Sample size matters in dietary gene expression studies—A case studyin the g…

One of the main concerns in gene expression studies is the calculation of statistical significance which inmost cases remains low due to limited sample size. Increasing biological replicates translates into moreeffective gains in power which, especially in nutritional experiments, is of great importance as individualvariation of growth performance parameters and feed conversion is high. The pre…

Identification of toxic cyclopeptides based on mass spectral library matching

Edisi

(2014), 1

ISBN/ISSN

Doi: 101016/j.ancr.2

Deskripsi Fisik

Analytical Chemistry Research 1 (2014), 8-15

Judul Seri

Analytical Chemistry Research

No. Panggil

-

Parameters affecting the determination of paraquat at silver rotating electro…

Edisi

(2014), 1

ISBN/ISSN

Doi: 101016/j.imic.2

Deskripsi Fisik

Analytical Chemistry Research 1 (2014), 16-21

Judul Seri

Analytical Chemistry Research

No. Panggil

-

Screening of children saliva samples for bisphenol A using stochastic, ampero…

Edisi

(2014), 1

ISBN/ISSN

Doi: 101016/j.ancr.2

Deskripsi Fisik

Analytical Chemistry Research 1 (2014), 1-7

Judul Seri

Analytical Chemistry

No. Panggil

-

Genetic characterization and relatedness of wild and farmed Eurasianperch (Pe…

Aquaculture of the Eurasian perch, Perca fluviatilis, in recirculating systems has emerged over the pastdecades to become a significant way of diversification for inland areas in Europe. The development of sucha production relies partly on the improvement of growth performance (i.e., reducing production costs),which requires suitable genetic management of broodstocks and the development of sele…

Evidence of vertical transmission and tissue tropism ofStreptococcosis from n…

Streptococcosis is a highly problematic disease in the aquaculture of freshwater fishes, especially fortilapia. The possibility of vertical transmission of streptococcosis and the pattern of tissue tropism of thispathogen in various organs was examined in red tilapia (Oreochromis sp.). Healthy broodstock withoutany clinical signs of Streptococcus spp. were selected from a farm earlier reported …

Impact of fishmeal replacement with Arthrospira platensis on growthperformanc…

In this study, we assessed the suitable level of replacement of fishmeal with a blue green microalga,Arthrospira platensis in feed for the post larvae (PL) of the freshwater prawn, Macrobrachium rosenbergiiby evaluating the growth performance, prawn proximate composition, feed utilization parameters andthe activity of digestive enzymes. The prawns were fed 5 different diets: a control diet and …

Regulation of vitellogenesis by selected endocrine modulators in crabOziothel…

Using vitellogenin (Vtg) gene as a biomarker, the possible role of selected endocrine modulators(EMs) such as methyl farnesoate (MF), 17-hydroxy progesterone (17-OHP), biochanin-A, methio-nine enkephaline (ME) and arachidonic acid on female reproduction in crab Oziothelphusa senex senex(O. senex senex) was elucidated in this study. The injections were given on 1st and 7th day of experi-ment (…

An outbreak of myxozoan parasites in farmed freshwater fishColossoma macropom…

The tambaqui (Colossoma macropomum) is a native fish species that is farmed most frequently and in thelargest quantities throughout Brazil. The high production of this species from fish farms has contributedto the occurrence of emerging parasites, which may compromise fish health and productivity. In a batchof 2500 tambaqui fry acquired for experimental farming procedures in Brazil, a mortality…

Alternative Solvents for Green Chemistry

Everyone is becoming more environmentally conscious and therefore, chemical processes are being developed with their environmental burden in mind. Of course, this also means that more traditional chemical methods are being replaced with new innovations. This includes new solvents. Solvents are everywhere, but should they be? They are used in most areas including synthetic chemistry, anal…

