Microarrays in molecular profiling of cancer - focus on head and neck squamous cell carcinoma

Microarrays have a wide range of applications in the biomedical field. From the beginning, arrays have mostly been utilized in cancer research, including classification of tumors into different subgroups and identification of clinical associations. In the microarray format, a collection of small features, such as different oligonucleotides, is attached to a solid support. The advantage of microarray technology is the ability to simultaneously measure changes in the levels of multiple biomolecules. Because many diseases, including cancer, are complex, involving an interplay between various genes and environmental factors, the detection of only a single marker molecule is usually insufficient for determining disease status. Thus, a technique that simultaneously collects information on multiple molecules allows better insights into a complex disease. Since microarrays can be custom-manufactured or obtained from a number of commercial providers, understanding data quality and comparability between different platforms is important to enable the use of the technology to areas beyond basic research. When standardized, integrated array data could ultimately help to offer a complete profile of the disease, illuminating mechanisms and genes behind disorders as well as facilitating disease diagnostics. In the first part of this work, we aimed to elucidate the comparability of gene expression measurements from different oligonucleotide and cDNA microarray platforms. We compared three different gene expression microarrays; one was a commercial oligonucleotide microarray and the others commercial and custom-made cDNA microarrays. The filtered gene expression data from the commercial platforms correlated better across experiments (r=0.78-0.86) than the expression data between the custom-made and either of the two commercial platforms (r=0.62-0.76). Although the results from different platforms correlated reasonably well, combining and comparing the measurements were not straightforward. The clone errors on the custom-made array and annotation and technical differences between the platforms introduced variability in the data. In conclusion, the different gene expression microarray platforms provided results sufficiently concordant for the research setting, but the variability represents a challenge for developing diagnostic applications for the microarrays. In the second part of the work, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 38 laryngeal and oral tongue squamous cell carcinoma cell lines and primary tumors. Our aim was to pinpoint genes for which expression was impacted by changes in copy number. The data revealed that especially amplifications had a clear impact on gene expression. Across the genome, 14-32% of genes in the highly amplified regions (copy number ratio >2.5) had associated overexpression. The impact of decreased copy number on gene underexpression was less clear. Using statistical analysis across the samples, we systematically identified hundreds of genes for which an increased copy number was associated with increased expression. For example, our data implied that FADD and PPFIA1 were frequently overexpressed at the 11q13 amplicon in HNSCC. The 11q13 amplicon, including known oncogenes such as CCND1 and CTTN, is well-characterized in different type of cancers, but the roles of FADD and PPFIA1 remain obscure. Taken together, the integrated microarray analysis revealed a number of known as well as novel target genes in altered regions in HNSCC. The identified genes provide a basis for functional validation and may eventually lead to the identification of novel candidates for targeted therapy in HNSCC.

Post head-emergence frost resistance of barley genotypes in the northern grain region of Australia.

Post head-emergence frost causes substantial losses for Australian barley producers. Varieties with improved resistance would have a significant positive impact on Australian cropping enterprises. Five barley genotypes previously tested for reproductive frost resistance in southern Australia were tested, post head-emergence, in the northern grain region of Australia and compared with the typical northern control cultivars, Gilbert and Kaputar. All tested genotypes suffered severe damage to whole heads and stems at plant minimum temperatures less than -8degreesC. In 2003, 2004 and 2005, frost events reaching a plant minimum temperature of ~-6.5degreesC did not result in the complete loss of grain yield. Rather, partial seed set was observed. The control genotype, Gilbert, exhibited seed set that was greater than or equal to that of any genotype in each year, as did Kaputar when tested in 2005. Thus, Gilbert and Kaputar were at least as resistant as any tested genotype. This contrasts with trial results from the southern grain region where Gilbert was reported to be less resistant than Franklin, Amagi Nijo and Haruna Nijo. Hence, rankings for post head-emergence frost damage in the northern grain region differ from those previously reported. These results indicate that Franklin, Amagi Nijo and Haruna Nijo are not likely to provide useful sources of frost resistance or markers to develop improved varieties for the northern grain region of Australia.

Queensland Coastal Wetland Resources: Round Hill Head to Tin Can Inlet

The wetland resources of the Queensland coastline have been mapped by the Resource Condition and Trend Unit, Fisheries Group, Department of Primary Industries Queensland. This process is being undertaken in order to provide a baseline dataset for Fish Habitat Area (FHA) declaration, Ramsar site nomination and continued monitoring of these important fish habitats. This report summarises the results of the mapping undertaken from Round Hill Head to Tin Can Inlet. The study was undertaken in order to: 1. document and map the coastal wetland communities from Round Hill Head (24°S) to Tin Can Inlet (26°S); 2. document levels of existing disturbance to and protection of the wetlands; 3. examine existing recreational and commercial fisheries in the region; and 4. evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important and/or threatened species.

