Genome-Wide Identification of Cyclin Dependent Kinase (CDK) Family Genes Influencing Adipocyte Differentiation in Cattle

Abstract Background: The cyclin dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. A variety of studies have shown that many CDK genes also played a critical role during adipogenic differentiation. However, there is a lack of systematic research on the CDK gene family regulating bovine adipocyte differentiation.Therefore, this study aimed to characterize CDK family genes in bovine and study the expression pattern during adipocyte differentiation.Results: We performed a genome-wide analysis and identified 25, 25, 22, 21, 22, 24, 22 and 24 CDK genes in Bos taurus, Bos indicus, Hybrid-Bos taurus, Hybrid bos indicus, Bos grunniens, Bos mutus, Bison and Bubalus bubalis, respectively. All the CDK genes classified into 8 subfamilies through phylogenetic analysis. Chromosome localization displayed 25 bovine CDK genes distributed on 16 chromosomes. Collinearity analysis revealed that CDK family genes of Bos taurus were extensively homologous with Bos indicus, Hybrid-Bos taurus, Hybrid bos indicus, Bos grunniens and Bubalus bubalis. Tanscriptome analysis showed that several of the CDK family genes had relatively high expression levels in preadipocytes compared with differentiated adipocytes, which is generally similar to qPCR, indicating that it could have a significant function in the growth of the emerging lipid droplets.Conclusion: We performed a comprehensive analysis for the CDK family genes including identification, phylogenetic classification, structural characterization, chromosomal distribution, collinearity analysis and expression profile analysis by tanscriptome sequencing and qPCR. The results provide a basis for further study to determine the roles of CDK family genes in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽

10.1186/s12864-021-07653-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cuili Pan ◽

Zhaoxiong Lei ◽

Shuzhe Wang ◽

Xingping Wang ◽

Dawei Wei ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Adipocyte Differentiation ◽

Bos Taurus ◽

Adipogenic Differentiation ◽

Critical Role ◽

Bos Indicus ◽

Specific Expression ◽

Genome Wide ◽

A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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Comparative analyses of copy number variations between Bos taurus and Bos indicus

BMC Genomics ◽

10.1186/s12864-020-07097-6 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yan Hu ◽

Han Xia ◽

Mingxun Li ◽

Chang Xu ◽

Xiaowei Ye ◽

...

Keyword(s):

Copy Number ◽

Muscle Development ◽

Reference Genome ◽

Bos Taurus ◽

Bos Indicus ◽

Copy Number Variations ◽

Genome Wide ◽

A Genome ◽

Detection Strategies ◽

Specific Sequences

Abstract Background Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. Results Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. Conclusions This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.

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A Genome-Wide Screen in Saccharomyces cerevisiae Reveals a Critical Role for Oxidative Phosphorylation in Cellular Tolerance to Lithium Hexafluorophosphate

Cells ◽

10.3390/cells10040888 ◽

2021 ◽

Vol 10 (4) ◽

pp. 888

Author(s):

Xuejiao Jin ◽

Jie Zhang ◽

Tingting An ◽

Huihui Zhao ◽

Wenhao Fu ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Oxidative Phosphorylation ◽

Cellular Response ◽

Critical Role ◽

Lithium Ion ◽

Deletion Mutants ◽

High Concentration ◽

Genome Wide ◽

A Genome ◽

Lithium Hexafluorophosphate

Lithium hexafluorophosphate (LiPF6) is one of the leading electrolytes in lithium-ion batteries, and its usage has increased tremendously in the past few years. Little is known, however, about its potential environmental and biological impacts. In order to improve our understanding of the cytotoxicity of LiPF6 and the specific cellular response mechanisms to it, we performed a genome-wide screen using a yeast (Saccharomyces cerevisiae) deletion mutant collection and identified 75 gene deletion mutants that showed LiPF6 sensitivity. Among these, genes associated with mitochondria showed the most enrichment. We also found that LiPF6 is more toxic to yeast than lithium chloride (LiCl) or sodium hexafluorophosphate (NaPF6). Physiological analysis showed that a high concentration of LiPF6 caused mitochondrial damage, reactive oxygen species (ROS) accumulation, and ATP content changes. Compared with the results of previous genome-wide screening for LiCl-sensitive mutants, we found that oxidative phosphorylation-related mutants were specifically hypersensitive to LiPF6. In these deletion mutants, LiPF6 treatment resulted in higher ROS production and reduced ATP levels, suggesting that oxidative phosphorylation-related genes were important for counteracting LiPF6-induced toxicity. Taken together, our results identified genes specifically involved in LiPF6-modulated toxicity, and demonstrated that oxidative stress and ATP imbalance maybe the driving factors in governing LiPF6-induced toxicity.

