Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes

This report describes a set of 21 polymerase chain reaction primers and amplification conditions developed to barcode practically any teleost fish species according to their mitochondrial cytochrome b and nuclear rhodopsin gene sequences. The method was successfully tested in more than 200 marine fish species comprising the main Actinopterygii family groups. When used in phylogenetic analyses, its combination of two genes with different evolutionary rates serves to identify fish at the species level. We provide a flow diagram indicating our validated polymerase chain reaction amplification conditions for barcoding and species identification applications as well as population structure or haplotyping analyses, adaptable to high‐throughput analyses.     

Efficiency and cost of economical brain functional networks

Brain anatomical networks are sparse, complex, and have economical small-world properties. We investigated the efficiency and cost of human brain functional networks measured using functional magnetic resonance imaging (fMRI) in a factorial design: two groups of healthy old (N = 11; mean age = 66.5 years) and healthy young (N = 15; mean age = 24.7 years) volunteers were each scanned twice in a no-task or “resting” state following placebo or a single dose of a dopamine receptor antagonist (sulpiride 400 mg). Functional connectivity between 90 cortical and subcortical regions was estimated by wavelet correlation analysis, in the frequency interval 0.06–0.11 Hz, and thresholded to construct undirected graphs. These brain functional networks were small-world and economical in the sense of providing high global and local efficiency of parallel information processing for low connection cost. Efficiency was reduced disproportionately to cost in older people, and the detrimental effects of age on efficiency were localised to frontal and temporal cortical and subcortical regions. Dopamine antagonism also impaired global and local efficiency of the network, but this effect was differentially localised and did not interact with the effect of age. Brain functional networks have economical small-world properties—supporting efficient parallel information transfer at relatively low cost—which are differently impaired by normal aging and pharmacological blockade of dopamine transmission.     

Biphenyl bicelle disks align perpendicular to magnetic fields on large temperature scales: a study combining synthesis, solid-state NMR, TEM, and SAXS

A phosphatidylcholine lipid (PC) containing a biphenyl group in one of its acyl chains (1-tetradecanoyl-2-(4-(4-biphenyl)butanoyl)-sn-glycero-3-PC, TBBPC) was successfully synthesized with high yield. Water mixtures of TBBPC with a short-chain C(6) lipid, dicaproyl-PC (DCPC), lead to bicelle systems formation. Freeze-fracture electron microscopy evidenced the presence of flat bilayered disks of 800 A diameter for adequate composition, hydration, and temperature conditions. Because of the presence of the biphenyl group, which confers to the molecule a positive magnetic anisotropy Delta chi, the disks align with their normal, n, parallel to the magnetic field B(0), as directly detected by (31)P, (14)N, (2)H solid-state NMR and also using small-angle x-ray scattering after annealing in the field. Temperature-composition and temperature-hydration diagrams were established. Domains where disks of TBBPC/DCPC align with their normal parallel to the field were compared to chain-saturated lipid bicelles made of DMPC(dimyristoylPC)/DCPC, which orient with their normal perpendicular to B(0). TBBPC/DCPC bicelles exist on a narrow range of long- versus short-chain lipid ratios (3%) but over a large temperature span around room temperature (10-75 degrees C), whereas DMPC/DCPC bicelles exhibit the reverse situation, i.e., large compositional range (22%) and narrow temperature span (25-45 degrees C). The two types of bicelles present orienting properties up to 95% dilution but with the peculiarity that water trapped in biphenyl bicelles exhibits ordering properties twice as large as those observed in the saturated-chains analog, which offers very interesting properties for structural studies on hydrophilic or hydrophobic embedded biomolecules.     

