bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying risk in the use of tumor markers to improve patient safety
Authors: Moreno-Campoy Elvira Eva , Mérida-De la Torre Francisco J. , Martos-Crespo Francisco , Plebani Mario
Published: March 2016

Background:

Tumor markers (TM) are a routine test that are not always used well, and can lead to unnecessary additional tests, which are not without risks for the patients. So, to implement appropriate strategies to improve the adequate use of TM and, therefore, improve patient safety, is required to analyze the use of TM, identifying risks and establishing if there are differences in their use as a function of their utility.

Methods:

The study was a descriptive, longitudinal, retrospective and systematic study in the area covered by the University Hospital of Padua. In the follow-up 2-year study, 23,059 analytical requests of TM, corresponding to 14,728 patients, were analyzed. For the level of statistical significance it applies an approximation of the normal law (Z statistic) and χ2-test.

Results:

Only 9196 requests (39.88%) out of a total of 23,059 on 5080 patients with neoplastic diseases have been classified as adecuate according to current guidelines. The number of requests per patient was variable (1.57±1.35). In patients with neoplastic diseases this increased to 1.80±1.68. The mean of number of TM per request was 2.4±1.73. The analysis showed an association between the number of requests and the type of marker used.

Conclusions:

The use of TM is variable, mainly of the follow-up markers, when they are used as screening. This inappropriate use, minimizes their utility favoring erroneous interpretations and increases the risk of damage to the patient. So it is essential to implement safe practices in the use of TM.
Mathematical Modeling and Investigation on the Temperature and Pressure Dependency of Permeation and Membrane Separation Performance for Natural gas Treatment
Authors: Hosseini Seyed Saeid , Dehkordi Javad Aminian , Kundu Prodip K.
Published: March 2016

Due to special features, modules comprising asymmetric hollow fiber membranes are widely used in various industrial gas separation processes. Accordingly, numerous mathematical models have been proposed for predicting and analyzing the performance. However, majority of the proposed models for this purpose assume that membrane permeance remains constant upon changes in temperature and pressure. In this study, a mathematical model is proposed by taking into account non-ideal effects including changes in pressure and temperature in both sides of hollow fibers, concentration polarization and Joule-Thomson effects. Finite element method is employed to solve the governing equations and model is validated using experimental data. The effect of temperature and pressure dependency of permeance and separation performance of hollow fiber membrane modules is investigated in the case of CO2/CH4. The effect of temperature and pressure dependence of membrane permeance is studied by using type Arrhenius type and partial immobilization equations to understand which form of the equations fits experimental data best. Findings reveal that the prediction of membrane performance for CO2/CH4 separation is highly related to pressure and temperature; the models considering temperature and pressure dependence of membrane permeance match experimental data with higher accuracy. Also, results suggest that partial immobilization model represents a better prediction to the experimental data than Arrhenius type equation.
Multi-objective Optimization of Preparation Conditions of Asymmetric Polyetherimide Membrane for Prevaporation of Isopropanol
Authors: Nabavi Seyed Reza
Published: March 2016

Multi-objective optimization is used in many chemical engineering fields that have conflict objective functions. Prevaporation is an effective process for removing trace or minor amount of the component of diluting solutions. This process is used for dehydration of alcohols containing small amounts of water. In this process membrane flux and separation factor have conflict with each other. So a multi-objective optimization approach can be used for optimization of the process. In this paper, in first stage a neural network based model was developed for preparation conditions for polyetherimide membrane in isopropanol prevaporation. Four major variables involved in the membrane preparation procedure, including polymer concentration, additive content, solvent evaporation temperature and time was considered. Membrane flux and separation factor were considered as objective functions. Elitist Non-dominated sorting genetic algorithm with jumping gene and altruistic adaptation (Alt-NSGA-aJG) was applied for simultaneous maximization of flux and separation factor. Pareto optimal solutions for membrane preparation conditions and effect of decision variables (four preparation variables) on Pareto front were investigated.
Ultrasound guided joint space distance changes during manual traction of acromioclavicular joint in young and healthy adults
Authors: Marciniak Tomasz , Brożyński Maciej , Wit Andrzej
Published: March 2016

Introduction: Manual traction is a commonly used technique in manual therapy. However, depicting changes in joint space distance via real time imaging during traction is seldomly applied. The aims of the study were to identify ACJ joint space distance changes during manual traction and creation of a classification of the techniques upon the largest change in the resultant parameter (l) representing joint space distance.

