Biological Communications 2021-11-12T16:53:46+03:00 Anton A. Nizhnikov 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> Transcriptomic analysis of <em>sym28</em> and <em>sym29</em> supernodulating mutants of pea (<em>Pisum sativum</em> L.) under complex inoculation with beneficial microorganisms 2021-11-12T16:53:40+03:00 Vladimir Zhukov Evgeny Zorin Aleksandr Zhernakov Alexey Afonin Gulnar Akhtemova Andrej Bovin Aleksandra Dolgikh Artemii Gorshkov Emma Gribchenko Kira Ivanova Anna Kirienko Anna Kitaeva Marina Kliukova Olga Kulaeva Pyotr Kusakin Irina Leppyanen Olga Pavlova Daria Romanyuk Elizaveta Rudaya Tatiana Serova Oksana Shtark Anton Sulima Anna Tsyganova Ekaterina Vasileva Elena Dolgikh Viktor Tsyganov Igor Tikhonovich <p>The garden pea (<em>Pisum sativum</em> L.), like most members of Fabaceae family, is capable of forming symbioses with beneficial soil microorganisms such as nodule bacteria (rhizobia), arbuscular mycorrhizal (AM) fungi and plant growth promoting bacteria (PGPB). The autoregulation of nodulation (AON) system is known to play an important role in controlling both the number of nodules and the level of root colonization by AM via root-to-shoot signaling mediated by CLAVATA/ESR-related (CLE) peptides and their receptors. In the pea, mutations in genes <em>Sym28</em> (<em>CLV2</em>-like) and <em>Sym29</em> (<em>CLV1</em>-like), which encode receptors for CLE peptides, lead to the supernodulation phenotype, i.e., excessive nodule formation. The aim of the present study was to analyze the response of pea cv. ‘Frisson’ (wild type) and mutants P64 (<em>sym28</em>) and P88 (<em>sym29</em>) to complex inoculation with rhizobia, AM fungi and PGPB, with regard to biomass accumulation, yield and transcriptomic alterations. The plants were grown in quartz sand for 2 and 4 weeks after inoculation with either rhizobia (Rh) or complex inoculation with Rh + AM, Rh + PGPB, and Rh+AM+PGPB, and the biomass and yield were assessed. Transcriptome sequencing of whole shoots and roots was performed using a modified RNAseq protocol named MACE (Massive Analysis of cDNA Ends). In the experimental conditions, P88 (<em>sym29</em>) plants demonstrated the best biomass accumulation and yield, as compared to the wild type and P64 (<em>sym28</em>) plants, whereas P64 (<em>sym28</em>) had the lowest rate of biomass and seed yield. The transcriptome analysis showed that both supernodulating mutants more actively responded to biotic and abiotic factors than the wild-type plants and demonstrated increased expression of genes characteristic to late stages of nodule development. The roots of P64 (<em>sym28</em>) plants responded to AM+Rh treatment with upregulation of genes encoding plastid proteins, which can be connected with the activation of carotenoid biosynthesis (namely, the non-mevalonate pathway that takes place in root plastids). The more active response to symbionts in P88 (<em>sym29</em>) plants, as compared to cv. ‘Frisson’, was associated with counterregulation of transcripts involved in chloroplast functioning and development in leaves, which accompanies successful plant development in symbiotic conditions. Finally, the effect of retardation of plant aging upon mycorrhization on a transcriptomic level was recorded for cv. ‘Frisson’ but not for P64 (<em>sym28</em>) and P88 (<em>sym29</em>) mutants, which points towards its possible connection with the AON system. The results of this work link the plant’s autoregulation with the responsiveness to inoculation with beneficial soil microorganisms.