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1. Molecular toxicity and defense mechanisms induced by silver nanoparticles in Drosophila melanogaster

Author:
Zhidi Wang; Liying Zhang; Xing Wang
Source:
Journal of environmental sciences (China) 2023 v.125 pp. 616-629
ISSN:
1001-0742
Subject:
sequence analysis,   etc   ; DNA damage; Drosophila melanogaster; cell viability; dose response; eclosion; fat body; fecundity; genes; hemocytes; metallothionein; nanosilver; pupation; toxicity; China;     Show all 15 Subjects
Abstract:
... The widely use of silver nanoparticles (AgNPs) as antimicrobial agents gives rise to potential environmental risks. AgNPs exposure have been reported to cause toxicity in animals. Nevertheless, the known mechanisms of AgNPs toxicity are still limited. In this study, we systematically investigated the toxicity of AgNPs exposure using Drosophila melanogaster. We show here that AgNPs significantly de ...
DOI:
10.1016/j.jes.2021.12.027

2. Prediction of intestinal stem cell regulatory genes from Drosophila gut damage model created using multiple inducers: Differential gene expression-based protein-protein interaction network analysis

Author:
Seung Hun Lee; Dooseon Hwang; Tae-Won Goo; Eun-Young Yun
Source:
Developmental and comparative immunology 2023 v.138 pp. 104539
ISSN:
0145-305X
Subject:
sequence analysis,   etc   ; Drosophila melanogaster; gene expression regulation; genes; homeostasis; innate immunity; intestines; models; oral administration; prediction; protein-protein interactions; stem cells;     Show all 12 Subjects
Abstract:
... Intestinal tissue functions in innate immunity to prevent the entry of harmful substances, and to maintain homeostasis through the constant proliferation of intestinal stem cells (ISC). To understand the mechanisms which regulate ISC in response to gut damage, we identified 81 differentially expressed genes (DEGs) through RNA-seq analysis after oral administration of three intestinal-damaging subs ...
DOI:
10.1016/j.dci.2022.104539

3. Morphological, physiological, biochemical, and transcriptome studies reveal the importance of transporters and stress signaling pathways during salinity stress in Prunus

Author:
Acharya Biswa R.; Sandhu Devinder; Dueñas Christian; Dueñas Marco; Pudussery Manju V.; Kaundal Amita; Ferreira Jorge F.S.; Suarez Donald L.; Skaggs Todd H.
Source:
Scientific reports 2022 v.12 no.1 pp. 1274
ISSN:
2045-2322
Subject:
sequence analysis,   etc   ; Prunus; almonds; chlorides; economic feasibility; electrical conductivity; gene expression regulation; genotype; ion channels; proline; salinity; salt stress; salt tolerance; transcriptome;     Show all 14 Subjects
Abstract:
... The almond crop has high economic importance on a global scale, but its sensitivity to salinity stress can cause severe yield losses. Salt-tolerant rootstocks are vital for crop economic feasibility under saline conditions. Two commercial rootstocks submitted to salinity, and evaluated through different parameters, had contrasting results with the survival rates of 90.6% for 'Rootpac 40' (tolerant ...
Handle:
10113/7709627
DOI:
10.1038/s41598-022-05202-1

4. Omic analysis of anthocyanin synthesis in wine grape leaves under low-temperature

Author:
Qianqian Pang; Wenbin Yu; Ehsan Sadeghnezhad; Xueqin Chen; Pingjing Hong; Tariq Pervaiz; Yanhua Ren; Yanping Zhang; Tianyu Dong; Haifeng Jia; Jinggui Fang
Source:
Scientia horticulturae 2023 v.307 pp. 111483
ISSN:
0304-4238
Subject:
sequence analysis,   etc   ; anthocyanins; autumn; carbohydrate metabolism; cold; energy metabolism; heat; hydrogen peroxide; lipid metabolism; metabolomics; protein kinases; salt stress; temperature; transcriptomics; wine grapes;     Show all 15 Subjects
Abstract:
... Anthocyanins can be induced by environmental factors such as low- temperature, and play an important role in adapting to abiotic stress. In this study, the leaves of 'Cabernet Gernischt' grapes with different colors under natural low-temperature in autumn were collected and grouped into Green (Gre), Light-red (L-Red), Red (Red), and Dark-red (D-Red). Results showed that the total anthocyanin conte ...
DOI:
10.1016/j.scienta.2022.111483

5. RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment.

Author:
Olawande C. Olagoke; Ana L.A. Segatto; Blessing A. Afolabi; Daniel Ardisson-Araujo; Michael Aschner; João B.T. Rocha
Source:
Comparative biochemistry and physiology 2023 v.263 pp. 110785
ISSN:
1096-4959
Subject:
sequence analysis,   etc   ; Nauphoeta cinerea; biomedical research; brain; glucose; hyperglycemia; insects; metabolism; non-specific serine/threonine protein kinase; peptides; ribosomal proteins; streptozotocin; transcription (genetics);     Show all 13 Subjects
Abstract:
... The use of insects to model molecular events that characterize degenerative conditions was originally met with scepticism. However, the discovery of insect insulin-like peptides in the 1970's and the demonstration of evolutionary conservation of insulin-related signalling from insects to mammals have highlighted the importance and reduced cost of insect models in biomedical research. Here, we expa ...
DOI:
10.1016/j.cbpb.2022.110785

6. Structure elucidation and in vitro rat intestinal fermentation properties of a novel sulfated glucogalactan from Porphyra haitanensis

Author:
Peilin Chen; Lu Liu; Zirun Cheng; Yi Zhang; Baodong Zheng; Xiaoke Hu; Hongliang Zeng
Source:
Food science and human wellness 2023 v.12 no.2 pp. 596-606
ISSN:
2213-4530
Subject:
sequence analysis,   etc   ; Desulfovibrio; Lactobacillus; Porphyra; algae; biochemical pathways; butyric acid; cholesterol metabolism; fermentation; food science; functional foods; humans; intestines; inulin; microorganisms; nucleotide sequences; prediction; rats;     Show all 18 Subjects
Abstract:
... This study was to investigate the structure and rat fecal microbial fermentation properties of a polysaccharide fraction (PHP2) isolated from the red marine alga Porphyra haitanensis. PHP2 was characterized as a sulfated glucogalactan, with a hypothetical backbone structure of →4)Gα(1→6)G4Sβ(1→4)Glc(1→ and a side chain of Man(1→6)Glc. PHP2 had an irregular spherical chain conformation. The 16S rRN ...
DOI:
10.1016/j.fshw.2022.07.062

7. Genome-resolved metagenomic analysis reveals different functional potentials of multiple Candidatus Brocadia species in a full-scale swine wastewater treatment system

Author:
Yabing Meng; Depeng Wang; Zhong Yu; Qingyun Yan; Zhili He; Fangang Meng
Source:
Frontiers of environmental science & engineering 2023 v.17 no.1 pp. 2
ISSN:
2095-2201
Subject:
sequence analysis,   etc   ; acetate kinase; acetates; ammonia; ammonium; anaerobic ammonium oxidation; carbon; cyanase; dominant species; ecological differentiation; hydroxylamine; metagenomics; nitrite reductase; nitrites; organic nitrogen; phylogeny; swine; urease; wastewater treatment;     Show all 19 Subjects
Abstract:
... The increasing application of anammox processes suggests their enormous potential for nitrogen removal in wastewater treatment facilities. However, the functional potentials and ecological differentiation of cooccurring anammox species in complex ecosystems have not been well elucidated. Herein, by utilizing functional reconstruction and comparative genome analysis, we deciphered the cooccurring m ...
DOI:
10.1007/s11783-023-1602-7

8. Polysaccharide extract from Rosa laevigata fruit attenuates inflammatory obesity by targeting redox balance and gut interface in high-fat diet-fed rats

Author:
Xuejiao Zhang; Chenzhong Jin; Han Liu; Yihong Hu; Yunyun Zhou; Weiguo Wu; Si Qin
Source:
Food science and human wellness 2023 v.12 no.2 pp. 442-453
ISSN:
2213-4530
Subject:
sequence analysis,   etc   ; Lachnospiraceae; Prevotella; Rosa laevigata; body weight changes; chemoprevention; digestive system; food science; fruits; functional foods; humans; intestinal microorganisms; liver function; metagenomics; multiomics; obesity; phenotype; polysaccharides; Asia;     Show all 19 Subjects
Abstract:
... Low-molecular-weight polysaccharides (RLPs) extracted from Rosa laevigata fruits showed multiple biofunctions in Asia. This study aimed to investigate its anti-inflammatory obesity effect in high-fat diet-fed rats and further elucidated the underlying molecular mechanism by multi-omics methods. The results showed that RLPs administration had significantly restored immune organ indexes and reduced ...
DOI:
10.1016/j.fshw.2022.07.046

9. DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk

Author:
Cynthia A. Kalita; Alexander Gusev
Source:
Genome biology 2022 v.23 no.1 pp. 152
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; alleles; risk;     Show all 3 Subjects
Abstract:
... Here, we propose DeCAF (DEconvoluted cell type Allele specific Function), a new method to identify cell-fraction (cf) QTLs in tumors by leveraging both allelic and total expression information. Applying DeCAF to RNA-seq data from TCGA, we identify 3664 genes with cfQTLs (at 10% FDR) in 14 cell types, a 5.63× increase in discovery over conventional interaction-eQTL mapping. cfQTLs replicated in ext ...
DOI:
10.1186/s13059-022-02708-9

10. TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

Author:
Dongshunyi Li; Jeremy J. Velazquez; Jun Ding; Joshua Hislop; Mo R. Ebrahimkhani; Ziv Bar-Joseph
Source:
Genome biology 2022 v.23 no.1 pp. 73
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; data collection; genome;     Show all 3 Subjects
Abstract:
... A major advantage of single cell RNA-sequencing (scRNA-Seq) data is the ability to reconstruct continuous ordering and trajectories for cells. Here we present TraSig, a computational method for improving the inference of cell-cell interactions in scRNA-Seq studies that utilizes the dynamic information to identify significant ligand-receptor pairs with similar trajectories, which in turn are used t ...
DOI:
10.1186/s13059-022-02629-7

11. An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development

Author:
Chun-Kai Huang; Wen-Dar Lin; Shu-Hsing Wu
Source:
Genome biology 2022 v.23 no.1 pp. 50
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; Arabidopsis; introns; photosynthesis;     Show all 4 Subjects
Abstract:
... BACKGROUND: Light switches on the photomorphogenic development of young plant seedlings, allowing young seedlings to acquire photosynthetic capacities and gain survival fitness. Light regulates gene expression at all levels of the central dogma, including alternative splicing (AS) during the photomorphogenic development. However, accurate determination of full-length (FL) splicing variants has bee ...
DOI:
10.1186/s13059-022-02620-2

12. Identification of lncRNAs involved in maternal‐to‐zygotic transition of in vitro‐produced porcine embryos by single‐cell RNA‐seq

Author:
Cai‐Xia Yang; Hao Liang; Zi‐Wei Wu; Li‐Jun Huo; Zhi‐Qiang Du
Source:
Reproduction in domestic animals 2022 v.57 no.1 pp. 111-122
ISSN:
0936-6768
Subject:
sequence analysis,   etc   ; blastomeres; embryogenesis; oocytes; swine;     Show all 5 Subjects
Abstract:
... Long non‐coding RNAs (lncRNAs) function through multiple tiers of molecular circuits and are vital to gamete maturation and early embryo development. However, in pig early embryos, identification and expression dynamics of lncRNAs remain less studied. Here, we systematically analysed the expression dynamics of lncRNAs based on our previously published single‐cell RNA‐seq data from pig mature oocyt ...
DOI:
10.1111/rda.14034

13. SEPHS1 is dispensable for pluripotency maintenance but indispensable for cardiac differentiation in mouse embryonic stem cells

Author:
Lu Qiao; So Hee Dho; Ji Young Kim; Lark Kyun Kim
Source:
Biochemical and biophysical research communications 2022 v.590 pp. 125-131
ISSN:
0006-291X
Subject:
sequence analysis,   etc   ; blastocyst; embryogenesis; mice; research;     Show all 5 Subjects
Abstract:
... Embryonic stem cells (ESCs) are derived from the inner cell mass of developing blastocysts, which have self-renewal ability and have the potential to develop or reconstitute into all embryonic lineages. Selenophosphate synthetase 1 (SEPHS1) is an essential protein in mouse early embryo development. However, the role of SEPHS1 in mouse ESCs remains to be elucidated. In this study, we generated Seph ...
DOI:
10.1016/j.bbrc.2021.12.091

14. Unveiling the evolution routes of TEM-type extended-spectrum β-lactamases

Author:
Qipeng Cheng; Yan Chu Cheung; Edward Wai Chi Chan; Kwok Yin Wong; Sheng Chen
Source:
International journal of antimicrobial agents 2022 v.59 no.1 pp. 106498
ISSN:
0924-8579
Subject:
sequence analysis,   etc   ; cephalosporins; evolution; mutagenesis; penicillins;     Show all 5 Subjects
Abstract:
... The TEM-1 β-lactamase can only cleave penicillin and the first-generation cephalosporins but it has evolved to become active against second-, third- and fourth-generation drugs. Through sequence analysis of natural TEM variants and those created by mutagenesis experiments, we described two distinct evolution routes of TEM-1 that has generated over 220 enzyme variants. One began with the Gly²³⁸Ser ...
DOI:
10.1016/j.ijantimicag.2021.106498

15. dsCellNet: A new computational tool to infer cell–cell communication networks in the developing and aging brain