Alkaloids: Chemistry, Biology, Ecology, and Applications

Recent progress in molecular biology leads to a better understanding of nature and natural life processes at the global and local scopes and opens new horizons for chemical and biological technology. Alkaloids, the subject of this book, are a group of very interesting and complex chemical and biological molecules having special tasks in the life machinery of our planet. They are also a good…

Immunological resilience of a freshwater Indian mollusc duringaestivation and…

Freshwater snail, Pila globosa is an edible mollusc which bears commercial and ethnomedicinal signifi-cance. During environmental aridity, P. globosa aestivates deep into the soil for four to five months. Wereport comparative analyses of immune associated parameters in the hemocytes and hemolymph of P.globosa during activity, experimental aestivation, arousal and starvation. Hemocyte is a major…

Evaluating contextual factors affecting the technical efficiency offreshwater…

The demand for animal protein, especially fish, is growing fast, perhaps due to the rapid expansion ofpopulations, increases in income and changes in eating habits and life styles. Capture fisheries, whichsupply over 70% of the fish for human consumption in Malaysia, are over-exploited or depleted. Theiryields have become stagnant over the last few decades and in some cases have even declined. …

Experimental induction of motile Aeromonas septicemia in channelcatfish (Icta…

Motile Aeromonas septicemia (MAS), caused by virulent clonal isolates of Aeromonas hydrophila (vAh), isemerging as a major disease in catfish (Ictalurus punctatus) aquaculture in the Southeastern United States.Predisposing conditions leading to vAh infection in catfish were however largely unknown. The objectiveof this study was to investigate factors that predispose catfish to vAh infection an…

Parental contribution and growth hormone gene polymorphismassociated with gro…

Red sea bream is one of the most important aquaculture fish species in Japan. To improve the productivityof this fish during seed production, improved growth traits and reduced size variation are needed. In thisstudy, we assessed parental contribution of fast- and slow-growing individuals observed in two differentrearing phases in a mass production lot: (1) 50 dph reared in a tank and (2) 200 d…

Effect of ingestion and waterborne routes under different shrimpdensities on …

A study was undertaken to evaluate some factors that are important for better management of the whitespot syndrome virus (WSSV). We examined the likelihood of that the mud crab (Scylla serrata) is a poten-tial carrier of WSSV in shrimp farms and then compared susceptibility of three shrimp species to WSSV,and finally tested the effects of shrimp stocking density and transmission routes on the i…

The effect of temperature on the embryonic development ofbarramundi, the Aust…

Lates calcarifer (barramundi or Asian seabass) has been farmed since the 1970s, yet despite its widespreadculture little has been documented on the species’ embryonic development and particularly how devel-opment relates to temperature. This is particularly the case for the Australian L. calcarifer genetic strain.Accordingly, embryonic development of fertilised barramundi eggs incubated at 26…

Growth rate analysis and protein identification of Kappaphycusalvarezii (Rhod…

Environmental pH is one of the factors contributing to abiotic stress which in turn influences the growthand development of macroalgae. This study was conducted in order to assess the growth and physio-logical changes in Kappaphycus alvarezii under different pH conditions: pHs 6, ∼8.4 (control) and 9. K.alvarezii explants exhibited a difference in the daily growth rate (DGR) among the differe…

A crustin isoform from black tiger shrimp, Penaeus monodon exhibitsbroad spec…

Crustaceans have a powerful non-specific immune mechanism that responds to pathogen invasion andtogether with cellular responses, generates powerful humoral factors such as antimicrobial peptides.Crustins are a diverse class of antimicrobial peptides that are expressed by the circulating haemocytesof crustaceans. Several isoforms of this molecule are reported and in this study, one isoform from…

Secondary stress responses of zebrafish to different pH: Evaluation ina seaso…

Stress is one of the most critical factors in fish health. The response to stress in fish is characterized bythe stimulation of the hypothalamus, which results in the activation of the neuroendocrine system anda subsequent cascade of metabolic and physiological changes. The present paper deals with the stressresponses of water pH on certain biochemical indices and hematological parameters of ze…

