journal
https://read.qxmd.com/read/38430379/genome-wide-identification-and-comparative-analysis-of-the-amino-acid-transporter-aat-gene-family-and-their-roles-during-phaseolus-vulgaris-symbioses
#21
JOURNAL ARTICLE
Kalpana Nanjareddy, María Fernanda Guerrero-Carrillo, Miguel Lara, Manoj-Kumar Arthikala
Amino acid transporters (AATs) are essential integral membrane proteins that serve multiple roles, such as facilitating the transport of amino acids across cell membranes. They play a crucial role in the growth and development of plants. Phaseolus vulgaris, a significant legume crop, serves as a valuable model for studying root symbiosis. In this study, we have conducted an exploration of the AAT gene family in P. vulgaris. In this research, we identified 84 AAT genes within the P. vulgaris genome sequence and categorized them into 12 subfamilies based on their similarity and phylogenetic relationships with AATs found in Arabidopsis and rice...
March 2, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38429576/draft-genome-of-novel-cyanobacteria-sphaerothrix-gracilis-isolated-from-coastal-microplastics-reveal-insights-to-chemical-ecology-bloom-and-plastic-utilization-potential
#22
JOURNAL ARTICLE
Emily Curren, Victor S Kuwahara, Teruaki Yoshida, Sandric Chee Yew Leong
Cyanobacteria are oxygenic photosynthetic organisms which are found across many ecosystems, including freshwater and marine habitats. They are also found on natural and artificial surfaces. In this study, we cultured and characterise a novel cyanobacterium from the surfaces of foam microplastics of tropical coastal waters. We study the chemical ecology of this cyanobacterium, Sphaerothrix gracilis gen. et sp. nov., together with its potential to form harmful cyanobacterial blooms and bioremediation applications to combat plastic pollution...
March 2, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38429550/codon-usage-bias-and-phylogenetic-analysis-of-chloroplast-genome-in-36-gracilariaceae-species
#23
JOURNAL ARTICLE
Tingting Li, Zheng Ma, Tiemei Ding, Yanxin Yang, Fei Wang, Xinjing Wan, Fangyun Liang, Xi Chen, Huipeng Yao
Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of chloroplast genomes in 36 species from Graciliaceae show that GC range from 0.284 to 0.335, the average GC3 range from 0.135 to 0.243 and the value of ENC range from 35.098 to 42.327, which indicates these genomes are rich in AT and prefer to use codons ending with AT in these species. Nc plot, PR2 plot, neutrality plot analyses and correlation analysis indicate that these biases may be caused by multiple factors, such as natural selection and mutation pressure, but prolonged natural selection is the main driving force influencing codon usage preference...
March 1, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38421529/harnessing-the-potential-of-mutation-breeding-crispr-genome-editing-and-beyond-for-sustainable-agriculture
#24
REVIEW
Nelissa Maisara Nor A'azizam, Sakshi Chopra, Praveen Guleria, Vineet Kumar, Muhamad Hafiz Abd Rahim, Jamilah Syafawati Yaacob
By 2050, the global population is projected to exceed 9.5 billion, posing a formidable challenge to ensure food security worldwide. To address this pressing issue, mutation breeding in horticultural crops, utilizing physical or chemical methods, has emerged as a promising biotechnological strategy. However, the efficacy of these mutagens can be influenced by various factors, including biological and environmental variables, as well as targeted plant materials. This review highlights the global challenges related to food security and explores the potential of mutation breeding as an indispensable biotechnological tool in overcoming food insecurity...
February 29, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38418630/de-novo-transcriptome-assembly-and-global-analysis-of-differential-gene-expression-of-aphid-tolerant-wild-mustard-rorippa-indica-l-hiern-infested-by-mustard-aphid-lipaphis-erysimi-l-kaltenbach
#25
JOURNAL ARTICLE
Lekha Bandopadhyay, Debabrata Basu, Samir Ranjan Sikdar
Rapeseed-mustard, the oleiferous Brassica species are important oilseed crops cultivated all over the globe. Mustard aphid Lipaphis erysimi (L.) Kaltenbach is a major threat to the cultivation of rapeseed-mustard. Wild mustard Rorippa indica (L.) Hiern shows tolerance to mustard aphids as a nonhost and hence is an important source for the bioprospecting of potential resistance genes and defense measures to manage mustard aphids sustainably. We performed mRNA sequencing of the R. indica plant uninfested and infested by the mustard aphids, harvested at 24 hours post-infestation...
