Molecular phylogeny of pectinase genes <Emphasis Type="Italic">PGU</Emphasis> in the yeast genus <Emphasis Type="Italic">Saccharomyces</Emphasis>

Using yeast genome databases and literature data, phylogenetic analysis of pectinase PGU genes from 112 Saccharomyces strains assigned to the biological species S. arboricola, S. bayanus (var. uvarum), S. cariocanus, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus, and the hybrid taxon S. pastorianus (syn. S. carlsbergensis) was carried out. A superfamily of divergent PGU genes was found. Natural interspecies transfer of the PGU gene both from S. cerevisiae to S. bayanus and from S. paradoxus to S. cerevisiae may, however, occur. Within the Saccharomyces species, identity of the PGU nucleotide sequences was 98.8–100% for S. cerevisiae, 86.1–95.7% for S. bayanus (var. uvarum), 94–98.3% for S. kudriavzevii, and 96.8–100% for S. paradoxus/S. cariocanus. For the first time, a family of polymeric PGU1b, PGU2b, PGU3b and PGU4b genes is documented for the yeast S. bayanus var. uvarum, a variety important for winemaking.     

New species of the buprestid genus <Emphasis Type="Italic">Endelus</Emphasis> Deyrolle (Coleoptera,Buprestidae) from China,India, and Laos

Endelus (Kubaniellus) indicus sp. n. from India, E. (K.) lao sp. n. and E. (K.) khnzoriani sp. n. from Laos, E. (s. str.) sausai sp. n. from China, and E. (s. str.) dembickyi sp. n. from India are described, the two latter species are included in the Endelus bicarinatus Théry, 1932 species-group recently established by the author. E. collinus Obenberger, 1922 is included in this group; lectotype of this species is designated. Keys to species of the subgenus Kubaniellus and of the E. collinus group are provided. E. (K.) kareni Kalashian is for the first time recorded for Shaanxi Prov., E. pacholatkoi Kalashian, E. smaragdinus Desc. et Vill., and E collinus Obenb., for Laos (the latter species, also for Myanmar).     

Mutations in <Emphasis Type="Italic">CsPID</Emphasis> encoding a Ser/Thr protein kinase are responsible for round leaf shape in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Key message

Two round-leaf mutants, rl-1 and rl-2, were identified from EMS-induced mutagenesis. High throughput sequencing and map-based cloning suggested CsPID encoding a Ser/Thr protein kinase as the most possible candidate for rl-1. Rl-2 was allelic to Rl-1.

Abstract

Leaf shape is an important plant architecture trait that is affected by plant hormones, especially auxin. In Arabidopsis, PINOID (PID), a regulator for the auxin polar transporter PIN (PIN-FORMED) affects leaf shape formation, but this function of PID in crop plants has not been well studied. From an EMS mutagenesis population, we identified two round-leaf (rl) mutants, C356 and C949. Segregation analysis suggested that both mutations were controlled by single recessive genes, rl-1 and rl-2, respectively. With map-based cloning, we show that CsPID as the candidate gene of rl-1; a non-synonymous SNP in the second exon of CsPID resulted in an amino acid substitution and the round leaf phenotype. As compared in the wild type plant, CsPID had significantly lower expression in the root, leaf and female flowers in C356, which may result in the less developed roots, round leaves and abnormal female flowers, respectively in the rl-1 mutant. Among the three copies of PID genes, CsPID, CsPID2 and CSPID2L (CsPID2-like) in the cucumber genome, CsPID was the only one with significantly differential expression in adult leaves between WT and C356 suggesting CsPID plays a main role in leaf shape formation. The rl-2 mutation in C949 was also cloned, which was due to another SNP in a nearby location of rl-1 in the same CsPID gene. The two round leaf mutants and the work presented herein provide a good foundation for understanding the molecular mechanisms of CsPID in cucumber leaf development.

