高原鼠兔有效洞穴密度对青藏高原高寒草甸群落植物生态位的影响

高原鼠兔(Ochotona curzoniae)有效洞穴密度扩增会引起高寒草甸植物群落组分的变化。采用野外调查方法研究了高原鼠兔有效洞穴密度对青藏高原高寒草甸群落植物生态位的影响。结果表明:随高原鼠兔有效洞穴密度增加,样方内植物种数逐渐增多,但主要是毒杂草,有效洞穴密度超过15个/625m2时豆科植物出现。优势种高山嵩草(Kobresia pygmaea)的重要值随有效洞穴密度增加呈单峰曲线,峰值出现在15个/625m2。有效洞穴密度低于或等于21个/625m2时,优势种高山嵩草生态位宽度位居第一,但有效洞穴密度达31个/625m2时,其生态位宽度降至并列第三,低于小米草(Euphrasia pectinata)和钝裂银莲花(Anemone obtusiloba),等同于小花草玉梅(Anemone rivularis)和乳浆大戟(Euphorbia esula)。有效洞穴密度分别为10个/625m2,15个/625m2,21个/625m2,31个/625m2时,与高山嵩草生态位重叠度最大的物种分别为莓叶委陵菜(Potentilla fragarioides)、圆叶筋骨草(Ajuga ovalifolia)、乳浆大戟、条叶垂头菊(Cremanthodium lineare)。有效洞穴密度为10个/625m2时,高山嵩草是群落内种群间竞争最激烈的一方,但有效洞穴密度超过或等于15个/625m2时,高山嵩草则退出了种群间竞争最激烈的双方。说明高原鼠兔有效密度增加严重影响了高寒草甸群落组分、重要值、生态位宽度和生态位重叠值。     

高原鼠兔有效洞穴密度对高寒草甸优势植物叶片和土壤氮磷化学计量特征的影响

采用有效洞穴密度代替高原鼠兔(Ochotona curzoniae)活动强度的方法,研究了高原鼠兔有效洞穴密度(10、15、21和31个/625 m~2)对高寒草甸优势植物高山嵩草(Kobresiapygmaea)、垂穗披碱草(Elymus nutans)、小花草玉梅(Anemone rivularis)叶片和土壤氮(N)磷(P)化学计量特征的影响。结果表明,3种优势植物叶片N含量随有效洞穴密度增加而显著增加(P0.05),但叶片P含量却出现分异,表现为高山嵩草和垂穗披碱草叶片P含量随有效洞穴密度增加而先增加后降低(P0.05),小花草玉梅叶片P含量逐渐增加(P0.05);高山嵩草叶片N:P随有效洞穴密度增加先降低后增加(P0.05),垂穗披碱草叶片N:P逐渐增加,小花草玉梅叶片N:P则先增加后降低。土壤0-10 cm和10-20 cm土层N含量随有效洞穴密度增加无明显变化;0—10cm土层P含量随有效洞穴密度增加先降低后增加,10—20 cm土层P含量逐渐降低;0—10 cm土层N:P随有效洞穴密度增加元明显变化,而10-20 cm土层N:P则逐渐增加。优势植物叶片N、P、N:P与土壤N、P、N:P的相关性受植物根系分布特征和生存微环境的约束。     

西宁南山4种灌木根际和非根际土壤微生物、酶活性和养分特征

西宁南山区植被退化情况严重,人工造林植被恢复被看作是最有效的恢复手段,其中选择合适造林树种尤为关键。选择人工种植的唐古特白刺Nitraria tangutorum、柠条Caragana korshinskii、西北小蘗Berberis vernae和短叶锦鸡儿Caragana brevifolia共4种灌木树种造林试验区为研究对象,通过测定根际和非根际土壤微生物数量、酶活性及养分含量,综合比较种植4种灌木树种根际和非根际土壤肥力差异,科学评价其对土壤的改善效果。研究表明:(1)土壤微生物数量和酶活性总体呈现出根际高于非根际的规律,仅放线菌数量和脲酶活性出现了根际低于非根际现象。(2)土壤养分方面,4种灌木根际土壤和非根际土壤p H值、全N、全P、全K含量差异不显著,有机质、有效P、速效K含量均呈现出根际非根际,而碱解N则是根际非根际。(3)土壤酶活性与土壤微生物数量相关性不显著,土壤有机质含量与土壤细菌、真菌数量呈极显著正相关,有效P含量与土壤细菌、真菌和放线菌数量呈极显著正相关,速效K含量与过氧化氢酶、酸性磷酸酶活性呈显著正相关,全N、碱解N含量均与脲酶活性呈显著正相关。(4)从土壤肥力综合水平来看,根际非根际,其中根际土壤中西北小蘗柠条短叶锦鸡儿唐古特白刺,研究结果表明西北小蘗和柠条能大幅提高土壤肥力,改良土壤效果较好。     