February 29, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38396290/comparative-plastome-analysis-and-taxonomic-classification-of-snow-lotus-species-saussurea-asteraceae-in-central-asia-and-southern-siberia
#26
JOURNAL ARTICLE
Nudkhuu Nyamgerel, Shukherdorj Baasanmunkh, Batlai Oyuntsetseg, Zagarjav Tsegmed, Gun-Aajav Bayarmaa, Georgy Lazkov, Elizaveta Pyak, Hee-Young Gil, Inkyu Park, Hyeok Jae Choi
Four species of Saussurea, namely S. involucrata, S. orgaadayi, S. bogedaensis, and S. dorogostaiskii, are known as the "snow lotus," which are used as traditional medicines in China (Xinjiang), Kyrgyzstan, Mongolia, and Russia (Southern Siberia). These species are threatened globally, because of illegal harvesting and climate change. Furthermore, the taxonomic classification and identification of these threatened species remain unclear owing to limited research. The misidentification of medicinal species can sometimes be harmful to health...
February 23, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38386088/fusarium-wilt-pandemic-current-understanding-and-molecular-perspectives
#27
REVIEW
Dalpat Lal, Devanshu Dev, Sarita Kumari, Saurabh Pandey, Aparna, Nilesh Sharma, Sudha Nandni, Ratnesh Kumar Jha, Ashutosh Singh
Plant diseases pose a severe threat to the food security of the global human population. One such disease is Fusarium wilt, which affects many plant species and causes up to 100% yield losses. Fusarium pathogen has high variability in its genetic constitution; therefore, it has evolved into different physiological races to infect different plant species spread across the different geographical regions of the world. The pathogen mainly affects plant roots, leading to colonizing and blocking vascular bundle cells, specifically xylem vessels...
February 22, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38383667/senp3-mediates-the-activation-of-the-wnt-%C3%AE-catenin-signaling-pathway-to-accelerate-the-growth-and-metastasis-of-oesophagal-squamous-cell-carcinoma-in-mice
#28
JOURNAL ARTICLE
Pengzeng Wang, Linan Yang, Yin Guo, Shuliang Qi, Jia Liang, Guo Tian, Ziqiang Tian
As a common malignant tumor, esophageal squamous cell carcinoma (ESCC) is occasionally seen in clinical practice. This type of disease has low incidence rate and mortality. The post-translational modification of small ubiquitin like modifiers (SUMO) can play a crucial role in regulating protein function, and can significantly impact the occurrence and development of diseases. SUMO-specific peptidase (SENP) affects cell activity by regulating the biological function of SUMO. SENP3 belongs to the SENP family, and available data indicate that many malignancies are associated with SENPs, it is currently unclear its role in ESCC...
February 22, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38381201/oscsn2-orchestrates-oryza-sativa-l-growth-and-development-through-modulation-of-the-ga-and-br-pathways
#29
JOURNAL ARTICLE
Shining Han, Weijie Yue, Anar Bao, Tongtong Jiao, Yanxi Liu, Hua Zeng, Kai Song, Ming Wu, Liquan Guo
The COP9 signalosome (CSN) is a conserved protein complex found in higher eukaryotes, consisting of eight subunits, and it plays a crucial role in regulating various processes of plant growth and development. Among these subunits, CSN2 is one of the most conserved components within the COP9 signalosome complex. Despite its prior identification in other species, its specific function in Oryza sativa L. (Rice) has remained poorly understood. In this study, we investigated the role of CSN2 in rice using gene editing CRISPR/Cas9 technology and overexpression techniques...
February 21, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38376551/dkc1-aggravates-gastric-cancer-cell-migration-and-invasion-through-up-regulating-the-expression-of-tnfaip6
#30
JOURNAL ARTICLE
Huihua Chen, Yibo Wu, Yancheng Jiang, Zixuan Chen, Tingjin Zheng
Gastric cancer (GC) is one hackneyed malignancy tumor accompanied by high death rate. DKC1 has been discovered to serve as a facilitator in several cancers. Additionally, it was discovered from one study that DKC1 displayed higher expression in GC tissues than in the normal tissues. Nevertheless, its role and regulatory mechanism in GC is yet to be illustrated. In this study, it was proved that DKC1 expression was upregulated in GC tissues through GEPIA and UALCAN databases. Moreover, we discovered that DKC1 exhibited higher expression in GC cells...
