Nelli Hovhannisyan

Yerevan State University

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Boris Gasparyan

National Academy of Sciences of Armenia

A. S. Sargsyan

National Polytechnic University of Armenia

Aleksandr Yesayan

Yerevan State University

Iosif Lazaridis

Harvard University

Astghik A. Shahkhatuni

Institute of Fine Organic Chemistry of Scientific - Technological Center of Organic and Pharmaceutical Chemistry

Marina Melkumyan

National Academy of Sciences of Armenia

Kristin Stewardson

Harvard University

Nick Patterson

Harvard University

Kendra Sirak

Harvard University

V. O. Topuzyan

Institute of Fine Organic Chemistry of Scientific - Technological Center of Organic and Pharmaceutical Chemistry

Cooperative Institutions

National Academy of Sciences of Armenia

Harvard University

Scientific Center of Zoology and Hydroecology

Yerevan State University

Pennsylvania State University

Romanian Academy

University of Bucharest

Howard Hughes Medical Institute

Centre National de la Recherche Scientifique

University of Vienna

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Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes

PLoS ONE (2019)

Stephen M. Richards Nelli Hovhannisyan Matthew Gilliham Joshua Ingram Birgitte Skadhauge

Hybridization capture with in-solution oligonucleotide probes has quickly become the preferred method for enriching specific DNA loci from degraded or ancient samples prior to high-throughput sequencing (HTS). Several companies synthesize sets of probes for in-solution hybridization capture, but these commercial reagents are usually expensive. Methods for economical in-house probe synthesis have been described, but they do not directly address one of the major advantages of commercially synthesised probes: that probe sequences matching many species can be synthesised in parallel and pooled. The ability to make "phylogenetically diverse" probes increases the cost-effectiveness of commercial probe sets, as they can be used across multiple projects (or for projects involving multiple species). However, it is labour-intensive to replicate this with in-house methods, as template molecules must first be generated for each species of interest. While it has been observed that probes can be used to enrich for phylogenetically distant targets, the ability of this effect to compensate for the lack of phylogenetically diverse probes in in-house synthesised probe sets has not been tested. In this study, we present a refined protocol for in-house RNA probe synthesis and evaluated the ability of probes generated using this method from a single species to successfully enrich for the target locus in phylogenetically distant species. We demonstrated that probes synthesized using long-range PCR products from a placental mammal mitochondrion (Bison spp.) could be used to enrich for mitochondrial DNA in birds and marsupials (but not plants). Importantly, our results were obtained for approximately a third of the cost of similar commercially available reagents.

Hybridization probe

Taxonomic rank

Oligomer restriction

Replicate

10.1371/journal.pone.0209499

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Citations (12)

Synthesis, Antiradical and Anticholinesterase Аctivity of Kетоamides of N-Substituted α,β-Dehydroamino Acids and Corresponding Imidazol-4-ones

Russian Journal of General Chemistry (2024)

A. G. Agababyan Nelli Hovhannisyan S. R. Tosunyan A. T. Makichyan A. A. Hovhannisyan

10.1134/s1070363224050062

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Recovery of Chloroplast Genomes from Medieval Millet Grains Excavated from the Areni-1 Cave in Southern Armenia

Research Square (Research Square) (2021)

Stephen M. Richards Leiting Li James Breen Nelli Hovhannisyan Oscar Estrada

Abstract Broomcorn millet ( Panicum miliaceum L.) was domesticated in northern China at least 7,000 years ago and was subsequentially adopted as a cereal in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, a region that has an important history in crop domestication. The rich botanical material found at Areni-1 includes grains identified by morphology as broomcorn millet that were 14 C dated to the medieval era (873 ± 36 CE and 1118 ± 35 CE). To retrace the demographic history of these broomcorn millet samples, we used ancient DNA extraction and hybridization capture enrichment to sequence and assemble three chloroplast genomes from the Areni-1 grains and then compared these sequences to 50 modern chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity and little inference on broomcorn demography could be made. However, in a phylogeny the chloroplast genomes separated into two clades with strong bootstrap support, similar to what has been reported for nuclear DNA from broomcorn millet. In a haplotype network, the chloroplast genomes of two accessions of wild (undomesticated) broomcorn millet contained a relatively large number of variants, 11 SNPs. These SNPs were not present in the domesticated varieties, suggesting these wild accessions may not be directly related to the lineages that underwent domestication or that broomcorn millet may have undergone a domestication bottleneck resulting in lost diversity in the chloroplast genome. These results demonstrate that broomcorn millet from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

Ancient DNA

Panicum miliaceum

Indel

10.21203/rs.3.rs-959635/v1

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Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia

Science (2022)

Iosif Lazaridis Songül Alpaslan-Roodenberg Ayşe Acar Ayşen Açıkkol Anagnostis P. Agelarakis

