Structural and functional studies of EpsC, a crucial component of the type 2 secretion system from Vibrio cholerae

The type 2 secretion system (T2SS) occurring in Gram-negative bacteria is composed of 12-15 different proteins which form large assemblies spanning two membranes and secreting several virulence factors in folded state across the outer membrane. The T2SS component EpsC of Vibrio cholerae plays an important role in this machinery. While anchored in the inner membrane, by far the largest part of EpsC is periplasmic, containing a so-called homology region (HR) domain and a PDZ domain. Here we report studies on the structure and function of both periplasmic domains of EpsC. The crystal structures of two variants of the PDZ domain of EpsC from V. cholerae were determined at better than 2 A resolution. Compared to the short variant, the longer variant contains an additional N-terminal helix, and reveals a significant difference in the position of helix alphaB with respect to the beta-sheet. Both our structures show that the PDZ domain of EpsC adopts a more open form than in previously reported structures of other PDZ domains. Most interestingly, in the crystals of the short EpsC-PDZ domain the peptide binding groove interacts with an alpha-helix from a neighboring subunit burying approximately 921 A2 solvent accessible surface. This makes it possible that the PDZ domain of this bacterial protein binds proteins in a manner which is altogether different from that seen in any other PDZ domain so far. We also determined that the HR domain of EpsC is primarily responsible for the interaction with the secretin EpsD, while the PDZ is not, or much less, so. This new finding, together with studies of others, leads to the suggestion that the PDZ domain of EpsC may interact with exoproteins to be secreted while the HR domain plays a key role in linking the inner-membrane sub-complex of the T2SS in V. cholerae to the outer membrane secretin.     

Staphylotrichum boninense, a new hyphomycete (Chaetomiaceae) from soils in the Bonin Islands, Japan

Staphylotrichum boninense, a new hyphomycete classified in the Chaetomiaceae (Ascomycota), was isolated from soils in the Bonin Islands, Japan. It is characterized morphologically by the production of yellow-orange colonies and subglobose holoblastic conidia. Morphologically the species is similar to S. coccosporum, but it is significantly different from S. coccosporum in phylogeny and also differs with respect to its secondary metabolite profile.     

Use of variability of the fungal ITS2 intergenic region for the identification of medically important yeast species

Yeasts are common fungal opportunistic pathogens in humans playing a significant role in the morbidity and mortality of immunocompromised patients. Number of resistant yeast species is responsible for infections and consequent infectious complications, but the final microbiological diagnosis can be affected by variability of their phenotype and may result in incorrect identification. For the purposes of this study, advanced applications of molecular genetic methods based on certain up-to-date knowledge of fungal internal transcribed spacer (ITS) regions have been employed, which could support a possibility of universal application of such methods for identification of any pure yeast culture. In this study, the targeted DNA was amplified by a couple of primers, and the products of PCR reaction were divided by capillary electrophoresis. In the cases, in which the measured sizes of fragments did not correspond with the anticipated sizes, fragments were used for the sequencing analysis and compared to the nucleotide databases using the BLAST tool. Out of 208 isolates, 7.2% (n = 16) of cases occurred to be incorrectly determined, particularly in the group of non-albicans Candida species accounting for as many as 21.7%.     

Virulence regions and virulence factors of the ovine footrot pathogen, Dichelobacter nodosus

Abstract Ovine footrot is a debilitating and highly infectious disease that is primarily caused by the Gram-negative, anaerobic bacterium Dichelobacter nodosus . The major antigens implicated in virulence are the type IV fimbriae and extracellular proteases. The fimbriae show sequence and structural similarity to other type IV fimbriae, this similarity extends to genes that are involved in fimbrial biogenesis. Several acidic and basic extracellular serine proteases are produced by both virulent and benign isolates of D. nodosus . Subtle functional differences in these proteases appear to be important in virulence. In addition, there are two chromosomal regions that have a genotypic association with virulence. The partially duplicated and rearranged vap regions appear to have arisen from the insertion of a plasmid into a tRNA gene via an integrase-mediated site-specific insertion event. The 27 kb vrl region has several genes often found on bacteriophages and has inserted into an ssrA gene that may have a regulatory role in the cell. The determination of the precise role that each of these genes and gene regions has in virulence awaits the development of methods for the genetic analysis and manipulation of D. nodosus .     

