Microbial Communities and Functional Genes in Periodontitis and Healthy Controls.

BACKGROUND: Periodontitis is a chronic progressive disease and the leading cause of tooth loss in adults. Recent studies have shown the impact of oral microbial communities on systemic health and diseases such as cancer, atherosclerosis, rheumatoid arthritis, inflammatory bowel disease, diabetes, hypertension, and Alzheimer's disease. In previous case control studies investigatin the relationship between periodontal disease and the oral microbiota, little attention has been paid to the intersections of these domains. METHODS: Here, we used high-throughput 16S rRNA sequencing to analyse the differences in the microbial composition in saliva between a group of patients with chronic periodontitis (C; n = 51) and a healthy control group (H; n = 61) and predicted the functional gene composition by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. RESULTS: We found significant alterations in oral microbial diversity between C and H (P = 0.002). Sixteen genera were significantly different between C and H, and 15 of them were enriched in C linear discriminant analysis (LDA > 2). Fifty functional genes were significantly different between C and H, and 34 of them were enriched in C (P < .025). CONCLUSIONS: Periodontitis is associated with significant changes in the oral microbial community.

Comparison of effectiveness and cost of different HCV testing strategies in high-risk populations in China.

High-risk populations are the predominant populations affected by hepatitis C virus (HCV) infection, and there is an urgent need for efficient and cost-effective HCV testing strategies for high-risk populations to identify potential undiagnosed HCV-infected individuals. This study compared several commonly used testing strategies and conducted effectiveness and cost analysis to select the appropriate testing strategy for diagnosing HCV infection in high-risk populations. Among the 2093 samples from high-risk populations in this study, 1716 were HCV negative, 237 were current HCV infection, 137 were past HCV infection, and three were acute early HCV infection. It was found that out of 237 patients with HCV current infection, Strategy A could detect 225 cases, with a missed detection rate of 5.06%, and the total cost was 33 299 RMB. In addition, Strategy B could detect 237 cases of current HCV infection, and the HCV missed detection rate was 0.00%, and the total cost was 147 221 RMB. While 137 cases of past HCV infection could be distinguished by strategy C, but 14 cases with current HCV infection were missed, with an HCV-positive missed detection rate of 5.91%, and the total cost for Strategy C was 43 059 RMB. In conclusion, in high-risk populations, the HCV positivity rate is typically higher. If feasible, the preferred approach is to directly conduct HCV RNA testing, which effectively minimizes the risk of missing cases. However, in situations with limited resources, it is advisable to initially choose a highly sensitive method for anti-HCV screening, followed by HCV RNA testing on reactive samples.

Pollen morphology of Clerodendrum L. (Lamiaceae) from China and its systematic implications.

Pollen morphology of 26 taxa of Clerodendrum, as well as one species of Volkameria from China, was investigated through a scanning electron microscope (SEM). Pollen grains of Clerodendrum are monads, radiosymmetric and tricolpate, with medium or large size. The equatorial view of the pollen grains is spheroidal or subprolate and the polar view is (sub) circular or rounded triangular. The colpus membrane of the investigated taxa is sunken (rarely even). Five varying pollen types are delimited on the basis of exine sculpturing: (1) spine-tectum perforatum; (2) spine-tectum imperforatum; (3) microspine-tectum perforatum; (4) microspine-tectum imperforatum; and (5) obtuser spine. The results indicate that Clerodendrum is closely related to several genera in Lamiaceae, including Aegiphila, Amasonia, Kalaharia, Tetraclea, Volkameria, Oxera, Faradaya, and Hosea, as supported by previous phylogenic studies. Additionally, the conventional infrageneric classification of Clerodendrum based on inflorescence and leaf characters is not supported by the results. However, the palynological data can be used to identify some closely related species with similar external characteristics. In conclusion, the investigation of pollen morphology not only contributes novel data from palynology for Clerodendrum but also provides a basis for future comprehensive classification of this genus.

Phylogenetic analysis and temporal diversification of the tribe Alsineae (Caryophyllaceae) with the description of three new genera, Hesperostellaria, Reniostellaria and Torreyostellaria.

