Search Results (17)

Background/Objectives: To establish a foundation for conserving and utilizing local frog germplasm resources in Zhejiang Province, for Quasipaa spinose, which has high commercial and nutritional value, a pan-genome analysis was performed. Methods: Herein, we characterized 405,263 SNPs for the giant spiny frog, Q. spinose, using the Illumina NovaSeq platform. Results: These loci were highly polymorphic in 59 individuals sampled from three different subpopulations, with 0.05 to 0.30 minor alleles per locus. The observed and expected heterozygosities were 0.2379 and 0.2683 (IBD), respectively. These polymorphic loci would be useful for assessing genetic diversity, population structure, gene flow, population assignment, and paternity in giant spiny frogs. Conclusions: Our investigation demonstrated that there are distinct genetic and evolutionary histories between Zhejiang and Jiangxi frogs. Phylogenetic inference effectively differentiated these three subpopulations based on their geographical origins, and the phylogenetic inference level of domesticated Zhejiang frogs was comparatively higher than that of the Jiangxi-derived population. Furthermore, by utilizing three selective signature methods, namely, Obs/Exp het, nucleotide diversity (Pi), and identical by state (IBS), across subpopulations, we concluded that these three breeds were from an identical population, and no genetic bottleneck occurred among these three lineages, in accordance with LD decay analysis. Finally, 2700 potential candidate genes were identified, including MAPK, calcium signaling pathway, Ras signaling pathway and regulation of actin cytoskeleton; we noted that the key genes associated with dilated cardiomyopathy or arrhythmogenic right ventricular cardiomyopathy in humans beings and GnRH signaling pathway-related genes (i.e., CD80, IFNA, and KCNK1) were highly enriched, which could impact cardiac function through immune-associated genes. Full article

This study developed a 60K single-nucleotide polymorphism (SNP) liquid-phase chip (‘Shenxin I’) based on genotyping by target sequencing (GBTS) technology. The chip was used to genotype 1451 individuals spanning five conserved local pig breeds: Fengjing (FJ), Meishan (MMS), Pudong White (PD), Shaowutou (SW), and Shanghai White (SHW), and newborn purebred Meishan offspring (MMS_New). The study assessed the genetic diversity, population structure, and genomic breed composition (GBC) of these breeds. The GBC analysis provided insights into genomic introgression within admixed individuals. Results indicate that PD and FJ breeds exhibited the higher fraction of the genome covered by runs of homozygosity (F_ROH) and slower linkage disequilibrium (LD) decay rate, suggesting higher genetic inbreeding level in these two breeds. The study conducted genetic distance of identity-by-state (IBS) analysis and molecular pedigree construction for the MMS population. Subsequently, purebred mating was implemented by selecting boars from different pedigrees to mate with sows and excluding individuals with high inbreeding coefficients from the breeding program. This resulted in a significant reduction in the overall inbreeding level of the born progeny and an increase in genetic diversity compared to the original population. Consequently, the study concludes that utilizing liquid-phase chip technology for genotyping, constructing molecular pedigrees, and optimizing mating combinations in small populations of locally conserved pig breeds contributes to enhancing the conservation effectiveness. Full article

Because of the advancement of IT, cross-domain environments have emerged where independent clouds with different security policies share data. However, sharing data between clouds with heterogeneous security levels is a challenging task, and most existing access control schemes focus on a single cloud domain. Among various access control models, RBAC is suitable for cross-domain data sharing, but existing RBAC schemes cannot provide strong role privacy and do not support freshness in role verification, so they are vulnerable to replay-based misuse of credentials. In this paper, we propose an RBAC scheme for cross-domain cloud environments based on a hash-chain-augmented zk-SNARK and identity-based signatures. The TA issues IBS-based role signing keys to users, and the user proves, through a zk-SNARK circuit, that there exists a valid role signing key satisfying the access policy without revealing the concrete role information to the CDS. In addition, a synchronized hash chain between the user and the CDS is embedded into the proof so that each proof is tied to the current hash-chain state and any previously used proof fails verification when replayed. We formalize role privacy, replay resistance, and MitM resistance in the cross-domain setting and analyze the proposed scheme by comparing it with Saxena and Alam’s I-RBAC, Xu et al.’s RBAC, MO-RBE, and PE-RBAC. The security analysis shows that the proposed scheme achieves robust role privacy against both the CDS and external attackers and prevents replay and man-in-the-middle attacks. Furthermore, the computational cost evaluation based on the number of pairing, exponentiation, point addition, and hash operations confirms that the verifier-side overhead remains comparable to existing schemes, while the additional prover cost is the price for achieving stronger privacy and security. Therefore, the proposed scheme can be applied to cross-domain cloud systems that require secure and privacy-preserving role verification, such as military, healthcare, and government cloud infrastructures. Full article

