In vivo detection and replication studies of α-anomeric lesions of 2′-deoxyribonucleosides

DNA damage, arising from endogenous metabolism or exposure to environmental agents, may perturb the transmission of genetic information by blocking DNA replication and/or inducing mutations, which contribute to the development of cancer and likely other human diseases. Hydroxyl radical attack on the C1′, C3′ and C4′ of 2-deoxyribose can give rise to epimeric 2-deoxyribose lesions, for which the in vivo occurrence and biological consequences remain largely unexplored. Through independent chemical syntheses of all three epimeric lesions of 2′-deoxyguanosine (dG) and liquid chromatography-tandem mass spectrometry analysis, we demonstrated unambiguously the presence of substantial levels of the α-anomer of dG (α-dG) in calf thymus DNA and in DNA isolated from mouse pancreatic tissues. We further assessed quantitatively the impact of all four α-dN lesions on DNA replication in Escherichia coli by employing a shuttle-vector method. We found that, without SOS induction, all α-dN lesions except α-dA strongly blocked DNA replication and, while replication across α-dA was error-free, replicative bypass of α-dC and α-dG yielded mainly C→A and G→A mutations. In addition, SOS induction could lead to markedly elevated bypass efficiencies for the four α-dN lesions, abolished the G→A mutation for α-dG, pronouncedly reduced the C→A mutation for α-dC and triggered T→A mutation for α-dT. The preferential misincorporation of dTMP opposite the α-dNs could be attributed to the unique base-pairing properties of the nucleobases elicited by the inversion of the configuration of the N-glycosidic linkage. Our results also revealed that Pol V played a major role in bypassing α-dC, α-dG and α-dT in vivo. The abundance of α-dG in mammalian tissue and the impact of the α-dNs on DNA replication demonstrate for the first time the biological significance of this family of DNA lesions.     

遥感在生物多样性研究中的应用进展

随着人口的持续增长, 人类经济活动对自然资源的利用强度不断升级以及全球气候变暖, 全球物种正以前所未有的速度丧失, 生物多样性成为了全球关注的热点问题。传统生物多样性研究以地面调查方法为主, 重点关注物种或样地水平, 但无法满足景观尺度、区域尺度以及全球尺度的生物多样性保护和评估需求。遥感作为获取生物多样性信息的另一种手段, 近年来在生物多样性领域发展迅速, 其覆盖广、序列性以及可重复性等特点使之在大尺度生物多样性监测和制图以及评估方面具有极大优势。本文主要通过文献收集整理, 从观测手段、研究尺度、观测对象和生物多样性关注点等方面综述了遥感在生物多样性研究中的应用现状, 重点分析不同遥感平台的技术优势和局限性, 并探讨了未来遥感在生物多样性研究的应用趋势。遥感平台按观测高度可分为近地面遥感、航空遥感和卫星遥感, 能够获取样地-景观-区域-洲际-全球尺度的生物多样性信息。星载平台在生物多样性研究中应用最多, 航空遥感的应用研究偏少主要受飞行成本限制。近地面遥感作为一个新兴平台, 能够直接观测到物种的个体, 获取生物多样性关注的物种和种群信息, 是未来遥感在生物多样性应用中的发展方向。虽然遥感技术在生物多样性研究中的应用存在一定的局限性, 未来随着传感器发展和多源数据融合技术的完善, 遥感能更好地从多个尺度、全方位地服务于生物多样性保护和评估。     

A new Illumina MiSeq high-throughput sequencing-based method for evaluating the composition of the Bacteroides community in the intestine using the rpsD gene sequence

Bacteroides is a bacterial genus that is known to closely interact with the host. The potential role of this genus is associated with its ecological status and distribution in the intestine. However, the current 16S V3–V4 region sequencing method can only detect the abundance of this genus, revealing a need for a novel sequencing method that can elucidate the composition of Bacteroides in the human gut microbiota. In this study, a core gene, rpsD, was selected as a template for the design of a Bacteroides-specific primer set. We used this primer set to develop a novel assay based on the Illumina MiSeq sequencing platform that enabled an accurate assessment of the Bacteroides compositions in complex samples. Known amounts of genomic DNA from 10 Bacteroides species were mixed with a complex sample and used to evaluate the performance and detection limit of our assay. The results were highly consistent with those of direct sequencing with a low Bacteroides DNA detection threshold (0.01 ng), supporting the reliability of our assay. In addition, the assay could detect all the known Bacteroides species within the faecal sample. In summary, we provide a sensitive and specific approach to determining the Bacteroides species in complex samples.     