Material and methods: Thirteen healthy volunteers were examined unilaterally. Acromioclavicular joint space distance changes were measured with dynamic ultrasound imaging during followingmanual traction techniques: International Academy of Orthopedic Medicine technique (IAOM AC), Karel Lewit’s Prague School of Manual Medicine & Rehabilitation technique (LAC) and author’s own proposition (B AC). The differences in joint space distance between resting position (RP) and the traction technique position, created three parameters of displacement - horizontal (x), vertical (y) and (l) - the resultant component.

Results: Parameters were not coherent with normal distribution. Statistical differences showed significance in the (x) parameter for IAOM AC compared with L AC (p<0,0183) and B AC (p<0,02). All techniques presented a significant increase of the resultant distance (l), compared with RP as the reference value - IAOM AC p<0,0036, L AC and B AC p<0,0000. In few cases L AC decreased the distance in the (x) parameter, but not significantly.

Conclusions:

1.Significant changes of (x) parameter did not correspond with the significance of the resultant parameter (l), which prevented authors from creating a classification of the techniques.

2.All traction techniques used in the study increased the joint space distance compared to RP, which confirms traction’s theoretical assumptions.

3.For clinical purpose the change of (x) parameter may prove crucial for therapy’s effectiveness, despite lack of change in the joint space distance in the resultant parameter (l) by itself.
The “CHILD” framework for the study of artisanal mercury mining communities
Authors: Van Brussel Evelyn , Carrizales Leticia , Flores-Ramirez Rogelio , Camacho Andrea , Leon-Arce Mauricio , Diaz-Barriga Fernando
Published: March 2016

In this paper, our group reports the use of a new framework in sites contaminated with mercury. This is significant because under the Minamata Convention on Mercury each Party shall endeavor to develop appropriate strategies for identifying and assessing sites contaminated by mercury or mercury compounds. This new approach, the “CHILD” framework has five steps: i) Community-based risk characterization; ii) Habilitation; iii) Intervention; iv) Laws and Regulation; and v) Development. We are using this framework in three mercury artisanal mining sites, and preliminary results are depicted in this report.
Arsenic projects in SE Asia
Authors: Navasumrit Panida , Chaisatra Krittinee , Ruchirawat Mathuros
Published: March 2016

Early life exposure to inorganic arsenic is associated with a wide range of malignant and chronic disease outcomes in humans. Prenatal arsenic exposure may give rise to adverse effects on child health and development as arsenic readily passes through the placenta in human beings. The impact of maternal arsenic exposure on fetal gene expression was conducted in pregnant women living in Southern Thailand. Arsenic exposed newborns had significantly higher levels of arsenic in cord blood, and a set of genes associated with numerous biological pathways, including cell signaling, apoptosis, inflammatory and stress response. A slight increase in promoter methylation of p53 in cord blood lymphocytes which correlated with arsenic accumulation in nails was observed in these exposed newborns. A follow-up study on these exposed children showed a significant increase in oxidative DNA damage, measured as 8-hydroxydeoxyguanosine (8-OHdG) in saliva. In addition, levels of urinary 8-OHdG excretion and salivary hOGG1 expression were significantly decreased in exposed children suggesting a defect in repair of 8-OHdG in arsenic-exposed children. Our study indicates that prenatal arsenic and continued exposure through early childhood can trigger various genetic and epigenetic alterations that may lead to disease development later in life.
Robust estimation of nonstationary, fractionally integrated, autoregressive, stochastic volatility
Authors: Jensen Mark J.
Published: March 2016

Empirical volatility studies have discovered nonstationary, long-memory dynamics in the volatility of the stock market and foreign exchange rates. This highly persistent, infinite variance, but still mean reverting, behavior is commonly found with nonparametric estimates of the fractional differencing parameter,
Toxic gain of function from mutant FUS protein is crucial to trigger cell autonomous motor neuron loss
Authors: Scekic‐Zahirovic Jelena , Sendscheid Oliver , El Oussini Hajer , Jambeau Mélanie , Sun Ying , Mersmann Sina , Wagner Marina , Dieterlé Stéphane , Sinniger Jérome , Dirrig‐Grosch Sylvie , Drenner Kevin , Birling Marie‐Christine , Qiu Jinsong , Zhou Yu , Li Hairi , Fu Xiang‐Dong , Rouaux Caroline , Shelkovnikova Tatyana , Witting Anke , Ludolph Albert C , Kiefer Friedemann , Storkebaum Erik , Lagier‐Tourenne Clotilde , Dupuis Luc
Published: March 2016

