https://biocomm.spbu.ru/issue/feed Biological Communications 2021-06-30T15:11:43+03:00 Anton A. Nizhnikov biocomm@spbu.ru Open Journal Systems <p>Biological Communications is a rebranded new title of the former journal «Vestnik of Saint Petersburg University. Series 3. Biology». The journal was founded as «Vestnik of Leningrad University» in 1946.&nbsp;Since 1953, it was published under several series. In 1956 the series «Biology» was first established.&nbsp;As its predecessors, Biological Communications is published at a quarterly&nbsp;basis.</p> https://biocomm.spbu.ru/article/view/8458 Structural organization of <em>TFL1</em>-like genes in representatives of the tribe Phaseoleae DC. 2021-06-30T15:11:32+03:00 Ekaterina Krylova e.krylova@vir.nw.ru Ksenia Strygina k.strygina@vir.nw.ru Elena Khlestkina director@vir.nw.ru <p>The type of stem growth is one of the key features in determining plant architectonics. Stem growth type is an economically important trait. It interconnects with stem length, flowering duration, yield, resistance to lodging, and suitability of mechanized cultivation. Mutations in the <em>TFL1</em> gene and its homologs have been demonstrated to change meristem indeterminacy across genera. The aim of this work was to characterize and compare the structural organization of <em>TFL1</em>-like genes in representatives of the tribe Phaseoleae (pigeonpea <em>Cajanus cajan</em>, soybean <em>Glycine max</em>, common bean <em>Phaseolus vulgaris</em>, adzuki bean <em>Vigna angularis</em>, mung bean <em>V. radiata</em>, and cowpea <em>V. unguiculata</em>) based on <em>in silico</em> analysis, including analysis of nucleotide sequences, predicted elements in promoter regions, predicted amino acid sequences, putative functional domains and 3D protein structures. We investigated <em>TFL1 </em>(one gene for adzuki bean, four copies for soybean, two copies for other studied species), <em>ATC </em>(two copies for soybean, one gene for other investigated species), and <em>BFT</em> (two copies for soybean, one gene for other studied species) gene family members found in whole-genome sequences databases available for representatives of the tribe Phaseoleae. The presence of duplicated copies for all genes in soybean may be a result of the last genome duplication event during the evolution of this species. Duplication of <em>TFL1 </em>gene to two copies in most of studied species of the tribe Phaseoleae is probably accompanied by the maintenance of the functional state of these genes. The exception is <em>VrTFL1.2</em> of <em>V. radiata</em>, which likely had lost its functionality. This work broadens the existing data about the number of gene copies, their structural divergence and evolution, and the expected functional differences. This information will be important for understanding the molecular genetic mechanisms underlying the maintenance of indeterminacy in the growth of the shoot apical meristem, as well as in the control of the transition to the reproductive phase of plant development.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Ekaterina Krylova, Ksenia Strygina, Elena Khlestkina https://biocomm.spbu.ru/article/view/8649 The application of Nanopore sequencing for variant calling on the human mitochondrial DNA 2021-06-30T15:11:29+03:00 Anton Shikov antonshikov96@gmail.com Viktoriya Tsay viktoriya14054@gmail.com Mikhail Fedyakov fedyakovma@mail.ru Yuri Eismont y-eis@inbox.ru Alena Rudnik rudnik.spb@mail.ru Stanislav Urasov urasta@list.ru Sergey Sherbak golotaa@yahoo.com Oleg Glotov olglotov@mail.ru <p>The emergence of long-read sequencing technologies has made a revolutionary step in genome biology and medicine. However, long reads are characterized by a relatively high error rate, impairing their usage for variant calling as a part of routine practice. Thus, we here examine different popular variant callers on long-read sequences of the human mitochondrial genome, convenient in terms of small size and easily obtained high coverage. The sequencing of mitochondrial DNA from 8 patients was conducted via Illumina (MiSeq) and the Oxford Nanopore platform (MinION), with the former utilized as a gold standard when evaluating variant calling’s accuracy. We used a conventional GATK3-BWA-based pipeline for paired-end reads and Guppy basecaller coupled with minimap2 for MinION data, respectively. We then compared the outputs of Clairvoyante, Nanopolish, GATK3, Longshot, DeepVariant, and Varscan tools applied on long-read alignments by analyzing false-positive and false-negative rates. While for most callers, raw signals represented false positives due to homopolymeric errors, Nanopolish demonstrated both high similarity (Jaccard coefficient of 0.82) and a comparable number of calls with the Illumina data (140 vs. 154) with the best performance according to AUC (area under ROC curve, 0.953) as well. In sum, our results, despite being obtained from a small dataset, provide evidence that sufficient coverage coupled with an optimal pipeline could make long reads of mitochondrial DNA applicable for variant calling.