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The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission

10.1101/2020.08.25.266775 ◽

2020 ◽

Cited By ~ 8

Author(s):

Yunkai Zhu ◽

Fei Feng ◽

Gaowei Hu ◽

Yuyan Wang ◽

Yin Yu ◽

...

Keyword(s):

Critical Role ◽

Surface Expression ◽

Spike Protein ◽

Hamster Model ◽

Entry Pathway ◽

Genome Wide ◽

A Genome ◽

Model Animal ◽

Public Health Challenges

SUMMARYThe global spread of SARS-CoV-2 is posing major public health challenges. One unique feature of SARS-CoV-2 spike protein is the insertion of multi-basic residues at the S1/S2 subunit cleavage site, the function of which remains uncertain. We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. This idea was supported by the identification of a suite of endosomal entry factors specific to Sdel virus by a genome-wide CRISPR-Cas9 screen. A panel of host factors regulating the surface expression of ACE2 was identified for both viruses. Using a hamster model, animal-to-animal transmission with the Sdel virus was almost completely abrogated, unlike with Sfull. These findings highlight the critical role of the S1/S2 boundary of the SARS-CoV-2 spike protein in modulating virus entry and transmission.

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273 OVUM PICKUP AT DIFFERENT TIMES OF A SYNCHRONIZED FOLLICULAR WAVE DID NOT AFFECT IVP IN BOS INDICUS, BOS TAURUS, OR BUBALUS BUBALIS

Reproduction Fertility and Development ◽

10.1071/rdv22n1ab273 ◽

2010 ◽

Vol 22 (1) ◽

pp. 293 ◽

Cited By ~ 5

Author(s):

L. U. Gimenes ◽

M. L. Ferraz ◽

A. Araujo ◽

P. Fantinato Neto ◽

M. R. Chiarati ◽

...

Keyword(s):

