Implications of hybridization, NUMTs, and overlooked diversity for DNA Barcoding of Eurasian ground squirrels

The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5-4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic 'mini-barcodes'.

Protocols for dry DNA storage and shipment at room temperature

The globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica(®) DNAstable(®) plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at -20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica(®) provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples. PVA was the second best protectant after Biomatrica(®) at room temperature, whereas trehalose was the second best protectant at 56 °C. In spite of lower PCR success, the DNA stored at -20 °C yielded longer sequence reads and stronger signal, indicating that temperature is a crucial factor for DNA quality which has to be considered especially for long-term storage. Although it is premature to advocate a transition to DNA storage at room temperature, dry storage provides an additional layer of security for frozen samples, protecting them from degradation in the event of freezer failure. All three forms of DNA preservation enable shipment of dry DNA and PCR products between barcoding facilities.

[Comparative efficacy of nitrofurans in children and adolescents with pyelonephritis in presence of crystalluria]

AIM

To evaluate the efficacy of nitrofurans in children and adolescents with pyelonephritis in the presence of crystalluria.

SUBJECTS AND METHODS

The study included 50 patients aged 4-14 years with chronic pyelonephritis in the presence of dysmetabolism. The patients underwent general blood test, general urinalysis with an urocytogram, bacteriological examination of urine, biochemical test of serum (uric acid, calcium, phosphorus, magnesium, urea, and creatinine) and 24-hour urinary excretion (uric acid, oxalates, calcium, phosphorus, and magnesium) at hospital admission and over time. The treatment regimen for Group 1 patients after antibiotic therapy involved furamag, Group 2 received furagin. The drugs were used in a dosage of 2 mg/kg/day in 2 divided doses for 14 days. Complaints, major clinical manifestations, crystalluria patterns, and a number of laboratory findings were analyzed over time.

RESULTS

The urinary sediment showed leukocyturia and bacteriuria in all the patients, oxaluria in 70% of the patients, uraturia in 10%, and mixed crystalluria in 20%. The main etiological agent of pyelonephritis was Escherichia coli (48.4%). Increased serum uric acid concentrations were revealed in 14% of the patients. Daily urine tests revealed hyperoxaluria, hyperuricosuria, and hypercalciuria in 86, 18, and 8% of the patients, respectively; urinary magnesium excretion was reduced in 86%. After treatment, Group 1 patients showed a more marked therapeutic effect in terms of a number of indicators (leukocyturia, crystalluria, uricosuria, magnesuria).

CONCLUSION

The results of the study showed that the antibacterial therapy involving antibiotics and nitrofurans for an exacerbation of chronic pyelonephritis in the presence of crystalluria not only provides an anti-inflammatory effect, but also leads to reductions in the level of crystalluria and the urinary content of uric acid and calcium. There was a significantly marked reduction in crystalluria, serum uric acid, and urinary oxalates and calcium in the children taking furamag. Out of nitrofurans, furamag may be recommended as the drug of choice to treat urinary tract infections in the presence of crystalluria.

Potential use of DNA barcodes in regulatory science: identification of the U.S. Food and Drug Administration's "Dirty 22," contributors to the spread of foodborne pathogens

The U.S. Food, Drug, and Cosmetic Act prohibits the distribution of food that is adulterated, and the regulatory mission of the U.S. Food and Drug Administration (FDA) is to enforce this Act. FDA field laboratories have identified the 22 most common pests that contribute to the spread of foodborne disease (the "Dirty 22"). The current method of detecting filth and extraneous material (tails, legs, carcasses, etc.) is visual inspection using microscopy. Because microscopy can be time-consuming and may yield inaccurate and/or nonspecific results due to lack of expertise, an alternative method of detecting these adulterants is needed. In this study, we sequenced DNA from the 5' region of the cytochrome oxidase I gene of these 22 common pests that contribute to the spread of foodborne pathogens. Here, we describe the generation of DNA barcodes for all 22 species. To date, this is the first attempt to develop a sequence-based regulatory database and systematic primer strategy to identify these FDA-targeted species. DNA barcoding can be a powerful tool that can aid the FDA in promoting the protection and safety of the U.S. food supply.

[Provisionality phenomenon in the histo- organo- and systemogenesis]

This review summarizes the results of the study of the provisionality phenomenon in the development of the organs of the urinary system (mesonephros, metanephros) in viviparous (human, rat) and oviparous (bird) amniotes, human organs of mixed origin (pituitary, ovary, stomodeum) reparative regeneration of supporting tissues (in humans and Syrian hamster), morphogenesis of primary hepatic cancer developing against the background of superinvasive opisthorchiasis. It is shown that during the development of tissues and organs, the stages of provisional and definitive histo- and organogenesis could be determined; saltatory mechanism is typical for embryonic organogenesis (formation of cartilaginous skeletal primordia, meso- and metanephrons) and foci of oncogenesis. Transformation zones of the type of tissue organization in the epithelium are located in the areas of contacts of the derivatives of different embryonic primordia. Mechanism of transformation of the epithelial layer of stomodeum and Rathke's pouch is provided by local activation of apoptosis and by the formation of the epithelial cells of a qualitatively new generation.

