16S Ribosomal DNA Research Articles

Characterization of the intestinal microbiota in MSM with HIV infection

BackgroundHIV-infected persons demonstrate notable disturbances in their intestinal microbiota; however, the impact of intestinal microbiota on HIV susceptibility in men who have sex with men (MSM), as well as the effects of HIV and antiretroviral therapy (ART) on their gut microbiota, remains under active study. Thus, our research focuses on clarifying the distinctions in intestinal microbiota composition among uninfected MSM and non-MSM healthy controls, investigating the alterations in early-stage intestinal microbial communities following HIV infection, and assessing how ART affects the intestinal microbiota.MethodsThis study enrolled four participant groups: uninfected MSM, Recent HIV-1 infection (RHI) MSM, MSM on ART, and non-MSM healthy controls, with 30 individuals in each group. We utilized 16S ribosomal DNA (16S rDNA) amplicon sequencing to analyze fecal microbiota and employed Luminex multiplex assays to measure plasma markers for microbial translocation (LBP, sCD14) and the inflammatory marker CRP.FindingsComparing uninfected MSM to non-MSM healthy controls, no substantial variances were observed in α and β diversity. Uninfected MSM had higher average relative abundances of Bacteroidetes, Prevotella, and Alloprevotella, while Bacteroides, Firmicutes, and Faecalibacterium had lower average relative abundances. MSM on ART had lower intestinal microbiota diversity than RHI MSM and uninfected MSM. In MSM on ART, Megasphaera and Fusobacterium increased, while Faecalibacterium and Roseburia decreased at genus level. Additionally, treatment with a non-nucleoside reverse transcriptase inhibitor (NNRTI) led to significant alterations in intestinal microbiota diversity and composition compared to RHI MSM. The random forest model showed that HIV infection biomarkers effectively distinguished between newly diagnosed HIV-infected MSM and HIV-negative MSM, with an ROC AUC of 76.24% (95% CI: 61.17-91.31%).ConclusionsMSM showed early intestinal microbiota imbalances after new HIV infection. MSM on ART experienced worsened dysbiosis, indicating a combined effect of HIV and ART. NNRTI-based treatment notably changed intestinal microbiota, suggesting a potential direct impact of NNRTI drugs on intestinal microbiota.

Effect of oral tryptamines on the gut microbiome of rats—a preliminary study

Background Psilocybin and related tryptamines have come into the spotlight in recent years as potential therapeutics for depression. Research on the mechanisms of these effects has historically focused on the direct effects of these drugs on neural processes. However, in addition to such neural effects, alterations in peripheral physiology may also contribute to their therapeutic effects. In particular, substantial support exists for a gut microbiome-mediated pathway for the antidepressant efficacy of other drug classes, but no prior studies have determined the effects of tryptamines on microbiota. Methods To address this gap, in this preliminary study, male Long Evans rats were treated with varying dosages of oral psilocybin (0.2 or 2 mg/kg), norbaeocystin (0.25 or 2.52 mg/kg), or vehicle and their fecal samples were collected 1 week and 3 weeks after exposure for microbiome analysis using integrated 16S ribosomal DNA sequencing to determine gut microbiome composition. Results We found that although treatment with neither psilocybin nor norbaeocystin significantly affected overall microbiome diversity, it did cause significant dose- and time-dependent changes in bacterial abundance at the phylum level, including increases in Verrucomicrobia and Actinobacteria, and decreases in Proteobacteria. Conclusion and Implications These preliminary findings support the idea that psilocybin and other tryptamines may act on the gut microbiome in a dose- and time-dependent manner, potentially identifying a novel peripheral mechanism for their antidepressant activity. The results from this preliminary study also suggest that norbaeocystin may warrant further investigation as a potential antidepressant, given the similarity of its effects to psilocybin.

Screening and Identification of Soil Selenium-Enriched Strains and Application in Auricularia auricula.

