Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “New genera”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13Linked to original sources
PubMedDate not supplied

Ultrastructure and development of Pleistophora ronneafiei n. sp., a microsporidium (Protista) in the skeletal muscle of an immune-compromised individual.

This report provides a detailed ultrastructural study of the life cycle, including proliferative and sporogonic developmental stages, of the first Pleistophora species (microsporidium) obtained from an immune-incompetent patient. In 1985, the organism obtained from a muscle biopsy was initially identified as belonging to the genus Pleistophora, based on spore morphology and its location in a sporophorous vesicle. Since that initial report, at least two new microsporidial genera, Trachipleistophora and Brachiola, have been reported to infect the muscle tissue of immunologically compromised patients. Because Trachipleistophora development is similar to Pleistophora, and as Pleistophora was only known to occur in cold-blooded hosts, the question of the proper classification of this microsporidium arose. The information acquired in this study makes it possible to compare Pleistophora sp. (Ledford et al. 1985) to the known human infections and properly determine its correct taxonomic position. Our ultrastructural data have revealed the formation of multinucleate sporogonial plasmodia, a developmental characteristic of the genus Pleistophora and not Trachipleistophora. A comparison with other species of the genus supports the establishment of a new species. This parasite is given the name Pleistophora ronneafiei n. sp.

Animals↗
PubMed2003

Molecular evolution of adenoviruses.

New advances in the field of genetic characterization of adenoviruses originating from different animal species are summarized. Variations seen in the host range and specificity, pathogenicity, genomic arrangement or gene complement are much wider than expected based on previous studies of human adenoviruses. Several exceptional adenoviruses from the two traditional conventional genera are now removed, and proposed to form at least two new genera. The eventual host origin of the new genera, however, is not clarified. Novel results from the genomic and phylogenetic analyses of adenoviruses originating from lower vertebrate species (including reptiles, amphibians and fish) seem to imply that probably five major clusters of adenoviruses exist corresponding to the five major classes of Vertebrata. Adenoviruses, which are now suspected to have common origin with enterobacterium phages from the family Tectiviridae, are perhaps very ancient indeed, and may have undergone a co-evolution with vertebrate hosts.

Adenoviridae↗
PubMed2026

Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.

Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250T, was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250T (=RGM 3146T = IMI 507634T).

Phylogeny↗
PubMed1999

Research on late Pliocene Oldowan sites at Kanjera South, Kenya.

The late Pliocene is notable for the appearance of two new hominid genera as well as the first archaeological sites, generally attributed to the Oldowan Industrial Complex. However, the behavioral ecology of Oldowan hominids has been little explored, particularly at sites older than 2.0 Ma. Moreover, debates on Oldowan hominid foraging ecology and behavior have centered on data from only two regions, and often from single site levels. Here we describe the preliminary results of our investigation of Oldowan occurrences at Kanjera South. These occurrences preserve the oldest known traces of hominid activity in southwestern Kenya, and unlike most of the Oldowan sites in the 2.0-2.5 Ma time interval, artefacts are found in spatial association with a well-preserved fauna. In 1996 and 1997, this project initiated the first excavation program for Kanjera South. Magneto- and biostratigraphy indicate that deposition began approximately 2.2 Ma, substantially earlier than previously thought. At Excavation 1, artefacts were found in spatial association with a taxonomically diverse faunal assemblage in Beds KS-1 and KS-2. Excavation 2 yielded a partial hippopotamus axial skeleton with artefacts in KS-3. Cores from both sites were incidentally flaked and represent a Mode I lithic technology indistinguishable from the Oldowan. Approximately 15% of the artefacts were manufactured from non-local raw materials, indicating a flow of resources into the area. Stable isotopic analysis of KS-1 and KS-2 pedogenic carbonates suggests that the Excavation 1 assemblages formed in a relatively open (>75% C4 grass) habitat. The Excavation 1 and 2 faunas contain a high proportion of equids relative to Oldowan accumulations from Bed I Olduvai Gorge, Tanzania. Beds KS-1 and KS-2 thus preserve traces of Oldowan hominid activities in a more open setting than has been previously documented.

