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Article: Editorial: Role of non-coding RNAs, metabolites, and extracellular vesicles in disease regulation and health.

Morenikeji, Olanrewaju B / Kutchy, Naseer A

2023 Volume 14, Page(s) 1206569

Language	English
Publishing date	2023-06-09
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1206569
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deciphering sperm functions using biological networks.

Kutchy, Naseer A / Morenikeji, Olanrewaju B / Memili, Aylin / Ugur, Muhammet R

Biotechnology & genetic engineering reviews

2023 , Page(s) 1–25

Abstract: The global human population is exponentially increasing, which requires the production of quality food through efficient reproduction as well as sustainable production of livestock. Lack of knowledge and technology for assessing semen quality and ... ...

Abstract	The global human population is exponentially increasing, which requires the production of quality food through efficient reproduction as well as sustainable production of livestock. Lack of knowledge and technology for assessing semen quality and predicting bull fertility is hindering advances in animal science and food animal production and causing millions of dollars of economic losses annually. The intent of this systemic review is to summarize methods from computational biology for analysis of gene, metabolite, and protein networks to identify potential markers that can be applied to improve livestock reproduction, with a focus on bull fertility. We provide examples of available gene, metabolic, and protein networks and computational biology methods to show how the interactions between genes, proteins, and metabolites together drive the complex process of spermatogenesis and regulate fertility in animals. We demonstrate the use of the National Center for Biotechnology Information (NCBI) and Ensembl for finding gene sequences, and then use them to create and understand gene, protein and metabolite networks for sperm associated factors to elucidate global cellular processes in sperm. This study highlights the value of mapping complex biological pathways among livestock and potential for conducting studies on promoting livestock improvement for global food security.
Language	English
Publishing date	2023-02-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	49457-4
ISSN	2046-5556 ; 0264-8725
ISSN (online)	2046-5556
ISSN	0264-8725
DOI	10.1080/02648725.2023.2168912
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Article: Evolutionary conservation of motifs within

Memili, Aylin / Kutchy, Naseer / Braimah, Olubumi A / Morenikeji, Olanrewaju B

Veterinary world

2022 Volume 15, Issue 10, Page(s) 2407–2413

Abstract: Background and aim: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. ...

Abstract	Background and aim: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Materials and methods: We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin ( Results: We observed the highest nucleotide sequence similarity of Conclusion: Resistance genes against vancomycin have highly conserved sequences between strains of
Language	English
Publishing date	2022-10-13
Publishing country	India
Document type	Journal Article
ZDB-ID	2456277-4
ISSN	2231-0916 ; 0972-8988
ISSN (online)	2231-0916
ISSN	0972-8988
DOI	10.14202/vetworld.2022.2407-2413
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Article ; Online: Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes.

Taiwo, Godstime / Morenikeji, Olanrewaju B / Idowu, Modoluwamu / Sidney, Taylor / Adekunle, Ajiboye / Cervantes, Andres Pech / Peters, Sunday / Ogunade, Ibukun M

BMC genomics

2024 Volume 25, Issue 1, Page(s) 245

Abstract: We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. ... ...

Abstract	We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.
MeSH term(s)	Animals ; Cattle ; Rumen ; Vascular Endothelial Growth Factor A ; Phenotype ; Bacteroidetes ; Eating ; RNA, Messenger
Chemical Substances	Vascular Endothelial Growth Factor A ; RNA, Messenger
Language	English
Publishing date	2024-03-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-024-10150-3
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Article: Molecular genotyping reveals mixed bovine and human trypanosomiasis in cattle from West Africa.

Morenikeji, Olanrewaju B / Metelski, Jessica L / Grytsay, Anastasia / Soulas, Jacob / Akinyemi, Mabel O / Thomas, Bolaji N

Veterinary world

2023 Volume 16, Issue 1, Page(s) 149–153

Abstract: Background and aim: Animal trypanosomiasis is a major contributor to agricultural and economic losses, especially in sub-Saharan Africa. We have shown that some animal species expressed genes that are significant players in immune response to bovine ... ...