     

New species of Telenominae (Hymenoptera,Scelionidae) from the palaearctic fauna

Four new species of Telenominae of the genera Telenomus and Platytelenomus, collected in the territory of the Ukraine, Hungary, and Japan, were described: Telenomus (T.) bicolorus Kononova, T. (T.) ardens Kononova, (T.) michaylovi Kononova, and Platytelenomus mirabilis Kononova. Brief morphological characteristics of the genera Telenomus and Platytelenomus are given, and some notes concerning biology and geographical distribution of the species are presented. Telenomus (T.) bicolorus differs from all the known species of the genus Telenomus in the two-colored body: head and thorax yellow with brownish tint ventrally, mesothorax and abdomen black. The main distinguishing feature of T. (T.) ardens is its smooth shining body, T. (T.) michaylovi is similar to T. (T.) rudis Kozlov. These species can be distinguished by the structure of their antenna. The second to fourth segments of the antennal clava are transverse in T. (T.) michaylovi and are as long as wide in T. (T.) rudis. In addition, the abdominal stem and abdominal tergite II are smooth and shining, while the abdominal stem in T. (T.) rudis is striate along the entire length, and tergite II is finely striate along half of its length. Platytelenomus mirabilis is closely related to P. danubialis Szelényi, but differs in the strongly flattened body, sculpture of the abdominal stem and tergite II, and coloration of the legs. The thorax of P. mirabilis is 4–5 times as wide as high, the abdominal stem is striate along the entire length, tergite II is striate at the base, and the legs, including coxae, are yellow. The thorax of P. danubialis is 4 times as wide as high, the abdominal stem and tergite II are smooth and shining, and the legs are brown.     

Reliability of the search for 19 common mutations in the <Emphasis Type="Italic">CFTR</Emphasis> gene in Russian cystic fibrosis patients and the calculated frequency of the disease in Russian Federation

A study of Russian cystic fibrosis (CF) patient DNA was conducted to assess the incidence frequency of 19 mutations, namely CFTRdele2,3(21kb), F508del, I507del, 1677delTA, 2143delT, 2184insA, 394delTT, 3821delT, L138ins, 604insA, 3944delGT, G542X, W1282X, N1303K, R334W, and 3849 + 10kbC > T, S1196X, 621 + 1g > t, and E92K of the CFTR gene. We also sought to determine the estimated CF frequency in Russian Federation. In addition, we determined the total information content of the approach for 19 common mutations registration in the CFTR gene, 84.6%, and the allelic frequencies of the examined mutations: three mutations were observed with a frequency exceeding 5% (F508del, 53.98%, E92K, 6.47%, CFTRdele2,3(21kb), 5.35%); other mutations were observed with frequencies ranging from 0.13 to 3.0%. The CF population carrier frequency was 1 in 38 subjects, while the predicted CF frequency was 1 in 5776 newborns.     

Foraminifera and their associations of a possibly Rhaetian section of the Nayband Formation in central Iran,northeast of Esfahan

The following paper describes the foraminiferal fauna and associated faunal assemblages of the bedded and reef carbonates of the Upper Triassic (most probably Rhaetian) Nayband Formation, which are exposed in a section south of the small town of Bagher-Abad, northeast of Esfahan. Foraminifers are extremely rare in sponge- or coral-dominated bioconstructions and in the bedded carbonates of the Nayband Formation in central Iran. Some carbonate beds are composed of bioclastic wackstone/packstone. These are exposed in the solenoporacean horizon at the uppermost part of the section. Here, the aulotortid- and trocholinid-type foraminifers are relatively abundant. The following foraminiferal taxa with different abundances were found within the carbonates of the investigated section: Trocholina umbo Frentzen, T. turris Frentzen, T. gracilis Blau, Aulotortus tumidus (Kristan-Tollmann), Aulotortus tenuis (Kristan), Aulotortus friedli (Kristan-Tollmann), Coronipora etrusca (Pirini), Semiinvoluta clari Kristan, Turrispirillina? licia variabilis Blau, Galeanella? laticarinata Al-Shaibani, Carter and Zaninetti, Ophthalmidium sp., Agathammina sp., “Sigmoilina” schaeferae Zaninetti, Planiinvoluta carinata Leischner, Planiinvoluta sp., Nubecularia sp., Endothyra sp., Paeolituonella sp. and some sessile agglutinated and nodosariid types. All mentioned taxa are very rare, except the involutinid and trocholinid types. The following species are described as new: Trocholina blaui nov. sp., Spirilina? iranica nov. sp., and Coronipora serraforma nov. sp. Trocholina blaui is usually attached to solenoporacean thalli. Four foraminiferal associations, which are named after the occurrence of the abundant species, were distinguished as Aulotortus tumidus association, Aulotortus friedli association, Trocholina umbo association, and Trocholina blaui association. Aulotortid types and Trocholina umbo were found within the bioclastic wackstone/packstone carbonates. Trocholina blaui is abundant in solenoporacean framestones. The foraminiferal association of investigated carbonates contains a mixed fauna, known from Upper Triassic–Liassic in the Tethyan realm. Carbonates of the whole investigated section are dated—due to occurrence of the genus Aulotortus, with species A. tumidus (Kristan-Tollmann), A. tenuis (Kristan), and A. friedli (Kristan-Tollmann)—as Upper Triassic (most probably Rhaetian). The “typical” foraminifers occurring in the reef biotopes in the northwestern Tethys are either missing or extremely rare in the Iranian bioconstructions.     

