Molecular analyses confirm Brevicellicium in Trechisporales.
Ontology highlight
ABSTRACT:
SUBMITTER: Telleria MT
PROVIDER: S-EPMC3719203 | biostudies-literature | 2013 Jul
REPOSITORIES: biostudies-literature
Publications
Molecular analyses confirm Brevicellicium in Trechisporales.
Telleria M Teresa MT Melo Ireneia I Dueñas Margarita M Larsson Karl-Henrik KH Paz Martín Maria P MP
IMA fungus 20130404 1
The genus Brevicellicium encompasses wood-inhabiting corticioid fungi characterized by isodiametric subhymenial hyphae, short basidia, and smooth, often subangular spores with a distinct apiculus. Eight new LSU nrDNA sequences and 13 new ITS nrDNA of this genus, including the type species, were aligned with 47 and 42 accessions respectively of species of Trechisporales obtained from GenBank, and phylogenetic analyses were performed. The order Trechisporales was confirmed as a monophyletic group; ...[more]
Similar Datasets
Project description:Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ? Y, e.g. A ? C; and X ? Y ? Z ? X, e.g. A ? C ? G ? A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.
| S-EPMC5094600 | biostudies-literature
Project description:The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699-30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401-2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system.
| S-EPMC6708575 | biostudies-literature
Project description:Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related groups) than to deuterostomes. For this reason, the lophophorate groups and Trochozoa were united to Lophotrochozoa. However, the relationships of the lophophorate lineages within Lophotrochozoa are still largely unresolved. Maximum-likelihood and Bayesian analyses were performed based on a dataset comprising 11,445 amino acid positions derived from 79 ribosomal proteins of 39 metazoan taxa including new sequences obtained from a brachiopod and a phoronid. These analyses show that the three lophophorate lineages are affiliated with trochozoan rather than deuterostome phyla. All hypotheses claiming that they are more closely related to Deuterostomia than to Protostomia can be rejected by topology testing. Monophyly of lophophorates was not recovered but that of Bryozoa including Ectoprocta and Entoprocta and monophyly of Brachiozoa including Brachiopoda and Phoronida were strongly supported. Alternative hypotheses that are refuted include (i) Brachiozoa as the sister group of Mollusca, (ii) ectoprocts as sister to all other Lophotrochozoa including Platyzoa, and (iii) ectoprocts as sister or to all other protostomes except chaetognaths.
| S-EPMC2593926 | biostudies-literature
Project description:The genus Rhizopogon includes species with hypogeous or subepigeus habit, forming ectomycorrhizae with naturally occurring or planted pines (Pinaceae). Species of the genus Rhizopogon can be distinguished easily from the other hypogeous basidiomycetes by their lacunose gleba without columella and their smooth elliptical spores; however, the limit between species is not always easy to establish. Rhizopogon luteolus, the type species of the genus, has been considered one of the species that are more abundant in Europe, as well as it has been cited in pine plantation of North and South America, different parts of Africa, Australia, and New Zealand. However, in this study, based on molecular analyses of the ITS nuclear ribosomal DNA (nrDNA) sequences (19 new sequences; 37 sequences from GenBank/UNITE, including those from type specimens), we prove that many GenBank sequences under R. luteolus were misidentified and correspond to Rhizopogon verii, a species described from Tunisia. Also, we confirm that basidiomes and ectomycorrhizae recently collected in Germany under Pinus sylvestris, as well as specimens from South of Brazil under Pinus taeda belong to R. verii. Thanks to the numerous ectomycorrhizal tips collected in Germany, a complete description of R. verii/P. sylvestris ectomycorrhiza is provided. Moreover, since in this paper the presence of R. verii in South America is here reported for the first time, a short description of basidiomes collected in Brazil, compared with collections located in different European herbaria, is included.
