Special Issue on ＂Biomarkers for Diseases＂

The journal Genomics Proteomics ＆ Bioinformatics （GPB） is now inviting submissions for a special issue （to be published in June of 2015） on the topic of ＂Biomarkers for Diseases＂.
As an emerging index, disease biomarkers have demonstrated the potential application in diagnosis and prognosis. The detection of the disease indicators at molecular level, DNA, RNA, protein or metabolites, could gain highly sensitive and specific signals that truly reflect the pathological changes and fully facilitate diagnostic analysis at early phase with invasive mode. Revolution of high-throughput techniques, such as genome-sequencing and mass spectrometers, greatly promotes the discovery and application of the disease biomarkers. The existing disease biomarkers have covered nearly all the macromolecular categories as well as their variants and modifications, including predisposing genetic variations （such as SNPs）, mutations, epigenetic modifications, miRNAs, splice isoforms, abnormal proteins and autoantibodies. Although some biomarkers have been adopted in clinical practice, there are still great needs for studies on identifying new ones, understanding the existing ones and applying the well-studied ones in practice.     

Special Issue on ＂Metagenomics of Marine Environments＂

We are pleased to announce a special issue on ＂Metagenomics of Marine Environments＂ of the journal Genomics, Proteomics ＆ Bioinformatics （GPB）, aiming to provide a platform for high-quality papers focusing on the topic and we invite submissions for this special issue （to be published in August of 2015）.
With most microbes being difficult or impossible to culture, metagenomic approaches based on culture- independent genomic sequencing provide the first real insight of the magnitude and diversity of microbial life that remains largely uncharted. The first metagenomic study of surface water of the Sargasso Sea revealed roughly 1800 species of microbes found in these samples, with 150 new bacterial species and over 1.2 million new genes. The astounding number of genes found in these samples suggests that microbial life in the ocean is far more abundant and diverse than one would expect.     

Comparative effects of insecticides with different mechanisms of action on Chrysoperla externa （Neuroptera＂ Chrysopidae）＂ Lethal,sublethal and dose-response effects

The comprehensive knowledge that the delayed systemic and reproduction side effects can be even more deleterious than acute toxicity, has caused a shift in focus toward sublethal effects assessment on physiology and behavior of beneficial insects. In this study, we assessed the risks posed by some insecticides with different mode of action through lethal and delayed systemic sublethal effects on the pupation, adult emergence, and repro- duction of the chrysopid Chrysoperla externa （Hagen, 1861; Neuroptera： Chrysopidae）, an important predator in pest biological control. The maximum field recommended dose （MFRD） and twice （2xMFRD） for chlorantraniliprole, tebufenozide, and pyriproxyfen were harmless to C. externa. In contrast, all the tested chitin synthesis inhibitors （CSIs） were highly detrimental to the predator, despite of their lack of acute lethal toxicity. There- fore, the safety assumed by using IGRs toward beneficial insects is not valid for chrysopids. Dose-response data showed that although all CSIs have a similar mechanism of action, the relative extent of toxicity may differ （novaluron 〉 lufenuron 〉 teflubenzuron）. For CSIs, the delayed systemic effects became obvious at adult emergence, where the predicted no observable effect dose （NOED） was 1/2 048 of the MFRD for novaluron （0.085 ng/insect）, and 1/256 of the MFRD for both lufenuron （0.25 ng/insect） and teflubenzuron （0.6 ng/insect）. Finally, this work emphasized the significance of performing toxicity risk assessments with an adequate posttreatment period to avoid underestimating the toxicities of insecticides, as the acute lethal toxicity assays may not provide accurate information regarding the long-range effects of hazardous compounds.     

