Horizontal Gene Transfer and Gene Duplication of Plant Cell Wall Degrading Enzyme Genes in an Invasive Insect Pest

Insects were long thought to lack endogenous genes encoding plant cell wall degrading enzymes (PCWDEs). However, this hypothesis has been challenged since symbiotic-independent PCWDE genes and enzymes were found in several insect species. As an economically-important wood-feeding beetle, how the invasive insect emerald ash borer (Agrilus planipennis) degrades plant cell walls and utilizes their contents is of high interest. We identified three glycoside hydrolase (GH) gene families and one polysaccharide lyase (PL) gene family within the A. planipennis genome, which putatively encode for α-L-arabinofuranosidases (GH43), endoglucanases (GH44), polygalacturonases (GH28) and Rhamnogalacturonases (PL4), respectively. Phylogenetic analysis showed that they exhibit close relationship with bacterial or fungal homologs, indicating that acquisition of these genes by the insect is through the horizontal gene transfer (HGT). Each family has multiple gene copies in the A. planipennis genome and they reside in the same clades, implying occurrence of the gene duplication events following HGT during evolution. To test the hypothesis that the HGT-associated gene duplication is adaptive, we selected one GH44 gene, two GH43 genes and one PL4 gene for quantitative RT-PCR analysis. The specific expression in the larval midgut and during larval stages of development, together with the presence of N-terminal signal peptides in the deduced protein sequences, suggest that these gene products are secreted into the larval midgut, facilitating digestion of the host plant cell walls.USDA-APHI

Secretory RING finger proteins function as effectors in a grapevine galling insect.

BackgroundAll eukaryotes share a conserved network of processes regulated by the proteasome and fundamental to growth, development, or perception of the environment, leading to complex but often predictable responses to stress. As a specialized component of the ubiquitin-proteasome system (UPS), the RING finger domain mediates protein-protein interactions and displays considerable versatility in regulating many physiological processes in plants. Many pathogenic organisms co-opt the UPS through RING-type E3 ligases, but little is known about how insects modify these integral networks to generate novel plant phenotypes.ResultsUsing a combination of transcriptome sequencing and genome annotation of a grapevine galling species, Daktulosphaira vitifoliae, we identified 138 putatively secretory protein RING-type (SPRINGs) E3 ligases that showed structure and evolutionary signatures of genes under rapid evolution. Moreover, the majority of the SPRINGs were more expressed in the feeding stage than the non-feeding egg stage, in contrast to the non-secretory RING genes. Phylogenetic analyses indicated that the SPRINGs formed clusters, likely resulting from species-specific gene duplication and conforming to features of arthropod host-manipulating (effector) genes. To test the hypothesis that these SPRINGs evolved to manipulate cellular processes within the plant host, we examined SPRING interactions with grapevine proteins using the yeast two-hybrid assay. An insect SPRING interacted with two plant proteins, a cellulose synthase, CSLD5, and a ribosomal protein, RPS4B suggesting secretion reprograms host immune signaling, cell division, and stress response in favor of the insect. Plant UPS gene expression during gall development linked numerous processes to novel organogenesis.ConclusionsTaken together, D. vitifoliae SPRINGs represent a novel gene expansion that evolved to interact with Vitis hosts. Thus, a pattern is emerging for gall forming insects to manipulate plant development through UPS targeting

CoupleNet: Coupling Global Structure with Local Parts for Object Detection

The region-based Convolutional Neural Network (CNN) detectors such as Faster R-CNN or R-FCN have already shown promising results for object detection by combining the region proposal subnetwork and the classification subnetwork together. Although R-FCN has achieved higher detection speed while keeping the detection performance, the global structure information is ignored by the position-sensitive score maps. To fully explore the local and global properties, in this paper, we propose a novel fully convolutional network, named as CoupleNet, to couple the global structure with local parts for object detection. Specifically, the object proposals obtained by the Region Proposal Network (RPN) are fed into the the coupling module which consists of two branches. One branch adopts the position-sensitive RoI (PSRoI) pooling to capture the local part information of the object, while the other employs the RoI pooling to encode the global and context information. Next, we design different coupling strategies and normalization ways to make full use of the complementary advantages between the global and local branches. Extensive experiments demonstrate the effectiveness of our approach. We achieve state-of-the-art results on all three challenging datasets, i.e. a mAP of 82.7% on VOC07, 80.4% on VOC12, and 34.4% on COCO. Codes will be made publicly available.Comment: Accepted by ICCV 201

A Ligation-PCR Approach for Generating Gene Replacement Constructs in Magnaporthe grisea

The conventional approach for generating gene replacement constructs involves several sequence-specific cloning steps and is time-consuming. A ligation-PCR approach was developed to efficiently generate gene replacement constructs. Two vectors useful for this ligation-PCR approach and another vector suitable for improving the efficiency of knockout mutant screens were constructed

