Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient’s treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing, but sequencing noise hinders accurate identification. The elimination of sequencing noise is a non-trivial task that still remains open. Here we propose CliqueSNV based on extracting pairs of statistically linked mutations from noisy reads. This effectively reduces sequencing noise and enables identifying minority haplotypes with the frequency below the sequencing error rate. We comparatively assess the performance of CliqueSNV using an in vitro mixture of nine haplotypes that were derived from the mutation profile of an existing HIV patient. We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms.     

洋葱伯克霍尔德菌感染家兔抗感染疗效与体外药物敏感性的比较

目的使用无CLSI完整解释标准的药物,哌拉西林/他唑巴坦、替卡西林/棒酸、头孢吡肟治疗洋葱伯克霍尔德菌感染的家兔模型,观察比较何种体外药物敏感试验更能准确反应临床疗效。方法 57株临床分离的洋葱伯克霍尔德菌,感染57只家兔腹腔。将感染家兔分成3组(A、B、C组),每组19只;分别在48、72、96、120和144 h注射药物:A组每只家兔注射1 mL浓度为2 g/mL哌拉西林/他唑巴坦;B组每只家兔注射1 mL浓度为0.1g/mL头孢吡肟;C组每只家兔注射1 mL浓度为0.6 g/mL替卡西林/棒酸。比较肉汤稀释法(MIC法)、K-B法及VITEK法检测的药物敏感性结果与体内药物治疗的疗效关系。结果哌拉西林/他唑巴坦治疗组(A组),K-B法检测结果与家兔感染模型治疗过程相符率为72.2%,MIC法66.7%,VITEK法为66.7%。替卡西林/棒酸治疗组(B组),MIC法83.3%,VITEK法为77.8%,K-B法检测结果与家兔感染模型治疗过程相符率为50.0%。头孢吡肟治疗组(C组),MIC法88.9%,VITEK法为77.8%,K-B法检测结果与家兔感染模型治疗过程相符率为72.2%。结论在3种药物敏感性检测法中,哌拉西林/他唑巴坦以K-B法检测结果与感染家兔的抗感染疗效最为接近;替卡西林/棒酸及头孢吡肟均以MIC法与感染家兔的抗感染疗效最为接近;针对洋葱伯克霍尔德菌的感染建议临床使用不同的方法检测不同的药物体外敏感性。     

Design,synthesis and biological evaluation of novel triazole,urea and thiourea derivatives of quinoline against Mycobacterium tuberculosis

A new series of 20 quinoline derivatives possessing triazolo, ureido and thioureido substituents have been synthesized and their antimycobacterial properties have been evaluated. Compounds 10, 22 and 24 inhibited Mycobacterium tuberculosis H37Rv up to 96%, 98% and 94% respectively, at a fixed concentration of 6.25 μg/mL. Minimum inhibitory concentration of 3.125 μg/mL was obtained for compound 10 and 24, while for compound 22 it was 6.25 μg/mL. Molecular docking calculations suggest critical hydrogen bonding and electrostatic interactions between polar functional groups (such as quinoline-nitrogen, urea-carbonyl and hydroxyl) of anti-mycobacterial (anti-TB) compounds and amino acids (Arg186 and Glu61) of ATP-synthase of M. tuberculosis, could be the probable reason for observed anti-mycobacterial action.     

Glutathione metabolism is modulated by postmortem interval, gender difference and agonal state in postmortem human brains

The equilibrium between antioxidant function and oxidative stress is implicated in brain pathology. However, human studies on oxidant and antioxidant markers rely on postmortem tissue that might be affected by pre and postmortem factors. To evaluate the effect of these variables, we tested whether antioxidant enzymes [superoxide dismutase (SOD), catalase] glutathione (GSH) and related enzymes [gamma glutamylcysteine ligase (GCL), GSH peroxidase (GPx), GSH reductase (GR), GSH-S-transferase (GST)] and malondialdehyde (MDA, marker of lipid peroxidation) are affected in postmortem human brains (n = 50) by increase in postmortem interval (2.5–26 h), gender difference and agonal state [based on Glasgow coma scale (GCS): range: 3–15] in different anatomical regions-frontal cortex (FC), cerebellum (CB) medulla oblongata (MO), substantia nigra (SN) and hippocampus (HC). While SOD and catalase activities were relatively unaltered, GR and GPx activities were affected by agonal state (GR in CB, p < 0.05; GPx in MO, p < 0.05) indicating altered GSH dynamics during the secondary events following neuronal injury. MO, SN and HC displayed low GSH compared to FC and CB. Total GSH level was decreased with PMI (MO, p = 0.02) which could be partly attributed to increase in MDA levels with increasing PMI in MO (p < 0.05). Total GSH level was higher in CB (p < 0.017) and MO (p < 0.04) in female brains compared to males. Interestingly, HC and SN regions showed significant stability in most of the markers tested. We suggest that while SOD and catalase were relatively unaffected by the pre and postmortem factors, GSH and its metabolic enzymes were significantly altered and this was more pronounced in MO of postmortem human brains. These data highlight the influence of pre and postmortem factors on GSH dynamics and the inherent differences in brain regions, with implications for studies on brain pathophysiology employing human samples.     

