Plant systems biology comes of age

'Omics' research approaches have produced copious data for living systems, which have necessitated the development of systems biology to integrate multidimensional biological information into networks and models. Applications of systems biology to plant science have been rapid, and have increased our knowledge about circadian rhythms, multigenic traits, stress responses and plant defenses, and have advanced the virtual plant project.     

Biomass estimation of orange roughy: a summary and evaluation of techniques for measuring stock size of a deep-water fish species in New Zealand

A number of techniques have been employed to measure biomass of orange roughy in New Zealand. Time series of stratified random trawl surveys in a number of areas over periods of 5–10 years have given relative abundance indices, which have been used in stock reduction analyses to estimate true biomass. This has given confident results for the Chatham Rise stock, and surveys have also shown strong trends in other regions. Acoustic surveys have been carried out on three grounds. They can give relative indices of orange roughy abundance in areas of fiat or medium sloping bottom, and have the potential for estimation of absolute biomass from a single survey. Egg production surveys have been employed on two grounds on the east coast of the North Island, where conditions of tight spawning aggregations and steep bottom topography have limited the success of other methods. Both daily fecundity reduction and annual egg production methods have been used. These have given estimates of true biomass from one-off surveys, although results are imprecise. Both unstandardized and standardized analyses of commercial catch-per-unit-effort data have given relative indices of abundance, which have formed an important part of stock assessment for several fisheries. No single technique used to measure the size of orange roughy stocks has proven ideal or appropriate in all New Zealand situations. All have advantages and disadvantages, depending on the characteristics of the fishing area and fish behaviour. For two areas, a combination of methods have been applied, which has given more confident results than those from a single technique.     

基因药物的前沿技术

基因药物的直接体内基因治疗发展迅速,新型基因药物不断产生。本文讨论了效果比较肯定的基因疫苗、反义ＲＮＡ药物、三链ＤＮＡ药物这三种新型基因药物技术的基本方法。分析了它们各自存在的优点和问题,并介绍了它们的应用范围及应用研究进展。     

Genome evolution of allopolyploids: a process of cytological and genetic diploidization

Allopolyploidy is a prominent mode of speciation in higher plants. Due to the coexistence of closely related genomes, a successful allopolyploid must have the ability to invoke and maintain diploid-like behavior, both cytologically and genetically. Recent studies on natural and synthetic allopolyploids have raised many discrepancies. Most species have displayed non-Mendelian behavior in the allopolyploids, but others have not. Some species have demonstrated rapid genome changes following allopolyploid formation, while others have conserved progenitor genomes. Some have displayed directed, non-random genome changes, whereas others have shown random changes. Some of the genomic changes have appeared in the F1 hybrids, which have been attributed to the union of gametes from different progenitors, while other changes have occurred during or after genome doubling. Although these observations provide significant novel insights into the evolution of allopolyploids, the overall mechanisms of the event are still elusive. It appears that both genetic and epigenetic operations are involved in the diploidization process of allopolyploids. Overall, genetic and epigenetic variations are often associated with the activities of repetitive sequences and transposon elements. Specifically, genomic sequence elimination and chromosome rearrangement are probably the major forces guiding cytological diploidization. Gene non-functionalization, sub-functionalization, neo-functionalization, as well as other kinds of epigenetic modifications, are likely the leading factors promoting genetic diploidization.     

《西北植物学报》2004～2006年载文来源基本信息分析

对《西北植物学报》2004~2006年载文来源基本信息进行统计分析,表明《西北植物学报》自2004年以来,投稿量逐年增加,稿源的地区分布范围进一步扩大,所载论文第一作者具有硕士以上学位的达55%,具有副高以上职称的占30.8%,40岁以下作者占76.4%,刊发论文的作者合作率达97%,论文项目的机构协作率达57%,基金论文达91%,学报影响因子逐年提高,2006年达到0.863.说明《西北植物学报》影响范围不断扩大,载文的作者具有较深厚的学术研究底蕴和较高的研究水平,论文能及时而真实地反映我国植物学领域的研究前沿动态和研究水平,载文的学术水平和影响力得到进一步提升.     

Colorectal carcinoma antigens detected by hybridoma antibodies.

Hybridoma cells which secrete colorectal carcinoma-specific antibodies have been produced and used to study the antigenic structure of these tumor cells. Nineteen antibodies have been studied in detail, and 15 of these are colorectal carcinoma specific. Only two antibodies reactive with carcinoembryonic antigen (CEA) have been discovered and five other antibodies that react with distinct epitopes on the cell surface have been defined. Several antigens with distinct molecular characteristics have been shown to exist by use of hybridoma antibodies. Six hybridoma antibodies have been shown to mediate antibody-dependent cell-mediated cytotoxicity (ADCC).     

Phage display in pharmaceutical biotechnology

Over the past year, methods for the construction of M13 phage-display libraries have been significantly improved and new display formats have been developed. Phage-displayed peptide libraries have been used to isolate specific ligands for numerous protein targets. New phage antibody libraries have further expanded the practical applications of the technology and phage cDNA libraries have proven useful in defining natural binding interactions. In addition, phage-display methods have been developed for the rapid determination of binding energetics at protein-protein interfaces.     

