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Affordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping-by-sequencing and more recently generated by low-coverage whole-genome-sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21x coverage) and low-coverage whole-genome-sequencing data from 8,760 heterogeneous stock rats (mean 0.27x coverage), we can impute 7.32 million bi-allelic single-nucleotide polymorphisms with a concordance rate >99.76% compared to high-coverage (mean 33.26x coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping-by-sequencing or low-coverage whole-genome-sequencing for accurate genotyping, and demonstrate techniques that may also be useful for other genetic studies in non-human subjects.

Genome-wide association studies typically evaluate the autosomes and sometimes the X Chromosome, but seldom consider the Y or mitochondrial (MT) Chromosomes. We genotyped the Y and MT Chromosomes in heterogeneous stock (HS) rats (Rattus norvegicus), an outbred population created from 8 inbred strains. We identified 8 distinct Y and 4 distinct MT Chromosomes among the 8 founders. However, only 2 types of each nonrecombinant chromosome were observed in our modern HS rat population (generations 81-97). Despite the relatively large sample size, there were virtually no significant associations for behavioral, physiological, metabolome, or microbiome traits after correcting for multiple comparisons. However, both Y and MT Chromosomes were strongly associated with the expression of a few genes located on those chromosomes, which provided a positive control. Our results suggest that within modern HS rats there are no Y and MT Chromosomes differences that strongly influence behavioral or physiological traits. These results do not address other ancestral Y and MT Chromosomes that do not appear in modern HS rats, nor do they address effects that may exist in other rat populations, or in other species.

Delay discounting refers to the behavioral tendency to devalue rewards as a function of their delay in receipt. Heightened delay discounting has been associated with substance use disorders and multiple co-occurring psychopathologies. Human and animal genetic studies have established that delay discounting is heritable, but only a few associated genes have been identified. We aimed to identify novel genetic loci associated with delay discounting through a genome-wide association study (GWAS) using Heterogeneous Stock (HS) rats, a genetically diverse outbred population derived from eight inbred founder strains. We assessed delay discounting in 650 male and female HS rats using an adjusting amount procedure in which rats chose between smaller immediate sucrose rewards or a larger reward at various delays. Preference switch points were calculated and both exponential and hyperbolic functions were fitted to these indifference points. Area under the curve (AUC) and the discounting parameter k of both functions were used as delay discounting measures. GWAS for AUC, exponential k, and one indifference point identified significant loci on chromosomes 20 and 14. The gene Slc35f1, which encodes a member of the solute carrier family, was the sole gene within the chromosome 20 locus. That locus also contained an eQTL for Slc35f1, suggesting that heritable differences in the expression might be responsible for the association with behavior. Adgrl3, which encodes a latrophilin subfamily G-protein coupled receptor, was the sole gene within the chromosome 14 locus. These findings implicate novel genes in delay discounting and highlight the need for further exploration.

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Affordable sequencing and genotyping methods are essential for large-scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, nonhuman model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping by sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping by sequencing and more recently generated by low-coverage whole-genome sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21× coverage) and low-coverage whole-genome sequencing data from 8,760 heterogeneous stock rats (mean 0.27× coverage), we can impute 7.32 million biallelic single-nucleotide polymorphisms with a concordance rate > 99.76% compared to high-coverage (mean 33.26× coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping by sequencing or low-coverage whole-genome sequencing for accurate genotyping and demonstrate techniques that may also be useful for other genetic studies in nonhuman subjects. [ABSTRACT FROM AUTHOR]

Background and Aims: Tick‐borne encephalitis (TBE) is a serious and acute central nervous system infection caused by the tick‐borne encephalitis virus (TBEV). In recent years, TBE has emerged as a growing public health threat, with cases reported across Europe, the Russian Far East, Japan and China. This study aims to assess the prevalence of TBEV infection and examine behaviours associated with an increased risk of infection among individuals who visited the Heilongjiang Red Cross Sengong General Hospital due to tick bites from 2020 to 2023. Methods and Results: We collected blood samples and administered survey questionnaires from tick‐bitten people. A total of 457 samples were screened using Nested PCR, and the detected TBEV prevalence rate was 29.54% (135/457). The symptoms of redness and swelling at the site of tick bite (42.57%), fever (28.71%) and headache (10.89%) were identified in the TBEV‐positive individuals when they visited the hospital by the physician. Phylogenetic analysis of the partial E gene of TBEV revealed that the predominant strains in the region are highly virulent Far Eastern subtype. However, they do not cluster with the three established evolutionary clades of the Far Eastern type. Questionnaires data analysis identified age and first tick bite as important factors associated with TBEV infection. Conclusions: This study provides basic information on the epidemiology of TBEV in Heilongjiang Province in recent years and identifies that the most related risk factor of infecting TBEV is tick exposure. Further research is needed to develop effective prevention and control measures. [ABSTRACT FROM AUTHOR]

