Ribosomal S6 Research Articles

Pseudocapillaria (Ichthyocapillaria) bumpi n. sp. (Nematoda: Capillariidae) Parasitising West African Lungfish Protopterus annectens (Owen, 1839) (Lepidosireniformes: Protopteridae) in Mozambique and Its Phylogenetic Position Within Capillariid Nematodes.

Pseudocapillaria (Ichthyocapillaria) bumpi n. sp. (Nematoda: Capillariidae) is described from specimens infecting the digestive tract of the West African lungfish, Protopterus annectens (Owen) (Lepidosireniformes: Protopteridae). Nematodes were collected in Karingani Game Reserve, Southern Mozambique and studied using light microscopy; obtained sequences of the 18S ribosomal (18S rRNA) gene used for phylogenetic studies. The new species is assigned to Pseudocapillaria Freitas, 1959 by having a stichosome consisting of a single row of stichocytes and ventrolateral lobes on the male tail as well as by lacking spines on the specular sheath, caudal alae, a membranous caudal bursa, and a lateral expansion of the caudal end. It is also assigned to the sub-genus Ichthyocapillaria Moravec, 1982 by having a membrane between the ventrolateral lobes and by lacking a vulvar appendage. Pseudocapillaria (I.) bumpi n. sp. differs from its nominal congeners by having a comparatively large body size with relatively long spicule, bearing the thin membrane non-extending further than ventrolateral lobes in males and relatively smaller eggs without protruding polar plugs. It is the 20th species of the genus, the first from the Afrotropical Realm, and the first from any lungfish species. Phylogenetic analyses suggested that P. (I.) bumpi is deeply nested in a clade that associates species of the genera Pearsonema, Aonchotheca and Baruscapillaria.

Multiplexing surface anchored functionalized iron carbide nanoparticle: A low molecular weight proteome responsive nano-tracer

Harvesting the low molecular weight (LMW) proteins from the cellular exudates is a big challenge for early disease detection. Here, we introduce a unique probe composed of surface-functionalized Fe2C NPs with different functional groups to harvest, identify and profile differentially expressed biomarker proteins. Three different functionalization of Fe2C NPs with Fe2C@NH2, Fe2C@COOH and Fe2C@PEG enabled to harvest 119 differentially expressed proteins from HeLa cell exudates. Among these proteins, 57 were LMW which 82.46 % were up-regulated and 17.54 % were down-regulated. The Fe2C@NH2 were able to separate 60S ribosomal proteins L7a, and L11, and leucine-rich repeat-containing protein 59. These proteins play a vital role in the maturation of large subunit ribosomal ribonucleic acid, mRNA splicing via spliceosome and cancer cell inhibitor, respectively. While, Fe2C@COOH identifies the 60S ribosomal protein types L7, 40S ribosomal protein S11, and 60S ribosomal protein L24. These proteins were important for large ribosomal subunit biogenesis, translational initiation, and assembly of large subunit precursor of pre-ribosome. Finally, the Fe2C@PEG extracted 40S ribosomal protein S2, splicing factor, arginine/serine-rich and 40S ribosomal protein S4, X isoform which were responsible for nonsense-mediated decay, oligodendrocyte differentiation and multicellular organism development. Thus, these results help us in defining oncogenic biomarkers for early disease detection.

Phylogeny and taxonomy of a novel species of Pseudocercospora from India

A new species of Pseudocercospora is described causing leaf spot disease on Crotalaria assamica from India. The identity of isolate was based on asexual morphs, cultural characteristics and phylogenetic analyses of partial nuclear ribosomal 28S large subunit and complete internal transcribed spacer rDNA sequence data with high statistical support value. Morphologically this species has characters similar to allied species in genus Pseudocercospora but differs in having catenate and branched conidia. Phylogenetic analysis using LSU and ITS reveals it a new species of >i>Pseudocercospora (Capnodiales, Mycosphaerellaceae).

