keyword
https://read.qxmd.com/read/38461236/genomic-dissection-of-the-correlation-between-milk-yield-and-various-health-traits-using-functional-and-evolutionary-information-about-imputed-sequence-variants-of-34-497-german-holstein-cows
#21
JOURNAL ARTICLE
Helen Schneider, Ana-Marija Krizanac, Clemens Falker-Gieske, Johannes Heise, Jens Tetens, Georg Thaller, Jörn Bennewitz
BACKGROUND: Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed settings. Still, little is known about the contribution of different functional and evolutionary genome partitioning subsets to milk production and dairy health...
March 9, 2024: BMC Genomics
https://read.qxmd.com/read/38460684/sequential-hydrotalcite-precipitation-microbial-sulfate-reduction-and-in-situ-hydrogen-sulfide-removal-for-neutral-mine-drainage-treatment
#22
JOURNAL ARTICLE
Ka Yu Cheng, Caroline Rubina Acuña, Anna H Kaksonen, Graeme Esslemont, Grant B Douglas
This study proposed and examined a new process flowsheet for treating neutral mine drainage (NMD) from an open-pit gold mine. The process consisted of three sequential stages: (1) in-situ hydrotalcite (HT) precipitation; (2) low-cost carbon substrate driven microbial sulfate reduction; and (3) ferrosol reactive barrier for removing biogenic dissolved hydrogen sulfide (H2 S). For concept validation, laboratory-scale columns were established and operated for a 140-days period with key process performance parameters regularly measured...
March 7, 2024: Science of the Total Environment
https://read.qxmd.com/read/38460210/ultrasimple-size-encoded-microfluidic-chip-for-rapid-simultaneous-multiplex-detection-of-dna-sequences
#23
JOURNAL ARTICLE
Man Tang, Kuan-Jie Zhu, Wei Sun, Xinyue Yuan, Zhipeng Wang, Ruyi Zhang, Zhao Ai, Kan Liu
Simultaneous multiplexed analysis can provide comprehensive information for disease diagnosis. However, the current multiplex methods rely on sophisticated barcode technology, which hinders its wider application. In this study, an ultrasimple size encoding method is proposed for multiplex detection using a wedge-shaped microfluidic chip. Driving by negative pressure, microparticles are naturally arranged in distinct stripes based on their sizes within the chip. This size encoding method demonstrates a high level of precision, allowing for accuracy in distinguishing 3-5 sizes of microparticles with a remarkable accuracy rate of up to 99%, even the microparticles with a size difference as small as 0...
March 1, 2024: Biosensors & Bioelectronics
https://read.qxmd.com/read/38459421/the-myc-nfatc2-axis-maintains-the-cell-cycle-and-mitochondrial-function-in-acute-myeloid-leukaemia-cells
#24
JOURNAL ARTICLE
Shaun D Patterson, Matthew E Massett, Xu Huang, Heather G Jørgensen, Alison M Michie
Acute myeloid leukaemia (AML) is a clonal haematological malignancy affecting the myeloid lineage, with generally poor patient outcomes owing to the lack of targeted therapies. The histone lysine demethylase 4A (KDM4A) has been established as a novel therapeutic target in AML, due to its selective oncogenic role within leukaemic cells. We identify that the transcription factor nuclear factor of activated T cells 2 (NFATC2) is a novel binding and transcriptional target of KDM4A in the human AML THP-1 cell line...
March 8, 2024: Molecular Oncology
https://read.qxmd.com/read/38453457/chromatin-immunoprecipitation-chip-using-drosophila-antennal-and-brain-samples
#25
JOURNAL ARTICLE
Chengcheng Du, Pelin Volkan
Chromatin immunoprecipitation (ChIP) is a common approach for studying the binding pattern of proteins on DNA sequences or the landscape of histones with different marks throughout the genome. ChIP is used on various organisms, including Drosophila This protocol provides a detailed overview of the immunoprecipitation portion of a ChIP procedure from samples of Drosophila nervous systems, specifically antennae and brains, that have already been fixed and sheared. These methods can be applied to other tissues of interest after optimizing for sample size and other relevant parameters...
March 7, 2024: Cold Spring Harbor Protocols
https://read.qxmd.com/read/38453456/using-chromatin-immunoprecipitation-chip-to-study-the-chromatin-state-in-drosophila
#26
JOURNAL ARTICLE
Chengcheng Du, Pelin Volkan
The chromatin state plays an important role in regulating gene expression, which affects organismal development and plasticity. Proteins, including transcription factors, chromatin modulatory proteins, and histone proteins, usually with modifications, interact with gene loci involved in cellular differentiation, function, and modulation. One molecular method used to characterize protein-DNA interactions is chromatin immunoprecipitation (ChIP). ChIP uses antibodies to immunoprecipitate specific proteins cross-linked to DNA fragments...
