The maize genome as a model for efficient sequence analysis of large plant genomes

The genomes of flowering plants vary in size from about 0.1 to over 100 gigabase pairs (Gbp), mostly because of polyploidy and variation in the abundance of repetitive elements in intergenic regions. High-quality sequences of the relatively small genomes of Arabidopsis (0.14 Gbp) and rice (0.4 Gbp) have now been largely completed. The sequencing of plant genomes that have a more representative size (the mean for flowering plant genomes is 5.6 Gbp) has been seen as a daunting task, partly because of their size and partly because of the numerous highly conserved repeats. Nevertheless, creative strategies and powerful new tools have been generated recently in the plant genetics community, so that sequencing large plant genomes is now a realistic possibility. Maize (2.4-2.7 Gbp) will be the first gigabase-size plant genome to be sequenced using these novel approaches. Pilot studies on maize indicate that the new gene-enrichment, gene-finishing and gene-orientation technologies are efficient, robust and comprehensive. These strategies will succeed in sequencing the gene-space of large genome plants, and in locating all of these genes and adjacent sequences on the genetic and physical maps.     

The effects of sloped surfaces on locomotion: an electromyographic analysis

Investigations using quadrupeds have suggested that the motor programs used for slope walking differ from that used for level walking. This idea has not yet been explored in humans. The aim of this study was to use electromyographic (EMG) signals obtained during level and slope walking to complement previously published joint angle and joint moment data in elucidating such control strategies. Nine healthy volunteers walked on an instrumented ramp at each of five grades (-39%, -15%, 0%, +15%, +39%). EMG activity was recorded unilaterally from eight lower limb muscles (gluteus maximus (GM), rectus femoris (RF), vastus medialis (VM), biceps femoris (BF), semimembranosus (SM), soleus (Sol), medial gastrocnemius (MG), and tibialis anterior (TA)). The burst onset, duration, and mean activity were calculated for each burst in every trial. The burst characteristics were then averaged within each grade and subject and submitted to repeated measures ANOVAs to assess the effect of grade (alpha=0.05, a priori). Power production increased during upslope walking, as did the mean activity and burst durations of most muscles. In this case, the changes in muscle activity patterns were not predictable based on the changes in joint moments because of the activation of biarticular muscles as antagonists. During downslope walking power absorption increased, as did knee extensor activity (mean and duration) and the duration of the ankle plantarflexor activity. The changes in muscle activity during this task were directly related to the changes in joint moments. Collectively these data suggest that the nervous system uses different control strategies to successfully locomote on slopes, and that joint power requirements are an important factor in determining these control strategies.     

Time of feeding and possible associated thermoregulatory benefits in bronze mannikins Lonchura cucullata

Birds with a small body size have a high surface area to volume ratio, and this means that they have a high rate of heat loss to the environment. Birds may employ behavioural strategies in order to counter this heat loss. The adjustment of feeding patterns in the short term is probably the least documented of all of these strategies. Feeding results in the specific dynamic effect (SDE) which increases the metabolic rate of animals after a feeding bout. This increase in metabolic rate has been reported to possibly substitute for thermoregulatory costs in a variety of endotherms, including house wrens (Troglodytes aedon) and a variety of finch species. The thermoneutral zone was described for bronze mannikins, Lonchura cucullata (T(lc)=33.7 degrees C), and the bronze mannikins' post-absorptive physiology was described within this thermoneutral zone. Bronze mannikin mean basal metabolic rate (0.043+/-0.0038 S.E. ml O(2) min(-1) g(-1)), daytime resting metabolic rates (0.0549+/-0.0088 S.E. ml O(2) min(-1) g(-1)), and diurnal metabolic responses were described. The SDE in bronze mannikins was demonstrated within the thermoneutral zone, and was quantified. The mean magnitude of the SDE was 26.42% of mean total metabolism of post-absorptive birds. The magnitude of this SDE was independent of meal size and bird body mass. Assuming a 100% substitution, the presence of the SDE may afford bronze mannikins a maximum thermoregulatory energy saving of approximately 71.76 J g(-1) over a 300-min period.     