Distinction between vaginal and cervical microbiota in high-risk human papilloma virus-infected women in China

BackgroundHigh-risk human papilloma virus (hrHPV) is the main causal factor of cervical precancer and cancer when persistent infection is left untreated. Previous studies have confirmed the vaginal microbiota is associated with HPV infection and the development of cervical lesions. The microbiota at different parts of the female genital tract is closely related but different from each other. To analyze the distinction between the vaginal and cervical microbiota of hrHPV(+) women in China, one hundred subjects were recruited, including 10 patients with HPV16/18(+) and cervical carcinoma, 38 patients with HPV16/18(+) but no cervical carcinoma, 32 patients with other hrHPV(+) and 20 healthy controls with HPV(−). Vaginal and cervical microbiota were separately tested through next-generation sequencing (NGS) targeting the variable region (V3-V4) of the bacterial ribosome 16S rRNA gene.ResultsHrHPV(+) subjects had higher percentages of vaginal douching history (P = 0.001), showed more frequent usage of sanitary pads (P = 0.007), had more sex partners (P = 0.047), were more sexually active (P = 0.025) and more diversed in ways of contraception (P = 0.001). The alpha diversity of the cervical microbiota was higher than that of the vagina. The cervical microbiota consisted of a lower percentage of Firmicutes and a higher percentage of Proteobacteria than the vagina at the phylum level. Sphingomonas, belonging to α-Proteobacteria, was almost below the detection limit in the vagina but accounted for five to 10 % of the bacteria in the hrHPV(−) cervix (P<0.001) and was inversely associated with hrHPV infection (P<0.05). Pseudomonas, belonging to γ-Proteobacteria, could hardly be seen in the normal vagina and shared a small percentage in the normal cervix but was significantly higher in the HPV16/18(+) (P<0.001) and cancerous cervix (P<0.05). No significant difference was shown in the percentage of BV associated anaerobes, like Gardnerella, Prevotella, Atopobium and Sneathia, between the cevix and vigina.ConclusionsThe proportion of Proteobacteria was significantly higher in the cervical microbiota than that of vagina. The hrHPV infection and cervical cancer was positively associated with Pseudomonas and negatively associated with Sphingomonas. It is of great improtance to deeply explore the cervical microbiota and its function in cervical cacinogenesis.

Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea.

Ribosomal protein L1 is a conserved two-domain protein that is involved in formation of the L1 stalk of the large ribosomal subunit. When there are no free binding sites available on the ribosomal 23S RNA, the protein binds to the specific site on the mRNA of its own operon (L11 operon in bacteria and L1 operon in archaea) preventing translation. Here we show that the regulatory properties of the r-protein L1 and its domain I are conserved in the thermophilic bacteria Thermus and Thermotoga and in the halophilic archaeon Haloarcula marismortui. At the same time the revealed features of the operon regulation in thermophilic bacteria suggest presence of two regulatory regions.

Three new species of Ametrodiplosis (Diptera: Cecidomyiidae) from Japan, with a key to the Japanese species and a molecular phylogenetic analysis.

Ametrodiplosis Rübsaamen (Diptera: Cecidomyiidae: Clinodiplosini) is a mostly Holarctic gall midge genus whose species are associated with a wide range of seed plant families, either as gall-inducers or inquilines. In this study, we describe three species of Ametrodiplosis from Japan: A. adetos n. sp. feeding in the flowers of Tylophora aristolochioides Miq. (Apocynaceae); A. aeroradicis n. sp. inducing aerial root galls on Trachelospermum asiaticum (Sieb. et Zucc.) Nakai and T. gracilipes var. liukiuense (Apocynaceae); and A. stellariae n. sp. forming leaf bud galls on Stellaria uliginosa Murray var. undulata (Thunb.) Ohwi (Caryophyllaceae). A molecular phylogenetic analysis using mitochondrial COI and ribosomal 16S genes and nuclear ribosomal 28S gene were conducted for the three new Ametrodiplisis species and other clinodiplosine taxa sequences available in GenBank. The analysis supported the monophyly of Ametrodiplosis despite the variable life history of the three species. In addition, it indicated very low intraspecific genetic divergence among the individuals from different localities and/or host plants. A taxonomic key to the three new Japanese species of Ametrodiplosis is provided.

HectD1 controls hematopoietic stem cell regeneration by coordinating ribosome assembly and protein synthesis.

