Multiomic study of the protective mechanism of Persicaria capitata (Buch.-Ham. ex D.Don) H.Gross against streptozotocin-induced diabetic nephropathy in Guizhou miniature pigs.

BACKGROUND: Persicaria capitata (Buch.-Ham. ex D.Don) H.Gross (P. capitata, PCB), a traditional drug of the Miao people in China, is potential traditional drug used for the treatment of diabetic nephropathy (DN). PURPOSE: The purpose of this study is to investigate the function of P. capitata and clarify its protective mechanism against DN. METHODS: We induced DN in the Guizhou miniature pig with injections of streptozotocin, and P. capitata was added to the pigs' diet to treat DN. In week 16, all the animals were slaughtered, samples were collected, and the relative DN indices were measured. 16S rRNA sequencing, metagenomics, metabolomics, RNA sequencing, and proteomics were used to explore the protective mechanism of P. capitata against DN. RESULTS: Dietary supplementation with P. capitata significantly reduced the extent of the disease, not only in term of the relative disease indices but also in hematoxylin-eosin-stained tissues. A multiomic analysis showed that two microbes (Clostridium baratii and Escherichia coli), five metabolites (oleic acid, linoleic acid, 4-phenylbutyric acid, 18-ß-glycyrrhetinic acid, and ergosterol peroxide), four proteins (ENTPD5, EPHX1, ARVCF and TREH), four important mRNAs (encoding ENTPD5, EPHX1, ARVCF, and TREH), six lncRNAs (TCONS_00024194, TCONS_00085825, TCONS_00006937, TCONS_00070981, TCONS_00074099, and TCONS_00097913), and two circRNAs (novel_circ_0001514 and novel_circ_0017507) are all involved in the protective mechanism of P. capitata against DN. CONCLUSIONS: Our results provide multidimensional theoretical support for the study and application of P. capitata.

The study on the impact of sex on the structure of gut microbiota of bamboo rats in China.

Introduction: Bamboo rats are rodents that eat bamboo, and their robust capacity for bamboo digestion is directly correlated with their gut flora. Chinese bamboo rat (Rhizomys sinensis) is a common bamboo rat in Chinese central and southern regions. As a single-stomach mammal, bamboo rats are a famous specificity bamboo-eating animal and their intestinal microbial composition may also play a key role in the digestion of cellulose and lignin. So, the gut microbiota of bamboo rat may play an important role in the adaptation of bamboo rats for digesting lignocellulose-based diet. Methods: To study the microbiome differences of bamboo rats from different sexes, the microbial genomic DNA was extracted from each fecal sample and the V4 region of 16S rRNA genes was amplified and sequencing on an IlluminaHiSeq6000 platform. The operational taxonomic units (OTUs) were classified, the OTUs in different sexes was identified and compared at phylum and genus levels. For isolation and screening of cellulose degradation bacteria from bamboo rats, fresh feces from randomly selected bamboo rats were collected and used for the isolation and screening of cellulose degradation bacteria using Luria Bertani (LB) Agar medium containing Carboxymethyl cellulose. The cellulase activity, biochemical characterization and phylogenetic analysis of the purified bacteria strains were characterized. Results and discussion: A total of 3,833 OTUs were classified. The total microbial diversity detected in the female and male rats was 3,049 OTUs and 3,452 OTUs, respectively. The Shannon index revealed significant differences between the two groups (p < 0.05), though they were all captive and had the same feeding conditions. At the phylum level, Firmicutes, Bacteroidota, and Proteobacteria were prominent in the microbial community. At the genus level, the microbial community was dominated by Lachnospiraceae, Lactobacillus, Bacteroides, and Prevotella, but there was a significant difference between the two groups of bamboo rats; ~90 bacteria genus in the female group was significantly higher than the male group. Among them, Bacteroides, Colidextribacter, and Oscillibacter were significantly higher genera, and the genera of Lachnoclostridium, Oscillibacter, and Papillibacter had the highest FC value among the male and female bamboo rats. The KEGG function annotation and different pathways analysis revealed that membrane transport, carbohydrate metabolism, and amino acid metabolism were the most enriched metabolic pathways in the two groups, and multiple sugar transport system permease protein (K02025 and K02026), RNA polymerase sigma-70 factor (K03088), and ATP-binding cassette (K06147) were the three different KEGG pathways (p < 0.05). Two cellulose degradation bacteria strains-Bacillus subtilis and Enterococcus faecalis-were isolated and characterized from the feces of bamboo rats.