Conservation and behavior of Africa＇s ＂Big Five＂

We examine the conservation status of Africa＇s ＂Big Five＂： lion, leopard, buffalo, black and white rhinoceros and elephant, and the role of behavioral knowledge in their conservation. Efforts to conserve these flagship species consist of in situ conservation, captive breeding and reintroductions. With a few exceptions, we find limited evidence that knowledge of behavior informs conservation programs targeted at these species. For management in the wild, knowledge of infanticide and ranging can provide guidelines for realistic hunting quotas and corridors between protected areas, respectively. For ex situ and reintroduction programs, behavioral knowledge is chiefly focused on improved animal husbandry. Despite a formidable understanding of these species＇ behavior, the practicalities of using such knowledge may be diminished because exploitation of these species is so forceful and the bulk of efforts aimed at conserving these species （and indeed most other African species） are primarily in situ where behaviorally driven interventions are limited. Our comparative findings suggest that behavior has been of rather narrow use in the conservation of these flagship species [Current Zoology 60 （4）： 486--499, 2014].     

Special Issue on ＂Translational Omics＂

The journal Genomics Proteomics ＆ Bioinformatics （GPB） is now inviting submissions for a special issue （to be published in autumn of 2014） on the topic of＂Translational Omics＂.     

A special issue on ＂Plant Molecular Biology＂

The use of molecular biology and genomics tools in plant biology research has greatly expanded our understandingof the molecular mechanisms that underlie plant development and physiology.The successful establishment of researchresources such as mutant populations has led to progress in a variety of fields,including plant reproductive develop-ment,signal transduction,hormone functions,defense responses and epigenetic control.In the future these advanceswill potentially facilitate crop improvement through molecular breeding.     

＂Unconventional＂ Neutralizing Activity of Antibodies Against HIV

Neutralizing antibodies are recognized to be one of the essential elements of the adaptive immune response that must be induced by an effective vaccine against HIV. However,only a limited number of antibodies have been identified to neutralize a broad range of primary isolates of HIV-1 and attempts to induce such antibodies by immunization were unsuccessful. The difficulties to generate such antibodies are mainly due to intrinsic properties of HIV-1 envelope spikes,such as high sequence diversity,heavy glycosylation,and inducible and transient nature of certain epitopes. In vitro neutralizing antibodies are identified using "conventional" neutralization assay which uses phytohe-magglutinin (PHA)-stimulated human PBMCs as target cells. Thus,in essence the assay evaluates HIV-1 replication in CD4 T cells. Recently,several laboratories including us demonstrated that some monoclonal antibodies and HIV-1-specific polyclonal IgG purified from patient sera,although they do not have neutralizing activity when tested by the "conventional" neutralization assay,do exhibit potent and broad neutralizing activity in "unconventional" ways. The neutralizing activity of these antibodies and IgG fractions is acquired through post-translational modifications,through opsonization of virus particles into macrophages and immature dendritic cells (iDCs),or through expression of antibodies on the surface of HIV-1-susceptible cells. This review will focus on recent findings of this area and point out their potential applications in the development of preventive strategies against HIV.     

（1,3;1,4）-β-D-Glucans in Cell Walls of the Poaceae,Lower Plants,and Fungi： A Tale of Two Linkages

（1,3;1,4）-β-D-Glucans consist of unbranched and unsubstituted chains of （1,3）- and （1,4）-β-glucosyl residues, in which the ratio of （1,4）-β-D-glucosyl residues to （1,3）-β-D-glucosyl residues appears to influence not only the physicochemical properties of the polysaccharide and therefore its functional properties in cell walls, but also its adoption by different plant species during evolution. The （1,3; 1,4）-β-D-glucans are widely distributed as non-cellulosic matrix phase polysaccharides in cell walls of the Poaceae, which evolved relatively recently and consist of the grasses and commercially important cereal species, but they are less commonly found in lower vascular plants, such as the horsetails, in algae and in fungi. The （1,3;1,4）-β-D-glucans have often been considered to be components mainly of primary cell walls, but recent observations indicate that they can also be located in secondary walls of certain tissues. Enzymes involved in the depolymerisation of （1,3;1,4）-β-D-glucans have been well characterized. In contrast, initial difficulties in purifying the enzymes responsible for （1,3;1,4）-β-D-glucan biosynthesis slowed progress in the identification of the genes that encode （1,3;1,4）-β-D-glucan synthases, but emerging comparative genomics and associated techniques have allowed at least some of the genes that contribute to （1,3;1,4）-β-D-glucan synthesis in the Poaceae to be identified. Whether similar genes and enzymes also mediate （1,3;1,4）-β-D-glucan biosynthesis in lower plants and fungi is not yet known. Here, we compare the different fine structures of （1,3;1,4）-β-D-glucans across the plant kingdom, present current information on the genes that have been implicated recently in their biosynthesis, and consider aspects of the cell biology of （1,3;1,4）-β-D-glucan biosynthesis in the Poaceae.     