Impaired ribosome function is the underlying etiology in a group of bone marrow failure syndromes called ribosomopathies. However, how ribosomes are regulated remains poorly understood, as are approaches to restore hematopoietic stem cell (HSC) function loss because of defective ribosome biogenesis. Here we reveal a role of the E3 ubiquitin ligase HectD1 in regulating HSC function via ribosome assembly and protein translation. Hectd1-deficient HSCs exhibit a striking defect in transplantation ability and exvivo maintenance concomitant with reduced protein synthesis and growth rate under stress conditions. Mechanistically, HectD1 ubiquitinates and degrades ZNF622, an assembly factor for the ribosomal 60S subunit. Hectd1 loss leads to accumulation of ZNF622 and the anti-association factor eIF6 on 60S, resulting in 60S/40S joining defects. Importantly, Znf622 depletion in Hectd1-deficient HSCs restored ribosomal subunit joining, protein synthesis, and HSC reconstitution capacity. These findings highlight the importance of ubiquitin-coordinated ribosome assembly in HSC regeneration.

Henneguya michiganensis n. sp. (Cnidaria: Myxosporea) from the gills of muskellunge Esox masquinongy Mitchill(Esociformes: Esocidae)

Henneguya Thélohan, 1892is the second most species rich genus of myxozoans, with reports from freshwater and marine fish worldwide. In the Great Lakes region of North America, muskellunge Esox masquinongy is an important game fish species that serves as an apex predator in the ecosystems of many inland lakes. The myxozoan fauna of esocid fish, especially muskellunge, remains largely understudied. During fish health assessments, muskellunge were examined for parasitic infections and myxozoan pseudocysts were observed on gill clip wet mounts. When ruptured under pressure, the intralamellar pseudocysts released thousands of myxospores consistent with those of the genus Henneguya. The myxospores were 67.3-96.6 (79.1 ± 5.9) µm in total length. The spore body was 18.6-22.6 (20.9 ± 1.0) µm × 5.4-6.9 (6.3 ± 0.4) µm in valvular view and 3.5-4.0 (3.8 ± 0.3) µm wide in sutural view. The two pyriform polar capsules positioned at the anterior of the spore body were 6.4-7.7 (7.0 ± 0.4) µm × 1.8-2.1 (2.0 ± 0.1) µm and each contained a tightly coiled polar filament with 9-10 turns. Two tapering caudal processes extended from the posterior of the spore body and were 47.3-75.6 (58.3 ± 5.8) µm in length. Histologically, large intralamellar polysporic plasmodia were surrounded by plump pillar cells and a distinct layer of plasma. Mild inflammation was present peripherally, with small numbers of necrotic germinative cells and intraplasmodial phagocytes internally. Ribosomal 18S rRNA gene sequence data were obtained from three gill pseudocysts. The three ~2000-bp sequences were identical, but shared no significant similarity with any publicly available sequence data. Phylogenetic analyses demonstrated sequence data from this Henneguya fell within a well-supported clade of Henneguya spp. reported from northern pike Esox lucius in Europe. Based on the distinct morphological, histological and molecular data, this species is designated as Henneguya michiganensis n. sp. from muskellunge in Michigan, USA.

DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters

AbstractThe application of DNA barcoding represents a complementary and efficient approach to identifying specimens at all stages of their life cycle when used in combination with traditional morphological methods. Due to difficulties obtaining samples from the deep sea (&amp;gt; 200 m), these methods have been less frequently applied to deep-water taxa. We used DNA-barcoding techniques to enhance large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico, a region that has recently been identified as one of the world’s four most hyperdiverse ocean ecosystems. This study was conceptualized in direct response to the Deepwater Horizon Oil Spill in 2010, which identified major knowledge gaps in our understanding of deep-sea biodiversity. We employed traditional Sanger sequencing and a genomic skimming approach to target the mitochondrial ribosomal large subunit 16S and the protein-coding cytochrome oxidase subunit 1 (COI). Alongside these molecular approaches, traditional taxonomic investigations allowed for advancements in biodiversity, evolutionary relationships, cryptic species complexes, and distributional records across four abundant and common deep-pelagic orders (Amphipoda, Euphausiacea, Lophogastrida, and Decapoda). DNA barcodes were successfully obtained from 82 species for a total of 158 and 169 new 16S and COI sequences, respectively. Evidence of cryptic diversity has been found in the genera EucopiaDana, 1852 (Lophogastrida) and Allosergestes Judkins &amp; Kensley, 2008 (Decapoda). New records for the Gulf of Mexico of species of LanceolaSay, 1818 (Amphipoda), Eupasiphae Wood-Mason in Wood-Mason &amp; Alcock, 1893, PasiphaeaSavigny, 1816, and MeningodoraSmith, 1882 (Caridea) are presented. Preliminary results allow us to reconsider the current classification and evolutionary relationships of several lineages. The urgency to document biodiversity in the deep-pelagic is pressing against a backdrop of future threats including oil spills and deep-sea drilling.