The Luhua chicken is an outstanding local breed in China that has been placed under conservation due to the impact of specialized breeding and the widespread adoption of commercial varieties. As such, this study analyzed reproductive traits across three consecutive generations and utilized whole-genome resequencing data from 60 Luhua chickens to assess conservation efficacy through genetic diversity, run of homozygosity (ROH) distribution, kinship, and population structure so as to better conserve the breed. The results show that, across generations, the body weight at first egg increased, the age at first egg was delayed, and the egg weight at first laying increased. No significant variations were found in the body weight at 300 d or the total egg number. The key genetic parameters of the polymorphism information content (PIC), expected heterozygosity (HE), observed heterozygosity (HO), and mean identical-by-state (IBS) distance were 0.234, 0.351, 0.277, and 0.782, respectively. The majority of ROHs ranged from 0.5 to 1 Mb, and the inbreeding coefficient based on ROHs was calculated at 0.021. The findings reveal that these traits remained unchanged across the three generations. Our research suggests that optimizing the mating plan of Luhua chickens is essential to minimize inbreeding risk. Furthermore, the methodology applied in this study provides a valuable reference for the conservation monitoring of other indigenous chicken breeds. Full article

Cloud computing has witnessed rapid growth and notable technological progress in recent years. Nevertheless, it is still regarded as being in its early developmental phase, with substantial potential remaining to be explored—particularly through integration with emerging technologies such as the Metaverse, Augmented Reality (AR), and Virtual Reality (VR). As the number of service users increases, so does the demand for computational resources, leading data owners to outsource processing tasks to remote cloud servers. The internet-based delivery of cloud computing services consequently expands the attack surface and impacts the trust relationship between the service user and the service provider. To address these challenges, this study proposes a restricted access control framework based on homomorphic encryption (HE) and identity-based encryption (IBE) mechanisms. A formal analysis of the proposed model is also conducted under an unauthenticated communication model. Simulation results indicate that the proposed approach achieves a 20–40% reduction in encryption and decryption times, respectively, compared with existing state-of-the-art homomorphic encryption schemes. The simulation was performed using a 2048-bit key and data size, consistent with current industry standards, to improve key management efficiency. Additionally, the role-based hierarchy was implemented in a Salesforce cloud environment to ensure secure and restricted access control. Full article

Background/Objectives: Kinship inference is commonly adopted in various forensic applications, but previous studies have often lacked precision. Methods: In this study, a new method for the nomenclature of kinship types, i.e., kinship chain (KC), was proposed, and then, six types of identity by state (IBS) scores were calculated for simulated and real families using four types of markers. Finally, several Bayesian network (BN)-based classifiers were constructed to investigate the efficiency of the kinship inference. Results: A total of 7, 22, 58, and 3 KCs were obtained for common first-, second-, and third-degree relatives and unrelated pairs, respectively. High accuracies could be achieved in distinguishing between related and unrelated pairs after combining the four types of genetic markers, with an accuracy of >99.99% for all 7 KCs of first-degree relationships and ~99% for 14 out of 22 KCs of second-degree relatives. When comparing relationships of the same degree, the accuracies were 99.28%, 42.31%, and 15.82% for first-, second-, and third-degree relationships, respectively. When it came to differentiating unspecific relationships, the overall accuracy was over 80%. All the results were validated on real family data. Conclusions: With the new nomenclature method of kinship types and the combination of autosomal and non-autosomal genetic markers, kinship inference can be realized with high accuracy and precision, which will be helpful in complex forensic cases, such as the identification of mass disaster victims. Full article

Background: Beagle dogs are widely used in biomedical research, but their genetic diversity and population structure require further investigation. This study aimed to assess genetic diversity, population structure, and selection signals in a foundational Beagle breeding population using genome-wide SNP genotyping. Methods: A total of 459 Beagle dogs (108 males, 351 females) were genotyped using the Canine 50K SNP chip. After quality control, 456 individuals and 31,198 SNPs were retained. Genetic diversity indices, principal component analysis (PCA), identity-by-state (IBS) distance, a genomic relationship matrix (G-matrix), runs of homozygosity (ROH), and Tajima’s D selection scans were analyzed. Results: The average minor allele frequency was 0.224, observed heterozygosity was 0.303, and expected heterozygosity was 0.305. A total of 2990 ROH segments were detected, with a mean inbreeding coefficient of 0.031. Phylogenetic analysis classified 106 stud dogs into 13 lineages. Selection signal analysis identified TTN (muscle function) and DLA-DRA, DLA-DOA, DLA-DMA (immune regulation) under selection. Conclusions: The Beagle population exhibits high genetic diversity and low inbreeding. To maintain genetic stability and ensure the long-term conservation of genetic resources, structured breeding strategies should be implemented based on lineage classifications. Full article