FUS is an RNA‐binding protein involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS‐containing aggregates are often associated with concomitant loss of nuclear FUS. Whether loss of nuclear FUS function, gain of a cytoplasmic function, or a combination of both lead to neurodegeneration remains elusive. To address this question, we generated knockin mice expressing mislocalized cytoplasmic FUS and complete FUS knockout mice. Both mouse models display similar perinatal lethality with respiratory insufficiency, reduced body weight and length, and largely similar alterations in gene expression and mRNA splicing patterns, indicating that mislocalized FUS results in loss of its normal function. However, FUS knockin mice, but not FUS knockout mice, display reduced motor neuron numbers at birth, associated with enhanced motor neuron apoptosis, which can be rescued by cell‐specific CRE‐mediated expression of wild‐type FUS within motor neurons. Together, our findings indicate that cytoplasmic FUS mislocalization not only leads to nuclear loss of function, but also triggers motor neuron death through a toxic gain of function within motor neurons.
suPAR level is associated with myocardial impairment assessed with advanced echocardiography in patients with type 1 diabetes with normal ejection fraction and without known heart disease or end-stage renal disease
Authors: Theilade Simone , Rossing Peter , Eugen-Olsen Jesper , Jensen Jan S , Jensen Magnus T
Published: March 2016

Aim

Heart disease is a common fatal diabetes-related complication. Early detection of patients at particular risk of heart disease is of prime importance. Soluble urokinase plasminogen activator receptor (suPAR) is a novel biomarker for development of cardiovascular disease. We investigate if suPAR is associated with early myocardial impairment assessed with advanced echocardiographic methods.

Methods

In an observational study on 318 patients with type 1 diabetes without known heart disease and with normal left ventricular ejection fraction (LVEF) (biplane LVEF >45%), we performed conventional, tissue Doppler and speckle tracking echocardiography, and measured plasma suPAR levels. Associations between myocardial function and suPAR levels were studied in adjusted models including significant covariates.

Results

Patients were 55±12 years (mean±s.d.) and 160 (50%) males. Median (interquartile range) suPAR was 3.4 (1.7) ng/mL and LVEF was 58±5%. suPAR levels were not associated with LVEF (P=0.11). In adjusted models, higher suPAR levels were independently associated with both impaired systolic function assessed with global longitudinal strain (GLS) and tissue velocity s′, and with impaired diastolic measures a′ and e′/a′ (all P=0.034). In multivariable analysis including cardiovascular risk factors and both systolic and diastolic measures (GLS and e′/a′), both remained independently associated with suPAR levels (P=0.012).

Conclusions

In patients with type 1 diabetes with normal LVEF and without known heart disease, suPAR is associated with early systolic and diastolic myocardial impairment. Our study implies that both suPAR and advanced echocardiography are useful diagnostic tools for identifying patients with diabetes at risk of future clinical heart disease, suited for intensified medical therapy.
O Nascimento de um Herói: análise da segunda cena do acto primeiro da ópera Ulisses em Lisboa de Francisco José Freire
Authors: Mateus Rui Miguel
Published: March 2016

A ópera de Cândido Lusitano, Ulisses em Lisboa, insere-se no Neoclassicismo e no contexto das Arcádias, nomeadamente da Arcádia Lusitana, da qual o autor fazia parte. Será aqui feito um breve estudo sobre o autor, a sua relevância para a literatura portuguesa e o seu papel no seio do período neoclássico. Propõe-se uma análise aprofundada de um excerto de Ulisses em Lisboa, enquadrado no primeiro acto. A segunda cena do primeiro acto pode ser estudada de um ponto de vista da cultura clássica, que serviu de influência a Cândido Lusitano. Tágio, a personagem em destaque na cena em análise, pode ser comparado com um pastor da Arcádia. O seu discurso alude a vários aspectos da vida na sociedade, tais como o nascimento e a família. Reunindo estes temas, defrontamo-nos com o vasto conhecimento que Francisco José Freire tinha da época clássica, da sua cultura, língua, religião e literatura.
Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast
Authors: Thierry Agnès , Khanna Varun , Dujon Bernard
Published: March 2016

Gene amplification has been observed in different organisms in response to environmental constraints, such as limited nutrients or exposure to a variety of toxic compounds, conferring them with specific phenotypic adaptations via increased expression levels. However, the presence of multiple gene copies in natural genomes has generally not been found in the absence of specific functional selection. Here, we show that the massive amplification of a chromosomal locus (up to 880 copies per cell) occurs in the absence of any direct selection, and is associated with low-order amplifications of flanking segments in complex chromosomal alterations. These results were obtained from mutants with restored phenotypes that spontaneously appeared from genetically engineered strains of the yeast Saccharomyces cerevisiae suffering from severe fitness reduction. Grossly extended chromosomes (macrotene) were formed, with complex structural alterations but sufficient stability to propagate unchanged over successive generations. Their detailed molecular analysis, including complete genome sequencing, identification of sequence breakpoints, and comparisons between mutants, revealed novel mechanisms causing their formation, whose combined action underlies the astonishing dynamics of eukaryotic chromosomes and their consequences.
Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium
Authors: Ramstein Guillaume P , Evans Joseph , Kaeppler Shawn M , Mitchell Robert B , Vogel Kenneth P , Buell C Robin , Casler Michael D
Published: March 2016

Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.
Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
Authors: McDonald Megan C , McGinness Lachlan , Hane James K , Williams Angela H , Milgate Andrew , Solomon Peter S
Published: March 2016

Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified < 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene.
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome
Authors: Gu Junchen , Stevens Michael , Xing Xiaoyun , Li Daofeng , Zhang Bo , Payton Jacqueline E , Oltz Eugene M , Jarvis James N , Jiang Kaiyu , Cicero Theodore , Costello Joseph F , Wang Ting
Published: March 2016

DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation, and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. Here, we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. We found that the ratio of methylated to unmethylated CpGs is relatively constant regardless of cell type. However, which CpGs made up the unmethylated complement was cell-type specific. We categorized the 26,000,000 human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs and found that 22.6% exhibited variable DNA methylation. These variably methylated CpGs formed 660,000 variably methylated regions (VMRs), encompassing 11% of the genome. By integrating a multitude of genomic data, we found that VMRs enrich for histone modifications indicative of enhancers, suggesting their role as regulatory elements marking cell type specificity. VMRs enriched for transcription factor binding sites in a tissue-dependent manner. Importantly, they enriched for GWAS variants, suggesting that VMRs could potentially be implicated in disease and complex traits. Taken together, our results highlight the link between CpG methylation variation, genetic variation, and disease risk for many human cell types.
Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains ofSaccharomyces cerevisiae
Authors: Borneman Anthony R , Forgan Angus H , Kolouchova Radka , Fraser James A , Schmidt Simon A
Published: March 2016

Humans have been consuming wines for more than 7000 yr . For most of this time, fermentations were presumably performed by strains of Saccharomyces cerevisiae that naturally found their way into the fermenting must . In contrast, most commercial wines are now produced by inoculation with pure yeast monocultures, ensuring consistent, reliable and reproducible fermentations, and there are now hundreds of these yeast starter cultures commercially available. In order to thoroughly investigate the genetic diversity that has been captured by over 50 yr of commercial wine yeast development and domestication, whole genome sequencing has been performed on 212 strains of S. cerevisiae, including 119 commercial wine and brewing starter strains, and wine isolates from across seven decades. Comparative genomic analysis indicates that, despite their large numbers, commercial strains, and wine strains in general, are extremely similar genetically, possessing all of the hallmarks of a population bottle-neck, and high levels of inbreeding. In addition, many commercial strains from multiple suppliers are nearly genetically identical, suggesting that the limits of effective genetic variation within this genetically narrow group may be approaching saturation.
Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes
Authors: Fu Yong-Bi , Peterson Gregory W , Dong Yibo
Published: March 2016

Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7–6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0–16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications.
Drak Is Required for Actomyosin Organization DuringDrosophilaCellularization
Authors: Chougule Ashish B , Hastert Mary C , Thomas Jeffrey H
Published: March 2016

The generation of force by actomyosin contraction is critical for a variety of cellular and developmental processes. Nonmuscle myosin II is the motor that drives actomyosin contraction, and its activity is largely regulated by phosphorylation of the myosin regulatory light chain. During the formation of the Drosophila cellular blastoderm, actomyosin contraction drives constriction of microfilament rings, modified cytokinesis rings. Here, we find that Drak is necessary for most of the phosphorylation of the myosin regulatory light chain during cellularization. We show that Drak is required for organization of myosin II within the microfilament rings. Proper actomyosin contraction of the microfilament rings during cellularization also requires Drak activity. Constitutive activation of myosin regulatory light chain bypasses the requirement for Drak, suggesting that actomyosin organization and contraction are mediated through Drak’s regulation of myosin activity. Drak is also involved in the maintenance of furrow canal structure and lateral plasma membrane integrity during cellularization. Together, our observations suggest that Drak is the primary regulator of actomyosin dynamics during cellularization.
Neurofibromin Loss of Function Drives Excessive Grooming in Drosophila
Authors: King Lanikea B , Koch Marta , Murphy Keith R , Velazquez Yoheilly , Ja William W , Tomchik Seth M
Published: March 2016