Methylated HNRNPK acts on RPS19 to regulate ALOX15 synthesis in erythropoiesis.

Post-transcriptional control is essential to safeguard structural and metabolic changes in enucleated reticulocytes during their terminal maturation to functional erythrocytes. The timely synthesis of arachidonate 15-lipoxygenase (ALOX15), which initiates mitochondria degradation at the final stage of reticulocyte maturation is regulated by the multifunctional protein HNRNPK. It constitutes a silencing complex at the ALOX15 mRNA 3′ untranslated region that inhibits translation initiation at the AUG by impeding the joining of ribosomal 60S subunits to 40S subunits. To elucidate how HNRNPK interferes with 80S ribosome assembly, three independent screens were applied. They consistently demonstrated a differential interaction of HNRNPK with RPS19, which is localized at the head of the 40S subunit and extends into its functional center. During induced erythroid maturation of K562 cells, decreasing arginine dimethylation of HNRNPK is linked to a reduced interaction with RPS19 in vitro and in vivo. Dimethylation of residues R256, R258 and R268 in HNRNPK affects its interaction with RPS19. In noninduced K562 cells, RPS19 depletion results in the induction of ALOX15 synthesis and mitochondria degradation. Interestingly, residue W52 in RPS19, which is frequently mutated in Diamond-Blackfan Anemia (DBA), participates in specific HNRNPK binding and is an integral part of a putative aromatic cage.

Bioremediation of various aromatic and emerging pollutants by Bacillus cereus sp. isolated from petroleum sludge.

The accumulation of toxic chemical constituents in sludge and wastewater has fuelled an interest in investigating efficient and eco-friendly wastewater remediation approaches. In this study, a set of bacterial samples were isolated from petroleum sludge and tested for their ability to degrade different aromatic pollutants, including azo dyes and emerging pollutants. Although exhibiting differential specificity, all bacterial isolates were able to degrade different classes of aromatic dyes efficiently. Ribosomal 16S rRNA sequencing of the 12 bacterial isolates showed that they belonged to two different bacterial genera: Bacillus cereus and Pseudomonas guariconensis. Of these 12 strains, MA1 (B. cereus) was the most promising and was chosen for further optimization and biochemical studies. The optimum culture and remediation conditions for MA1 was found to be at pH 7, with 100 ppm dye concentration, and under aerobic condition. In addition to efficiently degrading various aromatic dyes (e.g. Congo Red, Reactive Black 5, PBS, and Toluidine Blue), MA1 was also found to be capable of degrading various emerging pollutants (e.g. prometryn, fluometuron and sulfamethoxazole). Preliminary transcriptome analysis shows that MA1 grown on media containing a mixture of aromatic dyes appears to differentially express a number of genes. Data shown here strongly suggests that petroleum sludge is a rich reservoir of bacteria with powerful remediation abilities.