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Anton Shikov, Viktoriya Tsay, Mikhail Fedyakov, Yuri Eismont, Alena Rudnik, Stanislav Urasov, Sergey Sherbak, Oleg Glotov https://biocomm.spbu.ru/article/view/9265 Supply of acetyl-CoA to N<sub>2</sub>-fixing bacteroids: insights from the mutational and proteomic analyses of <em>Sinorhizobium meliloti</em> 2021-06-30T15:11:22+03:00 Olga Onishchuk olony@yandex.ru Oxana Kurchak okurchak@yahoo.com Elena Chizhevskaya chizhevskaya@yandex.ru Boris Simarov robb@yandex.ru Nikolay Provorov provorovnik@yandex.ru <p>Rhizobia represent a diverse group of gram-negative bacteria capable of fixing atmospheric nitrogen in symbiosis with leguminous plants. Mechanisms of symbiotic efficiency are important to study not only to reveal the “fine tuning” of the host–symbiont supra-organismal genetic system emergence, but also to develop agriculture with minimal environmental risks. In this paper we demonstrate that among seven genes whose inactivation by Tn5 insertions results in an increased efficiency of rhizobia (<em>Sinorhizobium meliloti</em>) symbiosis with alfalfa (Eff<sup>++</sup> phenotype), six genes are involved in the metabolism of small molecules. One of them (SMc04399) encodes for acetate-CoA transferase catalyzing the formation of acetyl-CoA from acyl-CoA. Since acetyl-CoA is required for operation of the Krebs cycle, providing ATP for symbiotic N<sub>2</sub> fixation, we suggest that a significant portion of this coenzyme utilized by bacteroids is provided by the plant cell supporting the energy-consuming nitrogenase reaction. Proteomic data analysis allow us to reveal the lability of enzymatic pathways which are involved in bacteroids in the production and catabolism of acetyl-CoA and which should be modified to obtain the Eff<sup>++</sup> phenotype. This phenotype was developed also after inactivation of NoeB protein which is involved in the host-specific nodulation and is characterized by an elevated production in wild type <em>S. meliloti </em>bacteroids, suggesting a multifunctional role of <em>noe</em>B in the symbiosis operation.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Olga Onishchuk, Oxana Kurchak, Elena Chizhevskaya, Boris Simarov, Nikolay Provorov https://biocomm.spbu.ru/article/view/7614 Plant species diversity in urban areas of Northwest Siberia 2021-06-30T15:11:40+03:00 Elena Koptseva e.koptseva@spbu.ru Olga Sumina o.sumina@spbu.ru Pavel Kirillov spbftu@gmail.com Alexandr Egorov egorovfta@yandex.ru Alexandr Pechkin a.pechkin.ncia@gmail.com <p>The flora of two towns and two settlements in the northern taiga and forest-tundra of Northwest Siberia (Russia) are considered. Urban species lists are limited (61–119 vascular plant species) and mainly consist of native species with a predominance of perennial herbs. Various urban functional zones (industrial, residential, recreational, vegetable patches) differ by species composition, and this difference increases in the course of city development. In the industrial zone, vegetation composition is closer to the native flora, because of the low number of adventive species. Maximal diversity is due to decorative plants, cultivars and southern weed distribution, and is typical to residential neighborhoods. Species diversity increases mainly because of woody plants introduction. Alien species are represented generally by a small number of individuals. The severe climate and poor soils limit their abilities to spread in the Far North. Urbanization forces the reduction of aboriginal biodiversity, but in northern areas where native species have the adaptive advantage, this effect is minimal. Changes in flora since 1995 were analyzed in the town of Novy Urengoy (Yamalo-Nenets Autonomous Okrug, Russia). Plant diversity increased by about 20 % in all functional zones, although some alien and natural species were not recorded in 2018.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Elena Koptseva, Olga Sumina, Pavel Kirillov, Alexandr Egorov, Alexandr Pechkin https://biocomm.spbu.ru/article/view/7443 Isolation of high-quality RNA from plant seeds 2021-06-30T15:11:43+03:00 Alisa Mishko mishko-alisa@mail.ru Maria Sundyreva taurim2012@yandex.ru Ilya Stepanov ivstepanof@gmail.com Sergey Efimenko efimenko-km@yandex.ru Vladimir Plotnikov vkpbio21@mail.ru Natalia Nenko nenko.nataliya@yandex.ru <p>The apple (<em>Malus domestica</em> Borkh.) is one of the major fruit tree crops, but it hasn’t been well-studied as a breeding object for molecular investigations. It is important to develop reliable and rapid methods that allow the preparation of plant material for future research. We introduce a quick and simple method for isolating high-quality RNA from lipid-rich apple seeds (<em>M. domestica</em> cv. Golden Delicious). Our method does not employ highly toxic reagents, because we exclude phenol, 2-mercaptoethanol and others. The chemical composition of the extraction buffer is simple and has a minimum level of toxicity. We showed that, in chaotropic conditions (i.e., with lithium chloride-urea), silica (SiO<sub>2</sub>) can bind with the lipids and RNA will remain in the solution. The extracted RNA was of high quality and we successfully used it for synthesizing cDNA and RT-PCR. The protocol developed by us can be useful for researchers working with RNA extraction from plant seeds.