Effect of Senecio scandens ethanol extract on gut microbiota composition in mice.

The gut microbiota inhabits the animal intestinal tract, and dysbiosis of the gut microbiota may result in disease. Senecio scandens has pharmaceutical antibacterial activities and is regarded as a broad-spectrum antibiotic in traditional Chinese medicine. Extracts of S. scandens are reported to show strong antimicrobial activity, and quercetin significantly decreases some species in the caecal microflora. However, the bactericidal effects of the extracts on the gut microbiota remain obscure. Here, we supplied ethanol extract of S. scandens, which might possibly be used as an alternative for chemical antibiotics, to mice to investigate the state of the intestinal microbiota. Our studies included a control group, low-, moderate-, and high-dose ethanol extract groups, and cefixime capsule group. The ethanol extract groups did not present reduced diversity or differences in the gut microbiota balance. There were significant differences between the ethanol extract and cefixime capsule groups in terms of the gut microbiota. The control and ethanol extract groups contained similar bacteria, which suggested that the ethanol extract has no inhibitory effect on the gut microbiota in vivo. Bifidobacteriales and Lactobacillus acidophilus were significantly increased in the high-dose group. Both secretory immunoglobulin A and mucin 2 concentrations increased as the dose of ethanol extract increased. The functional prediction differences between the control and ethanol extract groups decreased with increasing extract doses, which indicated that the low-dose and high-dose extract treatments might regulate different pathways and functions of the gut microbiota. The results also highlighted the prevention of bacterial drug resistance in the ethanol extract groups.

Significant Differences in the Gut Bacterial Communities of Hooded Crane (Grus monacha) in Different Seasons at a Stopover Site on the Flyway.

Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.

Variations in gut bacterial communities of hooded crane (Grus monacha) over spatial-temporal scales.

BACKGROUND: Microbes have been recognized as important symbionts to regulate host life. The animal gut harbors abundance and diverse bacteria. Numerous internal and external factors influence intestinal bacterial communities, including diet, seasonal fluctuations and habitat sites. However, the factors that influence the gut bacterial communities of wild bird is poorly characterized. METHODS: By high-throughput sequencing and statistical analysis, we investigated the variations in gut bacterial communities of the hooded cranes at three wintering stages in Caizi (CZL) and Shengjin Lake (SJL), which are two shallow lakes in the middle and lower Yangtze River floodplain. RESULTS: Our results revealed significant differences in gut bacterial community structure and diversity among different sampling sites and wintering stages. Seasonal changes have a significant impact on the gut microbe composition of hooded cranes in the two lakes. ANOSIM analysis demonstrated that the samples in CZL had greater differences in the gut bacterial composition than that in SJL. Our data showed strong evidence that the host's gut filtering might be an important factor in shaping bacterial community according to mean nearest taxon distance (MNTD). The PICRUSt analysis showed that the predicted metagenomes associated with the gut microbiome were carbohydrate metabolism, amino acid metabolism and energy metabolism over the entire wintering period at the two lakes. CONCLUSIONS: The results demonstrated that both seasonal changes and habitat sites have significant impact on the gut bacterial communities of hooded cranes. In addition, predictive function of gut microbes in hooded cranes varied over time. These results provide new insights into the gut microbial community of the cranes, which serves as a foundation for future studies.

Complete mitochondrial genome of Accipiter trivirgatus.

Crested goshawk (Accipiter trivirgatus) is a diurnal raptor tropical Asia which is a bird species in family Accipitridae. In the present study, we determined its complete mitochondrial genome by PCR-based method. The complete mitochondrial genome was 18,454 bp in length which overall base composition was 31.2% A, 24.4% T, 31.0% C, and 13.4% G. It consisted of the typical structure of 13 PCGs, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 2 control regions. All of the PCGs started with ATG codon, except for ND3 which was started with ATC. Most of the genes terminate with codons TAA. The non-coding regions include pseudo-control regions.

A new insight into the classification of dusky thrush complex: bearings on the phylogenetic relationships within the Turdidae.

