Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC.

Small RNA-mediated chromatin silencing is well characterized for repeated sequences and transposons, but its role in regulating single-copy endogenous genes is unclear. We have identified two small RNAs (30 and 24 nucleotides) corresponding to the reverse strand 3' to the canonical poly(A) site of FLOWERING LOCUS C (FLC), an Arabidopsis gene encoding a repressor of flowering. Genome searches suggest that these RNAs originate from the FLC locus in a genomic region lacking repeats. The 24-nt small RNA, which is most abundant in developing fruits, is absent in mutants defective in RNA polymerase IVa, RNA-DEPENDENT RNA POLYMERASE 2, and DICER-LIKE 3, components required for RNAi-mediated chromatin silencing. The corresponding genomic region shows histone 3 lysine 9 dimethylation, which was reduced in a dcl2,3,4 triple mutant. Investigations into the origins of the small RNAs revealed a polymerase IVa-dependent spliced, antisense transcript covering the 3' FLC region. Mutation of this genomic region by T-DNA insertion led to FLC misexpression and delayed flowering, suggesting that RNAi-mediated chromatin modification is an important component of endogenous pathways that function to suppress FLC expression.

Exclusion of linkage between schizophrenia and the D2 dopamine receptor gene region of chromosome 11q in 112 Irish multiplex families

A leading theory hypothesizes that schizophrenia arises from dysregulation of the dopamine system in certain brain regions. As this dysregulation could arise from abnormal expression of D2 dopamine receptors, the D2 receptor gene (DRD2) on chromosome 11q is a candidate locus for schizophrenia. We tested whether allelic variation at DRD2 and five surrounding loci cosegregated with schizophrenia in 112 small- to moderate-size Irish families containing two or more members affected with schizophrenia or schizoaffective disorder, defined by DSM-III-R. Evidence of linkage was assessed using varying definitions of illness and modes of transmission. Assuming genetic homogeneity, linkage between schizophrenia and large regions of 11q around DRD2 could be strongly excluded. Assuming genetic heterogeneity, variation at the DRD2 locus could be rejected as a major risk factor for schizophrenia in more than 50% of these families for all models tested and in as few as 25% of the families for certain models. The DRD2 linkage in fewer than 25% of these families could not be excluded under any of the models tested. Our results suggest that the major component of genetic susceptibility to schizophrenia is not due to allelic variation at the DRD2 locus or other genes in the surrounding chromosomal region.

Mutations within subdomain II of the extracellular region of epidermal growth factor receptor selectively alter TGF alpha binding

The interactions of epidermal growth factor (EGF) and transforming growth factor alpha (TGF alpha) with the epidermal growth factor receptor (EGFR) were examined by insertion mutagenesis of the receptor. Seventeen insertions were made throughout a construct containing only the extracellular domain. This truncated receptor (sEGFR) was secreted and had a dissociation constant similar to that of the full-length solubilized receptor. Receptors with insertions within subdomain III were not secreted. Two receptors with insertions at positions 291 and 474, which border subdomain III, have significantly decreased binding to both EGF and TGF alpha relative to wild type. This confirms previous work demonstrating that subdomain III forms the primary binding site for EGF and TGF alpha. Four of the mutants within subdomain II had a decreased binding to TGF alpha relative to wild type, but had wild type binding to EGF. These results suggest that a region within subdomain II may selectively regulate the binding of TGF alpha. Two receptors which contained insertions within subdomains II and IV, approximately equidistant from the center of subdomain III, bound twofold more ligand molecules than wild type receptor, with an affinity similar to that of wild type receptor. These findings suggest that insertion at these positions allows the access of more than one ligand molecule to the binding site.