March 7, 2024: Cold Spring Harbor Protocols
https://read.qxmd.com/read/38453052/ras-protein-activator-like-2-rasal2-initiates-peritubular-capillary-rarefaction-in-hypoxic-renal-interstitial-fibrosis
#27
JOURNAL ARTICLE
Yu Zhang, Yiqiong Yang, Xiuxiu Hu, Bizhen Wei, Qian Shen, Chuanbing Shi, Pingsheng Chen
The progression of chronic kidney disease (CKD) often involves renal interstitial fibrosis (RIF) and subsequent loss of peritubular capillaries (PTCs), which enhances disease severity. Despite advancements in our understanding of fibrosis, effective interventions for reversing capillary loss remain elusive. Notably, RIF exhibits reduced capillary density, whereas renal cell carcinoma (RCC) shows robust angiogenesis under hypoxic conditions. Using RNA sequencing and bioinformatics, we identified differentially expressed genes (DEGs) in hypoxic human renal tubular epithelial cells (HK-2) and renal cancer cells (786-0)...
March 5, 2024: Translational Research: the Journal of Laboratory and Clinical Medicine
https://read.qxmd.com/read/38447644/optimization-of-duplex-digital-pcr-for-the-measurement-of-sars-cov-2-rna
#28
JOURNAL ARTICLE
Sang-Soo Lee, Ah Leum Kim, Jae-Hyung Park, Da-Hye Lee, Young-Kyung Bae
Quantitative PCR (qPCR) is the gold standard for detecting nucleic acid sequences specific to the target pathogen. For COVID-19 diagnosis, several molecular assays have been developed. In this study, we present an optimization strategy for the measurement of SARS-CoV-2 RNA via multiplex qPCR and digital PCR (dPCR). Compared to qPCR, both droplet and chip-based dPCR, which are known to be more sensitive and accurate, showed a better resilience to suboptimal assay compositions and cycling conditions following the proposed optimizations...
March 4, 2024: Journal of Virological Methods
https://read.qxmd.com/read/38447229/dynamic-ipsc-derived-hepatic-tissue-tri-culture-system-for-the-evaluation-of-liver-physiology-in-vitro
#29
JOURNAL ARTICLE
Benedikt Scheidecker, Stéphane Poulain, Masahiro Sugimoto, Taketomo Kido, Takumi Kawanishi, Atsushi Miyajima, Soo Hyeon Kim, Hiroshi Arakawa, Yukio Kato, Masaki Nishikawa, Mathieu Danoy, Yasuyuki Sakai, Eric Leclerc
Availability of hepatic tissue for the investigation of metabolic processes is severely limited. While primary hepatocytes or animal models are widely used in pharmacological applications, a change in methodology towards more sustainable and ethical assays is highly desirable. Stem cell derived hepatic cells are generally regarded as a viable alternative for the above model systems, if current limitations in functionality and maturation can be overcome. By combining microfluidic organ-on-a-chip technology with individually differentiated, multicellular hepatic tissue fractions, we aim to improve overall functionality of hepatocyte-like cells, as well as evaluate cellular composition and interactions with non-parenchymal cell populations towards the formation of mature liver tissue...
March 6, 2024: Biofabrication
https://read.qxmd.com/read/38447046/long-noncoding-rna-gata2as-influences-human-erythropoiesis-by-transcription-factor-and-chromatin-landscape-regulation
#30
JOURNAL ARTICLE
Guoyou Liu, Juhyun Kim, Nicole Han Nguyen, Lecong Zhou, Ann Dean
LncRNAs are extensively expressed in eukaryotic cells and have been revealed to be important for regulating cell differentiation. Many lncRNAs have been found to regulate erythroid differentiation in the mouse. However, given the low sequence conservation of lncRNAs between mouse and human, our understanding of lncRNAs in human erythroid differentiation remains incomplete. LncRNAs are often transcribed opposite to protein coding genes and regulate their expression. Here we characterized a human erythrocyte-expressed lncRNA, GATA2AS, which is transcribed opposite to erythroid transcription regulator GATA2...