Dusky thrush complex comprises of two sister species breeding in SC Siberia, which is the member of thrush Turdus from Turdidae. The phylogenetic resolution of Dusky thrush complex remains controversial, and a detailed research is still necessary. In this research, we determined the complete mtDNAs of both species, and estimated phylogenetic trees based on the mtDNA alignment of these and 21 other Turdidae species, to clarify the taxa status of the Dusky thrush complex. The squenced lengths of these three mitochondrial genomes were 16,737, 16,788 and 16,750 bp. The mtDNAs are circular molecules, containing the 37 typical genes, with an identical gene order and arrangement as those of other Turdidae. The ATG and TAA, respectively, are observed the most commonly start and stop codon. Most of the tRNA could be folded into the canonical cloverleaf secondary structure except for tRNASer (AGY) and tRNALeu (CUN), which lose 'DHU' arm. The control region presented a higher A + T content than the average value for the whole mitogenome. The phylogenetic trees reconstructed by the concatenated nucleotide sequences of mtDNA genes (Cyt b, ND2 and COI) indicate the Dusky thrush complex cannot be divided into two species, but the relationships between Dusky thrush subspecies still need additional study. This study improves our understanding of mitogenomic structure and evolution of the Dusky thrush complex, which can provide further insights into our understanding of phylogeny and taxonomy in Turdidae.

Complete mitochondrial genome of Anser albifrons frontails (Anseriformes: Anatidae).

The mitochondrial genome of Anser albifrons frontails is 16740 bp in size, including 22 tRNAs, 2 rRNAs, 13 PCGs, and a CR. Except for tRNASer (AGY) and tRNALeu (CUN) without the dihydrouridine arm, all tRNAs could be folded into canonical cloverleaf structures. All PCGs start with ATG and the termination codon TAA is commonly observed. The CR is located between tRNAGlu and tRNAPhe. The result of the phylogenetic analysis suggests that Anser albifrons frontails is closely related to A. cygonoides and A. anser.

The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China.

Gut microbes of animals play critical roles in processes such as digestion and immunity. Therefore, identifying gut microbes will shed light on understanding the annual life of animal species, particularly those that are threatened or endangered. In the present study, we conducted nucleotide sequence analyses of the 16S rRNA genes of gut microbiome of the hooded cranes (Grus monacha) wintering at Shengjin Lake, China, by Illumina high-throughput sequencing technology. We acquired 503,398 high-quality sequences and 785 operational taxonomic units (OTUs) from 15 fecal samples from different cranes, representing 22 phyla that were dominated by Firmicutes, Proteobacteria, and Actinobacteria. A total of 305 genera were identified that were dominated by Clostridium, Lysinibacillus, and Enterobacter. The core gut microbiome comprised 26 genera, including many probiotic species such as Clostridium, Bacillus, Cellulosilyticum, and Cellulomonas that could catabolize cellulose. The findings reported here contribute to our knowledge of the microbiology of hooded cranes and will likely advance efforts to protect waterbirds that inhabit Shengjin Lake Reserve during winter.

Solution structure of Q388A3 PDZ domain from Trypanosoma brucei.

PDZ domains are abundant protein interaction modules that often recognize short amino acid motifs at the C-termini of target proteins and regulate multiple biological processes. So far, no PDZ domain in Trypanosoma brucei, an eukaryotic parasite causing sleeping sickness, has been studied. Q388A3, conserved in the related kinetoplastid parasites, is a 1634-residue protein containing a PDZ domain at its C-terminus. In this work, the solution structure of Q388A3 PDZ domain was solved by NMR spectroscopy. Q388A3 PDZ domain adopts a PDZ-like fold composed by a five-stranded ß-sheet capped by two α-helices, which is similar to the PDZ domains from HtrA family proteins. Meanwhile, Q388A3 PDZ domain shows some structural features quite different from HtrA PDZ domain.

The complete mitochondrial genome of the Black-headed Gull Chroicocephalus ridibundus (Charadriiformes: Laridae).

The Black-headed Gull Chroicocephalus ridibundus is a waterbird, which breeds from north-east North America and across much of Europe and Asia. In this study, we determined its complete mitochondrial DNA sequence by PCR-based approach. The complete mtDNA sequence is 16,807 bp in size. The overall-based composition was 30.8% A, 31.1% T, 14.2% C, 24.0% G, with an A + T content (54.8%) rich feature. The mitochondrial genome consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. All protein coding genes use the typical intiation codon ATN, except for COI. TAN is the most frequent stop codon, and AGG and T- - are also occurred very common. The tRNA(Ser(AGN)) and tRNA(Lys(CUN)) lacked the dihydrouridine (DHU) arm and formed a simple loop.