The significance of the chiral symmetry restoration is studied by considering the role of the modification of the nucleon mass in nuclear medium at finite density and temperature. Using the Korea-IBS-Daegu-SKKU density functional theory, we can create models that have an identical nuclear matter equation of state but different isoscalar and isovector effective masses at zero temperature. The effect of the effective mass becomes transparent at non-zero temperatures, and it becomes more important as temperature increases. The role of the effective mass is examined thoroughly by calculating the dependence of thermodynamic variables such as free energy, internal energy, entropy, pressure and chemical potential on density, temperature and proton fraction. We find that sensitivity to the isoscalar effective mass is several times larger than that of the isovector effective mass, so the uncertainties arising from the effective mass are dominated by the isoscalar effective mass. In the analysis of the relative uncertainty, we obtain that the maximum uncertainty is less than 2% for free energy, internal energy and chemical potential, but it amounts to 20% for pressure. Entropy shows a behavior completely different from the other four variables that the uncertainty is about 40% at the saturation density and increases monotonically as density increases. The effect of the uncertainty to properties of physical systems is investigated with the proto-neutron star. It is shown that temperature depends strongly on the effective mass at a given density, and substantial swelling of the radius occurs due to the finite temperature. The equation of state is stiffer with smaller isoscalar effective mass, so the effect of the effective mass appears clearly in the mass–radius relation of the proto-neutron star, where a larger radius corresponds to a smaller effective mass. Full article

The success of the Primitivo variety underscores the critical need for the managing of clone genetic conservation, utilization, and improvement. By combining genomic and environmental data, breeders can better predict the performance of varieties, thereby improving breeding efficiency and enabling more targeted development of high-quality grapevine cultivars. In this study, 35 Primitivo clones were analysed, including selected and certified clones that have been propagated over several years in Apulia. Genetic variability among the Primitivo clones was assessed through genotyping by sequencing. Using 38,387 filtered SNPs, pairwise identity-by-state (IBS) analysis demonstrated the uniqueness of the 35 clones (IBS < 0.75), indicating a high degree of variability among the samples. Genetic diversity analysis revealed three primary groups, which were differentiated based on geographic origin. The clones from Gioia del Colle were grouped into two distinct clusters, which aligns with the observed variation in grape-related traits. The fixation index (F_ST > 0.50) identified numerous loci putatively associated with stress responses and developmental traits, including genes involved in key plant biological processes, stress response regulation, and adaptation to environmental conditions such as glutamate receptors, auxin, and ethylene signalling. Full article

Background/Objectives: Infectious bronchitis (IB) is a highly infectious avian disease caused by the infectious bronchitis virus (IBV). The disease causes lesions mainly in the respiratory, reproductive, and renal systems and has a significant economic impact on the poultry industry worldwide. Methods: We discovered two unique IBV isolates (T-62: PP737794.1 and CL-61: PP783617.1) circulating in Canada and molecularly characterized them. Results: The phylogenetic analysis revealed that the IBV isolates belong to genotype I and fall between lineages 25 and 7. Further analysis of the T-62 IBV isolate indicated that it is a potential recombinant of the Iowa state isolate (IA1162/2020-MW) and that the CL-61 strain of the IBV is also a recombinant IBV with the Connecticut (Conn) vaccine strain as its major parent. The S1 glycoprotein of the CL-61 and T-62 strains of the IBV had 85.7% and 73.2% amino acid (aa) identities respectively compared to the Conn vaccine strain. There were 67 and 129 aa substitutions among the S1 glycoprotein of the CL-61 and T-62 strains of the IBV compared to the Conn vaccine, respectively. Importantly, two and nineteen of these aa variations were in hypervariable regions 1 (HVR1) and HVR3. Finally, the two IBV isolates possessed a higher affinity for the sialic acid ligand compared to the DMV/1639 and Mass/SES IBV strains. Conclusions: Genetic recombination in the IBV results in the continual emergence of new variants, posing challenges for the poultry industry. As indicated by our analyses, live attenuated vaccine strains play a role in the genetic recombination of the IBV, resulting in the emergence of variants. Full article