Background: Escherichia coli is an important intestinal flora, of which pathogenic E. coli is capable of causing many enteric and extra-intestinal diseases. Antibiotics are essential for the treatment of bacterial infections caused by pathogenic E. coli; however, with the widespread use of antibiotics, drug resistance in E. coli has become particularly serious, posing a global threat to human, animal, and environmental health. While the drug resistance and pathogenicity of E. coli carried by tigers and leopards in captivity have been studied intensively in recent years, there is an extreme lack of information on E. coli in these top predators in the wild environment. Methods: Whole genome sequencing data of 32 E. coli strains collected from the feces of wild Amur tiger (Panthera tigris altaica, n = 24) and North China leopard (Panthera pardus japonensis, n = 8) were analyzed in this article. The multi-locus sequence types, serotypes, virulence and resistance genotypes, plasmid replicon types, and core genomic SNPs phylogeny of these isolates were studied. Additionally, antimicrobial susceptibility testing (AST) was performed on these E. coli isolates. Results: Among the E. coli isolates studied, 18 different sequence types were identified, with ST939 (21.9%), ST10 (15.6%), and ST3246 (9.4%) being the most prevalent. A total of 111 virulence genes were detected, averaging about 54 virulence genes per sample. They contribute to invasion, adherence, immune evasion, efflux pump, toxin, motility, stress adaption, and other virulence-related functions of E. coli. Sixty-eight AMR genes and point mutations were identified. Among the detected resistance genes, those belonging to the efflux pump family were the most abundant. Thirty-two E. coli isolates showed the highest rate of resistance to tetracycline (14/32; 43.8%), followed by imipenem (4/32; 12.5%), ciprofloxacin (3/32; 9.4%), doxycycline (2/32; 6.3%), and norfloxacin (1/32; 3.1%). Conclusions: Our results suggest that E. coli isolates carried by wild Amur tigers and North China leopards have potential pathogenicity and drug resistance. [ABSTRACT FROM AUTHOR]

The widespread occurrence of Carboniferous Wuluate Formation volcanic rocks in the West Kunlun is closely related to the evolution of the Paleo-Tethys but has received little attention. In this study, we conducted detailed fieldwork on the Wuluate Formation in West Kunlun and performed zircon U‒Pb dating, whole-rock major and trace element analysis, whole-rock Sr-Nd isotope analysis, and in situ zircon Hf isotope analyses. The Wuluate Formation is characterized by a bimodal volcanic suite. Zircon U‒Pb dating indicates that the rhyolites erupted at ca. 348–353 Ma, which is coeval with the zircon U‒Pb dating result of 354 Ma for the basalt. The basalts show a tholeiitic magmatic evolution trend with flattened REE patterns and depleted whole-rock Sr-Nd and zircon Hf isotopes, indicating geochemical affinity to back-arc basin basalt (BABB). Trace element modelling results indicate that the primitive basaltic compositions fit well with the products of the DMM + sediments + H2O source under melting conditions of asthenospheric temperature and thin lithosphere thickness, and the REE modelling results show that the basalts underwent 40% to 95% crystallographic differentiation of olivine, monazite, hornblende, plagioclase, and magnetite. The silicic rocks are calcic to calcic-alkaline and meta/peraluminous. They exhibit flattened REE patterns and slightly enriched zircon Hf isotopes, which could originate from Precambrian metaigneous sources of West Kunlun. The Kungai bimodal suite is likely to have formed in a back-arc setting corresponding to the northward subduction of Paleo-Tethys. The subduction of Paleo-Tethys had already occurred, and a back-arc basin had developed before the Early Carboniferous. [ABSTRACT FROM AUTHOR]