Selenium (Se) is an essential trace element for human physiological metabolism. The application of organic Se as a source to cultivate Se-rich plants for micronutrient supplementation has been receiving increasing attention. In our study, a bacterial strain named H1 was isolated from the soil in Heilongjiang Province, China, and under optimal culture conditions, the unit Se content could reach 3000 μg·g-1 and its 16S ribosomal DNA sequence seemed to be a new molecular record of an Enterobacter species. After the domestication of Se tolerance and Se-rich experiments, H1 can be used as a Se source for cultivation of Se-rich Auricularia auricula. The results showed that soluble protein, soluble sugar, free amino acid and vitamin C contents in Auricularia auricula were notably increased by 28.7%, 21.8%, 32.5% and 39.2% under the treatment of Se concentration of 0.24 mg·kg-1, respectively. These findings enhance our understanding that H1 is more conducive to Se uptake and nutrient accumulation.

Mogroside Alleviates Diabetes Mellitus and Modulates Intestinal Microflora in Type 2 Diabetic Mice.

Mogroside, the main component of Siraitia grosvenorii (Swingle) C. Jeffrey (Cucurbitaceae) is a natural product with hypoglycemic and intestinal microbiota regulating properties. However, whether the alteration of intestinal microbiota is associated with the antidiabetic effect of mogroside remains poorly understood. This study investigated the mechanism underlying the hypoglycemic effect of mogroside in regulating intestinal flora and attenuating metabolic endotoxemia. Kunming mice with type 2 diabetes mellitus (T2DM) induced by high-fat diet and intraperitoneal injection of streptozotocin were randomly divided into model, pioglitazone (2.57 mg/kg) and mogroside (200, 100, and 50 mg/kg) groups. After 28 d of administration, molecular changes related to glucose metabolism and metabolic endotoxemia in mice were evaluated. The levels of insulin receptor substrate-1 (IRS-1), cluster of differentiation 14 (CD14) and toll-like receptor 4 (TLR4) mRNAs were measured, and the composition of intestinal microflora was determined by 16s ribosomal DNA (rDNA) sequencing. The results showed that mogroside treatment significantly improved hepatic glucose metabolism in T2DM mice. More importantly, mogroside treatment considerably reduced plasma endotoxin (inhibition rate 65.93%, high-dose group) and inflammatory factor levels, with a concomitant decrease in CD14 and TLR4 mRNA levels. Moreover, mogroside treatment reduced the relative abundance of Firmicutes and Proteobacteria (the inhibition rate of Proteobacteria was 85.17% in the low-dose group) and increased the relative abundance of Bacteroidetes (growth rate up to 40.57%, high-dose group) in the intestines of diabetic mice. This study reveals that mogroside can relieve T2DM, regulating intestinal flora and improving intestinal mucosal barrier, indicating that mogroside can be a potential therapeutic agent or intestinal microbiota regulator in the treatment of T2DM.

Effects of single-anastomosis duodenal-ileal bypass with sleeve gastrectomy on gut microbiota and glucose metabolism in rats with type 2 diabetes.

Bariatric and metabolic surgery often leads to significant changes in gut microbiota composition, indicating that changes in gut microbiota after bariatric and metabolic surgery might play a role in ameliorating type 2 diabetes (T2D). However, the effects of single-anastomosis duodenal-ileal bypass with sleeve gastrectomy (SADI-S) on gut microbiota in T2D remain unclear. To investigate the effects of SADI-S on gut microbiota and glucose metabolism in T2D rats. Nineteen T2D rats were randomly divided into the SADI-S group (n = 10) and the sham operation with pair-feeding group (sham-PF, n = 9). Fecal samples were collected to analyze the gut microbiota composition with 16S ribosomal DNA gene sequencing. The fasting blood glucose and glycated hemoglobin were measured to evaluate the effects of SADI-S on glucose metabolism. The Chao and ACE index results indicated the richness of the gut microbial community. The ACE and Chao index values were significantly lower in the SADI-S group than in the sham-PF group, indicating that indicating that species richness was significantly lower in the SADI-S group than in the sham-PF group (p < 0.05). Shannon and Simpson indices were used to estimate the species diversity of the gut microbiota. Compared with the sham-PF group, the SADI-S group showed significantly lower Shannon index and higher Simpson index values, indicating that the species diversity was significantly lower in the SADI-S group than in the sham-PF group (p < 0.05). At the genus level, SADI-S significantly changed the abundances of 33 bacteria, including the increased anti-inflammatory bacteria (Akkermansia and Bifidobacterium) and decreased pro-inflammatory bacteria (Bacteroides). SADI-S significantly decreased the fasting blood glucose and glycated hemoglobin levels. The blood glucose level of rats was positively correlated with the relative abundances of 12 bacteria, including Bacteroides, and negatively correlated with the relative abundances of seven bacteria, including Bifidobacterium. SADI-S significantly altered the gut microbiota composition of T2D rats, including the increased anti-inflammatory bacteria (Akkermansia and Bifidobacterium) and decreased pro-inflammatory bacteria (Bacteroides). The blood glucose level of rats was positively correlated with the abundances of 12 bacteria, including Bacteroides, but negatively correlated with the relative abundance of 7 bacteria, including Bifidobacterium. These alternations in gut microbiota may be the mechanism through which SADI-S improved T2D. More studies should be performed in the future to validate these effects.

