Zoological Research最新文献

{"title":"Obituary: Prof. Yun Zhang (1963-2023) - A scientist focused on toxins and their underlying mechanisms to decipher human diseases.","authors":"Wenhui Lee, Ren Lai","doi":"10.24272/j.issn.2095-8137.2023.415","DOIUrl":"10.24272/j.issn.2095-8137.2023.415","url":null,"abstract":"","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"45 1","pages":"230-232"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of letters to the editor and publications in 2023.","authors":"Xiu-Ping Zhang, Xue-Long Jiang, Yong-Gang Yao","doi":"10.24272/j.issn.2095-8137.2023.378","DOIUrl":"10.24272/j.issn.2095-8137.2023.378","url":null,"abstract":"","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"45 1","pages":"136-137"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138812756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs.","authors":"Cui-Hong Tong, Zhi-Peng Huo, Lu Diao, Dan-Yu Xiao, Ruo-Nan Zhao, Zhen-Ling Zeng, Wen-Guang Xiong","doi":"10.24272/j.issn.2095-8137.2023.012","DOIUrl":"10.24272/j.issn.2095-8137.2023.012","url":null,"abstract":"<p><p>Monitoring the prevalence of antimicrobial resistance genes (ARGs) is vital for addressing the global crisis of antibiotic-resistant bacterial infections. Despite its importance, the characterization of ARGs and microbiome structures, as well as the identification of indicators for routine ARG monitoring in pig farms, are still lacking, particularly concerning variations in antimicrobial exposure in different countries or regions. Here, metagenomics and random forest machine learning were used to elucidate the ARG profiles, microbiome structures, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs ( <i>P</i><0.05). <i>ANT(6)-Ib</i>, <i>APH(3')-IIIa</i>, and <i>tet</i>(40) were identified as shared core ARGs between the two pig populations. Furthermore, the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions. <i>Lactobacillus</i> and <i>Prevotella</i> were identified as the dominant genera in the core microbiomes of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100% and 98.7%, respectively. Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy ( <i>r</i>=0.72-0.88). <i>Escherichia flexneri</i> in both Chinese and European pig populations carried between 21 and 37 ARGs. The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"189-200"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic foraging strategy adaptation to heterogeneous environments contributes to social aggregation in snub-nosed monkeys.","authors":"Lan Zhao, Sheng-Nan Ji, Xiao-Bing Du, Jia-Hui Liu, Bo-Lun Zhang, Pei-Hua Li, Yi-Jun Yang, Bao-Guo Li, Yan-Qing Guo, Xiao-Guang Qi","doi":"10.24272/j.issn.2095-8137.2023.047","DOIUrl":"10.24272/j.issn.2095-8137.2023.047","url":null,"abstract":"<p><p>The dynamics of animal social structures are heavily influenced by environmental patterns of competition and cooperation. In folivorous colobine primates, prevailing theories suggest that larger group sizes should be favored in rainforests with a year-round abundance of food, thereby reducing feeding competition. Yet, paradoxically, larger groups are frequently found in high-altitude or high-latitude montane ecosystems characterized by a seasonal scarcity of leaves. This contradiction is posited to arise from cooperative benefits in heterogeneous environments. To investigate this hypothesis, we carried out a six-year field study on two neighboring groups of golden snub-nosed monkey ( <i>Rhinopithecus roxellana</i>), a species representing the northernmost distribution of colobine primates. Results showed that the groups adjusted their movement and habitat selection in response to fluctuating climates and spatiotemporal variability of resources, indicative of a dynamic foraging strategy. Notably, during the cold, resource-scarce conditions in winter, the large group occupied food-rich habitats but did not exhibit significantly longer daily travel distances than the smaller neighboring group. Subsequently, we compiled an eco-behavioral dataset of 52 colobine species to explore their evolutionary trajectories. Analysis of this dataset suggested that the increase in group size may have evolved via home range expansion in response to the cold and heterogeneous climates found at higher altitudes or latitudes. Hence, we developed a multi-benefits framework to interpret the formation of larger groups by integrating environmental heterogeneity. In cold and diverse environments, even smaller groups require larger home ranges to meet their dynamic survival needs. The spatiotemporal distribution of high-quality resources within these expanded home ranges facilitates more frequent interactions between groups, thereby encouraging social aggregation into larger groups. This process enhances the benefits of collaborative actions and reproductive opportunities, while simultaneously optimizing travel costs through a dynamic foraging strategy.