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Vladimir Zhukov, Evgeny Zorin, Aleksandr Zhernakov, Alexey Afonin, Gulnar Akhtemova, Andrej Bovin, Aleksandra Dolgikh, Artemii Gorshkov, Emma Gribchenko, Kira Ivanova, Anna Kirienko, Anna Kitaeva, Marina Kliukova, Olga Kulaeva, Pyotr Kusakin, Irina Leppyanen, Olga Pavlova, Daria Romanyuk, Tatiana Serova, Oksana Shtark, Anton Sulima, Anna Tsyganova, Ekaterina Vasileva, Elena Dolgikh, Viktor Tsyganov, Igor Tikhonovich Analysis of the polydispersity of soil-like bodies in glacier environments by the laser light scattering (diffraction) method 2021-11-12T16:53:20+03:00 Evgeny Abakumov Timur Nizamutdinov Viacheslav Polyakov <p>This study presents the results of polydispersity analysis of soil-like bodies from two various polar regions using the laser light scattering method. The differences in the particle size distribution of cryoconite samples from the Anuchin Glacier (Antarctica) and the Mushketov Glacier (Arctic) are described. The samples obtained from the Mushketov Glacier are characterized by a finer particle size distribution than samples collected on the Anuchin Glacier. While comparing our results with previously published studies, it was found that the method of laser light scattering shows a lower content of small fractions (&lt;0.05 mm) compared to the classical methods of sedimentation, since these methods are based on fundamentally different physical principles. The laser method used requires low amounts of samples (0.2–0.5 g), while the classical sedimentary method uses a higher gravimetric portion of cryoconite (5–10 g), which is critical for field sampling.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Evgeny Abakumov, Timur Nizamutdinov, Viacheslav Polyakov Protein glycation and drought response of pea (<em>Pisum sativum</em> L.) root nodule proteome: a proteomics approach 2021-11-12T16:53:31+03:00 Julia Shumilina Daria Gorbach Veronika Popova Alexander Tsarev Alena Kuznetsova Maria Grashina Mandy Dorn Elena Lukasheva Natalia Osmolovskaya Ekaterina Romanovskaya Vladimir Zhukov Christian Ihling Tatiana Grishina Tatiana Bilova Andrej Frolov <p>Because of ongoing climate change, drought is becoming the major factor limiting productivity of all plants, including legumes. As these protein-rich crops form symbiotic associations with rhizobial bacteria — root nodules — they readily lose their productivity under drought conditions. Understanding the underlying molecular mechanisms might give access to new strategies to preserve the productivity of legume crops under dehydration. As was shown recently, development of drought response is accompanied by alterations in the patterns of protein glycation and formation of advanced glycation end products (AGEs) that might be a part of unknown regulatory mechanisms. Therefore, here we address the effects of moderate drought on protein dynamics and AGE patterns in pea (<em>Pisum sativum</em>) root nodules. For this, plants inoculated with rhizobial culture were subjected to osmotic stress for one week, harvested, the total protein fraction was isolated from root nodules by phenol extraction, analyzed by bottom-up LC-MS-based proteomics, and AGE patterns were characterized. Surprisingly, despite the clear drought-related changes in phenotype and stomatal conductivity, only minimal accompanying expressional changes (14 rhizobial and 14 pea proteins, mostly involved in central metabolism and nitrogen fixation) could be observed. However, 71 pea and 97 rhizobial proteins (mostly transcription factors, ABC transporters and effector enzymes) were glycated, with carboxymethylation being the major modification type. Thereby, the numbers of glycated sites in nodule proteins dramatically decreased upon stress application. It might indicate an impact of glycation in regulation of transport, protein degradation, central, lipid and nitrogen metabolism. The data are available at Proteome Xchange (accession: PXD024042).</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Julia Shumilina, Daria Gorbach, Veronika Popova, Alexander Tsarev, Alena Kuznetsova, Maria Grashina, Elena Lukasheva, Natalia Osmolovskaya, Ekaterina Romanovskaya, Vladimir Zhukov, Christian Ihling, Tatiana Grishina, Tatiana Bilova, Andrej Frolov Species- and age-dependent distribution of retinol and α-tocopherol in the Canidae family during the cold season 2021-11-12T16:53:46+03:00 Irina Baishnikova Tatiana Ilyina Viktor Ilyukha Konstantin Tirronen <p>Vitamins A and E are known as nutrients involved in metabolic processes and facilitating the adaptation of animals. The metabolism of these vitamins is closely related to lipid metabolism, which has seasonal variations in animals inhabiting northern