Ancestral Origin Research Articles

A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations.

Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.

Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population.

COVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. The widespread clinical symptoms encompass a large group of asymptomatic COVID-19 patients, raising a crucial question regarding genetic susceptibility, e.g., whether individual differences in immunity play a role in patient symptomatology and how much human leukocyte antigen (HLA) contributes to this. To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. We identified two loci on chromosomes 5q32 and 11p12, which reach the significance threshold of suggestive association (p<1x10-5 threshold adjusted for multiple trait testing) and are associated with the COVID-19 susceptibility in the European ancestry (index rs17448496: odds ratio[OR] = 0.173; 95% confidence interval[CI], 0.08-0.36 for G allele; p = 5.15× 10-5 and index rs768632395: OR = 0.166; 95% CI, 0.07-0.35 for A allele; p = 4.25×10-6, respectively), which were associated with two genes, PPP2R2B at 5q32, and LRRC4C at 11p12, respectively. To explore the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases. Using In-silico binding predictions to map the binding of risk/protective HLA to the viral structural proteins, we found the differential presentation of viral peptides in both ancestries. Lastly, extrapolation of the identified HLA from the cohort to the worldwide population revealed notable correlations. The study uncovers possible differences in susceptibility to COVID-19 in different ancestral origins in the genetic background, which may provide new insights into the pathogenesis and clinical treatment of the disease.

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China.

The Qinghai Province of China is located in the northeast region of the Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. F ST values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and F ST methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.

ADGR: Admixture-Informed Differential Gene Regulation.

The regulatory elements in proximal and distal regions of genes are involved in the regulation of gene expression. Risk alleles in intronic and intergenic regions may alter gene expression by modifying the binding affinity and stability of diverse DNA-binding proteins implicated in gene expression regulation. By focusing on the local ancestral structure of coding and regulatory regions using the paired whole-genome sequence and tissue-wide transcriptome datasets from the Genotype-Tissue Expression project, we investigated the impact of genetic variants, in aggregate, on tissue-specific gene expression regulation. Local ancestral origins of the coding region, immediate and distant upstream regions, and distal regulatory region were determined using RFMix with the reference panel from the 1000 Genomes Project. For each tissue, inter-individual variation of gene expression levels explained by concordant or discordant local ancestry between coding and regulatory regions was estimated. Compared to European, African descent showed more frequent change in local ancestral structure, with shorter haplotype blocks. The expression level of the Adenosine Deaminase Like (ADAL) gene was significantly associated with admixed ancestral structure in the regulatory region across multiple tissue types. Further validations are required to understand the impact of the local ancestral structure of regulatory regions on gene expression regulation in humans and other species.

Cultural Practices of the Indigenous Peoples (IPS) of San Emilio Ilocos Sur: Then and Now

The cultural practices of the Indigenous Peoples (IPs) are a reflection of their ancestral origin. The performance of these practices indicates their sacredness and respect for their traditions. This investigation is an exploration of the cultural practices of the Indigenous People that have been performed in the past and in the present. This is a qualitative study employing an ethnographic approach with 12 key informants. These informants are elders, leaders, and residents of San Emilio, Ilocos Sur. Unstructured interviewing and Focus Group Discussion (FGD) were the means of obtaining data and were analyzed through Analytical Induction (AI) and Grounded theory. As a result, the performance of the cultural practices such as Pidis, Sakeb, Sawid, Legleg, Begnas, Paama, and Dwayya of the IPsin San Emilio, Ilocos Sur, has surpassed the challenges of modernization, technology and the existence of different religions in their place. With these circumstances, the Indigenous People of San Emilio collectively advocate these cultural practices for the younger generations. Despite uncontrollable factors affecting these traditions like religion, modernization, and the death of the elders who can perform these practices, they still aspire to their preservation. The theory of collectivism was deduced from the results obtained from their responses and observed behaviors during the performances of these cultural practices. The Indigenous People value their traditions as representations of their identity as a tribe.