Characterization of HPV-16 E6 DNA vaccines employing intracellular targeting and intercellular spreading strategies

Summary Human papillomavirus (HPV) E6 and E7 are consistently expressed and are responsible for the malignant transformation of HPV-associated lesions. Thus, E6 and E7 represent ideal targets for therapeutic HPV vaccine development. We have previously used the gene gun approach to test several intracellular targeting and intercellular spreading strategies targeting HPV-16 E7. These strategies include the use of the sorting signal of lysosome-associated membrane protein (LAMP-1), Mycobacterium tuberculosis heat shock protein 70 (HSP70), calreticulin (CRT) and herpes simplex virus type 1 (HSV-1) VP22 proteins. All of these strategies have been shown to be capable of enhancing E7-DNA vaccine potency. In the current study, we have characterized DNA vaccines employing these intracellular targeting or intercellular spreading strategies targeting HPV-16 E6 for their ability to generate E6-specific CD8⁺ T cell immune responses and antitumor effects against an E6-expressing tumor cell line, TC-1, in C57BL/6 mice. We found that all the intracellular targeting strategies (CRT, LAMP-1, HSP70) as well as the intercellular spreading strategy (VP22) were able to enhance E6 DNA vaccine potency, although the orientation of HSP70 linked to E6 antigen in the E6 DNA vaccine appears to be important for the HSP70 strategy to work. The enhanced E6-specific CD8⁺ T cell immune response in vaccinated mice also translated into potent antitumor effects against TC-1 tumor cells. Our data indicate that all of the intracellular targeting and intercellular spreading strategies that have been shown to enhance E7 DNA vaccine potency were also able to enhance E6 DNA vaccine potency.     

History and Future of Introduction of Exotic Arthropod Biological Control Agents in Spain: A Dilemma?

The first documented introduction of an exotic invertebrate biological control agent (IBCA) in Spain occurred in 1908. Sixty-four additional species have been introduced since then. Information, both previously recorded and original data, on the species introduced for pest control is summarized. Most of the introduced IBCAs focused on citrus pests and homopterans clearly predominate among target phytophagous species. Success has been more frequent for IBCAs used in seasonal inoculative strategies (50.0% of cases) than in classical biological control programs (17.1% of cases). Concerns about potential non-target effects of such species are increasing, but post-release evaluation has often been insufficient to draw any conclusions about them. Most of the beneficial species introduced in Spain were parasitoids (n = 53), and the remaining species were predators (n = 12). Only four parasitoids are considered specialized monophagous natural enemies. The mean number of host species parasitized by parasitoids is 15.2, whereas the mean number of prey species attacked by predators is 21.2. Therefore, polyphagy appears to be quite common among the IBCAs that have been introduced in Spain. The rationale guiding many of these introductions in the past would not be acceptable nowadays. Since classical biological control is such a valuable strategy for pest control, straightforward protocols to evaluate exotic candidate species are urgently needed.     

克服腺病毒载体介导免疫应答的新策略:关闭淋巴细胞反应

近年来随着分子免疫学的迅速发展,人们对于自身免疫耐受机制以及病毒逃逸免疫应答的策略有了较多的认识。基于这些研究,多种抵抗腺病毒载体介导免疫反应的新策略正在被探讨之中。这些策略包括:1口服或胸腺内应用腺病毒载体或其抽提物;2应用CTLA4Ig可溶性分子或其表达载体;3开发修饰腺病毒载体。所有这些策略其最终机制都在于特异性地阻止或中断针对腺病毒载体的T淋巴细胞反应。     

Retake the center stage--new development of rat genetics

The rat is a powerful model for the study of human physiology and diseases,and is preferred by physiologists,neuroscientists and toxicologists.However,the lack of robust genetic modification tools has severely limited the generation of rat genetic models over the last two decades.In the last few years,several gene-targeting strategies have been developed in rats using N-ethyl-N-nitrosourea(ENU), transposons,zinc-finger nucleases(ZFNs),bacterial artificial chromosome(BAC) mediated transgenesis,and recently established rat embryonic stem(ES) cells.The development and improvement of these approaches to genetic manipulation have created a bright future for the use of genetic rat models in investigations of gene function and human diseases.Here,we summarize the strategies used for rat genetic manipulation in current research.We also discuss BAC transgenesis as a potential tool in rat transgenic models.     