Exploration of the Changes in Facial Microbiota of Maskne Patients and Healthy Controls Before and After Wearing Masks Using 16S rRNA Analysis.

Whether in the field of medical care, or in people's daily life and health protection, the importance of masks has been paid more and more attention. Acne, the most common complication after wearing masks, which is also called maskne, has been successfully introduced into the common language as a common topic of dermatologist consultations. This study aims to study the changes of microflora in maskne patients and healthy controls before and after wearing masks. In the summer of 2023, we collected a total of 50 samples from 15 maskne patients and 10 healthy controls before and after wearing surgical masks for a long time. 16S ribosomal DNA sequencing and identification technology with V3-V4 variable region were adopted to explore the microbiome changes caused by mask wearing, analyze the changes in microbial diversity, and make interaction network. LDA effect size analysis was used to identify which bacteria showed significant changes in their relative abundance from phylum to genus. After wearing a mask, the microbiome of the maskne patients changed significantly more than that of the healthy controls, with both α diversity and β diversity lower than those of maskne patients before wearing masks and those of healthy controls after wearing masks. Co-occurrence network analysis showed that compared with other groups, the network of maskne patients after wearing masks for a long time had the lowest connectivity and complexity, but the highest clustering property, while the opposite was true for healthy controls. Many microbes that are potentially beneficial to the skin decreased significantly after wearing a mask. There was almost no difference in healthy controls before and after wearing a mask.

Myxotrichum persicum sp. nov., and two new combinations in the genus Myxotrichum

We describe Myxotrichum persicum sp. nov. as a seed endophyte of Aegilops triuncialis in Lorestan province of Iran, using morphological traits and sequences of the internal transcribed spacer regions 1 and 2 including the intervening 5.8S nuclear ribosomal DNA (ITS) and partial nuclear 28S ribosomal DNA (LSU) regions. Myxotrichum persicum is differentiated from its closest relative, M. deflexum, by possessing smaller ascomata bearing much shorter, usually unbranched appendages, and smaller, ellipsoidal to fusiform, smooth-walled ascospores. Based on morphology and the multilocus phylogeny of ITS, LSU, MCM7 and RPB1, we herein propose to combine two species of Malbranchea, namely M. circinata and M. flavorosea, into the genus Myxotrichum as Myxotrichum circinatum and M. flavoroseum, respectively.

A new species of the genus Paradistomum (Platyhelminthes: Trematoda) from Iwasaki's snail-eating snake Pareas iwasakii, with a note on morphological variations of Paradistomum megareceptaculum (Tamura, 1941).

Dicrocoeliid trematodes were detected from Iwasaki's snail-eating snake Pareas iwasakii in Iriomote Island, Okinawa Prefecture, Japan, and described as a new species Paradistomum dextra n. sp. in the present study. This new species can be distinguished from the type series of the other members of the genus based on size of eggs and morphological characteristics of body, oral and ventral suckers, and reproductive organs. However, the new species was hard to distinguish from Paradistomum megareceptaculum infecting snakes in Japan, including Iriomote Island where is the type locality of the new species, because it is closely similar to some part of the broad range of morphological variations in P. megareceptaculum. On the other hand, a partial sequence of 28S ribosomal DNA clearly distinguished these two species. Moreover, the new species' host snake Pareas iwasakii is reported to exclusively feed on land snails while host snakes of P. megareceptaculum feed on small vertebrates, indicating that the new species is also ecologically different from P. megareceptaculum. We also redescribed P. megareceptaculum based on adults sampled in this study and past studies to record the morphological variations of this species.

