Experimental assemblage of novel plant–herbivore interactions: ecological host shifts after 40 million years of isolation

Geographic isolation is the first step in insect herbivore diet specialization. Such specialization is postulated to increase insect fitness, but may simultaneously reduce insect ability to colonize novel hosts. During the Paleocene‐Eocene, plants from the order Zingiberales became isolated either in the Paleotropics or in the Neotropics. During the Cretaceous, rolled‐leaf beetles diversified in the Neotropics concurrently with Neotropical Zingiberales. Using a community of Costa Rican rolled‐leaf beetles and their Zingiberales host plants as study system, we explored if previous geographic isolation precludes insects to expand their diets to exotic hosts. We recorded interactions between rolled‐leaf beetles and native Zingiberales by combining DNA barcodes and field records for 7450 beetles feeding on 3202 host plants. To determine phylogenetic patterns of diet expansions, we established 20 experimental plots in the field, in which we planted plots five exotic Zingiberales, recording beetles feeding on these exotic hosts. In the laboratory, using both native and exotic host plants, we reared a subset of insect species that had expanded their diets to the exotic plants. The original plant–herbivore community comprised 24 beetle species feeding on 35 native hosts, representing 103 plant–herbivore interactions. After exotic host plant introduction, 20 percent of the beetle species expanded their diets to exotic Zingiberales. Insects only established on exotic hosts that belong to the same plant family as their native hosts. Laboratory experiments show that beetles are able to complete development on these novel hosts. In conclusion, rolled‐leaf beetles are preadapted to expand their diets to novel host plants even after millions of years of geographic isolation.     

Microbial Culture Collection (MCC) and International Depositary Authority (IDA) at National Centre for Cell Science,Pune

Culture collections are valuable resources for the sustainable use of microbial diversity and its conservation. Advances in biotechnology have further increased their importance and some of these have been recognized as International Depositary Authority (IDA) for the deposition of patent cultures. Microbial Culture Collection at National Centre for Cell Science was established by the Department of Biotechnology, Government of India is country’s newest culture collection with largest holdings. It is recognized as an IDA under the Budapest Treaty and Designated National Repository under the Biodiversity Act 2002. This article describes its various service related activities.     

Zeolites are effective ROS-scavengers in vitro

We report on the use of zeolites to limit the effects of reactive oxygen species (ROS) on human albumin under in vitro conditions. Zeolites of different structure type, channel size, channel polarity, and charge-compensating cation were screened for the elimination of ROS, notably HO, resulting from the Fenton reaction. A test based on ischemia-modified albumin (IMA) was used as a marker to monitor the activity of HO after co-exposure of human serum to these zeolites. Two commercial zeolites, faujasite (FAU 13×, channel opening 0.74 × 0.74 nm with Na⁺ as charge-compensating cation) and ferrierite (FER, channel opening 0.54 × 0.42 nm with H⁺ as charge-compensating cation), were found to reduce IMA formation by more than 65% due to removal of HO relative to reference values. It was established that partial ion exchange of the zeolites’ respective charge-compensating cation vs. Fe³⁺ implicated in the Fenton reaction plays a major role in HO deactivation process. Moreover, our results show that no saturation of the respective zeolite active sites occurred. This is possible only when ROS are actively converted to water molecules within the zeolite void system, which generates H⁺ ion transport.Because zeolites cannot be administered in blood, their use in medicine should be limited to extra corporeal circuits. Zeolites could be of use during cardiopulmonary bypass or hemodialysis procedures.     