Congruence between molecular and morphological systematics of Alpine non‐biting midges (Chironomidae, Diamesinae)

AbstractIn mountain regions, climate change is resulting in glacial retreat, causing biodiversity loss in glacial‐fed streams (kryal habitat). Diamesa species (Diptera Chironomidae), the main colonizers of the kryal in the Alps, are the aquatic insects more threatened by extinction. In recent years, DNA barcoding was successfully adopted to delimit species of chironomids and provided species identification. We highlighted that for the Diamesa genus, inconsistencies remain between identification on a morphological and molecular basis, mainly within cinerella and zernyi groups, raising doubts about the validity of head colour as a good diagnostic taxonomic character. Molecular phylogeny reconstruction based on mitochondrial (cytochrome oxidase subunits I and II) and one nuclear (ribosomal 18S rRNA) markers revealed that D. bohemani and D. zernyi on one hand, and D. cinerella and D. tonsa on the other hand, represent populations of the same species. Divergence times suggested that the radiation of these alpine species seems to have been driven by the climatic events with the alternation of glacial periods that happened in the Pliocene and Pleistocene. The initial separation of the oriental species D. steinboecki seems to be due to the tectonic movements of the Periadriatic fault system that probably favoured the emergence of lakes and streams, successively colonized by D. steinboecki. This study raises important concerns, from the validity of diagnostic characters used today to identify larval types up to the uncertainty about how many species of Diamesa inhabit the European Alps and what their fate will be within the scenario of climate change.

Taxonomy and phylogeny of the basidiomycetous hyphomycete genus Hormomyces.

The taxonomy of the genus Hormomyces, typified by Hormomyces aurantiacus, which based on circumstantial evidence was long assumed to be the hyphomycetous asexual morph of Tremella mesenterica (Tremellales, Tremellomycetes) or occasionally Dacrymyces (Dacrymycetales, Dacrymycetes), is revised. Phylogenies based on the three nuc rDNA markers [internal transcribed spacers (ITS), 28S large ribosomal subunit nrDNA (28S) and 18S small ribosomal subunit nrDNA (18S)], based on cultures from Canada and the United States, suggest that the genus is synonymous with Tulasnella (Cantharellales, Agaricomycetes) rather than Tremella or Dacrymyces. Morphological studies of 38 fungarium specimens of Hormomyces, including the type specimens of H. callorioides, H. fragiformis, H. paridiphilus and H. peniophorae and examination of the protologues of H. abieticola, H. aurantiacus and H. pezizoideus suggest that H. callorioides and H. fragiformis are conspecific with H. aurantiacus while the remaining species are unlikely to be related to Tulasnella. The conidial chains produced by H. aurantiacus are similar to monilioid cells of asexual morphs of Tulasnella species formerly referred to the genus Epulorhiza. The new combination Tulasnella aurantiaca is proposed and the species is redescribed, illustrated and compared with similar fungi. The ecological niche of T. aurantiaca and its possible relationship to orchid root endophytes is discussed. A key to asexual genera with similar conidium ontogeny to T. aurantiaca is provided. Citation: Mack J, Assabgui RA, Seifert KA (2021). Taxonomy and phylogeny of the basidiomycetous hyphomycete genus Hormomyces. Fungal Systematics and Evolution 7: 177-196. doi: 10.3114/fuse.2021.07.09.

The larvae of Chinese Hydropsychidae (Insecta: Trichoptera), Part II: Potamyia chinensis and Cheumatopsyche trifascia.

The larvae of Chinese caddisflies Potamyia chinensis and Cheumatopsyche trifascia were successfully associated with identifiable adults using independent DNA markers, mitochondrial COI barcodes and nuclear ribosomal 28S D2 genes. A total of 49 specimens collected in China were employed in the molecular analyses. The two markers were congruent on species boundaries for 11 distinctive haplogroups, while D2 failed in differentiating two closely related species. A brief summary for larval studies of both genera is given, followed by an introduction to the generic morphological characteristics, and detailed morphological descriptions and illustrations for the two successfully associated species. The larva of P. chinensis is re-described here based on Chinese materials, following the previous larval description for P. echigoensis, which was recently synonymized with P. chinensis.

Blueberry Polyphenol Extracts Enhance the Intestinal Antioxidant Capacity in Weaned Rats by Modulating the Nrf2-Keap1 Signal Pathway.