Molecular characterization and expression analysis of interferon (IFN-) gen…

Genes coding for interferon  (IFN-) has been cloned and studied for functional analysis in many species.Labeo rohita commonly known as rohu, is a commercially important and widely cultured fish in South-East Asia. IFN- of rohu was amplified with primers based on conserved regions of other related species.5and 3end were amplified using RACE PCR. The PCR products were cloned and sequenced. T…

Nutritional evaluation of groundnut oil cake in formulated diets forrohu, Lab…

De-oiled groundnut oil cake (GOC) was bio-processed through solid state fermentation (SSF) for 15 days at34 ± 1◦C by a tannase producing yeast, Pichia kudriavzevii (GU939629) isolated from the gut of a freshwa-ter carp, Cirrhinus cirrhosus. SSF of GOC was effective in significantly (P < 0.05) reducing crude fibre contentand antinutritional factors (e.g., tannin, phytic acid and trypsin inhib…

Mating behaviour of the orange mud crab, Scylla olivacea: The effect ofsex ra…

Mud crabs from the genus Scylla have high commercial value and are considered as one of the highlysought luxury seafood items. Thorough understanding about their biology and mating behaviour is vitalin providing important information for a sustainable exploitation and future incorporation into the aqua-culture industry. The mating process of S. olivacea lasted 82.0 ± 10.8 h was divided into fo…

Pathological assessment of farmed yellowtail tetra Astyanaxaltiparanae infest…

This study registers for the first time the copepod Acusicola sp. infesting the gills of farmed yellowtail tetraAstyanax altiparanae, as well as new information on gross pathology and gill alterations. Five specimens ofyellowtail tetra showing slow swimming, respiratory difficulty, scaleness and darkened skin were exam-ined. Fish were analysed in situ for ectoparasites diagnosis. Fragments of t…

Stress responses in rohu, Labeo rohita transported at differentdensities

Transportation of fish, although stressful, is an inevitable procedure in aquaculture practices. In thisstudy, we investigated the changes in biochemical and haematological indices in advanced fingerlingsof rohu, Labeo rohita in order to optimize the packing density as is imperative to avoid transportationstress and associated mortality. The fish (14.00–15.00 cm) were packed in sealed double …

Esophageal infection due to Kudoa sp. (Myxozoa) in mapara catfish,Hypophthalm…

The present study describes lesions caused by Kudoa sp. in the esophageal tissue of mapará catfishes(Hypophthalmus marginatus) collected from Cametá, Tocantins River in the northern Brazil. Fifty refriger-ated H. marginatus specimens were dissected and tissue samples were for embedded in paraffin andstained with hematoxylin-eosi, Masson’s trichrome and Giemsa. Pseudocysts of whitish color w…

Plasmid mediated tetracycline resistance of Vibrio parahaemolyticus associat…

Antimicrobial resistance is one of the most important problems in public health, veterinary medicine and aquaculture. Importantly, plasmid mediated antibiotic resistance of pathogenic Vibrio parahaemolyticus from shrimp can potentially be transferred through transposition, conjugation and plasmid uptake to different bacterial species in aquaculture systems. In this study, we evaluated the antib…

Genetic responses of the marine copepod Acartia tonsa (Dana) to heatshock and…

Expression of stress-related genes was investigated in the marine copepod Acartia tonsa in relation to heatshock at two different salinities (10 and 32‰), and it was furthermore investigated whether experimen-tally induced epibiont infestation led to elevated expression of stress-related genes. Expression of thegenes ferritin, Hsp90 and Hsp70 were analyzed in adult copepods by conducting reve…

Revealing gene regulation and associations through biologicalnetworks

tTraditionally, over the last 10,000 years, agriculture has relied on natural biological evolution and carefulselection of plant varieties by farmers that was used as the founder material by plant breeders in the last150 years for further genetic improvement. Plant breeders played an important role mainly by introgres-sion of a trait of interest, through the transfer of genetic loci, into an el…