Foraging strategies are related to skull morphology and life history traits of Melanerpes woodpeckers

Links between morphology and foraging strategies have been well established for many vertebrate groups. Foraging strategies of Melanerpes woodpeckers are especially variable, with at least six species being proficient flycatchers; the remainder of the better known species do not flycatch. Our objective was to examine variation in foraging tactics as it relates to skull morphology and other life history traits among these species to better understand the biology of these diverse woodpeckers. We measured eight skull characters from 241 individuals representing 19 species, but focused on eight species for which we had the most data. We used the log-geometric mean and a principal components analysis (PCA) to calculate size-scaled shape variables. Cluster analysis based on PCA scores clearly separated birds by foraging behavior. Species with similar foraging behaviors (i.e., flycatchers vs non-flycatchers) also share a number of other life history characteristics including similar plumage, diets, and migratory behavior. Diversity within Melanerpes may imply a high degree of plasticity or that species have been incorrectly placed in a polyphyletic group. Woodpeckers currently in the genus Melanerpes share few uniting characters and historically have been placed in as many as eight different genera. Additional life history, morphological, and genetic studies of the group, especially of Caribbean and Neotropical species, is warranted.     

利用微卫星标记分析我国13个地方灰羽鹅品种的遗传多样性

我国地方鹅品种具有很多优良性状,但长期以来由于没有形成科学的选育制度和培育方法,品种的遗传多样性没有得到完整保存。为了深入了解我国地方鹅品种的遗传结构,使之得到更好的保护和利用,作者选用31个多态性较高的微卫星标记(其中19个是首次用磁珠富集法从AFLP片段中分离),检测了我国13个地方灰羽鹅(An-sercygnnoides)品种的遗传多样性。利用等位基因频率计算出各群体的平均遗传杂合度(H)、多态信息含量(PIC)和群体间的遗传距离(DA)。结果表明:13个地方灰羽鹅品种中,平均多态信息含量为0.323–0.398,平均杂合度为0.4985–0.6727,各品种的杂合度都较高,最高的是狮头鹅(0.6727),最低的是雁鹅(0.4985)。用UPGMA法进行聚类分析的结果显示,13个品种被聚为4类:丰城灰鹅、武冈铜鹅、兴国灰鹅、狮头鹅、乌棕鹅、阳江鹅、马冈鹅、钢鹅、雁鹅聚为第1类;伊犁鹅自聚为第2类;长乐鹅、右江鹅聚为第3类;永康灰鹅自聚为第4类。本研究为鹅遗传育种提供了参考资料。     

The design and implementation of insect resistance management programs for Bt crops

Cotton and corn plants with insect resistance traits introduced through biotechnological methods and derived from the bacterium Bacillus thuringiensis (Bt) have been widely adopted since they were first introduced in 1996. Because of concerns about resistance evolving to these Bt crops, they have been released with associated IRM programs that employ multiple components and reflect the input of academic, industrial and regulatory experts. This paper summarizes the current status of Bt crop technologies in cotton and corn, the principles of IRM for Bt crops and what they mean for the design of IRM programs. It describes how these IRM programs have been implemented and some of the key factors affecting successful implementation. Finally, it suggests how they may evolve to properly steward these traits in different geographies around the world. The limited number of reported cases of resistance after more than 15 years of intensive global use of Bt crops suggest that this exercise has been broadly successful. Where resistance issues have been observed, they have been associated with first generation technologies and incomplete or compromised IRM programs (i.e., inadequate structured refuge). Next generation technologies with multiple pyramided modes of action, together with the implementation of IRM strategies that are more dependent upon manufacturing and less dependent upon grower behavior, such as seed mixes, should further enhance IRM programs for Bt crops.     