latitudes. The aim of this study was to investigate the concentrations of retinol (vitamin A) and α-tocopherol (vitamin E) in the cold season (October to February) in tissues of Canidae species that have different ecological characteristics: the blue fox (<em>Vulpes </em>syn<em>. Alopex lagopus</em>), silver fox (<em>Vulpes vulpes</em>), their interspecific hybrids (<em>Vulpes</em><em>×Vulpes</em>), raccoon dog (<em>Nyctereutes procyonoides</em>), and grey wolf (<em>Canis lupus</em>). In addition, age-related differences in the levels of these vitamins were determined. Results showed the distribution of retinol and α-tocopherol in the body of the canids was similar, with larger amounts being found in the liver and kidney cortex, which play a regulatory role in the metabolism of these nutrients. The higher retinol level in the liver of wolves and interspecific hybrids of blue fox and silver fox, as compared to the retinol level in the liver of other species, might be species-specific and could also be attributed to dietary differences. The blue fox and raccoon dog both have a higher capacity for α-tocopherol accumulation in the cold season, apparently due to their ability to store substantial fat reserves. Retinol and α-tocopherol levels were generally higher in the tissues of mature animals.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Irina Baishnikova, Tatiana Ilyina, Viktor Ilyukha, Konstantin Tirronen A biomechanical model to assess the injury risk of leopards (<em>Panthera pardus</em>) hunting by free falling from trees 2021-11-12T16:53:34+03:00 Rudemar Ernesto Blanco Daniel Eduardo Luzardo-Vera <p>Leopards have been observed to ambush prey by jumping down on it from trees. There are both anecdotal reports and video recordings of this hunting behavior. Here we conducted a biomechanical analysis of this technique to assess the degree of risk for the predator in such cases. We concluded that the risk of suffering severe injuries seems to be too high for this technique to be a usual way of predation on horned mammals such as male impalas. Our results can be useful in discussing proposed paleobiological hunting scenarios and living predators’ strategies of managing risks.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Rudemar Ernesto Blanco, Daniel Eduardo Luzardo-Vera Diet affects body color and energy metabolism in the Baikal endemic amphipod <em>Eulimnogammarus cyaneus</em> maintained in laboratory conditions 2021-11-12T16:53:26+03:00 Alexandra Saranchina Polina Drozdova Andrei Mutin Maxim Timofeyev <p>Proper diet is critical for laboratory-reared animals, as it may affect not only their welfare, but also experimental results. Amphipods (Crustacea: Amphipoda) play important roles in ecosystems and are often used in environmental research. Endemic amphipods from the ancient Lake Baikal are promising for laboratory bioassays; however, there are currently no laboratory cultures. In this work, we determine how different diets affect the color and metabolism of a laboratory-reared Baikal amphipod, <em>Eulimnogammarus cyaneus</em>. We found that in freshly collected blue-colored animals, body color correlated with total carotenoid content. Total carotenoid levels did not differ after long-term (two months) feeding with a close to natural carotenoid-enriched, or even a carotenoid-depleted diet. Nevertheless, antennae color was closer to red in the natural-like diet group. It is likely that the carotenoids from the commercial diet are not properly metabolized in <em>E. cyaneus</em>. The animals fed commercial diets had a higher glycogen content, which may signify a higher metabolic rate. Overall, we show that a carotenoid-enriched diet optimized for decapods is not optimal for amphipods, likely due to different carotenoid compositions, and the diet for long-term rearing of <em>E.&nbsp;cyaneus</em> and other Baikal amphipods requires supplementation.