Animals↗
PubMed2002

Primate canines from the early Miocene Pinturas Formation, Southern Argentina.

Previously undescribed canines from the Pinturas Formation (Santacrucian, early Miocene) in Patagonia, Argentina, indicate the presence of new primate taxa. These isolated teeth exhibit a generalized structure; the crowns are robust at the base, slightly or nonprojecting beyond the occlusal plane of the cheek teeth, with a relatively rounded or slightly sharp entocristid in the lowers. It is possible to distinguish at least one, possibly two, new primate genera. One taxon is slightly smaller than Soriacebus adrianae and morphologically distinct. The other may be an early relative of Alouatta, and if so it would expand the temporal and geographic range of this lineage. A third taxon is represented by an advanced pitheciin (? Soriacebus). Other isolated canines could be attributed to Carlocebus, but precise attribution remains uncertain. Despite the fragmentary nature of these specimens, and some unresolved taxonomic and phylogenetic questions, there is clear evidence for a greater diversity of fossil primates in Patagonia during the early Miocene than previously recognized.

Animals↗
PubMed2001

Natural occurrence of entomophthoralean fungi pathogenic to collembolans.

The aim of this study was to assess the natural occurrence of fungi from the order Entomophthorales (Zygomycetes) pathogenic to a range of collembolan species. A total of 11,709 collembolans representing a total of 15 species from all three subclasses within Collembola were collected and incubated. Infection with Neozygites-like spp. (Entomophthorales) was recorded in the two subclasses, Arthropleona and Symphypleona. The morphology of the primary conidia of the Neozygites-like fungi infecting collembolans showed a high degree of variation in shape and size, and the fungi were divisible into five groups. One group consisted of Neozygites sminthuri, while the other four groups, while still closely resembling the genus Neozygites, did not fit within the description of any known species and were preliminarily designated Neozygites sp. nov. 1 to 4. Neozygites sp. nov. 1, infecting Sphaeridia pumilis, was observed to form globular secondary conidia, which have not been observed before within the genus Neozygites. A formal species description needs, however, yet to be performed. The infection was mainly found in species from the subclass Symphypleona, where two new host genera for Neozygites, Deuterosminthurus and Sphaeridia, were recorded. However, the prevalence of Neozygites spp. was low, up to 10% in S. pumilis, 6% in Sminthurus viridis, and below 1% in Deuterosminthurus sulphureus. Infection with an obligatory entomopathogenic fungus was for the first time well documented within the subclass Arthropleona, where specimens of Orchesella cincta and Orchesella villosa sporulated with a N. sminthuri-like fungus. Additionally, infection with the facultative pathogen Conidiobolus coronatus was recorded from several hosts representing both the subclass Arthropleona (Isotoma anglicana and O. cincta) and the subclass Symphypleona (Dicyrtoma sp. and S. viridis). For most species the prevalence of C. coronatus resembled that of Neozygites spp. and did not exceed 8.8%. The only exception was Dicyrtoma sp., for which the only associated entomophthoralean fungus was C. coronatus, where the prevalence reached 17.8% infection.

Animals↗
PubMed2005

Different patterns of selection on the nuclear genes IRBP and DMP-1 affect the efficiency but not the outcome of phylogeny estimation for didelphid marsupials.

