Despite strong evidence for a role of biological factors in the etiology and pathology of suicide, the study of traditional neurotransmitter systems has been able to explain only a small proportion of the neurobiology of what is now recognized as a complex genetic trait. The use of microarrays to simultaneously examine the expression levels of thousands of gene transcripts has vastly expanded our capacity to detect the involvement of additional genes and pathways in suicidality, and has opened many new avenues for the discovery of the biological underpinnings of suicide completion. This review examines microarray studies which have been used to identify genes displaying altered expression in suicide completers, and highlights some of the important methodological considerations and metabolic pathways which have emerged from these analyses.

Iodine (I) is a micronutrient that mammals need for proper functionality of thyroid gland since it is the main component of thyroid hormones. Besides studies that have investigated the role of I in livestock nutrition, it is also important to know the transcriptomics changes in small ruminants following I supplementation. Therefore, the aim of this study was to investigate the effects of I on the whole blood transcriptome in sheep. Fifteen lactating cross-bred ewes (3 to 4-year-old, 55 to 65 kg BW) at their late lactation period were enrolled in this study. At the beginning, all the animals had a 2-week acclimation period where they were fed with a basal diet which includes an adequate level of I (2 mg I/animal per day) in the form of calcium iodate (CaI2O6). Then, the ewes were randomly divided into two groups and fed in individual troughs: the control group (n = 5) was maintained on basal diet and the experimental group (I, n = 10) was fed for 40 days with a diet containing a high I supplementation (equivalent to 30 mg I/animal per day), in the form of potassium iodide. Whole blood and milk were collected individually at the beginning (T0) and after the 40 days of supplementation (T40). Iodine quantification was assessed in serum and milk sample. Microarray gene expression analysis was performed on whole blood and, filtering data using a fold change >2 with an adjusted P < 0.05, we identified 250 differentially expressed genes (DEGs) in the I group (T40 v. T0). Looking for biological processes associated with our DEGs, we found significant association with cell growth regulation. Thus, our study unveils the role of I supplementation on gene expression in sheep improving the knowledge about micronutrients in animal nutrition.

The development of nutritional strategies to improve microbial homeostasis and gut health of piglets post-weaning is required to mitigate the high prevalence of post-weaning diarrhea and subsequent growth checks typically observed during the weaning transition. Therefore the objective of this study was to determine the effect of supplementing piglet creep and nursery feed with a yeast-derived mannan-rich fraction (MRF) on piglet growth performance, cecal microbial profiles, and jejunal morphology and gene expression. Ten litters of piglets (n=106) were selected on postnatal day (PND) 7 and assigned to diets with or without MRF (800 mg/kg) until weaning (n=5 litters/treatment; initial weight 3.0±0.1 kg). On PND 21, 4 piglets per litter (n=40) were selected and weaned into the nursery where they remained on their respective diets until PND 42. A two-phase feeding program was used to meet nutrient requirements, and pigs were switched from phase 1 to phase 2 on PND 28. Feed intake and piglet weights were recorded on PND 7, 14, 21, 28, 35 and 42. On PND 28 and 42, ten piglets per treatment were euthanized to collect intestinal tissue and digesta. Piglets supplemented with MRF had 21.5% greater (P<0.05) average daily feed intake between PND 14-21. However, MRF supplementation did not affect piglet growth performance compared to control. On PND 28, jejunal villus height was 16.8% greater (P<0.05) in piglets consuming MRF supplemented diets. Overall microbial community structure in cecal digesta on PND 28 tended to differ in pigs supplemented with MRF (P=0.076; analysis of similarities (ANOSIM)) with increased (P<0.05) relative abundance of Paraprevotellaceae genera YRC22 and CF231, and reduced (P<0.05) relative abundance of Sutterella and Prevotella. Campylobacter also tended to reduce (P<0.10) in MRF supplemented piglets. On PND 28 differential gene expression in jejunal tissue signified an overall effect of supplementing MRF to piglets. Downstream analysis of gene expression data revealed piglets supplemented with MRF had enriched biological pathways involved in intestinal development, function and immunity, supporting the observed improvement in jejunal villus architecture on PND 28. On PND 42 there was no effect of MRF supplementation on jejunal morphology or overall cecal microbial community structure. In conclusion, supplementing Actigen™, a MRF, to piglets altered cecal microbial community structure and improved jejunal morphology early post-weaning on PND 28, which is supported by enrichment of intestinal development pathways.