Complete mitochondrial genome of Tringa erythropus (Charadriiformes: Scolopacidae).

The spotted redshank Tringa erythropus is a shorebird in the large bird family Scolopacidae. In this study, we sequenced and characterized its complete mitochondrial genome. The mitogenome is a circular DNA molecule of 16,683 bp in length, containing 13 protein-coding genes, 22 tRNA, 2 rRNA genes, and an AT-rich region. Its gene arrangement pattern is identical with typical bird species. Based on our data combined with the mitgenome DNA sequences of 12 Scolopacidae birds from GenBank, phylogenetic analysis indicated that T. erythropus, Arenaria interpres, and Eurynorhynchus pygmeus formed a group.

Complete mitochondrial genome of white-throated rock-thrush Monticola cinclorhynchus gularis (Passeriformes: muscicapidae).

The white-throated rock-thrush Monticola cinclorhynchus gularis is a subspecies bird in the family Muscicapidae of the order Passeriformes, which is distributed in Southeast Siberia to Northeast China and Korea, winters to Southeast Asia. In this study, we determined its complete mitochondrial genome (mtDNA) by the PCR-based method. The complete mtDNA is a 16,801 bp circular molecule containing 37 typical genes. The gene order is identical with the standard avian gene order. All protein-coding genes start with a typical ATG codon except for COI. The termination codon is usually the standard TAA. The 12S rRNA is 984 bp, and the 16S rRNA is 1602 bp in length. All tRNAs possess the classic clover leaf secondary structure except for tRNASer (AGN) and tRNACys (CUN), which lack the 'DHU' stem, only forming a simple loop. The non-coding regions contain a 1222 bp long control region (D-loop) and a few intergenic spacers. The phylogenetic tree based on some mitogenomes from Muscicapidae and Turdidae indicates that M. cinclorhynchus gularis and Phoenicurus auroreus are in the same branch in the group Muscicapidae.

Effects of environmental factors on MSP21-25 aggregation indicate the roles of hydrophobic and electrostatic interactions in the aggregation process.

Merozoite surface protein 2 (MSP2), one of the most abundant proteins on the merozoite surface of Plasmodium falciparum, is recognized to be important for the parasite's invasion into the host cell and is thus a promising malaria vaccine candidate. However, mediated mainly by its conserved N-terminal 25 residues (MSP21-25), MSP2 readily forms amyloid fibril-like aggregates under physiological conditions in vitro, which impairs its potential as a vaccine component. In addition, there is evidence that MSP2 exists in aggregated forms on the merozoite surface in vivo. To elucidate the aggregation mechanism of MSP21-25 and thereby understand the behavior of MSP2 in vivo and find ways to avoid the aggregation of relevant vaccine in vitro, we investigated the effects of agitation, pH, salts, 1-anilinonaphthalene-8-sulfonic acid (ANS), trimethylamine N-oxide dihydrate (TMAO), urea, and sub-micellar sodium dodecyl sulfate (SDS) on the aggregation kinetics of MSP21-25 using thioflavin T (ThT) fluorescence. The results showed that MSP21-25 aggregation was accelerated by agitation, while repressed by acidic pHs. The salts promoted the aggregation in an anion nature-dependent pattern. Hydrophobic surface-binding agent ANS and detergent urea repressed MSP21-25 aggregation, in contrast to hydrophobic interaction strengthener TMAO, which enhanced the aggregation. Notably, sub-micellar SDS, contrary to its micellar form, promoted MSP21-25 aggregation significantly. Our data indicated that hydrophobic interactions are the predominant driving force of the nucleation of MSP21-25 aggregation, while the elongation is controlled mainly by electrostatic interactions. A kinetic model of MSP21-25 aggregation and its implication were also discussed.

Purification, crystallization and preliminary crystallographic analysis of the marine α-amylase AmyP.

AmyP is a raw-starch-degrading α-amylase newly identified from a marine metagenome library. It shares low sequence similarity with characterized glycoside hydrolases and was classified into a new subfamily of GH13. In particular, it showed preferential degradation to raw rice starch. Full-length AmyP was cloned and overexpressed in Escherichia coli, then purified and crystallized in the presence of its substrate analogue ß-cyclodextrin. X-ray diffraction data were collected to a resolution of 2.1 Å. The crystal belonged to space group P21212, with unit-cell parameters a=129.824, b=215.534, c=79.699 Å, α=ß=γ=90°, and was estimated to contain two molecules in one asymmetric unit.