Author:
Zhihong Song; Ting Wang; Yan Wu; Ming Fan; Haitao Wu
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 4072-4081
ISSN:
2001-0370
Subject:
sequence analysis,   etc   ; biotechnology; brain; cell communication;     Show all 4 Subjects
Abstract:
... Cell-cell interactions mediated by ligand-receptor complexes are critical to coordinating organismal development and functions. Majority of studies focus on the key time point, the mediator cell types or the critical genes during organismal development or diseases. However, most existing methods are specifically designed for stationary paired samples, there hasn’t been a repository to deal with in ...
DOI:
10.1016/j.csbj.2022.07.047

16. Mapping single-nucleotide m6A by m6A-REF-seq

Author:
Hong-Xuan Chen; Zhang Zhang; Dong-Zhao Ma; Li-Qian Chen; Guan-Zheng Luo
Source:
Methods 2022 v.203 pp. 392-398
ISSN:
1046-2023
Subject:
sequence analysis,   etc   ; DNA libraries; RNA; antibodies;     Show all 4 Subjects
Abstract:
... The past few years have witnessed rapid progress in the field of RNA modifications. As the most prevailing modification on eukaryotic mRNA, m⁶A is characterized to play a vital role in various cellular activities. However, limitations of the detection method impede functional studies of m⁶A. Here we introduce m⁶A-REF-seq, a powerful and straightforward method to identify m⁶A at single-nucleotide r ...
DOI:
10.1016/j.ymeth.2021.06.013

17. A novel dynamic simulation approach for Gas-Heat-Electric coupled system

Author:
Aobo Guan; Suyang Zhou; Wei Gu; Zhong Liu; Hengmen Liu
Source:
Applied energy 2022 v.315 pp. 118999
ISSN:
0306-2619
Subject:
sequence analysis,   etc   ; energy; equipment; heat transfer;     Show all 4 Subjects
Abstract:
... Dynamic simulation of Gas-Heat-Electric Coupled System (GHECS) can accurately describe the operation state of networks and equipment of the system, which can support the analysis of the stability and safety of GHECS. However, differences among simulation time-step of subsystems, computational complexities and lengthy simulation time make it difficult to precisely simulate the coupled system. To so ...
DOI:
10.1016/j.apenergy.2022.118999

18. Characterization of a Read-through Fusion Transcript, BCL2L2-PABPN1, Involved in Porcine Adipogenesis

Author:
Jiyuan Zhu; Zewei Yang; Wanjun Hao; Jiaxin Li; Liang Wang; Jiqiao Xia; Dongjie Zhang; Di Liu; Xiuqin Yang
Source:
Genes 2022 v.13 no.3 pp. -
ISSN:
2073-4425
Subject:
sequence analysis,   etc   ; adipogenesis; humans; microRNA; obesity; swine;     Show all 6 Subjects
Abstract:
... cis-Splicing of adjacent genes (cis-SAGe) has been involved in multiple physiological and pathological processes in humans. However, to the best of our knowledge, there is no report of cis-SAGe in adipogenic regulation. In this study, a cis-SAGe product, BCL2L2–PABPN1 (BP), was characterized in fat tissue of pigs with RT-PCR and RACE method. BP is an in-frame fusion product composed of 333 aa and ...
DOI:
10.3390/genes13030445

19. Comparison of confound adjustment methods in the construction of gene co-expression networks

Author:
Alanna C. Cote; Hannah E. Young; Laura M. Huckins
Source:
Genome biology 2022 v.23 no.1 pp. 44
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; data collection; gene expression; genes;     Show all 4 Subjects
Abstract:
... Adjustment for confounding sources of expression variation is an important preprocessing step in large gene expression studies, but the effect of confound adjustment on co-expression network analysis has not been well-characterized. Here, we demonstrate that the choice of confound adjustment method can have a considerable effect on the architecture of the resulting co-expression network. We compar ...
DOI:
10.1186/s13059-022-02606-0

20. Computational solutions for spatial transcriptomics

Author:
Iivari Kleino; Paulina Frolovaitė; Tomi Suomi; Laura L. Elo
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 4870-4884
ISSN:
2001-0370
Subject:
sequence analysis,   etc   ; biotechnology; gene expression; transcriptome; transcriptomics;     Show all 5 Subjects
Abstract:
... Transcriptome level expression data connected to the spatial organization of the cells and molecules would allow a comprehensive understanding of how gene expression is connected to the structure and function in the biological systems. The spatial transcriptomics platforms may soon provide such information. However, the current platforms still lack spatial resolution, capture only a fraction of th ...
DOI:
10.1016/j.csbj.2022.08.043