Isolation of endophytic fungi from tropical forest in Indonesia

Endophytic fungi (EPF) are an important contributor to fungal diversity. It is surmised that EPF colonizing plant roots have high diversity. This study aimed to alleviate the scarcity of information regarding EPF in tropical forests, by isolationg and identifying EPF from a tropical forests in Indonesia. Soils were collected from five forests: (1) Tectona grandis monoculture; (2) Swietenia macrophylla monoculture; (3) Gmelina sp., Artocarpus champeden, Dipterocarp mixed; (4) Dipterocarp primary; (5) Macaranga sp. secondary. Four trees (Calliandra calothyrsus, Paraserianthes falcataria, Sesbania grandiflora, and Cassia siamea) and three crops (Sorghum bicolor, Allium fistulosum, and Trifolium repens) were grown in the forest soils to trap EPF. EPF were isolated from roots and isolation rates were calculated. Based on the isolation rates, P. falcataria and S. bicolor were chosen and grown again in forest soils. EPF were isolated and identified by their rDNA ITS1 region. Twelve and 21 EPF were isolated from 250 roots of P. falcataria and 300 roots of S. bicolor, respectively. Identified EPF were from genera Acrocalymma, Fusarium, Tolypocladium, Penicillium, Talaromyces, Exophiala, Dictyosporium, Pseudochaetosphaeronema, Mariannaea, Trichoderma, and Mycoleptodiscus. Acrocalymma, Tolypocladium, Penicillium, Exophiala, Pseudochaetosphaeronema, Mariannaea, and Mycoleptodiscus spp. were isolated from only one forest. Fusarium, Talaromyces, and Trichoderma spp. were isolated from more than one forest. The numbers of EPF isolated from Gmelina sp., Artocarpus champeden, Dipterocarp mixed forest, and Macaranga sp. secondary forest were higher than those from other forests, suggesting that different plant species in forests affect the root EPF community.     

The <Emphasis Type="Italic">angora</Emphasis> gene weakens the effect of interaction of the mutant genes <Emphasis Type="Italic">wellhaarig</Emphasis> and <Emphasis Type="Italic">waved alopecia</Emphasis> in mice

The interaction of the mutant genes wellhaarig (we) and waved alopecia (wal) in mice was earlier demonstrated in our laboratory. The we gene significantly accelerates the appearance of alopecia in double we/wewal/wal homozygotes as compared to that in single +/+wal/wal homozygotes. It has been found in this work that the mutant gene angora-Y (Fgf5 ^go-Y ) weakens the effect of interaction of the we and wal genes. The first signs of alopecia appear in mice of the we/wewal/wal genotype at the age of 14 days, in triple Fgf5 ^go-Y /Fgf5 ^go-Y we/wewal/wal homozygotes alopecia is observed seven days later, i. e., in 21-day-old animals. The progression of alopecia in triple homozygotes is expressed to a lesser degree than in double +/+we/wewal/wal homozygotes. A single dose of the Fgf5 ^go-Y gene also decreases the effect of interaction of the we and wal genes, but less than a double dose of this gene. The first signs of alopecia in mice of the +/Fgf5 ^go-Y we/wewal/wal genotype appear only three days later than in double +/+we/wewal/wal homozygotes. The data obtained demonstrate that the Fgf5 ^go-Y gene is a powerful modifier of mutant genes determining the process of alopecia.     

