-stranded RNA (poly I:C) which exerts immune-mediated antitumor effects in mice and humans on intratumoral delivery. …”
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Development of a new data management system for the study of the gut microbiome of children who are small for their gestational age by Felix Manske, Magdalena Durda-Masny, Norbert Grundmann, Jan Mazela, Monika Englert-Golon, Marta Szymankiewicz-Bręborowicz, Joanna Ciomborowska-Basheer, Izabela Makałowska, Anita Szwed, Wojciech Makałowski

“…It supports short or long read data produced by virtually any sequencing instrument targeting (parts of) popular marker genes, such as the 16S rRNA gene and its variable regions. Classifications of these reads from the MetaG and Kraken 2 software are supported. …”
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Anti-PD-1 exacerbates bleomycin-induced lung injury in mice via Caspase-3/GSDME-mediated pyroptosis by Fei Wang, Haiyi Deng, Maolin Zhou, Yilin Yang, Jiankui Zhou, Yansheng Wang, Xiaohong Xie, Xinqing Lin, Ming Liu, Gengyun Sun, Chengzhi Zhou

“…Consistent with the findings in the animal model, immunofluorescence and RNA sequencing of lung tissue from ICI-LI patients revealed upregulation of the expression of genes related to the GSDME-related pyroptosis pathway. …”
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Genetic disruption of Blimp-1 drastically augments the antitumor efficacy of BCMA-targeting CAR T cells by Anthony M. Battram, Joan Mañé-Pujol, David F. Moreno, Aina Oliver-Caldés, Judit Carpio, Oriol Cardus, Luis Gerardo Rodríguez-Lobato, Álvaro Urbano-Ispizua, Carlos Fernández de Larrea

“…In this setting, Blimp-1 KO CAR T cells maintained a highly active state with high expression of memory markers, but, crucially, demonstrated enhanced effector function and increased energetic capacity. RNA-sequencing analysis of tumor-exposed Blimp-1 KO CAR T cells confirmed the presence of a memory-like transcriptomic signature and, additionally, revealed enhanced ribosome biogenesis and repressed CAR T-cell dysfunction as mechanisms that could contribute to improved antitumor activity. …”
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Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma by Olivia W Lee, Danielle M Karyadi, Stephen W Hartley, Weyin Zhou, Mitchell J Machiela, Shahriar A Zamani, Liudmyla Yu Zurnadzhy, John N Weinstein, Young Joo Park, Jeong-Sun Seo, Gerry A Thomas, Tetiana I Bogdanova, Mykola D Tronko, Lindsay M Morton, Stephen J Chanock

“…Our analysis confirmed that 22qDEL occurs more frequently with RAS point mutations (50.4%), particularly HRAS (70.3%), compared with other PTC drivers (9.3%), supporting the conclusion that 22qDEL is unlikely to be a solitary driver of PTC but possibly an important co-factor in carcinogenesis, particularly in PTCs with RAS driver mutations. Differential RNA expression analyses revealed downregulation of most genes located on chromosome 22 in cases with 22qDEL compared to those without 22qDEL. …”
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Antioxidant effect of Lactobacillus fermentum HFY02-fermented soy milk on D-galactose-induced aging mouse model by Tiantian Hu, Rui Chen, Yu Qian, Ke Ye, Xingyao Long, Kun-Young Park, Xin Zhao

“…The activities of GSH, GSH-Px, SOD, CAT and T-AOC in serum, brain and liver of soybean milk fermented by LF-HFY02 were significantly increased, while the content of MDA and the level of AGEs in hippocampal were significantly decreased compared with D-galactose induced group. Further more, the mRNA expression of GSH and SOD in mouse liver were obviously up-regulated by soybean milk fermented by LF-HFY02. …”
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Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial... by Frédérique Reverchon, Mariel García-Meléndez, Edgar Guevara-Avendaño, Oscar Mora-Chávez, Itzel A. Solís-García, Wesley Dáttilo, José A. Guererro-Analco, Alfonso Méndez-Bravo, Juan L. Monribot-Villanueva, Violeta Patiño-Conde, Fernando Pineda-García, Eria A. Rebollar