February 20, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38374301/gscit-smart-hash-table-based-mapping-equipped-genome-sequence-coverage-inspection
#31
LETTER
Samarth Godara, Shbana Begam, Ramcharan Bhattacharya, Hukam C Rawal, Anil Kumar Singh, Vijay Jangir, Sudeep Marwaha, Rajender Parsad
No abstract text is available yet for this article.
February 20, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38374244/mir-34c-5p-inhibited-fibroblast-proliferation-differentiation-and-epithelial-mesenchymal-transition-in-benign-airway-stenosis-via-mdmx-p53-pathway
#32
JOURNAL ARTICLE
Jinmei Wei, Yan Chen, Tingmei Feng, Yuihui Wei, Caizhen Yang, Changwen Zhang, Wentao Li, Guangnan Liu
Benign airway stenosis (BAS) means airway stenosis or obstruction that results from a variety of non-malignant factors, including tuberculosis, trauma, benign tumors, etc. In consideration of the currently limited research on microRNAs in BAS, this study aimed to explore the role and mechanism of miR-34c-5p in BAS. The expression of miR-34c-5p in BAS granulation tissues showed a significant down-regulation compared with the normal control group. Moreover, miR-34c-5p mimics suppressed the proliferation and differentiation of human bronchial fibroblasts (HBFs) and the epithelial-mesenchymal transition (EMT) of human bronchial epithelial cells (HBE)...
February 20, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38368303/pcdh8-is-a-novel-prognostic-biomarker-in-thyroid-cancer-and-promotes-cell-proliferation-and-viability
#33
JOURNAL ARTICLE
Ruida Yang, Nan Yang, Pan Yin, Zihan Xue, Feidi Sun, Ruihan Fan, JiaFu Liang, Xinru Lv, Shaobo Wu, Liankang Sun
Protocadherin 8 (PCDH8), a calcium-dependent transmembrane protein in the protocadherin family, regulates cell adhesion and signal transduction. While some studies have provided indirect evidence that PCDH8 has cancer-promoting properties, this association is controversial. In particular, its involvement in thyroid cancer (THCA) remains unclear. We aimed to elucidate the role of PCDH8 in THCA using bioinformatic analysis. Subsequently, the results were experimentally validated. The analysis conducted using the R programming language and online web tools explored PCDH8 expression levels, prognostic, and clinical implications, and its relationship with the tumor immune microenvironment in THCA...
February 17, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38365972/genetic-biofortification-advancing-crop-nutrition-to-tackle-hidden-hunger
#34
REVIEW
Usman Zulfiqar, Amman Khokhar, Muhammad Faisal Maqsood, Muhammad Shahbaz, Nargis Naz, Maheen Sara, Sana Maqsood, Sajila Sahar, Saddam Hussain, Muhammad Ahmad
Malnutrition, often termed "hidden hunger," represents a pervasive global issue carrying significant implications for health, development, and socioeconomic conditions. Addressing the challenge of inadequate essential nutrients, despite sufficient caloric intake, is crucial. Biofortification emerges as a promising solution by enhance the presence of vital nutrients like iron, zinc, iodine, and vitamin A in edible parts of different crop plants. Crop biofortification can be attained through either agronomic methods or genetic breeding techniques...
February 16, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38363406/unveiling-the-protective-effects-of-bmscs-anti-mir-124-3p-exosomes-on-lps-induced-endometrial-injury
#35
JOURNAL ARTICLE
Yihong Chen, Shan Zheng, Xiumei Zhao, Yi Zhang, Suchai Yu, Juanbing Wei
Researchers have reported that miR-124-3p is highly expressed in patients with chronic endometritis. However, the underlying mechanism of miR-124-3p in the development of endometritis remains unclear. This study constructed an in vitro endometrial cell injury model by treating HEECs with 2 μg/mL LPS for 48 h. Then, 1 mg/kg LPS was injected into both sides of the mouse uterus to construct an in vivo endometrial injury model. The expression of miR-124-3p in human endometrial epithelial cells (HEECs) was assessed using RT‒qPCR...