Abstract	Background and aim: Animal trypanosomiasis is a major contributor to agricultural and economic losses, especially in sub-Saharan Africa. We have shown that some animal species expressed genes that are significant players in immune response to bovine trypanosomosis, impeding signs and symptoms of the disease. We hypothesize that such animals are contributors to disease transmission dynamics and severe outcomes. Therefore, this study aims to ascertain trypanosome species diversity in cattle and their potential role as reservoirs for the transmission of human disease. Materials and methods: We performed a molecular genotyping of trypanosome internal transcribed spacer 1 (ITS-1) and 18S ribosomal RNA genes on genomic DNA extracts from randomly sampled N'Dama cattle from slaughterhouses in Nigeria. We identified trypanosome species circulating among the animals through polymerase chain reaction and genomic sequencing. We performed multiple sequence alignments as well as conducted a phylogenetic relationship between identified species. Results: In all, 9 of 127 (7.1%) samples were positively amplified (band sizes ranging from 250 bp to 710 bp), including an isolate with two distinct bands (700 and 710 bp), indicating two trypanosome types. Sequence similarity and homology analysis identified four species, namely: Conclusion: Overall, we observed different trypanosome species in our study area, with animals on the same farm infected with multiple species, which could complicate treatment and disease control strategies. Finding human trypanosome species strengthens the argument that disease transmission dynamics are modulated by other vertebrates, further complicating control programs.
Language	English
Publishing date	2023-01-23
Publishing country	India
Document type	Journal Article
ZDB-ID	2456277-4
ISSN	2231-0916 ; 0972-8988
ISSN (online)	2231-0916
ISSN	0972-8988
DOI	10.14202/vetworld.2023.149-153
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Article: In silico analyses of CD14 molecule reveal significant evolutionary diversity, potentially associated with speciation and variable immune response in mammals.

Morenikeji, Olanrewaju B / Thomas, Bolaji N

PeerJ

2019 Volume 7, Page(s) e7325

Abstract: The cluster differentiation gene (CD14) is a family of monocyte differentiating genes that works in conjunction with lipopolysaccharide binding protein, forming a complex with TLR4 or LY96 to mediate innate immune response to pathogens. In this paper, we ...

Abstract	The cluster differentiation gene (CD14) is a family of monocyte differentiating genes that works in conjunction with lipopolysaccharide binding protein, forming a complex with TLR4 or LY96 to mediate innate immune response to pathogens. In this paper, we used different computational methods to elucidate the evolution of CD14 gene coding region in 14 mammalian species. Our analyses identified leucine-rich repeats as the only significant domain across the CD14 protein of the 14 species, presenting with frequencies ranging from one to four. Importantly, we found signal peptides located at mutational hotspots demonstrating that this gene is conserved across these species. Out of the 10 selected variants analyzed in this study, only six were predicted to possess significant deleterious effect. Our predicted protein interactome showed a significant varying protein-protein interaction with CD14 protein across the species. This may be important for drug target and therapeutic manipulation for the treatment of many diseases. We conclude that these results contribute to our understanding of the CD14 molecular evolution, which underlays varying species response to complex disease traits.
Language	English
Publishing date	2019-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.7325
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Article ; Online: The differential plasma and ruminal metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers.

Idowu, Modoluwamu / Taiwo, Godstime / Sidney, Taylor / Morenikeji, Olanrewaju B / Pech Cervantes, Andres / Estrada-Reyes, Zaira M / Wilson, Matthew / Ogunade, Ibukun M

Translational animal science

2023 Volume 7, Issue 1, Page(s) txad054

Abstract: We applied ruminal and plasma metabolomics and ruminal 16S rRNA gene sequencing to determine the metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers. A group of 108 ... ...

Abstract	We applied ruminal and plasma metabolomics and ruminal 16S rRNA gene sequencing to determine the metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers. A group of 108 crossbred growing beef steers (average BW = 282.87 ± 30 kg) were fed a forage-based diet for a period of 56 d in a confinement dry lot equipped with GrowSafe intake nodes to determine their residual body weight gain (RADG) phenotype. After RADG identification, blood and rumen fluid samples were collected from beef steers with the highest RADG (most efficient;
Language	English
Publishing date	2023-05-23
Publishing country	England
Document type	Journal Article
ISSN	2573-2102
ISSN (online)	2573-2102
DOI	10.1093/tas/txad054
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Article ; Online: The functions of long non-coding RNA (lncRNA)-MALAT-1 in the pathogenesis of renal cell carcinoma.

Anbiyaee, Omid / Moalemnia, Arash / Ghaedrahmati, Farhoodeh / Shooshtari, Maryam Khombi / Khoshnam, Seyed Esmaeil / Kempisty, Bartosz / Halili, Shahla Ahmadi / Farzaneh, Maryam / Morenikeji, Olanrewaju B

BMC nephrology

2023 Volume 24, Issue 1, Page(s) 380

Abstract: Renal cell carcinoma (RCC), a prevalent form of renal malignancy, is distinguished by its proclivity for robust tumor proliferation and metastatic dissemination. Long non-coding RNAs (lncRNAs) have emerged as pivotal modulators of gene expression, ... ...

