Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi

The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification. </p

Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order

Amyloids are protein fibrils with a highly ordered spatial structure called cross-β. To date, amyloids were shown to be implicated in a wide range of biological processes, both pathogenic and functional. In bacteria, functional amyloids are involved in forming biofilms, storing toxins, overcoming the surface tension, and other functions. Rhizobiales represent an economically important group of Alphaproteobacteria , various species of which are not only capable of fixing nitrogen in the symbiosis with leguminous plants but also act as the causative agents of infectious diseases in animals and plants. Here, we implemented bioinformatic screening for potentially amyloidogenic proteins in the proteomes of more than 80 species belonging to the order Rhizobiales . Using SARP ( S equence A nalysis based on the R anking of P robabilities) and Waltz bioinformatic algorithms, we identified the biological processes, where potentially amyloidogenic proteins are overrepresented. We detected protein domains and regions associated with amyloidogenic sequences in the proteomes of various Rhizobiales species. We demonstrated that amyloidogenic regions tend to occur in the membrane or extracellular proteins, many of which are involved in pathogenesis-related processes, including adhesion, assembly of flagellum, and transport of siderophores and lipopolysaccharides, and contain domains typical of the virulence factors (hemolysin, RTX, YadA, LptD); some of them (rhizobiocins, LptD) are also related to symbiosis

Supplementary – Supplemental material for Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order <i>Rhizobiales</i>

<p>Supplemental material, Supplementary for Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order <i>Rhizobiales</i> by Kirill S Antonets, Sergey F Kliver and Anton A Nizhnikov in Evolutionary Bioinformatics</p

Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.

Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level

Recombination Is Responsible for the Increased Recovery of Drug-Resistant Mutants with Hypermutated Genomes in Resting Yeast Diploids Expressing APOBEC Deaminases

DNA editing deaminases (APOBECs) are implicated in generation of mutations in somatic cells during tumorigenesis. APOBEC-dependent mutagenesis is thought to occur during transient exposure of unprotected single-stranded DNA. Mutations frequently occur in clusters (kataegis). We investigated mechanisms of mutant generation in growing and resting diploid yeast expressing APOBEC from sea lamprey, PmCDA1, whose kataegistic effect was previously shown to be associated with transcription. We have found that the frequency of canavanine-resistant mutants kept raising after growth cessation, while the profile of transcription remained unchanged. Surprisingly, the overall number of mutations in the genomes did not elevate in resting cells. Thus, mutations were accumulated during vigorous growth stage with both intense replication and transcription. We found that the elevated recovery of can1 mutant clones in non-growing cells is the result of loss of heterozygosity (LOH) leading to clusters of homozygous mutations in the chromosomal regions distal to the reporter gene. We confirmed that recombination frequency in resting cells was elevated by orders of magnitude, suggesting that cells were transiently committed to meiotic levels of recombination, a process referred to in yeast genetics as return-to-growth. In its extreme, on day 6 of starvation, a few mutant clones were haploid, likely resulting from completed meiosis. Distribution of mutations along chromosomes indicated that PmCDA1 was active during ongoing recombination events and sometimes produced characteristic kataegis near initial breakpoints. AID and APOBEC1 behaved similar to PmCDA1. We conclude that replication, transcription, and mitotic recombination contribute to the recovered APOBEC-induced mutations in resting diploids. The mechanism is relevant to the initial stages of oncogenic transformation in terminally differentiated cells, when recombination may lead to the LOH exposing recessive mutations induced by APOBECs in cell’s history and to acquisition of new mutations near original break

Нормотермическая аутоперфузия сердечно‑легочного комплекса ex vivo: оценка функционального статуса и метаболизма

Objective: to carry out a comparative study of the efficacy of a 6-hour normothermic ex vivo heart and lung autoperfusion and cold cardioplegia using Bretschneider’s solution (Custodiol®, Germany).Materials and methods. Landrace pigs weighing 50 ± 5 kg at the age of 4–5 months (n = 10) were used as a model for a series of acute experiments. In the experimental group (n = 5), the cardiopulmonary complex was conditioned by autoperfusion for 6 hours. In the control group, the heart pumping function was restored after 6-hour cold cardioplegia using Bretschneider’s solution. The efficiency of graft preservation was assessed by measuring hemodynamic parameters, myocardial contractile function, and myocardial oxygen consumption.Results. After reperfusion and repeated isolation of the working cardiopulmonary complex, cardiac output was 0.63 [0.37; 0.8] L/min and 0.37 [0.23; 0.37] L/min in the experimental and control groups, respectively (p &lt; 0.05). Indicators – global left ventricular stroke work index and preload recruitable stroke work – were significantly higher in the experimental group (p &lt; 0.05).Conclusion. Normothermic autoperfusion is significantly more effective in preserving the morphofunctional status of a donor heart than static cold storage with Bretschneider solution for 6 hours.Цель: провести сравнительное исследование эффективности 6-часовой нормотермической аутоперфузии сердечного трансплантата ex vivo и фармакохолодовой консервации раствором Bretschneider (Custodiol®, Германия).Материалы и методы. В качестве модели для проведения серии острых экспериментов были использованы свиньи породы ландрас весом 50 ± 5 кг в возрасте 4–5 месяцев (n = 10). В экспериментальной группе (n = 5) кондиционирование сердечно-легочного комплекса проводили методом аутоперфузии в течение 6 часов. В контрольной группе восстановление насосной функции сердца выполняли после 6-часовой фармакохолодовой консервации раствором Bretschneider. Оценку эффективности консервации трансплантата проводили путем измерения параметров гемодинамики, сократительной функции миокарда, потребления миокардом кислорода.Результаты. После реперфузии и повторной изоляции работающего сердечно-легочного комплекса сердечный выброс составил 0,63 [0,37; 0,8] л/мин и 0,37 [0,23; 0,37] л/мин в экспериментальной и контрольной группах соответственно (р &lt; 0,05). Показатели – глобальная ударная работа левого желудочка и рекрутируемая преднагрузкой ударная работа сердца – были значительно выше в экспериментальной группе (р &lt; 0,05).Заключение. В ходе проведенного исследования было показано значительное преимущество нормотермической аутоперфузии в сохранении морфофункционального статуса донорского сердца по сравнению со статической фармакохолодовой консервацией раствором Bretschneider в течение 6 часов