Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas

Modularization of different functional segments in plasmid vectors eases creation of genetic tools á la carte for Pseudomonas.

     

模拟干旱胁迫下构树和桑树的生理特征比较

在不同浓度聚乙二醇(PEG 6000)的处理下,测定构树和桑树的碳酸酐酶活性、光响应曲线、二氧化碳响应曲线和叶绿素荧光等指标,比较它们的抗干旱能力.结果表明:(1)构树的碳酸酐酶活力变化不显著,而桑树的碳酸酐酶活力不同的PEG 6000浓度间差异较大.(2)构树的净光合速率受PEG 6000的影响较小,而桑树受到抑制较...     

Wheat genomic study for genetic improvement of traits in China

Science China Life Sciences - Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world’s population. Over the past several decades, advances in genomics have led to...     

The genetic control of fumarate hydratase (fumarase) in Drosophila melanogaster

Summary Using electrophoretic variants of fumarase, the genetic locus of this enzyme was determined to be at 1-19.9.     

The emerging role of deubiquitinating enzymes in genomic integrity,diseases, and therapeutics

The addition of mono-ubiquitin or poly-ubiquitin chain to signaling proteins in response to DNA damage signal is thought to be a critical event that facilitates the recognition of DNA damage lesion site, the activation of checkpoint function, termination and checkpoint response and the recruitment of DNA repair proteins. Despite the ubiquitin modifiers, removal of ubiquitin from the functional proteins by the deubiquitinating enzymes (DUBs) plays an important role in orchestrating DNA damage response as well as DNA repair processes. Deregulated ubiquitination and deubiquitination could lead to genome instability that in turn causes tumorigenesis. Recent TCGA study has further revealed the connection between mutations in alteration of DUBs and various types of tumors. In addition, emerging drug design based on DUBs provides a new avenue for anti-cancer therapy. In this review, we will summarize the role of deubiquitination and specificity of DUBs, and highlight the recent discoveries of DUBs in the modulation of ubiquitin-mediated DNA damage response and DNA damage repair. We will furthermore discuss the DUBs involved in the tumorigenesis as well as interception of deubiquitination as a novel strategy for anti-cancer therapy.     

The emerging role of poly(ADP-ribose) polymerase-1 in longevity

In the present paper, the involvement of the family of poly(ADP-ribose) polymerases (PARPs), and especially of PARP-1, in mammalian longevity is reviewed. PARPs catalyse poly(ADP-ribosyl)ation, a covalent post-translational protein modification in eukaryotic cells. PARP-1 and PARP-2 are activated by DNA strand breaks, play a role in DNA base-excision repair (BER) and are survival factors for cells exposed to low doses of ionising radiation or alkylating agents. PARP-1 is the main catalyst of poly(ADP-ribosyl)ation in living cells under conditions of DNA breakage, accounting for about 90% of cellular poly(ADP-ribose). DNA-damage-induced poly(ADP-ribosyl)ation also functions as a negative regulator of DNA damage-induced genomic instability. Cellular poly(ADP-ribosyl)ation capacity in permeabilised mononuclear blood cells (MNC) is positively correlated with life span of mammalian species. Furthermore PARP-1 physically interacts with WRN, the protein deficient in Werner syndrome, a human progeroid disorder, and PARP-1 and WRN functionally cooperate in preventing carcinogenesis in vivo. Some of the other members of the PARP family have also been revealed as important regulators of cellular functions relating to ageing/longevity. In particular, tankyrase-1, tankyrase-2, PARP-2 as well as PARP-1 have been found in association with telomeric DNA and are able to poly(ADP-ribosyl)ate the telomere-binding proteins TRF-1 and TRF-2, thus blocking their DNA-binding activity and controlling telomere extension by telomerase.     

Potential of Haplothrips brevitubus (Karny) (Thysanoptera: Phlaeothripidae) as a predator of mulberry thrips Pseudodendrothrips mori (Niwa) (Thysanoptera: Thripidae)