Proteogenomic analysis identifies neoantigens and bacterial peptides as immunotherapy targets in colorectal cancer

Considerable progress has recently been made in cancer immunotherapy, including immune checkpoint blockade, cancer vaccine, and adoptive T cell methods. The lack of effective targets is a major cause of the low immunotherapy response rate in colorectal cancer (CRC). Here, we used a proteogenomic strategy comprising immunopeptidomics, whole exome sequencing, and 16 S ribosomal DNA sequencing analyses of 8 patients with CRC to identify neoantigens and bacterial peptides that can serve as antitumor targets. This study directly identified several personalized neoantigens and bacterial immunopeptides. Immunoassays showed that all neoantigens and 5 of 8 bacterial immunopeptides could be recognized by autologous T cells. Additionally, T cell receptor (TCR) αβ sequencing revealed the TCR repertoire of epitope-reactive CD8+ T cells. Functional studies showed that T cell receptor-T (TCR-T) could be activated by epitope pulsed lymphoblastoid cells. Overall, this study comprehensively profiled the CRC immunopeptidome, revealing several neoantigens and bacterial peptides with potential to serve as immunotherapy targets in CRC.

Italian peninsula as a hybridization zone of Ixodes inopinatus and I. ricinus and the prevalence of tick-borne pathogens in I. inopinatus, I. ricinus, and their hybrids

BackgroundIxodes inopinatus was described from Spain on the basis of morphology and partial sequencing of 16S ribosomal DNA. However, several studies suggested that morphological differences between I. inopinatus and Ixodes ricinus are minimal and that 16S rDNA lacks the power to distinguish the two species. Furthermore, nuclear and mitochondrial markers indicated evidence of hybridization between I. inopinatus and I. ricinus. In this study, we tested our hypothesis on tick dispersal from North Africa to Southern Europe and determined the prevalence of selected tick-borne pathogens (TBPs) in I. inopinatus, I. ricinus, and their hybrids.MethodsTicks were collected in Italy and Algeria by flagging, identified by sequencing of partial TROSPA and COI genes, and screened for Borrelia burgdorferi s.l., B. miyamotoi, Rickettsia spp., and Anaplasma phagocytophilum by polymerase chain reaction and sequencing of specific markers.ResultsOut of the 380 ticks, in Italy, 92 were I. ricinus, 3 were I. inopinatus, and 136 were hybrids of the two species. All 149 ticks from Algeria were I. inopinatus. Overall, 60% of ticks were positive for at least one TBP. Borrelia burgdorferi s.l. was detected in 19.5% of ticks, and it was significantly more prevalent in Ixodes ticks from Algeria than in ticks from Italy. Prevalence of Rickettsia spotted fever group (SFG) was 51.1%, with significantly greater prevalence in ticks from Algeria than in ticks from Italy. Borrelia miyamotoi and A. phagocytophilum were detected in low prevalence (0.9% and 5.2%, respectively) and only in ticks from Italy.ConclusionsThis study indicates that I. inopinatus is a dominant species in Algeria, while I. ricinus and hybrids were common in Italy. The higher prevalence of B. burgdorferi s.l. and Rickettsia SFG in I. inopinatus compared with that in I. ricinus might be due to geographical and ecological differences between these two tick species. The role of I. inopinatus in the epidemiology of TBPs needs further investigation in the Mediterranean Basin.Graphical

Prevalence of tick infestation and molecular characterization of tick species of camels (Camelus dormedarius) from Al-Baha South Saudi Arabia

AbstractArthropods serve as efficient carriers for various life-threatening infections parasites, viruses and other harmful organisms throughout the world. In this study, Al-Aqiq Governorate of Al-Baha city served as the site where tick burden on camels (Camelus dromedarius) was assessed. The aim of the present investigation was to determine the diversity and prevalence of ticks. A total of 800 ticks, 756 adults and 44 nymphs were gathered and identified. Tick DNA was obtained from camels by utilizing commercially available kits. Polymerase chain reaction (PCR) was done on recovered DNA utilizing 12S rDNA and 16S ribosomal DNA fragments to analyze and identify the ticks. Three species of hard ticks were found in the two genera Hyalomma and Rhipicephalus. Hyalomma dromedarii (81.81%) and H. rufipes (17.35%) were the two species with the highest prevalence found on the domestic animal hosts, whereas R. sanguineus (had the lowest prevalence of 0.82%). This is a preliminary report of DNA barcode of tick species of camels (Camelus dormedarius) from Al-Baha in KSA and the Arabian Peninsula, which is a significant step towards broader phylogenetic studies on tick samples from this region. The results of our study provide valuable insights for healthcare administrators and government authorities regarding the frequency of hard ticks on mammalian hosts in Al-Aqiq Governorate of Al-Baha City, Saudi Arabia. This can also assist in regulating tick diseases, in particular during the epidemic time.