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Alisa Mishko, Maria Sundyreva, Ilya Stepanov, Sergey Efimenko, Vladimir Plotnikov, Natalia Nenko https://biocomm.spbu.ru/article/view/7833 Assessment of Macrophyte Biological Index for Rivers, and evaluation of physicochemical parameters in the Sakarya River Basin of Turkey 2021-06-30T15:11:36+03:00 Arda Acemi arda.acemi@kocaeli.edu.tr Halim Aytekin Ergül halim.ergul@kocaeli.edu.tr Melih Kayal melihkayal@dsi.gov.tr Fatih Ekmekçi fekmekci@dsi.gov.tr Fazıl Özen fazil.ozen@kocaeli.edu.tr <p>In this study, the Macrophyte Biological Index for Rivers (IBMR) method and physicochemical measurements were used to assess the trophic status of the Sakarya River Basin in Turkey. The most abundant macrophytes were <em>Phragmites australis</em>, <em>Thypa latifolia</em>, <em>Juncus</em> sp., and <em>Paspalum distichum</em>. The IBMR values varied between 6.00 and 13.00 in spring, and between 6.714 and 14.40 in the fall season. The sampling stations, which are under the influence of agricultural runoffs, domestic effluents, and industrial discharges, had hypoxia accompanied by eutrophic and/or hypertrophic conditions at least in one season. The individual trophy levels of the sampling sites in the basin have been assessed as mesotrophic to eutrophic. However, considering the average IBMR value of all stations, the general trophy level of the basin was close to eutrophic. The results indicate that the physicochemical parameters are affected by various effluents discharged to the basin as observed during field studies, and the obtained data would be useful to apply conservation measures.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Arda Acemi, Halim Aytekin Ergül, Melih Kayal, Fatih Ekmekçi, Fazıl Özen https://biocomm.spbu.ru/article/view/9633 Heterogeneity of the barrier properties of the colon in rat 2021-06-30T15:11:18+03:00 Viktoria Bekusova v.bekusova@spbu.ru Ilyas Fatyykhov st050188@student.spbu.ru Salah Amasheh salah.amasheh@fu-berlin.de Alexander Markov a.markov@spbu.ru <p>The incidence of colorectal cancer in different parts of the large intestine is not the same, as tumors more often appear in the distal part of the colon compared to the proximal one. The purpose of this study was to investigate heterogeneity of the barrier properties of the colon and clarify the effects of Prostaglandin E2 and interleukin-1beta on its different parts. An in-depth analysis of short circuit current, transepithelial electrical resistance and paracellular permeability for sodium fluorescein in Ussing chambers showed that the proximal part of the colon was less permeable compared to the distal one and the substances had different effects on the parameters of permeability in different parts of the colon. We suppose that heterogeneity of the barrier properties of the colon and various effects of their regulation by local molecular agents may determine different incidence of pathologies in the colon.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Viktoria Bekusova, Ilyas Fatyykhov, Salah Amasheh, Alexander Markov https://biocomm.spbu.ru/article/view/9214 Perception of static magnetic field by humans: a review 2021-06-30T15:11:25+03:00 Nikita Chernetsov Nikita.Chernetsov@gmail.com Inna Nikishena nikishena@mail.ru Natalia Zavarzina nzavarzina@mail.ru Olga Kulbach os_koulbakh@mail.ru <p>We review the scientific data available on the ability of humans to perceive static magnetic fields with intensities comparable to the intensity of the natural geomagnetic field. It is currently assumed that birds have at least two independent magnetoreceptory systems. Various authors have reported the existence of the sensory ability to perceive the Earth’s magnetic field and to use it for spatial orientation in different species of mammals. The question of whether this ability exists in humans has been raised repeatedly. During the past 40 years, serious scholarly titles have published the results of behavioral studies on humans’ ability to perform homing to their home range by magnetic cues, of the ability to point towards a certain magnetic compass direction, and claims of magnetic modulation of the ability to discriminate weak light flashes. Several research groups have tried to find out whether brain bioelectric activity responds to changes in the stationary magnetic field. Cortical activation following changes in the static magnetic field, which suggested transduction of the changes in the Earth’s magnetic field into neural responses, was found by analyzing event-related synchronization/desynchronization. However, no behavioral manifestation for the putative magnetoreception in humans is evident. All attempts to detect behavioral responses to magnetic field changes in humans have been less than convincing.</p> 2021-06-30T00:00:00+03:00 Copyright (c) 2021 Nikita Chernetsov, Inna Nikishena, Natalia Zavarzina, Olga Kulbach