Validation of a regional Indonesian seas model based on a comparison between model and INSTANT transports

The International Nusantara Stratification and Transport (INSTANT) program measured currents through multiple Indonesian Seas passages simultaneously over a three-year period (from January 2004 to December 2006). The Indonesian Seas region has presented numerous challenges for numerical modelers - the Indonesian Throughflow (ITF) must pass over shallow sills, into deep basins, and through narrow constrictions on its way from the Pacific to the Indian Ocean. As an important region in the global climate puzzle, a number of models have been used to try and best simulate this throughflow. In an attempt to validate our model, we present a comparison between the transports calculated from our model and those calculated from the INSTANT in situ measurements at five passages within the Indonesian Seas (Labani Channel, Lifamatola Passage, Lombok Strait, Ornbai Strait, and Timor Passage). Our Princeton Ocean Model (POM) based regional Indonesian Seas model was originally developed to analyze the influence of bottom topography on the temperature and salinity distributions in the Indonesian seas region, to disclose the path of the South Pacific Water from the continuation of the New Guinea Coastal Current entering the region of interest up to the Lifamatola Passage, and to assess the role of the pressure head in driving the ITF and in determining its total transport. Previous studies found that this model reasonably represents the general long-term flow (seasons) through this region. The INSTANT transports were compared to the results of this regional model over multiple timescales. Overall trends are somewhat represented but changes on timescales shorter than seasonal (three months) and longer than annual were not considered in our model. Normal velocities through each passage during every season are plotted. Daily volume transports and transport-weighted temperature and salinity are plotted and seasonal averages are tabulated.

Study of localized damage in composite laminates using micro-macro approach

A robust multiscale scheme referred to as micro–macro method has been developed for the prediction of localized damage in fiber reinforced composites and implemented in a finite element framework. The micro–macro method is based on the idea of partial homogenization of a structure. In this method, the microstructural details are included in a small region of interest in the structure and the rest is modeled as a homogeneous continuum. The solution to the microstructural fields is then obtained on solving the two different domains, simultaneously. This method accurately predicts local stress fields in stress concentration regions and is computationally efficient as compared with the solution of a full scale microstructural model. This scheme has been applied to obtain localized damage at high and low stress zones of a V-notched rail shear specimen. The prominent damage mechanisms under shear loading, namely, matrix cracking and interfacial debonding, have been modeled using Mohr–Coulomb plasticity and traction separation law, respectively. The average stress at the notch has been found to be 44% higher than the average stresses away from the notch for a 90 N shear load. This stress rise is a direct outcome of the geometry of the notch.

Study on risk assessment and management and prevention of conflicts of interest in the prevention and fight against betting-related match fixing in the EU 28: Final Report

This report concerns the provisions and practices on betting-related match fixing in sports
within the 28 Member States. Carried out in late 2013/early 2014, respondents in each Member
State reported on that state’s gambling-related provisions in respect of football and tennis and
(in each country) a third sport determined on the basis of either its popularity (in terms of
participation or television viewing) or the existence of betting-related “scandals” in that sport
within that particular jurisdiction. Those reports helped the authors to compare the Member
States’ regulatory and self-regulatory frameworks relating to risk assessment and conflict of
interest management, with a view to indicating areas of best practice, identifying particularly
good legislative frameworks and highlighting areas where change was either desirable or
necessary. While some individual Member States have legislation which might provide
templates that others could adapt for their own use, the authors were not convinced that “more
law”, whether at the national or European level, was desirable. Rather, more effective
cooperation among the stakeholders was identified as being more likely to provide tangible
benefits than would new legal frameworks.