Alsineae are one of the most taxonomically difficult tribes in Caryophyllaceae and consist of over 500 species distributed in the northern temperate zone. Recent phylogenetic results have improved our understanding on the evolutionary relationships among Alsineae members. Nevertheless, there are still some unresolved taxonomic and phylogenetic problems at the generic level, and the evolutionary history of major clades within the tribe was unexplored to date. In this study, we carried out phylogenetic analyses and divergence time estimation of Alsineae using the nuclear ribosomal internal transcribed spacer (nrITS) and four plastid regions (matK, rbcL, rps16, trnL-F). The present analyses yielded a robustly supported phylogenetic hypothesis of the tribe. Our results showed that the monophyletic Alsineae are strongly supported to be the sister of Arenarieae, and the inter-generic relationships within Alsineae were mostly resolved with strong support. Both molecular phylogenetic and morphological evidence supported the Asian species Stellaria bistylata and the two North American species Pseudostellaria jamesiana and Stellaria americana all should be recognized as new monotypic genera respectively, and three new genera Reniostellaria, Torreyostellaria, and Hesperostellaria were thereby proposed here. Additionally, molecular and morphological evidence also supported the proposal of the new combination Schizotechium delavayi. Nineteen genera were accepted within Alsineae and a key to these genera was provided. Molecular dating analysis suggested that Alsineae splitted from its sister tribe at ca. 50.2 million-years ago (Ma) during the early Eocene and began to diverge at ca. 37.9 Ma during the late Eocene, and divergent events within Alsineae occurred mainly since the late Oligocene. Results from the present study provide insights into the historical assembly of herbaceous flora in northern temperate regions.

Phylogenetic relationships and biogeography of Asia Callicarpa (Lamiaceae), with consideration of a long-distance dispersal across the Pacific Ocean -insights into divergence modes of pantropical flora.

There are about 140 species of Callicarpa L. 1753 (Lamiaceae), with more species richness in tropical to subtropical Asia and the New World. The genus might provide an insight into the amphi-Pacific disjunction pattern of tropical and subtropical vegetation. This study has greatly improved the phylogenetic underpinning for Callicarpa, derived from more inclusive taxonomic samplings, and employing data on both two-nuclear and eight-chloroplast regions. To address time and patterns of diversification in Callicarpa, we conducted divergence time and biogeographic analyses, and inferred shifts in the distribution areas across the phylogenetic clades. Our phylogenetic results show that Callicarpa is monophyletic with respect to the groups considered, and eight well-supported primary clades were discerned in the combined analyses. Our estimates indicated that the crown group of Callicarpa originates around the Late-Eocene (ca. 36.23 Ma) and diversification within most clades is concentrated in the Miocene and continued to the Pleistocene. In addition, our biogeographic analyses suggested that the probable ancestor of the Callicarpa crown clade originated in East Asia and Southeast Asia. Multiple dispersal and vicariance events contributed to the current distribution of the taxa. Furthermore, this genus expanded eastward out of East and Southeast Asia to the New World by long-distance dispersal, which inspired us to better understand the amphi-Pacific disjunct distribution.

Comprehensive molecular and morphological analysis of Brachystemmacalycinum and Stellariaovatifolia in the tribe Alsineae (Caryophyllaceae).

Over the course of the recent decade, the composition of Alsineae has been drastically changed by means of molecular phylogeny. However, the genus Brachystemma has not been sampled in any of the previous studies, and its phylogenetic position is still pending. In addition, the related species Stellariaovatifolia, which has at times been placed in Brachystemma, Schizotechium, or Stellaria, has also not been sampled. Here, nuclear ribosomal internal transcribed spacer (ITS) and four plastid regions (trnL-F, matK, rbcL, rps16) were used to conduct phylogenetic analyses within Caryophyllaceae and the tribe Alsineae. Ancestral characters (petal margin and number of seeds) were reconstructed in the tribe Alsineae based on the phylogenetic results. Our results indicate that Brachystemma is nested in the tribe Alsineae and forms a monophylum with S.ovatifolia, and apically lobed petals and numerous seeds may be the ancestral characters in the tribe Alsineae. Based on our study, Stellariaovatifolia should be considered within Brachystemma, and Brachystemma is clearly a separate genus and now includes two species.