The predation potential of Haplothrips brevitubus (Karny) for thrips was evaluated in the laboratory. When second stage larvae of Pseudodendrothrips mori (Niwa) were presented to an adult H. brevitubus at densities of 10, 20, 30, and 40 larvae per cage at 25 °C over 24 h, the number of larvae consumed per day increased with an increasing density up to 30. Predation of H. brevitubus exhibited the type II functional response. The mean development time of the egg, larva, and pupa of H. brevitubus were 4.5, 9.6, and 4.8 days, respectively, at 25 °C. The survival rate from egg to adult emergence was 94.7%. One H. brevitubus larva consumed 41.6 P. mori larvae on average during the total larval period. Adult longevity was 35.2 days in females and 34.6 days in males. The pre-oviposition period was 2.7 days and the oviposition period was 31.5 days. The lifetime fecundity was 120.1 eggs and the mean daily oviposition rate was 3.6 eggs. Calculated mean generation time (T) was 29.5 days, intrinsic rate of natural increase (r_m) was 0.162, and net reproductive rate (R₀) was 56.5. The r_m value of H. brevitubus was higher than that of Thrips palmi Karny and almost equal to that of Frankliniella occidentalis (Pergande). These results indicate that H. brevitubus has good potential as a predator of P. mori and is likely to be useful for controlling thrips.     

The population genetic structure of Ctenomys porteousi (Rodentia: Octodontidae)

Several aspects of the population biology and the population genetic structure of Ctenomys porteousi were studied. Chromosomal and allozyme polymorphisms in two local populations separated by 10 km were used to infer genetic structure. Heterochromatic addition/deletion rearrangements for six autosomal pairs were employed as genetic markers. Allozyme variants were analysed by the study of thirty-one presumptive loci. Thirteen loci (43%) were polymorphic, average observed heterozygosity per locus was 10%, and mean number of alleles per locus was 1.57. Chromosomal and allozyme frequencies were homogeneous across populations. The estimated F_st values were very low, 0.009 and 0.022 for chromosomal and allozyme data respectively. Gene flow was indirectly estimated by the method of Wright, Nm values (mean number of migrants per generation per deme) was very high (27.2 and 11.3 for chromosomal and allozyme data respectively). The F_is values suggest a significant defect of heterozygotes that could be explained by the Wahlund effect. The ecological data indicate the occurrence of sharp changes in density and in distribution pattern in short time. The genetic and ecological data suggest that the population structure of C. porteousi differs from that found in other species of Ctenomys affected by chromosomal mechanisms of speciation.     

Changing genetic paradigms: creating next-generation genetic databases as tools to understand the emerging complexities of genotype/phenotype relationships

Understanding genotype/phenotype relationships has become more complicated as increasing amounts of inter- and intra-tissue genetic heterogeneity have been revealed through next-generation sequencing and evidence showing that factors such as epigenetic modifications, non-coding RNAs and RNA editing can play an important role in determining phenotype. Such findings have challenged a number of classic genetic assumptions including (i) analysis of genomic sequence obtained from blood is an accurate reflection of the genotype responsible for phenotype expression in an individual; (ii) that significant genetic alterations will be found only in diseased individuals, in germline tissues in inherited diseases, or in specific diseased tissues in somatic diseases such as cancer; and (iii) that mutation rates in putative disease-associated genes solely determine disease phenotypes. With the breakdown of our traditional understanding of genotype to phenotype relationships, it is becoming increasingly apparent that new analytical tools will be required to determine the relationship between genotype and phenotypic expression. To this end, we are proposing that next-generation genetic database (NGDB) platforms be created that include new bioinformatics tools based on algorithms that can evaluate genetic heterogeneity, as well as powerful systems biology analysis tools to actively process and evaluate the vast amounts of both genomic and genomic-modifying information required to reveal the true relationships between genotype and phenotype.     

Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits

For lignocellulosic bioenergy to become a viable alternative to traditional energy production methods, rapid increases in conversion efficiency and biomass yield must be achieved. Increased productivity in bioenergy production can be achieved through concomitant gains in processing efficiency as well as genetic improvement of feedstock that have the potential for bioenergy production at an industrial scale. The purpose of this review is to explore the genetic and genomic resource landscape for the improvement of a specific bioenergy feedstock group, the C4 bioenergy grasses. First, bioenergy grass feedstock traits relevant to biochemical conversion are examined. Then we outline genetic resources available bioenergy grasses for mapping bioenergy traits to DNA markers and genes. This is followed by a discussion of genomic tools and how they can be applied to understanding bioenergy grass feedstock trait genetic mechanisms leading to further improvement opportunities.     