Current and emerging screening methods to identify post-head-emergence frost adaptation in wheat and barley

Cereal crops can suffer substantial damage if frosts occur at heading. Identification of post-head-emergence frost (PHEF) resistance in cereals poses a number of unique and difficult challenges. Many decades of research have failed to identify genotypes with PHEF resistance that could offer economically significant benefit to growers. Research and breeding gains have been limited by the available screening systems. Using traditional frost screening systems, genotypes that escape frost injury in trials due to spatial temperature differences and/or small differences in phenology can be misidentified as resistant. We believe that by improving techniques to minimize frost escapes, such ofalse-positive' results can be confidently identified and eliminated. Artificial freezing chambers or manipulated natural frost treatments offer many potential advantages but are not yet at the stage where they can be reliably used for frost screening in breeding programmes. Here we describe the development of a novel photoperiod gradient method (PGM) that facilitates screening of genotypes of different phenology under natural field frosts at matched developmental stages. By identifying frost escapes and increasing the efficiency of field screening, the PGM ensures that research effort can be focused on finding genotypes with improved PHEF resistance. To maximize the likelihood of identifying PHEF resistance, we propose that the PGM form part of an integrated strategy to (i) source germplasm;(ii) facilitate high throughput screening; and (iii) permit detailed validation. PGM may also be useful in other studies where either a range of developmental stages and/or synchronized development are desired.

Portrait of Ya'akov Meir [Jacob Meyer], Head of the Rabbinical Court and President of the Consistorium of the Community of Strasbourg; France.

Caption: J. Meyer, Grand-Rabbin et President du Consistoire Israelite du Department du Bas-Rhin a Strasbourg; also translated in Hebrew

Fusarium graminearum and Fusarium pseudograminearum caused the 2010 head blight epidemics in Australia

Wheat crops in southeast Queensland (Qld) and northern New South Wales (NSW) were infected with fusarium head blight (FHB)-like symptoms during the 201011 wheat growing season. Wheat crops in this region were surveyed at soft dough or early maturity stage to determine the distribution, severity, aetiology and toxigenicity of FHB. FHB was widespread on bread wheat and durum, and Fusarium graminearum and/or F.pseudograminearum were diagnosed from 42 of the 44 sites using species-specific PCR primers directly on spikelets or from monoconidial cultures obtained from spikelets. Stem base browning due to crown rot (CR) was also evident in some samples from both states. The overall FHB and CR severity was higher for NSW than Qld. Deoxynivalenol (DON) concentration of immature grains was more than 1 mg kg-1 in samples from 11 Qld and 14 NSW sites, but only 13 of 498 mature grain samples sourced from the affected areas had more than 1 mg kg-1 DON. DON concentration in straw also exceeded 1 mg kg-1 in eight Qld and all but one NSW sites but this was not linked to DON concentration of immature grains. The proportion of spikelets with positive diagnosis for F.graminearum and/or F.pseudograminearum and weather-related factors influenced DON levels in immature grains. The average monthly rainfall for AugustNovember during crop anthesis and maturation exceeded the long-term monthly average by 10150%. Weather played a critical role in FHB epidemics for Qld sites but this was not apparent for the NSW sites, as weather was generally favourable at all sites.

The relationship between forward head posture and cervical muscle performance in healthy individuals

Background Forward head postures (FHP) are proposed to adversely load cervical spine structures. Neck muscles provide support for the neck, and thus an imbalance in neck muscle performance could potentially contribute to the development of FHP. Previous studies have not considered the interaction of multiple muscle groups with regard to postural orientation. Given the interdependence of muscles along the cervical spine for optimal orientation and physical support of the vertebral column, the performance of a single muscle group may not accurately reflect the coordinated ability of the muscles to maintain a neutral neck posture. Purpose The purpose of this study was to investigate the relationship between FHP and the balance between the cervical extensor and flexor muscle groups in healthy individuals. We hypothesised that the magnitude of FHP would be associated with the strength and endurance performance ratios between the cervical extensor and flexor muscle groups. Methods Twenty male and 24 female volunteers were photographed in the sagittal plane wearing surface markers. The FHP of each participant was measured via the tragus-sternum marker distance over two conditions: (1)in relaxed standing and (2)during a sustained sitting task. Maximal strength (Nm) and endurance (s) performance of the extensor and flexor muscle groups were recorded at the upper (craniocervical flexion/extension (CCF/CCE)) and lower (cervicothoracic flexion/extension (CTF/CTE)) cervical regions. Muscle performance measures were expressed as extension:flexion ratios and their relation to FHP evaluated. A stepwise multiple regression analysis using backward elimination was utilised to examine the relationship between the postural measures and the muscle performance ratio measures. Separate models were used for the two different postural conditions (standing, sustained sitting). Gender was included as a constant correction factor in all regression models. Where gender was a significant variable in the model, analyses were repeated separately for males and females. Results Greater FHP in standing was significantly associated with reduced proportional CTE to CCF strength in females (R2 = 0.21, P = 0.03) and greater proportional CTE to CTF strength in males (R2 = 0.23, P = 0.03). A greater drift into FHP during sustained sitting was associated with a relative reduction in CCE endurance proportional to CTF endurance in females only (R2 = 0.27, P = 0.017). Conclusion(s) This initial study indicates that the balance in performance between the cervical flexor and extensor muscle groups may impact FHP in healthy individuals. However, the findings were inconsistent across different muscle performance ratios and gender. Larger scale studies are therefore now needed to further clarify the relationship between FHP and muscle performance. Implications The findings suggest that relative performance of the various cervical muscle groups needs to be accounted for when considering postural correction strategies in the clinical setting, as is often recommended.