| S-EPMC4909799 | biostudies-literature
Project description:Alternative hemiplegia of childhood (AHC) is a rare neurodevelopmental disorder with an extensive phenotypic variability, resulting in a challenging clinical diagnosis. About 75% of AHC cases are caused by pathogenic variants mapping in the ATP1A3, ATP1A2 or GLUT1 gene, leaving many AHC patients clinically and genetically undiagnosed. In this study, we report the case of a 9-year old proband clinically diagnosed with an atypical form of AHC presenting a suspected mitochondrial etiology and an obscure genetic diagnosis. Long-range PCR followed by next generation sequencing of the proband's mitochondrial genome identified a novel mitochondrial variant, m.12302C > A, mapping in the MT-TL2 gene with a low heteroplasmic level in blood and fibroblasts. Whole exome sequencing revealed three known and novel pathogenic variants with different parental inheritance, all involved in the mitochondrial energy metabolism and thus far not associated with AHC. Live-cell mitochondrial metabolic study showed dysregulated mitochondrial oxidative phosphorylation pathway and metabolic plasticity preventing an efficient switch to glycolysis to sustain ATP homeostasis, congruent with the suspected mitochondrial etiology. In conclusion, our comprehensive genetic and metabolic analyses suggest an oligogenic inheritance among the nuclear and mitochondrial variants for the mitochondrial etiology of proband's atypical form of AHC, thereby providing critical insight in terms of genetic clues and bioenergetic deficit. This approach also improves the diagnostic process of atypical form of AHC with an unclear genotype-phenotype correlation to personalize therapeutic interventions.
| S-EPMC7262444 | biostudies-literature
Project description:Sexual dimorphism in body size is often used as a correlate of social and reproductive behavior in Australopithecus afarensis. In addition to a number of isolated specimens, the sample for this species includes two small associated skeletons (A.L. 288-1 or "Lucy" and A.L. 128/129) and a geologically contemporaneous death assemblage of several larger individuals (A.L. 333). These have driven both perceptions and quantitative analyses concluding that Au. afarensis was markedly dimorphic. The Template Method enables simultaneous evaluation of multiple skeletal sites, thereby greatly expanding sample size, and reveals that A. afarensis dimorphism was similar to that of modern humans. A new very large partial skeleton (KSD-VP-1/1 or "Kadanuumuu") can now also be used, like Lucy, as a template specimen. In addition, the recently developed Geometric Mean Method has been used to argue that Au. afarensis was equally or even more dimorphic than gorillas. However, in its previous application Lucy and A.L. 128/129 accounted for 10 of 11 estimates of female size. Here we directly compare the two methods and demonstrate that including multiple measurements from the same partial skeleton that falls at the margin of the species size range dramatically inflates dimorphism estimates. Prevention of the dominance of a single specimen's contribution to calculations of multiple dimorphism estimates confirms that Au. afarensis was only moderately dimorphic.
| S-EPMC4419524 | biostudies-literature
Project description:IntroductionSystemic lupus erythematosus (SLE) is a multisystem autoimmune disease. Currently, numerous genetic loci of SLE have been confirmed. Here we try to further explore additional genes contributing to SLE susceptibility in this study.MethodsForty nine single nucleotide polymorphisms (SNPs) with moderate-risk for SLE in previous study were genotyped in a large-scale replication study with a total of 3,522 cases and 8,252 controls using the Sequenom Massarray system. Association analyses were performed using logistic regression with gender or sample cohorts as a covariate through PLINK 1.07 software.ResultsThis replication effort confirmed five reported SLE susceptibility loci reaching genome-wide levels of significance (P(meta) <5.00 × 10(-08)): TNFSF4 (rs1418190, odds ratio (OR) = 0.81, P(meta) = 1.08 × 10(-08); rs4916219, OR = 0.80, P(meta )= 7.77 × 10(-09)), IRF8 (rs2934498, OR = 1.25, P(meta) = 4.97 × 10(-09)), miR-146a (rs2431697, OR = 0.69, P(meta) = 1.15 × 10(-22)), CD44 (rs2732547, OR = 0.82, P(meta) = 1.55 × 10(-11)), and TMEM39A (rs12494314, OR = 0.84, P(meta) = 1.01 × 10(-09)). Further logistic regression analysis indicated that the genetic effects within TNFSF4 detected in this study are independent from our previously reported signals.ConclusionsThis study increases the number of established susceptibility loci for SLE in Han Chinese population and highlights the contribution of multiple variants of modest effect. Although further studies will be required to identify the causal alleles within these loci, the findings make a significant step forward in our understanding of the genetic contribution to SLE in Chinese population.