Neurofibromatosis I is a common genetic disorder that results in tumor formation, and predisposes individuals to a range of cognitive/behavioral symptoms, including deficits in attention, visuospatial skills, learning, language development, and sleep, and autism spectrum disorder-like traits. The nf1-encoded neurofibromin protein (Nf1) exhibits high conservation, from the common fruit fly, Drosophila melanogaster, to humans. Drosophila provides a powerful platform to investigate the signaling cascades upstream and downstream of Nf1, and the fly model exhibits similar behavioral phenotypes to mammalian models. In order to understand how loss of Nf1 affects motor behavior in flies, we combined traditional activity monitoring with video analysis of grooming behavior. In nf1 mutants, spontaneous grooming was increased up to 7x. This increase in activity was distinct from previously described dopamine-dependent hyperactivity, as dopamine transporter mutants exhibited slightly decreased grooming. Finally, we found that relative grooming frequencies can be compared in standard activity monitors that measure infrared beam breaks, enabling the use of activity monitors as an automated method to screen for grooming phenotypes. Overall, these data suggest that loss of nf1 produces excessive activity that is manifested as increased grooming, providing a platform to dissect the molecular genetics of neurofibromin signaling across neuronal circuits.
The Stress Granule RNA-Binding Protein TIAR-1 Protects Female Germ Cells from Heat Shock inCaenorhabditis elegans
Authors: Huelgas-Morales Gabriela , Silva-García Carlos Giovanni , Salinas Laura S , Greenstein David , Navarro Rosa E
Published: March 2016

In response to stressful conditions, eukaryotic cells launch an arsenal of regulatory programs to protect the proteome. One major protective response involves the arrest of protein translation and the formation of stress granules, cytoplasmic ribonucleoprotein complexes containing the conserved RNA-binding proteins TIA-1 and TIAR. The stress granule response is thought to preserve mRNA for translation when conditions improve. For cells of the germline—the immortal cell lineage required for sexual reproduction—protection from stress is critically important for perpetuation of the species, yet how stress granule regulatory mechanisms are deployed in animal reproduction is incompletely understood. Here, we show that the stress granule protein TIAR-1 protects the Caenorhabditis elegans germline from the adverse effects of heat shock. Animals containing strong loss-of-function mutations in tiar-1 exhibit significantly reduced fertility compared to the wild type following heat shock. Analysis of a heat-shock protein promoter indicates that tiar-1 mutants display an impaired heat-shock response. We observed that TIAR-1 was associated with granules in the gonad core and oocytes during several stressful conditions. Both gonad core and oocyte granules are dynamic structures that depend on translation; protein synthesis inhibitors altered their formation. Nonetheless, tiar-1 was required for the formation of gonad core granules only. Interestingly, the gonad core granules did not seem to be needed for the germ cells to develop viable embryos after heat shock. This suggests that TIAR-1 is able to protect the germline from heat stress independently of these structures.
Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis
Authors: Markert Matthew J , Zhang Ying , Enuameh Metewo S , Reppert Steven M , Wolfe Scot A , Merlin Christine
Published: March 2016

The eastern North American monarch butterfly, Danaus plexippus, is an emerging model system to study the neural, molecular, and genetic basis of animal long-distance migration and animal clockwork mechanisms. While genomic studies have provided new insight into migration-associated and circadian clock genes, the general lack of simple and versatile reverse-genetic methods has limited in vivo functional analysis of candidate genes in this species. Here, we report the establishment of highly efficient and heritable gene mutagenesis methods in the monarch butterfly using transcriptional activator-like effector nucleases (TALENs) and CRISPR-associated RNA-guided nuclease Cas9 (CRISPR/Cas9). Using two clock gene loci, cryptochrome 2 and clock (clk), as candidates, we show that both TALENs and CRISPR/Cas9 generate high-frequency nonhomologous end-joining (NHEJ)-mediated mutations at targeted sites (up to 100%), and that injecting fewer than 100 eggs is sufficient to recover mutant progeny and generate monarch knockout lines in about 3 months. Our study also genetically defines monarch CLK as an essential component of the transcriptional activation complex of the circadian clock. The methods presented should not only greatly accelerate functional analyses of many aspects of monarch biology, but are also anticipated to facilitate the development of these tools in other nontraditional insect species as well as the development of homology-directed knock-ins.
Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution
Authors: Chiang Charleston W K , Ralph Peter , Novembre John
Published: March 2016

