Dietary practices,site-specific tumors,and age-at-death relationships

When rats are given freedom of dietary choice, the quantity and composition of the diet selected varies from animal to animal, but the risk to the individual of developing a variety of neoplasms is greatly increased over that of rats fed fixed diets. The increase in frequency of tumors cannot be explained on the basis of the amount or the composition of the diet selected. However, the application of “variable selection” statistical procedures shows that there are combinations of temporal-specific interacting dietary and dietary-dependent variables that are closely linked with cancer mortality. The multi-variable statistical model for animals dying with one type of tumor is not applicable to those dying with tumors of other types or sites. In every case, the only data required to characterize the dates of death of tumor-bearing individuals are those describing the dietary practices and growth responses prior to maturity. The model for animals with pancreatic tumors is used to illustrate the extent to which dietary practices of early life are linked with the animals’ survival.     

Novel approach to engineer strains for simultaneous sugar utilization

Use of lignocellulosic biomass as a second generation feedstock in the biofuels industry is a pressing challenge. Among other difficulties in using lignocellulosic biomass, one major challenge is the optimal utilization of both 6-carbon (glucose) and 5-carbon (xylose) sugars by industrial microorganisms. Most industrial microorganisms preferentially utilize glucose over xylose owing to the regulatory phenomenon of carbon catabolite repression (CCR). Microorganisms that can co-utilize glucose and xylose are of considerable interest to the biofuels industry due to their ability to simplify the fermentation processes. However, elimination of CCR in microorganisms is challenging due to the multiple coordinating mechanisms involved. We report a novel algorithm, SIMUP, which finds metabolic engineering strategies to force co-utilization of two sugars, without targeting the regulatory pathways of CCR. Mutants of Escherichia coli based on SIMUP algorithm showed predicted growth phenotypes and co-utilized glucose and xylose; however, consumed the sugars slower than the wild-type. Some solutions identified by the algorithm were based on stoichiometric imbalance and were not obvious from the metabolic network topology. Furthermore, sequencing studies on the genes involved in CCR showed that the mechanism for co-utilization of the sugars could be different from previously known mechanisms.     

Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production

Genetically modified Saccharomyces cerevisiae strain (YPB-G) which secretes a bifunctional fusion protein that contains both Bacillus subtilis -amylase and Aspergillus awamori glucoamylase activities was used for the direct conversion of starch into ethanol. Starch was either supplied initially to different nutrient media or added instantaneously to the reactor at various discrete time instants (pulse feeding). Stoichiometric modeling was used to investigate the effects of initial substrate concentration and growth rate of the recombinant yeast culture on ethanol production. Reaction stoichiometries describing both the anabolism and catabolism of the microorganism were used as an input to flux balance analysis (FBA), the preferred metabolic modeling approach since the constructed stoichiometric network was underdetermined. Experiments for batch and fed-batch systems at different substrate concentrations were analyzed theoretically in terms of flux distributions using ethanol production rate as the maximization criteria. Calculated ethanol rates were in agreement with experimental measurements, suggesting that this recombinant microorganism is sufficiently evolved to optimize its ethanol production. The function of the main pathways of yeast metabolism (PPP, EMP, TCA) are discussed together with the node analyses of glucose-6-P and pyruvate branch points. Theoretical node analysis revealed that if the split ratio in G6P branch point is changed by genetic manipulations, the ethanol yield would be affected considerably.     

Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease

Coral reefs are deteriorating at an alarming rate mainly as a consequence of the emergence of coral diseases. The white plague disease (WPD) is the most prevalent coral disease in the southwestern Caribbean, affecting dozens of coral species. However, the identification of a single causal agent has proved problematic. This suggests more complex etiological scenarios involving alterations in the dynamic interaction between environmental factors, the coral immune system and the symbiotic microbial communities. Here we compare the microbiome of healthy and WPD-affected corals from the two reef-building species Diploria strigosa and Siderastrea siderea collected at the Tayrona National Park in the Caribbean of Colombia. Microbiomes were analyzed by combining culture-dependent methods and pyrosequencing of 16S ribosomal DNA (rDNA) V5-V6 hypervariable regions. A total of 20 410 classifiable 16S rDNA sequences reads were obtained including all samples. No significant differences in operational taxonomic unit diversity were found between healthy and affected tissues; however, a significant increase of Alphaproteobacteria and a concomitant decrease in the Beta- and Gammaproteobacteria was observed in WPD-affected corals of both species. Significant shifts were also observed in the orders Rhizobiales, Caulobacteriales, Burkholderiales, Rhodobacterales, Aleteromonadales and Xanthomonadales, although they were not consistent between the two coral species. These shifts in the microbiome structure of WPD-affected corals suggest a loss of community-mediated growth control mechanisms on bacterial populations specific for each holobiont system.     

海藻糖及其在生物工程方面的应用

自海藻糖发现以来对其化学性质、生理功能、作用机理、代谢途径等已进行了较为深入的研究,其分子生物学的研究也渐渐兴起。研究表明海藻糖能提高生物体对干旱、低温、高温、pH、盐渍等逆境条件下的抗性。离体试验表明海藻糖能保护生物膜、蛋白质的结构并能保持逆境下的酶活性,同时,外源海藻糖同样对生物体有保护作用。由于海藻糖具有这些独特的生物学功能,它已在许多方面得以应用,可作为食品工业的一种添加剂和甜味剂,使干燥食品在得水后保持原有的色、香、味;也可作为医药工业的非特异性生物制品和生化药品保护剂,使其在常温下保存,从而降低运输与储存费用;另外,在农业研究中可利用现代分子生物技术培育表达海藻糖的转基因作物,提高农作物的抗旱、抗冻等抗逆性能。     

代谢基因工程提高作物产量的分子靶标

应用基因工程技术对植物细胞内的代谢途径进行遗传修饰,已成功地使细胞代谢发生改变或合成新的化合物。光合作用,淀粉合成,氮素同化和水分利用等是形成作物产量的基础代谢。对这些代谢途径中的关键步骤和靶分子进行基因修饰以提高作物产量的研究已取得长足的进展,并正在发展成为提高作物产量的新途径。本文着重论述应用代谢基因工程提高作物产量的技术策略,研究现状,存在的问题,所面临的挑战和应用前景。     

Hematopoietic chimerism monitoring based on STRs: quantitative platform performance on sequential samples.