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"39-54"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini.","authors":"Yu-Ran Li, Zheng-Wei Wang, Richard T Corlett, Wen-Bin Yu","doi":"10.24272/j.issn.2095-8137.2023.169","DOIUrl":"10.24272/j.issn.2095-8137.2023.169","url":null,"abstract":"<p><p>The insect mitogenome is typically a compact circular molecule with highly conserved gene contents. Nonetheless, mitogenome structural variations have been reported in specific taxa, and gene rearrangements, usually the tRNAs, occur in different lineages. Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences, comparative analyses of mitogenomes have been given increasing attention. However, most studies use a very few species to represent the whole genus, tribe, family, or even order, overlooking potential variations at lower taxonomic levels, which might lead to some incorrect inferences. To provide new insights into mitogenome organizations and their implications for phylogenetic inference, this study conducted comparative analyses for mitogenomes of three social bee tribes (Meliponini, Bombini, and Apini) based on the phylogenetic framework with denser taxonomic sampling at the species and population levels. Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type, while those of Meliponini show diverse variations in mitogenome sizes and organizations. Large inverted repeats (IRs) cause significant gene rearrangements of protein coding genes (PCGs) and rRNAs in Indo-Malay/Australian stingless bee species. Molecular evolution analyses showed that the lineage with IRs have lower <i>d</i> _N/ <i>d</i> _S ratios for PCGs than lineages without IRs, indicating potential effects of IRs on the evolution of mitochondrial genes. The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution. Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini, tRNA rearrangements are common across all three tribes of social bees, and are significant even at the species level, indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements, and their implications for phylogenetic inference.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"45 1","pages":"160-175"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139418745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancient DNA unravels species identification from Laosicheng site, Hunan Province, China, and provides insights into maternal genetic history of East Asian leopards.","authors":"Ming Zhang, Cai-Hui Wang, Yu-Xin Zheng, Qi-Gao Jiangzuo, Ye-Mao Hou, Peng Cao, Qing-Yan Dai, Ruo-Wei Yang, Feng Liu, Xiao-Tian Feng, Lin-Heng Mo, Qiao-Mei Fu","doi":"10.24272/j.issn.2095-8137.2023.292","DOIUrl":"10.24272/j.issn.2095-8137.2023.292","url":null,"abstract":"","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"45 1","pages":"226-229"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiplex gene editing reduces oxalate production in primary hyperoxaluria type 1.","authors":"Rui Zheng, De-Xin Zhang, Yan-Jiao Shao, Xiao-Liang Fang, Lei Yang, Ya-Nan Huo, Da-Li Li, Hong-Quan Geng","doi":"10.24272/j.issn.2095-8137.2022.495","DOIUrl":"10.24272/j.issn.2095-8137.2022.495","url":null,"abstract":"<p><p>Targeting key enzymes that generate oxalate precursors or substrates is an alternative strategy to eliminate primary hyperoxaluria type I (PH1), the most common and life-threatening type of primary hyperoxaluria. The compact Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) from the <i>Prevotella</i> and <i>Francisella 1</i> (Cpf1) protein simplifies multiplex gene editing and allows for all-in-one adeno-associated virus (AAV) delivery. We hypothesized that the multiplex capabilities of the Cpf1 system could help minimize oxalate formation in PH1 by simultaneously targeting the hepatic hydroxyacid oxidase 1 ( <i>Hao1</i>) and lactate dehydrogenase A ( <i>Ldha</i>) genes. Study cohorts included treated PH1 rats ( <i>Agxt</i> ^<i>Q84X</i> rats injected with AAV-AsCpf1 at 7 days of age), phosphate-buffered saline (PBS)-injected PH1 rats, untreated PH1 rats, and age-matched wild-type (WT) rats. The most efficient and specific CRISPR RNA (crRNA) pairs targeting the rat <i>Hao1</i> and <i>Ldha</i> genes were initially screened <i>ex vivo</i>. <i>In vivo</i> experiments demonstrated efficient genome editing of the <i>Hao1</i> and <i>Ldha</i> genes, primarily resulting in small deletions. This resulted in decreased transcription and translational expression of <i>Hao1</i> and <i>Ldha</i>. Treatment significantly reduced urine oxalate levels, reduced kidney damage, and alleviated nephrocalcinosis in rats with PH1. No liver toxicity, ex-liver genome editing, or obvious off-target effects were detected. We demonstrated the AAV-AsCpf1 system can target multiple genes and rescue the pathogenic phenotype in PH1, serving as a proof-of-concept for the development of multiplex genome editing-based gene therapy.