Macrosomia, not only is closely associated with short-term, birth-related problems, but also has long-term consequences for the offspring. We investigated the expression of long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in the placenta of macrosomia births using a microarray profile. The data showed that 2929 lncRNAs and 4574 mRNAs were upregulated in the placenta of macrosomia births compared with the normal birth weight group (fold change ⩾2.0, P<0.05), and 2127 lncRNAs and 2511 mRNAs were downregulated (fold change ⩾2.0, P<0.05). To detect the function of the differentially expressed lncRNAs and their possible relationship with the differentially expressed mRNAs, we also performed gene ontology analysis and pathway analysis. The results demonstrated that the PI3K-AKT signalling pathway, the mitogen-activated protein kinase (MAPK) signalling pathway, the focal adhesion pathway, the B cell receptor signalling pathway, and the protein processing in endoplasmic reticulum and lysosome pathway were significantly differentially expressed in the macrosomia placenta. Four lncRNAs were randomly chosen from the differentially expressed lncRNAs to validate the microarray data by quantitative polymerase chain reaction (qPCR). The qPCR results were consistent with the microarray data. In conclusion, lncRNAs were significantly differentially expressed in the placenta of macrosomia patients, and may contribute to the pathogenesis of macrosomia.

Mammalian oocyte maturation is achieved when oocytes reach metaphase II (MII) stage, and accumulate mRNA and proteins in the cytoplasm following fertilization. It has been shown that oocytes investigated before and after in vitro maturation (IVM) differ significantly in transcriptomic and proteomic profiles. Additionally, folliculogenesis and oogenesis is accompanied by morphogenetic changes, which significantly influence further zygote formation and embryo growth. This study aimed to determine new transcriptomic markers of porcine oocyte morphogenesis that are associated with cell maturation competence. An Affymetrix microarray assay was performed on an RNA template isolated from porcine oocytes before (n = 150) and after (n = 150) IVM. The brilliant cresyl blue (BCB) staining test was used for identification of cells with the highest developmental capacity. DAVID (Database for Annotation, Visualization, and Integrated Discovery) software was used for the extraction of the genes belonging to a cell morphogenesis Gene Ontology group. The control group consisted of freshly isolated oocytes. In total, 12,000 different transcripts were analysed, from which 379 genes were downregulated and 40 were upregulated in oocytes following IVM. We found five genes, SOX9, MAP1B, DAB2, FN1, and CXCL12, that were significantly upregulated in oocytes after IVM (in vitro group) compared with oocytes analysed before IVM (in vivo group). In conclusion, we found new transcriptomic markers of oocyte morphogenesis, which may be also recognized as significant mediators of cellular maturation capacity in pigs. Genes SOX9, MAP1B, DAB2, FN1, and CXCL12 may be involved in the regulation of the MII stage oocyte formation and several other processes that are crucial for porcine reproductive competence.

The buffalo has a seasonal reproduction activity with mating and non-mating periods occurring from late autumn to winter and from late spring to beginning of autumn, respectively. Sperm glycocalyx plays an important role in reproduction as it is the first interface between sperm and environment. Semen quality is poorer during non-mating periods, so we aimed to evaluate if there were also seasonal differences in the surface glycosylation pattern of mating period spermatozoa (MPS) compared with non-mating period spermatozoa (NMPS). The complexity of carbohydrate structures makes their analysis challenging, and recently the high-throughput microarray approach is now providing a new tool into the evaluation of cell glycosylation status. We adopted a novel procedure in which spermatozoa was spotted on microarray slides, incubated with a panel of 12 biotinylated lectins and Cy3-conjugated streptavidin, and then signal intensity was detected using a microarray scanner. Both MPS and NMPS microarrays reacted with all the lectins and revealed that the expression of (i) O-glycans with NeuNAcα2-3Galβ1,3(±NeuNAcα2-6)GalNAc, Galβ1,3GalNAc and GalNAcα1,3(l-Fucα1,2)Galβ1,3/4GlcNAcβ1 was not season dependent; (ii) O-linked glycans terminating with GalNAc, asialo N-linked glycans terminating with Galβ1,4GlcNAc, GlcNAc, as well as α1,6 and α1,2-linked fucosylated oligosaccharides was predominant in MPS; (iii) high mannose- and biantennary complex types N-glycans terminating with α2,6 sialic acids and terminal galactose were lower in MPS. Overall, this innovative cell microarray method was able to identify specific glycosylation changes that occur on buffalo bull sperm surface during the mating and non-mating periods.