With the rapid development of the Internet of Things (IoT), ensuring secure communication between devices has become a crucial challenge. This paper proposes a novel secure communication solution by extracting wireless channel state information (CSI) features from IoT devices to generate a device identity. Due to the instability of the wireless channel, the CSI features are fuzzy and time-varying; thus, we a employ locally sensitive hashing (LSH) algorithm to ensure the stability of the generated identity in a dynamically changing wireless channel environment. Furthermore, zero-knowledge proofs are utilized to guarantee the authenticity and effectiveness of the generated identity. Finally, the identity generated using the aforementioned approach is integrated into an IBE communication scheme, which involves the fuzzy extraction of channel state information from IoT devices, stable identity extraction for fuzzy IoT devices using LSH, and the use of zero-knowledge proofs to ensure the authenticity of the generated identity. This identity is then employed as the identity information in identity-based encryption (IBE), constructing the device’s public key for achieving confidential communication between devices. Full article

The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analysis certified that they belong to the same population. The outer point of the breed demarcation was a single Hungarian Wire-haired Vizsla (HWV) individual, which was the closest animal genetically to the HSV population in the PCA analysis. Three programs were used for the breed assignment calculations, including the widely used GeneClass2.0 software and two additional approaches developed here: the ‘PCA-distance’ and ‘IBS-central’ methods. Both new methods calculate a single number that represents how closely a dog fits into the actual reference population. The former approach calculates this number based on the PCA distances from the median of HSV animals. The latter calculates it from identity by state (IBS) data, measuring the distance from a central animal that is the best representative of the breed. Having no mixed-breed dogs with known HSV genome proportion, admixture animals were simulated by using data of HSV and HWV individuals to calibrate the inclusion/exclusion probabilities for the assignment. The numbers generated from these relatively simple calculations can be used by breeders and clubs to keep their populations under genetic supervision. Full article

Durian (Durio zibethinus L.) is a crop of economic and health importance globally. Efforts are being made to revamp China’s only successful commercial-scale durian plantations in Hainan; however, their genetic base is unknown. Therefore, the present study was undertaken to assess the genetic base and population structure of 32 genotypes in durian plantation sites in Hainan, China, and develop simple sequence repeat (SSR) markers by whole genome sequencing through restriction site-associated DNA sequencing technology to facilitate germplasm conservation and breeding. The results from identity by state (IBS), phylogenetic tree, population structure, and principal component analysis grouped the 32 genotypes into two clusters/sub-populations. Based on IBS, genotypes in Cluster I are largely duplicated genotypes; however, results from the model-based population structure demonstrated that most of the genotypes in Sub-population II shared a common genetic background with those in Sub-population I/Cluster I. The results revealed that the core durian collection in the plantation sites in Hainan include D24, D101, MSW, JH, D163, HFH, and NLX-5. In addition, we developed a total of 79,178 SSR markers with varied lengths and amplicon sizes. The genetic diversity and population structure reported in this study will be useful for durian conservation and utilization. In addition, the discovered and developed SSR markers will lay the foundation for molecular breeding via marker-assisted selection, quantitative trait loci mapping, and candidate gene discovery and validation. Full article

Across the globe, wireless devices with Internet facilities such as smartphones and tablets have become essential assets for communication and entertainment alike for everyday life for millions of people, which increases the network traffic and the demand for low-latency communication networks. The fourth-generation (4G)/long-term evolution (LTE)/ fifth-generation (5G) communication technology offers higher bandwidth and low latency services, but resource utilization and resiliency cannot be achieved, as transmission control protocol (TCP) is the most common choice for most of the state-of-art applications for the transport layer. An extension of TCP—multipath TCP (MPTCP)—offers higher bandwidth, resiliency, and stable connectivity by offering bandwidth aggregation and smooth handover among multiple paths. However, MPTCP uses multiple disjointed paths for communication to offer multiple benefits. A breach in the security of one of the paths may have a negative effect on the overall performance, fault-tolerance, robustness, and quality of service (QoS). In this paper, the research focuses on how MPTCP options such as MP_CAPABLE, ADD_ADDR, etc., can be used to exploit the vulnerabilities to launch various attacks such as session hijacking, traffic diversion, etc., to compromise the availability, confidentiality, and integrity of the data and network. The probable security solutions for securing MPTCP connections are analyzed, and the secure key exchange model for MPTCP (SKEXMTCP) based on identity-based encryption (IBE) is proposed and implemented. The parameters exchanged during the initial handshake are encrypted using IBE to prevent off-path attacks by removing the requirement for key exchange before communication establishment by allowing the use of arbitrary strings as a public key for encryption. The experiments were performed with IBE and an elliptic curve cryptosystem (ECC), which show that IBE performs better, as it does not need to generate keys while applying encryption. The experimental evaluation of SKEXMTCP in terms of security and performance is carried out and compared with existing solutions. Full article

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies. Full article