Specific shoot formation in Miscanthus sacchariflorus (Poaceae) under different environmental factors and DNA passportization using ISSR markers

The generic complex Miscanthus Anderss. (Poaceae) is a unique example among herbaceous plants characterized by high values of growth of aboveground vegetative mass and practical use as a valuable source of alternative energy. Miscanthus is one of the most efficient solar energy accumulators, and since phytomeliorative use implies the cultivation of these resource plants in inconvenient and semi-shady areas, the question about the effect of insufficient lighting on the productivity of Miscanthus arises. As a result of a long-lasing introduction effort, the Central Siberian Botanical Garden SB RAS created a population of Miscanthus sacchariflorus (Maxim.) Benth., which has good prospects for growing under the conditions of the forest-steppe area in Western Siberia. The goals of our study were: (1) to determine the peculiarities of shoot formation, (2) to assess the cellulose and lignin accumulation in M. sacchariflorus populations under different lighting conditions and (3) to perform a DNA passportization of the Miscanthus population by ISSR marking. Evaluation of shoot formation and the amount of accumulated cellulose and lignin in plants was carried out under different degrees of illumination: one variant was grown in a sunny area, and the other, in partial shade. As a result of analysis of variance, it was found that the number of shoots does not depend on environmental conditions, but on the age of the plant, while environmental conditions have a significant effect on plant height. Although the samples of both M. sacchariflorus variants were characterized by different rates of creation of a continuous projective cover, plants in semi-shaded areas formed up to 89.34 % of shoots compared to their peers in illuminated areas, which did not affect significantly the size of the aboveground mass and the cellulose content in it. As a result of ISSR-analysis of genomic DNA in the M. sacchariflorus population, unique molecular polymorphic fragments were identified, which can be used for identification and DNA passportization at the inter-population level. Thus, the complex use of M. sacchariflorus as a valuable meliorative and bioenergetic culture is due to the high adaptive potential of this species. It was found that the illumination factor has virtually no effect on the amount of the cellulose content in the shoot, and a reduced content of the technologically undesirable lignin was observed in plants growing in the partial shade conditions

Features of the resource species Miscanthus sacchariflorus (Maxim.) Hack. when introduced in West Siberia

Here we provide a scientific justification and experimental support for the choice of easily renewable cellulosic feedstock Miscanthus sacchariflorus (Maxim.) Hack. in order to obtain high-quality nutrient broths therefrom for bacterial cellulose biosynthesis. The plant life-forms promising for breeding were screened under introduction conditions at the Central Siberian Botanical Garden, SB RAS, and this study was thus aimed at investigating the full and reduced ontogenetic patterns; cellulose and noncellulosic contents, including lignin; and duraminization of vegetative (feedstock source) organs throughout the seasonal development. The full ontogenetic patterns of the plants grown from seeds that had been collected in native habitats were compared to show that M. sacchariflorus and M. sinensis Anderss. accessions are distinguished by longer being at the most vulnerable developmental stages: seedlings and plantlets. Hence, it is preferable to cultivate seedlings on protected ground, and plantations are advisable to establish with more stable cloned vegetative material. The chemical compositions of the whole plant, leaf and stem separately, from seven M. sacchariflorus harvests were examined to reveal a rise in cellulose content and a drop in noncellulosic content with plantation age. The Miscanthus stem was found to contain more cellulose than the leaf, regardless of the plant age. The overall cellulose content was 48−53 %, providing a rationale for studies of bacterial cellulose biosynthesis in a M. sacchariflorusderived nutrient medium. Since high lignin content is undesirable for technological processes concerned with biosynthesis of bacterial cellulose, we performed histochemical assays of transverse sections of the culms to monitor the seasonal course of lignification. Our results suggest that the specific time limits for harvesting the aboveground biomass as a feedstock be validated by histochemical data on the seasonal course of lignification of M. sacchariflorus sprouts. To sum up, the examined chemical composition of M. sacchariflorus grown in the Siberian climate conditions demonstrated its prospects as a source of glucose substrate, the basic component of good-quality nutrient media for biosynthesis of bacterial cellulose

Characterization of Hepatitis B Virus and Human Immunodeficiency Virus among HIV/HBV Co-Infected Patients from the Republic of Guinea