Why is the beautyberry so colourful? Evolution, biogeography, and diversification of fruit colours in Callicarpa (Lamiaceae).

Fruit colour is essential to seed dispersal, speciation, and biological diversity in global ecosystems. The relationship between fruit-colour variation and species diversification has long been of interest in evolutionary biology, but remains poorly understood at the genus level. Here, we used Callicarpa, a typical representative of pantropical angiosperm, to analyse whether fruit colours are correlated with biogeographic distribution, dispersal events, and diversification rate. We estimated a time-calibrated phylogeny for Callicarpa and reconstructed ancestral fruit colour. Utilizing phylogenetic methods, we estimated the major dispersal events across the phylogenetic tree and the most likely fruit colours related to each dispersal event, and tested whether the dispersal frequencies and distances of the four fruit colours between major biogeographical areas were equal. We then tested whether fruit colours are correlated with latitude, elevation, and diversification rate. Biogeographical reconstructions showed that Callicarpa originated in the East Asia and Southeast Asia during the Eocene (∼35.53 Ma) and diverse species diverged mainly in the Miocene and lasted into the Pleistocene. Large-scale dispersal events were significantly associated with violet-fruited lineages. Furthermore, different fruit colours were markedly correlated with different latitudes and elevations (e.g., violet fruits were correlated with higher latitudes and elevations; red fruits and black fruits with lower latitudes; white fruits with higher elevations). Notably, violet fruits were statistically associated with highest diversification rates, driving fruit colour variation among different regions globally. Our results contribute to further understanding why fruit colour is so variable at the genus level of angiosperms in different areas around the world.

Integerrima A-E, phenylethanoid glycosides from the stem of Callicarpa integerrima.

Five new phenylethanoid glycosides integerrima A-E (1-5) were isolated from the stem of Callicarpa integerrima for the first time. Their structures were elucidated by extensive spectroscopic analyses. In addition, cytotoxicity, anti-adipogenic and antioxidant activities were evaluated. All the phenylethanoid glycosides would be nontoxic to the normal human hepatocytes LO-2 and pre-adipocytes 3T3-L1 cell lines, significantly promote the proliferation of normal hepatocytes, thus displaying the potential for hepatoprotective. Integerrima A (1), C (3) and D (4) exhibited selectively moderate cytotoxic activity against the hepatoma cell lines Bel-7402, with the IC50 value at 72.66, 80.43 and 84.88 µmol/L, respectively. Moreover, integerrima D (4) had significant activities on reducing lipid droplet formation, with the inhibition rate of 48.02% on the concentration of 200 µg/mL. Finally, the result of FRAP assays exhibited remarkable antioxidant activity in integerrima E (5), which was close to the positive control ascorbic acid with the concentration of 100 µg/mL.

Callicarpa stoloniformis (Lamiaceae), a new species from Southeast China based on morphological characters and phylogenetic evidence.

Callicarpa stoloniformis sp. nov. (Lamiaceae) is described as a new species from Fujian Province of China on the basis of both morphological and molecular data. The new species is morphologically most close to C. hainanensis. However, it can be distinguished from the latter by its unique procumbent life form, adventitious roots at nodes, papery leaves, cup-shaped or campanulate calyx, truncate or shallow fissure calyx lobes, and smaller fruits. In addition, the new species is also similar with C. basitruncata, a species only known from the original description and the photograph of holotype, but it can differ from the latter by its procumbent shrub, purple terete branchlets with apparent linear lenticels, adventitious roots at nodes, and papery larger leaves with prominently cordate leaf base. Original photographs, illustration, distribution map, and a comparative morphological table, as well as an identification key of the related taxa are provided.

HSPA1A, HSPA2, and HSPA8 Are Potential Molecular Biomarkers for Prognosis among HSP70 Family in Alzheimer's Disease.

