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This article analyzes the genetic variants in protein-coding genes of the Aoluguya reindeer, a subspecies of reindeer facing the threat of extinction. The study collected blood samples from healthy and unrelated male adult individuals and sequenced their DNA. The analysis revealed a significant number of single nucleotide polymorphisms (SNPs) and indels in the reindeer population. The findings provide valuable insights into the genetic variation and adaptation of the Aoluguya reindeer and the entire reindeer species. [Extracted from the article]

Wagyu is recognized for producing marbled beef with high nutritional value and flavor. Reportedly, Wagyu has been widely used to improve the meat quality of local breeds around the world. However, studies on the genetic mechanism of meat quality in Wagyu at the whole‐genome level are rarely reported. Here, whole‐genome sequencing data of 11 Wagyu and 115 other individuals were used to explore the genomic variations and genes under selection pressure in Wagyu. A total of 31 349 non‐synonymous variants and 53 102 synonymous variants were identified in Wagyu. The population structure analysis showed that Wagyu had the closest genetic relationship with Mishima–Ushi cattle and was apparently separated from other cattle breeds. Then, composite likelihood ratio (CLR), integrated haplotype score, fixation index and cross‐population composite likelihood ratio (XP‐CLR) tests were performed to identify the candidate genes under positive selection in Wagyu. In total, 770 regions containing 312 genes were identified by at least three methods. Among them, 97 regions containing 27 genes were detected by all four methods. We specifically illustrate a list of interesting genes, including LRP2BP, GAA, CACNG6, CXADR, GPCPD1, KLF2, KLF13, SOX5, MYBPC1, SLC25A10, ATP8A1 and MYH15, which are associated with lipid metabolism, fat deposition, muscle development, bone development, feed intake and growth traits in Wagyu. This is the first study to explore the genomic variations and selection signatures of Wagyu at the whole‐genome level. These results will provide significant help to beef cattle improvement and breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: The Chinese Red Steppe Cattle (CRS) is a well-known dual-purpose (meat and milk) cattle breed. Here, the genetic variation and population structure of CRS were studied using 100 K SNP genotyping data. The results show that the genetic structure of CRS is different from other populations, the level of genetic diversity is high, and the level of inbreeding is low. In conclusion, our research provides the genetic basis for the prominent characteristics of CRS, which can be used to improve the breeding program of CRS in the future. Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding. [ABSTRACT FROM AUTHOR]

With the increasing scale of crowds in public places, the study of modeling crowd evacuation has become a significant research field. However, most previous research ignores to incorporate behavioral heterogeneity of individuals into the modeling framework, making it hard to replicate more realistic evacuation processes. Therefore, a behavioral heterogeneity-based social force model (BHSFM) is proposed to reveal the heterogeneity characteristics from the aspect of individual behavior. Numerical experiments show that the BHSFM provides a general mathematical framework for describing behavioral heterogeneity and forms a more reasonable and elaborate evacuation process. Notably, some interesting evacuation phenomena can emerge by integrating the behavioral heterogeneity coefficient with temporal-spatial dynamic risk indexes. Compared with the social force model (SFM), higher frequencies of small-scale displacements are performed by BHSFM due to more pushing behaviors. Furthermore, the periods and areas of a potential crowd disaster are revealed by our model under different numbers of pedestrians, which has important guiding significance for formulating reasonable evacuation schemes in specific scenarios. [ABSTRACT FROM AUTHOR]

The GSE54514 dataset included gene expression profiling based on arrays of whole blood from 26 sepsis survivors (days 1-5), 9 sepsis patients who died, and 18 healthy controls. Challenges in assessing the burden of sepsis and understanding the inequalities of sepsis outcomes between National Health Systems: secular trends in sepsis and infection incidence and mortality in Germany. A total of 3355 DEGs were common to adult and pediatric sepsis patients, while 4477 genes may be specific to pediatric sepsis and 2961 genes may be specific to adult sepsis (Figure 2C, Table S3). Sequencing data from sepsis patients and controls in GSE54514 and GSE25504 datasets were analyzed by bioinformatics in order to identify early potential biomarkers of sepsis. [Extracted from the article]

Recently, the introduction of specialized commercial breeds such as Boer and Saanen goats has sharply decreased the population size of purebred LUB, so there is an urgent need to assess the present population structure and genetic diversity. The Lubei White (LUB) goat is an indigenous dual-purpose meat and skin breed kept mainly in the Shandong province of China. Assessing the current genetic status of Lubei white goat based on the whole-genome data. [Extracted from the article]

As one of the most common self-organizing phenomena in social systems, queueing has been attracting a lot of interest. Understanding the local interaction mechanism in queueing behaviors is a critical issue in the field of crowd dynamics. However, most studies ignore the heuristic decision during queueing processes. Even less is known about the effect of queueing behaviors on the collective movement. Therefore, an extended social force queueing model is proposed, which is based on vision and morality. Guided by visual and moral information, the desired speed and direction are heuristically adjusted in the self-driven force. Numerical simulations indicate that our model constructs a more realistic and detailed framework for the interpretation of pedestrian queueing. This model successfully predicts the emergence of the "detours" phenomenon, which is beneficial for reducing crowd pressure. Furthermore, our model may provide guidance for crowd management in safety science and navigation in autonomous robots. • A queueing behavior-based social force model for crowd evacuation is proposed. • Vision and morality information are incorporated to achieve a queueing motion. • Self-organized phenomenon appeared is in agreement with empirical observations. • The queuing behavior apparently reduces the local pressure that indicates risk. [ABSTRACT FROM AUTHOR]

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits., Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions., Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity., Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

Introduction: Northeast Merino (NMS) is a breed developed in Northeast China during the 1960s for wool and meat production. It exhibits excellent traits such as high wool yield, superior meat quality, rapid growth rate, robust disease resistance, and adaptability to cold climates. However, no studies have used whole-genome sequencing data to investigate the superior traits of NMS. Methods: In this study, we investigated the population structure, genetic diversity, and selection signals of NMS using whole-genome sequencing data from 20 individuals. Two methods (integrated haplotype score and composite likelihood ratio) were used for selection signal analysis, and the Fixation Index was used to explore the selection signals of NMS and the other two breeds, Mongolian sheep and South African meat Merino. Results: The results showed that NMS had low inbreeding levels, high genomic diversity, and a pedigree of both Merino breeds and Chinese local breeds. A total length of 14.09 Mb genomic region containing 287 genes was detected using the two methods. Further exploration of the functions of these genes revealed that they are mainly concentrated in wool production performance ( IRF2BP2 , MAP3K7 , and WNT3 ), meat production performance ( NDUFA9 , SETBP1 , ZBTB38, and FTO ), cold resistance ( DNAJC13 , LPGAT1 , and PRDM16 ), and immune response ( PRDM2 , GALNT8 , and HCAR2 ). The selection signals of NMS and the other two breeds annotated 87 and 23 genes, respectively. These genes were also mainly focused on wool and meat production performance. Conclusion: These results provide a basis for further breeding improvement, comprehensive use of this breed, and a reference for research on other breeds., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Yi, Hu, Shi, Li, Bai, Sun, Ma, Zhao and Yan.)

Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1 , PRKG2 , DGAT1 , PARP10 , TONSL , ADCK5 , and BMP3 , most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.