Aroid scarabs in the genus Peltonotus Burmeister (Coleoptera,Scarabaeidae, Dynastinae): key to species and new distributional data

The southeast Asian scarab beetle genus Peltonotus Burmeister (Scarabaeidae, Dynastinae, Cyclocephalini) is reviewed. New country records for Peltonotus morio Burmeister (Myanmar and Vietnam), Peltonotus nasutus Arrow (southern China and Cambodia), and Peltonotus favonius Jameson and Wada (Myanmar) are reported, including a new record in the Palearctic/Sino-Japanese biogeographic region. The first female specimen of Peltonotus favonius is described. Biological associations with aroid inflorescences are reviewed, and human consumption of Peltonotus beetles is reported. A key to all species, paralectotype designations for Peltonotus nasutus, diagnoses, and distributions using dynamic mapping tools are included.     

Description of a new species and redescription of two species of the genus Limoniscus Reitter (Coleoptera,Elateridae, Dendrometrinae) from Japan

We presented a revised taxonomy of two allied species, Limoniscus mitokiiKishii, 2004 and L. ogatai (Kishii, 1985), from western Japan. Through this revision, we found a new species, L. spelunca sp. n., from the type series of L. ogatai. The new species is different in its frons, antennae, prosternum, and aedeagus compared with L. mitokii and L. ogatai. We also reviewed the current understanding of Japanese Limoniscus species, and provided a key to the 23 Limoniscus species found in Japan. urn:lsid:zoobank.org:pub:56104650-EAA9-42E9-AFC3-91D7DCA53938.     

Corrections to the identification key to species of Pertusius Mantilleri, 2016 (Coleoptera : Curculionoidea,Brentidae)

In the identification key proposed by Mantilleri in 2016 for the genus Pertusius, some mistakes were introduced in references to figures. They are corrected here.     

Evolutionary Relationships of the Limnochromini, a Tribe of Benthic Deepwater Cichlid Fish Endemic to Lake Tanganyika, East Africa

Lake Tanganyika harbors an enormous diversity of cichlid fish that stem from eight distinct ancestral lineages, which colonized the lake after its formation 9 to 12 million years ago. Six of twelve currently described tribes are assigned to the H-lineage, an assemblage of exclusively mouthbrood-ing cichlids, all of which evolved during a short period of time during the course of the primary radiation of lacustrine species. Our study focuses on the deepwater tribe Limnochromini, comprising bi-parental mouthbrooders, and is based on phylogenetic analysis of two mitochondrial gene segments. We confirm the polyphyletic origin of the Limnochromini as they are defined to date, in that Gnathochromis pfefferi is placed among the Tropheini, whereas the genus Benthochromis is presented as an independent lineage. The remaining nine species were unambiguously resolved as monophyletic and should be redefined as the tribe Limnochromini. Concerning generic assignments, the genus Greenwoodochromis appeared as monophyletic, Limnochromis as paraphyletic, and the genera Reganochromis and Baileychromis as monophyletic sister genera. The linearized tree analysis and the comparison of average sequence divergences to that of the remaining tribes of the H-lineage revealed a relatively recent but simultaneous proliferation of the Limnochromini, suggesting that the same environmental changes triggered the radiation of particular deepwater, benthic, pelagic, and littoral lineages. By using a preliminary calibration of a molecular clock based on gamma-corrected amino acid distances of the NADH2 gene, the diversification of the Limnochromini could tentatively be dated to 2.9–3.5 MYA, coinciding with a period of aridification in East Africa between 2.5 and 3 MYA. The lack of geographic color morphs and the structural uniformity and resource scarcity of deepwater habitats suggest that competition and resource partitioning leading to differential trophic specialization promoted speciation within the Limnochromini, rather than an allopatric model.Reviewing Editor: Dr. Axel Meyer     

Drakensbergianella rudebecki, New Genus and New Species from the Mountains of Southern Africa, and Taxonomic Observations on Gabonia Jacoby and Related Genera (Insecta, Coleoptera, Chrysomelidae, Alticinae)