Host defense mechanisms of cephalopods

Humoral and cellular mechanisms of defense have been described for cephalopods, a relatively advanced group of mollusks. Typical of other mollusks, cephalopod agglutinins are the most documented component of humoral immunity. Lectins, which have agglutinating properties, have been described and characterized from octopuses. Agglutinins from cephalopod hemolymph have also been shown to agglutinate a variety of vertebrate red blood cells, as well as potential bacterial pathogens. Hemocytes are the primary component of cellular immunity. Although the hemocyte role in phagocytosis has been extensively studied in other mollusks, the mechanisms of phagocytosis have not been described extensively for cephalopods. Cephalopod hemocytes have phagocytic capabilities and may function in encapsulation and neutralization of foreign substances; however, the effects of environmental factors and the full extent of phagocytic capabilities of cephalopod hemocytes have not been reported. Hemocytes from cephalopods have a role in wound healing and inflammation which have been reported in detail by several investigators.     

Optical fiber-based sensors: application to chemical biology

Optical fibers have been used to develop sensors based on nucleic acids and cells. Sensors employing DNA probes have been developed for various genomics applications and microbial pathogen detection. Live cell-based sensors have enabled the monitoring of environmental toxins, and have been used for fundamental studies on populations of individual cells. Both single-core optical fiber sensors and optical fiber sensor arrays have been used for sensing based on nucleic acids and live cells.     

Expanded-capacity adenoviral vectors--the helper-dependent vectors

Significant advances have recently been made in the development of vectors and gene-delivery systems for gene therapy. Experiments performed over the past decade have revealed how vectors will have to be modified to make them a clinically viable treatment option. In the case of adenovirus (Ad) vectors, which have been particularly useful as gene delivery vehicles, the main drawback associated with their use is vector-mediated immunogenicity. Recent modifications of the Ad backbone have led to the development of helper-dependent (HD) Ad vectors, which are completely devoid of all viral protein-coding sequences. These modifications have significantly reduced the immunogenicity of Ad vectors and have enhanced their safety. It is expected that HD vectors will become important tools for future clinical gene therapy.     

Biodiversity among haptophyte algae

The division Haptophyta is represented only by about 300 extant species showing wide diversity in morphology, biochemistry and ecology. They have a world-wide distribution and are numerically important in phytoplankton populations in nearly all marine environments. Evidence from the geological record shows that they have been the major constituent of calcareous deposits since the Late Triassic and, as they have evolved quickly through time, their coccoliths have always shown wide morphological diversity. In today's oceans they occasionally produce extensive blooms, visible by satellite imagery, which have ecological impact. As a consequence of these blooms the haptophyte algae are now receiving greater attention, as their role in the global sulphur and carbon cycles may influence the world's climate, and their potential as nuisance bloom algae have implications for commercial fishing and the marine ecosystem. As it is likely that these organisms have always produced such blooms, these effects may have been in operation for the last 200 million years.     

Means and extremes: building variability into community‐level climate change experiments

Experimental studies assessing climatic effects on ecological communities have typically applied static warming treatments. Although these studies have been informative, they have usually failed to incorporate either current or predicted future, patterns of variability. Future climates are likely to include extreme events which have greater impacts on ecological systems than changes in means alone. Here, we review the studies which have used experiments to assess impacts of temperature on marine, freshwater and terrestrial communities, and classify them into a set of ‘generations’ based on how they incorporate variability. The majority of studies have failed to incorporate extreme events. In terrestrial ecosystems in particular, experimental treatments have reduced temperature variability, when most climate models predict increased variability. Marine studies have tended to not concentrate on changes in variability, likely in part because the thermal mass of oceans will moderate variation. In freshwaters, climate change experiments have a much shorter history than in the other ecosystems, and have tended to take a relatively simple approach. We propose a new ‘generation’ of climate change experiments using down‐scaled climate models which incorporate predicted changes in climatic variability, and describe a process for generating data which can be applied as experimental climate change treatments.     

Proteomic analysis of mitochondria from the Bos taurus heart. III. Identification of mitochondrial inner memrane proteins

We have conducted a research of mitochindrial internal membrane proteins. This fraction has been received in the form of submitochondrial particles (SMP). SMP have been processed by trypsinum, and the received peptides have been separated from so-called "smoothfaced vesicles". "Smoothfaced vesicles" were blasted, proteinse and peptides were processed by cyanogen bromide and trypsinum. We have received two groups of tryptic peptides and analyzed them separately with the help of proteomic methods, such as chromatography, mass spectrometry and protein identification in different databases. To identify more proteins and find minor components of mitochindrial proteome we have considered possible non-specific fragmentation of proteins. 298 proteins have been identified, we also have conducted the analisys of their functions and cell localization.     