植物中活性氧的产生及清除机制

环境胁迫使植物细胞中积累大量的活性氧,从而导致蛋白质、膜脂、DNA及其它细胞组分的严重损伤。植物体内有效清除活性氧的保护机制分为酶促和非酶促两类。酶促脱毒系统包括超氧化物歧化酶(SOD)、抗坏血酸过氧化物酶(APX)、过氧化氢酶(CAT)和谷胱甘肽过氧化物酶(GPX)等。非酶类抗氧化剂包括抗坏血酸、谷胱甘肽、甘露醇和类黄酮。利用基因工程策略增加这些物质在植物体内的含量,从而获得耐逆转基因植物已取得一定的进展。     

Effects of Pharmacological Concentrations of Dietary Zinc Oxide on Growth of Post-weaning Pigs: A Meta-analysis

Pharmacological dietary zinc (Zn) concentrations of 1,000 to 3,000 mg/kg diet from Zn oxide have been found to increase growth in post-weaning pigs. However, results were inconsistent among studies. A frequentist meta-analysis, in which effects were numerically described with standardized effect sizes (Hedges's g), was conducted in order to identify and quantify the responses in average daily gain (ADG), average daily feed intake (ADFI), and gain to feed ratio (G/F) in post-weaning pigs upon dietary Zn supplementation from Zn oxide. The inability of independent continuous variables to explain significant heterogeneity obtained with fixed effect models necessitated the use of random effects models to calculate summary statistics. Dietary Zn supplementation increased (P?<?0.05) ADG (mean effect size?=?1.086, 95 % confidence intervals?=?0.905–1.266, 26 studies, 72 comparisons), ADFI (mean effect size?=?0.794, 95 % confidence intervals?=?0.616–0.971, 25 studies, 71 comparisons), and G/F (mean effect size?=?0.566, 95 % confidence intervals?=?0.422–0.710, 24 studies, 70 comparisons). Zinc oxide provided a feasible alternative to in-feed antibiotics to improve growth in post-weaning pigs, and its reduction in diets due to potential environmental pollution will have to be negated by alternative feed additives and management strategies in order to prevent economic losses.     

An immunomodulation strategy targeted towards immunocompetent cells or cytokines in inflammatory bowel diseases (IBD)

Many immunological abnormalities have been described in inflammatory bowel diseases (IBD). Even though, no clear cut primary defects have yet been described, some therapeutic trials have targeted either immunocompetent cells or overproduction of cytokines. Preliminary results have shown that antisense oligonucleotides (anti-ICAM), anti-cytokine antibodies (anti-TNF) or recombinant human cytokines (IL-10 or IL-11) are effective in some patients with Crohn's disease refractory to steroids. However, these data need to be confirmed and the potential side effects of these treatments must be further considered. These drugs need to be more precisely defined in particular compared to corticotherapy. Finally, data from immunomodulation strategies should help us understand the aetiology of abnormal immune responses in Crohn's disease (CD) and ulcerative colitis (UC).     

超氧化物歧化酶(SOD)研究进展

环境胁迫使植物细胞中积累大量的活性氧,从而导致蛋白质、膜脂、DNA及其它细胞组分的严重损伤。植物体内有效清除活性氧的酶类包括超氧化物歧化酶(SOD)、抗坏血酸过氧化物酶(APX)、过氧化氢酶(CAT)等,其中研究最深入的是SOD。利用基因工程策略增加这些物质在植物体内的含量,从而获得抗逆转基因植株。     

Evaluation of different sources of DNA for use in genome wide studies and forensic application

In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA™ cards. However, using unamplified–degraded genomic DNA reduced the call rate to a mean of 42.6% compared to amplified DNA extracted from FTA card (mean of 96.6%). This study establishes the utility of FTA™ cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.     