Background: The roundworms, Parascaris spp., are important nematode parasites of foals and were historically model organisms in the field of cell biology, leading to many important discoveries. According to karyotype, ascarids in Equus are commonly divided into Parascaris univalens (2n = 2) and Parascaris equorum (2n = 4). Methods: Here, we performed morphological identification, karyotyping and sequencing of roundworms from three different hosts (horses, zebras and donkeys). Phylogenetic analysis was performed to study the divergence of these ascarids based on cytochrome c oxidase subunit I (COI) and internal transcribed spacer (ITS) sequences. Results: Karyotyping, performed on eggs recovered from worms of three different Equus hosts in China, showed two different karyotypes (2n = 2 in P. univalens collected from horses and zebras; 2n = 6 in Parascaris sp. collected from donkeys). There are some differences in the terminal part of the spicula between P. univalens (concave) and Parascaris sp. (rounded). Additionally, it was found that the egg's chitinous layer was significantly thicker in Parascaris sp. (> 5 μm) than P. univalens (< 5 μm) (F(2537) = 1967, P < 0.01). Phylogenetic trees showed that the sequences of Parascaris from Equus hosts were divided into two distinct lineages based on sequences of the COI and ITS. Conclusions: Comparing the differences in roundworms collected from three different Equus hosts, this study describes a Parascaris species (Parascaris sp.) with six chromosomes in donkeys. It is worth noting that the thickness of the chitinous layer in the Parascaris egg may serve as a diagnostic indicator to distinguish the two roundworms (P. univalens and Parascaris sp.). The Parascaris sp. with six chromosomes in donkeys in the present study may be a species of P. trivalens described in 1934, but the possibility that it is a new Parascaris species cannot be ruled out. Both karyotyping and molecular analysis are necessary to solve the taxonomic problems in Parascaris species. [ABSTRACT FROM AUTHOR]

The geological evolution of the Proto-Tethys Ocean remains vague. The Tianshuihai Terrane (TSHT), a subterrane of the West Kunlun, distributed to the south of the Proto-Tethys Ocean during the Early Palaeozoic, records abundant information on the geological evolution of the Proto-Tethys Ocean. In this study, we reported SHRIMP and LA-ICP-MS zircon U–Pb ages, whole-rock major and trace element composition data, and Sr-Nd-Hf isotopes of a suite of monzogranites and the monzonitic-syenitic enclaves in Zankan and syenogranites in Laobing regions of the TSHT, West Kunlun Orogenic Belt. The syenogranites in the Laobing region yielded SHRIMP zircon U-Pb ages of 550.4 ± 6.4 Ma to 547.5 ± 5.3 Ma, which were the earliest age records of subduction-related magmatism in the TSHT during the Late Neoproterozoic-Early Palaeozoic. The host monzogranites in the Zankan area yielded SHRIMP and LA-ICP-MS zircon U-Pb ages of 542.6 ± 8.4 Ma to 540.5 ± 2.8 Ma, which is coeval with the monzonitic-syenitic enclaves ages of 533.8 ± 3.4 Ma to 534.7 ± 3.0 Ma. We speculated that an active margin developed along the TSHT during the Cambrian and the initial subduction of the Proto-Tethys oceanic slab must have occurred prior to the Early Cambrian (>550 Ma). The TSHT and the Southern Kunlun Terrane were distributed between the northern margin of the East Gondwana continent and the Tarim Block. Additionally, the coexistence of two branches of the Proto-Tethys Ocean represented by the Kangxiwa Fault and Kudi Ophiolite Belt during the Early Palaeozoic. Based on the chronological statistics of micro-continental blocks in the northern margin of the East Gondwana continent, subduction of the Proto-Tethys Ocean could be diachronous, initially originating in the northwestern part of the East Gondwana continent, and gradually propagating to the east of the East Gondwana continent. [ABSTRACT FROM AUTHOR]

This study aims to identify risk factors associated with central lymph node metastasis (CLNM) in individuals with papillary thyroid carcinoma (PTC) and to develop a predictive nomogram model, thereby offering clinicians a valuable tool for guiding surgical treatment decisions in PTC management.Clinical and ultrasound data were collected from 348 patients with PTC who underwent surgical treatment at our hospital between July 2022 and November 2023. The cohort was randomly divided into a training group (n = 243) and a validation group (n = 105 cases). Independent risk factors for CLNM were identified using multivariate logistic regression analysis, which was subsequently used to construct a predictive nomogram. The performance of the model was internally validated, and its predictive accuracy was evaluated using receiver operating characteristic (ROC) curves, decision curve analysis (DCA), and calibration curves.Among the 348 patients, CLNM was observed in 115 (47.33%) patients in the training group and 48 (45.71%) patients in the validation group. Univariate and multivariate logistic regression analyses revealed that male sex, age under 55 years, nodular anteroposterior diameter of ≥1 cm, BRAF-V600E gene mutation, and tumor capsule invasion were independent risk factors for CLNM in PTC (P < 0.05). The constructed nomogram demonstrated strong predictive capability, with areas under the ROC curve (AUC) of 0.84 (95% CI, 0.78–0.89) for the training group and 0.85 (95% CI, 0.78–0.93) for the validation group.The nomogram constructed based on ultrasound and BRAF-V600E gene mutation status is a reliable predictive tool for CLNM in patients with PTC, potentially aiding clinicians in the formulation of personalized surgical treatment strategies. [ABSTRACT FROM AUTHOR]