林麝及其近缘物种编码区微卫星分布规律及功能分析

麝科和鹿科动物均属于偶蹄反刍类动物,具有重要的经济价值。通过系统的微卫星序列 (Simple sequences repeats, SSRs) 从基因组水平揭示物种间的系统进化关系,探索微卫星序列的基因功能及其富集的信号通路,目前仍缺乏相关研究。随着林麝 (Moschus berezovskii)、原麝 (Moschus moschiferus)、小麂 (Muntiacus reevesi)、赤麂 (Muntiacus vaginalis) 和马鹿 (Cervus elaphus) 基因组测序的完成,本文利用生物信息学方法提取了这些动物蛋白质编码区 (coding sequences, CDS) 序列,统计和分析了其CDS区微卫星序列分布规律及其生物学功能,探索了含SSR 基因富集的信号通路及其与疾病的关联性。结果表明,林麝、原麝、小麂、赤麂和马鹿蛋白质编码区含SSR序列的基因所占比例分别为6.96% (1 696个)、7.18% (2 359个)、7.29% (3 005个)、7.36% (1 916个) 和7.48% (1 924个),并且这5种动物CDS区SSRs分布模式具有相似性,均是三倍体核苷酸 (即三核苷酸和六核苷酸) SSRs最多,分别为96.85%、94.87%、65.44%、64.23%和88.04%。GO功能富集表明,林麝与其他4种动物蛋白质编码区SSR序列在分子功能、细胞组成和生物学过程3个方面具有较多共同显著富集的功能,包括DNA结合、染色质和生长发育等。KEGG 通路分析表明,林麝及其他4种动物蛋白质编码区SSR序列具有7个共同显著富集的KEGG通路,包括遗传信息调控蛋白家族、转录因子、染色体及相关蛋白、剪接体、转录机制和Notch信号通路和成体糖尿病。通过对林麝编码区含SSR关键免疫基因及其相关联的KEGG通路进行分析,发现10个含SSR的关键免疫基因对应的KEGG通路与疾病密切相关。     

Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs have been accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA prediction tools. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users in selecting promising miRNA candidates in an interactive mode, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for the annotation of miRNAs in plant species with reference genomes. We also illustrate the application of iwa-miRNA for miRNA annotation using data from plant species with varying genomic complexity. The source codes and web server of iwa-miRNA are freely accessible at http://iwa-miRNA.omicstudio.cloud/.     

Verification of meiotic gynogenesis in Siberian sturgeon (Acipenser baeri Brandt) using microsatellite DNA and cytogenetical markers

Diploid gynogenesis was induced in Siberian sturgeon Acipenser baeri using ultra violet (UV)-irradiated bester ( Huso huso × Acipenser ruthenus ) sperm. The higher survival rate of meiotic diploids was noted after 1350 ergs mm⁻² UV irradiation. A total of 80 meiotic diploids of known parentage from two different experimental treatments were screened using microsatellite DNA and cytogenetical analysis, and uniparental transmission in meiotic diploids was confirmed.     

Late Permian phylloclades of the new genus <Emphasis Type="Italic">Permophyllocladus</Emphasis> and problems of the evolutionary morphology of peltasperms

Phylloclades from the Upper Permian (Tatarian) deposits of the Sokovka locality, Vladimir Region, showing gradational transformation of a planate scale-leaved shoot into a foliar organ, are assigned to the new genus Permophyllocladus (Peltaspermales?). The phylloclades are distinctly dorsoventral: scaly leaves and their rudiments are developed on the lower side and are only marked by suture lines on the cuticle of the opposite side. In epidermal characteristics, the phylloclades are similar to the leaves of peltasperms from coeval deposits. It is supposed that peltasperm leaves are of phylloclade origin and were formed by cohesion of units of a coniferoid scale-leaved shoot that resembles shoots of the Mesozoic family Hirmerellaceae (Cheirolepidiaceae), which also tend to develop phylloclades.     

Siberian crane chick calls reflect their thermal state

Chicks can convey information about their needs with calls. But it is still unknown if there are any universal need indicators in chick vocalizations. Previous studies have shown that in some species vocal activity and/or temporal-frequency variables of calls are related to the chick state, whereas other studies did not confirm it. Here, we tested experimentally whether vocal activity and temporal-frequency variables of calls change with cooling. We studied 10 human-raised Siberian crane (Grus leucogeranus) chicks at 3–15 days of age. We found that the cooled chicks produced calls higher in fundamental frequency and power variables, longer in duration and at a higher calling rate than in the control chicks. However, we did not find significant changes in level of entropy and occurrence of non-linear phenomena in chick calls recorded during the experimental cooling. We suggest that the level of vocal activity is a universal indicator of need for warmth in precocial and semi-precocial birds (e.g. cranes), but not in altricial ones. We also assume that coding of needs via temporal-frequency variables of calls is typical in species whose adults could not confuse their chicks with other chicks. Siberian cranes stay on separate territories during their breeding season, so parents do not need to check individuality of their offspring in the home area. In this case, all call characteristics are available for other purposes and serve to communicate chicks’ vital needs.     