Dynamic flexibility metrics for capability and capacity

In production environments, such as Flexible Manufacturing Systems (FMSs), the schedule can be disturbed by the occurrence of unplanned events. Machines stop for major failures, maintenance, tool changes due to wear, or tool reassignments. The rescheduling process, however, can be costly. In this study, a dynamic measure of flexibility which helps to determine an appropriate time for rescheduling an FMS has been defined and investigated. Flexibility is defined as a function of Capability and Capacity. Accordingly, two metrics have been developed to monitor the capability and capacity efficiency of each machine in the system for responding to the dynamic system status. The value of each metric falls between 0 and 1 at all times. Higher values in the capability metric mean better machine selection and part distribution strategies among the machines. Higher values for the capacity metric mean higher machine utilization in the production plan. Based on the interaction between the metrics and their respective behavior in the system, four states have been identified and characterized. Simulations of various scenarios can be used to demonstrate the use of these metrics for monitoring FMS operations and determining appropriate times for rescheduling and tool reassignment.     

Breeding Systems of Three Tree Ferns: Alsophila firma (Cyatheaceae), Cyathea stipularis (Cyatheaceae), and Lophosoria quadripinnata (Lophosoriaceae)

Abstract Breeding-system data have been available for a large number and diverse array of angio-sperms for a relatively long time. In contrast, breeding systems of ferns and their allies (pteridophytes) have only recently been examined, and breeding-system data from natural populations of sporophytes are still lacking for pteridophytes representing many life-history strategies. Few studies, for example, have examined breeding systems of tropical pteridophytes, and no breeding-system data are available for tree ferns. We therefore examined the breeding systems of three species of tree ferns from Costa Rica, Alsophila firma (Cyatheaceae), Cyathea stipularis (Cyatheaceae), and Lophosoria quadripinnata (Lophosoriaceae) using enzyme electro-phoresis. Genetic data were used to estimate intragametophytic self-fertilization and F , the fixation index. Analysis of genetic data indicates that the gametophytes of these three species predominantly cross-fertilize; all three species would be characterized as outcrossers. However, some population-to-population variation in breeding system was detected in all three species. Outcrossing also typifies a diverse array of temperate ferns. Thus, despite the potential for self-fertilization, outcrossing appears to characterize the majority of pteridophytes representing a variety of evolutionary lineages, life-history strategies, and environments.     

Behavioral,Ecological and Genetic Differentiation in an Open Environment—A Study of a Mysid Population in the Baltic Sea

Diel vertical migration (DVM) is often assumed to encompass an entire population. However, bimodal nighttime vertical distributions have been observed in various taxa. Mysid shrimp populations also display this pattern with one group concentrated in the pelagia and the other near the bottom. This may indicate alternative migratory strategies, resembling the seasonal partial migrations seen in birds, fishes and amphibians, where only a subset of the population migrates. To assess the persistence of these alternative strategies, we analyzed the nitrogen and carbon stable isotope signatures (as proxies for diet), biochemical indices (as proxies for growth condition), and genetic population divergence in the Baltic mysid Mysis salemaai collected at night in the pelagia and close to the bottom. Stable isotope signatures were significantly different between migrants (pelagic samples) and residents (benthic samples), indicating persistent diet differences, with pelagic mysids having a more uniform and carnivorous diet. Sequencing of the mitochondrial cytochrome subunit I (COI) gene showed genetic differentiation attributable to geographic location but not between benthic and pelagic groups. Divergent migration strategies were however supported by significantly lower gene flow between benthic populations indicating that these groups have a lower predisposition for horizontal migrations compared to pelagic ones. Different migration strategies did not convey measurable growth benefits as pelagic and benthic mysids had similar growth condition indices. Thus, the combination of ecological, biochemical and genetic markers indicate that this partial migration may be a plastic behavioral trait that yields equal growth benefits.     

Isolation and characterization of microsatellite markers from the acacia-ant Crematogaster mimosae

We describe 10 microsatellite loci developed from Crematogaster mimosae, an ant species that nests mutualistically in Acacia drepanolobium trees in east Africa. Polymorphism ranged from 4 to 16 alleles per locus (mean = 7.3). Observed and expected heterozygosities ranged from 0.485 to 0.813 (mean 0.626), and from 0.502 to 0.894 (mean 0.674), respectively. These markers will foster studies of the population structure, colony structure, and reproductive strategies of these ants.