Identity-by-descent (IBD) is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to share an IBD segment if that segment is inherited from a recent shared common ancestor without intervening recombination. Segments several cM long can be efficiently detected by a number of algorithms using high-density SNP array data from a population sample, and there are currently efforts to detect shorter segments from sequencing. Here, we study a problem of identifiability: because existing approaches detect IBD based on contiguous segments of identity-by-state, inferred long segments of IBD may arise from the conflation of smaller, nearby IBD segments. We quantified this effect using coalescent simulations, finding that significant proportions of inferred segments 1–2 cM long are results of conflations of two or more shorter segments, each at least 0.2 cM or longer, under demographic scenarios typical for modern humans for all programs tested. The impact of such conflation is much smaller for longer (> 2 cM) segments. This biases the inferred IBD segment length distribution, and so can affect downstream inferences that depend on the assumption that each segment of IBD derives from a single common ancestor. As an example, we present and analyze an estimator of the de novo mutation rate using IBD segments, and demonstrate that unmodeled conflation leads to underestimates of the ages of the common ancestors on these segments, and hence a significant overestimate of the mutation rate. Understanding the conflation effect in detail will make its correction in future methods more tractable.
The Genetic Basis of Baculum Size and Shape Variation in Mice
Authors: Schultz Nicholas G , Ingels Jesse , Hillhouse Andrew , Wardwell Keegan , Chang Peter L , Cheverud James M , Lutz Cathleen , Lu Lu , Williams Robert W , Dean Matthew D
Published: March 2016

The rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three dimensions is not straightforward. Here, we develop a novel morphometric approach to quantify size and shape variation from three-dimensional micro-CT scans taken from 369 bacula, representing 75 distinct strains of the BXD family of mice. We identify two quantitative trait loci (QTL) that explain ∼50% of the variance in baculum size, and a third QTL that explains more than 20% of the variance in shape. Together, our study demonstrates that baculum morphology may diverge relatively easily, with mutations at a few loci of large effect that independently modulate size and shape. Based on a combination of bioinformatic investigations and new data on RNA expression, we prioritized these QTL to 16 candidate genes, which have hypothesized roles in bone morphogenesis and may enable future genetic manipulation of baculum morphology.
Genomic Bayesian Prediction Model for Count Data with Genotype × Environment Interaction
Authors: Montesinos-López Abelardo , Montesinos-López Osval A , Crossa José , Burgueño Juan , Eskridge Kent M , Falconi-Castillo Esteban , He Xinyao , Singh Pawan , Cichy Karen
Published: March 2016

Genomic tools allow the study of the whole genome, and facilitate the study of genotype-environment combinations and their relationship with phenotype. However, most genomic prediction models developed so far are appropriate for Gaussian phenotypes. For this reason, appropriate genomic prediction models are needed for count data, since the conventional regression models used on count data with a large sample size (nT) and a small number of parameters (p) cannot be used for genomic-enabled prediction where the number of parameters (p) is larger than the sample size (nT). Here, we propose a Bayesian mixed-negative binomial (BMNB) genomic regression model for counts that takes into account genotype by environment (G×E) interaction. We also provide all the full conditional distributions to implement a Gibbs sampler. We evaluated the proposed model using a simulated data set, and a real wheat data set from the International Maize and Wheat Improvement Center (CIMMYT) and collaborators. Results indicate that our BMNB model provides a viable option for analyzing count data.
PROBIOTIC ATTRIBUTES OF THE NEWLY ISOLATED LACTIC ACID BACTERIA FROM INFANTS’GUT
Authors: Kumar Bajaj Bijender , Razdan Konika , JJ Claes Ingmar , Lebeer Sarah
Published: March 2016

The gut microbiota intimately interacts with the host and influences physiological, metabolic, genetic, and immunological attributes. In the current study, analysis of fecal samples from healthy breast fed infants showed that lactic acid bacteria constitute the most abundant bacterial spp. in the infant gut (Lactobacillus plantarum being the most predominant) contrary to the established reports that Bifidobacterium spp. are mostly predominant in the infants’ gut. Evaluation of lactic acid bacteria (LAB) isolates for important probiotic characteristics showed that several of the isolates were well equipped with desirable probiotic attribute viz. ability to grow at the gut pH, and at high NaCl, bile and phenol concentrations. Some of the LAB isolates expressed functional properties like high hydrophobicity, cholesterol lowering ability, exopolysacharide producing ability, and antimicrobial potential against human pathogens. Three LAB isolates found to be superlative on probiotics attributes were identified as Enterococcus faecium FS-1.1, E. faecium FS-2.0, and E. faecium FS-4.0, based on 16S rDNA sequence analysis. Furthermore, the fecal samples of breast fed infants showed lower level of β-glucuronidase and higher level of β-glucosidase as compared to the formula fed infants, thus, reflecting the importance of breast-feeding towards general health and well being of infants.
EVALUATION OF A LOOP-MEDIATED ISOTHERMAL AMPLIFICATION (LAMP) ASSAY FOR THE DETECTION OF VIRUSES IN READY-TO-EAT FOODS
Authors: Birmpa Angeliki , Kalogeropoulos Konstantinos , Kokkinos and Apostolos Vantarakis Petros
Published: March 2016