Abstract C054: Characterizing differences in the chromatin accessibility landscape by donor ancestry in human triple-negative breast cancer cell lines

Abstract African American (AA) women are at increased risk of developing and dying from Triple-Negative Breast Cancer (TNBC), an aggressive breast cancer subtype, compared to European American (EA) women in the United States. In addition to social determinants, further investigation into biologic factors that contribute to these disparities is needed to fully understand this multi-factorial problem. In particular, the epigenetics of racial/population diversity and its influence on breast cancer incidence and outcomes remain underexplored. Using ATAC-sequencing, we characterized differences in chromatin accessibility between EA-derived versus AA-derived breast cancer cell lines across a range of breast cancer subtypes. Interestingly, our principal component analysis of the top 50,000 peaks with the most variance revealed separation of chromatin profiles by genetic ancestry specifically in TNBC cell lines (N=10). Digital footprinting analysis of differentially open chromatin regions using TOBIAS revealed significant differences in transcription factor (TF) binding by ancestry (61 TFs with a differential binding score &amp;gt; 0.25 or &amp;lt; -0.25 and FDR &amp;lt; 0.01). AA TNBC cell lines exhibited increased binding of transcription factors associated with epithelial-to-mesenchymal transition (ZEB1, SNAI1, GRHL2), cancer stemness and chemotherapeutic resistance (TFAP2C, NRF1), and others such as KAISO, whose aberrant expression has been previously linked to a distinct biology and poor outcomes in AA breast and prostate cancer patients. Pathway analysis of genes located within promoters of differentially open chromatin regions reveals enrichment of the following KEGG pathways in AA TNBC cells: inflammatory mediator regulation of TRP channels (p-adj = 0.009), Hippo signaling (p-adj = 0.006), Wnt signaling (p-adj = 0.031), and Rap-1 signaling (p-adj = 0.046). Together, these data reveal a differential chromatin landscape associated with the aberrant activity of critical TFs and downstream gene expression changes that may contribute to worsened TNBC biology in women of African ancestry. Additionally, as many of these cell lines are used routinely in biomedical research, these findings also indicate that the ancestral origin of patient derived cell lines matters and may contribute to biologic variation in experimental data, suggesting that inclusion of diversely sourced cell lines should be considered in experimental design. Citation Format: Alexandra R. Harris, Vishal Koparde, Gatikrushna Panigrahi, Maeve Bailey-Whyte, Tiffany Dorsey, Stefan Ambs. Characterizing differences in the chromatin accessibility landscape by donor ancestry in human triple-negative breast cancer cell lines [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C054.

Molecular characterization of Brucella melitensis detected in blood and Serum samples of sheep and Goats

The incidence of brucellosis was investigated in sheep and goats with a history of abortions. Out of 550 blood samples collected from small ruminants, a total of 113 samples including 44 blood and 69 serum samples tested positive for brucellosis by using i-enzyme linked immunosorbent assay. Further, these samples were subjected to molecular detection of Brucella spp by BCSP31 and IS711/BM polymerase chain reaction (PCR) assays. The reference strains B. abortus S19, B. abortus 544 and B. melitensis Rev 1 were included in PCR assay as controls. The reference strains B. abortus S19 and B. abortus 544 produced amplification product of 223 bp. Moreover, 223 bp amplicon was observed in 12 (27.27%) blood and 14 (20.29%) serum samples confirming the presence of Brucella spp. In IS711/BM PCR B. melitensis Rev 1, 10 (22.73%) blood and 10 (14.49%) serum samples produced amplicons of 731 bp confirming the presence of B. melitensis. Phylogenetic analysis of four IS711/BM gene sequences of B. melitensis detected the ancestral origin of organism. It was inferred that BCSP31 and IS711/BM PCR assays were found useful in direct detection of Brucella organisms from whole blood and serum samples of sheep and goats.

Abstract IA031: AGEing and RAGEing in prostate cancer: Integrating ancestral tumor biology into the multilevel framework of health inequity constructs to inform on cancer disparity outcomes