Aim. Molecular genetic characterization of hepatitis B virus and human immunodeficiency virus in patients with HIV / HBV co-infection living in the Republic of Guinea. Materials and methods. 2168 blood serum samples obtained from the Republic of Guinea residents – blood donors and conditionally healthy people, without suspicion of Ebola virus disease, UK RUSAL employees and their families, as part of their routine medical examination. The presence of serological and molecular biological markers of HIV and HBV was examined. When HIV/HBV co-infection was detected, the nucleotide sequences of the complete HBV genomes and the HIV pol gene fragment were sequenced. Results and discussion. HIVserological markers were detected in 239 people (11.02 %). HIV RNA was detected in 31 people, which accounted for 12.9 % of patients in the seropositive group (1.43 % of the total group). HBV serological markers among HIV RNAs-positive individuals were detected in 29.03 % of patients, including 16.12 % HBsAg and 12.9 % anti-HBcore IgG. HBV DNA was detected in all HBsAg-positive and in two anti-HBcore IgG-positive patients, as well as in 12 people negative for all HBV serological markers analyzed in the work. Thus, HBV DNA was found in 61.29 % of HIV RNA-positive individuals. Based on the pol gene fragment nucleotide sequences analysis of 19 HIV samples, it was shown that the HIV circulating recombinant form CRF02_AG  prevails in the examined group (52.63 %) compared with HIV A1 (42.1 %), one sample was an independent recombinant of genotypes A1 and G. HBV phylogenetic analysis of the studied samples showed that genotype E prevails – 47.36 %, compared with HBV D1 – 21.05 %, D2 – 15.78 %, D3 – 10.52 % and A2 – 5.26 %. HIV and HBV samples have been detected that carry drug resistance mutations despite the antiretroviral therapy absence. HIV and HBV drug resistance mutations identification in ART-naive patients emphasizes the need for HIV surveillance programs as well as routine testing for HBV and HIV and HBV drug resistance before starting antiretroviral therapy in the clinical management of patients in the country

Determination of HIV Tropism in Patients with Antiretroviral Therapy Failure in Arkhangelsk Region

The aim of the study was to determine the tropism of the human immunodeficiency virus in patients with virological failure of antiretroviral therapy (ART) from the Arkhangelsk Region based on the analysis of the env gene V3 loop nucleotide sequence.Materials and methods. We used blood plasma samples obtained from 76 HIV-infected persons from the Arkhangelsk Region with virological failure of antiretroviral therapy. The nucleotide sequences of the HIV env gene C2-V3-C3 region were studied by PCR followed by sequencing. The genotype of the studied strains was determined based on the analysis of their phylogenetic relations with reference sequences from the international GenBank database, as well as using specialized programs. To predict viral tropism, the Garrido rule and the online bioinformatic tool Geno2Pheno[coreceptor] were used. The Geno2Pheno[coreceptor] algorithm, determines the false positive rate (FPR) based on the analysis of the env gene V3 loop nucleotide sequence. Results and discussion. Significantly lower representation of R5X4/X4-tropic HIV variants in long-term infected persons with subsubtype A6 virus compared to subtype B virus has been shown. For all FPR cut-off algorithms, a significant correlation between subtype and HIV tropism was observed (p=0.0014 and p=0.013 for FPR 10 % and FPR 20 %, respectively). While among subtype B strains, at least 57 % were identified as R5X4/X4-tropic variants (for an FPR of 10 %), including two strains classified as X4-tropic; among HIV subsubtype A6 even at an FPR of 20 %, the frequency of R5X4/X4-tropic samples only slightly exceeded 22 %. It can be assumed that the dynamics of changes in HIV tropism depends on the virus subtype. Significant differences in the distribution of amino acid residues of the V3 region sequences in the examined group between R5-tropic and R5X4/X4-tropic strains of subsubtype A6 for positions 18 (χ2=7.616, p=0.0058), 21 (χ2=7.281, p=0.007), 24 (χ2=5.587, p=0.0181), and 34 (χ2=5.144, p=0.0233) have been demonstrated. Among the R5X4/X4-tropic strains of the A6 subsubtype, amino acid substitutions were registered at positions 6, 19, 21, 26, 29, 30, which were not found in the R5-tropic A6 strains. The high occurrence frequency of a number of mutations previously described as presumably associated with resistance to maraviroc and similar drugs may indicate a natural polymorphism characteristic of the A6 subsubtype, which does not correlate with resistance to CCR5 co-receptor antagonists

Resource potential of some species of the genus Miscanthus Anderss. under conditions of continental climate of West Siberian forest-steppe