Microarray analysis was used to follow changes in gene expression coinciding with seasonal changes in the dormancy status of crown buds of field-grown leafy spurge. Known cold-regulated genes were induced, and numerous gibberellic acid–responsive genes were down-regulated during the transition from paradormancy to endodormancy. Genes involved in photomorphogenesis were induced during endodormancy. Also, ethylene signaling responses were observed during ecodormancy rather than endodormancy. These results provide additional insights into the signals regulating expression of several genes previously associated with transition from paradormancy to growth in root buds.

Arabidopsis complementary DNA (cDNA) microarrays were hybridized with labeled cDNA from mature leaves and emerging tillers of wild oat to determine if they could identify gene expression profiles in distantly related species. More than 23% of the > 11,000 cDNAs on the array hybridized to the wild oat probe. Transcription patterns detected by hybridization to the arrays are indicators for physiological processes in the tissues tested. Coordinated expression patterns for these genes in Arabidopsis indicate common signals involved in their regulation. The results demonstrate that probing cDNA-based arrays from well-characterized species can provide valuable insight into the signal transduction processes regulating growth and development of poorly characterized species.

Microarray analysis was used to identify changes in gene expression in corn leaves collected from plants at the V11–14 growth stage that resulted from competition with velvetleaf. The plants were grown in field plots under adequate N (addition of 220 kg N ha−1) and irrigation to minimize N and water stress. Consequently, only differences resulting from competition for micronutrients, light, and perhaps allelopathic stress were anticipated. Genes involved in carbon and nitrogen utilization, photosynthesis, growth and development, oxidative stress, signal transduction, responses to auxin and ethylene, and zinc transport were repressed in corn growing in competition with velvetleaf. Very few genes were induced because of competition with velvetleaf, and those that were provided little indication of the physiological response of corn. No differences were observed in genes responsive to water stress or sequestering/transporting micronutrients other than zinc, indicating that these stresses were not a major component of velvetleaf competition with corn at the developmental stage tested.

An overview of bioinformatics is presented with an emphasis on describing a set of tools, databases, and ontologies useful to the weed science community. These tools can be used to identify genes whose product may be the target site of a herbicide or in the degradation pathway of a xenobiotic. They may identify receptors responsible for pathogen recognition or enzymes in the metabolic pathway for allelopathic compounds. Whatever the gene of interest, bioinformatics allows researchers to assemble complete or partial genes from expressed sequence tags (ESTs), complete cDNAs, or complete genomes and then translate them into their corresponding amino acid sequences. Similarity searches can be used to find other proteins with homology to the gene of interest, which can provide clues to its function from the annotation of these database hits. The use of protein domain databases can also provide insight into the functional capabilities of the protein in question and delineate those portions essential for activity. Enzyme Commission (EZ) numbers or gene ontology (GO) descriptors allow placement of the protein within the larger network context of a biological system. These capabilities allow the scientist to probe deeper into the function of their protein of interest to gain a novel understanding of the biology.