Abstract Black/African American (AA) men have a 70% higher risk of prostate cancer (PCa) and are more than twice as likely to die of their disease as non-Hispanic White men (NHW). While the negative impacts of health inequity on PCa incidence and mortality are undeniable, ancestry specific tumor biology also plays a significant role. The circumstances and environments where individuals are born, live, work, and play, likely cause molecular changes that are synergistic or at least additive in their biological effects when combined with ancestral tumor biology. However, studies that assess how ethnic and racial disparities in health inequity constructs can exacerbate ancestry specific tumor biology are lacking. Through their ability to perpetuate a reactive stroma, this study defines the increased bioavailability of reactive metabolites called advanced glycation end products (AGEs) as a pro-tumorigenic consequence of interrelated health inequity risk factors that influence ancestry specific tumor biology. AGEs are significant because AA communities who often bear the highest cancer burden are more likely to be exposed to health inequity risk factors that greatly increase AGE exposure. For example, AAs communities often have the highest poverty rates, be more sedentary, and are more likely to live in designated food deserts. This promotes the consumption of unhealthy foods that are AGE laden, lead to weight gain, obesity, and increase cancer risk. In mice, chronic AGE consumption caused a rapid progression through prostate intra-epithelial neoplasia (p=0.049), adenocarcinoma (p=0.042) and metastatic disease (p=0.001). Mechanistically, AGEs recapitulated a regulatory program of ‘activated’ stroma similar to that observed in AA prostate tumors. Specifically, increased AGE bioavailability caused receptor for AGE (RAGE) dimerization in resident prostate fibroblasts leading to a regulatory program of immune, metabolic, and oxidative dysregulation and the downregulation of matrix regulatory proteins. Functionally, AGE treated AA-derived fibroblasts were able to increase epithelial cell migratory potential to a much greater extent than NHW-derived fibroblasts irrespective of the ancestral origin of the cocultured epithelial cells. In collaborative epidemiological studies, cancer patients in the highest quartile of past AGE consumption associated with both aggressive disease and increased all-cause mortality. The irreversible nature of AGE adducts, their association with health inequity, and their ability to impact the tumor microenvironment supports the premise that “increased AGE bioavailability contributes to the rapid tumor progression and poor outcomes observed in AA men with PCa”. AGE bioavailability provides an unexploited opportunity to consider how ethnic and racial disparities in health inequity can exacerbate ancestral tumor biology. Multidisciplinary educational, interventional, and pharmacological studies aimed at reducing AGE exposure may be viewed as novel cancer preventive and/or therapeutic initiatives. Citation Format: David P. Turner. AGEing and RAGEing in prostate cancer: Integrating ancestral tumor biology into the multilevel framework of health inequity constructs to inform on cancer disparity outcomes [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr IA031.

Multiple introductions and recombination events underlie the emergence of a hyper-transmissible Cryptosporidium hominis subtype in the USA

The parasite Cryptosporidium hominis is a leading cause of the diarrheal disease cryptosporidiosis, whose incidence in the United States has increased since 2005. Here, we show that the newly emerged and hyper-transmissible subtype IfA12G1R5 is now dominant in the United States. In a comparative analysis of 127 newly sequenced and 95 published C.hominis genomes, IfA12G1R5 isolates from the United States place into three of the 14 clusters (Pop6, Pop13, and Pop14), indicating that this subtype has multiple ancestral origins. Pop6 (IfA12G1R5a) has an East Africa origin and has recombined with autochthonous subtypes after its arrival. Pop13 (IfA12G1R5b) is imported from Europe, where it has recombined with the prevalent local subtype, whereas Pop14 (IfA12G1R5c) is a progeny of secondary recombination between Pop6 and Pop13. Selective sweeps in invasion-associated genes have accompanied the emergence of the dominant Pop14. These observations offer insights into the emergence and evolution of hyper-transmissible pathogens.

Visiting ‘home’: Considering diasporic practices through assemblage dynamics

AbstractVisiting ‘home’ as a migrant may not always be about going home. Exploring a case where visiting is motivated by tourism as much as – or more than – migration, I argue for using assemblage as a set of ontological premises enables alternative appreciations of how practices of ‘visiting home’ evolve. Starting from a primacy of relationality and of malleable materialities, this perspective does not rely on migration‐defined polarities to frame the spectrum of belonging in a homeland but allows for influences from many sources to interact and generate new formations that exceed the sum of their parts. Within this case, I analyse diasporic practices of visiting through three entwined dynamics: a contradictory sense of attachment to a place of ancestral origin, a desire for embodied leisure on vacation, and an instinct to insulate oneself from certain others. All three simultaneously contribute to the potency and perpetuation of diasporic visiting in Morocco.

Genome-wide association study analysis to resolve the key regulatory mechanism of biomineralization in Pinctada fucata martensii.

Biomineralization-controlled exo-/endoskeleton growth contributes to body growth and body size diversity. Molluscan shells undergo ectopic biomineralization to form the exoskeleton and biocalcified "pearl" involved in invading defence. Notably, exo-/endoskeletons have a common ancestral origin, but their regulation and body growth are largely unknown. This study employed the pearl oyster, Pinctada fucata marntensii, a widely used experimental model for biomineralization in invertebrates, to perform whole-genome resequencing of 878 individuals from wild and breeding populations. This study characterized the genetic architecture of biomineralization-controlled growth and ectopic biomineralization. The insulin-like growth factor (IGF) endocrine signal interacted with ancient single-copy transcription factors to form the regulatory network. Moreover, the "cross-phylum" regulation of key long noncoding RNA (lncRNA) in bivalves and mammals indicated the conserved genetic and epigenetic regulation in exo-/endoskeleton growth. Thyroid hormone signal and apoptosis regulation in pearl oysters affected ectopic biomineralization in pearl oyster. These findings provide insights into the mechanism underlying the evolution and regulation of biomineralization in exo-/endoskeleton animals and ectopic biomineralization.