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"44 6","pages":"993-1002"},"PeriodicalIF":4.0,"publicationDate":"2023-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/22/5c/zr-44-5-993.PMC10559083.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41154541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic revision of genus <i>Rohanixalus</i> (Anura: Rhacophoridae) in China with description of one new species.","authors":"Xiao-Long Liu, Jun-Kai Huang, Bryan L Stuart, Ren-Da Ai, Justin M Bernstein, Chatmongkon Suwannapoom, Siriwadee Chomdej, Jing Che, Zhi-Yong Yuan","doi":"10.24272/j.issn.2095-8137.2023.179","DOIUrl":"10.24272/j.issn.2095-8137.2023.179","url":null,"abstract":"","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"44 6","pages":"1146-1151"},"PeriodicalIF":4.0,"publicationDate":"2023-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107592998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of long-term <i>ex vivo</i> expansion of tree shrew spermatogonial stem cells.","authors":"Cong Li, Rui Bi, Lin Wang, Yu-Hua Ma, Yong-Gang Yao, Ping Zheng","doi":"10.24272/j.issn.2095-8137.2023.317","DOIUrl":"10.24272/j.issn.2095-8137.2023.317","url":null,"abstract":"<p><p>Tree shrews ( <i>Tupaia belangeri chinensis</i>) share a close relationship to primates and have been widely used in biomedical research. We previously established a spermatogonial stem cell (SSC)-based gene editing platform to generate transgenic tree shrews. However, the influences of long-term expansion on tree shrew SSC spermatogenesis potential remain unclear. Here, we examined the <i>in vivo</i> spermatogenesis potential of tree shrew SSCs cultured across different passages. We found that SSCs lost spermatogenesis ability after long-term expansion (>50 passages), as indicated by the failure to colonize the seminiferous epithelium and generate donor spermatogonia (SPG)-derived spermatocytes or spermatids marking spermatogenesis. RNA sequencing (RNA-seq) analysis of undifferentiated SPGs across different passages revealed significant gene expression changes after sub-culturing primary SPG lines for more than 40 passages on feeder layers. Specifically, DNA damage response and repair genes (e.g., <i>MRE11</i>, <i>SMC3</i>, <i>BLM</i>, and <i>GEN1</i>) were down-regulated, whereas genes associated with mitochondrial function (e.g., <i>NDUFA9</i>, <i>NDUFA8</i>, <i>NDUFA13</i>, and <i>NDUFB8</i>) were up-regulated after expansion. The DNA damage accumulation and mitochondrial dysfunction were experimentally validated in high-passage cells. Supplementation with nicotinamide adenine dinucleotide (NAD ⁺) precursor nicotinamide riboside (NR) exhibited beneficial effects by reducing DNA damage accumulation and mitochondrial dysfunction in SPG elicited by long-term culture. Our research presents a comprehensive analysis of the genetic and physiological attributes critical for the sustained expansion of undifferentiated SSCs in tree shrews and proposes an effective strategy for extended <i>in vitro</i> maintenance.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"44 6","pages":"1080-1094"},"PeriodicalIF":4.0,"publicationDate":"2023-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials.","authors":"Gao-Ming Liu, Qi Pan, Juan Du, Ping-Fen Zhu, Wei-Qiang Liu, Zi-Hao Li, Ling Wang, Chun-Yan Hu, Yi-Chen Dai, Xiao-Xiao Zhang, Zhan Zhang, Yang Yu, Meng Li, Peng-Cheng Wang, Xiao Wang, Ming Li, Xu-Ming Zhou","doi":"10.24272/j.issn.2095-8137.2023.189","DOIUrl":"10.24272/j.issn.2095-8137.2023.189","url":null,"abstract":"<p><p>The timing of mammalian diversification in relation to the Cretaceous-Paleogene (KPg) mass extinction continues to be a subject of substantial debate. Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples. In the present study, we improved an existing dataset from the landmark study of Meredith et al. (2011) by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers. Using these two datasets, we then constructed phylogenies for extant mammalian families, providing improved resolution of many conflicting relationships. Moreover, the timetrees generated, which were calibrated using appropriate molecular clock models and multiple fossil records, indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period. Additionally, intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary, supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification. Thus, our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"44 6","pages":"1064-1079"},"PeriodicalIF":4.0,"publicationDate":"2023-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}