DNA Barcode for the Parthenogenetic Surinam Cockroach Pycnoscelus surinamensis (Linnaeus, 1758) (Blattodea: Blaberidae) from India

DNA Barcoding is one of the emerging tools in molecular identification of faunal diversity, specifically insect fauna. The Surinam cockroach, Pycnoscelus surinamensis is the only known roach to be obligatorily parthenogenetic, with reported haplotypes. P. surinamensis is well established in Indomalayan, tropical and subtropical regions and substantially documented from India with a phenetic approach. Herewith we report the first set of mt DNA barcode from a vouchered collection for the species from southern Western Ghats India. Discussions are made on the identity of two sequences each of Blatteria species and Pycnoscelus species reported from USA.

OROK OR ULTA: NOTES TO THE ETHNONYM AND ETHNOGENESIS

Ороки — жители Сахалина, говорящие на одном из тунгусо-маньчжурских языков (южная группа), близкого к ульчскому и нанайскому. Не позднее конца XVII века они заселили Сахалин, практикуя транспортное оленеводство, в сочетании с охотой, рыболовством и добычей морского зверя. Цель работы, — анализ некоторых фактов, оказавшихся вне поля зрения предшественников. Это особый счет возраста оленей, который сближает их с восточными эвенами, структура календаря, имеющая аналогии с календарями амурских эвенков (название января), и с календарями орочей, ульчей и негидальцев (названия летних месяцев). Мозаичность ороков (субэтносы), наряду с особенностями природных условий острова и длительной изоляцией, обеспечили своеобразие космогонических представлений, пантеона, базовых ритуалов (летний медвежий праздник и др.). Выявлено существование названия северного оленя, в форме (ы,у,и)л(в/б)(э/е)л у коряков, юкагиров, чукчей, алеутов, чуванцев, северных хантов, тундровых ненцев с неизвестной этимологией (кроме ненецкого тундрового илебць — средство к жизни). Орокское название дикого оленя сиро можно связать с подготовкой к гону (обдирка рогов сирки / ситчи) взрослых самцов дикого оленя. Название домашнего оленя (ула/я) у ороков, ранее возводимое к понятию река (ул / уил), близко к алеутскому улинах, северохантыйскому ули и иле в тундровом диалекте юкагирского, могло быть заимствовано пра — «ороками» напрямую, или через промежуточную контактную группу, на Саяно-Алтае, или в процессе миграции на восток. Данные популяционной генетики, роднят их с этносами Саяно-Алтая (тувинцы-тоджинцы, тофалары и др.) практикующих до сих пор охоту, собирательство и кочевое транспортное оленеводство. Примерно близкий (и невысокий 11,5–17,4 %), уровень частотности «тунгусской» гаплогруппы С, у ороков, ульчей, удэгейцев, негидальцев, указывает, по-видимому, на малое участие эвенкиек в формировании мтДНК ороков (женский генофонд). Oroks are residents of Sakhalin who speak one of the Tungus-Manchu languages (southern group), close to Ulchi and Nanai. Since the end of the 16th century, they have inhabited Sakhalin, practicing transport reindeer husbandry, combined with hunting, fishing and hunting of sea animals. The purpose of this work is to analyze some facts that were out of the field of view of their predecessors. This is a special account of the age of deer, which brings them closer to the Eastern evens, a calendar structure that has analogies with the calendars of the Amur Evenks (the name of January), and with the calendars of the Orochi, Ulchi and Negidals (the names of the summer months). Mosaic Oroks (subethnoses), along with the peculiarities of the island's natural conditions and long-term isolation, provided the uniqueness of cosmogonic representations, Pantheon, basic rituals (summer bear festival, etc.). The existence of the name of the reindeer, in the form *(I, u,e)l(v/b) (э/e)l in Koryaks, Yukagirы, Chukchis, Aleuts, Chuvans, Northern Khants, tundra Nenets with unknown etymology (except for the Nenets tundra ilebts — a means to life). The name of the wild deer siro can be associated with the preparation for the rut (stripping the horns of sirki / sitchе) of adult male wild deer. The name of the domestic deer (ula / ylja) among the Oroks, previously raised to the concept of river (ul / uil), close to the Aleutian ulinakh, North Khanty uli and Il in the tundra dialect of Yukagir, could be borrowed by the Oroks directly, or through an intermediate contact group. Data from population genetics make them related to the ethnic groups of the Sayano-Altai (tuvians-todzhins, tofalars, etc.) who still practice hunting, gathering, and nomadic transport reindeer husbandry. The approximately close (and low) frequency level of Tungusian haplogroup C in Oroks, Ulchi, Udege, and Negidals (frequency within 11.5–17.4%) seems to indicate a small participation of Evenki in the formation of mt DNA of Oroks (female gene pool).

