Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus).

To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.

Keeping Students Connected and Engaged in a Wet-Lab Research Experience during a Time of Social Distancing via Mobile Devices and Video Conferencing Software.

Two major COVID-19 pandemic challenges presented for in-person instruction included adhering to social distancing guidelines and accommodating remote learners who were temporarily isolated or permanently participating from afar. At Binghamton University, our First-year Research Immersion (FRI) program was challenged with providing students with a wet lab course-based undergraduate research experience (CURE), an intense hands-on experience that emphasized student teamwork, lab protocol development, iteration, troubleshooting, and other elements of the scientific process that could not be replicated in a fully remote environment. We developed an innovative technology approach to maximize all students' connection to the lab research experience, utilizing dedicated mobile devices (iPod Touch) and video conferencing software (Zoom) to synchronously connect remote learners to in-person learners, peer mentors, and instructors in our FRI research labs. In this way, despite limited lab capacities and fluctuating remote learning populations, we were able to connect remote learners to their peers and mentors in real-time and give them responsibilities that allowed them to be engaged and feel like meaningful participants in the research process. Although our students reported a preference for in-person labs, they noted that this hybrid model was better than other traditionally employed remote-learning lab options. We believe that the lessons learned here can be applied to improve access to research in all situations and allow us to be prepared for other catastrophic disruptions to the educational system.

Recent kuru-induced female gene flow disrupted the coevolution of genes and languages in the Papua New Guinea highlands.

OBJECTIVES: The island of New Guinea was settled by modern human over 50,000 years ago, and is currently characterized by a complex landscape and contains one-seventh of the world's languages. The Eastern Highlands of New Guinea were also the home to the devastating prion disease called kuru that primarily affected Fore-speaking populations, with some 68% of cases involving adult females. We characterized the mitochondrial DNA (mtDNA) diversity of highlanders from Papua New Guinea (PNG) to: (a) gain insight into the coevolution of genes and languages in situ over mountainous landscapes; and (b) evaluate the recent influence of kuru mortality on the pattern of female gene flow. MATERIALS AND METHODS: We sequenced the mtDNA hypervariable segment 1 of 870 individuals from the Eastern and Southern Highlands of PNG using serums collected in the 1950s to 1960s. These highlanders were selected from villages representing 15 linguistic groups within the Trans-New Guinea phylum. Genetic, linguistic, and geographic distances were calculated separately and correlations among those distance matrices were assessed using the Mantel test. RESULTS: Geographic, genetic, and linguistic patterns were independently correlated with each other (p < .05). Increased mtDNA diversity in kuru-affected populations and low Fst estimates between kuru-affected linguistic groups were observed. DISCUSSION: In general, the genetic structure among the Highland populations was shaped by both geography and language, and language is a good predictor of mtDNA affinity in the PNG Highlands. High kuru female mortality increased female gene flow locally, disrupting coevolutionary pattern among genes, languages, and geography.

Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions.

Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA findings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defined by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found.

Genomic insights into the origin of farming in the ancient Near East.

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Association of myeloperoxidase -463 G/A polymorphism with clinical outcome of Helicobacter pylori infection in Iranian patients with gastrointestinal diseases.

BACKGROUND: Polymorphisms in the immune related genes are important in the clinical outcome of Helicobacter pylori infection. Myeloperoxidase -463 G/A polymorphism has been shown to reduce enzyme expression and activity. OBJECTIVE: the aim of the present study is to investigate the association of myeloperoxidase G-463A polymorphism with clinical outcome of Helicobacter pylori infection. METHODS: two hundred and eighty five patients with positive culture of Helicobacter pylori from their gastric biopsies are included in this study. Human leukocyte DNA was extracted using salting out method and myeloperoxidase G-463A polymorphism was investigated by PCR-RFLP. All clinicopathological data were collected from individual records. RESULTS: When the patients were categorized according to the high (GG) and low + intermediate (AG+AA) genotypes of myeloperoxidase producers, there was a significant association between myeloperoxidase G-463A genotypes and clinical outcome of Helicobacter pylori infection (p=0.006). In search for combined effect of cagA status and myeloperoxidase genotypes on clinical presentations, only in cagA- Helicobacter pylori infected patients a significant association between myeloperoxidase genotypes and clinical outcome was found (p=0.0001). Also this association was found only in patients infected with vacA s1m1 genotype (p=0.008). CONCLUSIONS: Our findings suggest that the myeloperoxidase G-463A polymorphism is a host genetic factor which determines the clinical outcome of Helicobacter pylori infection. Moreover, the combination of host and bacterial genetics could provide a better understanding of clinical outcome after infection with Helicobacter pylori.