Alzheimer's disease (AD) is a chronic neurodegenerative disease, which leads to impairment of cognition and memory. The heat shock protein 70 (HSP70) family plays an important role in the pathogenesis of AD. It is known to regulate protein misfolding in a variety of diseases, including inhibition of Aß aggregation and NFT formation in AD. As yet, the diagnostic molecular markers of AD remain unclear. Herein, we sought to investigate molecular markers of HSP70 family that can affect diagnosis and treatment in AD through computational analysis. In this study, the intersection between HSP70 family members and immune molecules was taken to screen immune-related HSP70 family genes. Based on the datasets from the NCBI-Gene Expression Omnibus (GEO) database, we found that the expression levels of HSPA1A and HSPA2 were significantly increased in AD samples, while HSPA8 significantly decreased. Surprisingly, the combination of the 3 hub genes had a good diagnosis of AD via receiver operating characteristic curve (ROC). Moreover, the clinical value of the 3 hub genes was further assessed by the Spearman correlation analysis with AD-related genes, ß-secretase activity, and γ-secretase activity. In terms of immune cell infiltration, we showed that the distribution of seven immune cell types (macrophages M2, neutrophils, T cells CD4 memory activated, macrophages M0, NK cells activated, plasma cells, and T cells follicular helper) was associated with the occurrence of AD by CIBERSORT. Furthermore, our data suggested that EP300, MYC, TP53, JUN, CREBBP, and ESR1 might be key transcription factors (TFs) for the 3 hub genes. In general, these findings suggest that HSPA1A, HSPA2, and HSPA8 are potential molecular biomarkers for prognosis among HSP70 family in AD, and it provides a new perspective on diagnostic and therapeutic targets for AD.

The signal-to-cutoff ratios to predict HCV infection among people who inject drugs.

People who inject drugs (PWIDs) are primarily the high-risk population for HCV infection. This study aims to determine the optimal cut-off values for predicting HCV infection status based on the Signal-to-Cutoff (S/CO) ratio. In this study, a total of 719 PWIDs' samples were collected, and performed for screening test by ELISA assay, and followed by RIBA assay and NAT assay to detect HCV antibody and HCV RNA levels, respectively. The findings revealed that the prevalence of HCV infection among PWIDs was 54.66% (393/719), and the false-positive rate of HCV antibody detection by ELISA assay among PWIDs was only 3.85% (16/416). In addition, when the optimal cut-off value for S/CO ratio was 2.0, the sensitivity and specificity of HCV antibody were 100.00% and 93.55%, respectively. And when the optimal cut-off value for S/CO ratio was 21.36, the sensitivity and specificity of HCV RNA positive were 89.90% and 72.73%, respectively. In conclusion, the status of HCV infection can be predicted based on the S/CO ratios of the ELISA assay, which can improve diagnosis and facilitate timely treatment to effectively prevent the spread of HCV infection.

The complete plastid genome of Cheniella didyma (H.Y.Chen) R.Clark & Mackinder (Leguminosae).

We report here for the first time the complete plastid genome of Cheniella didyma of the legume family. The plastid genome has a typical circular structure with a total length of 157,186 bp and contains two inverted repeat regions (IRs, 24,455 bp), a large single-copy region (LSC, 89,410 bp), and a small single-copy region (SSC, 18,866 bp). This is the first report of the complete plastid genome sequence of Cheniella, a genus recently segregated from Bauhinia s.l. The phylogenetic analysis based on 77 coding regions of the plastome of this species and those of the related species strongly suggested that C. didyma is sister to Lysiphyllum and is not directly related to Bauhinia s.s.

Baseline Characteristics of Mitochondrial DNA and Mutations Associated With Short-Term Posttreatment CD4+T-Cell Recovery in Chinese People With HIV.

