A new frog species of the genus Odorrana (Anura: Ranidae) from Yunnan, China.

Huia absita, new species, is described from Xe Sap National Biodiversity Conservation Area, southern Laos. Huia absita very closely resembles H. masonii, a species endemic to the Indonesian island of Java about 2,500 km away. The description of the holotype of H. masonii is expanded. Huia absita differs from H. masonii by having an outer metatarsal tubercle, having the third and fifth toes equal in length, and having supernumerary tubercles on the fingers. Huia melasma, new species, is described from Tham Tarn Lot (= Chalerm Rattanakosin) National Park and Kaeng Krachan National Park, western Thailand, and is distinguished by having males with SVL 53.5–55.1, no visible pineal body, a black spot on the side of the snout separated from the black canthal streak extending from nostril to eye, the first and second fingers equal in length, and all toes webbed to base of discs. The description of H. absita and H. melasma brings the number of species of Huia from five to seven.

A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compared with its morphologically similar and geographically proximate congeners. Molecular phylogeny derived from mitochondrial DNA sequences revealed that although the new species – designated here as Microhyla nilphamariensis sp. nov. – forms a clade with M. ornate, it is highly divergent from M. ornata and all of its congeners, with 5.7 – 13.2% sequence divergence at the 16S rRNA gene. The new species can be identified phenotypically on the basis of a set of diagnostic (both qualitative and quantitative) characters as follows: head length is 77% of head width, distance from front of eyes to the nostril is roughly six times greater than nostril–snout length, internarial distance is roughly five times greater than nostril–snout length, interorbital distance is two times greater than internarial distance, and distance from back of mandible to back of the eye is 15% of head length. Furthermore, inner metacarpal tubercle is small and ovoid-shaped, whereas outer metacarpal tubercle is very small and rounded. Toes have rudimentary webbing, digital discs are absent, inner metatarsal tubercle is small and round, outer metatarsal tubercle is ovoid-shaped, minute, and indistinct.

BackgroundAccurate identification of molecular transmission clusters (MTCs) and understanding the dynamics of human immunodeficiency virus (HIV) transmission are necessary to develop targeted interventions to prevent HIV transmission. We evaluated the characteristics of antiretroviral therapy-naïve individuals who belonged to HIV-1 MTCs in the China–Myanmar border region to inform targeted effective HIV intervention.MethodsPhylogenetic analyses were undertaken on HIV-1 pol sequences to characterize subtypes or circulating recombinant forms and identify MTCs. MTCs were defined as those with 2 or more sequences having bootstrap support > 80% and a pairwise gene distance less than or equal to 0.03. Factors correlated with MTCs were evaluated using logistic regression analysis. The chi-square test was used to compare differences between Chinese and Burmese participants belonging to MTCs.ResultsA total of 900 people had their pol gene successfully sequenced. Twenty-one MTCs were identified and included 110 individuals (12.2%). Individuals in MTCs were more likely to be Burmese [aOR = 2.24 (95% CI: 1.33, 3.79), P = 0.003], be younger [aOR = 0.34 (95% CI: 0.20, 0.58), P < 0.001 for age 26–50 vs. 25 years or younger], have a lower CD4 T cell count [aOR = 2.86 (95% CI: 1.34, 6.11), P = 0.007 for < 200 vs. 350 or greater], and have subtypes CRF07_BC or C [CRF07_BC: aOR = 7.88 (95% CI: 3.55, 17.52), P < 0.001; C: aOR = 2.38 (95% CI: 1.23, 4.62), P = 0.010 compared to CRF01_AE]. In MTCs, Burmese were younger (89.7 vs. 57.7% for age 25 years or younger), had a lower education level (41.0 vs. 8.5% for illiterate), were more likely to be infected through injection drug use (35.9 vs. 12.7%), and had a higher proportion of subtype BC (33.3 vs. 15.5%) and CRF01_AE (20.5 vs. 8.5%) compared to Chinese (P < 0.05 for all).ConclusionBurmese participants were more likely to belong to MTCs, and most MTCs had both Burmese and Chinese participants. These data highlight the bidirectional transmission of HIV-1 frequently transmission and close relationship among immigrants in the China–Myanmar border region. Local health departments should pay more attention to HIV screening and intervention to immigrants Burmese with the characteristics of younger age, having lower CD4 T cell count and infected with HIV subtypes CRF07_ BC or C.