Selection at the protein-level can influence nucleotide substitution patterns for protein-coding genes, which in turn can affect their performance as phylogenetic characters. In this study, we compare two protein-coding nuclear genes that appear to have evolved under markedly different selective constraints and evaluate how selection has shaped their phylogenetic signal. We sequenced 1,100+ bp of exon 6 of the gene encoding dentin matrix protein 1 (DMP1) from most of the currently recognized genera of New World opossums (family: Didelphidae) and compared these data to an existing matrix of sequences from the interphotoreceptor retinoid-binding protein gene (IRBP) and morphological characters. In comparison to IRBP, DMP1 has far fewer sites under strong purifying selection and exhibits a number of sites under positive directional selection. Furthermore, selection on the DMP1 protein appears to conserve short, acidic, serine-rich domains rather than primary amino acid sequence; as a result, DMP1 has significantly different nucleotide substitution patterns from IRBP. Using Bayesian methods, we determined that DMP1 evolves almost 30% faster than IRBP, has 2.5 times more variable sites, has less among-site rate heterogeneity, is skewed toward A and away from CT (IRBP has relatively even base frequencies), and has a significantly lower rate of change between adenine and any other nucleotide. Despite these different nucleotide substitution patterns, estimates of didelphid relationships based on separate phylogenetic analyses of these genes are remarkably congruent whether patterns of nucleotide substitution are explicitly modeled or not. Nonetheless, DMP1 contains more phylogenetically informative characters per unit sequence and resolves more nodes with higher support than does IRBP. Thus, for these two genes, relaxed functional constraints and positive selection appear to improve the efficiency of phylogenetic estimation without compromising its accuracy.

Amino Acid Sequence↗
PubMed2006

E pluribus unum: A phylogenetic and phylogeographic reassessment of Laevapex (Pulmonata: Ancylidae), a North American genus of freshwater limpets.

The North American freshwater limpet genus Laevapex (Walker, 1903) is a ubiquitous inhabitant of lentic and slow-moving lotic habitats east of the Rocky Mountains, but uncertainty clouds its systematic affinities, the phylogenetic validity of its constituent nominal species, and its degree of genetic connectivity among drainages. We addressed these issues by sampling the genus throughout much of its collective range and constructing representative nuclear and mitochondrial (mt) gene trees, in addition to performing morphometric analyses of shell shape variation. Our results identify neotropical Gundlachia and South American Uncancylus as sister lineages for Laevapex and reveal a pronounced sub-familial dichotomy within the Ancylidae, separating these three New World genera from a Holarctic (Ferrissia (Ancylus, Rhodacmea)) sister clade. Five nominal taxa (L. fuscus, L. diaphanus, L. peninsulae, L. sp., and "F."arkansasensis), indistinguishable in our morphometric analyses, were polyphyletic in the mt gene trees, exhibited modest levels (< 3.9%) of genetic divergence in the primary (103 of 109 individuals) mt clade and, with one minor exception, they appeared fixed for a single nuclear ITS-2 genotype. Although complicated by the presence of rare, highly divergent mt lineages (of either introgressive or persistent ancestral polymorphic origin) in some populations, the molecular data were consistent with a taxonomic conclusion that these five nominal taxa represent a single polymorphic lineage of the type species L. fuscus. AMOVA analyses indicated that 56% of the observed mt variation could be attributed to among population differences, only two of 36 haplotypes were detected in more than one sampling location, and estimates of among-population mt gene flow were generally low at both regional and continental scales. Unrooted network analyses revealed a number of mt tip clades, one restricted to the southwestern part of the range, the remainder having overlapping distributions in eastern North America. All of the eastern tip clades occurred in the Mid-Atlantic region, and these samples displayed by far the highest levels of collective mt diversity. However, directional gene flow estimates indicated that this region has been a recipient (especially from Alabama populations), rather than a source of haplotypic diversity, implying that it likely represents a center of overlap, not a primary ice age refugium, for this limpet species.

Amino Acid Sequence↗
PubMed1999

Molecular evidence for multiple origins of woodiness and a new world biogeographic connection of the Macaronesian island endemic Pericallis (Asteraceae: senecioneae).

The prevalence of woody species in oceanic islands has attracted the attention of evolutionary biologists for more than a century. We used a phylogeny based on sequences of the internal-transcribed spacer region of nuclear ribosomal DNA to trace the evolution of woodiness in Pericallis (Asteraceae: Senecioneae), a genus endemic to the Macaronesian archipelagos of the Azores, Madeira, and Canaries. Our results show that woodiness in Pericallis originated independently at least twice in these islands, further weakening some previous hypotheses concerning the value of this character for tracing the continental ancestry of island endemics. The same data suggest that the origin of woodiness is correlated with ecological shifts from open to species-rich habitats and that the ancestor of Pericallis was an herbaceous species adapted to marginal habitats of the laurel forest. Our results also support Pericallis as closely related to New World genera of the tribe Senecioneae.

