Comparative genetic mapping reveals synteny and collinearity between the American cranberry and diploid blueberry genomes

Cranberry and blueberry are closely related and recently domesticated fruit crops in the genus Vaccinium. Both have a presumed American origin and likely evolved from a common ancestor; however, details of their adaptive radiation and the extent of their genomic divergence remains little understood. To better understand their evolutionary and genomic relationships, a set of 323 cross-transferable simple sequence repeat (SSR) markers were identified, added to existing marker datasets, and used to construct linkage maps for cranberry (582 SSRs) and an interspecific diploid blueberry population (V. darrowii x V. corymbosum) x V. corymbosum (409 markers, densest blueberry SSR map currently available). The maps allowed for the first comparative genetic mapping study in Vaccinium, and revealed a surprisingly high degree of macro-synteny and collinearity between the cranberry and blueberry genomes. Approximately 93% of the blueberry linkage map was collinear with cranberry, while the remaining 7% (66.3 cM) was spread across 15 non-collinear regions detected in eight of the 12 linkage groups. These observations suggest that large-scale genome differentiation between the cranberry and blueberry genomes has not occurred during their evolution, and that sequence information will be highly transferable between the species in future genetic research and breeding. Finally, the set of 323 cross-transferable SSRs and linkage maps they were used to construct can serve as a shared resource for the Vaccinium research community, enabling additional comparative mapping studies, the identification and transfer of quantitative trait loci and candidate genes between species, and future exploration of evolutionary relationships in Vaccinium.     

Graphene Doping Induced Tunability of Nanoparticles Plasmonic Resonances

Interest in graphene has been widely increasing since its discovery in 2004. Research on graphene for plasmonic applications has also boomed due to the high potential of these systems. In this article, we discuss the possible interaction between metallic NPs and graphene monolayer. We show how the contact between metallic NPs and graphene results in graphene doping. More importantly, we experimentally put into evidence the possible modulation of the plasmonic resonance of NPs by graphene doping. Understanding and evidencing this interaction is highly important both from a fundamental point of view and for specific applications such as active plasmonic devices.

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Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

Background

Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases.

Methods

To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria.

Results

Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features.

Conclusion

Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis.

     

Construction of a recombinant BHV-1 expressing the VP1 gene of foot and mouth disease virus and its immunogenicity in a rabbit model

Foot-and-mouth disease (FMD) and infectious bovine rhinotracheitis (IBR) are two important infectious diseases of cattle. Using bovine herpesvirus type 1 (BHV-1) as a gene delivery vector for development of live-viral vaccines has gained widespread interest. In this study, a recombinant BHV-1 was constructed by inserting the synthetic FMDV (O/China/99) VP1 gene in the the gE locus of BHV-1 genome under the control of immediately early gene promoter of human cytomegalovirus (phIE CMV) and bovine growth hormone polyadenylation (BGH polyA) signal. After homologous recombination and plaque purification, a recombinant virus named BHV-1/gE⁻/VP1 was acquired and identified. The immunogenicity was confirmed in a rabbit model by virus neutralization test and enzyme-linked immunosorbent assay (ELISA). The result indicated that the BHV-1/gE⁻/VP1 has the potential for being developed as a bivalent vaccine for FMD and IBR.     

鲤科鱼类6个正反交人工异源三倍体胚胎的染色体变化及其发育命运

采用静水压休克保留第二极体的方法,在鲤(♀)×鲢(?)、鲫(♀)×鲢(?)、白鲫(♀)×鲢(?)和鲢(♀)×鲤(?)、鲢(♀)×鲫(?)、鲢(♀)×白鲫(?)6个正反交组合中都诱导出了异源三倍体,但只有正交鲤(♀)×鲢(?)、鲫(♀)×鲢(?)和白鲫(♀)×鲢(?)3个处理组中整倍性的异源三倍体胚胎才有可能正常发育,孵化出苗;而反交鲢(♀)×鲤(?)、鲢(♀)×鲫(?)和鲢(♀)×白鲫(?)3个处理组中的异源三倍体胚胎在发育过程中不断发生染色体排除和丢失,形成非整倍体而死亡,只有少数雌核发育二倍体鲢才能孵化出苗。结果表明,鱼类人工异源三倍体胚胎的发育命运与杂交物种间的基因组大小有关。     

A new genotyping method for detecting low abundance single nucleotide mutations based on gap ligase chain reaction and quantitative PCR assay

We tested applicability of a new genotyping technique to detect a low abundance CD17 (A → T) mutation of β-globin gene. The technique utilized a combined gap ligase chain reaction (Gap-LCR) and quantitative PCR (qPCR) methods. One pair of Gap-LCR primers was modified by adding specific sequences to the 5′ end of the upstream and the 3′ end of the downstream primer which served as a combining sequence for qPCR. First, specific mutation is detected using Gap-LCR; then, ligation products are detected by qPCR. Our results show that the amount of LCR products is directly proportional to the amount of template DNA. We further demonstrate that this technique detects a low abundance mutant DNA with a mutant/normal allele ratio as low as 1:10000. This technique was applied to detect a paternally inherited CD17 mutation from 53 maternal plasma samples. The results were consistent with those obtained by PCR/reverse dot blot of amniotic fluid cell DNA. In conclusion, by combining Gap-LCR and qPCR technology we successfully established a highly sensitive technique to detect low abundance point mutations. This technique can be applied to detect fetal DNA point mutation in maternal plasma.     

