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Article ; Online: Diversified Mammalian Visuasl Adaptations to Bright- or Dim-Light Environments.

Gai, Yulin / Tian, Ran / Liu, Fangnan / Mu, Yuan / Shan, Lei / Irwin, David M / Liu, Yang / Xu, Shixia / Yang, Guang

2023 Volume 40, Issue 4

Abstract: ... by three visual pigments, two (SWS1 and M/LWS) of them for color vision and rhodopsin (RH1) for dim-light ...

Abstract	Photic niche shifts of mammals are associated with changing visual capabilities, primarily mediated by three visual pigments, two (SWS1 and M/LWS) of them for color vision and rhodopsin (RH1) for dim-light vision. To further elucidate molecular mechanisms of mammalian visual adaptations to different light environments, a systematic study incorporating evolutionary analyses across diverse groups and in vitro assays have been carried out. Here, we collected gene sequences for the three opsins from 220 species covering all major mammalian clades. After screening for cone opsin gene losses, we estimated selective pressures on each of the three genes and compared the levels of selection experienced by species living in bright- and dim-light environments. SWS1 pigment is shown to experience accelerated evolution in species living in bright-light environments as has RH1 in aquatic cetaceans, indicating potential shifts for ecological adaptations. To further elucidate the functional mechanisms for these two pigments, we then carried out site-directed mutagenesis in representative taxa. For SWS1, violet and ultraviolet sensitivities in the pika and mouse are mainly affected by substitutions at the critical sites 86 and 93, which have strong epistatic interaction. For RH1, the phenotypic difference between the sperm whale and bovine sequences is largely contributed by a substitution at site 195, which could be critical for dim-light sensation for deep-diving species. Different evolutionary patterns for the visual pigments have been identified in mammals, which correspond to photic niches, although additional phenotypic assays are still required to fully explain the functional mechanisms.
MeSH term(s)	Animals ; Cattle ; Mice ; Phylogeny ; Evolution, Molecular ; Mammals ; Opsins/genetics ; Rhodopsin/genetics
Chemical Substances	Opsins ; Rhodopsin (9009-81-8)
Language	English
Publishing date	2023-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msad063
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Article ; Online: Hybrid origin of a primate, the gray snub-nosed monkey.

Wu, Hong / Wang, Zefu / Zhang, Yuxing / Frantz, Laurent / Roos, Christian / Irwin, David M / Zhang, Chenglin / Liu, Xuefeng / Wu, Dongdong / Huang, Song / Gu, Tongtong / Liu, Jianquan / Yu, Li

Science (New York, N.Y.)

2023 Volume 380, Issue 6648, Page(s) eabl4997

Abstract: Hybridization is widely recognized as promoting both species and phenotypic diversity. However, its role in mammalian evolution is rarely examined. We report historical hybridization among a group of snub-nosed monkeys ( ...

Abstract	Hybridization is widely recognized as promoting both species and phenotypic diversity. However, its role in mammalian evolution is rarely examined. We report historical hybridization among a group of snub-nosed monkeys (
MeSH term(s)	Animals ; China ; Genome ; Genomics ; Presbytini/anatomy & histology ; Presbytini/genetics ; Hybridization, Genetic ; Biological Evolution ; Chimera ; Reproductive Isolation ; Biological Variation, Population ; Pigmentation/genetics
Language	English
Publishing date	2023-06-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abl4997
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Article ; Online: Night shift schedule alters endogenous regulation of circulating cytokines.

Liu, Peter Y / Irwin, Michael R / Krueger, James M / Gaddameedhi, Shobhan / Van Dongen, Hans P A

Neurobiology of sleep and circadian rhythms

2021 Volume 10, Page(s) 100063

Abstract: Night shift work is a risk factor for viral infection, suggesting that night shift schedules compromise host defense mechanisms. Prior studies have investigated changes in the temporal profiles of circulating cytokines important for priming and ... ...

Abstract	Night shift work is a risk factor for viral infection, suggesting that night shift schedules compromise host defense mechanisms. Prior studies have investigated changes in the temporal profiles of circulating cytokines important for priming and restraining the immune response to infectious challenges from night shift work, but not by way of a 24-h constant routine of continuous wakefulness devoid of behavioral or environmental influences. Hence the true
Language	English
Publishing date	2021-03-05
Publishing country	United States
Document type	Journal Article
ISSN	2451-9944
ISSN (online)	2451-9944
DOI	10.1016/j.nbscr.2021.100063
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Article ; Online: Accelerated evolution of dim-light vision-related arrestin in deep-diving amniotes

Xin Guo / Yimeng Cui / David M. Irwin / Yang Liu

Frontiers in Ecology and Evolution, Vol

2022 Volume 10

Abstract: Arrestins are key molecules involved in the signaling of light-sensation initiated by visual pigments in retinal photoreceptor cells. Vertebrate photoreceptor cells have two types of arrestins, rod arrestin, which is encoded by SAG and is expressed in ... ...