Dormancy is a state of shifted physiological activities with cessation of growth. It occurs in seeds and vegetative propagules and enables plants to survive in adverse growing conditions. Traditional studies on dormancy-related problems have mostly focused on hormone changes along with environmental factors that have achieved great insight on these processes at the physiological level. The molecular nature and cellular basis of signals that carry out the processes of dormancy or dormancy breaking are largely unknown. Recent advances in plant genetics and genomics have provided assorted ways to investigate questions concerning dormancy. Various approaches such as developing genetic maps with DNA-based markers, e.g., amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP), analyzing mutant lines, conducting quantitative trait loci (QTL) analysis, two-dimensional polyacrylamide gel electrophoresis, differential display, microarray, have been performed to resolve different issues related to dormancy. The phenotypic variation in dormant seeds or buds is continuous instead of discrete, and thus QTL analysis is desirable to identify the association between genetically determined phenotypes and specific genetic markers (RFLPs). Some aspects of QTL will be introduced. DNA microarray is a recently developed technology that is used to detect and quantitate large numbers of differences in gene expression simultaneously. We have used the DNA microarray technology to study underground bud dormancy and growth in leafy spurge (Euphorbia esula L.). The principle and versatility of DNA microarray will be introduced, and the strategy for applying this technology will be discussed.

Leafy spurge seeds are responsive to alternating temperature rather than constant temperature for germination. Transcriptome changes of dry leafy spurge seeds and seeds imbibed for 1 and 3 d at 20 C constant (C) and 20 : 30 C alternating (A) temperature were determined by microarray analysis to examine temperature responsiveness. Principal component analysis revealed differences in the transcriptome of imbibed seeds based on the temperature regime. Computational methods in bioinformatics parsed the data into overrepresented AraCyc pathways and gene regulation subnetworks providing biological context to temperature responses. After 1 d of imbibition, the degradation of starch and sucrose leading to anaerobic respiration were common pathways at both temperature regimes. Several overrepresented pathways unique to 1 d A were associated with generation of energy, reducing power, and carbon substrates; several of these pathways remained overrepresented and up-regulated at 3 d A. At 1 d C, pathways for the phytohormones jasmonic acid and brassinosteroids were uniquely overrepresented. There was little similarity in overrepresented pathways at 1 d C between leafy spurge and arabidopsis seeds, indicating species-specific effects upon imbibition of dry seeds. Overrepresented gene subnetworks at 1 d and 3 d at both temperature regimes related to signaling processes and stress responses. A major overrepresented subnetwork unique to 1 d C related to photomorphogenesis via the E3 ubiquitin ligase COP1. At 1 d A, major overrepresented subnetworks involved circadian rhythm via LHY and TOC1 proteins and expression of stress-related genes such as DREB1A, which is subject to circadian regulation. Collectively, substantial differences were observed in the transcriptome of leafy spurge seeds imbibed under conditions that affect the capacity to germinate.

The objective was to study the effect of maternal supplementation with a yeast cell wall-based product containing a mannan-rich fraction (MRF) during gestation and lactation on piglet intestinal gene expression. First parity sows were fed experimental gestation and lactation diets with or without MRF (900 mg/kg). After farrowing, piglets were fostered within treatment, as necessary. Sow and litter production performance data were collected until weaning. On day 10 post farrowing, jejunum samples from piglets were collected for gene expression analysis using the Affymetrix Porcine GeneChip array. Most performance parameters did not differ between the treatments. However, protein (P<0.01), total solids less fat (P<0.03) and the concentration of immunoglobulin G (IgG) in milk were greater (P<0.05) in the MRF-supplemented group. Gene expression results using hierarchical clustering revealed an overall dietary effect. Further analysis elucidated activation of pathways involved in tissue development, functioning and immunity, as well as greater cell proliferation and less migration of cells in the jejunum tissue. In conclusion, feeding the sow MRF during pregnancy and lactation was an effective nutritional strategy to bolster colostrum and milk IgG that are essential for development of piglet immune system and gut. In addition, the gene expression patterns affected by the passive immunity transfer showed indicators that could benefit animal performance long term.