Peripheral Blood Mitochondrial DNA Levels Were Modulated by SARS-CoV-2 Infection Severity and Its Lessening Was Associated With Mortality Among Hospitalized Patients With COVID-19

IntroductionDuring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the virus hijacks the mitochondria causing damage of its membrane and release of mt-DNA into the circulation which can trigger innate immunity and generate an inflammatory state. In this study, we explored the importance of peripheral blood mt-DNA as an early predictor of evolution in patients with COVID-19 and to evaluate the association between the concentration of mt-DNA and the severity of the disease and the patient’s outcome.MethodsA total 102 patients (51 COVID-19 cases and 51 controls) were included in the study. mt-DNA obtained from peripheral blood was quantified by qRT-PCR using the NADH mitochondrial gene.ResultsThere were differences in peripheral blood mt-DNA between patients with COVID-19 (4.25 ng/μl ± 0.30) and controls (3.3 ng/μl ± 0.16) (p = 0.007). Lower mt-DNA concentrations were observed in patients with severe COVID-19 when compared with mild (p= 0.005) and moderate (p= 0.011) cases of COVID-19. In comparison with patients with severe COVID-19 who survived (3.74 ± 0.26 ng/μl) decreased levels of mt-DNA in patients with severe COVID-19 who died (2.4 ± 0.65 ng/μl) were also observed (p = 0.037).ConclusionHigh levels of mt-DNA were associated with COVID-19 and its decrease could be used as a potential biomarker to establish a prognosis of severity and mortality of patients with COVID-19.

Oscillatory movement of a dynein-microtubule complex crosslinked with DNA origami

During repetitive bending of cilia and flagella, axonemal dynein molecules move in an oscillatory manner along a microtubule (MT), but how the minus-end-directed motor dynein can oscillate back and forth is unknown. There are various factors that may regulate the dynein activities, e.g., the nexin-dynein regulatory complex, radial spokes, and central apparatus. In order to understand the basic mechanism of the oscillatory movement, we constructed a simple model system composed of MTs, outer-arm dyneins, and DNA origami that crosslinks the MTs. Electron microscopy (EM) showed patches of dynein molecules crossbridging two MTs in two opposite orientations; the oppositely oriented dyneins are expected to produce opposing forces. The optical trapping experiments showed that the dynein-MT-DNA-origami complex actually oscillate back and forth after photolysis of caged ATP. Intriguingly, the complex, when held at one end, showed repetitive bending motions. The results show that a simple system composed of ensembles of oppositely oriented dyneins, MTs, and inter-MT crosslinkers, without the additional regulatory structures, has an intrinsic ability to cause oscillation and repetitive bending motions.

Circulating mitochondrial DNA copy numbers represent a sensitive marker for diagnosis and monitoring of disease activity in systemic lupus erythematosus

ObjectivesCell-free DNA is involved in the pathogenesis of systemic lupus erythematosus (SLE) but the clinical value of cell-free DNA measurements in SLE is unknown. Our aim was therefore to examine the utility of mitochondrial (mt) DNA and nuclear (n) DNA quantification in SLE.MethodsEDTA plasma was drawn from 103 consecutive patients with SLE and from 56 healthy blood donors. mtDNA and nDNA copy numbers were quantified by PCR from cell-free plasma. Clinical parameters were recorded prospectively.ResultsCirculating mtDNA copy numbers were increased 8.8-fold in the plasma of patients with SLE (median 6.6×107 /mL) compared with controls (median 7.6×106 /mL, p<0.0001). Among all 159 individuals, a cut-off set at 1.8×107 mtDNA copies in a receiver operated curve identified patients with SLE with 87.4% sensitivity and 94.6% specificity; the area under the curve was 0.95 (p<0.0001). mtDNA levels were independent of age or gender, but correlated with Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) on multivariable analysis (p=0.004). Conversely, SLEDAI was associated with prednisone dose (p<0.001), anti-double stranded DNA-titres (p=0.003) and mtDNA levels (p=0.005), but not nDNA copy numbers. In 33 patients with SLE with available follow-up, the changes of mtDNA, but not those of nDNA concentrations, robustly correlated with the evolution of the SLEDAI (r=0.55, p=0.001).ConclusionsCirculating mtDNA unlike nDNA molecules are markedly increased in SLE plasma. Regardless of disease activity, circulating mtDNA levels distinguish patients with SLE from healthy controls with high sensitivity and represent an independent marker of SLE activity.

Novel primer targeting the mitochondrial NADH dehydrogenase subunit 4 (ND4) and NADH dehydrogenase subunit 5 (ND5) for detection of porcine (Sus scrofa) DNA fragments in food products for halal authentication

In this research, a pair primer targeting NADH dehydrogenase subunit 4 (ND4) gene of porcine (Sus scrofa) mt-DNA was designed and tested for its specificity. The ND4 primer was compared for its robustness against an established primer pair designed to amplify the NADH dehydrogenase subunit 5 (ND5) gene. The samples include non-halal meat animals (dog, porcine, and rat) and halal meat animals (chicken, cow, and horse). DNA from raw meat was isolated by modified Chloroform Isoamyl-Alcohol method and then was analyzed quantitatively with NanoDrop™ spectrophotometer followed by amplification using PCR technique. The amplification results proved that the two pairs of primers were specific, resulting in amplification of 120 bp DNA target for ND4 and 227 bp for ND5. It can be concluded that the two primers can differentiate between halal and non-halal animals. However, to determine the sensitivity of each primer, further research is needed.

Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae)

Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA–Rag-1; mt-DNA– 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island’s aseasonal ‘wet zone’ and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges–ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.

Evolving in the darkness: phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

Troglomorphism-morphological adaptation enabling life in constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism in freshwater fish requires a sound understanding of the evolutionary relationships among surface, troglomorphic, and intermediate lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to probe deeper into the evolution of the Sinocyclocheilus fishes of China. They comprise the largest cavefish diversification in the world with a remarkable array of derived troglomorphic traits, and are currently considered as an emerging multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals from throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497 bp per individual, including 4378 loci and 67,983 SNPs (61,023 parsimony-informative) shared across more than at least 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs only under a coalescent model (SVDquartets) showed a high degree of congruence and high node support (> 95) for most nodes in the phylogeny. The major clades we recovered conform to a pattern established previously using Sanger-based mt-DNA sequences, however, with a few notable exceptions. With an increased representation of the genome sequenced, we now recognize 6 major clades in this group, two additional clades than before. The blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus are now recognized as distinct clades due to their deep divergence from other clades. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identity were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. Our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.5 Mya, but most speciation events happened in the last 2 Mya, likely favored by the uplift of Qinghai-Tibetan Plateau and a climate driven aridification event forcing cave occupation during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.

The genetic diversity of the genus Mus (Linnaeus, 1758) in the eastern part of the North Caucasus

Background There are two species of Mus in the Caucasus: M. musculus and M. macedonicus. M. musculus is widespread in the Caucasus, where the species is found everywhere from the Black to the Caspian Sea. M. macedonicus is ubiquitous Transcaucasia. The most north-astern border of its distribution in the Caucasus, according to the literature, is located in the Derbent region, near the border between Dagestan and Azerbaijan. Results Cytochrome b mt-DNA of genus Mus research in this study in the Eastern Caucasus. About 70% of M. musculus haplotypes from the lowlands of Dagestan were recorded for the first time. One of these haplotypes accounts for approximately 25% of the total species diversity of haplotypes. M. macedonicus was found in only one locality, the Sarykum barchans, where this species prevails in number and accounts for 70% of the total number mice of the genus Mus. The species is characterized by low values of genetic diversity and nucleotide variability, which may indicate that the population originated from a small number of founders and may explain its relative isolation from the main range. The dating of the appearance of the ancestors of M. musculus in the east of the Russian Caucasus corresponds to 99-66 thousand years ago (at a mutation rate of 3-10% per million years). Conclusion The results obtained suggest that the history of the appearance of M. musculus in the Eastern Caucasus is more ancient and is not associated with human agricultural activities. We believe that possibly the ancestral range of M. musculus covered the eastern and western coasts of the Caspian Sea in the territory of southern Dagestan, Azerbaijan, and Iran. In this paper M. macedonicus, a Balkan-Asia Minor species, was registered for the first time in the North Caucasus. This species was registered in the center of Dagestan, where it inhabits sympatrically (on the territory) and syntopically (on the same biotope) with M. musculus. The low values of genetic diversity of M. macedonicus in the North Caucasus suggest that the population originated from a small group of founders.

Promising Epigenetic Biomarkers for the Early Detection of Colorectal Cancer: A Systematic Review

In CRC, screening compliance is decreased due to the experienced discomfort associated with colonoscopy, although this method is the gold standard in terms of sensitivity and specificity. Promoter DNA methylation (hypomethylation or hypermethylation) has been linked to all CRC stages. Study objectives: to systematically review the current knowledge on approved biomarkers, reveal new potential ones, and inspect tactics that can improve performance. This research was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines; the risk of bias was evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies criteria (QUADAS-2). The Web of Science® Core Collection, MEDLINE® and Scopus® databases were searched for original articles published in peer-reviewed journals with the specific keywords “colorectal cancer”, “early detection”, “early-stage colorectal cancer”, “epigenetics”, “biomarkers”, “DNA methylation biomarkers”, “stool or blood or tissue or biopsy”, “NDRG4”, “BMP3”, “SEPT9”, and “SDC2”. Based on eligibility criteria, 74 articles were accepted for analysis. mSDC2 and mSEPT9 were frequently assessed in studies, alone or together as part of the ColoDefense panel test—the latter with the greatest performance. mBMP3 may not be an appropriate marker for detecting CRC. A panel of five methylated binding sites of the CTCF gene holds the promise for early-stage specific detection of CRC. CRC screening compliance and accuracy can be enhanced by employing a stool mt-DNA methylation test.