March 6, 2024: Blood
https://read.qxmd.com/read/38443156/-nasp-gene-contributes-to-autism-by-epigenetic-dysregulation-of-neural-and-immune-pathways
#31
JOURNAL ARTICLE
Sipeng Zhang, Jie Yang, Dandan Ji, Xinyi Meng, Chonggui Zhu, Gang Zheng, Joseph Glessner, Hui-Qi Qu, Yuechen Cui, Yichuan Liu, Wei Wang, Xiumei Li, Hao Zhang, Zhanjie Xiu, Yan Sun, Ling Sun, Jie Li, Hakon Hakonarson, Jin Li, Qianghua Xia
BACKGROUND: Epigenetics makes substantial contribution to the aetiology of autism spectrum disorder (ASD) and may harbour a unique opportunity to prevent the development of ASD. We aimed to identify novel epigenetic genes involved in ASD aetiology. METHODS: Trio-based whole exome sequencing was conducted on ASD families. Genome editing technique was used to knock out the candidate causal gene in a relevant cell line. ATAC-seq, ChIP-seq and RNA-seq were performed to investigate the functional impact of knockout (KO) or mutation in the candidate gene...
March 5, 2024: Journal of Medical Genetics
https://read.qxmd.com/read/38440920/ap-1-c-fos-and-ap-1-fra2-differentially-regulate-early-and-late-adipogenic-differentiation-of-mesenchymal-stem-cells
#32
JOURNAL ARTICLE
Ganesh Suraj Bose, Garima Kalakoti, Abhijeet P Kulkarni, Smriti Mittal
Obesity is defined as an abnormal accumulation of adipose tissue in the body and is a major global health problem due to increased morbidity and mortality. Adipose tissue is made up of adipocytes, which are fat-storing cells, and the differentiation of these fat cells is known as adipogenesis. Several transcription factors (TFs) such as CEBPβ, CEBPα, PPARγ, GATA, and KLF have been reported to play a key role in adipogenesis. In this study, we report one more TF AP-1, which is found to be involved in adipogenesis...
March 5, 2024: Journal of Cellular Biochemistry
https://read.qxmd.com/read/38439081/a-genotyping-array-for-the-globally-invasive-vector-mosquito-aedes-albopictus
#33
JOURNAL ARTICLE
Luciano Veiga Cosme, Margaret Corley, Thomas Johnson, Dave W Severson, Guiyun Yan, Xiaoming Wang, Nigel Beebe, Andrew Maynard, Mariangela Bonizzoni, Ayda Khorramnejad, Ademir Jesus Martins, José Bento Pereira Lima, Leonard E Munstermann, Sinnathamby N Surendran, Chun-Hong Chen, Kevin Maringer, Isra Wahid, Shomen Mukherjee, Jiannon Xu, Michael C Fontaine, Elizabet L Estallo, Marina Stein, Todd Livdahl, Patricia Y Scaraffia, Brendan H Carter, Motoyoshi Mogi, Nobuko Tuno, James W Mains, Kim A Medley, David E Bowles, Richard J Gill, Roger Eritja, Ranulfo González-Obando, Huynh T T Trang, Sébastien Boyer, Ann-Marie Abunyewa, Kayleigh Hackett, Tina Wu, Justin Nguyễn, Jiangnan Shen, Hongyu Zhao, Jacob E Crawford, Peter Armbruster, Adalgisa Caccone
BACKGROUND: Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases...
March 4, 2024: Parasites & Vectors
https://read.qxmd.com/read/38433131/genetic-correlations-shared-risk-genes-and-immunity-landscapes-between-covid-19-and-venous-thromboembolism-evidence-from-gwas-and-bulk-transcriptome-data
#34
JOURNAL ARTICLE
Langchao Yan, Shifu Li, Qian Hu, Di Liao
BACKGROUND: Patients with coronavirus disease 2019 (COVID-19) were vulnerable to venous thromboembolism (VTE), which further increases the risk of unfavorable outcomes. However, neither genetic correlations nor shared genes underlying COVID-19 and VTE are well understood. OBJECTIVE: This study aimed to characterize genetic correlations and common pathogenic mechanisms between COVID-19 and VTE. METHODS: We used linkage disequilibrium score (LDSC) regression and Mendelian Randomization (MR) analysis to investigate the genetic associations and causal effects between COVID-19 and VTE, respectively...
March 3, 2024: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://read.qxmd.com/read/38433110/first-report-of-cryptostroma-corticale-causing-sooty-bark-disease-in-california-and-first-worldwide-report-of-silver-maple-as-a-host
#35
JOURNAL ARTICLE
Matteo Garbelotto, Douglas Schmidt, Tina Popenuck, Suzanne Rooney-Latham, Curtis Ewing, Tom Smith
In November 2022 and February 2023, CAL FIRE tree health experts examined four maples (Acer spp.) planted decades earlier in a residential setting in Elk Grove, Sacramento Co., California (USA). Three of the trees were silver maples (Acer saccharinum ) and one was a Norway maple (A. platanoides); both species are exotic to California. The trees were in an irreversible state of decline, with the canopy substantially thinned and browning. Extensive bark cankers elongating longitudinally along the stem were visible on all trees (Fig...