Abstract	Arrestins are key molecules involved in the signaling of light-sensation initiated by visual pigments in retinal photoreceptor cells. Vertebrate photoreceptor cells have two types of arrestins, rod arrestin, which is encoded by SAG and is expressed in both rods and cones, and cone arrestin, encoded by ARR3 in cones. The arrestins can bind to visual pigments, and thus regulate either dim-light vision via interactions with rhodopsin or bright-light vision together with cone visual pigments. After adapting to terrestrial life, several amniote lineages independently went back to the sea and evolved deep-diving habits. Interestingly, the rhodopsins in these species exhibit specialized phenotypes responding to rapidly changing dim-light environments. However, little is known about whether their rod arrestin also experienced adaptive evolution associated with rhodopsin. Here, we collected SAG coding sequences from >250 amniote species, and examined changes in selective pressure experienced by the sequences from deep-diving taxa. Divergent patterns of evolution of SAG were observed in the penguin, pinniped and cetacean clades, suggesting possible co-adaptation with rhodopsin. After verifying pseudogenes, the same analyses were performed for cone arrestin (ARR3) in deep-diving species and only sequences from cetacean species, and not pinnipeds or penguins, have experienced changed selection pressure compared to other species. Taken together, this evidence for changes in selective pressures acting upon arrestin genes strengthens the suggestion that rapid dim-light adaptation for deep-diving amniotes require SAG, but not ARR3.
Keywords	vertebrates ; SAG ; ARR3 ; scotopic vision ; molecular evolution ; visual adaptation ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Subject code	580
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Evolution and expression patterns of the neo-sex chromosomes of the crested ibis.

Xu, Lulu / Ren, Yandong / Wu, Jiahong / Cui, Tingting / Dong, Rong / Huang, Chen / Feng, Zhe / Zhang, Tianmin / Yang, Peng / Yuan, Jiaqing / Xu, Xiao / Liu, Jiao / Wang, Jinhong / Chen, Wu / Mi, Da / Irwin, David M / Yan, Yaping / Xu, Luohao / Yu, Xiaoping /

Li, Gang

Nature communications

2024 Volume 15, Issue 1, Page(s) 1670

Abstract: Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels ... ...

Abstract	Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels of inter-sexual conflict, yet their sex chromosome evolution remains poorly understood. Here, by we analyse of a chromosome-level assembly of a female crested ibis (Nipponia nippon), a typical core waterbird. We identify neo-sex chromosomes resulting from fusion of microchromosomes with ancient sex chromosomes. These fusion events likely occurred following the divergence of Threskiornithidae and Ardeidae. The neo-W chromosome of the crested ibis exhibits the characteristics of slow degradation, which is reflected in its retention of abundant gametologous genes. Neo-W chromosome genes display an apparent ovary-biased gene expression, which is largely driven by genes that are retained on the crested ibis W chromosome but lost in other bird species. These results provide new insights into the evolutionary history and expression patterns for the sex chromosomes of bird species.
MeSH term(s)	Animals ; Female ; Birds/genetics ; Sex Chromosomes/genetics
Language	English
Publishing date	2024-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46052-x
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Article ; Online: Succinylation proteomic analysis identified differentially expressed succinylation sites affecting porcine muscle fiber type function.

Tan, Xiaofan / Liu, Kaiqing / He, Yu / Yan, Zhiwei / Chen, Jing / Zhao, Ruixue / Sui, Xin / Zhang, Junpeng / Irwin, David M / Zhang, Shuyi / Li, Bojiang

Food chemistry: X

2023 Volume 20, Page(s) 100962

Abstract: Muscle fiber type is a major factor in pork meat quality, however, the role of post-translational protein modifications, especially succinylation, in the regulation of muscle fiber type is not fully understood. Here we performed protein succinylation ... ...

Abstract	Muscle fiber type is a major factor in pork meat quality, however, the role of post-translational protein modifications, especially succinylation, in the regulation of muscle fiber type is not fully understood. Here we performed protein succinylation profiles of fast-type biceps femoris (BF) and slow-type soleus (SOL) muscles. A total of 4,221 succinylation sites were identified from these samples, of which 294 sites were differentially expressed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these succinylated proteins were mainly involved in glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Succinylation modification of the CRAT and RAB10 proteins was verified by co-immunoprecipitation. Protein-protein interaction (PPI) network analysis unveiled the interactions of these succinylated proteins that regulate pig myofiber type conversion. This investigation offers fresh perspectives into the molecular roles of protein succinylation in the regulation of pig myofiber type transformation and meat quality.
Language	English
Publishing date	2023-10-27
Publishing country	Netherlands
Document type	Journal Article
ISSN	2590-1575
ISSN (online)	2590-1575
DOI	10.1016/j.fochx.2023.100962
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Article ; Online: Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla.

