Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach
J Appl Genet. 2024 Feb 15. doi: 10.1007/s13353-024-00843-6. Online ahead of print.ABSTRACTHead and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, some associated with carcinomas. Chromobox (CBX) family is known to modulate physiological and oncological processes. In our study, we analyzed AQPs and CBXs having significant expression followed by their prognostic and mutational assessment. Next, we performed enrichment and tumor infil...
Source: J Appl Genet - February 15, 2024 Category: Genetics & Stem Cells Authors: Rishabh Gurung Mohammad Masood Prithvi Singh Prakash Jha Anuradha Sinha Swati Ajmeriya Milin Sharma Ravins Dohare Mohammad Mahfuzul Haque Source Type: research
Triticale field phenotyping using RGB camera for ear counting and yield estimation
J Appl Genet. 2024 Feb 14. doi: 10.1007/s13353-024-00835-6. Online ahead of print.ABSTRACTTriticale (X Triticosecale Wittmack), a wheat-rye small grain crop hybrid, combines wheat and rye attributes in one hexaploid genome. It is characterized by high adaptability to adverse environmental conditions: drought, soil acidity, salinity and heavy metal ions, poorer soil quality, and waterlogging. So that its cultivation is prospective in a changing climate. Here, we describe RGB on-ground phenotyping of field-grown eighteen triticale market-available cultivars, made in naturally changing light conditions, in two consecutive win...
Source: J Appl Genet - February 14, 2024 Category: Genetics & Stem Cells Authors: Piotr Stefa ński Sajid Ullah Przemys ław Matysik Krystyna Rybka Source Type: research
Featured lncRNA-based signature for discriminating prognosis and progression of hepatocellular carcinoma
In conclusion, the 18-lncRNA signature was a robust predictive biomarker for the prognosis and progression of HCC.PMID:38347289 | DOI:10.1007/s13353-024-00836-5 (Source: J Appl Genet)
Source: J Appl Genet - February 12, 2024 Category: Genetics & Stem Cells Authors: Huiyuan Qiu Bo Jiang Yinqi Chen Zhaoyi Lin Wenjie Zheng Xianglei Cao Source Type: research
Transcriptome meta-analysis-based identification of hub transcription factors and RNA-binding proteins potentially orchestrating gene regulatory cascades and crosstalk in response to abiotic stresses in Arabidopsis thaliana
This study highlighted the gene/protein candidates that could be considered for multiplexed genetic manipulation - a promising approach to develop robust, multi-stress-resilient plant varieties.PMID:38337133 | DOI:10.1007/s13353-024-00837-4 (Source: J Appl Genet)
Source: J Appl Genet - February 10, 2024 Category: Genetics & Stem Cells Authors: M J Nishanth Source Type: research
The role of multidisciplinary diagnostic and therapeutic model of care in Lamb-Shaffer syndrome - case report
J Appl Genet. 2024 Feb 10. doi: 10.1007/s13353-024-00838-3. Online ahead of print.ABSTRACTThis case study illustrates a multidisciplinary diagnostic and therapeutic model of care for a 7-year-old male with Lamb-Shaffer syndrome (LAMSHF). LAMSHF is an ultra-rare genetic neurodevelopmental disorder, caused by heterozygous alterations in the SOX5 gene. An integrative model of therapy of cognitive functions and speech is described. The presented approach allows the development of language competences through stimulation of basic cognitive functions, which allows the learning of the abstract rules of an inflected language. A su...
Source: J Appl Genet - February 10, 2024 Category: Genetics & Stem Cells Authors: Urszula Sajewicz-Radtke Ariadna Łada-Maśko Ma łgorzata Lipowska Bartosz M Radtke Beata S Lipska-Zi ętkiewicz Katarzyna Krempla-Patron Source Type: research
Peptidylprolyl isomerase D circular RNA sensitizes breast cancer to trastuzumab through remodeling HER2 N4-acetylcytidine modification
In this study, a novel circular RNA derived from peptidylprolyl isomerase D (PPID) is identified as a negative regulator of trastuzumab resistance. Circ-PPID is highly stable and significantly downregulated in trastuzumab-resistant cells and tissues. Restoration of circ-PPID markedly enhances HER2-positive breast cell sensitivity to trastuzumab in vitro and in vivo. Circ-PPID directly binds to N-acetyltransferase 10 (NAT10) in the nucleus and blocks the interaction between NAT10 and HER2 mRNA, reducing N4-acetylcytidine (ac4C) modification on HER2 exon 25, leading to HER2 mRNA decay. Intriguingly, the subcellular localizat...