Abstract	Renal cell carcinoma (RCC), a prevalent form of renal malignancy, is distinguished by its proclivity for robust tumor proliferation and metastatic dissemination. Long non-coding RNAs (lncRNAs) have emerged as pivotal modulators of gene expression, exerting substantial influence over diverse biological processes, encompassing the intricate landscape of cancer development. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1), an exemplar among lncRNAs, has been discovered to assume functional responsibilities within the context of RCC. The conspicuous expression of MALAT-1 in RCC cells has been closely linked to the advancement of tumors and an unfavorable prognosis. Experimental evidence has demonstrated the pronounced ability of MALAT-1 to stimulate RCC cell proliferation, migration, and invasion, thereby underscoring its active participation in facilitating the metastatic cascade. Furthermore, MALAT-1 has been implicated in orchestrating angiogenesis, an indispensable process for tumor expansion and metastatic dissemination, through its regulatory influence on pro-angiogenic factor expression. MALAT-1 has also been linked to the evasion of immune surveillance in RCC, as it can regulate the expression of immune checkpoint molecules and modulate the tumor microenvironment. Hence, the potential utility of MALAT-1 as a diagnostic and prognostic biomarker in RCC emerges, warranting further investigation and validation of its clinical significance. This comprehensive review provides an overview of the diverse functional roles exhibited by MALAT-1 in RCC.
MeSH term(s)	Humans ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/pathology ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Cell Proliferation/genetics ; Prognosis ; Cell Line, Tumor ; Tumor Microenvironment/genetics
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2023-12-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2041348-8
ISSN	1471-2369 ; 1471-2369
ISSN (online)	1471-2369
ISSN	1471-2369
DOI	10.1186/s12882-023-03438-1
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Article ; Online: SNP Diversity in

Morenikeji, Olanrewaju B / Capria, Anna L / Ojurongbe, Olusola / Thomas, Bolaji N

Genes

2020 Volume 11, Issue 1

Abstract: Immune response to infections has been shown to be mediated by genetic diversity in pattern recognition receptors, leading to disease tolerance or susceptibility. We elucidated naturally occurring variations within the ... ...

Abstract	Immune response to infections has been shown to be mediated by genetic diversity in pattern recognition receptors, leading to disease tolerance or susceptibility. We elucidated naturally occurring variations within the bovine
MeSH term(s)	Adaptation, Biological/genetics ; Animals ; Breeding ; Cattle/genetics ; Cattle Diseases/genetics ; Disease Susceptibility ; Female ; Genetic Predisposition to Disease/genetics ; Genome/genetics ; Genomics/methods ; Genotype ; Lipopolysaccharide Receptors/genetics ; Male ; Nigeria ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Promoter Regions, Genetic/genetics ; Tick Infestations/genetics ; Trypanosoma/genetics ; Trypanosoma/pathogenicity
Chemical Substances	Lipopolysaccharide Receptors
Language	English
Publishing date	2020-01-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11010112
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Article: Urine metabolome reveals candidate biomarkers for divergent residual feed intake in beef cattle

Taiwo , Godstime / Idowu , Modoluwamu / Sidney , Taylor / Morenikeji , Olanrewaju B. / Ogunade , Ibukun M.

URINE. 2022, v. 4

2022

Abstract: We analyzed the amine/phenol-metabolome of urine samples to identify urinary metabolic biomarkers associated with residual feed intake in beef cattle. A group of 56 crossbred growing beef steers (average BW = 261 ± 18.5 kg) were adapted to a high- ... ...

Abstract	We analyzed the amine/phenol-metabolome of urine samples to identify urinary metabolic biomarkers associated with residual feed intake in beef cattle. A group of 56 crossbred growing beef steers (average BW = 261 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake classification (RFI). After RFI determination, weekly urine samples were collected three times from beef steers with negative RFI (most efficient (HFE); RFI = - 1.93 kg/d, n = 8) and positive RFI (least efficient (LFE); RFI = + 2.01 kg/d, n = 8). Urine samples collected were then composited for each steer. Metabolome analysis was conducted using a chemical isotope labeling/liquid chromatography–mass spectrometry, specifically for the analysis of metabolites containing amine/phenol-chemical groups, which are metabolites associated with metabolisms of amino acids. A total number of 557 amine/phenol-containing metabolites were detected and identified. Biomarker analysis of the urinary amine/phenol-metabolome identified N-acetyl-l-tyrosine, O-methyl-l-threonine, uridine, and threoninyl-hydroxyproline as candidate biomarkers of RFI (false discovery rate ≤0.05; Area Under the Curve ≥0.85). In conclusion, the results of our study revealed that alteration in urine amine/phenol-metabolome is associated with selection for low or high RFI in beef steers and urine is a potential source of metabolite biomarkers associated with RFI in beef cattle.
Keywords	beef ; beef cattle ; biomarkers ; feed intake ; isotopes ; liquid chromatography ; mass spectrometry ; metabolites ; metabolome ; metabolomics ; steers ; uridine ; urine
Language	English
Size	p. 7-13.
Publishing place	Elsevier BV
Document type	Article
ISSN	2590-2806
DOI	10.1016/j.urine.2022.04.002
Database	NAL-Catalogue (AGRICOLA)

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