Contrasting seasonal dynamics in fleas of the Siberian flying squirrel (Pteromys volans) in Finland

Abstract.  1. The seasonal and spatial variation of the adult flea fauna (Siphonaptera) was examined in connection with live-trapping studies of the Siberian flying squirrel ( Pteromys volans ) in three study areas in southern Finland between 1997 and 2005.
2. The numerically dominant flea species of the Siberian flying squirrel were Tarsopsylla octodecimdentata octodecimdentata and Ceratophyllus (Monopsyllus) indages indages (Ceratophyllidae); the latter being a host specialist of the Siberian flying squirrel. Tarsopsylla octodecimdentata , which also commonly occurs on the red squirrel ( Sciurus vulgaris ), infected a large proportion of the host population throughout the winter, whereas C. indages occurred predominantly during the summer and autumn, being practically the only flea species in nests during the flying squirrels' breeding season and on juveniles still inhabiting their natal nest.
3. The use of nest boxes by flying squirrels did not have any positive effects on flea populations, but it may have had a negative impact on T.   octodecimdentata .
4. The potentially vulnerable C.   i.   indages is a predictable, widespread component in the flea fauna of the Siberian flying squirrel at various spatial scales, and it is likely to occur in most of the permanent flying squirrel populations in Finland.     

High-value chemicals obtained from selective photo-oxidation of glucose in the presence of nanostructured titanium photocatalysts

Glucose was oxidized in the presence of powdered TiO(2) photocatalysts synthesized by an ultrasound-promoted sol-gel method. The catalysts were more selective towards glucaric acid, gluconic acid and arabitol (total selectivity approx. 70%) than the most popular photocatalyst, Degussa P-25. The photocatalytic systems worked at mild reaction conditions: 30°C, atmospheric pressure and very short reaction time (e.g. 5 min). Such relatively good selectivity towards high-valued molecules are attributed to the physico-chemical properties (e.g. high specific surface area, nanostructured anatase phase, and visible light absorption) of novel TiO(2) materials and the reaction conditions. The TiO(2) photocatalysts have potential for water purification and energy production and for use in the pharmaceutical, food, perfume and fuel industries.     

Diet affects resting, but not basal metabolic rate of normothermic Siberian hamsters acclimated to winter

We examined the effect of different dietary supplements on seasonal changes in body mass (m_b), metabolic rate (MR) and nonshivering thermogenesis (NST) capacity in normothermic Siberian hamsters housed under semi-natural conditions. Once a week standard hamster food was supplemented with either sunflower and flax seeds, rich in polyunsaturated fatty acids (FA), or mealworms, rich in saturated and monounsaturated FA. We found that neither of these dietary supplements affected the hamsters' normal winter decrease in m_b and fat content nor their basal MR or NST capacity. NST capacity of summer-acclimated hamsters was lower than that of winter-acclimated ones. The composition of total body fat reflected the fat composition of the dietary supplements. Resting MR below the lower critical temperature of the hamsters, and their total serum cholesterol concentration were lower in hamsters fed a diet supplemented with mealworms than in hamsters fed a diet supplemented with seeds. These results indicate that in mealworm-fed hamsters energy expenditure in the cold is lower than in animals eating a seed-supplemented diet, and that the degree of FA unsaturation of diet affects energetics of heterotherms, not only during torpor, but also during normothermy.     

Organic compositions of the embryo-bearing lowermost Cambrian Kuanchuanpu formation on the northern Yangtze platform, China

We investigated the origin of organic matter and paleoceanographic conditions of the embryo-bearing lowermost Cambrian Kuanchuanpu Formation in Shaanxi Province, China, in terms of sedimentary facies, fossil morphometry, and organic geochemistry, including biomarker compositions. The results indicated the abundance of algae and eukaryotic phytoplankton that fueled a diverse ecosystem including cnidarians and small shelly fossils. The water column contained enough oxygen to provide habitat for benthic cnidarians such as Olivooides. On the other hand, low pristane/phytane ratios, detection of squalane, and hopane composition indicate reductive conditions within the sediments, and that the redox front was likely near the water-sediment interface. Common occurrences of pyrite and barite indicate that redox reactions of sulfur species were activated at the water-sediment interface. Such circumstances and the high phosphate concentration in ambient water may recall the presence of sulfur-oxidizing bacteria that promoted the phosphatization of animal embryos, as suggested for in the Neoproterozoic Doushantuo Formation. Nitrogen was the limiting nutrient for primary productivity, and the high phosphate concentration in the ocean promoted the phosphatization of animal embryos at the reductive water–sediment interface.     

Morphogenesis,origin, and paleoecology of the bryozoans of the family Medvedkellidae fam. nov. (Upper Carboniferous,East European Platform)

A new family of the order Rhabdomesida, Medvedkellidae fam. nov., is described. This family consists of a new genus, Medvedkella gen. nov., comprising three species transferred from the genus Rhombopora Meek, 1872: the type species M. riasanensis (Schulga-Nesterenko, 1955), M. diaphragmata (Schulga-Nesterenko, 1955), and M. mariae (Dunaeva, 1961). The morphogenesis of the first two species is studied. For the first time axial zooecia are revealed in the suborder Golgdfussitrypina, which existed in parallel with the suborder Rhabdomesina of the order Rhabdomesida. A hypothesis that the new family evolved from the subfamily Nicklesoporinae Gorjunova, 1985 of the family Goldfussitrypidae, 1985 is proposed. Some questions of the ecological adaptation of these bryozoans in the Late Carboniferous marine basin of the East European Platform are discussed.