蚯蚓中抗肿瘤蛋白组分的提取分离及其抗肿瘤活性

以赤子爱胜蚓为原料 ,通过蛋白质的丙酮沉淀和凝胶过滤 ,分离得到一组抗肿瘤活性蛋白成分 (简称蚯蚓抽提物 ) ;这组成分富含Fe、Zn、Cu以及Se等微量元素 ,蛋白含量为 6 0 4 3± 2 36 %(n =5 ) .体外实验中 ,通过MTT法和SRB法测定了蚯蚓抽提物对多种人癌细胞株 (HCT 116、SY5Y、K5 6 2、MGc80 3和HeLa)以及正常细胞株 (HEK2 93和COS 7)的抑制杀伤率 .结果表明 ,蚯蚓抽提物对癌细胞的杀伤有一定的选择性 ,受试人癌细胞达到 5 0 %生长抑制率所需作用浓度约 6 0～110mg L ;但是 ,10 0℃煮沸 5min后 ,该抑制活性完全消失 .通过纤维蛋白平板法 ,测得蚯蚓抽提物同时具有纤溶酶和纤溶酶原激活酶的活性 .体外测得丝氨酸蛋白酶抑制剂aprotinin和PMSF能显著抑制蚯蚓抽提物的细胞杀伤活性 .体内实验中 ,蚯蚓抽提物能有效延长荷瘤 (S180 )小鼠的生存时间 ,并使其身体机能得到明显改善 .腹膜内注射剂量为 2 8mg kg和 36mg kg时 ,生命延长率分别为135 3%和 12 3 5 % ,和标准药物 (环磷酰胺 )治疗后结果 (76 5 % )相比 ,有显著性差异     

Enhancement of butanol production and reducing power using a two-stage controlled-pH strategy in batch culture of Clostridium acetobutylicum XY16

The effects of pH control on the process of acetone/butanol/ethanol (ABE) production in batch cultures of Clostridium acetobutylicum XY16 have been investigated. Based on the specific acid- and solvent-forming rates in batch fermentation at different pH values (from 4.3 to 6.0), a two-stage controlled-pH strategy was developed in which the pH was shifted from 5.5 to 4.9 after a dry cell weight of 0.5 g L(-1) was achieved. By applying this strategy, the maximum ABE concentration and productivity reached 20.3 g L(-1) and 0.63 g L(-1) h (-1), and were significantly improved by 12.2 and 40.1 %, respectively, compared with the process with no pH control. In addition, reducing power capability was significantly enhanced by this strategy. The two-stage controlled-pH strategy was a convenient and rapid method for high intensity ABE production.     

Proteomic Analysis of Interactions Between the Generalist Herbivore <Emphasis Type="Italic">Spodoptera exigua</Emphasis> (Lepidoptera: Noctuidae) and <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

In this study, comparative proteomics was used to investigate the interaction of Spodoptera exigua and Arabidopsis thaliana. By using 2-D electrophoresis of differentially expressed proteins, combined with high-throughput matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and MALDI-TOF/TOF MS, the changes in the abundance of proteins induced by insect feeding were studied in A. thaliana. More than 1,100 protein spots were reproducibly detected on each gel. The intensities of 30 protein spots in particular changed significantly, showing differences in volume of at least twofold. Among these, 17 protein spots were upregulated, and 13 were downregulated following an 8-h insect feeding period. Nineteen insect-feeding-responsive proteins were identified, all of which were involved in metabolic regulation, binding functions or cofactor requirement of protein, cell rescue, and defense and virulence, as assessed by Munich Information Center for Protein Sequences function category. About 50% of these were involved in metabolism, including transketolase, S-adenosylmethionine synthase 3, 2,3-biphosphoglycerate-independent phosphoglycerate mutase, beta-ureidopropionase, GDP-d-mannose 3′,5′-epimerase, and fatty acid synthase. The identification of insect-feeding-responsive proteins on Arabidopsis provides not only new insights into insect stress but also a good start for further investigation of their functions. Understanding how the plant responses to insects in the proteomic level will provide tools for a better management of insect pest in the field.     

Competitive binding of Fe<Superscript>3+</Superscript>, Cr<Superscript>3+</Superscript>, and Ni<Superscript>2+</Superscript> to transferrin

Competitive binding of Fe³⁺, Cr³⁺, and Ni²⁺ to transferrin (Tf) was investigated at various physiological iron to Tf concentration ratios. Loading percentages for these metal ions are based on a two M ⁿ⁺ to one Tf (i.e., 100% loading) stoichiometry and were determined using a particle beam/hollow cathode–optical emission spectroscopy (PB/HC-OES) method. Serum iron concentrations typically found in normal, iron-deficient, iron-deficient from chronic disease, iron-deficient from inflammation, and iron-overload conditions were used to determine the effects of iron concentration on iron loading into Tf. The PB/HC-OES method allows the monitoring of metal ions in competition with Fe³⁺ for Tf binding. Iron-overload concentrations impeded the ability of chromium (15.0 μM) or nickel (10.3 μM) to load completely into Tf. Low Fe³⁺ uptake by Tf under iron-deficient or chronic disease iron concentrations limited Ni²⁺ loading into Tf. Competitive binding kinetic studies were performed with Fe³⁺, Cr³⁺, and Ni²⁺ to determine percentages of metal ion uptake into Tf as a function of time. The initial rates of Fe³⁺ loading increased in the presence of nickel or chromium, with maximal Fe³⁺ loading into Tf in all cases reaching approximately 24%. Addition of Cr³⁺ to 50% preloaded Fe³⁺–Tf showed that excess chromium (15.0 μM) displaced roughly 13% of Fe³⁺ from Tf, resulting in 7.6 ± 1.3% Cr³⁺ loading of Tf. The PB/HC-OES method provides the ability to monitor multiple metal ions competing for Tf binding and will help to understand metal competition for Tf binding.