Mixed Model ◽

Bos Taurus ◽

Bos Indicus ◽

Cumulus Cell ◽

Bubalus Bubalis ◽

Genetic Group ◽

Cleavage Rate ◽

Follicular Wave ◽

Counting Data ◽

Initial Hypothesis

One important factor in the success of ovum pickup (OPU)/IVP in Bos taurus is the follicular status at OPU concerning the dominance period (Hendriksen et al. 2000 Theriogenology 53, 11-20). The hypothesis of the present study is that OPU performed after follicle deviation, when follicles show a mild level of atresia, improves competence for IVP in Nelore (NE), Holstein (HO), and buffaloes (BU). Objectives were to determine effects of OPU done at different times of synchronized follicular wave (1, 3, or 5 d after expected emergence) and of genetic group (NE, HO, and BU) on IVP. A total of 27 heifers (9 of each genetic group) were maintained in contemporary nutritional and environmental conditions during experiment, in a cross-over design, performed in 6 replicates. Recovered oocytes with at least one cumulus cell layer were matured in TCM-199 supplemented with 10% of FCS plus 50 μM of cysteamin and 0.3 mM of cystine, at 38.5°C with 5% CO2 in air for 24 h. IVF was done with 2 × 106 spermatozoa per mL of NE (for bovine oocytes) or BU semen (for BU oocytes), for 20 h at the same incubator conditions of IVM. After IVF, presumptive zygotes were denuded and cultured in SOF under the same previous atmosphere conditions. Medium was changed 3 d after IVF when cleavage rate (CR) was assessed. Blastocyst (BR) and hatching rates (HR) were evaluated 7 and 9 days after IVF, respectively. About 50% of hatched blastocysts were fixed until nuclei counting. Data were analyzed by ANOVA using the Proc Mixed model. No effects of interaction or time of synchronization were observed in any of the variables. Concerning genetic group, NE had better results than HO and BU (mean ± SEM / heifer / replicate), respectively, for visualized follicles (41.0a ± 2.1, 22.1b ± 1.3, 18.8b ± 0.9), total oocytes (37.1a ± 2.5, 15.4b ± 1.2, 14.8b ± 1.0), oocytes at IVM (30.8a ± 2.4, 10.7b ± 1.0, 7.9b ± 0.7), oocytes at IVC (18.7a ± 0.8, 8.0b ± 0.5, 7.5b ± 0.4), cleaved embryos (15.4a ± 0.7, 4.6b ± 0.4, 4.4b ± 0.3),CR(81.8a, 59.1b, 62.3b), blastocysts on Day 7 (5.1a ± 0.6, 1.0b ± 0.2, 0.6b ± 0.1), BR (25.8a, 13.6b, 9.1b), and hatched blastocysts on Day 9 (2.6a ± 0.4, 0.3b ± 0.1, 0.3b ± 0.1). Recovery rate and HR were greater for NE (89.4 and 50.6%, respectively) than for HO (73.3 and 23.2%), but neither differed from BU (82.8 and 31.9%). Also, the percentage of viable was greater for NE (83.0) than for HO (66.9) and BU (53.1). No effects were observed for nuclei counting (NE = 176.6 ± 5.3, HO = 168.9 ± 13.7 and BU = 206.1 ± 23.1). Results demonstrate that Nelore had a better efficiency for IVP than Holstein and buffaloes. OPU performed at different times of synchronized follicular wave did not influence IVP, conversely to the initial hypothesis of this study. FAPESP (06/59550-6, 07/04782-2), Tortuga Cia Zootecnica®, Santa Adele and São Caetano Farms, LMMD, PCAPS, HOVET (Dr. Ubiraem Schalch), VRA, VNP (Prof. Dr. Francisco de Palma Rennó).

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Clínica e hematologia de Bos indicus, Bos taurus e Bubalus bubalis inoculados com oocistos de Toxoplasma gondii (Apicomplexa: Toxoplasmatinae)

Ciência Rural ◽

10.1590/s0103-84782001000400010 ◽

2001 ◽

Vol 31 (4) ◽

pp. 621-626 ◽

Cited By ~ 6

Author(s):

Francisco Carlos Rodrigues de Oliveira ◽

Alvimar José da Costa ◽

Gustavo Adolfo Sabatini

Keyword(s):

Toxoplasma Gondii ◽

Bos Taurus ◽

Bos Indicus ◽

Bubalus Bubalis

Três animais de cada espécie (Bos indicus, Bos taurus e Bubalus bubalis) foram inoculados, via oral, com 2,0 x 10(5) oocistos de Toxoplasma gondii. Seis outros animais, dois de cada espécie, foram mantidos como testemunhas. As alterações clínicas surgidas a partir do 3º dia após inoculação (DAI) foram: hipertermia, taquicardia, taquipnéia, anorexia, prostração, corrimento nasal e lacrimejamento. Estes sinais foram mais evidentes nos taurinos, espécie que apresentou, ainda, diarréia, fotofobia e conjuntivite. Foi possível isolar T. gondii da corrente sangüínea em todas as espécies. Nos taurinos, a partir do 5º DAI até o final do experimento, o parasito foi isolado de todas as amostras de sangue colhidas semanalmente, com exceção do 14º, 35º e 63º DAI. Os bubalinos apresentaram parasitemia no 7º, 14º, 35º e 70º DAI e os zebuínos apenas no 7º e 28º DAI, correspondendo aos picos de temperatura, em todas as espécies, sendo mais evidente em taurinos. Os parâmetros clínico-laboratoriais demonstraram que os taurinos foram mais sensíveis ao T. gondii do que os zebuínos e estes não diferiram significativamente dos bubalinos, que tiveram aparente normalidade clínico-laboratorial.

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