“…During the infection process, we measured plant morphological and physiological variables and collected rhizosphere soil samples for bacterial and fungal amplicon sequencing, bacterial RNA-seq and metabolomic analyses. Conclusions Collectively, our data elucidate the shifts in the avocado rhizosphere microbiome after infection by P. cinnamomi and when inoculated with a BCA, and help understand how a pathogen or a beneficial bacterium can alter plant-microbiome crosstalk. …”
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Comparative transcriptomic rhythms in the mouse and human prefrontal cortex by Jennifer N. Burns, Jennifer N. Burns, Aaron K. Jenkins, Xiangning Xue, Kaitlyn A. Petersen, Kaitlyn A. Petersen, Kyle D. Ketchesin, Kyle D. Ketchesin, Megan S. Perez, Megan S. Perez, Chelsea A. Vadnie, Madeline R. Scott, Madeline R. Scott, Marianne L. Seney, Marianne L. Seney, George C. Tseng, Colleen A. McClung, Colleen A. McClung

“…However, investigation into the potential circadian mechanisms underlying these diseases in animal models must contend with the fact that the human PFC is highly evolved and specialized relative to that of rodents.MethodsHere, we use RNA sequencing to lay the groundwork for translational studies of molecular rhythms through a sex-specific, cross species comparison of transcriptomic rhythms between the mouse medial PFC (mPFC) and two subregions of the human PFC, the anterior cingulate cortex (ACC) and the dorsolateral PFC (DLPFC).ResultsWe find that while circadian rhythm signaling is conserved across species and subregions, there is a phase shift in the expression of core clock genes between the mouse mPFC and human PFC subregions that differs by sex. …”
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Characterization of three novel Helicobacter species infecting stomachs of dogs and cats: Helicobacter gastrocanis sp. nov., Helicobacter gastrofelis sp. nov., and Helicobacter fel... by Emiko Rimbara, Sae Aoki, Masato Suzuki, Hirotaka Kobayashi, Taisuke Nakagawa, Yuko Goto-Koshino, Sachiyo Nomura, Sachiyo Nomura, Wan-Ying Du, Hidenori Matsui, Shigetarou Mori, Keigo Shibayama, Tsuyoshi Kenri, Koichi Ohno

“…In the present study conducted in Japan, among the nine Helicobacter strains that we isolated from dogs and cats, NHP19-003T from a dog, and strains NHP19-012T and NHP21-005T from cats were identified to be the strains most closely related to Helicobacter heilmannii ASB1T based on a 16S rRNA comparison (98.7–99.2% similarity with H. heilmannii ASB1T). …”
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Suppressing recurrence in Sonic Hedgehog subgroup medulloblastoma using the OLIG2 inhibitor CT-179 by Yuchen Li, Chaemin Lim, Taylor Dismuke, Daniel S. Malawsky, Sho Oasa, Zara C. Bruce, Carolin Offenhäuser, Ulrich Baumgartner, Rochelle C. J. D’Souza, Stacey L. Edwards, Juliet D. French, Lucy S. H. Ock, Sneha Nair, Haran Sivakumaran, Lachlan Harris, Andrey P. Tikunov, Duhyeong Hwang, Coral Del Mar Alicea Pauneto, Mellissa Maybury, Timothy Hassall, Brandon Wainwright, Santosh Kesari, Gregory Stein, Michael Piper, Terrance G. Johns, Marina Sokolsky-Papkov, Lars Terenius, Vladana Vukojević, Leon F. McSwain, Timothy R. Gershon, Bryan W. Day

“…Single cell transcriptomic studies (scRNA-seq) confirm that CT-179 increases differentiation and implicate Cdk4 up-regulation in maintaining proliferation during treatment. …”
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Epidemiology of bacterial biofilms on polyps and normal tissues in a screening colonoscopy cohort by Julia L. Drewes, Samara B. Rifkin, Madison McMann, Sara Glass, Emma Spence, Caroline R. Wensel, Abby L. Geis, Courtney Stevens, Joell J. Gills, Hao Wang, Linda M. Hylind, Gerard Mullin, David Kafonek, David Cromwell, Louis La Luna, Francis M. Giardiello, Cynthia L. Sears

“…Here we evaluated potential procedural and demographic risk factors associated with biofilm status using a cross-sectional observational cohort.Methods Histologically normal colonic biopsies from 2,051 individuals undergoing screening colonoscopy were evaluated for biofilm status using fluorescence in situ hybridization with oligonucleotide probes targeting bacterial 16S rRNA. Polyp tissues from 21 individuals were also examined. …”
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