Background: Mitochondrial DNA (mtDNA) profiles and contributions of mtDNA variants to CD4+T-cell recovery in Euramerican people living with HIV (PLWH) may not be transferred to East-Asian PLWH, highlighting the need to consider more regional studies. We aimed to identify mtDNA characteristics and mutations that explain the variability of short-term CD4+T-cell recovery in East-Asian PLWH. Method: Eight hundred fifty-six newly reported antiretroviral therapy (ART)-naïve Chinese PLWH from the Comparative HIV and Aging Research in Taizhou (CHART) cohort (Zhejiang Province, Eastern China) were enrolled. MtDNA was extracted from peripheral whole blood of those PLWH at HIV diagnosis, amplified, and sequenced using polymerase chain reaction and gene array. Characterization metrics such as mutational diversity and momentum were developed to delineate baseline mtDNA mutational patterns in ART-naïve PLWH. The associations between mtDNA genome-wide single nucleotide variants and CD4+T-cell recovery after short-term (within ~48 weeks) ART in 724 PLWH were examined using bootstrapping median regressions. Results: Of 856 participants, 74.18% and 25.82% were male and female, respectively. The median age was 37 years; 94.51% were of the major Han ethnicity, and 69.04% and 28.62% were of the heterosexual and homosexual transmission, respectively. We identified 2,352 types of mtDNA mutations and mtDNA regions D-loop, ND5, CYB, or RNR1 with highest mutational diversity or volume. Female PLWH rather than male PLWH at the baseline showed remarkable age-related uptrends of momentum and mutational diversity as well as correlations between CD4+T <200 (cells/µl) and age-related uptrends of mutational diversity in many mtDNA regions. After adjustments of important sociodemographic and clinical variables, m.1005T>C, m.1824T>C, m.3394T>C, m.4491G>A, m.7828A>G, m.9814T>C, m.10586G>A, m.12338T>C, m.13708G>A, and m.14308T>C (at the Bonferroni-corrected significance) were negatively associated with short-term CD4+T-cell recovery whereas m.93A>G, m.15218A>G, and m.16399A>G were positively associated with short-term CD4+T-cell recovery. Conclusion: Our baseline mtDNA characterization stresses the attention to East-Asian female PLWH at risk of CD4+T-cell loss-related aging and noncommunicable chronic diseases. Furthermore, mtDNA variants identified in regression analyses account for heterogeneity in short-term CD4+T-cell recovery of East-Asian PLWH. These results may help individualize the East-Asian immune recovery strategies under complicated HIV management caused by CD4+T-cell loss.

Case Report: Metagenomics Next-Generation Sequencing Can Be Performed for the Diagnosis of Disseminated Mucormycosis.

Mucormycosis is an infection caused by a group of filamentous molds with in the order Mucorales. In developing countries, most cases of mucormycosis occur in persons with poorly controlled diabetes mellitus or subjects with normal post-traumatic immune function. Mucormycosis exhibits a marked propensity for invading blood vessels. The mortality rate of invasive mucormycosis is very high (>30-50%), and 90% of mortality is related to disseminated diseases. We report a 62-year-old man with underlying diseases, such as diabetes and psoriatic arthritis, with a history of trauma before admission. Chest CT showed multiple cavities. Based on the suspected clinical manifestation of mucormycosis infection, the patient received a microbiological culture of bronchoalveolar lavage fluid, and metagenomics next generation sequencing (mNGS) was performed. The results suggested Klebsiella pneumoniae infection. However, Rhizopus microsporus strains were shown by the mNGS of transpulmonary puncture tissue. Therefore, we report a case in which rare pathogens are identified by mNGS.

The complete chloroplast genome of Callicarpa rubella Lindl. (Lamiaceae) from Guangxi, China: genome structure and phylogenetic analysis.

The relationship between Callicarpa rubella Lindl. and its infraspecific taxa has troubled researchers for a long time. Here, we reported for the first time the complete chloroplast (cp) genome of C. rubella to investigate its phylogenetic position and provide more sequencing information for further studies about the relationship between C. rubella and its related species. The cp genome of C. rubella was 154,202 bp in length and displayed a typical quadripartite angiosperm structure, containing two inverted repeat (IR) regions of 25,701 bp, a large single-copy (LSC) region of 84,968 bp and a small single-copy (SSC) region of 17,832 bp. It contained 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The analysis fully resolved C. rubella was in a clade with C. bodinieri and C. nudiflora. The results indicated Callicarpa formed a sister relationship with Dicrastylis parvifolia in Lamiaceae.

Effects of Smoking on Inflammatory Markers in a Healthy Population as Analyzed via the Gut Microbiota.