In the meantime, search for environmentally friendly renewable energy sources alternative to fossil fuel has been driven by energy security challenges including limited availability of fuel and energy price fluctuations. Therefore herbal perennial grasses with their rapid growth and prominent biomass yield increasingly make it a favorite choice as a valuable agricultural crop usable for cellulosic ethanol production. As an example, the genus Miscanthus Anderss. (silvergrass) comprises ca. 14–20 species including M. sacchariflorus (Maxim.) Hack., M. sinensis Anderss., M. purpurascens Anderss, and M. × giganteus, which appear to be an almost inexhaustible source of sustainable raw material, and several Miscanthus species were investigated as a potential biofuel energy crop with commercially viable way of its producing. Introduction and investigation of Miscanthus species were initiated in the Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences (CSBG SB RAS, Novosibirsk, Russia) based on the grass and ornamental plant collection in the late 1990s. The paper objective is studying the biological traits of three Miscanthus species introduced into the CSBG SB RAS, selection and genetic identification of cultivars and varieties as the most perspective agricultural crop. To evaluate the potential crop yield and selection prospects of Miscanthus species being competitive as a valuable biofuel energy crop, the authors have estimated seasonal rhythms of model species development in the continental climate conditions of West Siberia. The article characterizes different Miscanthus varieties obtained either by the ex situ or in situ methods; presents the biochemical analysis of plant material and molecular identification of three Miscanthus species introduced into the CSBG SB RAS. The seasonal development analysis of three selected varieties of Miscanthus (M. sacchariflorus, M. sinensis, and M. purpurascens) proved the hydrometeorological conditions to be advantageous for prominent biomass yield, e. g. contributory to use Miscanthus in West Siberia as an easy to grow cellulose-rich grass. Molecular markers applicable in DNA-identification and genetic passportization of Miscanthus varieties have been established, which are perspective as such an economically available plant material as alternative non-woody source of cellulose

The formation and the study of a collection of the Miscanthus resource species gene pool in the conditions of the West Siberian forest steppe

Several species of the genus Miscanthus Anderss. (elephant grass) characterized by a high rate of growth of the aboveground vegetative mass are currently in the focus of attention due to their high practical application as a source of bioethanol and cellulose. The main goals of this study were: (1) molecular genetic identification and (2) histochemical analysis of the genus Miscanthus Anderss. species in the collection of Central Siberian Botanical Garden SB RAS in order to identify the most perspective and technically valuable individuals. To study the collection of Miscanthus samples, a multi-disciplinary approach was applied. To collect the samples of different species from native habitats, traditional systematic and geobotanical methods (comparative morphological and phytocenological) were used. According to the results of the ISSR-analysis, 16 samples of three Miscanthus species were divided into two clades: Sinensis and Sacchariflorus, the former including two subclades. For the samples of M. purpurascens_I and II, a hybrid origin of this species was confirmed by ISSR data. The molecular data obtained from the study allowed us to hypothesize that the samples involved in the subclade I of the Sinensis clade could be used as donors of resistance to adverse environments, and the samples of the subclade II, as donors of high biomass productivity. Based on histochemical analysis, sclerenchyma cells were characterized by the most lignin-rich thickened membranes, so the most appropriate direction in Miscanthus selection should be based on identification and using less lignin-containing samples

Profile of Hepatitis B Virus Mutations Associated with HBsAg-Negative Disease in Patients of Hemodialysis Centers