<Emphasis Type="Italic">Halomonas tibetensis</Emphasis> sp. nov., isolated from saline lakes on Tibetan Plateau

Strains pyc13^T and ZGT13 were isolated from Lake Pengyan and Lake Zigetang on Tibetan Plateau, respectively. Both strains were Gram-negative, catalase- and oxidase-positive, aerobic, rod-shaped, nonmotile, and nonflagellated bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains pyc13^T and ZGT13 belong to the genus Halomonas, with Halomonas alkalicola 56-L4-10aEn^T as their closest neighbor, showing 97.4% 16S rRNA gene sequence similarity. The predominant respiratory quinone of both strains was Q-9, with Q-8 as a minor component. The major fatty acids of both strains were C_18:1ω6c/C_18:1ω7c, C_16:1ω6c/C_16:1ω7c, C_16:0, and C_12:0 3OH. The polar lipids of both strains consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, glycolipid, phospholipids of unknown structure containing glucosamine, and unidentified phospholipids. The DNA G + C content of pyc13^T and ZGT13 were 62.6 and 63.4 mol%, respectively. The DNA-DNA hybridization values of strain pyc13^T were 34, 41, 61, 35, and 35% with the reference strains H. alkalicola 56-L4-10aEn^T, H. sediminicola CPS11^T, H. mongoliensis Z-7009^T, H. ventosae Al12^T, and H. fontilapidosi 5CR^T, respectively. Phenotypic, biochemical, genotypic, and DNA-DNA hybridization data showed that strains pyc13^T and ZGT13 represent a new species within the genus Halomonas, for which the name H. tibetensis sp. nov. is proposed. The type strain is pyc13^T (= CGMCC 1.15949^T = KCTC 52660^T).     

Effects of Two Chinese Herbal Formulae for the Treatment of Moderate to Severe Stable Chronic Obstructive Pulmonary Disease: A Multicenter,Double-Blind,Randomized Controlled Trial

Objective

The study aims to evaluate the efficacy and safety of two Chinese herbal formulae for the treatment of stable COPD.

Methods

A multicenter, double-blind, double-dummy, and randomized controlled trial (RCT) was conducted. All groups were treated with additional conventional medicines. There were a 6-month treatment and a 12-month follow-up for 5 times. Primary outcomes included lung function test, exacerbation frequency, score of SGRQ. Second outcomes consisted of 6MWD, BODE index, psychological field score, inflammatory factors and cortisol.

Results

A total of 331 patients were randomly divided into two active treatment groups (Bushen Yiqi (BY) granule group, n = 109; Bushen Fangchuan (BF) tablet group, n = 109) and a placebo group (n = 113). Finally 262 patients completed the study. BY granule & BF tablet increased the values of VC, FEV₁ (%) and FEV₁/FVC (%), compared with placebo. BY granule improved PEF. Both treatments reduced acute exacerbation frequency (P = 0.067), BODE index and psychological field score, while improved 6MWD. In terms of descent rang of SGRQ score, both treatments increased (P = 0.01). Both treatments decreased inflammatory cytokines, such as IL-8, and IL-17(P = 0.0219). BY granule obviously descended IL-17(P<0.05), IL-1β (P = 0.05), IL-6, compared with placebo. They improved the level of IL-10 and cortisol. BY granule raised cortisol (P = 0.07) and decreased TNF-α. Both treatments slightly descended TGF-β1. In terms of safety, subject compliance and drug combination, there were no differences (P>0.05) among three groups.

Conclusions

BY granule and BF tablet were positively effective for the treatment of COPD, and the former performed better in general.