Asteraceae↗
PubMed1998

Cloning and expression of a novel dominant-negative-acting estrogen response element-binding protein in the heterogeneous nuclear ribonucleoprotein family.

Most genera of New World primates exhibit a compensated form of resistance to steroid hormones produced by the adrenal gland, gonads, and kidney. Estrogen resistance in New World primate cells is associated with the relative overexpression of a nonreceptor-related estrogen response element-binding protein (ERE-BP) that competes with estrogen receptor for ERE binding. Using the concatamerized ERE half-site (AGGTCAcag) in DNA affinity chromatography, we purified to homogeneity a 40-42-kDa ERE-BP. The affinity-purified ERE-BP bound specifically to either single- or double-stranded DNA bearing the consensus ERE half-site motif AGGTCA. Four distinct internal tryptic peptides from this protein were generated and shown to exhibit sequence similarity to proteins in the heterogeneous nuclear ribonucleoprotein family. These tryptic peptide fragments were used to generate a series of degenerate oligonucleotides that were successfully employed in isolating a full-length ERE-BP cDNA by polymerase chain reaction. Although a member of a family of proteins generally recognized for their ability to bind single strand RNA, the estrogen resistance-associated protein ERE-BP can effectively bind double strand DNA and competitively squelch estrogen receptor-directed transactivation.

Amino Acid Sequence↗
PubMed2005

Hylid frog phylogeny and sampling strategies for speciose clades.

How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed.

Animals↗
PubMed1996

Metabolism of reproductive steroids during the ovarian cycle in two species of callitrichids, Saguinus oedipus and Callithrix jacchus, and estimation of the ovulatory period from fecal steroids.

Gonadal steroids were measured in daily fecal samples providing comparative data on steroid metabolism in two genera of New World primates. Circulating bioactive LH and progesterone concentrations and fecal progesterone, pregnanediol, estradiol, and estrone concentrations were measured by collecting blood and daily fecal samples from four captive common marmoset females and four cotton-top tamarin females for 30 days. High recoveries (> 80%) of labeled steroids that were added directly to the feces before extraction were recovered from feces of both species. Because of the presence of complex steroid conjugates, only one fifth the amount of estradiol was measured without solvolysis as compared to the amount measured with solvolysis. In tamarins, steroids were metabolized rapidly, with all postovulatory increases occurring within two days after the circulating LH peak (an increase of 2 SD higher than mean follicular levels). In marmosets, steroid excretion was slower; increased steroid levels occurred 2-4 days after the LH peak except in the case of estrone, which did not consistently increase after the LH peak. Circulating estrone and estradiol both contributed to the high excretion of estradiol in the feces from both species. The timing in the delay in excretion of fecal steroids was used to accurately determine the ovulatory period to within a 2-day window. This degree of accuracy is possible when the duration of the delay to the LH peak is known for a given species. Additionally, steroid concentrations were highly correlated between frozen and lyophilized fecal samples (0.81 +/- 0.07 SEM), indicating that fluid removal from the feces did not effectively alter steroid profiles.

Animals↗
PubMed2000

16S-23S rDNA spacer of Pectinatus, Selenomonas and Zymophilus reveal new phylogenetic relationships between these genera.

The 16S-23S rDNA spacer regions of two Pectinatus species, two Zymophilus species and one Selenomonas species were cloned after PCR amplification. The results of PCR amplification showed that these species had two types of spacer regions which differ in molecular size (long and short). Only the long spacer regions in these bacteria contained one or two tRNA genes (alanine and/or isoleucine). The spacer regions in these bacteria had a relatively high level of homology. Homology was particularly high for bacteria belonging to the same genus. Interestingly, the order of the two tRNA genes present in the long spacer regions of Pectinatus and Selenomonas was the reverse of that which had been previously reported for other bacteria. The results of spacer homology analysis and the order of the tRNA genes suggest that the taxonomic classification of anaerobic bacteria isolated from the brewing process should be re-examined.