Genotypic characterization of Lactic acid bacteria in gut microbiome of freshwater fish

The present study focused on identification and genotypic characterization of Lactic acid bacteria (LAB) in the intestine of freshwater fish. 76 strains of LAB were isolated and identified by 16S rRNA gene sequences and hsp60 gene sequences as different strains of Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus fermentum, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus brevis, Lactobacillus reuteri, Lactobacillus salivarius, Pediococcus pentosaceus, Pediococcus acidilactici, Weissella paramesenteroides, Weissella cibaria, Enterococcus faecium, and Enterococcus durans. The hsp60 gene showed a higher level of sequence variation among the isolates examined, with lower interspecies sequence similarity providing more resolutions at the species level than the 16S rRNA gene. Phylogenetic tree derived from hsp60 gene sequences with higher bootstrap values at the nodal branches was more consistent as compared to phylogenetic tree constructed from 16S rRNA gene sequences. Closely related species L. plantarum and L. pentosus as well as species L. delbrueckii subsp. bulgaricus and L. fermentum were segregated in different cluster in hsp60 phylogenetic tree whereas such a distribution was not apparent in 16S rRNA phylogenetic tree. In silico restriction analysis revealed a high level of polymorphism within hsp60 gene sequences. Restriction pattern with enzymes AgsI and MseI in hsp60 gene sequences allowed differentiation of all the species including closely related species L. plantarum and L. pentosus, E. faecium and E. durans. In general, hsp60 gene with higher evolutionary divergence proved to be a better phylogenetic marker for the group LAB.     

Generation of Chinese cabbage resistant to bacterial soft rot by heterologous expression of <Emphasis Type="Italic">Arabidopsis WRKY75</Emphasis>

Soft rot caused by Pectobacterium carotovorum subsp. carotovorum (Pcc) is a serious disease in Chinese cabbage (Brassica rapa L. subsp. pekinensis). To reduce the severity of soft rot symptoms in Chinese cabbage, Arabidopsis AtWRKY75 was introduced into Chinese cabbage by Agrobacterium-mediated transformation, which was previously reported to reduce susceptibility to Pcc infection in Arabidopsis. Three independent Chinese cabbage transgenic lines carrying AtWRKY75 were obtained. The growth phenotypes of AtWRKY75 overexpression (OE) lines were normal. Bacterial soft rot symptoms and Pcc growth were reduced in AtWRKY75-OE Chinese cabbage lines compared with WT plants. In contrast, overexpression of AtWRKY75 had no effect on infection with a hemibiotrophic pathogen, Xanthomonas campestris pv. campestris (Xcc) causing black rot disease. These results are consistent with those observed in the transgenic Arabidopsis. We found that AtWRKY75 activated a subset of Chinese cabbage genes related to defense against Pcc infection, such as Meri15B, BrPR4, and BrPDF1.2 (but not BrPGIP2). Moreover, overexpression of AtWRKY75 caused H₂O₂ production and activation of H₂O₂ scavenge enzyme genes, suggesting that H₂O₂ played a role in AtWRKY75-mediated resistance to Pcc. Together, these results demonstrated that AtWRKY75 decreased the severity of Pcc-caused bacterial soft rot and activated a subset of Pcc infection defense-related genes in Chinese cabbage similar to in Arabidopsis. It is suggested that AtWRKY75 is a candidate gene for use in crop improvement, because it results in reduced severity of disease symptoms without concurrent growth abnormalities.     

