Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)

After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus , in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi . Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus . As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.

A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen

Genomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evolution in the plant pathogenic fungus Verticillium dahliae. We identified incomplete DNA methylation of repetitive elements, associated with specific genomic compartments originally defined as Lineage-Specific (LS) regions that contain genes involved in host adaptation. Further chromatin characterization revealed associations with features such as H3 Lys-27 methylated histones (H3K27me3) and accessible DNA. Machine learning trained on chromatin data identified twice as much LS DNA as previously recognized, which was validated through orthogonal analysis, and we propose to refer to this DNA as adaptive genomic regions. Our results provide evidence that specific chromatin profiles define adaptive genomic regions, and highlight how different epigenetic factors contribute to the organization of these regions.

Changes in the cell-free DNA characteristics of the of patients with catatonic and paranoid schizophrenia compared with a healthy control

Исследованы характеристики вкДНК в плазмах крови подвыборок больных кататонической (КШ, N=46) и параноидной формой (ПШ, N=54) шизофрении в сравнении с выборкой психически здоровых людей соответствующего возраста. Обнаружено, что независимо от типа шизофрении, концентрация вкДНК возрастает почти в 2 раза по сравнению с контролем, и нуклеазная активность плазм крови больных также повышена. Мы определили, что уровень 8-oxodG в мононуклеарах больных КШ и ПШ не различается и значительно выше контроля, и содержание гистонов Н2АХ в двух подвыборках больных шизофренией также значительно выше, чем в лимфоцитах здоровых людей, при этом уровень двунитевых разрывов в подгруппе КШ выше, чем в ПШ. Клетки с двунитевыми разрывами гибнут, пополняя пул вкДНК. Повышенная нуклеазная активность способствует выведению быстро расщепляемых АТ-богатых фрагментов и накоплению GC-богатых фрагментов в составе вкДНК. ВкДНК больных шизофренией обогащена ГЦ-богатыми фрагментами теломерного повтора по сравнению с вкДНК здоровых доноров. В составе вкДНК больных КШ число копий ГЦ-богатого рибосомного повтора увеличено по сравнению с выборкой ПШ и контрольной выборкой. Все исследованные показатели в большей степени изменены в группе пациентов с кататонической формой шизофрении, что может свидетельствовать о более выраженном воспалительном процессе при кататонии. CfDNA parameters of SZ patients with paranoid (N=54) and catatonic SZ (N=46) forms have been analyzed and compared with those of healthy controls. In the subjects from the both SZ forms, the mean cfDNA plasma concentration was twofold higher and NA of the plasma was higher than those in the healthy controls. In addition, peripheral blood lymphocytes of both SZ forms showed elevated levels of oxidized dna (8-OHDG) as well as increased number of double-stranded DNA breaks (flow Cytometry), and the ds-breaks level is higher in catatonic SZ. The cells with genomic DNA damages can undergo to unprogrammed cell death and contribute to circulating cfDNA. Increased DNase I activity in patients with schizophrenia promotes to cleave primarily AT-rich DNA-fragments and the accumulation of GC-rich fragments. Compared to those of healthy controls, plasma cfDNA samples of both SZ forms patients contained increased copy numbers of telomere DNA, as well as ribosomal RNA genes, and cf-rDNA concentration is higher in catatonic SZ group. Changes in cfDNA parameters was significantly higher in the catatonic SZ group, which may indicate a more pronounced inflammatory process.

CRISPR-Cas9 Dual-gRNA Attack Causes Mutation, Excision and Inversion of the HIV-1 Proviral DNA

Although several studies demonstrated that the HIV proviral DNA can be effectively targeted and inactivated by the CRISPR-Cas9 system, the precise inactivation mechanism has not yet been analyzed. Whereas some studies suggested efficient proviral DNA excision upon dual-gRNA/Cas9 treatment, we previously demonstrated that hypermutation of the target sites correlated with permanent virus inactivation. To better understand the mechanism underlying HIV inactivation, we analyzed the proviral DNA upon Cas9 attack with gRNA pairs. We observed that dual-gRNA targeting resulted more frequently in target site mutation than fragment excision, while fragment inversion was rarely observed. The frequencies varied for different gRNA combinations without an obvious relationship with the distance between the target sites, indicating that other gRNA and target DNA characteristics influence the DNA cleavage and repair processes.