Does flexibility of the cervical and thoracic spine influence forward head posture in healthy individuals?

Background: Forward head posture (FHP) is a commonly reported deviation from a neutral neck posture, usually implying a protracted head position in the sagittal plane. Habitual FHP has been associated with a higher incidence of painful neck disorders, changes in joint mobility and muscle behaviour within the cervicothoracic regions. One factor that has received attention in the literature with regards to FHP is flexibility of the neck. A number of previous studies have previously investigated the relationship between neck flexibility and neck posture under different conditions, but at present this relationship is unclear.

A Framework for Detecting Glaucomatous Progression in the Optic Nerve Head of an Eye Using Proper Orthogonal Decomposition

Glaucoma is the second leading cause of blindness worldwide. Often, the optic nerve head (ONH) glaucomatous damage and ONH changes occur prior to visual field loss and are observable in vivo. Thus, digital image analysis is a promising choice for detecting the onset and/or progression of glaucoma. In this paper, we present a new framework for detecting glaucomatous changes in the ONH of an eye using the method of proper orthogonal decomposition (POD). A baseline topograph subspace was constructed for each eye to describe the structure of the ONH of the eye at a reference/baseline condition using POD. Any glaucomatous changes in the ONH of the eye present during a follow-up exam were estimated by comparing the follow-up ONH topography with its baseline topograph subspace representation. Image correspondence measures of L-1-norm and L-2-norm, correlation, and image Euclidean distance (IMED) were used to quantify the ONH changes. An ONH topographic library built from the Louisiana State University Experimental Glaucoma study was used to evaluate the performance of the proposed method. The area under the receiver operating characteristic curves (AUCs) was used to compare the diagnostic performance of the POD-induced parameters with the parameters of the topographic change analysis (TCA) method. The IMED and L-2-norm parameters in the POD framework provided the highest AUC of 0.94 at 10 degrees. field of imaging and 0.91 at 15 degrees. field of imaging compared to the TCA parameters with an AUC of 0.86 and 0.88, respectively. The proposed POD framework captures the instrument measurement variability and inherent structure variability and shows promise for improving our ability to detect glaucomatous change over time in glaucoma management.

Post-head-emergence frost in wheat and barley: defining the problem, assessing the damage, and identifying resistance

Radiant frost is a significant production constraint to wheat (Triticum aestivum) and barley (Hordeum vulgare), particularly in regions where spring-habit cereals are grown through winter, maturing in spring. However, damage to winter-habit cereals in reproductive stages is also reported. Crops are particularly susceptible to frost once awns or spikes emerge from the protection of the flag leaf sheath. Post-head-emergence frost (PHEF) is a problem distinct from other cold-mediated production constraints. To date, useful increased PHEF resistance in cereals has not been identified. Given the renewed interest in reproductive frost damage in cereals, it is timely to review the problem. Here we update the extent and impacts of PHEF and document current management options to combat this challenge. We clarify terminology useful for discussing PHEF in relation to chilling and other freezing stresses. We discuss problems characterizing radiant frost, the environmental conditions leading to PHEF damage, and the effects of frost at different growth stages. PHEF resistant cultivars would be highly desirable, to both reduce the incidence of direct frost damage and to allow the timing of crop maturity to be managed to maximize yield potential. A framework of potential adaptation mechanisms is outlined. Clarification of these critical issues will sharpen research focus, improving opportunities to identify genetic sources for improved PHEF resistance.