Characteristics of the oral microbiota in patients with primary Sjögren's syndrome.

Primary Sjögren's syndrome (pSS) is an autoimmune disease with unknown etiology that is considered to be related to environmental and genetic factors. The aim of this study was to clarify the oral microflora characteristics of pSS patients and to reveal the connection between oral bacterial composition and dental caries using a high-throughput sequencing technique. Thirty-five pSS patients and 20 healthy controls were enrolled in this study. We collected saliva and plaque samples from pSS patients and saliva samples from healthy controls. We used 16S ribosomal DNA (16S rDNA) high-throughput sequencing targeting the V3-V4 hypervariable region to determine the composition and structure of the microbiota in the three sample sets. Finally, bioinformatics analyses, including the diversity of the microbiota, species differences, and functional prediction were performed. In the alpha diversity and beta diversity analysis, the Chao1 (P < 0.01), observed species (P < 0.01), and PD whole tree indices (P < 0.01) were significantly lower in the saliva and plaque samples of pSS patients than in the saliva samples of healthy controls, but the Shannon (P < 0.01) and Simpson indices (P < 0.01) were significantly higher in the healthy controls, and their total diversity significantly differed. In the main flora composition at the genus level (top 10), we identified Prevotella and Veillonella as more enriched in the saliva of pSS patients and Fusobacterium, Actinomyces, and Leptotrichia as more enriched in the plaque of pSS patients. Predictive functional analysis showed that the oral microbiota of pSS patients was related to translation, metabolism of cofactors and vitamins, and nucleotide metabolism. The oral microbial ecology of patients with pSS is dysregulated, resulting in a decrease in overall diversity. Prevotella and Veillonella may be related to pSS, while Fusobacterium, Actinomyces, and Leptotrichia may be related to dental caries in pSS patients. Key Points • This study revealed differences in the oral microbial composition of patients with pSS compared to healthy controls. • We included a plaque group of pSS patients to identify the microbiota related to pSS and dental caries. • Prevotella and Veillonella may contribute to pSS, and Fusobacterium, Actinomyces, and Leptotrichia are associated with dental caries in pSS patients.

Treatment Effect of Long-Term Subsurface-Flow Constructed Wetland on Mariculture Water and Analysis of Wetland Bacterial Community

To improve the quality of natural seawater to meet the needs of aquaculture production, a large-scale subsurface-flow constructed wetland (HSFCW) was constructed and operated stably for 2 years to understand the reasons for its purification effect on natural seawater. The results of the study showed that the system could maintain a high purification effect on natural seawater during aquaculture; the average removal rates of COD, TSS, TN, NH4+-N, and DON (organic nitrogen) were 22.29%, 49.33%, 36.94%, 10.88%, and 44.08%, respectively. Additionally, the HSFCW could effectively remove harmful algae such as Cyanobacteria; the removal rate of dominant algae species in Cyanobacteria was 90.33–97.93%. The pyrosequencing of 16S ribosomal DNA revealed that Proteobacteria, Nitrospirae, and Chloroflexi were the main and key bacterial phyla in the system. Members of these key gates are regarded as playing important roles in resisting water purification. The study results suggest that the subsurface-flow wetland system can effectively improve seawater quality and reduce the density of harmful algae cells.

A full-length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing.