Domestication of Blue Swimming Crab for Sustainability: Growth and Genetic Change

Blue swimming crabs (Portunus pelagicus) are a fisheries resource which is currently threatened by over-exploitation. Crab culture is one approach which can contribute towards sustainable use of blue swimming crab (BSC) populations. In this context, BSC domestication is considered necessary. The purpose of this study was to evaluate the genetic and growth changes occurring during initial stages of a BSC domestication program. The DNA of selected strains was examined using Random Amplified Polymorphism DNA (RAPD). Five OPA primers were used to generate a fragment pattern from the samples collected. The RAPD results showed that BSC domestication combined with selection for fast growth resulted in genetic change, with a genetic distance of 0.1053 – 0.3158 between 1st and 4th generations. This distance was associated with significantly higher growth rates after the 4th generation. After 100 days grow-out, mean growth in carapace width was 103 mm for 1st generation crabs and 109 mm in the 4th generation, with respective growth rates of 1.0 mm/day and 1.1 mm/ day. Domestication with selection of fast growing individuals as BSC broodstock resulted in a positive shift towards DNA characteristics associated with faster growth in subsequent BSC generations.Keywords: Blue swimming crab, Sustainability, Domestication, Selective breeding, Growth rate, RAPD

Assessing alignment-based taxonomic classification of ancient microbial DNA

The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.

Activation of interferon-α signaling by resveratrol, genistein and quercetin

Resveratrol, genistein and quercetin from the group of polyphenols from secondary plant metabolites reveal cancer preventive and antivirus effects realized via their pleiotropic influence on the different macromolecules in cells. These compounds can interact with DNA without the formation of covalent bonds. This process is usually followed by changes in spatial, physical-chemical and structural DNA characteristics that can result in disfunction of DNA metabolism enzymes and chromatin destabilization. Similar effects were described for anticancer drug Curaxine CBL0137 in association with activation of interferon-α signaling. We demonstrated dose-dependent stimulating effects of resveratrol, genistein and quercetin on interferon-α signaling using HeLa cells expressed mCherry protein with interferon-stimulated response elements (ISRE) in promoter. Furthermore, it was shown by live-cell fluorescent microscopy in HT1080 cells with mCherry-labeled histone H1.5 that described polyphenols induced the redistribution of this linker histone in cell nuclei. The data obtained suggest an existence of DNA-dependent mechanism of anticancer effects of plant polyphenols and a need for further study of crosslinks between the polyphenols’ influence on chromatin structure and the changes in genome function, in particular, induction of interferon- interferon-α signaling.

Experimental evolutionary studies on the genetic autonomy of the cytoplasmic genome “plasmon” in the Triticum (wheat)–Aegilops complex

The term “plasmon” is used to indicate the whole cytoplasmic genetic system, whereas “genome” refers to the whole nuclear genetic system. Although maternal inheritance of the plasmon is well documented in angiosperms, its genetic autonomy from the coexisting nuclear genome still awaits critical examination. We tested this autonomy in two related studies: One was to determine the persistence of the genetic effect of the plasmon of Aegilops caudata (genome CC) on the phenotype of common wheat, Triticum aestivum strain “Tve” (genome AABBDD), during 63 y (one generation per year) of repeated backcrosses of Ae. caudata and its offspring with pollen of the same Tve wheat, and the second was to reconstruct an Ae. caudata strain from the genome of this strain and its plasmon that had been resident in Tve wheat for 50 generations, and to compare the phenotypic and organellar DNA characteristics between the native and reconstructed strains. Results indicated no change in the effect of Ae. caudata plasmon on Tve wheat during its stay in wheat for more than half a century, and no difference between the native and reconstructed caudata strains in their phenotype and simple sequence repeats in their organellar DNAs, thus demonstrating the prolonged genetic autonomy of the plasmon from the coexisting genomes of wheat and several other species that were used in the reconstruction of Ae. caudata. The relationship between the proven genetic autonomy of the plasmon under changing nuclear conditions and its diversification during evolution of the Triticum–Aegilops complex is discussed.