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Alexandra Saranchina, Polina Drozdova, Andrei Mutin, Maxim Timofeyev Sexual dimorphism patterns of the White Sea threespine stickleback (<em>Gasterosteus aculeatus</em>) 2021-11-12T16:53:24+03:00 Ahmed Dorgham Ulrika Candolin Tatiana Ivanova Mikhail Ivanov Ekaterina Nadtochii Anastasia Yurtseva Dmitry Lajus <p>Sexual dimorphism (SD) in the threespine stickleback <em>Gasterosteus aculeatus</em> reflects the different roles of the sexes in reproduction and their adaptations to different ecological niches. We quantified SD in one population of marine stickleback from the White Sea, collected during the spawning period from three spawning grounds, each at a distance of 5 km or less from the others. We used a landmark-based approach to quantify variation in 44 morphometric linear traits. In total, 749 females and 693 males were analyzed. In males, anterior body parts are larger — the base of the caudal fin and armor structures such as the first and second dorsal spines and the pelvic spine. Females have larger posterior bodies — the abdomen, pelvic girdle and the third dorsal spine. The SD of caudal body parts exhibits complex patterns. In White Sea threespine stickleback, SD patterns are generally similar to other populations of the species, but more often show male-biased patterns. Female-biased size SD may be associated with the female biased sex ratio of White Sea stickleback.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Ahmed Dorgham, Ulrika Candolin, Tatiana Ivanova, Mikhail Ivanov, Ekaterina Nadtochii, Anastasia Yurtseva, Dmitry Lajus Wild-type p53-induced phosphatase sensitizes acute myeloid leukemia cells to conventional chemotherapy 2021-11-12T16:53:37+03:00 Vasily Golotin Ekaterina Belotserkovskaya Larisa Girshova Alexey Petukhov Andrey Zaritsky Oleg Demidov <p>Recently wild-type p53-induced phosphatase was implicated in the pathogenesis of acute myeloid leukemia (AML) and “pre-leukemia” myeloproliferative conditions. Here we decided to check how the strategy directed to phosphatase inhibition affected sensitivity to conventional chemotherapy. All experiments were conducted on AML cell lines cultivated in vitro. The levels of wild-type p53-induced phosphatase vary in different AML cell lines. The chemical compound GSK2830371 reduced levels of phosphatase and diminished its activity. GSK2830371 did not significantly change the cell cycle distribution of AML cells when used alone or in combination with the anti-cancer chemotherapeutic drug Cytosar but increased caspase-dependent PARP1 cleavage. In contrast with previous studies, we did not observe the negative effect of phosphatase activity inhibition and depletion on cells when a chemical inhibitor was used as monotherapy. Using a combination of GSK2830371 with Cytosar we were able to reduce the threshold of chemotherapy-dependent cytotoxicity and more efficiently eliminate leukemic cells. We propose considering inhibition of wild-type p53-induced phosphatase as a prospective strategy in improving anti-AML therapy.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Vasily Golotin, Ekaterina Belotserkovskaya, Larisa Girshova, Alexey Petukhov, Andrey Zaritsky, Oleg Demidov Presence of <em>Notahypsibius pallidoides</em> (Tardigrada: Hypsibiidae) in the fauna of Russia confirmed with the methods of DNA barcoding 2021-11-12T16:53:43+03:00 Denis Tumanov <p>A brief report is given on the tardigrade species <em>Notahypsibius pallidoides</em>, discovered in a moss cushion in the vicinity of Saint Petersburg. Morphological identification of the species is supported with the analysis of obtained sequences of nuclear and mitochondrial DNA barcode genes (ITS-2 and COI). The current state of knowledge of Russian fauna of Tardigrada is characterised, and all available data on the distribution of <em>Notahypsibius pallidoides</em> and its genetic variability are summarised. The data obtained in this study by methods of DNA barcoding demonstrated that studied specimens of the tardigrada population isolated in Russia belong to the same species (<em>Notahypsibius pallidoides</em>) as the control specimens isolated in Austria though represent another haplotype thus confirming the presence of <em>Notahypsibius pallidoides</em> for the fauna of Russia.</p> 2021-11-12T00:00:00+03:00 Copyright (c) 2021 Denis Tumanov