Amphiboreality and Distribution of Snailfishes (Cottiformes: Liparidae) in the Arctic and the North Atlantic

The marine ichthyofauna of the Arctic Ocean has an ancestral origin from the Pacific Ocean and, to a lesser extent, from the Atlantic Ocean, which is explained by the amphiboreal concept, developed on groups of fish and invertebrates. Snailfishes (Liparidae) of the Arctic and the North Atlantic are analyzed in the context of this amphiboreal concept. The review is based on the data of many years of research on their taxonomy using various material of morphological differences/similarities of the taxa and patterns of species distribution against the background of biogeographic representations. For the Arctic area, 33 species of the family are known: Liparis (5), Careproctus (21), Paraliparis (2), Rhodichthys (2), and Psednos (3). For the Atlantic fauna, with the same number of species, their composition differs: Liparis (6), Careproctus (3), Paraliparis (12), Psednos (11), and Eutelichthys (1). The amphiboreal concept explains the speciation of Liparis and the majority of Careproctus as the result of trans-Arctic preglacial migrations. For other (deep-sea) species, the hypothesis of a transoceanic dispersal route is applicable; it passed from the North Pacific through the Southern Ocean and then north across the Atlantic.

The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions

Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.

Genomics, Origin and Selection Signals of Loudi Cattle in Central Hunan.

Due to the geographical, cultural and environmental variability in Xiangxi, China, distinctive indigenous cattle populations have formed. Among them, Loudi cattle and Xiangxi cattle are the local cattle in Hunan, and the environment in Loudi is relatively more enclosed and humid than that in Xiangxi. To study the genome and origin of Loudi cattle in hot and humid environments, 29 individuals were collected and sequenced by whole-genome resequencing. In addition, genomic data were obtained from public databases for 96 individuals representing different cattle breeds worldwide, including 23 Xiangxi cattle from western Hunan. Genetic analysis indicated that the genetic diversity of Loudi cattle was close to that of Chinese cattle and higher than that of other breeds. Population structure and ancestral origin analysis indicated the relationship between Loudi cattle and other breeds. Loudi has four distinctive seasons, with a stereoscopic climate and extremely rich water resources. Selective sweep analysis revealed candidate genes and pathways associated with environmental adaptation and homeostasis. Our findings provide a valuable source of information on the genetic diversity of Loudi cattle and ideas for population conservation and genome-associated breeding of local cattle in today's extreme climate environment.

Retraction: The ancestral origin of the critically endangered Quadricorna sheep as revealed by genome-wide analysis.

Retraction: The ancestral origin of the critically endangered Quadricorna sheep as revealed by genome-wide analysis.

Elucidating genetic diversity and population structure in jamun [Syzygium cumini (L.) Skeels] using morpho-physiological traits and CAAT box-derived polymorphism

• Assessment of morpho-physiological and molecular diversity in Syzygium cumini . • Population structure analysis using CBDP markers. • CBDP markers were highly informative in detecting the polymorphism. • Evidence for high levels of gene flow and less genetic differentiation. The use of molecular markers has received little attention in jamun [ Syzygium cumini (L.) Skeels], an underutilized fruit crop highly valued for its medicinal and nutraceutical properties. In this study, 50 jamun accessions from four different populations were analyzed using 21 morpho-physiological traits and 22 polymorphic gene-targeted CAAT box-derived polymorphism (CBDP) markers. The morpho-physiological variability was fairly high among the jamun accessions. The UPGMA analysis based on morpho-physiological traits produced three clusters with a cophenetic correlation of 0.75, reflecting a good fit between the original matrix and the clustering algorithm. The average polymorphism of 91.17% and the wide-ranging heterozygosity values (0.282-0.499) for the CBDP markers revealed considerable genetic variation among jamun genotypes. The average PIC of 0.352 evinced a high discriminatory power of the CBDP markers in distinguishing the accessions. CDBP data-based UPGMA clustering and population structure analysis identified four distinct populations; albeit with overlaps among them. This, together with the existence of admixed types in all four populations, indicated a fairly high degree of gene flow within jamun populations sampled in this study. It is therefore likely that despite widely differing geographic origins, some accessions in all the populations have a shared ancestral origin. Analysis of Molecular Variance also supports this assumption, as an exceedingly higher within-population variance (84%) than among-population variance (16%) reflected a high degree of gene flow and low genetic differentiation for the Jamun populations examined. Our findings improve the existing understanding vis-à-vis genetic diversity and population structure in jamun, and are expected to increase the use of CBDP and similar marker techniques in cultivar development programs.