Lake Level Changes Recorded by Tree Rings of Lakeshore Shrubs： A Case Study at the Lake West-Juyan, Inner Mongolia, China

Variation in water resources is a main factor influencing ecohydrological processes and sustainable development in arid regions. Lake level changes are a useful indicator of the variability in water resources. However, observational records of changes in lake levels are usually too short to give an understanding of the long-term variability. In the present study, we investigated the tree rings of shrubs growing on the lakeshore of Lake West-Juyan, the terminus of the Heihe River in western China, and found that Lake West-Juyan had undergone degradation three times over the past 200 years. The lake level decreased from 904.3 to 896.8 m above sea level （a.s.1.） during the period 1800-1900, to 892.0 m a.s.1, from around 1900 to the late 1950s, and the lake dried out in 1963. The trend for changes in lake levels, which was represented by the composite chronology of three beach bars, showed that the phases of increasing lake levels over the past 150 years were during the periods 1852-1871, 1932-1952, 1973-1982, and 1995-1999. Comparison with the history of regional economic development showed that human activity has played an important role in regulating the water resources of the lower reaches of the Heihe watershed over the past 200 years.     

The Arabidopsis Spontaneous Cell Death1 gene, encoding a ζ-carotene desaturase essential for carotenoid biosynthesis, is involved in chloroplast development,photoprotection and retrograde signalling

Carotenoids, a class of natural pigments found in all photosynthetic organisms, are involved in a variety of physiological processes, including coloration, photoprotection, biosynthesis of abscisic acid （ABA） and chloroplast biogenesis. Although carotenoid biosynthesis has been well studied biochemically, the genetic basis of the pathway is not well understood. Here, we report the characterization of two allelic Arabidopsis mutants, spontaneous cell death1-1 （spcl-1） and spc1-2. The weak allele spc1-1 mutant showed characteristics of bleached leaves, accumulation of superoxide and mosaic cell death. The strong mutant allele spc1-2 caused a complete arrest of plant growth and development shortly after germination, leading to a seedling-lethal phenotype. Genetic and molecular analyses indicated that SPC1 encodes a putative ζ-carotene desaturase （ZDS） in the carotenoid biosynthesis pathway. Analysis of carotenoids revealed that several major carotenoid compounds downstream of SPC 1/ZDS were substantially reduced in spc1-1, suggesting that SPC 1 is a functional ZDS. Consistent with the downregulated expression of CAO and PORB, the chlorophyll content was decreased in spc1-1 plants. In addition, expression of Lhcb1. 1, Lhcbl. 4 and RbcS was absent in spc1-2, suggesting the possible involvement of carotenoids in the plastid-to-nucleus retrograde signaling. The spc1-1 mutant also displays an ABA-deficient phenotype that can be partially rescued by the externally supplied phytohormone. These results suggest that SPC1/ZDS is essential for biosynthesis of carotenoids and plays a crucial role in plant growth and development.     

Nesting season,nest age,and disturbance,but not habitat characteristics,affect nest survival of Chinese grouse