Protist diversity studies are frequently conducted using DNA metabarcoding methods. Currently, most studies have utilized short read sequences to assess protist diversity. One limitation of using short read sequences is the low resolution of the markers. For better taxonomic resolution longer sequences of the 18S rDNA are required because the full-length has both conserved and hypervariable regions. In this study, a new primer pair combination was used to amplify the full-length 18S rDNA and its efficacy was validated with a test community and then validated with field samples. Full-length sequences obtained with the Nanopore MinION for protist diversity from field samples were compared with Illumina MiSeq V4 and V8-V9 short reads. Sequences generated from the high-throughput sequencers are Amplicon Sequence Variants (ASVs). Metabarcoding results show high congruency among the long reads and short reads in taxonomic annotation at the major taxonomic group level; however, not all taxa could be successfully detected from sequences. Based on the criteria of ≥95% similarity and ≥1000 bp query length, 298 genera were identified by all markers in the field samples, 250 (84%) were detected by 18S, while only 226 (76%) by V4 and 213 (71%) by V8-V9. Of the total 85 dinoflagellate genera observed, 19 genera were not defined by 18S dinoflagellate ASVs compared to only three among the total 52 diatom genera. The discrepancy in this resolution is due to the lack of taxonomically available 18S reference sequences in particular for dinoflagellates. Overall, this preliminary investigation demonstrates that application of the full-length 18S rDNA approach can be successful in field studies.

Evaulation of Effective Antagonistic Yeasts in Kalasin Province, a Biocontrol Agent against the Fungal Colletotrichum capsici Caused Anthracnose Diseases in Chili Fruits

Primary screening of epiphytic and endophytic yeasts, the majority yeast was found from rhizosphere soil (21 isolates, 31.81%), and 5 antagonistic yeasts can have inhibited the growth of mycelia of C. capsici up to 60%. Efficacy of five antagonistic yeasts were screened under plant nurseries conditions. The result found all isolates were tested and compared with control and chemical plots. The result of plant height showed that, yeast isolate KS34 had highest of plant height at 45.80 cm. For the result of branch per plant of chili plant found isolate KS37 showed highest of branch per plant at 16.60 branches and the flower of chili per plant presented that isolate KS37 had highest of flower at 18.60 flowers. The result of anthracnose disease control by antagonistic yeasts in disease incidence and category mean as plant resistance. These results found that, Isolates KS46 had a great disease incidence at 7.80% that mean this isolate prove chili plant to resistance to C. capsisci. Addition, isolate KS46 had highest of activity of chitinase enzyme at 170.72 U/ml. Isolate KS46 identified by D1/D2 domain of 26S ribosomal DNA sequencing. The sequence analysis showed maximum identity of 100% with Candida haemulonii. This assumed C. haemulonii was showed the best to control C. capsici. For confirmed this result, all isolates were determined the mode of action by studied in relationship between antagonist isolates. The action of yeast isolate could competition the nutrient with mycelia of pathogen. This mode effect to C. capsici loss nutrient caused the pathogen get stuck to braked and died later.

Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool.

Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women. Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed. MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing. In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women's health.

Multi-Locus Sequence Analysis Indicates Potential Cryptic Speciation in the Chigger Mite Neoschoengastia gallinarum (Hatori, 1920) Parasitising Birds in Asia.

Neoschoengastia gallinarum is widely distributed in Asia, preferentially parasitising birds, and heavy infestations have clinical impacts on domestic fowl. In common with other trombiculid mites, the genetic diversity and potential variation in host preferences or pathology induced by N. gallinarum are poorly understood. This study aimed to unravel the geographical variation and population structure of N. gallinarum collected from galliform birds in Peninsular Malaysia and Thailand by inference from concatenated mitochondrial-encoded cytochrome c oxidase subunit I (COI), and nuclear-encoded internal transcribed spacer 2 (ITS2) and 18S ribosomal DNA gene sequences, including a comparison with previously published data from southeastern China. Our multi-locus sequence analysis revealed three monophyletic clades comprising (A) specimens from Peninsular Malaysia, (B) the samples from Thailand together with a minority of Chinese sequences, and (C) the majority of sequences from China. Similarly, most species delimitation approaches divided the specimens into three operational taxonomic units. Analysis of molecular variance revealed 96.41% genetic divergence between Malaysian and Thai populations, further supported by the absence of gene flow (Nm = 0.01). In conclusion, despite the two countries sharing a land border, populations of N. gallinarum from Peninsular Malaysia and Thailand appear to be genetically segregated and may represent distinct cryptic species.