DNase I hypersensitivity mapping, genomic footprinting, andtranscription fact…

Understanding gene regulatory networks in plants requires knowledge of cis-regulatory DNA, trans-actingfactors, and their dynamics across development and in response to stimuli. Active cis-regulatory elementsare hypersensitive to cleavage by the endonuclease DNase I. Motifs within DNase I hypersensitive sitesindicate potential trans-acting factor occupancy and, when combined with DNase I cleava…

CressInt: A user-friendly web resource for genome-scale explorationof gene re…

tThe thale cress Arabidopsis thaliana is a powerful model organism for studying a wide variety of biologicalprocesses. Recent advances in sequencing technology have resulted in a wealth of information describingnumerous aspects of A. thaliana genome function. However, there is a relative paucity of computationalsystems for efficiently and effectively using these data to create testable hypothes…

Towards a comprehensive and dynamic gynoecium gene regulatorynetwork

tThe Arabidopsis thaliana gynoecium arises at the center of the flower as a simple structure, which willsuccessively develop novel cell types and tissues, resulting in a complex organ. Genetic and hormonalfactors involved in this process have been identified, but we are still far from understanding how theseelements interact, and how these interactions rearrange according to spatial and tempora…

A systems approach to understand shoot branching

Shoots are ramifying systems with regular initiation of new growth axils called shoot branches. In seedplants, shoot buds initiate in leaf axils from axillary meristems (AMs) containing stem cells. The activitiesof AMs and buds play vital roles in plant architecture and crop yield. Whereas recent years have witnessedenormous progress the control of bud outgrowth, our knowledge of AM initiation …

Transcriptional networks governing plant metabolism

Efficiently obtaining and utilizing energy and elements is critical for an organism to maximize its fitness.Optimizing these processes requires precise regulation and coordination of an organism’s metabolic net-works in response to diverse environmental conditions and developmental stages. Metabolic regulationis often considered to largely occur by allosteric feedback where the metabolites di…

A longphotoperiodrelaxesenergymanagementin Arabidopsis leaf six

Plants adapt to the prevailing photoperiod by adjustinggrowthandfloweringtotheavailabilityofenergy. To understand the molecul archanges involved in adaptation to along-dayconditionwecomprehensively profiled leaf six at the end of the day and theend of the night at four development al stages on Arabidopsis thaliana plants grownin a 16 hphotoperiod,andcompared the profilest othose from leaf 6of …

Enhanced resistance in wheat against stem rust achieved by markerassisted bac…

Marker assisted backcrossing (MABC) was used to transfer the three stem rust (Puccinia graminis tritici)resistant genes Sr25, SrWeb and Sr50 into the popular Indian wheat cv. HUW234. The donor was theCIMMYT breeding line PMBWIR4, and each of the target genes was marked by a simple PCR assay. Athree step screening strategy was adopted: the first screen comprised foreground selection, the secondu…

Computational approaches to identify regulators of plant stressresponse using…

Insight into biological stress regulatory pathways can be derived from high-throughput transcriptomicdata using computational algorithms. These algorithms can be integrated into a computational approachto provide specific testable predictions that answer biological questions of interest. This review conceptu-ally organizes a wide variety of developed algorithms into a classification system base…

The KnownLeaf literature curation system captures knowledge aboutArabidopsis …

The information that connects genotypes and phenotypes is essentially embedded in research articleswritten in natural language. To facilitate access to this knowledge, we constructed a framework for thecuration of the scientific literature studying the molecular mechanisms that control leaf growth anddevelopment in Arabidopsis thaliana (Arabidopsis). Standard structured statements, called relat…