Nest survival is a vital component of breeding success,and affects population dynamics,as the loss of nests is the main cause of reproductive failure in birds.To identify key factors for the conservation of Chinese grouse Tetrastes sewerzowi,we tested the effects of nest concealment,nest age,nesting season,and habitat edge on nest daily survival rate(DSR)of Chinese grouse using 54 nests found at Lianhuashan Nature Reserve,Gansu,China,2009-2012.Moreover,we controlled for the effect of research activity by testing the effect of nest checks on DSR.Overall,mammal predation caused 93%of nest failures.DSR was 0.986±0.0038 in the constant model and the probability of a nest with a full clutch of 6 eggs surviving the entire 40-day nesting period was 0.526±0.090.DSR decreased with nest age and nesting season(from 19 May to 3 July).Mammals instead of avian predators being responsible for most nest failures suggest that nest sites might be selected to avoid visual avian predators,but not olfactory mammalian predators,and the decreasing trend of DSR with nest age and nesting season could attribute to an additive exposure effect.Moreover,nest checks conducted by investigators significantly lowered nest DSR,especially during the late period of nesting season and for older nests.Mammalian predators might locate the nest site by following the investigator's odor.Based on our results,we suggest that the late incubation stage is a particularly vulnerable period for nest survival of Chinese grouse and those researchers should adjust their activities around nests to balance the need of acquiring accurate data and decreasing nest predation risk.     

First Announcement of and Call for Papers for ＂Forum on Genetics Progress and Human Health＂

＂Forum on Genetics Progress and Human Health＂ will be held at Yunnan University in Kunming, Yunnan Province, China, in November, 2007. The forum focuses on the current progress and future directions in all major aspects of human genetics and medical genetics. The submitted papers written in English will be considered for publication in Journal of Genetics and Genomics after peer-review and papers in Chinese in Hereditas （Beijing）. Papers＇ in the following areas are encouraged for submission and outstanding papers will be selected for oral presentation in the forum.     

Cloning and Expression of Low Molecular Weight Glutenin Genes from the Chinese Elite Wheat Cultivar ＂Xiaoyan 54＂

The low molecular weight （LMW） glutenln subunlts account for 40% of wheat gluten protein content by mass and these proteins are considered to significantly affect dough quality characteristics. Five new full-length LMW glutenln genes （designated LMW-5, LMW-7, LMW-42, LMW-58, and LMW-34） were isolated from the Chinese elite wheat cultivar ＂Xlaoyan 54＂ by PCR amplification of genomlc DNA using a pair of degenerate primers designed from the conserved sequences of the N- and C-terminal regions of published LMW glutenln genes. Deduced amino acid sequence analysis showed that LMW-5 belongs to the LMW-i type genes and that the other four belong to LMW-m type genes. Sequence comparisons revealed that point mutations occasionally occurred in signal peptide and N-terminus domains and often existed in domain III and domain V. Small insertions and deletions are represented in the repetitive domain. There is a stop codon after amino acid position 110 In the repetitive domain of LMW.34, indicating that It is a pseudogene. The other four genes have complete open reading frames and the putative mature regions of these genes were subcloned Into pET-30a expression vector and successfully expressed in Escherlchla coll. Protein sodium dodecyl sulfate-polyacrylamlde gel electro- phoresls analysis showed that all proteins expressed in E. coil by the four genes could be related to B-group LMW glutenln subunits of wheat.     

First Announcement of and Call for Papers for ＂Forum on Genetics Progress and Human Health＂

＂Forum on Genetics Progress and Human Health＂ will be held at Yunnan University in Kunming, Yunnan Province, China, in November, 2007. The forum focuses on the current progress and future directions in all major aspects of human genetics and medical genetics. The submitted papers written in English will be considered for publication in Journal of Genetics and Genomics after peer-review and papers in Chinese in Hereditas （Beijing）. Papers in the following areas are encouraged for submission and outstanding papers will be selected for oral presentation in the forum.     

Characterization of a novel α4/4-conotoxin,Qcl.2, from vermivorous Conus quercinus

As part of continuing studies of the identification of gene organization and cloning of novel α-conotoxins, the first α4/4-conotoxin identified in a vermivorous Conus species, designated Qcl.2, was originally obtained by cDNA and genomic DNA cloning from Conus quercinus collected in the South China Sea. The predicted mature toxin of Qc1.2 contains 14 amino acid residues with two disulfide bonds （Ⅰ-Ⅲ, Ⅱ-Ⅳ connectivity） in a native globular configuration. The mature peptide of Qcl.2 is supposed to contain an N-terminal post-translationally processed pyroglutamate residue and a free carboxyl C-terminus. This peptide was chemically synthesized and refolded for further characterization of its functional properties. The synthetic Qcl.2 has two interconvertible conformations in aqueous solution, which may be due to the cis-trans isomerization of the two successive Pro residues in its first Cys loop. Using the Xenopus oocyte heterologous expression system, Qcl.2 was shown to selectively inhibit both rat neuronal α3β2 and α3β4 subtypes of nicotinic acetylcholine receptors with low potency. A block of -63% and 37% of the ACh-evoked currents was observed, respectively, and the toxin dissociated rapidly from the receptors. Compared with other characterized α-conotoxin members, the unusual structural features in Qcl.2 that confer to its receptor recognition profile are addressed.     