Draft Genome Sequence of Achromobacter piechaudii Strain HLE

Achromobacter piechaudii strain HLE is a betaproteobacterium (previously known as Alcaligenes faecalis) that was an early isolate with arsenite oxidase activity. This draft genome of 6.89 Mb is the second available genome for this species in the opportunistic pathogen Alcaligenaceae family.     

Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR

SYBR Green I (SG) is widely used in real-time PCR applications as an intercalating dye and is included in many commercially available kits at undisclosed concentrations. Binding of SG to double-stranded DNA is non-specific and additional testing, such as DNA melting curve analysis, is required to confirm the generation of a specific amplicon. The use of melt curve analysis eliminates the necessity for agarose gel electrophoresis because the melting temperature (T_m) of the specific amplicon is analogous to the detection of an electrophoretic band. When using SG for real-time PCR multiplex reactions, discrimination of amplicons should be possible, provided the T_m values are sufficiently different. Real-time multiplex assays for Vibrio cholerae and Legionella pneumophila using commercially available kits and in-house SG mastermixes have highlighted variability in performance characteristics, in particular the detection of only a single product as assessed by T_m analysis but multiple products as assessed by agarose gel electrophoresis. The detected T_m corresponds to the amplicon with the higher G+C% and larger size, suggesting preferential binding of SG during PCR and resulting in the failure to detect multiple amplicons in multiplex reactions when the amount of SG present is limiting. This has implications for the design and routine application of diagnostic real-time PCR assays employing SG.     

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions

Background

Colorectal cancer is the second leading cause of cancer death in the United States, with over 50,000 deaths estimated in 2014. Molecular profiling for somatic mutations that predict absence of response to anti-EGFR therapy has become standard practice in the treatment of metastatic colorectal cancer; however, the quantity and type of tissue available for testing is frequently limited. Further, the degree to which the primary tumor is a faithful representation of metastatic disease has been questioned. As next-generation sequencing technology becomes more widely available for clinical use and additional molecularly targeted agents are considered as treatment options in colorectal cancer, it is important to characterize the extent of tumor heterogeneity between primary and metastatic tumors.

Results

We performed deep coverage, targeted next-generation sequencing of 230 key cancer-associated genes for 69 matched primary and metastatic tumors and normal tissue. Mutation profiles were 100% concordant for KRAS, NRAS, and BRAF, and were highly concordant for recurrent alterations in colorectal cancer. Additionally, whole genome sequencing of four patient trios did not reveal any additional site-specific targetable alterations.

Conclusions

Colorectal cancer primary tumors and metastases exhibit high genomic concordance. As current clinical practices in colorectal cancer revolve around KRAS, NRAS, and BRAF mutation status, diagnostic sequencing of either primary or metastatic tissue as available is acceptable for most patients. Additionally, consistency between targeted sequencing and whole genome sequencing results suggests that targeted sequencing may be a suitable strategy for clinical diagnostic applications.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0454-7) contains supplementary material, which is available to authorized users.     

Genetic diversity of Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae,Rhodophyta) in Southeast Asia

The commercial importance of carrageenophytes Kappaphycus and Eucheuma is well known, with much interest in terms of cultivation, marketing, and research. Considering the many lucrative prospects, these red seaweeds were introduced into various parts of the world for farming, where merely a few were comprehensively documented. Despite being extensively cultivated throughout Southeast Asia, the genetic diversity of Kappaphycus and Eucheuma is poorly studied, where heavy reliance is placed on the use of local or commercial names for identifications. This study used the mitochondrial-encoded cox1 and cox2–3 spacer genetic markers to investigate the Kappaphycus and Eucheuma haplotypes, cultivated and wild, available throughout Southeast Asia. Concatenated cox1–cox2–3 spacer datasets were also analyzed. The near full-length cox1 gene is preferred at revealing the genetic diversity of Kappaphycus and Eucheuma, provided a larger reference database is available. Both molecular markers were capable of delineating common members of the genus Kappaphycus (i.e., Kappaphycus alvarezii, Kappaphycus striatus, and Kappaphycus cottonii) and Eucheuma denticulatum, and revealed interesting genotypes and new species which may be potential alternatives to the common cultivars as well as materials for research. The relative scarcity of Eucheuma species is discussed and future sites for sampling are recommended.     