March 3, 2024: Plant Disease
https://read.qxmd.com/read/38432146/aberrant-h3k4me3-modification-of-immune-response-genes-in-cd4-t-cells-of-patients-with-systemic-lupus-erythematosus
#36
JOURNAL ARTICLE
Delong Feng, Hongjun Zhao, Qian Wang, Jiali Wu, Lianlian Ouyang, Sujie Jia, Qianjin Lu, Ming Zhao
BACKGROUND: Increasing evidence has highlighted the significant role of histone modifications in pathogenesis of systemic lupus erythematosus (SLE). However, few studies have comprehensively analyzed trimethylation of histone H3 lysine 4 (H3K4me3) features at specific immune gene loci in SLE patients. METHODS: We conducted H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) on CD4+ T cells from SLE patients and healthy controls (HC). Differential H3K4me3 peaks were identified, followed by enrichment analysis...
March 2, 2024: International Immunopharmacology
https://read.qxmd.com/read/38429845/single-cell-deconvolution-algorithms-analysis-unveils-autocrine-il11-mediated-resistance-to-docetaxel-in-prostate-cancer-via-activation-of-the-jak1-stat4-pathway
#37
JOURNAL ARTICLE
Bisheng Cheng, Lingfeng Li, Tianlong Luo, Qiong Wang, Yong Luo, Shoumin Bai, Kaiwen Li, Yiming Lai, Hai Huang
BACKGROUND: Docetaxel resistance represents a significant obstacle in the treatment of prostate cancer. The intricate interplay between cytokine signalling pathways and transcriptional control mechanisms in cancer cells contributes to chemotherapeutic resistance, yet the underlying molecular determinants remain only partially understood. This study elucidated a novel resistance mechanism mediated by the autocrine interaction of interleukin-11 (IL-11) and its receptor interleukin-11 receptor subunit alpha(IL-11RA), culminating in activation of the JAK1/STAT4 signalling axis and subsequent transcriptional upregulation of the oncogene c-MYC...
March 1, 2024: Journal of Experimental & Clinical Cancer Research: CR
https://read.qxmd.com/read/38428071/label-free-single-cell-analysis-in-microdroplets-using-a-light-scattering-based-optofluidic-chip
#38
JOURNAL ARTICLE
Li Liang, Minhui Liang, Zewen Zuo, Ye Ai
Droplet-based single-cell analysis is a very powerful tool for studying phenotypic and genomic heterogeneity at single-cell resolution for a variety of biological problems. In conventional two-phase droplet microfluidics, due to the mismatch in optical properties between oil and aqueous phases, light scattering mainly happens at the oil/water interface that disables light-scattering-based cell analysis confined in microdroplets. Detection and analysis of cells in microdroplets thus mostly rely on the fluorescence labeling of cell samples, which may suffer from complex operation, cytotoxicity, and low fluorescence stability...
February 20, 2024: Biosensors & Bioelectronics
https://read.qxmd.com/read/38425797/growth-regulating-factor-15-mediated-vascular-cambium-differentiation-positively-regulates-wood-formation-in-hybrid-poplar-populus-alba-%C3%A3-p-glandulosa
#39
JOURNAL ARTICLE
Houjun Zhou, Xueqin Song, Meng-Zhu Lu
INTRODUCTION: Hybrid poplars are industrial trees in China. An understanding of the molecular mechanism underlying wood formation in hybrid poplars is necessary for molecular breeding. Although the division and differentiation of vascular cambial cells is important for secondary growth and wood formation, the regulation of this process is largely unclear. METHODS: In this study, mPagGRF15 OE and PagGRF15-SRDX transgenic poplars were generated to investigate the function of PagGRF15 ...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38424624/il6-stat3-c-ebp%C3%AE-il6-positive-feedback-loop-in-tumor-associated-macrophages-promotes-the-emt-and-metastasis-of-lung-adenocarcinoma
#40
JOURNAL ARTICLE
Zhengyang Hu, Qihai Sui, Xing Jin, Guangyao Shan, Yiwei Huang, Yanjun Yi, Dejun Zeng, Mengnan Zhao, Cheng Zhan, Qun Wang, Zongwu Lin, Tao Lu, Zhencong Chen
BACKGROUND: Lung cancer is one of the most common tumors in the world, and metastasis is one of the major causes of tumor-related death in lung cancer patients. Tumor-associated macrophages (TAMs) are a major component of the tumor microenvironment (TME) and are frequently associated with tumor metastasis in human cancers. However, the regulatory mechanisms of TAMs in lung cancer metastasis remain unclear. METHODS: Single-cell sequencing analysis of lung cancer and normal tissues from public databases and from 14 patients who underwent surgery at Zhongshan Hospital was performed...
February 29, 2024: Journal of Experimental & Clinical Cancer Research: CR
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