Molecular characterization of Brucella species detected from clinical samples of cattle and buffaloes

The present study was undertaken for molecular characterization of Brucella species of cattle and buffaloes. Clinical samples (1145) of unvaccinated cattle and buffaloes (200 blood samples, 710 sera, 190 vaginal swabs, 20 abomasal contents of foetus, 25 foetal tissues) and 146 blood samples of vaccinated animals were collected from dairy farms in and around Mumbai and Pune region. These samples were processed for isolation of Brucella organisms and further characterized by PCR and sequencing. A total of 26 (11.06%) Brucella isolates were recovered from 235 samples. Also, 5 isolates received from human cases were included in the study. BCSP 31 PCR showed an amplicon of 223 bp in all 31 isolates, 123 (61.5%) blood samples, 123 (64.73%) vaginal swabs and 27 (60%) aborted foetal material. IS711/AB and BM PCR showed an amplicon of 498 bp and 731 bp in 17 and 14 isolates, 42 (21%) and 38 (19%) blood samples, 43 (22.63%) and 34 (17.89%) vaginal swabs, while 7(15.55%) and 6 (13.33%) aborted foetal material, respectively. The phylogenetic analysis detected the ancestral origin of the organism. Rapid and correct diagnosis of brucellosis and vaccination is important to eradicate the disease. The molecular methods used in the present study speed up the diagnosis of the disease.

The ancestral origin of the critically endangered Quadricorna sheep as revealed by genome-wide analysis.

Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds’ biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Among primitive breeds, aside from sharing common ancestral genomic components, they also show several traits such as the policeraty, large horns in the ram, short tail, and a moulting fleece, considered as ancestral. Although most of the primitive breeds characterized by these traits are confined on the very edge of Northern Europe, several residual populations are also scattered in the Mediterranean region. In fact, although in Italy a large number of local breeds are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterized by several ancestral traits. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 33 primitive traits-related, Mediterranean and Middle-East breeds, with the specific aim to reconstruct its origin. After retaining 35,680 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds’ distances and by the maximum likelihood tree as implemented in treemix. Multiple convergent evidence from all our population genetics analyses, indicated that the two Quadricorna populations differ from all the other Italian breeds, while they resulted to be very close to the Middle Eastern and primitive European breeds. In addition, the genetic diversity indices highlighted values comparable with those of most of the other analyzed breeds, despite the two populations exhibit slightly different genetic indices suggesting different levels of genomic inbreeding and drift (FIS and FROH). The admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of the two populations, while on the other hand the treemix analysis seems to suggest an ancient admixture with other primitive European breeds. Finally, all these evidences seem to trace back the residual Quadricorna sheep to an early Neolithic spread, probably following a Mediterranean route and that urgent conservation actions are needed in order to keep the breed and all related cultural products alive.

A Preliminary Study of the Social History of the Cantonese Chinese Community in Singapore

Abstract This paper aims to provide a historical study of the development of the Cantonese community in Singapore. Through an archival study of various Cantonese associations, it will focus on the connotations of what it means to be Cantonese and the lives of Cantonese people in the context of Singapore. According to a 2020 Singapore population census, the “Cantonese” are currently the third largest Chinese-dialect group, making up almost fifteen percent of the Chinese population on the island state. The term Cantonese, in Singapore, commonly refers to those originating from the vicinity of China’s Guangdong Province, mainly from the south-west region of Guangdong, along the Pearl River Delta. Outnumbered by the Hokkien and Teochew communities, the Cantonese were largely centralized in the Kreta Ayer area and were the dominant dialect group there. Yet, the definition of the term “Cantonese” involves two major issues of geographical location and language system. Being Cantonese, as per the administrative control of Guangdong Province, encompasses all of Chinese descent whose respective ancestral origins are from Guangdong. Moreover, the Cantonese are defined by the unique characteristics of the Cantonese language as well. Therefore, this paper will attempt to differentiate the multiple definitions of the term Cantonese, followed by an overall history of the Cantonese people in Singapore.

Structure of SARS-CoV-2 M protein in lipid nanodiscs.

SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 Å resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity in a simple lipid bilayer and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.