Hematopoietic stem cell transplantation (HSCT) creates a donor-recipient cellular chimerism in the patient, which is quantitatively assayed from peripheral blood based on STR-DNA. Since chimerism values often vary across a patient's samples, it is important to determine to what extent this variability reflects technical aspects of platform performance. This issue is systematically assessed in the current study for the first time. Using the SGM Plus multiplex PCR kit and ABI platform, the longitudinal performance of STR markers was quantitatively evaluated in two chimeric models with true values, and in patient samples (n >500 marker loci). Computation of percent chimerism for each marker, and mean (sample) percent chimerism, standard deviation, and coefficient of variance was performed by our ChimerTrack utility. In chimeric models with known values, individual markers exhibited an accuracy (observed/true) of 88-98%; replication precision was 92-100% true, with a mean error of 2%. Fragment size calling was greater than 99% accurate and precise. Patient results were comparable for markers, relaive to sample means. One source of technical variability in chimerism estimation was allelic differential amplification efficiency. The latter was influenced by signal amplitude, dye label, marker size, and allelic size interval. It can be concluded that long-term chimeric tracking is routinely feasible using this platform in conjunction with ChimerTrack software. Importantly, mean percent chimerism, for any sample, should closely approximate the true chimeric status, with a technical accuracy of 98%. Guidelines are presented for selecting an optimized marker profile.     

从代谢流量分析角度探讨培养条件改变下对放射型根瘤茵WSH2601合成辅酶Q10的影响

分析了放射型根瘤菌(R．radiobacter)WSH2601生物合成辅酶Q10的代谢途径网络,并在溶氧条件改变和培养基中添加玉米浆条件下对辅酶Q10发酵细胞内代谢途径流量变化作定量的分析,结果表明：提高溶氧浓度(20％)5-磷酸核酮糖(RuSP)物流(r7)增加26．6,即糖酵解途径(EMP)途径向磷酸戊糖途径(HMP)转移;添加1％玉米浆r7增加17．2,EMP与HMP途径物流比值与三羧酸循环(TCA)途径物流都下降,而癸异戊烯基焦磷酸(DPP)生成物流通量(绝对值)变化都较小,即辅酶Q10的生物合成更大程度地取决于辅酶Q10生物合成途径中催化DPP的合成和4-羟基苯甲酸(PHB)与DPP的缩合反应的两种关键酶活性。6-磷酸葡萄糖(G6P)节点是辅酶Q10生物合成代谢途径的柔性节点,而丙酮酸节点是半柔性节点。细胞生物量的提高与HMP途径物流增加有关。     

The historical biogeography of co-evolution: emerging infectious diseases are evolutionary accidents waiting to happen

Ecological fitting refers to interspecific associations characterized by ecologically specialized, yet phylogenetically conservative, resource utilization. During periods of biotic expansion, parasites and hosts may disperse from their areas of origin. In conjunction with ecological fitting, this sets the stage for host switching without evolving novel host utilization capabilities. This is the evolutionary basis of emerging infectious diseases (EIDs). Phylogenetic analysis for comparing trees (PACT) is a method developed to delineate both general and unique historically reticulated and non‐reticulated relationships among species and geographical areas, or among parasites and their hosts. PACT is based on ‘Assumption 0’, which states that all species and all hosts in each input phylogeny must be analysed without modification, and the final analysis must be logically consistent with all input data. Assumption 0 will be violated whenever a host or area has a reticulated history with respect to its parasites or species. PACT includes a Duplication Rule, by which hosts or areas are listed for each co‐evolutionary or biogeographical event affecting them, which satisfies Assumption 0 even if there are reticulations. PACT maximizes the search for general patterns by using Ockam's Razor – duplicate only enough to satisfy Assumption 0. PACT applied to the host and geographical distributions of members of two groups of parasitic helminths infecting anthropoid primates indicates a long and continuous association with those hosts. Nonetheless, c. 30% of the host associations are due to host switching. Only one of those involves non‐primate hosts, suggesting that most were constrained by resource requirements that are phylogenetically conservative among primates (ecological fitting). In addition, most of the host switches were associated with episodes of biotic expansion, also as predicted by the ecological fitting view of EIDs.     

硫氧还蛋白与心血管疾病

硫氧还蛋白是细胞内最重要的二硫键还原酶,对维持细胞内蛋白质的还原状态并正常发挥功能着重要的作用,此外。硫氧还蛋白、硫氧还蛋白还原酶和硫氧还蛋白过氧化物酶组成了细胞内最重要的抗氧化系统之一,在对抗细胞的氧化应激上起着重要作用。心血管疾病是威胁人类健康的主要疾病,它与炎症反应和氧化应激有着密切的联系。文章将从硫氧还蛋白的抗氧化、抗炎、抗细胞凋亡,调控与炎症基因表达有关的核转录因子的转录活性,以及调节细胞内蛋白质的亚硝基化等诸多方面阐述硫氧还蛋白在防御心血管疾病方面可能具有的生物学功能。