A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance

The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5' end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.

[Results of macular zone assessment with optical coherent tomography in patients with anterior endogenous uveitis]

45 patients (50 eyes) with anterior endogenous uveitis of various ethiology were included into the study. Examination included traditional ophthalmologic evaluation, laboratory testing and Optical Coherent Tomography (Stratus OCT 3000 "Carl Zeiss Meditec"). Retinal foveola thickness was showed to be 194-350 microm in 38 eyes (76%) compared with control group (everage value 172+21 microm). The average central macular thickness in examined group was 222+26 microm, it is more than in control group by 50 microm (p < 0.05). These results allow us to suggest that the majority of patients with anterior eye inflammation have inflammatory changes in posterior segment.

The role of DNA barcodes in understanding and conservation of mammal diversity in southeast Asia

Background

Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning.

Methodology and Principal Findings

DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized.

Conclusions

DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.

[Genetic diversity of ixodid tick-borne pathogens in Tomsk City and suburbs]

We studied two urban and two suburban biotypes of Tomsk City for tick-transmitted diseases prevalence in naturally collected ticks. Tick-borne encephalitis virus (TBEV) was found in 6.5% of tick samples, West Nile virus (WNV) in 2.2%, Borrelia spp. in 8%, Rickettsia spp. in 2.5%, and Ehrlichia spp. in 1.7% of samples. Genetic markers of Powassan virus, Bartonella spp., and Balbesia spp. were not found. Analysis of the genetic diversity of revealed pathogens resulted in the following conclusions: 1. TBEV strains belong to Siberian and Far-Eastern subtypes, and Far-Eastern subtype of TBEV is most frequent in urban biotypes (up to 43 % of urban strains of TBEV); 2. WNV strains belong to genotype la; 3. Borrelia spp. were classified as B. garinii; 4. Rickettsia spp. were classified as R. tarasevichiae and probably as a new Rickettsia raoultii subspecies; 5. Ehrlichia spp. were classified as E. muris. The coexistence of several pathogens was found in 5.7% of tick samples, and the most frequent combination was TBEV + Borrelia spp.

Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes

The freshwater fish fauna of Mexico and Guatemala is exceptionally diverse with >600 species, many endemic. In this study, patterns of sequence divergence were analysed in representatives of this fauna using cytochrome c oxidase subunit 1 (COI) DNA barcodes for 61 species in 36 genera. The average divergence among conspecific individuals was 0.45%, while congeneric taxa showed 5.1% divergence. Three species of Poblana, each occupying a different crater lake in the arid regions of Central Mexico, have had a controversial taxonomic history but are usually regarded as endemics to a single lake. They possess identical COI barcodes, suggesting a very recent history of isolation. Representatives of the Cichlidae, a complex and poorly understood family, were well discriminated by barcodes. Many species of Characidae seem to be young, with low divergence values (<2%), but nevertheless, clear barcode clusters were apparent in the Bramocharax-Astyanax complex. The symbranchid, Opisthernon aenigmaticum, has been regarded as a single species ranging from Guatemala to Mexico, but it includes two deeply divergent barcode lineages, one a possible new endemic species. Aside from these special cases, the results confirm that DNA barcodes will be highly effective in discriminating freshwater fishes from Central America and that a comprehensive analysis will provide new important insights for understanding diversity of this fauna.

[Detection of the West Nile Virus and its genetic typing in ixodid ticks (Parasitiformes: Ixodidae) in Tomsk City and its suburbs]

Four tick species, Ixodes persulcatus, I. pavlovskyi, I. trianguliceps, and Dermacentor reticulatus, were found in Tomsk and its suburbs in 2006. The species I. pavlovskyi was found to be dominant in the localities situated in Tomsk City, and I. persulcatus was dominant in its suburbs. Viral RNA and viral antigen of the West Nile virus (WNV) were detected in the ticks I. pavlovskyi and I. persulcatus collected in the city and its suburbs by the RT PCR method and enzyme immunoassay with monoclonal antibodies against protein E of the WNV. Average rate of the WNV infected ticks varied from 5.2 up to 11.7% in different localities. Identification of the nucleotide sequence of the protein E gene fragment allowed classifying the cDNA obtained as genotype Ia of the WNV. The sequences are proved similar to the strain LEIV-Vlg99-27889-human of the WNV isolated in Volgograd. The obtained data showed that natural foci of the WNV virus can appear in the city and its suburbs probably involving two dominant tick species. The WNV infected imagoes, larvae, and nymphs of I. persulcatus and I. pavlovskyi were collected from small mammals, lizards, and birds. Therefore we presume that these hosts can be involved in the circulation and distribution of WNV on the territory of Tomsk Region.