Usefulness of the Non-conventional <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> Model to Assess <Emphasis Type="Italic">Candida</Emphasis> Virulence

Invasive candidiasis is caused mainly by Candida albicans, but other Candida species have increasing etiologies. These species show different virulence and susceptibility levels to antifungal drugs. The aims of this study were to evaluate the usefulness of the non-conventional model Caenorhabditis elegans to assess the in vivo virulence of seven different Candida species and to compare the virulence in vivo with the in vitro production of proteinases and phospholipases, hemolytic activity and biofilm development capacity. One culture collection strain of each of seven Candida species (C. albicans, Candida dubliniensis, Candida glabrata, Candida krusei, Candida metapsilosis, Candida orthopsilosis and Candida parapsilosis) was studied. A double mutant C. elegans AU37 strain (glp-4;sek-1) was infected with Candida by ingestion, and the analysis of nematode survival was performed in liquid medium every 24 h until 120 h. Candida establishes a persistent lethal infection in the C. elegans intestinal tract. C. albicans and C. krusei were the most pathogenic species, whereas C. dubliniensis infection showed the lowest mortality. C. albicans was the only species with phospholipase activity, was the greatest producer of aspartyl proteinase and had a higher hemolytic activity. C. albicans and C. krusei caused higher mortality than the rest of the Candida species studied in the C. elegans model of candidiasis.     

Role of Gene-Gene Interactions in the Chromosomal Instability in Workers at Coal Thermal Power Plants

The 23 polymorphic variants in genes encoding the enzymes of xenobiotics biotransformation (CYP1A1 (rs4646903), CYP1A2 (rs762551), GSTP1 (rs1138272, rs1695), GSTM1 (del), and GSTT1 (del)), DNA repair (XRCC1 (rs25489, rs25487), APEX1 (rs1130409), hOGG1 (rs1052133), ADPRT (rs1136410), XPD (rs13181), XPG (rs17655), XPC (rs2228001), ATM (rs1801516), NBS (rs1805794), XRCC2 (rs3218536), and XRCC3 (rs861539)), antioxidant system (MnSOD (rs4880) and GPx1 (rs1050450)), cell cycle control and apoptosis (TP53 (rs1042522)), DNA methylation (MTHFR (rs1801133) and MTR (rs1805087)), and chromosomal aberrations in lymphocytes in the workers at thermal power plants were analyzed. We found that allelic variants in the CYP1A1 (rs4646903), hOGG1 (rs1052133), XRCC1 (rs25487), and APEX1 (rs1130409) genes were associated with an increased level of chromosomal aberrations in workers. Informative models of gene-gene interactions including CYP1A1 (rs4646903, T>C), CYP1A2 (rs762551, C>A), GSTT1 (del); XRCC1 (rs25487, G>A), MTHFR (rs1801133, C>T), GSTT1 (del); XRCC1 (rs25487, G>A), APEX1 (rs1130409, T>G), TP53 (rs1042522, G>C) determining the formation of the increased frequency of chromosomal aberrations in the workers at coal thermal power plants were discovered.     

New palaearctic species of the subgenus <Emphasis Type="Italic">Telenomus</Emphasis> (Hymenoptera,Scelionidae, Telenominae), having the mesoscutum with parapsidal furrows

Five new species of the genus Telenomus, subgenus Telenomus [Telenomus (T.) decoratus Kononova, sp. n., T. (T.) erectus Kononova, sp. n., T. (T.) notus Kononova, sp. n., T. (T.) clarus Kononova, sp. n., and T. (T.) gratus Kononova, sp. n.], collected from the Ukraine, Bulgaria, and Russia (Kunashir Island), are described for the first time. T. (T.) decoratus differs from the species with the mesoscutum bearing parapsidal furrows in the oblong tergite II with alveolate sculpture. T. (T.) erectus is closely related to T. (T.) lachesis Kozlov et Kononova and can be distinguished by the longer thorax and abdominal tergite I with longitudinal rugae. T. (T.) notus differs from the similar T. (T.) erectus in the sculpture and shape of the abdomen and coloration of the legs. T. (T.) clarus differs from T. (T.) lineolatus Kozlov in the sculpture of the frontal depression: granulate in T. (T.) clarus and smooth and lustrous in T. (T.) lineolatus. T. (T.) gratus is similar to T. (T.) atropos; its specific features are the head much wider than long and the smooth and lustrous tergite I.     