The number of people who smoke has increased in recent years, and the incidence of smoking-related diseases increases annually. This study was conducted to explore whether smoking affects diseases via changes in the gut microbiota. We enrolled 33 smokers and 121 non-smokers. We collected fecal samples from all participants and performed whole-genome sequencing. Smoking significantly affected the gut microbiota. At the phylum through genus levels, the smokers' microbiotas showed slight changes compared with those of the non-smokers. The α- and ß-diversities differed significantly between the smokers and non-smokers, and the smokers' gut microbiota compositions differed significantly from those of the non-smokers. At the species level, the relative abundances of Ruminococcus gnavus (P=0.00197) and Bacteroides vulgatus (P=0.0468) were significantly greater in the smokers than in the non-smokers, while the relative abundances of Faecalibacterium prausnitzii (P=0.0000052) and Akkermansia muciniphila (P=0.0057) were significantly lower in the smokers. Smoking increases inflammation in the body by inducing an increased abundance of proinflammatory bacteria. Non-smokers had higher abundances of anti-inflammatory microorganisms than did smokers; these microorganisms can produce short-chain fatty acids, which inhibit inflammation.

Case Report: Metagenomics Next-Generation Sequencing Can Help Define the Best Therapeutic Strategy for Brain Abscesses Caused by Oral Pathogens.

Brain abscesses are associated with an increased long-term risk of new seizures and increased mortality within several years after infection. Common microorganisms that cause brain abscesses include bacteria, fungi, and mycoplasma. We report a 75-year-old man with a brain abscess caused by Prevotella denticola, an oral pathogen. Based on the clinical condition, we suspected that the patient had a blood-borne brain abscess, and he received antibiotics and systemic supportive treatment. The patient developed shock for the second time after negative Gram-staining results. Metagenomics next-generation sequencing showed one strain from the oral microbiome, confirming our hypothesis, and targeted antibiotic treatment was administered quickly. Thus, we report a case in which genomic analysis was the critical factor in determining the best antimicrobial therapy for administration.

Evaluation of seven rapid diagnostic tests for detection of hepatitis C virus antibodies in China.

Rapid diagnostic tests as an attractive alternative to enzyme immunoassay could identify hepatitis C virus (HCV) infected persons more expeditiously. The availability of high performing and quality-assured rapid diagnostic tests are essential to scale-up HCV screening. The study was undertaken to evaluate the performance of seven domestic HCV rapid diagnostic tests kits. The kits were evaluated by using HCV serum panels, including HCV basic panel, analytical specificity panel, mixed titre performance panel, characteristic panel, seroconversion panel, and genotype qualification panel. The results showed that clinical sensitivity, clinical specificity and analytical specificity of seven rapid diagnostic tests kits ranged from 94% (95% CI: 83.2-98.6) to 100% (95% CI: 91.5-100). Furthermore, specimens with HCV genotypes 1b, 2a, 3a, 4a, 5a, 6 could be detected by HCV rapid diagnostic tests kits, whereas specimens with genotypes 1a and 2b could not be detected. Additionally, most HCV rapid diagnostic tests kits had great performance in diagnosing different titres and/or different bands samples, but some low S/CO value specimens may not be fully detected by few rapid diagnostic test kits. In conclusion, seven HCV rapid diagnostic tests reagents presented high sensitivity, specificity, good anti-interference and detection ability of early infection, which could meet the requirements of clinical HCV antibody screening.

The complete plastid genome of Delonix regia (Hook.) Raf. (Leguminosae).

Delonix regia, a plant species of the legume family native to Madagascar, has been widely cultivated in the tropical and subtropical regions as an ornamental tree due to its remarkable showy orange-red flowers over summer. Here we report for the first time the complete plastid genome of this species, which has a typical circular structure with a total length of 162,756 bp and contains two inverted repeat regions (IRs, 25,544 bp), a large single copy region (LSC, 92,490 bp), and a small single copy region (SSC, 19,178 bp). The phylogenetic analysis based on the complete plastome sequences of this species and those of the related species from GenBank strongly suggested that D. regia is nested in the subfamily Caesalpinioideae and is sister to a clade consisting of Erythrophlium fordii and the old-sense Mimosoideae.