Thrips, the sole vector of plant Tospovirus, are major pests of many agricultural crops throughout the world. Molecular approaches have been applied in recent decades to identify these minute and morphologically difficult to distinguish insects. In this study, sequences of internal transcribed spacer 1 (ITS1) region of 15 agronomically important thrips, including several virus transmission species, have been analyzed in order to design species-specific primers for multiplex PCR and probes for microarray assay. That the ITS1 sequence distances within species were smaller than those among species suggests that the ITS1 fragment can be used for thrips species identification. The specificity and stability of these primers, combined with universal paired primers, were tested and verified in multiplex PCR. Using these specific primers as probes, microarray assay showed that PCR products of all thrips species hybridized consistently to their corresponding probes, though some signals were weak. We have demonstrated that multiplex PCR using specific primers based on ITS1 sequences is a simple, reliable, and cost-effective diagnostic tool for thrips species identification. Moreover, the DNA microarray assay is expected to extend into a reliable high-throughput screening tool for the vast numbers of thrips.

Chickens (Gallus gallus) were the first avian species selected for whole genome sequencing because of their economic value, use as a food source, livelihood security and research importance. Any living organism contains a galaxy of genes which express all the phenotypes or characters by encoding proteins and peptides, and playing regulatory roles in the biological system. Functional genomics in turn, is a multidisciplinary approach to identify and demonstrate the functional roles of genes and other regulatory molecules such as microRNA and CpG methylation in biological pathways. In the last two decades, the chicken genome database has made significant advancements in accruing large amounts of genomic information through employing advanced bio-informatic tools. Several techniques such as cDNA microarray, serial analysis of gene expression, massively parallel signature sequencing, cDNA subtractive hybridisation and next generation sequencing have been utilised to investigate the genome-wide expression profile instead of revealing expression pattern of one or a few genes in various avian species. Expressed sequence tag or cDNA sequences are the key factors for identification of novel genes and understanding the complex molecular cascades of ontology. A large-scale cDNA library has been constructed from embryonic and adult tissues and consequently identified the presence of about 19,000 functional genes in chickens. The micro RNAs play crucial role in gene expression and to date, approximately 496 micro RNAs have been characterised. The non-coding RNA alters gene expression involved in cellular process, by modulating the chromatin architecture, transcription, RNA splicing, editing, translation and turnover. Functional genomics studies have been extensively used to identify genes associated with several production traits, immuno-genetic mechanism, host-pathogen interaction, pathogen biology etc. Nutrigenomics have determined the genomic mechanism involved in feed utilisation, metabolism and cholesterol synthesis etc., which ultimately reveal potential applications for improving the nutritional efficiency of birds. This review discusses the tools and utility of functional genomics approaches in chicken.

Differential gene expression analyses typically focus on departures across mathematical expectations (i.e. mean) from two or more groups of microarrays, without considering alternative patterns of departure. Nevertheless, recent studies in humans and great apes have suggested that differential gene expression could also be characterized in terms of heterogeneous dispersion patterns. This must be viewed as a very interesting genetic phenomenon clearly linked to the regulation mechanisms of gene transcription. Unfortunately, we completely lack information about the incidence and relevance of dispersion-specific differential gene expression in livestock species, although a specific Bayes factor (BF) for testing this kind of differential gene expression (i.e. within-probe heteroskedasticity) has been recently developed. Within this context, our main objective was to characterize the incidence of dispersion-specific differential gene expression in pigs and, if possible, providing the first evidence of this phenomenon in a livestock species. We evaluated dispersion-specific differential gene expression on ovary, uterus and hypophysis samples from 22 F2 Iberian × Meishan sows, where a total of 15 252 probes were interrogated. For each tissue, heteroskedasticity of probe-specific residual variances was evaluated by three pairwise comparisons involving three physiological stages, that is, heat, 15 days of pregnancy and 45 days of pregnancy. Between 2.9% and 37.4% of the analyzed probes provided statistical evidence of within-tissue across-physiological stages dispersion-specific differential gene expression (BF >1), and between 0.1% and 3.0% of them reported decisive evidence (BF >100). It is important to highlight that <8% of the heteroskedastic probes were also linked to differential gene expression in terms of departures among the probe-specific mathematical expectation of each physiological stage. This discarded the disturbance of scale effects in a high percentage of probes and suggested that probe-specific heteroskedasticity must be viewed as an independent phenomenon within the context of differential gene expression. As a whole, our results report a remarkable incidence of dispersion-specific differential gene expression across the whole genome of the pig, establishing a very interesting starting point for further studies focused on deciphering the genetic mechanisms underlying heteroskedasticity.