Post-head-emergence frost in wheat and barley: defining the problem, assessing the damage, and identifying resistance

Radiant frost is a significant production constraint to wheat (Triticum aestivum) and barley (Hordeum vulgare), particularly in regions where spring-habit cereals are grown through winter, maturing in spring. However, damage to winter-habit cereals in reproductive stages is also reported. Crops are particularly susceptible to frost once awns or spikes emerge from the protection of the flag leaf sheath. Post-head-emergence frost (PHEF) is a problem distinct from other cold-mediated production constraints. To date, useful increased PHEF resistance in cereals has not been identified. Given the renewed interest in reproductive frost damage in cereals, it is timely to review the problem. Here we update the extent and impacts of PHEF and document current management options to combat this challenge. We clarify terminology useful for discussing PHEF in relation to chilling and other freezing stresses. We discuss problems characterizing radiant frost, the environmental conditions leading to PHEF damage, and the effects of frost at different growth stages. PHEF resistant cultivars would be highly desirable, to both reduce the incidence of direct frost damage and to allow the timing of crop maturity to be managed to maximize yield potential. A framework of potential adaptation mechanisms is outlined. Clarification of these critical issues will sharpen research focus, improving opportunities to identify genetic sources for improved PHEF resistance.

New yellow head virus genotype (YHV7) in giant tiger shrimp Penaeus monodon indigenous to northern Australia

ABSTRACT: In 2012, giant tiger shrimp Penaeus monodon originally sourced from Joseph Bonaparte Gulf in northern Australia were examined in an attempt to identify the cause of elevated mortalities among broodstock at a Queensland hatchery. Nucleic acid extracted from ethanol-fixed gills of 3 individual shrimp tested positive using the OIE YHV Protocol 2 RT-PCR designed to differentiate yellow head virus (YHV1) from gill-associated virus (GAV, synonymous with YHV2) and the OIE YHV Protocol 3 RT-nested PCR designed for consensus detection of YHV genotypes. Sequence analysis of the 794 bp (Protocol 2) and 359 bp (Protocol 3) amplicons from 2 distinct regions of ORF1b showed that the yellow-head-complex virus detected was novel when compared with Genotypes 1 to 6. Nucleotide identity on the Protocol 2 and Protocol 3 ORF1b sequences was highest with the highly pathogenic YHV1 genotype (81 and 87%, respectively) that emerged in P. monodon in Thailand and lower with GAV (78 and 82%, respectively) that is enzootic to P. monodon inhabiting eastern Australia. Comparison of a longer (725 bp) ORF1b sequence, spanning the Protocol 3 region and amplified using a modified YH30/31 RT-nPCR, provided further phylogenetic evidence for the virus being distinct from the 6 described YHV genotypes. The virus represents a unique seventh YHV genotype (YHV7). Despite the mortalities observed, the role of YHV7 remains unknown.

Head motion and Inattention/Hyperactivity share common genetic influences: Implications for fMRI studies of ADHD

Head motion (HM) is a well known confound in analyses of functional MRI (fMRI) data. Neuroimaging researchers therefore typically treat HM as a nuisance covariate in their analyses. Even so, it is possible that HM shares a common genetic influence with the trait of interest. Here we investigate the extent to which this relationship is due to shared genetic factors, using HM extracted from resting-state fMRI and maternal and self report measures of Inattention and Hyperactivity-Impulsivity from the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scales. Our sample consisted of healthy young adult twins (N = 627 (63% females) including 95 MZ and 144 DZ twin pairs, mean age 22, who had mother-reported SWAN; N = 725 (58% females) including 101 MZ and 156 DZ pairs, mean age 25, with self reported SWAN). This design enabled us to distinguish genetic from environmental factors in the association between head movement and ADHD scales. HM was moderately correlated with maternal reports of Inattention (r = 0.17, p-value = 7.4E-5) and Hyperactivity-Impulsivity (r = 0.16, p-value = 2.9E-4), and these associations were mainly due to pleiotropic genetic factors with genetic correlations [95% CIs] of rg = 0.24 [0.02, 0.43] and rg = 0.23 [0.07, 0.39]. Correlations between self-reports and HM were not significant, due largely to increased measurement error. These results indicate that treating HM as a nuisance covariate in neuroimaging studies of ADHD will likely reduce power to detect between-group effects, as the implicit assumption of independence between HM and Inattention or Hyperactivity-Impulsivity is not warranted. The implications of this finding are problematic for fMRI studies of ADHD, as failing to apply HM correction is known to increase the likelihood of false positives. We discuss two ways to circumvent this problem: censoring the motion contaminated frames of the RS-fMRI scan or explicitly modeling the relationship between HM and Inattention or Hyperactivity-Impulsivity