Molecular characterization of HAO3, the homologue of the Bm86 tick vaccine antigen,from the Iranian isolate of Hyalomma anatolicum anatolicum

Hyalomma anatolicum anatolicum tick is widely distributed in many parts of Iran and while the commercial vaccines based on the application of midgut-derived recombinant Bm86 antigen are used for its control, limited information about the efficiency of this vaccination in Iran is available. Herein, with the final aim of evaluation of Bm86-based heterologous vaccination, as the primary step the Bm86 homologue of the H. a. anatolicum (Hao3) from an Iranian isolate was characterized and compared with the commercialized Bm86 and other Bm86 homologoue sequences available in GenBank.     

Availability peak of caloric fruits coincides with energy-demanding seasons for resident and non-breeding birds in restinga, an ecosystem related to the Atlantic forest,Brazil

We evaluated temporal variation and quality of food resources available to birds especially in two energy-demanding seasons: one when there is a peak of molting residents and another when non-breeding individuals are the bulk of biomass of captured birds. Birds were captured and observed, as well as fruits counted and collected, in two restinga sites for 2 years. Molting resident birds may rely basically on the regularly produced Clusia hilariana and Erythroxylum spp. fruits as lipid-sources, while non-breeders count on Ocotea notata fruits (also rich in lipids) during their passage by the study site. We found that fruits with sugars, lipids or proteins were available throughout the whole period, but a more intense seasonal variation was observed for the before mentioned plant species. The birds studied are known to be potential seed dispersers of these plant species, which are important components of restinga plant community structure.     

普通鹿蹄草品质与根际和非根际土壤的关系

以野外调查和室内分析相结合,采用相关分析、主成分分析、回归分析、通径分析等多种分析方法,对秦岭太白山区不同生境下野生普通鹿蹄草有效成分(总黄酮、单宁、金丝桃苷、槲皮素和抗氧化活性(DPPHIC50)与其根际和非根际土壤性质的关系做了研究。结论如下:(1)根际土壤速效钾、pH和脲酶与单个有效成分含量之间呈现出显著或极显著作用,而非根际土壤速效钾与5种有效成分均达到显著或极显著正相关。(2)根际土壤速效钾、pH、转化酶和脲酶是影响普通鹿蹄草有效成分含量的主导因子,而非根际土壤有效氮、速效钾、pH和转化酶是综合影响其含量的主导因子。(3)根际土壤速效钾是影响普通鹿蹄草有效成分含量的主要决策因素,而pH、转化酶和脲酶是其主要限制因素;非根际土壤有效氮和速效钾是影响普通鹿蹄草有效成分含量的主要决策因素,而pH和转化酶是其主要限制因素。由此得出,普通鹿蹄草有效成分含量受根际和非根际多种土壤因子的综合影响,且土壤速效钾含量、pH、转化酶是影响其含量的共同因子。     

Explicit reformulations of time-dependent solution for a Michaelis-Menten enzyme reaction model

The exact closed-form solution to the Michaelis-Menten equation is expressed in terms of the Lambert W(x) function. However, the utility of this solution is limited because the W(x) function is not widely available in curve-fitting software. Based on various approximations to the W(x) function, different explicit equations expressed in terms of the elementary functions are proposed here as useful shortcuts to fit time depletion of substrate concentration directly to progress curves using commonly available nonlinear regression computer programs. The results are compared with those obtained by fitting other algebraic equations that have been proposed previously in the literature.     

Development of a Synthetic Minimal Medium for Listeria monocytogenes

A defined solid and liquid minimal medium, HTM, which contained methionine and cysteine as the sole amino acids, was developed for Listeria monocytogenes. Complex broth-grown L. monocytogenes had to adapt to HTM by inducing amino acid biosyntheis. HTM is the simplest minimal medium available for growth of L. monocytogenes.     

Biochemical basis of radiation-sensitivity in mutants of Neurospora crassa

The available UV-sensitive mutants of Neurospora crassa were examined for their ability to excise and photoreactive cytosine-containing dimers invivo. All strains exhibited in vivo photoreactivation, including upr-1, which was originally thought to be deficient in photoreactivation. Two strains, uvs-2 and upr-1 were shown to be deficient in excision repair; uvs-3 was shown to contain a residual amount of excision capabilit. The remaining strains, uvs-1, uvs-5, and uvs-6, were normal in their ability to excise dimers. Based on these results, tentative analogies were drawn between the Neurospora mutants and the known classes of UV-sensitive mutants in E. coli. Accordingly, the N. crassa mutants were classified as uvs-1, -lon; uvs-2, -uvr; uvs-3, -uvr (rec?); uvs-5, -lon; uvs-6, -rec; and upr-1, -uvr. A comparison was made between the biochemical responses and the available published data on mutation induction in the Neurospora mutants. Althoughsome relationships were seen between repair defects and mutation induction, too little data were available for any definitive conclusions.     