Introgression of the high grain protein gene Gpc-B1 in an elite wheatvariety …

Grain protein content (GPC) in wheat has been a major trait of interest for breeders since it has enormousend use potential. In the present study, marker-assisted backcrossing (MABC) was successfully used toimprove GPC in wheat cultivar HUW468. The genotype Glu269 was used as the donor parent for intro-gression of the gene Gpc-B1 that confers high GPC. In a segregating population, SSR marker Xu…

Plant speciation through chromosome instability and ploidy change:Cellular me…

Plant speciation and diversification strongly rely on structural changes in the nuclear genome, both at the whole ploidy and individual chromosome level. Phylogenetic, comparative mapping and cytological studies have provided insights into the evolutionary mechanisms that shape the plant genome. These include major genome alterations, such as whole genome duplication and hybridization (auto- an…

Application of iPBS in high-throughput sequencing for thedevelopment of retro…

Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retro-transposons are especially predominant. Thus, numerous LTR retrotransposon families with high copynumbers exist in most plant genomes. As the integrated copies of these retrotransposons are geneticallyinherited, their insertion polymorphisms among crop cultivars have been used as functional molec…

Paleogenomics in Triticeae for translational research

Recent access to Triticeae genome sequences as well as high resolution gene-based genetic maps recentlyoffered the opportunity to compare modern Triticeae genomes and model their evolutionary history fromtheir reconstructed founder ancestors. In silico paleogenomic data have revealed the evolutionary forcesthat have shaped present-day Triticeae and allowed to gain insight into how wheat, barley…

Expression of a transferred nuclear gene in a mitochondrial genome

tTransfer of mitochondrial genes to the nucleus, and subsequent gain of regulatory elements for expres-sion, is an ongoing evolutionary process in plants. Many examples have been characterized, which insome cases have revealed sources of mitochondrial targeting sequences and cis-regulatory elements. Incontrast, there have been no reports of a nuclear gene that has undergone intracellular transf…

Gene and genome duplications and the origin of C4photosynthesis:Birth of a tr…

tC4photosynthesis is a trait that has evolved in 66 independent plant lineages and increases the efficiencyof carbon fixation. The shift from C3to C4photosynthesis requires substantial changes to genes andgene functions effecting phenotypic, physiological and enzymatic changes. We investigate the role ofancient whole genome duplications (WGD) as a source of new genes in the development of this …

Biological process annotation of proteins across the plant kingdom

tAccurate annotation of protein function is key to understanding life at the molecular level, but auto-mated annotation of functions is challenging. We here demonstrate the combination of a method forprotein function annotation that uses network information to predict the biological processes a proteinis involved in, with a sequence-based prediction method. The combined function prediction is b…

The repetitive component of the sunflower genome

The sunflower (Helianthus annuus) and species belonging to the genus Helianthus are emerging as amodel species and genus for a number of studies on genome evolution. In this review, we report on therepetitive component of the H. annuus genome at the biochemical, molecular, cytological, and genomiclevels. Recent work on sunflower genome composition is described, with emphasis on different typeso…

Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an S…

Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular…

Characterization of QTL for unique agronomic traits of new-plant-type rice va…

To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived) line of IR64, YTH288, was developed using a new-plant-type cultivar,IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F…

Interpreting genotype × environment interactions for grain yield of rainfed …

Clustering genotype × environment (GE) interactions and understanding the causes of GE interactions are among the most important tasks in crop breeding programs. Pattern analysis (cluster and ordination techniques) was applied to analyze GE interactions for grain yield of 24 durum wheat (Triticum turgidum L. var. durum) genotypes (breeding lines and old and new cultivars) along with a popular …

Responses in gas exchange and water status between drought-tolerant and -susc…

The purpose of this studywas to investigate the physiological responses of drought-tolerant and drought-susceptible soybean genotypes to exogenous abscisic acid (ABA) application during progressive soil drying at seedling stages. Five-day old soybean seedlings were transplanted into PVC tubes filledwith soilmixture. Seedlingswerewatered dailywith similarwater volumes until second trifoliate lea…