OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes

OligoWiz 2.0 is a powerful tool for microarray probe design that allows for integration of sequence annotation, such as exon/intron structure, untranslated regions (UTRs), transcription start site, etc. In addition to probe selection according to a series of probe quality parameters, cross-hybridization, T(m), position in transcript, probe folding and low-complexity, the program facilitates automatic placement of probes relative to the sequence annotation. The program also supports automatic placement of multiple probes per transcript. Together these facilities make advanced probe design feasible for scientists inexperienced in computerized information management. Furthermore, we show that probes designed using OligoWiz 2.0 give rise to consistent hybridization results ()

Functional Associations by Response Overlap (FARO), a Functional Genomics Approach Matching Gene Expression Phenotypes

The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving ‘Functional Association(s) by Response Overlap’ (FARO) between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability between studies that is typical for methods that rely on correlation in gene expression. We apply FARO to a compendium of 242 diverse Arabidopsis microarray experimental factors, including phyto-hormones, stresses and pathogens, growth conditions/stages, tissue types and mutants. We also use FARO to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates the usefulness of our approach for exploiting public microarray data to derive biologically meaningful associations between experimental factors. Finally, our results indicate that FARO is more powerful in associating mutants in common pathways than existing methods such as co-expression analysis

Transcriptome profiling of mice testes following low dose irradiation

BACKGROUND: Radiotherapy is used routinely to treat testicular cancer. Testicular cells vary in radio-sensitivity and the aim of this study was to investigate cellular and molecular changes caused by low dose irradiation of mice testis and to identify transcripts from different cell types in the adult testis. METHODS: Transcriptome profiling was performed on total RNA from testes sampled at various time points (n = 17) after 1 Gy of irradiation. Transcripts displaying large overall expression changes during the time series, but small expression changes between neighbouring time points were selected for further analysis. These transcripts were separated into clusters and their cellular origin was determined. Immunohistochemistry and in silico quantification was further used to study cellular changes post-irradiation (pi). RESULTS: We identified a subset of transcripts (n = 988) where changes in expression pi can be explained by changes in cellularity. We separated the transcripts into five unique clusters that we associated with spermatogonia, spermatocytes, early spermatids, late spermatids and somatic cells, respectively. Transcripts in the somatic cell cluster showed large changes in expression pi, mainly caused by changes in cellularity. Further investigations revealed that the low dose irradiation seemed to cause Leydig cell hyperplasia, which contributed to the detected expression changes in the somatic cell cluster. CONCLUSIONS: The five clusters represent gene expression in distinct cell types of the adult testis. We observed large expression changes in the somatic cell profile, which mainly could be attributed to changes in cellularity, but hyperplasia of Leydig cells may also play a role. We speculate that the possible hyperplasia may be caused by lower testosterone production and inadequate inhibin signalling due to missing germ cells

Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

Background Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking. Results In this study, we report genome-scale transcript response diversity of 10 A. thaliana ecotypes originating from different geographical locations to non-freezing cold stress (10°C). To analyze the transcriptional response diversity, we initially compared transcriptome changes in all 10 ecotypes using Arabidopsis NimbleGen ATH6 microarrays. In total 6061 transcripts were significantly cold regulated (p < 0.01) in 10 ecotypes, including 498 transcription factors and 315 transposable elements. The majority of the transcripts (75%) showed ecotype specific expression pattern. By using sequence data available from Arabidopsis thaliana 1001 genome project, we further investigated sequence polymorphisms in the core cold stress regulon genes. Significant numbers of non-synonymous amino acid changes were observed in the coding region of the CBF regulon genes. Considering the limited knowledge about regulatory interactions between transcription factors and their target genes in the model plant A. thaliana, we have adopted a powerful systems genetics approach- Network Component Analysis (NCA) to construct an in-silico transcriptional regulatory network model during response to cold stress. The resulting regulatory network contained 1,275 nodes and 7,720 connections, with 178 transcription factors and 1,331 target genes. Conclusions A. thaliana ecotypes exhibit considerable variation in transcriptome level responses to non-freezing cold stress treatment. Ecotype specific transcripts and related gene ontology (GO) categories were identified to delineate natural variation of cold stress regulated differential gene expression in the model plant A. thaliana. The predicted regulatory network model was able to identify new ecotype specific transcription factors and their regulatory interactions, which might be crucial for their local geographic adaptation to cold temperature. Additionally, since the approach presented here is general, it could be adapted to study networks regulating biological process in any biological systems

Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α proteobacteria, subsequently evolving into the mitochondrial organelle of our cells. The consensus is based upon genetic and metabolic similarities between mitochondria and aerobic α proteobacteria but fails to explain the origin of several enzymes found in the mitochondria-derived organelles of anaerobic eukaryotes such as Trichomonas and Entamoeba. These enzymes are thought to derive from bacterial lineages other than α proteobacteria, e.g., Clostridium - an obligate anaerobe. [FeFe]-hydrogenase constitues the characteristic enzyme of this anaerobic metabolism and is present in different types also in Entamoeba and other anaerobic eukaryotes. Here we show that α proteobacteria derived from metagenomic studies possess both the cytosolic and organellar type of [FeFe]-hydrogenase, as well as all the proteins required for hydrogenase maturation. These organisms are related to cultivated members of the Rhodospirillales order previously suggested to be close relatives of mitochondrial ancestors. For the first time, our evidence supports an α proteobacterial ancestry for both the anaerobic and the aerobic metabolism of eukaryotes. Reviewers: This article was reviewed by William Martin and Nick Lane, both suggested by the Authors. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13062-016-0136-3) contains supplementary material, which is available to authorized users

Palaeoclimatic and regional implications of Older Dryas and Younger Dryas local glacier activity in the low-Arctic valley Finnkongdalen, Andøya, northern Norway

Continuous glacier margin and equilibrium-line altitude fluctuations of a former glacier on central Andøya, northern Norway, are reconstructed during the Lateglacial based on moraines and AMS 14C-dated sediments from the distal glacier-fed lake Ner-Finnkongdalsvatnet. The results indicate that a valley glacier occupied the entire valley during the Last Glacial Maximum (before 21 970±620 cal. a BP). The glacier remained large throughout the early Lateglacial until a significant glacier retreat took place about 14 300±330 cal. a BP. Major advances occurred during the Older Dryas (OD) and during the Younger Dryas (YD), while minor advances are suggested to have taken place during the Intra Allerød Cold Period and the Late Allerød Cooling. Additionally, three smaller glacier retreats/re-advances within the YD are suggested to have taken place, the latter being the largest. The glacier re-formations/advances during the Lateglacial are consistent with increases in temperature, and they are thus suggested to be the result of increased winter precipitation. Comparing the results with relevant glacier and sea-surface temperature records, a south–north migration of storm tracks may have occurred between 12 100–11 810±220 cal. a BP. The high temporal resolution of local glacier activity in Finnkongdalen improves our understanding of the climate forcing of the regional glacier fluctuations of the northwestern sector of the Scandinavian Ice Sheet during the Skarpnes- (OD) and Tromsø-Lyngen (YD) re-advances.publishedVersio

Shoulder rotational strength profiles of danish national level badminton players

Background Increased age has been shown to be associated with weaker external rotators and stronger internal rotators of the shoulder in pitchers and tennis players. Whether this age-associated change is present in elite badminton players is unknown. Purpose To compare the internal and external rotation strength of the shoulder in adolescent and adult elite badminton players. Study design Cross-sectional. Methods Thirty-one adolescent (12 females aged 16.8 ± 1.6 years and 19 males aged 17.1 ± 1.6 years) and 29 adult (10 females aged 25 ± 2.9 years and 19 males aged 26.2 ± 4.6 years) national level badminton players were tested pre-seasonally for external rotation (ER) and internal rotation (IR) isometric muscle strength bilaterally, using a hand-held dynamometer. Within-group ER to IR strength ratios were calculated (ER/IR×100%). Results The adolescents had stronger shoulder ER than the adults on both sides (p < 0.05). The adult males tended to have stronger IR of the dominant shoulder than the adolescent males (p = 0.071). In the dominant shoulders, the strength ratios for adult females and males were 77% and 78%, respectively, while the same ratio for adolescent females and males were 85% and 99%, respectively. In the non-dominant shoulders, the ER/IR strength ratios for adult females and males were 90% and 87%, respectively, while the ratios for adolescent females and males were 116% and 102%, respectively. Conclusion This study is the first to demonstrate that in shoulder injury-free national team badminton players, adolescents have stronger shoulder ER than adults on both sides. Therefore, increased age appears to be associated with weaker shoulder ER muscles in elite badminton players.publishedVersio