Ecotypes of wild rooibos (Aspalathus linearis (Burm. F) Dahlg., Fabaceae) are ecologically distinct

Aspalathus linearis (Burm. F) Dahlg., Fabaceae is cultivated by small- and large-scale commercial farmers of the Cederberg and Bokkeveld Plateau in the Cape Floristic Region of South Africa, for the production of an herbal beverage called ‘rooibos’ or ‘rooibos tea’. Small-scale farmers also harvest A. linearis from the wild and market the tea as an organic and fair-trade certified product. However, little is known about the apparent ecotypes of wild A. linearis. We hypothesized that 1) rooibos ecotypes are ecologically distinct (occurring in different plant communities defined by environmental variables); 2) rooibos ecotypes are functionally distinct due to variance in water use efficiency; and 3) rooibos ecotypes are associated with threatened vegetation types/species, making populations of wild rooibos ecotypes worthy of conservation. Ecotypes of wild rooibos were identified based on plant habit and local knowledge. Plant communities were classified using Twinspan, environmental factors were tested as predictors of ecotype distribution and water use efficiency of ecotypes growing across a rainfall gradient was determined from foliar natural abundance of ¹³C. Wild rooibos was not generally associated with endangered vegetation types but was associated with plant species having endangered status. Wild rooibos occurred in four plant communities and comprised five wild rooibos ecotypes: shrub, tree, upright, salignus and prostrate types. Although some ecotypes clearly co-occurred, evidence is provided for habitat preference between the ecotypes: Prostrate and upright ecotypes occurred at higher elevations (> 400-600 m). Shrub ecotypes occurred at lower rainfall sites (< 200 mm p.a.) and the salignus ecotype occurred at higher rainfall sites (> 500 mm p.a.). Foliar ¹³C indicated greater water use efficiencies by ecotypes in relatively drier areas. The extent to which this is a plastic or inherent response requires further investigation. Considering that wild rooibos ecotypes differ both ecologically and possibly also functionally and genetically, it is concluded that populations of wild rooibos ecotypes should be considered as distinct and worthy of conservation. This distinctness should be considered when farmers apply for both harvesting and ploughing rights on land with wild rooibos ecotypes.     

在墨尔本召开的第18届国际植物学大会做出的有关名称发表要求的变化——电子出版物对你意味着什么？

《国际植物命名法规》的修订由每六年一次的国际植物学大会（IBC）命名分会来决定。第18届国际植物学大会在澳大利亚墨尔本举行;命名分会于2011年7月18日至22日召开,其决议获得7月30日的全体会议通过。“墨尔本法规”有几个重要的变化,将影响新名称的发表。这些变化中的两个将在“墨尔本法规”出版前的几个月,即于2012年1月1日起生效。通过以移动文档格式（Portable Document Format;pdf）在线发表的具有国际标准连续出版物号（ISSN）或国际标准图书编号（ISBN）的电子出版物,将构成有效发表。新分类群名称的合格发表所必须的拉丁文描述或特征集要将更改为拉丁文或英文描述或特征集要。此外,自2013年1月1日起,被处理为真菌的生物的新名称必须在原始资料（某一名称合格发表时与之有关的所有资料）中引证一个由一家公认的存储库（例如MycoBank）签发的标识码,才构成合格发表。本文提供了有关电子出版物的新规则的草案文本,并概述了相应的最佳做法。     

Structure based virtual screening of MDPI database: Discovery of structurally diverse and novel DPP-IV inhibitors

Inhibition of dipeptidyl peptidase IV (DPP-IV) has been emerged as a promising approach for the treatment of type 2 diabetes (T2D). Structure based virtual screening (SBVS) of Molecular Diversity Preservation International (MDPI) database was performed using Glide and Gold against DPP-IV enzyme. Six promising hits were identified and tested for DPP-IV inhibition. Three compounds were found to be active at low micromolar concentration. The 3-(1-hydrazinyl-1-(phenylamino)ethyl)-4-hydroxy-1-methylquinolin-2(1H)-one (compound A) was found to be the most potent hit with an IC₅₀ of 0.73 μM. These three compounds (A, B and D) were then assessed for their glucose lowering effects in glucose fed hyperglycemic female Wistar rats. The glucose lowering effects of compounds also confirms their potential as anti-diabetic agents. The present study demonstrates a successful utilization of in silico SBVS tools in identification of novel and potential DPP-IV inhibitor.     