CanGeneBase (CGB) ‐ a database on cancer related genes

The advent of genomic and proteomic technologies in this post-genomic era has urged the researchers to develop novel research strategies against cancer by targeting the human genes that would greatly facilitate to identify more promising treatment and to develop accurate early diagnosis for cancer. To harness the power of cancer genetic information towards better treatment we have developed a cancer gene database called CanGeneBase (CGB). It is a comprehensive data collection of cancer-related genes with the intention of helping the researchers to stay on a single platform to gain exclusive information on the genes of their interest. According to the Cancer Gene Data Curation Project, about 4,700 genes have been identified as being related to cancer. The present CanGeneBase covers about 12 different types of cancer which includes 190 unique gene entries. Each entry encompasses about 33 useful parameters to provide detailed information about specific gene. CanGeneBase is made in such a way that it can be easily accessed by either gene symbol or by the type of cancer.

Availability

The database is freely available at http://122.165.25.137/bioinfo/cancerdb/     

扇贝糖胺聚糖对感染HSV-I小鼠免疫功能的影响研究

目的：研究扇贝裙边糖胺聚糖（glycosaminoglycan from Scallop Skirt,SS—GAG）对感染单纯疱疹病毒I型（herpes simplex virustype,HSV-I）小鼠免疫功能的影响。方法：通过在无菌条件下给予小鼠注射扇贝糖胺聚糖SS．GAG,连续11天,并在给药第三天给小鼠腹腔注射HSV—I病毒悬液建立小鼠感染模型,用MTT等方法观察SS—GAG对HSV—I感染小鼠腹腔巨噬细胞吞噬活性的影响、对脾脏指数、胸腺指数的影响以及对脾淋巴细胞转化能力等免疫指标的影响。结果：与病毒对照组相比,扇贝糖胺聚糖SS-GAG低剂量组、中剂量组、高剂量组均能显著增强HSV．I感染小鼠的腹腔巨噬细胞的吞噬活性和HSV—I感染小鼠的脾脏指数和胸腺指数（P〈0．01）,并且能促进其脾淋巴细胞转化增殖能力（P〈0．01）。结论：扇贝糖胺聚糖在体内有一定的抗I型单纯疱疹病毒作用。其抗病毒作用可能与增强机体免疫功能有关。     

Proteomic analysis of larval integument, trachea and adult scale from the silkworm, Bombyx mori

Multidimensional LC-tandem MS was used to investigate the protein compositions of three tissues of silkworm, Bombyx mori. A total of 162, 259, and 175 peptides from silkworm larval integument and trachea, and adult scale obtained by database search were matched to 48, 51, and 40 proteins, respectively. Forty-one cuticular proteins were identified from three tissues and covered all five cuticular protein families of silkworm. In the adult scale, all seven cuticular proteins were identified for the first time in the final pellet after SDS extraction. The majority of cuticular proteins were found in each tissue differentially, suggesting that tissue-specific cuticular proteins were involved in the building of the specialized tissues. Seventy-three non-cuticular proteins were also identified in this analysis mainly including muscular proteins, proteinases, inhibitors, transport proteins, and redox-related proteins.     

Bioethanol fermentation of concentrated rice straw hydrolysate using co-culture of Saccharomyces cerevisiae and Pichia stipitis

Rice straw is one of the abundant lignocellulosic feed stocks in the world and has been selected for producing ethanol at an economically feasible manner. It contains a mixture of sugars (hexoses and pentoses).Biphasic acid hydrolysis was carried out with sulphuric acid using rice straw. After acid hydrolysis, the sugars, furans and phenolics were estimated. The initial concentration of sugar was found to be 16.8 g L⁻¹. However to increase the ethanol yield, the initial sugar concentration of the hydrolysate was concentrated to 31 g L⁻¹ by vacuum distillation. The concentration of sugars, phenols and furans was checked and later detoxified by over liming to use for ethanol fermentation. Ethanol concentration was found to be 12 g L⁻¹, with a yield, volumetric ethanol productivity and fermentation efficiency of 0.33 g L⁻¹ h⁻¹, 0.4 g g⁻¹ and 95%, respectively by co-culture of OVB 11 (Saccharomyces cerevisiae) and Pichia stipitis NCIM 3498.