Source: J Appl Genet - February 10, 2024 Category: Genetics & Stem Cells Authors: Shengting Wang Qian Li Yufang Wang Xiaoming Li Xinghua Feng Yuxuan Wei Jiaman Wang Xin Zhou Source Type: research
Assessing cytotoxicity and endoplasmic reticulum stress in human blood-brain barrier cells due to silver and copper oxide nanoparticles
We examined ER stress in immortalized human cerebral microvascular cells (hCMEC/D3) after exposure to silver-NPs (Ag-NPs)- and copper oxide-NPs (CuO-NPs) induced toxicity at < 10 nm and < 40 nm or < 50 nm diameters, respectively. In cytotoxicity assessments, cells were exposed to different CuO-NPs (5-400 µg/mL) or Ag-NPs (1-10 µg/mL) concentration ranges for 24 h and 72 h, and tetrazole salt reduction assays (EZ4U) were performed. Also, Ag-NP or CuO-NP effects on cell proliferation, apoptosis (caspase 3/7 assays), and ER stress and cell morphology were evaluated. In ER stress assessments, RNA-like endoplasmic re...
Source: J Appl Genet - February 9, 2024 Category: Genetics & Stem Cells Authors: Luiza Chojnacka-Puchta Dorota Sawicka Lidia Zapor Katarzyna Miranowicz-Dzierzawska Source Type: research
Bioinformatics to analyze the differentially expressed genes in different degrees of Alzheimer's disease and their roles in progress of the disease
J Appl Genet. 2024 Feb 5. doi: 10.1007/s13353-024-00827-6. Online ahead of print.ABSTRACTEmploying bioinformatics approaches, this investigation pinpointed pivotal differentially expressed genes (DEGs) across the spectrum of Alzheimer's disease (AD), from incipient to severe stages, using the GSE28146 dataset from the GEO repository. Analytical methods included DEG identification via the limma package in R, coupled with GO and KEGG pathway analyses through clusterProfiler, to discern biological processes and pathway involvements. Key findings spotlighted the roles of proteasome subunits PSMB4, PSMB8, PSMC4, and PSMD6 in th...
Source: J Appl Genet - February 5, 2024 Category: Genetics & Stem Cells Authors: Yanfang Niu Yunyun Zhang Qin Zha Jingfei Shi Qiuyan Weng Source Type: research
Genetic analysis of milk minerals in dairy cattle: a review
J Appl Genet. 2024 Jan 30. doi: 10.1007/s13353-024-00832-9. Online ahead of print.ABSTRACTMineral composition in milk can affect its nutritional as well as physio-chemical properties of milk and is considered an important trait in the evaluation of milk quality. The composition and concentration of milk minerals could be altered with natural source of variation including nutrition and genetics. The effect of diet on milk minerals is well studied. However, genetic effects on the milk minerals have recently gained the attention. This review provides an overview of the genetic variation of milk minerals, and the genomic regio...
Source: J Appl Genet - January 29, 2024 Category: Genetics & Stem Cells Authors: Akansha Singh Amit Kumar Mohan Singh Thakur Vaishali Khare Asit Jain Sita Prasad Tiwari Source Type: research
Pharmacogenetic study of CES1 gene and enalapril efficacy
J Appl Genet. 2024 Jan 23. doi: 10.1007/s13353-024-00831-w. Online ahead of print.ABSTRACTEnalapril is an orally administered angiotensin-converting enzyme inhibitor which is widely prescribed to treat hypertension, chronic kidney disease, and heart failure. It is an ester prodrug that needs to be activated by carboxylesterase 1 (CES1). CES1 is a hepatic hydrolase that in vivo biotransforms enalapril to its active form enalaprilat in order to produce its desired pharmacological impact. Several single nucleotide polymorphisms in CES1 gene are reported to alter the catalytic activity of CES1 enzyme and influence enalapril me...