The effects of mycotoxins in the production of animal feed were investigated using broiler chickens. For the feeding trial, naturally Fusarium mycotoxin-contaminated wheat was used, which mainly contained deoxynivalenol (DON). The main effects of DON are reduction of the feed intake and reduced weight gain of broilers. At the molecular level, DON binds to the 60 S ribosomal subunit and subsequently inhibits protein synthesis at the translational level. However, little is known about other effects of DON, for example, at the transcriptional level. Therefore, a microarray analysis was performed, which allows the investigation of thousands of transcripts in one experiment. In the experiment, 20 broilers were separated into four groups of five broilers each at day 1 after hatching. The diets consisted of a control diet and three diets with calculated, moderate concentrations of 1.0, 2.5 and 5.0 mg DON/kg feed, which was attained by exchanging uncontaminated wheat with naturally mycotoxin-contaminated wheat up to the intended DON concentration. The broilers were held at standard conditions for 23 days. Three microarrays were used per group to determine the significant alterations of the gene expression in the liver (P < 0.05), and qPCR was performed on the liver and the jejunum to verify the results. No significant difference in BW, feed intake or feed conversion rate was observed. The nutrient uptake into the hepatic and jejunal cells seemed to be influenced by genes: SLC2A5 (fc: −1.54, DON2.5), which facilitates glucose and fructose transport and SLC7A10 (fc: +1.49, DON5), a transporter of d-serine and other neutral amino acids. In the jejunum, the palmitate transport might be altered by SLC27A4 (fc: −1.87, DON5) and monocarboxylates uptake by SLC16A1 (fc: −1.47, DON5). The alterations of the SLC gene expression may explain the reduced weight gain of broilers chronically exposed to DON-contaminated wheat. The decreased expressions of EIF2AK3 (fc: −1.29, DON2.5/5) and DNAJC3 (fc: −1.44, DON2.5) seem to be related to the translation inhibition. The binding of DON to the 60 S ribosomal subunit and the subsequent translation inhibition might be counterbalanced by the downregulation of EIF2AK3 and DNAJC3. The genes PARP1, MPG, EME1, XPAC, RIF1 and CHAF1B are mainly related to single-strand DNA modifications and showed an increased expression in the group with 5 mg DON/kg feed. The results indicate that significantly altered gene expression was already occurring at 2.5 mg DON/kg feed.

The aim of this study was to determine the effects of supplementing unprotected dietary unsaturated fatty acids (UFAs) from different plant oils on gene expression in the mammary gland of grazing dairy cows. A total of 28 Holstein–Friesian dairy cows in mid-lactation were blocked according to parity, days in milk, milk yield and fat percentage. The cows were then randomly assigned to four UFA sources based on rapeseed, soybean, linseed or a mixture of the three oils for 23 days, after which, all 28 cows were switched to a control diet for an additional 28 days. On the last day of both periods, mammary gland biopsies were taken to study genome-wide differences in gene expression on Affymetrix GeneChip® Bovine Genome Arrays (no. 900493) by ServiceXS (Leiden, The Netherlands). Supplementation with UFAs resulted in increased milk yield but decreased milk fat and protein percentages. Furthermore, the proportion of de novo fatty acids (FAs) in the milk was reduced, whereas that of long-chain FAs increased. Applying a statistical cut-off of false discovery rate of q-values <0.05 together with an absolute fold change of 1.3, a total of 972 genes were found to be significantly affected through UFA supplementation, indicating that large transcriptional adaptations occurred in the mammary gland when grazing dairy cows were supplemented with unprotected dietary UFA. Gene sets related to cell development and remodeling, apoptosis, nutrient metabolic process, as well as immune system response were predominantly downregulated during UFA supplementation. Such molecular knowledge on the physiology of the mammary gland might provide the basis for further functional research on dairy cows.