Drakensbergianella rudebecki, a new genus and new species of flea beetle (Chrysomelidae, Alticinae) found at high elevations from Southern Africa (Drakensberg mountains) is described. This new genus is closely related to the genus Gabonia Jacoby, 1893 but is easily distinguishable mainly by: the metasternum shorter than the length of the middle coxal cavities; the legs with femora and tibiae clearly elongate, especially the hind ones; the antennae generally longer than body in both sexes, especially in males; the metafemoral spring with inner side of the ventral lobe not angled; the metathoracic wings strongly reduced. Line drawings of male and female genitalia, metafemoral springs, and scanning electronic micrographs of particular morphological aspects of the taxa considered are provided. Finally, a brief discussion about Gabonia and related genera in the Afrotropical region with a key for the identification, is also reported. Moreover, the following new combination is proposed: Longitarsus ruandensis Weise, 1910 = Montiaphthona ruandensis Weise, 1910 n. comb.     

Description of a new species of the genus Glenea from Tibet, China (Coleoptera, Cerambycidae, Lamiinae, Saperdini)

A new species, Glenea jinisp. n. is described from Tibet, China. It can be separated from other species of the genus Glenea Newman by the complicated black and ochre markings as well as characters of the genitalia.     

马铃薯抗晚疫病基因Rpi-blb2的LRR区域多态性及分子进化分析

马铃薯抗晚疫病基因Rpi-blb2是来源于马铃薯野生种Solanum bulbocastanum中的一个具有广谱抗性的NBS-LRR类抗病基因。文章用PCR的方法从20个高抗晚疫病的马铃薯栽培种和20个高感晚疫病的马铃薯栽培种以及7个马铃薯野生种中克隆了Rpi-blb2基因的LRR区段。采用生物信息学方法对这些序列的相似性、多态性位点、核酸多样性指数等参数进行了分析,发现Rpi-blb2的LRR区域在核酸水平上变异程度很高,而且存在多处热点突变位点;通过对该区域的Ka/Ks值进行估算,发现Rpi-blb2的LRR区域总体上受到纯化选择,功能保守,但是LRR区域的不同部位所受到的选择压力却不尽相同。同时,从核酸水平来看,Rpi-blb2基因的LRR区域在马铃薯栽培种和马铃薯野生种之间没有发现明显的分化。     

湖北大巴山东部蚤类区系组成及垂直分布

采用常规与沿雪线调查方法,对大巴山东部具代表性的7个不同海拔梯度及6个不同生境类型,连续进行了11年调查和研究。结果表明：1)在所获得的8科28属51种9 974只蚤类中,有25种隶属于古北界,占49.02%,21种属于东洋界,占41.18%,5种广布,占9.80%; 经个体数量区系处理,古北和东洋两界蚤类区系数量（37.97%,50.30%）并不完全与物种区系相吻合,但东洋蚤类区系数量与古北物种区系相当;2）大巴山东部蚤类垂直分布的区系特点是,1 500 m以下东洋成分占绝对优势,1 600～2 300 m古北成分达44.82%～56.41%,但个体区系数量却在33.47%～60.16%之间,物种区系成分与数量区系分布并不完全一致; 一些东洋界特有指示性质的巴山盲鼠蚤和它的寄主猪尾鼠,仍可分布到这一地带;当海拔上升到2 600 m,古北成分已稳定达55.00%,此地带已不见东洋界特有指示性质的巴山盲鼠蚤和它的寄主猪尾鼠的踪迹,当海拔上升到2 800～2 980 m,古北成分和个体数量分别已达65.00%和89.51%;3）在大巴山东部51种蚤类中,有24种在秦岭有分布,占秦岭已知34种的70.58%,两座山系古北成分也相当,分别为49.02%及52.94%。最后按区系、宿主动物、植被带谱和地理状况相近原则,对张金桐等（1989）对秦岭南坡的蚤类海拔高度划线1 000～2 000 m进行修订,并上移至2 600 m左右地带,修订后的划线,其具体位置及走向大体与暗针叶林的下限保持一致。此线以上,无论蚤种或是数量都以古北界成分为主,低于此线,古北、东洋成分和一些特有指示性质的种类相互渗透。     

Fibroblast growth factor-2 and vascular endothelial growth factor expression in the ileocecal region of quail (Coturnix coturnix japonica)

Abstract

We undertook this study to immunolocalize in quail vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF-2) in the ileocecal region, which is a significant entry point for intestinal immunity. Diffuse cytoplasmic reaction for FGF-2 and VEGF was observed in the epithelial cells of the distal ileum and proximal cecal mucosa. VEGF immunoreactive cells, which give strong intracytoplasmic immunoreaction, were observed in the lamina propria of both intestinal parts. FGF-2 immunoreactive cells were seen in the lamina propria and germinative centers of lymph follicles in the cecum mucosa. Expressions of FGF-2 and VEGF in healthy quail intestines indicate that these factors have physiological roles in quail.     