The emerging role of APC/CCdh1 in development

The function of APC/C (anaphase-promoting complex/cyclosome) was initially implicated with the onset of anaphase during mitosis, where its association with Cdc20 targets securin for destruction, thereby allowing the separation of two duplicated daughter genomes. When combined with Cdh1, APC regulates G1/S transition and DNA replication during cell cycle. Beyond cell cycle control, results from recent biochemical and mouse genetic studies have attracted our attention to the unexpected impact of APC/C(Cdh1) in cellular differentiation, genomic integrity and pathogenesis of various diseases. This review will aim to summarize current understanding of APC/C(Cdh1) in regulating crucial events during development.     

Radiation damage and induced tetraploidy in mulberry (Morus Alba L.)

Vigorously growing mulberry shoots were exposed to 5 kR of gamma rays at the rate of 0·2 kR/hr and 5·0 kR/hr and successively pruned three times in two growing seasons. The most radiosensitive part of both the apical and axillary meristems was the second cell layer. The younger axillary bud primordia were more sensitive to radiation than the older ones. Recovery from radiation damage was assumed to be from the flank meristem in the shoot apex. The frequency of mutations was much lower than that of tetraploidy. Among the tetraploids 50% were 2-4-4 chimeras.     

Photosynthetic characteristics involved in adaptability to Karst soil and alien invasion of paper mulberry (Broussonetia papyrifera (L.) Vent.) in comparison with mulberry (Morus alba L.)

Unlike mulberry (Morus alba, M.a.), paper mulberry (Broussonetia papyrifera, B.p.) can acclimate to Karst soil and incline to alien invasion. The photosynthetic parameters, diurnal changes of carbonic anhydrase, and chlorophyll fluorescence induction, and water potential were measured on sunny days (SD) and cloudy days (CD). Photosynthetic midday depression occurred in B.p. but not in M.a. The irradiance-and CO₂-saturated photosynthetic rates of B.p. were significantly higher than those of M.a. There was no significant difference in water use efficiency between the two species on a SD. The maximum fluorescence, maximum quantum yield, photochemical quenching, and relative electron transport rate in the leaves of B.p. were much higher than those in M.a. The activity of carbonic anhydrase (CA) of B.p., on either an SD or a CD, was much greater than that of M.a. Higher transpiration rate (E) and net photosynthetic rate (P _N) of B.p. resulted in the lack of water in mesophyll cells. Although a higher CA activity of B.p. supplied both water and CO₂ for the photosynthesis of mesophyll cells, water in mesophyll cells was the factor limiting photosynthesis, and the intercellular CO₂ concentration of B.p. was high and stable.     

The defensive role of scutes in juvenile fluted giant clams (Tridacna squamosa)

This study tests the hypothesis that the scaly projections (scutes) on the shells of juvenile giant fluted clams, Tridacna squamosa, are an adaptation against crushing predators such as crabs. The forces required to crush scutes and clams were measured with a universal testing machine whereas crab chela strength was measured with a digital force gauge connected to a set of lever arms. Results for shell properties and chela strength are used to create two, non-mutually exclusive, predator–defense models. In Model 1, scutes increase the overall shell size, consequently reducing the number of crab predators with chelae that are large enough to seize and crush the prey. In Model 2, the chela has to open more to grasp a prey with these projecting structures which leads to a loss of claw-closing force such that crabs fail to crush the scutes, and consequently the clam. Clam scutes may also deter crab predators by increasing the risk of claw damage and/or handling time.     

The biological role of octopine in the squid,Loligo vulgaris (Lamarck)

Summary The enzymatic activities of glyceraldehyde-3-phosphate dehydrogenase, octopine dehydrogenase and lactate dehydrogenase were determined fromLoligo vulgaris. Octopine dehydrogenase displays the highest activity yet recorded for this enzyme, exceeding glyceraldehyde-3-phosphate dehydrogenase sixfold and lactate dehydrogenase 365-fold (Table 1).During jet propulsion swimming octopine accumulates instead of lactate (Table 2), while phosphoarginine, the phosphagen of the squid, is depleted (Table 3).The formation of octopine is discussed in relation to anaerobic metabolism which might occur during burst activity in cephalopods.The following abbreviations are used AK arginine kinase (2.7.3.3) - GAPDH glyceraldehyde-3-phosphate dehydrogenase (1.2.1.12) - LDH L-lactate - NAD oxidoreductase (1.1.1.27) - ODH octopine - NAD oxidoreductase (1.5.1.11) - DTT dithiothreitol - dw dry weight (about 20% of the fresh weight) This investigation was generously supported by The Deutsche Forschungsgemeinschaft grant No.: (Ze 40/13)