From infection to cancer: how DNA tumour viruses alter host cell central carbon and lipid metabolism

Infections cause 13% of all cancers globally, and DNA tumour viruses account for almost 60% of these cancers. All viruses are obligate intracellular parasites and hijack host cell functions to replicate and complete their life cycles to produce progeny virions. While many aspects of viral manipulation of host cells have been studied, how DNA tumour viruses manipulate host cell metabolism and whether metabolic alterations in the virus life cycle contribute to carcinogenesis are not well understood. In this review, we compare the differences in central carbon and fatty acid metabolism in host cells following infection, oncogenic transformation, and virus-driven cancer of DNA tumour viruses including: Epstein–Barr virus, hepatitis B virus, human papillomavirus, Kaposi''s sarcoma-associated herpesvirus and Merkel cell polyomavirus.     

A statistical approach for the enhanced production of thermostable alkaline protease showing detergent compatibility activity from Bacillus circulans

Abstract

Response surface methodology (RSM) was employed to enhance the production of a thermostable alkaline protease from Bacillus circulans. Significant influences of peptone, yeast extract, and glucose on protease production were noted with a one-variable-at-a-time optimization strategy. Then, a full factorial central composite design (CCD) was applied to study the effects of glucose, peptone, and yeast extract to determine the optimal concentrations of these compounds for protease production by B. circulans under shake flask fermentation conditions. The statistical reliability and significance of the model was validated by an F-test for analysis of variance (ANOVA); enzyme production was improved significantly under optimized conditions. The enzyme was purified by ammonium sulphate fractionation, and gel filtration chromatography. Maximum enzyme activity was observed at 60°C temperature, and at pH 10. Alkaline protease from B. circulans showed excellent compatibility and stability in the presence of commercial detergents like Ariel, Surf Excel, Tide, Rin, Nirma, Wheel, and Doctor and showed excellent blood destaining effectiveness with commercial detergents.     

Effects and statistical optimization of fermentation conditions on growth and poly (vinyl alcohol)-degrading enzyme production of Streptomyces venezuelae GY1

The effects of environmental conditions, including temperature, pH and dissolved oxygen, on growth and production of polyvinyl alcohol (PVA)-degrading enzymes of the newly-isolated strain Streptomyces venezuelae GY1 were investigated. The medium composition for strain GY1 was studied first by single factorial design and then optimized using a central composite design. PVA with high saponification is better for growth of, and PVA-degrading enzyme production by S. venezuelae GY1 compared with PVA with low saponification, in contrast with the characteristics of other bacteria producing PVA-degrading enzymes. The optimal temperature and initial pH for production of PVA-degrading enzyme by strain GY1 was 30°C and 7.0, respectively. The optimal medium composition for PVA-degrading enzyme production is: 1.01 g L^?1 of PVA1799, 0.307 g L^?1 of NaNO₃ and 0.512 g L^?1 of MgSO₄?7H₂O.     

The plant landscape as inferred from a basket of the Roman town of Privernum (Latium,central Italy)

Abstract

Privernum was a rich Roman colony located 70 km southwest of Rome (southern Latium, central Italy). The archaeobotanical investigations focused on the garden and related structures of the luxury domus della Soglia nilotica. They are archaeologically and radiocarbon dated to the second half of the 1st century AD. The remains of a charred basket were found in the filling of the euripus, an ornamental water basin of the garden. The weaving was made with twisted strands of the leaves of Ampelodesmos mauritanicus (Poir.) T. Durand and Schinz; for the bottom and the handle/s of the basket, wood of evergreen oaks and ash and/or elm, respectively were probably used. The basket contained Pinus pinea seeds and cone scales, and Prunus persica endocarps, which were probably burnt in summer. The sediment in the drainage system and in the kitchen was processed for macro- and microremains. The results indicate the presence of spontaneous ruderal and weed flora elements, typical of human settlement areas, and crops.     

Diversity of saproxylic bryophytes in old‐growth and managed beech forests in the central Balkans

Abstract

The diversity of saproxylic bryophyte species in beech forest stands from the wide region of the central Balkans (i.e. Serbia and Montenegro) was studied, and this study is the first of such a type in SE Europe. Comparison of preserved old‐growth and managed forests were made. Bryophyte species diversity is higher in primeval forest stands where the spectra of dead wood in various decaying stages of its dynamics are present. The ecological group of epixylic specialists is predominant among the bryophytes recorded. Threatened bryophyte species occur in old‐growth beech stands. The dead wood as habitat together with some other factors are extremely important for the surviving of epixylic bryophyte; so these species can be used as bioindicator bryophyte species of old‐growth or managed and structured forest ecosystems.     

Half of the European fruit fly species barcoded (Diptera,Tephritidae); a feasibility test for molecular?identification

A feasibility test of molecular identification of European fruit flies (Diptera: Tephritidae) based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences – almost 20% of the total – this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification.We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to BLAST against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification.     

Lysoglycerophospholipids in chronic inflammatory disorders: The PLA2/LPC and ATX/LPA axes

Lysophosphatidylcholine (LPC) and lysophosphatidic acid (LPA), the most prominent lysoglycerophospholipids, are emerging as a novel class of inflammatory lipids, joining thromboxanes, leukotrienes and prostaglandins with which they share metabolic pathways and regulatory mechanisms. Enzymes that participate in LPC and LPA metabolism, such as the phospholipase A₂ superfamily (PLA₂) and autotaxin (ATX, ENPP2), play central roles in regulating LPC and LPA levels and consequently their actions. LPC/LPA biosynthetic pathways will be briefly presented and LPC/LPA signaling properties and their possible functions in the regulation of the immune system and chronic inflammation will be reviewed. Furthermore, implications of exacerbated LPC and/or LPA signaling in the context of chronic inflammatory diseases, namely rheumatoid arthritis, multiple sclerosis, pulmonary fibrosis and hepatitis, will be discussed. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.     

DPSN：扩增子测序引物标准化命名数据库

扩增子测序是目前用来衡量微生物多样性时使用最广泛的测序手段。因为其扩增的需要,所以选择合适的特定引物是必需的,且其对结果影响甚大。probeBase是目前最常用的记录了人工校正后的rRNA探针和引物的数据库。然而,我们发现probeBase中63.58%的引物存在不同程度的注释错误,包括命名重复、命名无规律以及匹配位置错误等。更严重的是,目前主流的短命名方式不具有唯一性,导致对应关系模糊不清。因此,我们定义了更简单可行的短命名标准并开发了新的引物科学命名数据库（DPSN）,并对probeBase里的所有173个引物进行了校正,并新加入了4个新的改良引物以及38个针对大亚基的新引物。新的短命名规则包含3个基本要素：在正链5''端的位置、版本号和方向。此外在前面加入了识别大/小亚基以及主要针对的菌界的标志。使用DPSN,可以快速查找感兴趣区域对应的引物并比较不同版本的差异选择合适的引物。同时还能建立命名与序列的明确一一对应关系,避免歧义。