An Ensemble Multilabel Classification for Disease Risk Prediction

It is important to identify and prevent disease risk as early as possible through regular physical examinations. We formulate the disease risk prediction into a multilabel classification problem. A novel Ensemble Label Power-set Pruned datasets Joint Decomposition (ELPPJD) method is proposed in this work. First, we transform the multilabel classification into a multiclass classification. Then, we propose the pruned datasets and joint decomposition methods to deal with the imbalance learning problem. Two strategies size balanced (SB) and label similarity (LS) are designed to decompose the training dataset. In the experiments, the dataset is from the real physical examination records. We contrast the performance of the ELPPJD method with two different decomposition strategies. Moreover, the comparison between ELPPJD and the classic multilabel classification methods RAkEL and HOMER is carried out. The experimental results show that the ELPPJD method with label similarity strategy has outstanding performance

Weight control behaviors in overweight/obese U.S. adults with diagnosed hypertension and diabetes

<p>Abstract</p> <p>Background</p> <p>Obesity is a major risk factor for development and progression of hypertension and diabetes, which often coexist in obese patients. Losing weight by means of energy restriction and physical activity has been effective in preventing and managing these diseases. However, weight control behaviors among overweight/obese adults with these conditions are poorly understood.</p> <p>Methods</p> <p>Using self-reported data from 143,386 overweight/obese participants (aged ≥ 18 years) in the 2003 Behavioral Risk Factor Surveillance System, we examined the proportion of overweight/obese adults who tried to lose weight and their weight control strategies by hypertension and/or diabetes status.</p> <p>Results</p> <p>Among all participants, 58% of those with hypertension, 60% of those with diabetes, and 72% of those with both diseases tried to lose weight, significantly higher than the 50% of those with neither condition (Bonferroni corrected P < 0.017 for all comparisons). The multivariate-adjusted odds ratio (AOR) for trying to lose weight was 1.11 (95% confidence interval [CI]: 1.05–1.17) in participants with hypertension, 1.02 (95% CI: 0.90–1.15) in participants with diabetes, and 1.18 (95% CI: 1.07–1.29) in participants with both diseases (participants with neither condition as the referent). Among 78,446 participants who tried to lose weight, 23% of those with hypertension only and 28% of those with both hypertension and diabetes reported adopting a low fat/low calorie (LF/LC) diet in controlling their weight, significantly higher than 19% of those with neither disease (Bonferroni corrected P < 0.017 for all comparisons). Participants with both diseases had a significantly lower percentage of adopting physical activity in controlling their weight than those with neither condition (6% versus 12%, P < 0.01). After multivariate adjustment, the AOR for adopting a LF/LC diet plus physical activity to lose weight was 1.46 (95% CI: 1.15–1.84) in participants with both diseases. The AOR for adopting a LF/LC diet only to lose weight was 1.72 (95% CI: 1.35–2.20) in participants with both diseases and was 1.21 (95% CI: 1.03–1.40) in participants with hypertension only.</p> <p>Conclusion</p> <p>The proportion of overweight/obese patients with diagnosed hypertension and/or diabetes who attempted to lose weight remains suboptimal and the weight control strategies varied significantly among these patients.</p

Factors Associated with Vitamin D Deficiency and Inadequacy among Women of Childbearing Age in the United States

Objective. To examine the prevalence and correlates of vitamin D deficiency and inadequacy among US women of childbearing age. Methods. Data from 1,814 female participants (20–44 y) in the 2003–2006 NHANES were analyzed to estimate the age-adjusted prevalence and prevalence ratios with 95% confidence intervals (CIs) for vitamin D deficiency (defined as serum 25-hydroxyvitamin D [25(OH)D] <12.0 ng/mL) and inadequacy (defined as 25(OH)D: 12.0–<20.0 ng/mL). Results. The age-adjusted prevalence was 11.1% (95% CI: 8.8–14.0%) for vitamin D deficiency and 25.7% (95% CI: 22.3–29.5%) for vitamin D inadequacy. Race/ethnicity other than non-Hispanic white and obesity were associated with increased risks, whereas dietary supplement use, milk consumption of ≥1 time/day, and potential sunlight exposure during May-October were associated with decreased risks for both vitamin D deficiency and inadequacy (P < 0.05). Current smoking and having histories of diabetes and cardiovascular disease were also associated with an increased risk for vitamin D deficiency (P < 0.05). Conclusions. Among women of childbearing age, periconceptional intervention programs may focus on multiple risk factors for vitamin D deficiency and inadequacy to ultimately improve their vitamin D nutrition

Serum Non-high-density lipoprotein cholesterol concentration and risk of death from cardiovascular diseases among U.S. adults with diagnosed diabetes: the Third National Health and Nutrition Examination Survey linked mortality study