Trial Registration

Chinese Clinical Trial Register center ChiCTR-TRC-09000530     

Role of Tomato Lipoxygenase D in Wound-Induced Jasmonate Biosynthesis and Plant Immunity to Insect Herbivores

In response to insect attack and mechanical wounding, plants activate the expression of genes involved in various defense-related processes. A fascinating feature of these inducible defenses is their occurrence both locally at the wounding site and systemically in undamaged leaves throughout the plant. Wound-inducible proteinase inhibitors (PIs) in tomato (Solanum lycopersicum) provide an attractive model to understand the signal transduction events leading from localized injury to the systemic expression of defense-related genes. Among the identified intercellular molecules in regulating systemic wound response of tomato are the peptide signal systemin and the oxylipin signal jasmonic acid (JA). The systemin/JA signaling pathway provides a unique opportunity to investigate, in a single experimental system, the mechanism by which peptide and oxylipin signals interact to coordinate plant systemic immunity. Here we describe the characterization of the tomato suppressor of prosystemin-mediated responses8 (spr8) mutant, which was isolated as a suppressor of (pro)systemin-mediated signaling. spr8 plants exhibit a series of JA-dependent immune deficiencies, including the inability to express wound-responsive genes, abnormal development of glandular trichomes, and severely compromised resistance to cotton bollworm (Helicoverpa armigera) and Botrytis cinerea. Map-based cloning studies demonstrate that the spr8 mutant phenotype results from a point mutation in the catalytic domain of TomLoxD, a chloroplast-localized lipoxygenase involved in JA biosynthesis. We present evidence that overexpression of TomLoxD leads to elevated wound-induced JA biosynthesis, increased expression of wound-responsive genes and, therefore, enhanced resistance to insect herbivory attack and necrotrophic pathogen infection. These results indicate that TomLoxD is involved in wound-induced JA biosynthesis and highlight the application potential of this gene for crop protection against insects and pathogens.     

CARD9-Dependent Neutrophil Recruitment Protects against Fungal Invasion of the Central Nervous System

Candida is the most common human fungal pathogen and causes systemic infections that require neutrophils for effective host defense. Humans deficient in the C-type lectin pathway adaptor protein CARD9 develop spontaneous fungal disease that targets the central nervous system (CNS). However, how CARD9 promotes protective antifungal immunity in the CNS remains unclear. Here, we show that a patient with CARD9 deficiency had impaired neutrophil accumulation and induction of neutrophil-recruiting CXC chemokines in the cerebrospinal fluid despite uncontrolled CNS Candida infection. We phenocopied the human susceptibility in Card9 ^-/- mice, which develop uncontrolled brain candidiasis with diminished neutrophil accumulation. The induction of neutrophil-recruiting CXC chemokines is significantly impaired in infected Card9 ^-/- brains, from both myeloid and resident glial cellular sources, whereas cell-intrinsic neutrophil chemotaxis is Card9-independent. Taken together, our data highlight the critical role of CARD9-dependent neutrophil trafficking into the CNS and provide novel insight into the CNS fungal susceptibility of CARD9-deficient humans.     

Diurnal Expression Pattern,Allelic Variation,and Association Analysis Reveal Functional Features of the E1 Gene in Control of Photoperiodic Flowering in Soybean

Although four maturity genes, E1 to E4, in soybean have been successfully cloned, their functional mechanisms and the regulatory network of photoperiodic flowering remain to be elucidated. In this study, we investigated how the diurnal expression pattern of the E1 gene is related to photoperiodic length; and to what extent allelic variation in the B3-like domain of the E1 gene is associated with flowering time phenotype. The bimodal expression of the E1 gene peaked first at around 2 hours after dawn in long-day condition. The basal expression level of E1 was enhanced by the long light phase, and decreased by duration of dark. We identified a 5bp (3 SNP and 2-bp deletion) mutation, referred to an e1-b3a, which occurs in the middle of B3 domain of the E1 gene in the early flowering cultivar Yanhuang 3. Subcellular localization analysis showed that the putative truncated e1-b3a protein was predominately distributed in nuclei, indicating the distribution pattern of e1-b3a was similar to that of E1, but not to that of e1-as. Furthermore, genetic analysis demonstrated allelic variations at the E1 locus significantly underlay flowering time in three F₂ populations. Taken together, we can conclude the legume specific E1 gene confers some special features in photoperiodic control of flowering in soybean. Further characterization of the E1 gene will extend our understanding of the soybean flowering pathway in soybean.     