The aim of this study was to characterize mutations in the hepatitis B virus (HBV) genome associated with HBsAg-negative form of the disease in patients receiving hemodialysis replacement therapy. Materials and methods. We used blood plasma samples obtained from hemodialysis centers in St. Petersburg, Russia – 173 patients and 108 patients from Belgrade, Republic of Serbia. The samples were examined for the presence of serological (HBsAg, antibodies anti-HBs IgG, anti-HBcore IgG) and molecular-genetic (HBV DNA) markers of HBV followed by whole-genome sequencing and determination of clinically significant virus mutations. Results and discussion. Antibodies to hepatitis B were detected in 7.5 % and 11.1 % of patients from St. Petersburg and Belgrade, respectively. HBsAg was identified only in 1.1 % of cases in the group from Russia and in 0.9 % of cases in the group from Serbia. HBV DNA was determined in 2.8 % of the studied samples from both, patients from Saint-Petersburg and Belgrade. Phylogenetic analysis of 9 viral isolates showed that genotype D virus (88.9 %) prevailed as compared to genotype A (11.1 %) in the examined group. Among the samples obtained from patients from St. Petersburg, four belonged to the D2 sub-genotype, one to the D3 genotype. Four samples obtained from Belgrade patients belonged to different sub-genotypes – D1, D2, D3, A2, respectively. When analyzing the nucleotide sequences of the HBV genomes, mutations in the MHR region were detected in all cases, but only in HBsAg-negative isolates, mutations were revealed in the region of 124–147 amino acids, including mutations P120T, R122K, A128V, Q129R, M133I, G145R affecting the recognition of HBsAg by anti-HBs antibodies and associated with the resistance of the virus to the vaccine. The results of this study indicate that transmission of blood-borne viral hepatitis agent in the hemodialysis departments of the Russian Federation and the Republic of Serbia still exists. The prevalence of the latent chronic hepatitis B, coupled with the presence of vaccine escape mutations in all identified cases, indicates the need to pay close attention to the occurrence of the virus mutant variants in hemodialysis centers

Monitoring of coronavirus infection in the kyrgyz population

Purpose of the study: to study the dynamics of developing herd immunity against SARS-CoV-2 in the population of the Republic of Kyrgyzstan during COVID-19. Materials and methods. The work was carried out using the methodology for assessing population immunity developed by Rospotrebnadzor (Russia) as well as the Ministry of Health (Kypgyzstan) and the St. Petersburg Pasteur Institute. The selection of participants was carried out by questionnaire using a cloud (Internet server) service. To monitor population immunity, a cohort of 2421 subjects was formed, who participated in all stages of seromonitoring. Volunteers were randomized according to age groups (1–17, 18–29, 30–39, 40–49, 50–59, 60–69, 70+ years), regional and professional factors. Antibodies (Abs) against SARS-CoV-2 nucleocapsid (Nc) and the receptor binding domain (RBD) of S-glycoprotein were determined by qualitative and quantitative methods. The study was carried out in 3 stages according to a single scheme: 1st stage — 06/28–07/03/2021, 2nd — 21–25/02/2022 and 3rd — 31/10–04/11/2022. Since 2021, Kyrgyzstan has been vaccinating the population against SARS-CoV-2 mainly using inactivated whole-virion vaccines. Results. Population immunity against SARS-CoV-2 was predominantly accounted for by both Ab types (Nc+RBD+). By the 3rd stage, the percentage of such persons reached 99.2%, Nc–RBD– volunteers — up to 0.8%. At the 1st stage, middle-aged people dominated, but age differences were leveled out by the 2nd stage. The greatest impact on seroprevalence was found among medical workers, the smallest — among businessmen and industrial workers. Populational vaccination significantly impacted on the state of herd immunity that reached 25% by the 3rd stage. The refusals of the population in Kyrgyz Republic from vaccination noted at the 2nd and especially 3rd stages did not significantly affect level of herd immunity, which could probably be associated with asymptomatic cases of COVID-19, against which primary vaccination had a booster effect. Conclusion. The dynamics of population humoral immunity against SARS-CoV-2 included a number of changes in the level of circulating antibodies (Nc, RBD), caused by both primary infection and vaccination. The herd immunity formed in population of Kyrgyzstan allowed to reduce the incidence of COVID-19 to almost sporadic level

Корреляционный анализ морфофункциональных и иммунологических параметров у пациентов с продвинутыми стадиями первичной открытоугольной глаукомы