On the identity of strychnicine

Evidence is presented for the probable identity of strychnicine, a Strychnos alkaloid isolated by Boorsma in 1902 but no longer available, with vomicine (4-hydroxy-N-methyl-sec.-pseudostrychnine). A product obtained in 1966 by Hifny Saber et al. and identified by them as strychnicine is different from Boorsma's compound and its nature remains uncertain.     

Génomique quantitative chez Caenorhabditis elegans : stratégies pour l’identification de nouvelles cibles thérapeutiques et de nouveaux mécanismes moléculaires chez l’homme

Because the entire genome of Caenorhabditis elegans (C. elegans) is available for exploration since 1998, several information have been retrieved about the global interest of this organism when it became apparent that the similarity of genes in this 1 mm length nematode and those in humans is remarkable, with approximately 67% of genes that are associated with human disease having homologues in the worm genome. C. elegans worms can be easily maintained on various food-sources and culture media allowing testing for molecules or treatments in combination with different genetic mutants backgrounds as well as RNA interference (RNAi). Because of regulatory pathways conservation between humans and worms, several interesting strategies can be developed to facilitate drugs screenings on specific targets as well as to decipher complex physiological programmed traits with potential identification of new therapeutic targets interesting for human health. By using specific examples, we propose to introduce how to use the already available C. elegans data-cross that can be used as a basis for developing new therapeutic targets identification strategies.     

Candida Sepsis: a New Entity?

Despite progress in the field of biological sciences, a definitive diagnosis of Candida sepsis remains an elusive target. Candida, which is frequently found in non-immunocompromised patients in intensive care units, causes severe sepsis, septic shock, and multiple-organ failure in a similar fashion as bacteria. Despite its imprecision, the blood and/or sterile-site culture is still the gold standard for diagnosis, although new biological markers are becoming available for earlier and more accurate diagnosis of invasive candidiasis. Mortality remains high due to a number of factors, and early initiation of appropriate antifungal therapy is a critical factor in positive outcomes. Echinocandins are the drug of choice for severe Candida infections in hospitalized patients. Antifungal stewardship programs may decrease the likelihood of resistance strains, and preventive measures are becoming available to lower the rate of fungal infections in intensive care units.     

The Relative Concentrations of Nutrients and Toxins Dictate Feeding by a Vertebrate Browser,the Greater Glider Petauroides volans

Although ecologists believe that vertebrate herbivores must select a diet that allows them to meet their nutritional requirements, while avoiding intoxication by plant secondary metabolites, this is remarkably difficult to show. A long series of field and laboratory experiments means that we have a good understanding of the factors that affect feeding by leaf-eating marsupials. This knowledge and the natural intraspecific variation in Eucalyptus chemistry allowed us to test the hypothesis that the feeding decisions of greater gliders (Petauroides volans) depend on the concentrations of available nitrogen (incorporating total nitrogen, dry matter digestibility and tannins) and of formylated phloroglucinol compounds (FPCs), potent antifeedants unique to Eucalyptus. We offered captive greater gliders foliage from two species of Eucalyptus, E. viminalis and E. melliodora, which vary naturally in their concentrations of available nitrogen and FPCs. We then measured the amount of foliage eaten by each glider and compared this with our laboratory analyses of foliar total nitrogen, available nitrogen and FPCs for each tree offered. The concentration of FPCs was the main factor that determined how much gliders ate of E. viminalis and E. melliodora, but in gliders fed E. viminalis the concentration of available nitrogen was also a significant influence. In other words, greater gliders ate E. viminalis leaves with a particular combination of FPCs and available nitrogen that maximised the nutritional gain but minimised their ingestion of toxins. In contrast, the concentration of total nitrogen was not correlated with feeding. This study is among the first to empirically show that browsing herbivores select a diet that balances the potential gain (available nutrients) and the potential costs (plant secondary chemicals) of eating leaves. The major implication of the study is that it is essential to identify the limiting nutrients and relevant toxins in a system in order to understand feeding behaviour.