February 16, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38363405/vegfr-affects-mir-3200-3p-mediated-regulatory-t-cell-senescence-in-tumour-derived-exosomes-in-non-small-cell-lung-cancer
#36
JOURNAL ARTICLE
Kaiyuan Hui, Changhong Dong, Chenxi Hu, Jiawen Li, Dongyue Yan, Xiaodong Jiang
Numerous studies have demonstrated that regulatory T (Treg) cells play an important role in the tumour microenvironment (TME). The aim of this study was to investigate whether VEGFR2 affects the expression of miR-3200-3p in exosomes secreted by tumour cells, thereby influencing Treg senescence in the TME. The results showed that VEGFR2 expression level was the highest in Calu-1 cells, and after transfection with si-VEGFR2, the exosomes secreted from Calu-1 cells were extracted and characterised with no significant difference from the exosomes of the untransfected group, but the expression of miR-3200-3p in the exosomes of the transfected si-VEGFR2 group was elevated...
February 16, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38363382/the-novel-mir-873-5p-ywhae-pi3k-akt-axis-is-involved-in-non-small-cell-lung-cancer-progression-and-chemoresistance-by-mediating-autophagy
#37
JOURNAL ARTICLE
Zhifeng Li, Jinglei Liu, Ping Wang, Boyu Zhang, Guanghui He, Liwei Yang
Non-small cell lung cancer (NSCLC) encompasses approximately 85% of all lung cancer cases and is the foremost cancer type worldwide; it is prevalent in both sexes and known for its high fatality rate. Expanding scientific inquiry underscores the indispensability of microRNAs in NSCLC. Here, we probed the impact of miR-873-5p on NSCLC development and chemoresistance. qRT‒PCR was used to measure the miR-873-5p level in NSCLC cells with or without chemoresistance. A model of miR-873-5p overexpression was constructed...
February 16, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38358412/a-prognostic-marker-ltbp1-is-associated-with-epithelial-mesenchymal-transition-and-can-promote-the-progression-of-gastric-cancer
#38
JOURNAL ARTICLE
Xinju Jiang, Shengjie Yin, Xin Yin, Yufei Wang, Tianyi Fang, Shuo Yang, Xiulan Bian, Guoli Li, Yingwei Xue, Lei Zhang
LTBP1 is closely related to TGF-β1 function as an essential component, which was unclear in gastric cancer (GC). Harbin Medical University (HMU)-GC cohort and The Cancer Genome Atlas (TCGA) dataset were combined to form a training cohort to calculate the connection between LTBP1 mRNA expression, prognosis and clinicopathological features. The training cohort was also used to verify the biological function of LTBP1 and its relationship with immune microenvironment and chemosensitivity. In the tissue microarrays (TMAs), immunohistochemical (IHC) staining was performed to observe LTBP1 protein expression...
February 15, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38353724/linc00942-inhibits-ferroptosis-and-induces-the-immunosuppression-of-regulatory-t-cells-by-recruiting-igf2bp3-slc7a11-in-hepatocellular-carcinoma
#39
JOURNAL ARTICLE
Dong Jin, Yongfeng Hui, Di Liu, Nan Li, Junzhi Leng, Genwang Wang, Qi Wang, Zhenhui Lu
Hepatocellular carcinoma (HCC) is a common malignant tumor with a high recurrence rate and a poor prognosis. Long intergenic nonprotein coding RNA 942 (LINC00942) is reported to be related to ferroptosis and the immune response in HCC and serves as an oncogene in various cancers. This research aimed to explore the contribution of LINC00942 in HCC progression. Functional assays were used to evaluate the functional role of LINC00942 in vitro and in vivo. Mechanistic assays were conducted to assess the association of LINC00942 with insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) and solute carrier family 7 member 11 (SLC7A11) and the regulatory pattern of LINC00942 in HCC cells...
February 14, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38340226/ubiquitination-specific-protease-7-enhances-stemness-of-hepatocellular-carcinoma-by-stabilizing-basic-transcription-factor-3
#40
JOURNAL ARTICLE
Mingchao Hu, Chengchen Dai, Xieyin Sun, Yinqi Chen, Nuo Xu, Zhaoyi Lin, Shiyu Xu, Chun Cheng, Zhonghua Tan, Saiyan Bian, Wenjie Zheng
This study aims to explore the molecular regulation mechanism of ubiquitination-specific protease 7 (USP7) in facilitating the stemness properties of hepatocellular carcinoma (HCC). Gain-of-function and loss-of-function assays were conducted in SK-Hep1 and HepG2 cells transfected with USP7 overexpression/knockdown plasmids and USP7 inhibitor P22077. The proliferation, migration, invasion, and self-renewal capacity of hepatocellular carcinoma cells were detected by CCK-8, colony formation, Transwell, scratch, and tumor sphere formation, respectively...
February 10, 2024: Functional & Integrative Genomics
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