Lang, Datian / Wang, Xiaoping / Liu, Chunbing / Geng, Weihang / Irwin, David M / Chen, Shanyuan / Li, Chunqing / Yu, Li / Xiao, Heng

Science China. Life sciences

2022 Volume 66, Issue 5, Page(s) 1170–1182

Abstract: RNase9 plays a reproductive function and has been recognized as an important member of the ribonuclease (RNase) A superfamily, a gene family that is widely used as a model for molecular evolutionary studies. Here, we identified 178 RNase9 genes from 95 ... ...

Abstract	RNase9 plays a reproductive function and has been recognized as an important member of the ribonuclease (RNase) A superfamily, a gene family that is widely used as a model for molecular evolutionary studies. Here, we identified 178 RNase9 genes from 95 Cetartiodactyla species that represent all four lineages and 21 families of this clade. Unexpectedly, RNase9 experienced an evolutionary scenario of "birth and death" in Ruminantia, and expression analyses showed that duplicated RNase9A and RNase9B genes are expressed in reproductive tissues (epididymis, vas deferens or prostate). This expression pattern combined with the estimate that these genes duplicated during the middle Eocene, a time when Ruminantia become a successful lineage, suggests that the RNase9 gene duplication might have been advantageous for promoting sperm motility and male fertility as an adaptation to climate seasonality changes of this period. In contrast, all RNase9 genes were lost in the Cetacean lineage, which might be associated with their high levels of prostatic lesions and lower reproductive rates as adaptations to a fully aquatic environment and a balance to the demands of ocean resources. This study reveals a complex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla, providing new insights into the evolution of the RNaseA superfamily and molecular mechanisms for organismal adaptations to the environment.
MeSH term(s)	Animals ; Artiodactyla/genetics ; Ribonucleases/genetics ; Phylogeny ; Amino Acid Sequence ; Molecular Sequence Data ; Sequence Alignment ; Genome ; Male
Chemical Substances	Ribonucleases (EC 3.1.-)
Language	English
Publishing date	2022-11-25
Publishing country	China
Document type	Journal Article
ZDB-ID	2546732-3
ISSN	1869-1889 ; 1674-7305
ISSN (online)	1869-1889
ISSN	1674-7305
DOI	10.1007/s11427-022-2195-x
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Article ; Online: A review of the impact of energy balance on triple-negative breast cancer.

Akingbesote, Ngozi D / Owusu, Dennis / Liu, Ryan / Cartmel, Brenda / Ferrucci, Leah M / Zupa, Michelle / Lustberg, Maryam B / Sanft, Tara / Blenman, Kim R M / Irwin, Melinda L / Perry, Rachel J

Journal of the National Cancer Institute. Monographs

2023 Volume 2023, Issue 61, Page(s) 104–124

Abstract: Cancer cells cannot proliferate without sufficient energy to generate biomass for rapid cell division, as well as to fuel their functions at baseline. For this reason, many recent observational and interventional studies have focused on increasing energy ...

Abstract	Cancer cells cannot proliferate without sufficient energy to generate biomass for rapid cell division, as well as to fuel their functions at baseline. For this reason, many recent observational and interventional studies have focused on increasing energy expenditure and/or reducing energy intake during and after cancer treatment. The impact of variance in diet composition and in exercise on cancer outcomes has been detailed extensively elsewhere and is not the primary focus of this review. Instead, in this translational, narrative review we examine studies of how energy balance impacts anticancer immune activation and outcomes in triple-negative breast cancer (TNBC). We discuss preclinical, clinical observational, and the few clinical interventional studies on energy balance in TNBC. We advocate for the implementation of clinical studies to examine how optimizing energy balance-through changes in diet and/or exercise-may optimize the response to immunotherapy in people with TNBC. It is our conviction that by taking a holistic approach that includes energy balance as a key factor to be considered during and after treatment, cancer care may be optimized, and the detrimental effects of cancer treatment and recovery on overall health may be minimized.
MeSH term(s)	Humans ; Triple Negative Breast Neoplasms/therapy ; Triple Negative Breast Neoplasms/drug therapy ; Immunotherapy ; Energy Metabolism
Language	English
Publishing date	2023-05-04
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1745-6614
ISSN (online)	1745-6614
DOI	10.1093/jncimonographs/lgad011
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Article ; Online: Adaptive Evolution of the Fox Coronavirus Based on Genome-Wide Sequence Analysis.