MITOCHONDRIAL DNA (mtDNA) contains genes for the ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) used in mitochondrial protein synthesis and for a limited number of proteins of the mitochondrial inner membrane1–4. By a combination of genetic and physical mapping, the location of most of these genes on yeast mtDNA has been determined3,4. There is a single gene for the RNA from the large subunit of yeast mitochondrial ribosomes5, but, nevertheless, this RNA hybridises to non-adjacent fragments on the physical map of mtDNA6. Although this suggested that the gene for this RNA is split, like some eukaryotic nuclear genes7, the presence of partial gene duplications complicated the interpretation of our hybridisation experiments6. By electron microscopy of RNA–DNA hybrids we now present direct evidence for an insertion in this rRNA gene.

Colour change is a well-known phenomenon in many amphibians. Most of these changes involve transient darkening, lightening, or attainment of breeding colours. Nuptial calosities may become lighter outside the main breeding season. Depigmentation as an extreme form of lightening has been documented also for keratinized structures of tadpole mouths. Here I report a hitherto overlooked type of colour change: darkening of metatarsal tubercles from white to almost black. At Kinchega National Park in New South Wales, individuals of the Australian borrowing frog Neobatrachus pictus emerging from their aestivation burrows after rains had white outer metatarsal tubercles. Within a few hours to two days the metatarsal tubercles had turned completely black. This indicates that the extent of black colouration of the outer metatarsal tubercle hitherto used to discriminate the species N. centralis from N. pictus and N. sudelli is unreliable.

Paradoxical frogs (Pseudae) have been difficult to characterize morphologically, and their phylogenetic affinities have long remained elusive despite several taxonomic revisions of the group. Based on the analysis of 1388 specimens we evaluate morphological characters used to identify and group species throughout their distributions. We also suggest other, previously unreported phylogenetically informative morphological characters and evaluate morphometric differences among species. The geographic distribution of Pseudae in Brazil confirms, to a certain degree, their association with hydrographic basins. Geographic variation in morphology is extensive in some species. Some characters traditionally used to identify species (e.g. stripes on the ventral surface of the thigh) vary extensively among populations, and in most cases do not distinguish among species. Body shape differences, skin texture, size and number of carpal and metatarsal tubercles, supernumerary tubercles, vocal sac structure, dorsal coloration, ventral stripes on the thigh, and geographic distribution need to be considered together to correctly identify species. Size of reproductive Pseudis varies considerably, most likely as a response to local conditions altering larval size at metamorphosis, given that postmetamorphic growth is reduced or absent in Pseudis. The previously suggested suite of ecological characters that allow disproportionate larval growth are therefore substantiated, while the paradox of a conserved body plan coupled with extensive character variation is implicated as the cause for confusion in the taxonomy of paradoxical frogs.

Objective To detect clinical strain by amplifying 16S ribosomal RNA(16S rRNA) gene with polymerase chain reaction (PCR) method. Methods 16S rRNA gene was amplifyied by universal primers P1, P2 with polymerase chain reaction, and the polymerase chain reaction products were sequenced to achieve the DNA sequences. Results PCR products were about 1 465bp, and the PCR sequences were blasted in NCBI web to achieve the proper strain name, with the use of this method, the unkown gram-positive bacilli strain was identified as corynebacterium jeikeium strain, ATCC25923 was identified as a strain of staphylococcus aureus and negative control was also specific. Conclusion 16S rRNA gene detection can be used as strain identification, and especially for some less common clinical strains. Key words: Bacteria; RNA, 16S, ribosomal; Polymerase chain reaction

The first complete mitochondrial genome of a sunbird was determined for Gould’s sunbird Aethopyga gouldiae. The identity of the sample was verified by conducting nucleotide blast for each mitochondrial ribosomal RNA and protein-coding gene, and by estimating its phylogenetic position using five genes (12S, ND2, ATP6, ND3, CYTb) and 52 passerines (including 17 sunbirds and allies). The mitogenomic length of A. gouldiae was 16,893 bp, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The nucleotide composition of the genome shows a bias toward A + T. Since the sunbirds and allies form a large bird group that feeds on nectar, along with the hummingbirds and honeyeaters, the mitogenome of A. gouldiae could contribute to understand the evolution of feeding behavior in birds and the phylogenetic position of the sunbirds.

Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication

Simple SummaryDNA transposons are parasitic DNA segments that can move or duplicate themselves from one site to another in the genome. Dada is a unique group of DNA transposons, which specifically insert themselves into multicopy RNA genes such as transfer RNA (tRNA) genes or small nuclear RNA (snRNA) genes to avoid the disruption of single-copy functional genes. However, only a few Dada families have been characterized along with their target sequences. Here, vertebrate genomes were surveyed to characterize new Dada transposons, and over 120 Dada families were characterized from diverse fishes. They were classified into 12 groups with confirmed target specificities. Various tRNA genes, as well as 5S ribosomal RNA (rRNA) genes were inserted by Dada transposons. Phylogenetic analysis revealed that Dada transposons inserted in the same RNA genes are closely related. Phylogenetically related Dada transposons inserted in different RNA genes show the sequence similarity around their insertion sites, indicating Dada proteins recognize DNA nucleotide sequences to find their targets. Understanding how Dada discovers the targets would help develop target-specific insertions of foreign DNA segments.Dada is a unique superfamily of DNA transposons, inserted specifically in multicopy RNA genes. The zebrafish genome harbors five families of Dada transposons, whose targets are U6 and U1 snRNA genes, and tRNA-Ala and tRNA-Leu genes. Dada-U6, which is inserted specifically in U6 snRNA genes, is found in four animal phyla, but other target-specific lineages have been reported only from one or two species. Here, vertebrate genomes and transcriptomes were surveyed to characterize Dada families with new target specificities, and over 120 Dada families were characterized from the genomes of actinopterygian fish. They were classified into 12 groups with confirmed target specificities. Newly characterized Dada families target tRNA genes for Asp, Asn, Arg, Gly, Lys, Ser, Tyr, and Val, and 5S rRNA genes. Targeted positions inside of tRNA genes are concentrated in two regions: around the anticodon and the A box of RNA polymerase III promoter. Phylogenetic analysis revealed the relationships among actinopterygian Dada families, and one domestication event in the common ancestor of carps and minnows belonging to Cyprinoidei, Cypriniformes. Sequences targeted by phylogenetically related Dada families show sequence similarities, indicating that the target specificity of Dada is accomplished through the recognition of primary nucleotide sequences.

Human mitochondrial DNA (mtDNA) is 16,569 base pairs (bp) in length, coding for 37 genes. During the course of evolution, nearly all the genes expressing ribosomal proteins and ribosomal RNAs (rRNA) genes have been transferred from the mitochondria to the nucleus. However, mitochondrial DNA contains two ribosomal RNAs genes (12S and 16S), which have not yet transferred to the nucleus. These two, should, soon or later, end up in the nucleus. What does the future likely hold for these genes? In the nucleus everything has already been prepared, since all of the ribosomal protein genes are now chromosomally encoded, and nucleolar organizers, the nucleolus, and 45 rDNA are developed waiting for 12S rRNA and I6S rRNA genes to join them, thus enabling the formation of the third DNA-containing organelle, the ribosomal compartment. What could be the reason for this major event in the existence of life on Earth as it is currently understood? The advent of the ribosomal organelle will likely have an enormous impact on reproductive characteristics and on intellectual (thoughts, abstract and complex ideas, imagination, dreams, spirit) activity of the brain. Could this be the answer to the question: Are humans still evolving?

We describe a new species of Phrynobatrachus from the eastern part of the Upper Guinea forest region, Ghana, West Africa. Morphologically, the new species can be distinguished from all of its congeners by the combination of a slender body, short and pointed snout, a relatively warty dorsum, a black-spotted throat in both sexes, a gular flap in males, a dark spotted chest, a white-greyish venter with occasional blackish spots, rudimentary pedal webbing, none to slightly dilated finger tips and strongly delated toe tips, presence of both inner and outer metatarsal tubercles and absence of a dark face mask, eyelid tubercles and longer dorsal ridges. We collected mitochondrial DNA (mtDNA) sequence data from the 16S rRNA gene to measure the genetic diversity of the new species, and to estimate phylogenetic relationships. The new species is a distinct and monophyletic evolutionary lineage most closely related to Phrynobatrachus gutturosus, P. fraterculus and P. maculiventris. The discovery of this new species highlights that the biodiversity of West African forests is still incompletely known and that the few remaining forests need urgent protection.

Genome Sequence Resource of Bacillus velezensis Strain HC-8, a Native Bacterial Endophyte with Biocontrol Potential Against the Honeysuckle Powdery Mildew Causative Pathogen Erysiphe lonicerae var. lonicerae.

The organization of the ribosomal RNA (rRNA) genes of the mouse was determined by Southern blot hybridization using cloned rDNA fragments as probes, which could encompass the entire spacer region between two rRNA gene regions. The rRNA genes are organized into tandem repeats of nearly uniform length of about 44 kb. The heterogeneity detected in the nontranscribed spacer appears to be caused by its sequence rather than its length difference. At least three kinds of repetitive sequences are present in the non-transcribed spacer region; two of them are located 13 kb upstream from the 5'-end of 18S RNA gene and the other located 1 to 4 kb downstream from the 3'-end of 28S RNA gene.

Physical linkage between 5 s, 16 s and 23 s ribosomal RNA genes in Bacillus subtilis