Source: J Appl Genet - January 23, 2024 Category: Genetics & Stem Cells Authors: Misbah Hussain Sehrish Basheer Adila Khalil Qurat Ul Ain Haider Hafsa Saeed Muhammad Faizan Source Type: research
Up-regulated mRNA expression of VEGFA receptors (FLT1 and KDR) in placentas after assisted reproductive technology fertilization
J Appl Genet. 2024 Jan 18. doi: 10.1007/s13353-023-00823-2. Online ahead of print.ABSTRACTPlacental angiogenesis is a pivotal process for feto-maternal circulation and ensures efficient development of the placenta throughout pregnancy. Many factors during in vitro fertilization and embryo transfer procedures may affect placental gene expression and fetus development. The present study aimed to identify differences in angiogenesis-related gene (VEGFA, FGF2, FLT1, and KDR) expression profiles in placentas after assisted reproductive technology fertilization and natural conception in healthy women. In a case-control study, te...
Source: J Appl Genet - January 18, 2024 Category: Genetics & Stem Cells Authors: Aleksandra E Mrozikiewicz Gra żyna Kurzawińska Micha ł Walczak Marzena Skrzypczak-Zieli ńska Marcin O żarowski Piotr J ędrzejczak Source Type: research
Prognostic analysis and risk assessment based on RNA editing in hepatocellular carcinoma
In this study, we aimed to develop a personalized prognostic model for HCC based on RNA editing. RNA editing is a post-transcriptional process that can affect gene expression and, in some cases, play a role in cancer development. By analyzing RNA editing sites in HCC, we sought to identify a set of sites associated with patient prognosis and use them to create a prognostic model. We gathered RNA editing data from the Synapse database, comprising 9990 RNA editing sites and 250 HCC samples. Additionally, we collected clinical data for 377 HCC patients from the Cancer Genome Atlas (TCGA) database. We employed a multi-step app...
Source: J Appl Genet - January 13, 2024 Category: Genetics & Stem Cells Authors: Xintong Shi Xiaoyuan Bu Xinyu Zhou Ningjia Shen Yanxin Chang Wenlong Yu Yingjun Wu Source Type: research
Review of applications of artificial intelligence (AI) methods in crop research
J Appl Genet. 2024 Jan 13. doi: 10.1007/s13353-023-00826-z. Online ahead of print.ABSTRACTSophisticated and modern crop improvement techniques can bridge the gap for feeding the ever-increasing population. Artificial intelligence (AI) refers to the simulation of human intelligence in machines, which refers to the application of computational algorithms, machine learning (ML) and deep learning (DL) techniques. This is aimed to generalise patterns and relationships from historical data, employing various mathematical optimisation techniques thus making prediction models for facilitating selection of superior genotypes. These...
Source: J Appl Genet - January 12, 2024 Category: Genetics & Stem Cells Authors: Suvojit Bose Saptarshi Banerjee Soumya Kumar Akash Saha Debalina Nandy Soham Hazra Source Type: research
Genetic analysis of purple pigmentation in rice seed and vegetative parts - implications on developing high-yielding purple rice (Oryza sativa L.)
J Appl Genet. 2024 Jan 8. doi: 10.1007/s13353-023-00825-0. Online ahead of print.ABSTRACTPigmentation in rice grains is an important quality parameter. Purple-coloured rice (Oryza sativa L.) indicates the presence of high anthocyanin with benefits of antioxidant properties. However, the genetic mechanism of grain colour is not fully understood. Therefore, the study focused on understanding pigmentation in grain pericarp and vegetative parts, and its relationship with blast resistance and enhanced grain yield. Three local cultivars from the northeastern region (NER) of India - Chakhao Poireiton (purple), Mang Meikri (light ...
Source: J Appl Genet - January 9, 2024 Category: Genetics & Stem Cells Authors: Bharati Lap P Magudeeswari Wricha Tyagi Mayank Rai Source Type: research
Genetic analysis of purple pigmentation in rice seed and vegetative parts - implications on developing high-yielding purple rice (Oryza sativa L.)
J Appl Genet. 2024 Jan 8. doi: 10.1007/s13353-023-00825-0. Online ahead of print.ABSTRACTPigmentation in rice grains is an important quality parameter. Purple-coloured rice (Oryza sativa L.) indicates the presence of high anthocyanin with benefits of antioxidant properties. However, the genetic mechanism of grain colour is not fully understood. Therefore, the study focused on understanding pigmentation in grain pericarp and vegetative parts, and its relationship with blast resistance and enhanced grain yield. Three local cultivars from the northeastern region (NER) of India - Chakhao Poireiton (purple), Mang Meikri (light ...
Source: J Appl Genet - January 9, 2024 Category: Genetics & Stem Cells Authors: Bharati Lap P Magudeeswari Wricha Tyagi Mayank Rai Source Type: research