<p>Abstract</p> <p>Background</p> <p>Non-high-density lipoprotein cholesterol (non-HDL-C) measures all atherogenic apolipoprotein B-containing lipoproteins and predicts risk of cardiovascular diseases (CVD). The association of non-HDL-C with risk of death from CVD in diabetes is not well understood. This study assessed the hypothesis that, among adults with diabetes, non-HDL-C may be related to the risk of death from CVD.</p> <p>Methods</p> <p>We analyzed data from 1,122 adults aged 20 years and older with diagnosed diabetes who participated in the Third National Health and Nutrition Examination Survey linked mortality study (299 deaths from CVD according to underlying cause of death; median follow-up length, 12.4 years).</p> <p>Results</p> <p>Compared to participants with serum non-HDL-C concentrations of 35 to 129 mg/dL, those with higher serum levels had a higher risk of death from total CVD: the RRs were 1.34 (95% CI: 0.75-2.39) and 2.25 (95% CI: 1.30-3.91) for non-HDL-C concentrations of 130-189 mg/dL and 190-403 mg/dL, respectively (<it>P </it>= 0.003 for linear trend) after adjustment for demographic characteristics and selected risk factors. In subgroup analyses, significant linear trends were identified for the risk of death from ischemic heart disease: the RRs were 1.59 (95% CI: 0.76-3.32) and 2.50 (95% CI: 1.28-4.89) (<it>P </it>= 0.006 for linear trend), and stroke: the RRs were 3.37 (95% CI: 0.95-11.90) and 5.81 (95% CI: 1.96-17.25) (<it>P </it>= 0.001 for linear trend).</p> <p>Conclusions</p> <p>In diabetics, higher serum non-HDL-C concentrations were significantly associated with increased risk of death from CVD. Our prospective data support the notion that reducing serum non-HDL-C concentrations may be beneficial in the prevention of excess death from CVD among affected adults.</p

Avirulence effector discovery in a plant galling and plant parasitic arthropod, the Hessian fly (Mayetiola destructor)

Citation: Aggarwal R, Subramanyam S, Zhao C, Chen M-S, Harris MO, et al. (2014). Avirulence Effector Discovery in a Plant Galling and Plant Parasitic Arthropod, the Hessian Fly (Mayetiola destructor). PLoS ONE 9(6): e100958. doi:10.1371/journal.pone.0100958Highly specialized obligate plant-parasites exist within several groups of arthropods (insects and mites). Many of these are important pests, but the molecular basis of their parasitism and its evolution are poorly understood. One hypothesis is that plant parasitic arthropods use effector proteins to defeat basal plant immunity and modulate plant growth. Because avirulence (Avr) gene discovery is a reliable method of effector identification, we tested this hypothesis using high-resolution molecular genetic mapping of an Avr gene (vH13) in the Hessian fly (HF, Mayetiola destructor), an important gall midge pest of wheat (Triticum spp.). Chromosome walking resolved the position of vH13, and revealed alleles that determine whether HF larvae are virulent (survive) or avirulent (die) on wheat seedlings carrying the wheat H13 resistance gene. Association mapping found three independent insertions in vH13 that appear to be responsible for H13-virulence in field populations. We observed vH13 transcription in H13-avirulent larvae and the salivary glands of H13-avirulent larvae, but not in H13-virulent larvae. RNA-interference-knockdown of vH13 transcripts allowed some H13-avirulent larvae to escape H13-directed resistance. vH13 is the first Avr gene identified in an arthropod. It encodes a small modular protein with no sequence similarities to other proteins in GenBank. These data clearly support the hypothesis that an effector-based strategy has evolved in multiple lineages of plant parasites, including arthropods

Use of folic acid and vitamin supplementation among adults with depression and anxiety: a cross-sectional, population-based survey

<p>Abstract</p> <p>Background</p> <p>Evidence suggests that folate deficiency may be causatively linked to depressive symptoms. However, little is known on the status of use of folic acid and vitamin supplements among people with mental disorders. This study examined the prevalence and the likelihood of use of folic acid or vitamin supplements among adults with depression and anxiety in comparison to those without these conditions.</p> <p>Methods</p> <p>Using data from 46, 119 participants (aged ≥ 18 years) in the 2006 Behavioral Risk Factor Surveillance System survey, we estimated the adjusted prevalence and odds ratios with 95% confidence intervals for taking folic acid and vitamin supplements among those with ever diagnosed depression (n = 8, 019), ever diagnosed anxiety (n = 5, 546) or elevated depressive symptoms (n = 3, 978, defined as having a depression severity score of ≥ 10 on the Patient Health Questionnaire-8 diagnostic algorithm).</p> <p>Results</p> <p>Overall, women were more likely than men to take folic acid supplements 1-4 times/day (50.2% versus 38.7%, P < 0.001) and vitamin supplements (62.5% versus 49.8%, P < 0.001). After multivariate adjustment, men with ever diagnosed depression or anxiety were 42% and 83%, respectively, more likely to take folic acid supplements < 1 time/day; 44% and 39%, respectively, more likely to take folic acid supplements 1-4 times/day; and 40% and 46%, respectively, more likely to take vitamin supplements compared to men without these conditions (P < 0.05 for all comparisons). Women with ever diagnosed depression were 13% more likely to take folic acid supplements 1-4 times/day and 15% more likely to take vitamin supplements than women without this condition (P < 0.05 for both comparisons). Use of folic acid and vitamin supplements did not differ significantly by elevated depressive symptoms in either sex.</p> <p>Conclusion</p> <p>The prevalence and the likelihood of taking folic acid and vitamin supplements varied substantially by a history of diagnosed depression among both men and women and by a history of diagnosed anxiety among men, but not by presence of elevated depressive symptoms in either sex.</p