Partial shoeprint retrieval using multiple point-of-interest detectors and SIFT descriptors

Shoeprint evidence collected from crime scenes can play an important role in forensic investigations. Usually, the analysis of shoeprints is carried out manually and is based on human expertise and knowledge. As well as being error prone, such a manual process can also be time consuming; thus affecting the usability and suitability of shoeprint evidence in a court of law. Thus, an automatic system for classification and retrieval of shoeprints has the potential to be a valuable tool. This paper presents a solution for the automatic retrieval of shoeprints which is considerably more robust than existing solutions in the presence of geometric distortions such as scale, rotation and scale distortions. It addresses the issue of classifying partial shoeprints in the presence of rotation, scale and noise distortions and relies on the use of two local point-of-interest detectors whose matching scores are combined. In this work, multiscale Harris and Hessian detectors are used to select corners and blob-like structures in a scale-space representation for scale invariance, while Scale Invariant Feature Transform (SIFT) descriptor is employed to achieve rotation invariance. The proposed technique is based on combining the matching scores of the two detectors at the score level. Our evaluation has shown that it outperforms both detectors in most of our extended experiments when retrieving partial shoeprints with geometric distortions, and is clearly better than similar work published in the literature. We also demonstrate improved performance in the face of wear and tear. As matter of fact, whilst the proposed work outperforms similar algorithms in the literature, it is shown that achieving good retrieval performance is not constrained by acquiring a full print from a scene of crime as a partial print can still be used to attain comparable retrieval results to those of using the full print. This gives crime investigators more flexibility is choosing the parts of a print to search for in a database of footwear.

Fingerprint Volatile Organic Compounds (VOC) analysis in Goat’s Milk and Halloumi Cheese as Marker for Authentication of Region of Origin

Goats’ milk is responsible for unique traditional products such as Halloumi cheese. The characteristics of Halloumi depend on the original features of the milk and on the conditions under which the milk has been produced such as feeding regime of the animals or region of production. Using a range of milk (33) and Halloumi (33) samples collected over a year from three different locations in Cyprus (A, Anogyra; K, Kofinou; P, Paphos), the potential for fingerprint VOC analysis as marker to authenticate Halloumi was investigated. This unique set up consists of an in-injector thermo desorption (VOCtrap needle) and a chromatofocusing system based on mass spectrometry (VOCscanner). The mass spectra of all the analyzed samples are treated by multivariate analysis (Principle component analysis and Discriminant functions analysis). Results showed that the highland area of product (P) is clearly identified in milks produced (discriminant score 67%). It is interesting to note that the higher similitude found on milks from regions “A” and “K” (with P being distractive; discriminant score 80%) are not ‘carried over’ on the cheeses (higher similitude between regions “A” and “P”, with “K” distinctive). Data have been broken down into three seasons. Similarly, the seasonality differences observed in different milks are not necessarily reported on the produced cheeses. This is expected due to the different VOC signatures developed in cheeses as part of the numerous biochemical changes during its elaboration compared to milk. VOC however it is an additional analytical tool that can aid in the identification of region origin in dairy products.

New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Cyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3-62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means.

Privacy Region Protection for H.264/AVC with Enhanced Scrambling Effect and a Low Bitrate Overhead

While video surveillance systems have become ubiquitous in our daily lives, they have introduced concerns over privacy invasion. Recent research to address these privacy issues includes a focus on privacy region protection, whereby existing video scrambling techniques are applied to specific regions of interest (ROI) in a video while the background is left unchanged. Most previous work in this area has only focussed on encrypting the sign bits of nonzero coefficients in the privacy region, which produces a relatively weak scrambling effect. In this paper, to enhance the scrambling effect for privacy protection, it is proposed to encrypt the intra prediction modes (IPM) in addition to the sign bits of nonzero coefficients (SNC) within the privacy region. A major issue with utilising encryption of IPM is that drift error is introduced outside the region of interest. Therefore, a re-encoding method, which is integrated with the encryption of IPM, is also proposed to remove drift error. Compared with a previous technique that uses encryption of IPM, the proposed re-encoding method offers savings in the bitrate overhead while completely removing the drift error. Experimental results and analysis based on H.264/AVC were carried out to verify the effectiveness of the proposed methods. In addition, a spiral binary mask mechanism is proposed that can reduce the bitrate overhead incurred by flagging the position of the privacy region. A definition of the syntax structure for the spiral binary mask is given. As a result of the proposed techniques, the privacy regions in a video sequence can be effectively protected by the enhanced scrambling effect with no drift error and a lower bitrate overhead.