Tea Consumption and Cognitive Impairment: A Cross-Sectional Study among Chinese Elderly

Background

Laboratorial and epidemiological researches suggested that tea exhibited potential neuroprotective effect which may prevent cognitive impairment, but there were few data among the elderly aged 60 years and above in China.

Objective

The objective was to explore the relationship between characteristics of tea consumption and cognitive impairment.

Design

We analyzed the baseline data from Zhejiang Major Public Health Surveillance Program (ZPHS) which was conducted in 2014. Totally 9,375 residents aged 60 years and above were recruited in this study. Face-to-face interview based on a self-developed questionnaire was performed for each participant. Detailed tea consumption habits were included in the questionnaire. Cognitive impairment screening was performed by using Mini-Mental State Examination (MMSE). Education-specific cut-off points for Chinese were applied to determine the status of cognitive impairment. Logistic regression analysis was used to calculate odds ratios (ORs) of cognitive impairment associated with tea consumption.

Results

The means (SD) of MMSE scores for the subjects who did not consume tea and consumed <2 cups/d, 2–4 cups/d, ≥4 cups/d were 23.3 (SD = 5.61), 23.8 (SD = 5.60), 24.5 (SD = 5.63) and 25.0 (SD = 5.08), respectively. An inverse correlation was found between tea consumption (of all types) and prevalence of cognitive impairment. Volume of tea consumption was significantly associated with cognitive impairment: compared with non-consumption participants, those who consumed < 2 cups/d, 2–4 cups/d, and ≥4 cups/d were observed ORs of 0.77 (95% CI: 0.56, 1.07), 0.62 (95% CI: 0.47, 0.81), and 0.49 (95% CI: 0.36, 0.66), respectively. Compared with non-consumption, black tea presented a positive correlation with cognitive function after controlling for potential confounders (OR = 0.52, 95% CI: 0.28, 0.95), while green tea showed no significant difference (OR = 1.04, 95% CI: 0.72, 1.51). Participants who consumed weak tea, moderate tea or strong tea more often were observed a better cognitive status when compared with those who did not have tea, with an OR of 0.51 (95% CI: 0.28, 0.92), 0.32 (95% CI: 0.19, 0.56) and 0.42 (95% CI: 0.22, 0.78) after adjusting for the potential confounders. But there was no statistically significant difference between any two of these ORs.

Conclusion

Black tea consumption was association with better cognitive performance among the elderly aged 60 years and above in China, while green tea presented no correlation. The positive association of cognitive status with tea consumption was not limited to particular type of concentration.     

Prediction of river ecological integrity after cascade hydropower dam construction on the mainstream of rivers in Longitudinal Range-Gorge Region (LRGR), China

Dam construction is considered the major factor contributing to significant modification of river ecosystems. The related ecological effects of these constructions on flow patterns, water quality, sediment etc. have led to increased concerns in recent years. Most of the works so far focus on the assessment of vulnerability, risk, and damages to single factors, such as soil conservation, fish reproduction or vegetation. Few works have been done on to analyzing and predicting the changes of the river ecosystem integrity (REI). Taking three important international rivers, Lancang River, Nu River and Yuan River in LRGR as a case study, the relationship between cascade dam construction and REI is analyzed. A model of the cascade dam construction and the REI is developed on Lancang River after cascade construction, and then it is applied on the Nu River and Yuan River to predict the changes of REI after the planned cascade construction. The results show that there are significant relationships between the cascade construction and the change of the REI. Before the cascade development, REI index of Nu River is the highest with a value of 0.844. Yuan River, the worst of the three before the cascade construction (0.719), is found to be the best one after the cascade construction (0.389). After the cascade construction, the REI index value of the Lancang River is likely to dramatically decrease from 0.825 to 0.274.