Beer↗
PubMed2003

Novel anamorphic mite-associated fungi belonging to the Ustilaginomycetes: Meira geulakonigii gen. nov., sp. nov., Meira argovae sp. nov. and Acaromyces ingoldii gen. nov., sp. nov.

Three novel mite-associated basidiomycetous species are described in two new anamorph genera as Meira geulakonigii gen. nov., sp. nov. (type CBS 110052(T)=NRRL Y-27483(T)=AS 004(T)), Meira argovae sp. nov. (type CBS 110053(T)=NRRL Y-27482(T)=AS 005(T)) and Acaromyces ingoldii gen. nov., sp. nov. (type CBS 110050(T)=NRRL Y-27484(T)=AS 001(T)). Morphologically, these fungi are similar to the yeast-like fungi classified in the Ustilaginales, such as Pseudozyma species. However, analysis of the D1/D2 domain of the LSU rDNA suggests that they belong to two different lineages within the Exobasidiomycetidae of the Ustilaginomycetes (Basidiomycota). Furthermore, these fungi may be of interest for the biocontrol of mites, as they reduced mite numbers by approximately 80 % after inoculation.

Animals↗
PubMed1998

Isolation of myxobacteria from the marine environment.

In an attempt to isolate indigenous marine myxobacteria from coastal samples, we obtained two swarm forming bacteria. Both isolates formed cell aggregates which, at least in one isolate, developed to fruiting body-like structures consisting of a mass of myxospore-like cells. The optimum NaCl concentrations for their growth were between 2 and 3%, comparable to the NaCl concentration of seawater. This growth characteristic strongly suggests that the two isolates are specific marine bacteria. The 16S rDNA sequence studies indicated that the two isolates were related to the genus Nannocystis. Based on the phylogenetic distances between branches, we concluded that the isolates should be assigned to two new myxobacterial genera.

Culture Media↗
PubMed2004

Sequence and organization of the Neodiprion lecontei nucleopolyhedrovirus genome.

All fully sequenced baculovirus genomes, with the exception of the dipteran Culex nigripalpus nucleopolyhedrovirus (CuniNPV), have previously been from Lepidoptera. This study reports the sequencing and characterization of a hymenopteran baculovirus, Neodiprion lecontei nucleopolyhedrovirus (NeleNPV), from the redheaded pine sawfly. NeleNPV has the smallest genome so far published (81,755 bp) and has a GC content of only 33.3%. It contains 89 potential open reading frames, 43 with baculovirus homologues, 6 identified by conserved domains, and 1 with homology to a densovirus structural protein. Average amino acid identity of homologues ranged from 19.7% with CuniNPV to 24.9% with Spodoptera exigua nucleopolyhedrovirus. The conserved set of baculovirus genes has dropped to 29, since NeleNPV lacks an F protein homologue (ac23/ld130). NeleNPV contains 12 conserved lepidopteran baculovirus genes, including that for DNA binding protein, late expression factor 11 (lef-11), polyhedrin, occlusion derived virus envelope protein-18 (odv-e18), p40, and p45, but lacks 21 others, including lef-3, me53, immediate early gene-1, lef-6, pp31, odv-e66, few polyhedra 25k, odv-e25, protein kinase-1, fibroblast growth factor, and ubiquitin. The lack of identified baculovirus homologues may be due to difficulties in identification, differences in host-virus interactions, or other genes performing similar functions. Gene parity plots showed limited colinearity of NeleNPV with other baculoviruses, and phylogenetic analysis indicates that NeleNPV may have existed before the lepidopteran nucleopolyhedrovirus and granulovirus divergence. The creation of two new Baculoviridae genera to fit hymenopteran and dipteran baculoviruses may be necessary.

Animals↗