A let-7 microRNA-binding site polymorphism in 3'-untranslated region of KRAS gene predicts response in wild-type KRAS patients with metastatic colorectal cancer treated with cetuximab monotherapy

PURPOSE: recent studies have found that KRAS mutations predict resistance to monoclonal antibodies targeting the epidermal growth factor receptor in metastatic colorectal cancer (mCRC). A polymorphism in a let-7 microRNA complementary site (lcs6) in the KRAS 3' untranslated region (UTR) is associated with an increased cancer risk in non-small-cell lung cancer and reduced overall survival (OS) in oral cancers. We tested the hypothesis whether this polymorphism may be associated with clinical outcome in KRAS wild-type (KRASwt) mCRC patients treated with cetuximab monotherapy.

PATIENTS AND METHODS: the presence of KRAS let-7 lcs6 polymorphism was evaluated in 130 mCRC patients who were enrolled in a phase II study of cetuximab monotherapy (IMCL-0144). Genomic DNA was extracted from dissected formalin-fixed paraffin-embedded tumor tissue, KRAS mutation status and polymorphism were assessed using direct sequencing and PCR restriction fragment length polymorphism technique.

RESULTS: KRAS let-7 lcs6 polymorphism was found to be related to object response rate (ORR) in mCRC patients whose tumors had KRASwt. The 12 KRASwt patients harboring at least a variant G allele (TG or GG) had a 42% ORR compared with a 9% ORR in 55 KRASwt patients with let-7 lcs6 TT genotype (P = 0.02, Fisher's exact test). KRASwt patients with TG/GG genotypes had trend of longer median progression-free survival (3.9 versus 1.3 months) and OS (10.7 versus 6.4 months) compared to those with TT genotypes.

CONCLUSIONS: these results are the first to indicate that the KRAS 3'UTR polymorphism may predict for cetuximab responsiveness in KRASwt mCRC patients, which warrants validation in other clinical trials.

Identification of descendants of an extinct bovine population from the Algarve region of Portugal using numerical taxonomy analysis of morphological traits

The morphology of a sample of four bulls and 43 cows, presumed to be descendants of the extinct cattle breed ‘Algarvia’ (AG), was used to assign their relationship with animals from other Portuguese autochthonous breeds – Arouquesa (AR), Barrosa˜ (BA), Cachena (CA), Marinhoa (MA), Maronesa (MO), Minhota (MN), Mirandesa (MI), (only bulls), Alentejana (AL), Garvonesa (GA), Mertolenga (ME) and Preta (PR). Standard numerical taxonomic methods were applied to a set of 183 (cows) and 170 (bulls) traits, to derive average pairwise taxonomic distances among the sample of 257 cows and 76 bulls. Distance coefficients (morphological index of distance) ranged from 0.22 to 2.62 (cows) and from 0.49 to 2.13 (bulls). Unweighted pair group method using arithmetic averages (UPGMA)-based phenograms and a principal coordinate analysis showed that bulls were highly clustered and cows showed a tendency to cluster according to their geographical and breed origin. The AG population grouped together with GA, AL, ME and MN breeds in the Red Convex group. The average taxonomic distance among breeds was 1.02, the highest being 1.39 (ME versus BA) and the lowest being 0.64 (MA versus AR). The approach allowed for the identification of a phenotypically differentiated set of animals, comprising 19 cows and four bulls representative of the AG breed, and which can be targeted in further studies aiming at the recovery of this extinct breed.