The ability of viruses to persist in the environment and on fresh produce, as well as their low infectious doses, allows even a small amount of contamination to cause foodborne viral outbreaks. Human Adenoviruses (hAdVs) of subgroup F (enteric serotypes 40 and 41) are known to be associated with 5–20% worldwide of acute gastroenteritis cases among infants and young children. The present study aimed to evaluate a simple and cost-effective, one-step, single-tube adenovirus type 40/41 specific loop-mediated isothermal amplification (LAMP) assay for the detection of hAdV40/41 DNA in a series of ready-to-eat food samples (strawberries, sour cherries, lettuce, cherry tomatoes and green onions). No LAMP assay has previously been reported for the detection of these virus types in food samples. Results were obtained within 60 min, under isothermal conditions at 69°C. After amplification, the products were detected either by observing a ladder pattern following gel electrophoresis, or a color change with the addition of SYBR Green I to the reaction tube. The limits of detection of hAdV40/41 in food samples were found to be >30 GCs per reaction, when a nucleic acids extraction step was included in the analysis. A 1 log higher (>100 GCs/reaction) detection limit was found for lettuce, cherry tomatoes and green onions, without a nucleic acids extraction step included before the isothermal amplification. The LAMP assay for the virological analysis of food samples is expected to provide a robust, innovative, powerful, cheap and fast monitoring tool, without the need of sophisticated equipment, which will be available for food safety testing by the food industry and the public food health authorities.
ISOLATION OF SEED-BORNE AND SEED ASSOCIATED FUNGI OF Lablab purpureus (L.) SWEET AND THEIR BIOLOGICAL CONTROL
Authors: Biswas Sudhangshu , Roy Apurba , Islam Rezuanul , Alam Nadia , Chowdhury Samanandro , Rahman Mafizur
Published: March 2016

Lablab purpureus (L.) Sweet is one of the most important and nutritious vegetables as well as pulse in Bangladesh and is grown extensively all over the country. It suffers from various fungal infections, which reduce greatly its quality and quantity. Seed-borne and seed associated fungi are one of the factors of substantial damages of the bean genotypes. Seed- borne and seed associated fungi of eleven genotypes of L. purpureus (L.) Sweet and their various controlling methods were studied. From eleven bean seed samples, seven types of fungal pathogens were isolated and identified. The most predominant fungi species were Aspergillus spp. followed by Fusarium sp. and Rhizopus sp. Comparatively less frequent fungi were Penicillium sp., Curvularia sp., Colletotrichum sp. and Alternaria sp. Plant extracts (Lawsonia inermis, Azadirachta indica and Allium sativum), cow urine, hot water and chemical fungicides (Bavistin, redomil and dithane M-45) were used to observe the efficacy of them against different species of fungi and their effect on germination rate and vigour index of bean seeds. Among the controlling measures, considering fungal infection controlling capacity, germination rate, vigour index as well as cheap, easy, environment friendly, easily available and easily applicable controlling measures, Azadirachta indica leaf extract was the best. Genotype GBLB-6, GBLB-11 and GBLB-13 showed more better performance through all the controlling measures and these genotypes may be used in the breeding program for their higher germination rate, higher vigour index and comparatively lower susceptibility to fungal pathogen.
PECTIN – CANDELILLA WAX: AN ALTERNATIVE MIXTURE FOR EDIBLE FILMS
Authors: B. Alvarez-Pérez Olga , Montañez Julio , N. Aguilar CristÃ³bal , Rojas Romeo
Published: March 2016

Edible films and coatings have received special attention in recent years due to the advantages that represent their use as edible packaging over synthetics materials. This contributes in high degree to reduce the environmental pollution with non-biodegradable materials. By functioning as barriers, such edible films and coatings can improve the recycling and/or substitute some synthetic packaging materials. New packaging materials have been developed and characterized by some scientists from natural sources (biomaterials); however, it is necessary the manufacture tailor-made to every food. The main objective of this review is to provide basic and applied information and benefits that can be generate the use of two products with low cost (candelilla wax and pectin), but with great importance in the food industry and that can be used to manufacture edible films and coatings.
EFFECT OF DRYING METHODS ON CONTENT OF SOME NATURAL PIGMENTS IN URTICA DIOICA L. AND MELISSA OFFICINALIS L.
Authors: Droštinová Lenka , Braniša Jana , Bončíková Dominika , Jomová Klaudia
Published: March 2016