Species identification in cell culture: a two-pronged molecular approach

Species identification of cell lines and detection of cross-contamination are crucial for scientific research accuracy and reproducibility. Whereas short tandem repeat profiling offers a solution for a limited number of species, primarily human and mouse, the standard method for species identification of cell lines is enzyme polymorphism. Isoezymology, however, has its own drawbacks; it is cumbersome and the data interpretation is often difficult. Furthermore, the detection sensitivity for cross-contamination is low; it requires large amounts of the contaminant present and cross-contamination within closely related species may go undetected. In this paper, we describe a two-pronged molecular approach that addresses these issues by targeting the mitochondrial genome. First, we developed a multiplex PCR-based assay to rapidly identify the most common cell culture species and quickly detect cross-contaminations among these species. Second, for speciation and identification of a wider variety of cell lines, we amplified and sequenced a 648-bp region, often described as the "barcode region" by using a universal primer mix targeted at conserved sequences of the cytochrome C oxidase I gene (COI). This method was challenged with a panel of 67 cell lines from 45 diverse species. Implementation of these assays will accurately determine the species of cell lines and will reduce the problems of misidentification and cross-contamination that plague research efforts.

[The molecular-genetic study of juvenile endogenous attack-like psychoses]

Polymorphisms of the following genes (dopamine receptors D2 (Taq1A), D3 (Ser/Glu), D4 (VNTR, -521T/C, -616 G/C, -809A/G), catechol-O-methyltransferase, serotonin receptor type 2A (T102C), serotonin transporter (5-HTTLPR small i, Cyrillic VNTR) and brain-derived neurotrophic factor) have been studied in 260 men with juvenile endogenous attack-like psychoses and 145 age- and sex-matched controls. Type of psychopathological syndrome, PANSS scores and cognitive traits have been assessed. Only the T102C 5-HTR2A polymorphism was associated with some changes in the progress of this type of psychosis. As compared to the TT genotype, patients with 1 or 2 copies of the C allele were characterized by the absence of or less pronounced affective symptoms and more cognitive impairment that implies severity of illness. Moreover, the higher frequency of the C allele was found in the group of patients with chronic course of disease. In conclusion, the T102C polymorphism can be taken into account in prediction of juvenile endogenous attack-like psychosis.

Critical factors for assembling a high volume of DNA barcodes

Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR amplification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.

[Development of a PCR-based method for diagnostics of mycoses]

Since the express-diagnostics of mycoses in immune-deficit patients still remains an acute problem, we developed an effective test system (Kan-Am) to detect DNA Candida albicans, which is a leader in the list of causative agents of candidosis. A comparison study of three PCR-systems used to detect a broad spectrum of fungoid pathogens was carried out, and a universal system (FungAm), which ensures the detection of DNAs of above 78 strains of 25 types of pathogenic fungi, was selected. The results of clinical testing of the species-specific and universal PCR-systems are well confirmed by the culture method, and they are indicative of the efficacy of applying them for the diagnostics of mycoses in neonatology. The use of the mentioned systems is a promising factor for the express-diagnostics of mycoses in immunodeficiency patients. The high sensitivity of the method makes it possible to detect 10 to 100 cells of a causative agent in 100 mcl of the examined biological material, which is compatible with the culture method. A kit of dry reagents (IonoMix) designed for an accelerated sample preparation and isolation, from them, of DNAs on the basis of Chelex-100 and of proteinase K was worked out; the kit is portable and meant for a long-term storing.

[Clinical presentation of connective tissue dysplasia in adults]

Connective tissue dysplasia (CTD) markers (anthropometric parameters, joint hypermobility, state of the skin, osteomuscular system, etc.) as well as external respiration function, echocardiography, occlusive plethysmography data were assessed in 402 healthy subjects (142 males and 260 females, mean age 28.4 +/- 0.5 years). Four basic CTD symptom complexes were identified: ligamentous-articular, cutaneous, osteomuscular and cardial. Control group consisted of subjects free of CTD markers (n = 61). Combination of the above four symptom complexes occurred in 8.5% examinees. These show psychoemotional disorders, impaired function of external respiration, decreased size of the heart, low arterial pressure, affection of capillary and venous circulation.

Mitochondrial 12S rDNA sequence relationships suggest that the enigmatic bovid "Linh Duong" Pseudonovibos spiralis is closely related to buffalo

The phylogenetic position and taxonomic status of the recently described Southeast Asian endemic bovid Pseudonovibos spiralis were deduced from nearly complete 12S mitochondrial rDNA sequences of this species and Bubalus bubalis alongside 26 sequences of Bovidae from GenBank using Cervus elaphus (Cervidae) as outgroup. Maximum-likelihood analyses performed by PUZZLE and fastDNAml nested P. spiralis at the base of the subtribe buffalo Bovini, suggesting the close relationship of this enigmatic species with buffalo and enabling its distinction into the separate