Heterologous expression of an RNA-binding protein affects flowering time as well as other developmental processes in <Emphasis Type="Italic">Solanaceae</Emphasis>

Flowering time in members of the Solanaceae plant family, such as pepper (Capsicum spp.) and tomato (Solanum lycopersicum), is an important agronomic trait for controlling shoot architecture and improving yield. To investigate the feasibility of flowering time regulation in tomato, an RNA-binding protein (RBP) encoding gene homologous to human Nucleolar protein interacting with the forkhead-associated (FHA) domain of pKI-67 (NIFK), CaRBP, was isolated from hot pepper. The function of CaRBP was determined in transgenic tomato. The deduced amino acid sequence includes an RNA recognition motif (RRM) and showed most similarity to the RRM present in a putative RBP encoded by human NIFK. CaRBP was highly expressed in the vegetative and reproductive tissues, such as leaves and fruits, respectively. Subcellular localization analysis indicated that CaRBP is a nucleolar protein. Heterologous expression of CaRBP under 35S promoter in tomato plants induced severe alteration of flowering with additional defects of vegetative organs. This floral retardation was associated with the alteration of SFT/SP3D and SlSOC1s as floral integrators. Furthermore, CaRBP reduces the expression levels of SlCOLs/TCOLs via changes in the expression of SlCDF3, SlFBHs, and SlFKF1s. This indicates a repressive effect of CaRBP on the regulation of flowering time in tomato. Overall, these results suggest that alteration in CaRBP expression levels may provide an effective means of controlling flowering time in day-neutral Solanaceae.     

The mathematical model of concentration polarization coefficient in membrane transport and volume flows

In this paper, the authors investigate the membrane transport of aqueous non-electrolyte solutions in a single-membrane system with the membrane mounted horizontally. The purpose of the research is to analyze the influence of volume flows on the process of forming concentration boundary layers (CBLs). A mathematical model is provided to calculate dependences of a concentration polarization coefficient (ζ _s ) on a volume flux (J _vm ), an osmotic force (Δπ) and a hydrostatic force (ΔP) of different values. Property ζ _s ?=?f(J _vm ) for J _vm ?>?0 and for J _vm ?≈?0 and property ζ _s ?=?f(ΔC ₁) are calculated. Moreover, results of a simultaneous influence of ΔP and Δπ on a value of coefficient ζ _s when J _vm ?=?0 and J _vm ?≠?0 are investigated and a graphical representation of the dependences obtained in the research is provided. Also, mathematical relationships between the coefficient ζ _s and a concentration Rayleigh number (R _C ) were studied providing a relevant graphical representation. In an experimental test, aqueous solutions of glucose and ethanol were used.     

New data on the taxonomy,distribution, and ecology of the weevil genus <Emphasis Type="Italic">Otiorhynchus</Emphasis> germar (Coleoptera,Curculionidae)

The subgenus Pocusogetus Rtt. of the genus Otiorhynchus Germ. is revised. The subgenus includes O. rosti Strl., O. shapovalovi Davidian et Yunakov, O. obsulcatus Strl., O. fischtensis Rtt., and O. gusakovi sp. n. closely related to O. fischtensis (both from Mt. Fisht, the Western Caucasus). O. fischtensis is transferred from the subgenus Vicoranius Rtt., its lectotype is designated. A key to species of Pocusogetus is given. The systematic position of the subgenera Pocusogetus and Vicoranius in the genus Otiorhynchus is discussed. New data on the geographical distribution and ecology of the little-known species of the subgenera Obvoderus Rtt., Pseudoprovadilus Magnano, and Clypeorhynchus Yunakov et Arzanov are given. Some features of ecological differentiation between Otiorhynchus species in the alpine and subalpine zones of the Caucasus are discussed.