| S-EPMC4404072 | biostudies-literature
Project description:INTRODUCTION:In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone. METHODOLOGY/PRINCIPAL FINDINGS:To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea. CONCLUSIONS/SIGNIFICANCE:Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea.
| S-EPMC3235110 | biostudies-literature
Project description:Banana (Musa spp. L.) is an important staple food and cash crop for about 30% of the population in Tanzania; however, the burrowing plant-parasitic nematode Radopholus similis causes black head disease and toppling in banana plants, which results in yield losses. We collected and identified 80 specimens of R. similis from four agro-ecological zones in Tanzania using morphological characters. We then used universal and specific R. similis primers to amplify the small subunit, internal transcribed spacer and large subunit of ribosomal DNA regions of these specimens. The amplicons were subsequently sequenced and analyzed using Bayesian inference. We identified two major clades, one that comprised all R. similis sequences derived from this study and another that included R. similis and Radopholus spp. sequences obtained from GenBank, indicating the separation of this species from congeneric sequences. Our findings provide a useful, simple and rapid method for identifying burrowing nematodes. This outcome could contribute to the development of permanent, integrated pest management strategies for the control of R. similis in banana and other crops in order to reduce associated yield losses in Tanzania. To our knowledge, this is the first study of nematodes to use combined morphological and molecular methods for the identification of R. similis in Tanzania.Banana (Musa spp. L.) is an important staple food and cash crop for about 30% of the population in Tanzania; however, the burrowing plant-parasitic nematode Radopholus similis causes black head disease and toppling in banana plants, which results in yield losses. We collected and identified 80 specimens of R. similis from four agro-ecological zones in Tanzania using morphological characters. We then used universal and specific R. similis primers to amplify the small subunit, internal transcribed spacer and large subunit of ribosomal DNA regions of these specimens. The amplicons were subsequently sequenced and analyzed using Bayesian inference. We identified two major clades, one that comprised all R. similis sequences derived from this study and another that included R. similis and Radopholus spp. sequences obtained from GenBank, indicating the separation of this species from congeneric sequences. Our findings provide a useful, simple and rapid method for identifying burrowing nematodes. This outcome could contribute to the development of permanent, integrated pest management strategies for the control of R. similis in banana and other crops in order to reduce associated yield losses in Tanzania. To our knowledge, this is the first study of nematodes to use combined morphological and molecular methods for the identification of R. similis in Tanzania.
| S-EPMC7266020 | biostudies-literature
Project description:Background: SARS-CoV-2 infection may not provide long lasting post-infection immunity. While hundreds of reinfections have reported only a few have been confirmed. Whole genome sequencing (WGS) of the viral isolates from the different episodes is mandatory to establish reinfection. Methods: Nasopharyngeal (NP), oropharyngeal (OP) and whole blood (WB) samples were collected from paired samples of four individuals who were suspected of SARS-CoV-2 reinfection based on distinct clinical episodes and RT-PCR tests. Details from their case record files and investigations were documented. RNA was extracted from the NP and OP samples and subjected to WGS, and the nucleotide and amino acid sequences were subjected to genome and protein-based functional annotation analyses. Serial serology was performed for Anti-N IgG, Anti- S1 RBD IgG, and sVNT (surrogate virus neutralizing test). Findings: Three patients were more symptomatic with lower Ct values and longer duration of illness. Seroconversion was detected soon after the second episode in three patients. WGS generated a genome coverage ranging from 80.07 to 99.7%. Phylogenetic analysis revealed sequences belonged to G, GR and "Other" clades. A total of 42mutations were identified in all the samples, consisting of 22 non-synonymous, 17 synonymous, two in upstream, and one in downstream regions of the SARS-CoV-2 genome. Comparative genomic and protein-based annotation analyses revealed differences in the presence and absence of specific mutations in the virus sequences from the two episodes in all four paired samples. Interpretation: Based on the criteria of genome variations identified by whole genome sequencing and supported by clinical presentation, molecular and serological tests, we were able to confirm reinfections in two patients, provide weak evidence of reinfection in the third patient and unable to rule out a prolonged infection in the fourth. This study emphasizes the importance of detailed analyses of clinical and serological information as well as the virus's genomic variations while assessing cases of SARS-CoV-2 reinfection.
| S-EPMC7985553 | biostudies-literature