Medicinal plants are usually marketed to the public in a dried form and in this form they can also be used for the needs of the pharmaceutical industry. Since the drying process can affect chemical changes in the plants several drying methods and conditions have been tested to preserve the quality and quantity of biologically active components. The objective of this study was to investigate the effect of convection oven drying at 25°C ± 1°C for 65 hours, microwave oven drying at 800 W for 45 seconds, and air drying with sun exposure at 25°C ± 1°C for 65 hours on the content of chlorophylls and carotenoids in leaves of two medicinal plants. The plants selected were stinging nettle (Urtica dioica L.) and lemon balm (Melissa officinalis L.). The content of the natural pigments was investigated in the prepared extracts by the UV-VIS spectrophotometric method. Results showed higher content of pigments in Melissa officinalis when microwave drying procedure was applied compared to the oven dried samples and the sun dried samples (air dried with sun exposure) but a significant difference was only observed in the content of chlorophyll b. In Urtica dioica the air drying technique with sun exposure can be considered to be a more suitable drying procedure which preserves a higher amount of all pigments. Sun dried Urtica dioica samples had significantly higher chlorophylls and carotenoids content compared to the oven dried and microwave dried samples. In general, air drying with sun exposure seems to be the most suitable drying method in terms of preservation of pigments under study. This technique represents the simplest and most energy efficient drying procedure.
IMPROVEMENT OF AFRICAN TRADITIONAL SORGHUM BEERS QUALITY AND POTENTIAL APPLICATIONS OF PLANTS EXTRACTS FOR THEIR STABILIZATION: A REVIEW
Authors: Tétédé  Rodrigue KONFO Christian , Worou CHABI NicodÃ¨me , DAHOUENON-AHOUSSI Edwige , CAKPO-CHICHI Martial , Mansourou SOUMANOU Mohamed , Coco Kodjo SOHOUNHLOUE Dominique
Published: March 2016

In Africa, various kinds of traditional alcoholic beverages commonly named sorghum beers or opaque beers, have been recorded and described. These drinks have a central role in peoples' cultures and play fundamental socioeconomic function. Their brewing involves malting, mashing, souring, straining, boiling and two successive steps of fermentation which occur at ambient conditions. A primary lactic fermentation, or souring stage, confers the souring taste and storage longevity. The alcoholic fermentation is usually initiated by pitching wort with a portion of previous brew. The beverage thus obtained is unstable. Since the African sorghum beers fermentation process is run by uncontrolled inoculation under no standard hygienic conditions, producers have a major problem to make a good beer with a long shelf-life. In other hand, recently the disappearance of many active synthetic substances in foods protection has resulted to a renewed interest in naturally occurring substances. In parallel to these disappearances, the regulatory environment incites strongly to increase the use of alternative methods to chemical control. This review aims to summarize works about African traditional sorghum beers stabilization and potential applications of plants extract for their natural preservatives.
PURIFICATION AND STRUCTURAL CHARACTERIZATION OF A PHTHALATE ANTIBIOTIC FROM BURKHOLDERIA GLADIOLI OR1 EFFECTIVE AGAINST MULTI-DRUG RESISTANT STAPHYLOCOCCUS AUREUS
Authors: Bharti Pratibha , Tewari Rupinder
Published: March 2016

A soil isolate, identified as Burkholderia gladioli OR1, has been reported in our earlier study, to possess broad spectrum antimicrobial activity against drug resistant clinical isolates of bacteria and fungi. The 16S rRNA gene sequence data of B. gladioli strain OR1 has been deposited in the GenBank databases (MTCC) under the accession number MTCC11251. Thin layer chromatography and bioautography studies of chloroform extract of the cell free supernatant of this organism, showed at least four different antimicrobial compounds. The silica gel column chromatography and high performance liquid chromatography led to the isolation of one compound that exhibited growth inhibitory activity against multi-antibiotic resistant clinical isolates of Staphylococcus aureus (resistant to amikacin, ciprofloxacin, clindamycin, clinafloxacin, erythromycin, gentamicin and methicillin). On the basis of mass, infra-red (IR), 1H nuclear magnetic resonance (NMR), 13C NMR and 2D NMR spectral studies, we propose the structure of this antibiotic to be bis-(2-ethylhexyl) phthalate, isolated for the first time from the species of the genus Burkholderia.