Feng, Chunyu / Liu, Yuting / Lyu, Guangqi / Shang, Songyang / Xia, Hongyue / Zhang, Junpeng / Irwin, David M / Wang, Zhe / Zhang, Shuyi

BioMed research international

2022 Volume 2022, Page(s) 9627961

Abstract: ... among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes ... respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively ...

Abstract	Purpose: To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV. Methods: Anal swab samples were collected from 35 foxes to detect the presence of CoV and obtain the virus sequence. Phylogenetic analysis was conducted using MrBayes. The possibility of recombination within these sequences was assessed using GARD. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Data Monkey platforms. Results: Of the 35 samples, two were positive, and complete genome sequences for the viruses were obtained. Phylogenetic analysis, using Bayesian methods, of these sequences, together with other CoV sequences, revealed that the fox CoV sequences clustered with canine coronavirus (CCoV) sequences, with sequences from other carnivores more distantly related. In contrast to the feline, ferret and mink CoV sequences that clustered into species-specific clades, the fox CoV fell within the CCoV clade. Minimal evidence for recombination was found among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes, respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively. Conclusion: The complete genome sequence of fox CoV has been obtained for the first time. The results suggest that the genome sequence of fox CoV may have experienced adaptive evolution in the genes replication, entry, and virulence. The number of sites in each gene that experienced negative selection is far greater than the number that underwent positive selection, suggesting that most of the sequence is highly conserved and important for viral survive. However, positive selection at a few sites likely aided these viruses to adapt to new environments.
MeSH term(s)	Animals ; Bayes Theorem ; Cats ; Coronavirus/genetics ; Coronavirus Infections/genetics ; Coronavirus, Canine/genetics ; Dogs ; Ferrets/genetics ; Genome, Viral/genetics ; Phylogeny ; Sequence Analysis, DNA
Language	English
Publishing date	2022-04-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2022/9627961
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Article ; Online: Discovery and identification of a novel canine coronavirus causing a diarrhea outbreak in Vulpes.

Liu, Yuting / Deng, Yao / Niu, Sheng / Zhu, Na / Song, Jingdong / Zhang, Xiaoshuang / Su, Weiting / Nie, Wenhui / Lu, Roujian / Irwin, David M / Gao, George Fu / Wang, Wenling / Wang, Qihui / Tan, Wenjie / Zhang, Shuyi

Science bulletin

2023 Volume 68, Issue 21, Page(s) 2598–2606

Abstract: Cross-species transmission of viruses from wildlife animal reservoirs, such as bats, poses a threat to human and domestic animal health. Previous studies have shown that domestic animals have important roles as intermediate hosts, enabling the ... ...

Abstract	Cross-species transmission of viruses from wildlife animal reservoirs, such as bats, poses a threat to human and domestic animal health. Previous studies have shown that domestic animals have important roles as intermediate hosts, enabling the transmission of genetically diverse coronaviruses from natural hosts to humans. Here, we report the identification and characterization of a novel canine coronavirus (VuCCoV), which caused an epidemic of acute diarrhea in Vulpes (foxes) in Shenyang, China. The epidemic started on November 8, 2019, and caused more than 39,600 deaths by January 1, 2022. Full-length viral genomic sequences were obtained from 15 foxes with diarrhea at the early stage of this outbreak. The VuCCoV genome shared more than 90% nucleotide identity with canine coronavirus (CCoV) for three of the four structural genes, with the S gene showing a larger amount of divergence. In addition, 67% (10/15) of the VuCCoV genomes contained an open reading frame (ORF3) gene, which was previously only detected in CCoV-I genomes. Notably, VuCCoV had only two to three amino acid differences at the partial RNA-dependent RNA polymerase (RdRp) level to bat CoV, suggesting a close genetic relationship. Therefore, these novel VuCCoV genomes represent a previously unsampled lineage of CCoVs. We also show that the VuCCoV spike protein binds to canine and fox aminopeptidase N (APN), which may allow this protein to serve as an entry receptor. In addition, cell lines were identified that are sensitive to VuCCoV using a pseudovirus system. These data highlight the importance of identifying the diversity and distribution of coronaviruses in domestic animals, which could mitigate future outbreaks that could threaten livestock, public health, and economic growth.
MeSH term(s)	Animals ; Dogs ; Humans ; Foxes ; Coronavirus, Canine/genetics ; Animals, Wild ; SARS-CoV-2/genetics ; Animals, Domestic ; Disease Outbreaks/veterinary ; Diarrhea/epidemiology
Language	English
Publishing date	2023-09-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2816140-3
ISSN	2095-9281 ; 2095-9273
ISSN (online)	2095-9281
ISSN	2095-9273
DOI	10.1016/j.scib.2023.09.011
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