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

Mesopotamia

Ancient DNA

10.1126/science.abq0762

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Citations (29)

Oleanolic acid glycosides from Scabiosa caucasica and Scabiosa ochroleuca: Structural analysis and cytotoxicity

Planta Medica (2023)

Samvel Nazaryan Antoine Bruguière Nelli Hovhannisyan Loı̈c Briand Anne‐Claire Mitaine‐Offer

10.1055/s-0043-1774034

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THE INFLUENCE OF NON-PROTEIN AMINO ACIDS AND PEPTIDES ON BACTERIAL COLLAGENASE

Proceedings of the YSU B Chemical and Biological Sciences (2022)

A. S. Sargsyan Ani J. Karapetyan Liana A. Hayriyan Anahit M. Hovhannisyan Marina Melkumyan

Bacterial collagenolytic proteases have drawn increasing attention due to their essential role in the global nitrogen cycling and their virulent role in some diseases. The inhibition of these enzymes is attractive, as it does not attack the pathogen directly but rather blocks the colonization and infiltration of the host by the clostridia. Optically active non-protein α-amino acids have been screened for their ability to inhibit collagenase of Clostridium histolyticum. Both structure-based drug design approach (modeling) and that of determining enzyme activity in the presence of amino acids have been used to identify low molecular weight inhibitors of collagenase. The compounds able to inhibit collagenase activity have been revealed and IC50 values have been estimated.

Clostridia

Microbial collagenase

10.46991/pysu:b/2022.56.2.126

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Callus culture of oleander retains pharmacological activities of the plant

Natural products : an Indian journal (2011)

Nelli Hovhannisyan M.Mkrumyan Aleksandr Yesayan Rouben Aroutiounian Rebecca Newman

There is growing interest in the proposed antineoplastic activity of Nerium oleander components. Earlier we have developed an oleander callus culture. The objectives of this work were to reveal whether the cultured tissue is able to generate secondarymetabolites representative of the parent plant under in vitro conditions and whether these products retain biological activities of the source. The callus tissue produces oleandrin, oleandrigenin and odoroside, the main oleander secondary metabolites. The levels of cytotoxicity of callus and plant leaf extracts for human cell lines in vitro are comparable. Callus extract expresses species-specific cytotoxicity characteristic of the parent plant. The both extracts tested are toxic for human (normal embryo fibroblasts, Jurkat,K-562, L-41,KB cell lines) andmonkey (COS-7 cell line) cells, while rat PC-12 cell line has low sensitivity to the extract of leaves and is fully resistant to callus extract. The extracts were shown to induce apoptosis. The anti-genotoxic and anti-mutagenic activity of polysaccharide fractions of oleander leaves and callus culture was revealed and can be considered to be novel findings. Thus, oleander callus culture retains the main activities of the plant. This culture can be used as a biotechnological source of biologically/pharmacologically active compounds of oleander.

Callus

Plant tissue culture

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Armenian grape varieties SSR fingerprinting by using Qiaxcel DNA fragment analysis system

M. Dallakyan S. S. Yesoyan G. Melyan Aleksandr Yesayan Nelli Hovhannisyan

The applicability of QIAxcel System for SSR fingerprinting of grape varieties exploiting the internationally accepted 9 microsatellite markers was investigated. To optimize the allele sizing, a comparative genotyping of seven reference varieties with known sizes of microsatellite alleles, proposed by GENRES 081 project consortium, was performed. Ուսումնասիրվել և գնահատվել է QIAxcel համակարգի կիրառելիությունը խաղողի սորտերի՝ միջազգայնորեն ընդունված 9 միկրոսատելիտային մարկերներով ուսումնասիրությունների համար: Изучена и оценена применяемость системы QIAxcel для микросателлитного генотипироания сортов винограда с применением 9 междунороднопризнанных микросателлитных маркеров. В целях оптимизации определения длины аллелей было проведено сравнительное генотипирование семи стандартных сортов с известной длиной микросателлитных аллелей, предложенных консорцием проекта GENRES 081.

DNA profiling

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The genetic history of the Southern Arc: A bridge between West Asia and Europe

Science (2022)

Iosif Lazaridis Songül Alpaslan-Roodenberg Ayşe Acar Ayşen Açıkkol Anagnostis P. Agelarakis

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

Steppe

Pastoralism

Homeland

Chalcolithic

10.1126/science.abm4247

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Citations (85)

A new method for the synthesis of 2,3-aryl-5-arylideneimidazol-4-ones using N-trimethylsilylimidazole

Журнал Общей Химии (2023)

V. O. Topuzyan S. R. Tosunyan E. R. Aleksanyan E. H. Hakobyan Nelli Hovhannisyan

Oxazolone

Microwave heating

Dimethyl formamide

10.31857/s0044460x23100074

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