Divergence of tRNA genes in chloroplast DNA of higher plants

The saturation hybridization between spinach chloroplast (ct) DNA and spinach ¹²⁵I-labelled chloroplast tRNA has shown that about 1.1% of the spinach ctDNA codes for tRNAs. The observed hybridization is a result of specific base-pairing as shown by competition hybridization experiments and thermal stability of the ctDNA-tRNA hybrids. The amount of hybridization shows that spinach ctDNA contains about 40 tRNA genes. Similar hybridization studies have shown that corn ctDNA contains about 28 tRNA genes. The cross-hybridizations between ctDNA and tRNAs of corn, spinach and pea have shown that tRNAs in chloroplasts of higher plants have undergone significant divergence. The pea and spinach tRNAs have been found to have 50% of the base sequences in common. The corn tRNAs have been found to have only about 30% of the base sequences in common with pea and spinach. These data have been confirmed by extensive heterologous competition experiments and thermal stability of the heterologous DNA-tRNA hybrids. The experiments have also shown that the base sequences of tRNAs common in all three plants are the same.     

小肠结肠炎耶尔耶尔森氏菌血清群的研究：Ⅱ.我国小肠...

Since 1980, we have collected 1120 strains of Yersinia enterocolitica, from the different parts of China. These strains have been obtained from various sources in man, animals and natural environment accompanied by their clinical or ecological information of Yersinia enterocolitica. The results of our tests have shown that the 747 strains have exhibited the clinical morphological and biochemical characteristics of Yersinia enterocolitica. Through comparing under the same conditions, out of the 747 strains 335 have been selected out with better antigenicity and have been produced antisera from their representative strains. This set of antisera is very satisfactory for its potency and specificity. This set of antisera is ready to supply and have good efficacy and application facilitated for control strains on identifying strains and their epidemiologic observation.     

Comparing G matrices: are common principal components informative?

Common principal components (CPC) analysis is a technique for assessing whether variance-covariance matrices from different populations have similar structure. One potential application is to compare additive genetic variance-covariance matrices, G. In this article, the conditions under which G matrices are expected to have common PCs are derived for a two-locus, two-allele model and the model of constrained pleiotropy. The theory demonstrates that whether G matrices are expected to have common PCs is largely determined by whether pleiotropic effects have a modular organization. If two (or more) populations have modules and these modules have the same direction, the G matrices have a common PC, regardless of allele frequencies. In the absence of modules, common PCs exist only for very restricted combinations of allele frequencies. Together, these two results imply that, when populations are evolving, common PCs are expected only when the populations have modules in common. These results have two implications: (1) In general, G matrices will not have common PCs, and (2) when they do, these PCs indicate common modular organization. The interpretation of common PCs identified for estimates of G matrices is discussed in light of these results.     

Are extrafloral nectaries efficient against herbivores? Herbivory and plant defenses in contrasting tropical species

植物用于防御的资源有限，而那些具有生物防御的物种，其叶片可能会较少地用于其他类型的防御。我们比较了机械防御能力较弱，但具有花外蜜腺的植物，与没有花外蜜腺但叶片更有韧性的植物是否更不容易被取食。我们通过分析文献数据，调查有无花外蜜腺的植物被取食的情况。在巴西南部的热带稀树草原植被中，我们采集了6种热带植物的叶片数据，并测定了被取食情况和比叶面积。我们进一步评估了有无花外蜜腺的物种之间以及植物之间被取食情况和比叶面积的差异。为了检验动物取食与叶片韧性之间的关系，我们对单株平均被取食情况和平均叶片韧性进行了回归。研究结果表明，植物表现出不同程度的叶片损伤，但没有蚂蚁防御的植物因被取食造成的叶面积损失最大。不同植物的机械防御水平也不相同。无花外蜜腺的植株更坚韧，比叶面积值更小。虽然无花外蜜腺的植物有更多的坚硬叶片，但这种机械防御不足以损害和/或减少食草动物的取食，这表明由蚂蚁形成的生物防御可能比用于与叶片适口性相关的机械防御更有效。     

Cyclooxygenase enzymes: catalysis and inhibition

Scientists working in the field of cyclooxygenase enzymes have witnessed several major advances in the past two years. Crystal structures of fatty acid substrate and prostaglandin product complexes have been elucidated. Elegant site-directed mutagenesis studies have pinpointed the roles of key amino acids within the active site. Together, these results have provided key insights into the overall reaction mechanism. Detailed kinetics, spectroscopic and crystallographic studies have shed new light on the complex mechanism of inhibition of these fascinating enzymes. Finally, novel substrates of cyclooxygenase-2 have been identified.     

Protein redesign.

It has been demonstrated that, for a number of proteins, it is possible to dramatically alter the connectivities between elements of secondary structure. Remarkably large loop insertions are tolerated and many redesigns have generated proteins that successfully fold to stable, active structures. Some redesigns have been entirely the choice of the investigators, whereas others have incorporated a randomization and selection step to identify optimal sequences. These studies have provided basic guidelines for the rational manipulation of protein structure and stability, they have allowed the dissection of folding pathways and they have generated proteins with the potential for practical therapeutic applications.