Mathematical modeling in assessing the risk of restenosis after carotid endarterectomy

Carotid endarterectomy is the main way to combat atherosclerosis of the carotid arteries, which disrupts cerebral circulation. The generally accepted marker of atherogenesis risk are hemodynamic indices associated with near-wall shear stress. The purpose of the work is to conduct a comparative analysis of hemodynamic indices in various carotid bifurcation models. The influence of a virtual change in the geometric shape of the model in order to optimize hemodynamic indices is also being studied. On the basis of computed angiography data, carotid bifurcation models are constructed, in which critical zones of hemodynamic indices are built using computational fluid dynamics. A comparative analysis of the critical zones for different classes of models is carried out. Comparison of averaged indices for critical zones between 'normal' and post-operative groups gave more than 5-x worse results for the latter. The same results for the near-bifurcation parts of the zones give a 25% better result for postoperative models. Virtual 'removal' of insignificant plaques leads to a deterioration of the indices of up to 40% in the places of the plaque's former location. The described method makes it possible to build the indices critical zones and compare them for various types of models. A technique for virtual changing the shape of a vessel (virtual surgery) is proposed. The novelty of the approach lies in the use for comparative analysis both real vessel models and hypothetical 'improved' virtual ones, as well in the proposed division of post-operative model's critical zones into subzones of different genesis.

Message in a Bottle-Metabarcoding enables biodiversity comparisons across ecoregions

Background

Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning 3 Canadian ecoregions.

Results

This study revealed the presence of 26,263 arthropod species in the 3 ecoregions and indicated that at least another 3,000–5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall α-diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site, with turnover greater than nestedness, suggesting the presence of many transient species.

Conclusions

Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.

[Rehabilitation problems in Top Rated Databases]

Development of medical rehabilitation technologies are the investments into «human capital». The effectiveness criterion of the scientific institutions work dealing with the problems of rehabilitation is the scientific publication activity of their employees in this subject in high-ranking international databases (DB).

Purpose of the study. Analysis of the state of the scientific publication flow in the field of rehabilitation.

MATERIAL AND METHODS

Data from the Web of Science and Scopus databases for November 2019, depth from 1991 to 2018 were used.

RESULTS

It was revealed that the high level of the publication rating of Russia, which was noted in 1991-1992, has not yet been achieved in the Scopus database for medical rehabilitation. Measures have been identified to enhance it by increasing the growth rate of the Russian publication flow. It also noted the necessity to reduce Russia's dependence on the monopoly of foreign publishing corporations by creating domestic Russian resources and borrowing the experience of foreign colleagues.

CONCLUSION

The necessary measures should be taken at the level of authors, scientific organizations, the scientific community and the State in order to increase the Russian scientific publication flow in the direction of «Rehabilitation» in foreign top-rated databases. Authors of interdisciplinary articles need to correctly present metadata indicating the relation of the work to the problem of rehabilitation. The necessity is substantiated not only to increase the share of Russian scientific journals in international databases, but also to create domestic high-rating databases, as well as to harmonize the existing regulatory legal acts in regards of terms and definitions in the field of rehabilitation, to bring the headings of the Universal Decimal Classification aligned with the headings of high-ranking international databases. Given the high social significance of the «Rehabilitation» area, it is necessary to include it in the priority list and funded areas at a level corresponding to global trends.

[Medical rehabilitation: domestic scientific publication stream]

The formation of a high-tech healthcare system is provided for by national projects. The expected effectiveness of the implementation of these projects is possible only with full-fledged scientific support, which is reflected in the publication scientific rating of Russia in highly rated international databases (DB).

THE PURPOSE

Of this work is to analyze the Russian scientific publication stream on medical rehabilitation against the background of the world array of publications and its forecast for the near future.

MATERIAL AND METHODS

The data of Web of Science and Scopus DB has investigated. Analysis of Russian scientific publications was carried out at various hierarchical levels of the DB: for Web of Science - across the entire DB (5 sections), under the section «Life Sciences and Biomedicine», under the subsection «Rehabilitation»; for Scopus - in the division of knowledge «Medicine» (SUBJAREA (medi)), as well as in the subject area «Rehabilitation». The publication scientific rating of Russia was evaluated against the background of the world rating. Analysis of DB information was carried out for the period 1991-2018.

RESULTS AND CONCLUSION

For the period 1991-2018, the highest quantity of domestic publications on rehabilitation in the international rating databases Web of Science and Scopus was in 1991: 5.5% (3rd place out of 53 in the world ranking) and 2.3% (6th place out of 64), respectively. The forecast of the dynamics of the quantity, taking into account the data of this period, showed that Russia has practically reached this high level in Scopus, and at the current rate of growth in the publication activity of Russian scientists, in the Web of Science, it can only reach it by 2028.