Weaning causes the generation of excessive reactive oxygen species in the body, which could lead to oxidative stress. Polyphenols, for which blueberries are an important dietary source, are known for various health benefits including antioxidant properties. Here, we sought to elucidate the effects of blueberry polyphenol extracts (BPE) on intestinal antioxidant capacity and possible underlying mechanisms in weaned rats. Ninety-six rats were assigned to two groups and fed either a standard diet or a standard diet supplemented with BPE (200 mg/kg). The results showed that BPE supplementation increased (P < 0.05) catalase and superoxide dismutase activities and decreased (P < 0.05) interleukin-1 and interferon-γ contents in the jejunum and ileum. The abundances of mammalian target of rapamycin, ribosomal p70 S6 kinase and eukaryotic initiation factor 4E-binding protein 1 mRNA were elevated in the jejunum and ileum (P < 0.05) after BPE supplementation. Additionally, BPE supplementation decreased (P < 0.05) Kelch-like ECH-associated protein 1 (Keap1) gene transcription and enhanced (P < 0.05) NF-E2-related factor 2 (Nrf2) gene transcription in the jejunum and ileum. According to our results, BPE-induced protective effects against oxidative stress appear through the promotion of the jejunal and ileal antioxidant defense system in weaned rats, which was associated with the Nrf2–Keap1 signaling pathway.

A new species of Neoheterobothrium Price, 1943 (Monogenea, Diclidophoridae) from Syacium papillosum (Linnaeus) (Pleuronectiformes, Paralichthyidae) in the Yucatan Shelf, with notes on the validity of the subfamilies in the Diclidophoridae

Neoheterobothrium papillosum n. sp. (Monogenea: Diclidophoridae) is described based on specimens collected from the gills of the dusky flounder Syacium papillosum (Linnaeus) (Paralichthyidae) in the Yucatan Shelf. The new species can be differentiated from other congeneric species by the following characteristics: (1) number of hooks in the genital atrium (8 hooks), (2) number of testes (20-34), (3) pharynx size, (4) peduncle length, and (5) egg size. Neoheterobothrium papillosum n. sp. resembles Neoheterobothrium syacii; however, detailed morphological analysis allowed for their separation into two different species. Sequences of the nuclear ribosomal DNA partial 28S and ITS1 were obtained and compared with available sequences of other species and genera of the family Diclidophoridae from GenBank. A phylogenetic analysis was conducted, including 33 sequences, 18 of which represented 17 species and 11 genera of the family Diclidophoridae. The phylogenetic tree showed that Diclidophoridae is a monophyletic family and species of Diclidophora were grouped as the sister group of Neoheterobothrium papillosum n. sp. Our phylogenetic analyses were consistent with Mamaev's hypothesis, who divided Diclidophoridae into Diclidophorinae and Choricotylinae and concluded that Neoheterobothrium was a genus belonging to Diclidophorinae.

A first for Southern Africa: description of a new Heterobothrium (Monogenea: Diclidophoridae) parasitizing the evileye pufferfish Amblyrhynchotes honckenii (Tetraodontiformes: Tetraodontidae).

The monogenean genus Heterobothrium (Monogenea: Diclidophoridae) currently consists of 12 accepted species described globally from various pufferfishes (Tetraodontidae). This includes the economically important Heterobothrium okamotoi Ogawa 1991 that causes severe disease in the cultured tiger puffer Takifugu rubripes in Japan. During parasitological surveys targeting near shore marine fishes of South Africa, a new Heterobothrium was discovered on the gills of five evileye pufferfish Amblyrhynchotes honckenii with a prevalence of 100% and mean intensity of 23 (4-72). Specimens were morphologically studied using both light and scanning electron microscopy and molecularly characterized by sequencing the partial ribosomal gene 28S. Heterobothrium victorwepeneri n. sp. differs from its 12 congeners by a combination of morphological characters, such as fourth clamp pair (anteriormost, 180° inverted) as the smallest with some of the sclerites differing in shape from the other pairs, 8 to 9 genital hooks, number of testes 40-50, and absent isthmus. The 28S tree depicted two main branches, one clustering together species of mazocraeidean families while the other clustered together only species of the Diclidophoridae. Heterobothrium victorwepeneri n. sp. is the first species of its genus to be recorded and described from South Africa and from the tetraodontid A. honckenii. This study also provides for the first time 28S sequence for a species of this highly host-specific genus.