Sampling genetic diversity in the sympatrically and allopatrically speciating Midas cichlid species complex over a 16 year time series

Background  

Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different strengths as populations diverge. The Central American Midas cichlid fish species complex is an important case study for understanding the processes of speciation. Previous analyses have demonstrated that allopatric processes led to species formation among the lakes of Nicaragua as well as sympatric speciation that is occurring within at least one crater lake. However, since speciation is an ongoing process and sampling genetic diversity of such lineages can be biased by collection scheme or random factors, it is important to evaluate the robustness of conclusions drawn on individual time samples.     

Isolation and cross‐familial amplification of 41 microsatellites for the brook charr (Salvelinus fontinalis)

The brook charr (Salvelinus fontinalis; Osteichthyes: Salmonidae) is a phenotypically diverse fish species inhabiting much of North America. But relatively few genetic diagnostic resources are available for this fish species. We isolated 41 microsatellites from S. fontinalis polymorphic in one or more species of salmonid fish. Thirty‐seven were polymorphic in brook charr, 15 in the congener Arctic charr (Salvelinus alpinus) and 14 in the lake charr (Salvelinus namaycush). Polymorphism was also relatively high in Oncorhynchus, where 21 loci were polymorphic in rainbow trout (Oncorhynchus mykiss) and 16 in cutthroat trout (Oncorhynchus clarkii) but only seven and four microsatellite loci were polymorphic in the more distantly related lake whitefish (Coregonus clupeaformis) and Atlantic salmon (Salmo salar), respectively. One duplicated locus (Sfo228Lav) was polymorphic at both duplicates in S. fontinalis.     

Assessing the reliability of eBURST using simulated populations with known ancestry

Background  

The program eBURST uses multilocus sequence typing data to divide bacterial populations into groups of closely related strains (clonal complexes), predicts the founding genotype of each group, and displays the patterns of recent evolutionary descent of all other strains in the group from the founder. The reliability of eBURST was evaluated using populations simulated with different levels of recombination in which the ancestry of all strains was known.     

刺梨提取物在卷烟中的应用及其致香成分的双柱分析

将刺梨提取物用于卷烟加料,用二氯甲烷同时蒸馏萃取刺梨提取物,分别用极性柱和非极性柱进行GC/MS分析.结果表明,刺梨提取物与烟香谐调,具有增加香气质和香气量、掩盖杂气、改善余味的作用,是安全有效的天然烟用香料;采用双柱分析的方法共检出62种化合物,比用单一极性柱分析更能相对客观、全面的反映刺梨提取物中的致香成分的状况;...     

The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone

Escherichia coli ST131 is a globally disseminated, multidrug resistant clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with antibiotic resistance; however, this phenotype alone is unlikely to explain its dominance amongst multidrug resistant uropathogens circulating worldwide in hospitals and the community. Thus, a greater understanding of the molecular mechanisms that underpin the fitness of E. coli ST131 is required. In this study, we employed hyper-saturated transposon mutagenesis in combination with multiplexed transposon directed insertion-site sequencing to define the essential genes required for in vitro growth and the serum resistome (i.e. genes required for resistance to human serum) of E. coli EC958, a representative of the predominant E. coli ST131 clonal lineage. We identified 315 essential genes in E. coli EC958, 231 (73%) of which were also essential in E. coli K-12. The serum resistome comprised 56 genes, the majority of which encode membrane proteins or factors involved in lipopolysaccharide (LPS) biosynthesis. Targeted mutagenesis confirmed a role in serum resistance for 46 (82%) of these genes. The murein lipoprotein Lpp, along with two lipid A-core biosynthesis enzymes WaaP and WaaG, were most strongly associated with serum resistance. While LPS was the main resistance mechanism defined for E. coli EC958 in serum, the enterobacterial common antigen and colanic acid also impacted on this phenotype. Our analysis also identified a novel function for two genes, hyxA and hyxR, as minor regulators of O-antigen chain length. This study offers novel insight into the genetic make-up of E. coli ST131, and provides a framework for future research on E. coli and other Gram-negative pathogens to define their essential gene repertoire and to dissect the molecular mechanisms that enable them to survive in the bloodstream and cause disease.