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

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.

Validation of COI metabarcoding primers for terrestrial arthropods

Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40-60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).

Idiotypic and anti-idiotypic antibodies against polycyclic aromatic hydrocarbon in human blood serum are new biomarkers of lung cancer

Evaluation of epidemiologic risk factor in relation to lung cancer invoked by polycyclic aromatic hydrocarbons has been inconsistent. To address this issue, we conducted a prospective evaluation of new biomarkers for lung cancer classified according levels of idiotypic and anti-idiotypic antibodies against polycyclic aromatic hydrocarbons in human blood serum. The blood serums of 557 lung cancer patients and 227 healthy donors were analysis of these antibodies by ELISA. Collected data were regrouped and analyzed by gender, smoking, and age as predictors of risk lung cancer factors. Also, the data of lung cancer patients were additionally analyzed by stages and types of lung cancer, surgery, and chemotherapy. It was suggested to use ratio of idiotypic and anti-idiotypic antibodies rather than distinguish level each of them separately. The ratio of levels in healthy people was 3.32 times higher than in lung cancer patients. This approach gave more precisely results and great prognostic value. The logistic regression model (AUC = 0.9) and neural networks (AUC = 0.95) were built to compare lung cancer patients and healthy donors by predictors. The ELISA data of 49 people random sampled from the originally ELISA data and ELISA data of 52 coal miners as a group of lung cancer risk were confirmed logistic regression model. So, suggested idiotypic and anti-idiotypic antibodies against polycyclic aromatic hydrocarbons were not only shown difference between healthy donors and lung cancer patients also elicited group of lung cancer risk among healthy people.

[Transepithelial corneal collagen crosslinking in patients with progressive keratoconus]

PURPOSE

To assess the effectiveness of transepithelial collagen crosslinking (CXL) in patients with keratoconus.

MATERIAL AND METHODS

The study involved 44 patients (44 eyes) with stage I-II progressive keratoconus. Patients were divided into two groups. The 1^st group included 22 patients that had underwent transepithelial CXL. The 2^nd group included 22 patients that had underwent traditional CXL.

RESULTS AND DISCUSSION

All patients of the group 2 all patients had corneal syndrome, which lasted 2-4 days. In the 1^st group, 98% of the patients did not have corneal syndrome and their visual acuity (VA) was same as preoperative on the next day after the surgery. In the 2^nd group, the mean level of postoperative pain was 1.7 times higher than in group 1 (p<0.05). Six months after the treatment, uncorrected VA (UCVA) in the 1^st group has increased by 52%, the best corrected VA (BCVA) - by 17%, in the 2^nd group UCVA increased by 53%, BCVA - by 20% (p<0.05). The demarcation line in the 2^nd group was 2.2 times deeper than in the 1^st group (p<0.05). Six months after the treatment in the 1^st group mean K1, K2 and K_m decreased by 1.5%, 2.3% and 1.7% respectively (p>0.05); in the 2^nd group - by 3.6%, 3.9% and 4.1% (p<0.05) compared with the data before the surgery. One year after the treatment, mean K_max in the 1^st group decreased by 2.1%, in the 2^nd group - by 3.9%. Differences with preoperative values were statistically significant only in the 2^nd group.

CONCLUSION

Transepitelial CXL is a safe procedure well tolerated by patients and leading to a rapid restoration of visual function. Transepithelial CXL proved to have reduced effectiveness in inducing improvement in keratometric values, its effect on visual acuity was likely to be similar to that of epithelium-off CXL.

[Method of preventing late hemorrhagic complications after surgical treatment of secondary neovascular glaucoma]

The existing methods of surgical treatment of secondary neovascular glaucoma (NVG) in 50-55% of cases are accompanied by hemorrhagic complications, which lead to persistent increase of intraocular pressure (IOP), complete loss of vision and even eye death. Decreasing the risks of hemorrhagic complications after surgical treatment of secondary NVG is one of topical problems of ophthalmology.

PURPOSE

To study the effectiveness of a new method of preventing late hemorrhagic complications of surgical treatment of secondary NVG after central retinal vein occlusion (CRVO).

MATERIAL AND METHODS

The study included 148 patients (150 eyes) with secondary NVG after CRVO. The patients were divided into two groups: 98 patients (100 eyes) of the 1^st group underwent sinustrabeculectomy with cyclovitrectomy and traditional surgery preparation and post-op treatment; the second group consisted of 50 patients (50 eyes) who received surgical treatment in combination with interferon therapy. All patients were observed for 1.5 years with necessary ophthalmic examination methods.