Comments on duck circovirus (DuCV) genotype definition

A standardised methodology has been used to define genotypes based on pairwise sequence comparisons (PASC). PASC is a widely accepted method in virus taxonomy, which is based on the histogram of pairwised differences among sequences. Recently, Zhang et al. (2013) concluded that the average p-distance of duck circovirus (DuCV) between genotypes 1 and 2 was 0.170, and subtype distance thresholds were 0.032 in DuCV-1 and 0.018 in DuCV-2, respectively. However, there might be some concerns on the methodology application to define the genotype of DuCV. Taking into account the concerns mentioned above, our authors conducted the PASC analyses of 54 capsid gene (ORF2) and genomic sequences including all the sequences from Zhang et al. (2013). Our results confirmed the existence of two DuCV genotypes (1 and 2) and, we suggest that DuCV ORF2 and genomic distance genotype thresholds were 0.061 and 0.038, respectively.     

Association analysis of ERBB2 amplicon genetic polymorphisms and STARD3 expression with risk of gastric cancer in the Chinese population

The purpose of this study was to investigate whether risk of gastric cancer (GC) was associated with single nucleotide polymorphisms (SNPs) in a gene cluster on the chromosome 17q12-q21 (ERBB2 amplicon) in the Chinese Han population. We detected twenty-six SNPs in this gene cluster containing steroidogenic acute regulatory-related lipid transfer domain containing 3 (STARD3), protein phosphatase 1 regulatory subunit 1B (PPP1R1B/DARPP32), titin-cap (TCAP), per1-like domain containing 1(PERLD1/CAB2), human epidermal growth factor receptor-2 (ERBB2/HER2), zinc-finger protein subfamily 1A 3 (ZNFN1A3/IKZF3) and DNA topoisomerase 2-alpha (TOP2A) genes in 311 patients with GC and in 425 controls by Sequenom. We found no associations between genetic variations and GC risk. However, haplotype analysis implied that the haplotype CCCT of STARD3 (rs9972882, rs881844, rs11869286 and rs1877031) conferred a protective effect on the susceptibility to GC (P = 0.043, odds ratio [OR] = 0.805, 95% confidence intervals [95% CI] = 0.643–0.992). The STARD3 rs1877031 TC genotype endued histogenesis of gastric mucinous adenocarcinoma and signet-ring cell carcinoma (P = 0.021, OR = 2.882, 95% CI = 1.173–7.084). We examined the expression of STARD3 in 243 tumor tissues out of the 311 GC patients and 20 adjacent normal gastric tissues using immumohistochemical (IHC) analysis and tissue microarrays (TMA). The expression of STARD3 was observed in the gastric parietal cells and in gastric tumor tissues and significantly correlated with gender (P = 0.004), alcohol drinking (P < 0.001), tumor location (P = 0.007), histological type (P = 0.005) and differentiation (P = 0.023) in GC. We concluded that the combined effect of haplotype CCCT of STARD3 might affect GC susceptibility. STARD3 expression might be related to the tumorigenesis of GC in the Chinese population.     

Challenges in assessing pathogenicity based on frequency of variants in mismatch repair genes: an extreme case of a MSH2 variant and a meta-analysis

The clinical interpretation of variants in mismatch repair (MMR) genes associated with Lynch syndrome can be confusing when the functional nature of the variant is not clearly defined. We report an extreme case where a polymorphism in the MSH2 gene which had a low minor allele frequency, was misclassified as a mutation based on low evidential methods in the database and previous publications. We expanded this experience to perform a systematic meta-analysis in order to investigate other variants that have potentially been misclassified. Our results suggested that the interpretation of pathogenicity should be more cautious and emphasized the need for solid validation through multiple analyses including functional analysis for variants in MMR genes.     

Taxonomic investigation of five streptomycete cultures belonging to ISP standards

The taxonomic investigation of five streptomycete cultures belonging to the International Streptomyces Project (ISP) standards was carried out using the methods of population analysis, DNA-DNA hybridization, and multilocus DNA fingerprinting. Two species with names considered to be synonymous,S. alboviridis ISP 5326 andS. oligocarbophilus ISP 5589, were found to be actually identical. Three other species investigated,S. krainskii ISP 5321,S. craterifer ISP 5296, and 5.anulatus ISP 5361, whose names are usually referred to as synonymous, were shown to be different species.