PURPOSE. To study the correlations between the immunological data and the indicators of electroretinography (ERG) and optical coherence tomography (OCT) in patients with advanced stages of primary open-angle glaucoma (POAG).METHODS. Previously, we conducted a multimodal study of patients with advanced stages of glaucoma involving ERG, morphometric and immunological studies. In this new study we performed a correlation analysis of the immunological and morphofunctional data of patients with advanced stages of POAG. The study included 35 patients (35 eyes), among them 19 women and 16 men, who were divided into two groups: group 1 — stage II POAG (12 patients, 12 eyes), and group 2 — stage III POAG (23 patients, 23 eyes). The average age of the subjects was 64.2±6.5 years. Intraocular pressure was compensated in all study patients. The Pearson's correlation coefficient was used to calculate the linear relationship between continuous features.RESULTS. In the subgroup with stage II POAG significant correlations of moderate strength (according to the Chaddock scale) were found between the parameters of pattern ERG (PERG) and photopic negative response (PhNR) and the level of VEGF-A in the blood serum (BS), EGF in the tear fluid (TF) and aqueous humor (AH); strong correlations — for the concentrations of EGF and TGF-β2 in the AH. In group 2, moderate correlations between PERG and PhNR parameters and the level of IL-1RA in the TF were found, as well as moderate correlation of TGF-β2 expression in the AH with PnHR amplitude from the baseline. In patients with stage II glaucoma, the levels of MIP-1β/CCL4 in the TF, IL-1RA in the intraocular fluid correlated with the thickness of the retinal nerve fiber layer (RNFL) and retinal ganglion cell layer (GCL), while the EGF in the TF and AH correlated with RNFL thickness. In the group with stage III POAG, correlations of moderate strength were found for the expression level of TNF-α, IL-8/CXCL8 in the TF and RNFL thickness, and strong correlations — for the level of IP-10/CXCL10, HGF/SF, TGF-β2 in AH and the thickness of RNFL and GCL.CONCLUSION. Comparison of ERG, OCT findings and the level of cytokines of various biological effects in the BS, TF and AH confirmed the high informativeness of PERG and PhNR indicators and immunological data as markers of advanced stages of POAG, and allow EGF to be considered as the most promising pathogenetically oriented immunological marker of II and III stages of glaucoma.ЦЕЛЬ. Изучить корреляционные взаимосвязи между данными иммунологических исследований и показателей электроретинографии (ЭРГ) и оптической когерентной томографии (ОКТ) у пациентов с продвинутыми стадиями первичной открытоугольной глаукомой (ПОУГ).МЕТОДЫ. Ранее нами было выполнено мультимодальное исследование пациентов с продвинутыми стадиями глаукомы, включающее электроретинографию, морфометрические и иммунологические исследования. В настоящей работе проведен корреляционный анализ данных иммунологических и морфофункциональных исследований у больных с продвинутыми стадиями ПОУГ. Проанализированы результаты исследований 35 пациентов (35 глаз), в том числе 19 женщин и 16 мужчин, в двух группах: 1 — с развитой (12 больных, 12 глаз), и 2 — далекозашедшей стадией ПОУГ (23 пациента, 23 глаза). Средний возраст исследуемых составил 64,2±6,5 лет. Внутриглазное давление было компенсировано у всех обследуемых. Для вычисления линейной зависимости между непрерывными признаками использовали коэффициент корреляции Пирсона.РЕЗУЛЬТАТЫ. В подгруппе с развитой глаукомой выявлены достоверные корреляции «заметной» силы (по шкале Чеддока) между параметрами паттерн-ЭРГ (ПЭРГ) и фотопического негативного ответа (ФНО) и уровнем VEGF-A в сыворотке крови (СК), EGF в слезной жидкости (СЖ) и внутриглазной жидкости (ВГЖ); и взаимосвязи «высокой» силы – для концентраций EGF и TGF-β2 в ВГЖ. В группе больных с далекозашедшей ПОУГ выявлены корреляции «умеренной» силы для параметров ПЭРГ и ФНО и содержания IL-1RA в СЖ, и «заметная» корреляция экспрессии TGF-β2 в ВГЖ с амплитудой ФНО от изолинии. У пациентов со развитой стадией глаукомы уровни содержания MIP-1β/CCL4 в СЖ, IL-1RA в ВГЖ коррелируют с толщиной слоя нервных волокон сетчатки (СНВС) и ганглиозных клеток сетчатки (ГКС), а концентрации EGF в СЖ и ВГЖ — с толщиной СНВС. В группе с далекозашедшей ПОУГ обнаружены корреляции «умеренной» силы для уровня экспрессии TNF-α, IL-8/CXCL8 в СЖ и толщины СНВС и «заметной» силы — для содержания  IP-10/CXCL10,  HGF/SF,  TGF-β2  в  ВГЖ  и  толщины СНВС и слоя ГКС.ЗАКЛЮЧЕНИЕ. Сопоставление результатов электроретинографии, ОКТ и уровня цитокинов разнообразного биологического действия в СК, СЖ и ВГЖ подтверждают клинически значимую информативность параметров ПЭРГ и ФНО и показателей иммунологических исследований как маркеров продвинутых стадий ПОУГ и позволяют выделить EGF в качестве наиболее перспективного патогенетически ориентированного иммунологического маркера II и III стадии глаукомы