A Method For Producing Airborne Pollen Source Inventories: An Example of Ambrosia (Ragweed) on the Pannonian Plain

We present here a simple methodology for calculating species inventories for allergenic pollen that can be used by atmospheric transport models. Ragweed (Ambrosia) species distribution or infection level on the Pannonian Plain has been used as an example of how the methodology can be used. The Pannonian Plain is one of the three main regions in Europe recognized as being polluted by Ambrosia. The methodology relies on spatial variations in annual Ambrosia pollen counts, knowledge on ragweed ecology and detailed land cover information. The results of this analysis showed that some of the highest mean annual ragweed pollen concentrations were witnessed around Kecskemét in central Hungary and Novi Sad in northern Serbia. These areas are also the areas with the highest density of Ambrosia habitats. The resulting inventory can be entered into atmospheric transport models in combination with other components such as a phenological model and a model for daily pollen release, in order to simulate the movement of ragweed pollen from the Pannonian Plain. The methodology is likely to be generally applicable for creating inventories of species distribution of allergenic plants. The main requirement is availability of: detailed land cover information; pollen indexes; a list of the most important habitats; and a region of interest that is mainly influenced by local sources.

Enzymatic grafting: A novel approach to develop multifunctional materials of interest

Today more than 99% of plastics are petroleum-based because of the availability and cost of the raw material. The durability of disposed plastics contributes to the environmental problems as waste and their persistence in the environment causes deleterious effects on the ecosystem. Environmental pollution awareness and the demand for green technology have drawn considerable attention of both academia and industry into biodegradable polymers. In this regard green chemistry technology has the potential to provide solution to this issue. Enzymatic grafting has recently been the focus of green chemistry technologies due to the growing environmental concerns, legal restrictions, and increasing availability of scientific knowledge. Over the last several years, research covering various applications of robust enzymes like laccases and lipases has been increased rapidly, particularly in the field of polymer science, to graft multi-functional materials of interest. In principle, enzyme-assisted grafting may modify/impart a variety of functionalities to the grafted composites which individual materials fail to demonstrate on their own. The modified polymers through grafting have a bright future and their development is practically boundless. In the present study series of graft composites with poly(3-hydroxybutyrate) (P(3HB) as side chain and cellulose as a backbone polymer were successfully synthesised by introducing enzymatic grafting technique where laccase and lipase were used as model catalysts [1-3]. Subsequently, the resulting composites were removed from the casting surface under ambient environment and characterised by Fourier-transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), and X-ray diffraction (XRD) in detail. Moreover, the thermo-mechanical behaviours of the grafted composites were investigated by differential scanning calorimetry (DSC) and dynamic mechanical analyser (DMA) measurements, respectively. In addition, hydrophobic and hydrophilic characteristics of the grafted polymers were studied through drop contour analysis using water contact angle (WCA). In comparison to the individual counterparts improvement was observed in the thermo- mechanical properties of the composites to varied extent. The tensile strength, elongation at break, and Young’s modulus values of the composites reached their highest levels in comparison to the films prepared with pure P(3HB) only which was too fragile to measure any of the above said characteristics. Interestingly, untreated P(3HB) was hydrophobic in nature and after lipase treatment P(3HB) and P(3HB)-EC-based graft composite attained higher level of hydrophilicity. This is a desired characteristic that enhances the biocompatibility of the materials for proper cell adhesion and proliferation therefore suggesting potential candidates for tissue engineering/bio-medical type applications [3]. The present research will be a first step in the biopolymer modification. To date no report has been found in literature explaining the laccase/lipase assisted grafting of P(3HB) [1-3]. The newly grafted composites exhibit unique functionalities with wider range of potential applications in bio-plastics, pharmaceutical, and cosmetics industries, tissue engineering, and biosensors. [1] H.M.N. Iqbal, G. Kyazze, T. Tron and T. Keshavarz, Cellulose 21, 3613-3621 (2014). [2] H.M.N. Iqbal, G. Kyazze, T. Tron and T. Keshavarz, Carbohydrate Polymers 113, 131-137 (2014). [3] H.M.N. Iqbal, G. Kyazze, T. Tron and T. Keshavarz, Polymer Chemistry In-Press, DOI: 10.1039/C4PY0 0857J (2014).