RESULTS

At the end of the follow-up, the second group showed statistically significant (p<0.01) reduction in the rates of hemorrhagic complications by 80%, progression of neovascularization of the iris and structures of the angle of anterior chamber of the eye by 50%, progression of neovascularization of the retina accompanied by the development of fibrosis of posterior hyaloid membrane by 37%. Reduction of the rate of complications positively affected the functional and tonometric results leading to improved visual acuity and preservation or even widening of the field of vision by 118%, as well as 60% improvement of tonometric results.

CONCLUSION

The newly developed method of preventing post-surgical complications allowed significant reduction of the risks of hemorrhagic complications and improvement of functional and tonometric results of surgical treatment of patients with secondary NVG after CRVO.

Metabarcoding a diverse arthropod mock community

Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR‐amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Environmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish and tilapia. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184–187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM or S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, six fish species represent new records for the study area, while two require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods would enable its detection. In summary, we developed protocols that recovered eDNA from tropical oligotrophic aquatic ecosystems and confirmed their effectiveness in detecting fishes and diverse species of vertebrates.

Approaches to integrating genetic data into ecological networks

As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here, we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rica dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci, for example from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally, for mixed templates such as faecal contents of insectivorous bats, we use DNA metabarcoding targeting two sequence lengths (157 and 407 bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse, and we discuss the implications of this type of resolution on network analysis. Using these data, we construct the first molecular-based network of networks containing 3,304 interactions between 762 nodes of eight trophic functions and involving parasitic, mutualistic and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.

Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding 1

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.

A Sequel to Sanger: amplicon sequencing that scales

BACKGROUND

Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system.

RESULTS

By examining templates from more than 5000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL can reduce greatly reduce sequencing costs in comparison to first (Sanger) and second generation platforms (Illumina, Ion).

CONCLUSIONS

SMRT analysis generates high-fidelity sequences from amplicons with varying GC content and is resilient to homopolymer tracts. Analytical costs are low, substantially less than those for first or second generation sequencers. When implemented on the SEQUEL platform, SMRT analysis enables massive amplicon characterization because each instrument can recover sequences from more than 5 million DNA extracts a year.

Molecular phylogenetics and taxonomy of dwarf hamsters Cricetulus Milne-Edwards, 1867 (Cricetidae, Rodentia): description of a new genus and reinstatement of another

The taxonomy of the genus Cricetulus has been controversial. The phylogenetic relationships both within the genus and among Cricetulus lineages and other genera were examined using a set of five nuclear and two mitochondrial genes. The results demonstrate that Cricetulus in its current treatment is a polyphyletic assemblage because the subgenus Urocricetus is phylogenetically unrelated to all other Cricetulus and is a distant sister group to Phodopus. The grey hamster (C. migratorius) proved to be closer to Cricetus and Allocricetulus than to Cricetulus proper, which includes C. barabensis C. sokolovi and C. longicaudatus. Based on these results Urocricetus is elevated to the rank of a full genus and a new genus Nothocricetulus gen.nov. is described for the grey hamster.

Mono- and Combined Therapy of Metastasizing Breast Carcinoma 4T1 with Zoledronic Acid and Doxorubicin

The efficiency of monotherapy with zoledronic acid (Resorba), doxorubicin, and their combination was studied on the model of metastasizing breast carcinoma in BALB/c mice. Doxorubicin monotherapy was accompanied by a significant increase in median survival up to 57 days (vs. 34 and 35 days in control groups); 27% animals survived for 90 days (duration of the study). Bioluminescence area of the primary tumor significantly decreased on days 21 and 28; the total number of visceral metastases also decreased according to magnetic-resonance imaging data. Resorba monotherapy produced no general toxic effect, the median survival increased to 64 days, and 90-day survival was 33%. Imaging techniques (magnetic-resonance imaging, microtomography, bioluminescent analysis) showed that Resorba delayed the development of the primary tumor (regression of luminescence area on days 21 and 28, regression of standardized bioluminescence intensity on day 28) and significantly reduced the number of visceral metastases in comparison with the control. Combination therapy was less effective than monotherapy with the same medications. Median survival was 55 days, 90-day survival was 13%, but magnetic-resonance imaging and bioluminescence analysis after combination therapy also showed delayed growth of the primary tumor and reduced number of visceral metastases. Microtomography revealed bone metastases in ~30% animals of the control group; in experimental groups, no bone metastases were found. The experiment with periosteal (distal epiphysis of the femur) injection of 4T1-Luc2 tumor cells demonstrated pronounced selective effectiveness of Resorba in relation to bone metastases. Monotherapy with Resorba can prevent the development of not only bone, but also visceral metastases of breast cancer.

Authentication of Herbal Supplements Using Next-Generation Sequencing

BACKGROUND

DNA-based testing has been gaining acceptance as a tool for authentication of a wide range of food products; however, its applicability for testing of herbal supplements remains contentious.