Erwinia carotovora ssp. carotovora Infection Induced ＂Defense Lignin＂ Accumulation and Lignin Biosynthetic Gene Expression in Chinese Cabbage （Brassica rapa L. ssp. pekinensis）

Erwinia carotovora subsp, carotovora （Ecc） infects and causes soft rot disease in hundreds of crop species including vegetables, flowers and fruits. Lignin biosynthesis has been implicated in defensive reactions to injury and pathogen infection in plants. In this work, variations of lignin content and gene expression in the molecular interaction between Chinese cabbage and Ecc were investigated. H2O2 accumulation and peroxidase activity were detected by 3, 3＇- Dimethoxybenzidine staining at mocked and Ecc-inoculated sites of Chinese cabbage leafstalks. Klason lignin content in inoculated plants increased by about 7.84%, 40.37%, and 43.13% more than that of the mocked site at 12, 24 and 72 h after inoculation, respectively. Gas chromatography detected more p-coumaryl （H） and less coniferyl （G） and sinapyl （S） monolignins in leafstalks of Chinese cabbage. All three monomers increased in Ecc-infected leafstalks, and the Ecc-induced ＂defense lignin＂ were composed of more G and H monolignins, and less S monolignin. After searching the expressed sequence tags （EST） data of Chinese cabbage, 12 genes putatively encoding enzymes involved in lignin biosynthesis were selected to study their expression. All of these genes could be induced by mock inoculation and Ecc infection, while the gene expression lasted for several more hours in the infected samples than in mocked and untreated plants. Our results indicated that ＂defense lignin＂ was different from the developmental lignin in composition; G and S monolignins were significantly induced in plants in response to the soft rot Ecc; thus, lignin biosynthesis was differentially regulated and played a role in plant response to the soft rot Ecc.     

Circadian rhythms of feeding, oviposition, and emergence of the boll weevil （Coleoptera： Curculionidae）

Circadian rhythm of feeding, oviposition, and emergence of boll weevil adults were determined at five different photophases （24, 14, 12, 10, and 0 hours） and a constant 27℃ temperature, 65% RH in the laboratory. Squares from Petri dishes, where they were exposed to boll weevil females, were removed and examined for feeding and oviposition punctures every 4 hours during daylight （0700-1900 h） and every 12 h at night （1900-0700 h） over eight consecutive days. Cohorts of randomly selected egg-punctured squares were sampled from ovipositing females at 0700, 1100, 1500, and 1900 during 24 hours and under different photophase treatments, and maintained in Petri dishes at 27 ＋ I℃, 65% RH. Dishes were observed twice daily （1900 and 0700 h） for adults emerging at day or night. Circadian rhythm of oviposition was not affected by the length of the photophase. The boll weevil has round-the-clock circadian rhythm of oviposition, with a daytime preference. We observed that 82.4%-86.0% of the boll weevil eggs were deposited between 0700 and 1900 h, and 14.0%-17.6% between 1900 and 0700 h during a 24-h period. Feeding of boll weevil females in photoperiods 24：0 h （complete light） and 0：24 h （complete darkness） did not significantly change between 0700-1900 h versus 1900-0700 h, while the d .ally cycle of light and darkness in other photoperiods significantly increased the feeding punctures from 0700-1900 compared with 1900-0700 h. The circadian rhythm of emergence depended significantly on the time of oviposition and the length of the photophase. Investigation of boll weevil circadian rhythm provides a better understanding of boll weevil ecology and reveals potential weak links for improving control technologies targeting their reproductive strategies.