Molecular characterization of spiny hedgehogs of the Iberian Peninsula: the missing link in the postglacial colonization of the western European hedgehog

The western European hedgehog Erinaceus europaeus is the most representative species among spiny Iberian hedgehogs. The Algerian hedgehog Atelerix algirus and the four-toed hedgehog Atelerix albiventris are other spiny hedgehogs that can be found on the Iberian Peninsula. Whereas A. algirus has a limited distribution in a narrow stretch of east Iberia and a doubtful native/introduced origin, A. albiventris is considered an exogenous species potentially introduced because of their commercialization as pets. Because all three species are kept in captivity, we may found unpredictable phenotypic appearance of breeding specimens, making the use of molecular markers necessary to unequivocally identify hedgehog species. We used two mitochondrial genes (cytochrome b and ribosomal 12S) to identify species that distributed on the Iberian Peninsula. We identified some Algerian hedgehogs, A. algirus, and delimited the current distribution of this specie to the eastern Iberian coast from Barcelona southwards. We found a few A. albiventris exemplars in natural populations, which represent the first record of this exotic species in Europe. We focused on gene diversity and phylogenetic analyses of the most abundant species E. europaeus and aimed to reconstruct phylogenetic relationships and putative routes of colonization from the Iberian glacial refuges. We found two divergent lineages of an ancient origin with a geographical pattern of distribution delimited by the Ebro River. The northeast lineage was indicated as the glacial refuge that contributed to a rapid postglacial colonization of west Europe from the Iberian Peninsula.

The evolutionary relationship of S15/NS1RNA binding domains with a similar protein domain pattern - A computational approach

Abstract RNA binding proteins are involved in many functions, though the majority of them are composed into small RNA binding domains. The S15/NS1 RNA binding domain is a ribosomal S15 and the non-structural NS1 protein. In this study, an attempt was made to find the evolutionarily related protein fold of the S15/NS1 RNA binding domain using structural and sequence-based analysis, and it was found that several protein domain folds similar to this fold. Apart from these, different support vector machine (SVM) based methods were also developed for the analysis of these folds. According to the results of the structure, sequence and SVM-based analysis, several domain folds are evolutionarily related to the S15/NS1 RNA binding domain fold.

Molecular Placement of an Outbreak-Causing Gall Wasp,Zapatella davisae(Hymenoptera: Cynipidae), with Comments on Phylogenetic Arrangements in the Tribe Cynipini

AbstractGall wasps (Hymenoptera: Cynipidae) have fascinated researchers for centuries due to the elaborate diversity of charismatic galls they produce, the presence of unique reproductive systems (e.g., a form of cyclical parthenogenesis), the possible convergent evolution of semiparasitic gall wasp forms (i.e., “inquilines”), and their multitrophic interactions. While many classifications for gall wasps have been proposed, recent DNA sequence efforts combined with taxonomic revisions are beginning to clarify the evolutionary relationships of this group. To date, however, a well resolved phylogeny is lacking, complicating the study of outbreak-causing pest species. Outbreaks by one such species, the black oak gall wasp, Zapatella davisae Buffington &amp; Melika (Hymenoptera: Cynipidae: Cynipini), have led to extensive damage and mortality of black oaks, Quercus velutina L. (Fagales: Fagaceae), in the northeastern United States. Here we sequenced fragments of the nuclear ribosomal gene 28S, and the nuclear protein coding gene long-wavelength opsin from samples of Z. davisae collected on Cape Cod, MA, and Long Island, NY. Using these sequences and sequences previously published from the mitochondrial locus cytochrome b, we performed Bayesian and maximum likelihood multilocus phylogenetic reconstructions based on a concatenated alignment including species of gall wasps in the tribe Cynipini from which all three loci were present in the GenBank database. Confirming morphological work, we find that Z. davisae is most closely related to species in the genera Callirhytis and Neuroterus, and appears to be a basal member of the “Quercus” section of the tribe Cynipini. We find that recent generic reclassifications within the Cynipini have made great progress towards clarifying the taxonomic relationships of species of gall-inducing wasps in this tribe, and we comment on several classifications that require additional research.