Karyotype evolutionary diversification in marine fishes. First classical and molecular cytogenetic data on four Atlantic species

ABSTRACT Fishes present an exceptional level of diversification among vertebrates, whose adaptive instructions contained in their genome are physically organised in their chromosomes. Although cytogenetic data are useful to help understand the evolutionary processes, they are restricted or unavailable for many fish families. Cytogenetic characteristics of one Atlantic member of the Kyphosidae, Cirrhitidae, Pempheridae and Bythitidae families – about which little or no prior data is known – are described here. Conventional chromosomal analysis and the mapping of the 18S and 5S ribosomal DNA sequences revealed substantial variations in the diploid number (2n = 38–48) and structure of the chromosomes (FN = 48–84; i.e. number of chromosome arms), as well as in the rDNA distribution (simple, multiple and polymorphic sites). The findings extend the cytogenetic data for reef fish groups across a wider phylogenetic range and reveal the various ways in which karyotype evolution has taken place in the marine environment.

Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein.

Eukaryotic retrotransposons encode a reverse transcriptase that binds RNA to template DNA synthesis. The ancestral non-long terminal repeat (non-LTR) retrotransposons encode a protein that performs target-primed reverse transcription (TPRT), in which the nicked genomic target site initiates complementary DNA (cDNA)synthesis directly into the genome. The best understood model system for biochemical studies of TPRT is the R2 protein from the silk moth Bombyx mori. The R2 protein selectively binds the 3' untranslated region of its encoding RNA as template for DNA insertion to its target site in 28S ribosomal DNA. Here, binding and TPRT assays define RNA contributions to RNA-protein interaction, template use for TPRT and the fidelity of template positioning for TPRT cDNA synthesis. We quantify both sequence and structure contributions to protein-RNA interaction. RNA determinants of binding affinity overlap but are not equivalent to RNA features required for TPRT and its fidelity of template positioning for full-length TPRT cDNA synthesis. Additionally, we show that a previously implicated RNA-binding protein surface of R2 protein makes RNA binding affinity dependent on the presence of two stem-loops. Our findings inform evolutionary relationships across R2 retrotransposon RNAs and are a step toward understanding the mechanism and template specificity of non-LTR retrotransposon mobility.

Protective effect of Tao Hong Si Wu Decoction against inflammatory injury caused by intestinal flora disorders in an ischemic stroke mouse model

Background and aimsRecent studies have shown that intestinal flora are involved in the pathological process of ischemic stroke (IS). The potential protective effect of the traditional Chinese prescription, Tao Hong Si Wu Decoction (THSWD), against inflammatory injury after IS and its underlying mechanisms of action were investigated in the current study.MethodsFifty SPF(Specefic pathogen Free) male C57 mice were randomly assigned to sham operation, model, THSWD low-dose (6.5 g/kg), medium-dose (13 g/kg) and high-dose (26 g/kg) groups (10 mice per group). Mouse models of transient middle cerebral artery occlusion were prepared via thread embolism. Neurological function score, hematoxylin-eosin (HE) staining, immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), 16S ribosomal DNA (rDNA) sequencing, quantitative reverse transcription PCR (qRT-PCR) and other methods were employed to elucidate the underlying molecular mechanisms.ResultsNotably, THSWD induced a reduction in the neurological function score (P < 0.01) and neuronal injury in brain tissue, increase in protein expression of Claudin-5 and zonula occludens-1 (ZO-1) in brain tissue(P < 0.01), and decrease in serum lipopolysaccharide (LPS)(P < 0.01), diamine oxidase (DAO)(P < 0.01) and D-lactic acid(P < 0.01, P < 0.05) levels to a significant extent. THSWD also inhibited the levels of tumor necrosis factor-α (TNF-α)(P < 0.01) and interleukin − 1β (IL-1β)(P < 0.01) in brain tissue, and increased alpha and beta diversity in ischemic stroke mice, along with a certain reversal effect on different microflora. Finally, THSWD inhibited the polarization of microglia cells(P < 0.01) and decreased the protein and gene expression of toll-like receptor-4 (TLR-4)(P < 0.01, P < 0.05) and nuclear factor kappa B (NF-κB)(P < 0.01) in brain tissue.ConclusionOur data indicate that THSWD may interfere with inflammatory response in ischemic stroke by regulating intestinal flora and promoting intestinal barrier repair.