Intron size, abundance, and distribution within untranslated regions of genes

Most research concerning the evolution of introns has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes. Here, we directly determined intron size, abundance, and distribution in UTRs of genes using full-length cDNA libraries and complete genome sequences for four species, Arabidopsis thaliana, Drosophila melanogaster, human, and mouse. Overall intron occupancy (introns/exon kbp) is lower in 5' UTRs than CDSs, but intron density (intron occupancy in regions containing introns) tends to be higher in 5' UTRs than in CDSs. Introns in 5' UTRs are roughly twice as large as introns in CDSs, and there is a sharp drop in intron size at the 5' UTR-CDS boundary. We propose a mechanistic explanation for the existence of selection for larger intron size in 5' UTRs, and outline several implications of this hypothesis. We found introns to be randomly distributed within 5' UTRs, so long as a minimum required exon size was assumed. Introns in 3' UTRs were much less abundant than in 5' UTRs. Though this was expected for human and mouse that have intron-dependent nonsense-mediated decay (NMD) pathways that discourage the presence of introns within the 3' UTR, it was also true for A. thaliana and D. melanogaster, which may lack intron-dependent NMD. Our findings have several implications for theories of intron evolution and genome evolution in general.     

Contributions to the taxonomy of the genera Pachysternum and Cyrtonion (Coleoptera, Hydrophilidae, Sphaeridiinae)

Pachysternum loxodonta sp. n. from the Republic of the Congo and Pachysternum sulawesicum sp.n. from Sulawesi Island, Indonesia are described. The generic status of Pachysternum sculpticolle (Régimbart, 1907) is revised, the species is transferred to the genus Cyrtonion and its differences from C. ghanense Hansen, 1989 are discussed. Taxonomy of Pachysternum is discussed, dividing the genus prelusively into three species groups, one comprising all known Oriental and Eastern Palearctic species, and two comprising the Afrotropical species. Species with unclear positions within the genus Pachysternum or with questionable generic status are left as “Species incertae sedis”.     

Presence of an acidic glycoprotein in the serum of arthritic rats: Modulation by capsaicin and curcumin

Voltage-dependent L-type Ca²⁺ channels form highly selective pores for Ca²⁺ ions in the membranes of excitable cells. We investigated the functional role of negatively charged residues, within or near the selectivity region, in ion permeation of a human cardiac L-type Ca²⁺ channel. Glutamates in each of the four repeats, and an aspartate in repeat IV, were substituted with positively charged lysine. Wild-type and mutant Ca²⁺ channels were expressed in Xenopus oocytes. Block by Ca²⁺ and Mg² of inward Li⁺ currents through the channels was used to assess the effects of amino acid substitutions on high-affinity divalent cation binding. The rank order of IC₅₀'s for Ca²⁺ block of I_Li was: E677K > E1086K > E334K > E1387K > D1391K > wild-type. The order of IC₅₀'s for Mg²⁺ block of I_Li indicated differential involvement of the same residues in Mg²⁺ binding: E1387K > E334K > E1086K > E677K > D1391K wild-type. Mutants E1387K and D1391K effectively permeated Ba²⁺, but exhibited a decreased single-channel conductance. The unitary current amplitude carried by Na+, in the absence of external divalent cations, was slightly decreased in the E1387K mutant but not in the D1391K mutant. The results confirm that each of the four glutamates participate unequally in high-affinity Ca²⁺ binding. Additionally, our results indicate that these glutamate residues participate in Mg²⁺ binding. The glutamate at position 1387 may be only peripherally involved in the formation of a high-affinity Ca²⁺ -binding site but is central to a Mg²⁺ binding site accessible from the external side of the pore. The aspartate at position 1391 is most likely located just external to the selectivity region. (Mol Cell Biochem 166: 125-134, 1997)