METHODS

We utilized Sanger and Next-Generation Sequencing (NGS) for taxonomic authentication of fifteen herbal supplements representing three different producers from five medicinal plants: Echinacea purpurea, Valeriana officinalis, Ginkgo biloba, Hypericum perforatum and Trigonella foenum-graecum. Experimental design included three modifications of DNA extraction, two lysate dilutions, Internal Amplification Control, and multiple negative controls to exclude background contamination. Ginkgo supplements were also analyzed using HPLC-MS for the presence of active medicinal components.

RESULTS

All supplements yielded DNA from multiple species, rendering Sanger sequencing results for rbcL and ITS2 regions either uninterpretable or non-reproducible between the experimental replicates. Overall, DNA from the manufacturer-listed medicinal plants was successfully detected in seven out of eight dry herb form supplements; however, low or poor DNA recovery due to degradation was observed in most plant extracts (none detected by Sanger; three out of seven-by NGS). NGS also revealed a diverse community of fungi, known to be associated with live plant material and/or the fermentation process used in the production of plant extracts. HPLC-MS testing demonstrated that Ginkgo supplements with degraded DNA contained ten key medicinal components.

CONCLUSION

Quality control of herbal supplements should utilize a synergetic approach targeting both DNA and bioactive components, especially for standardized extracts with degraded DNA. The NGS workflow developed in this study enables reliable detection of plant and fungal DNA and can be utilized by manufacturers for quality assurance of raw plant materials, contamination control during the production process, and the final product. Interpretation of results should involve an interdisciplinary approach taking into account the processes involved in production of herbal supplements, as well as biocomplexity of plant-plant and plant-fungal biological interactions.

Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve

BACKGROUND

Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada.

NEW INFORMATION

The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.

[Spatial Distribution Features of the Root Biomass of Some Tree Species (Picea abies, Pinus sylvestris, Betula sp.)]

The effect of intra- and interspecific competition on the spatial distribution of the biomass and mortmass of woody plant roots in mixed tree stands has been studied. It has been found that the mass of roots in the samples from tree pairs of different species is higher than in the samples from monospecific pairs. Species-specific differences in the vertical distribution of roots and the effect of intra- and interspecific competition on the spatial structure of biomass have been shown. It has been noted that the proportion of dead roots increases almost linearly with depth.

[Factors limiting distribution of the rare lichen species Lobaria pulmonaria (in forests of the Kologriv Forest Nature Reserve)]

The distribution patterns and coenotic confines ofthe epiphytic lichen Lobaria pulmonaria have been studied. The factors limiting the habitat of this rare lichen species in the Kologriv Forest Nature Reserve (southern taiga subzone) have been revealed. It has been shown that L. pulmonaria is attracted to forest areas, which are less affected by humans and characterized by better light conditions than other communities. It has been found that L. pulmonaria is able to colonize trees at various ontogenetic states, beginning from virginal ones.

Modeling and integral X-ray, optical, and MRI visualization of multiorgan metastases of orthotopic 4T1 breast carcinoma in BALB/c mice

A model of highly metastasizing orthotopic allogeneic breast carcinoma was reproduced and standardized in experiments on BALB/c mice. 4T1 cells characterized by high metastatic activity were transfected with red fluorescent protein (RFP) gene or firefly luciferase (Luc2) gene. Unmodified 4T1 cells and modified 4T1-RFP and 4T1-Luc2 cells were subcutaneously injected to mature female mice into the second mammary fat pads. Quantitative evaluation of the primary node and visceral metastases was performed using magnetic-resonance imaging, X-ray and optical tomography. Modification of 4T1 cells with RFP gene considerably reduced their invasive and metastatic potential and led to spontaneous regression of the primary tumor in 20% cases. Modification of 4T1 cells with Luc2 gene had practically no effect on proliferative, invasive, and metastatic characteristics of the tumor and provided the possibility of quantitative analysis of the primary tumor dynamics by the luminescence intensity. The survival median in mice receiving unmodified 4T1 cells and transfected 4T1-RFP and 4Т1-Luc2 cells was 32, 42, and 38 days, respectively. Neither primary node nor tumor metastases accumulated gadolinium-containing contrast agent and Alasens fluorescent tracer. After implantation of 4T1 and 4Т1-Luc2 cells, multiple metastases were more often detected in the lungs, liver, spleen, spine, and regional lymph nodes and less frequently in the brain, which corresponded to metastasizing profile of human breast cancer. The developed model of orthotopic breast carcinoma 4T1 in BALB/c mice with complex detection of multiple organ metastases using X-ray microCT, optical, and MRI can be recommended for preclinical studies of new antitumor preparations.

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