Molecular evolution and phylogeographic analysis of wheat dwarf virus

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10−4 substitutions/site/year (95% credibility interval, 2.828 × 10−4–5.723 × 10−4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517–1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China

The effects of circularly polarized light on mating behavior and gene expression in Anomala corpulenta (Coleoptera: Scarabaeidae)

Light is an important abiotic factor affecting insect behavior. In nature, linearly polarized light is common, but circularly polarized light is rare. Left circularly polarized (LCP) light is selectively reflected by the exocuticle of most scarab beetles, including Anomala corpulenta. Despite our previous research showing that this visual signal probably mediates their mating behavior, the way in which it does so is not well elucidated. In this study, we investigated how LCP light affects not only mating behavior but also gene expression in this species using RNA-seq. The results indicated that disruption of LCP light reflection by females of A. corpulenta probably affects the process by which males of A. corpulenta search for mates. Furthermore, the RNA-seq results showed that genes of the environmental signaling pathways and also of several insect reproduction-related amino acid metabolic pathways were differentially expressed in groups exposed and not exposed to LCP light. This implies that A. corpulenta reproduction is probably regulated by LCP light-induced stress. Herein, the results show that LCP light is probably perceived by males of the species, further mediating their mating behavior. However, this hypothesis needs future verification with additional samples

Obesity and Overweight Are Independently Associated with Greater Survival in Critically Ill Diabetic Patients: A Retrospective Cohort Study

Background. The relationship between obesity and the outcomes of critically ill diabetic patients is not completely clear. We aimed to assess the effects of obesity and overweight on the outcomes among diabetic patients in the intensive care unit (ICU). Methods. Critically ill diabetic patients in the ICU were classified into three groups according to their body mass index. The primary outcomes were 30-day and 90-day mortality. ICU and hospital length of stay (LOS) and incidence and duration of mechanical ventilation were also assessed. Cox regression models were developed to evaluate the relationship between obesity and overweight and mortality. Results. A total of 6108 eligible patients were included. The 30-day and 90-day mortality in the normal weight group were approximately 1.8 times and 1.5 times higher than in the obesity group and overweight group, respectively (P<0.001, respectively). Meanwhile, the ICU (median (IQ): 2.9 (1.7, 5.3) vs. 2.7 (1.6, 4.8) vs. 2.8 (1.8, 5.0)) and hospital (median (IQ): 8.3 (5.4, 14.0) vs. 7.9 (5.1, 13.0) vs. 8.3 (5.3, 13.6)) LOS in the obesity group and overweight group were not longer than in the normal weight group. Compared with normal weight patients, obese patients had significantly higher incidence of mechanical ventilation (58.8% vs. 64.7%, P<0.001) but no longer ventilation duration (median (IQ): 19.3 (7.0, 73.1) vs. 19.0 (6.0, 93.7), P=1). Multivariate Cox regression showed that obese and overweight patients had lower 30-day (HR (95% CI): 0.62 (0.51, 0.75); 0.76 (0.62, 0.92), respectively) and 90-day (HR (95% CI): 0.60 (0.51, 0.70); 0.79 (0.67, 0.93), respectively) mortality risks than normal weight patients. Conclusions. Obesity and overweight were independently associated with greater survival in critically ill diabetic patients, without increasing the ICU and hospital LOS. Large multicenter prospective studies are needed to confirm our findings and the underlying mechanisms warrant further investigation

High innate preference of black substrate in the chive gnat, Bradysia odoriphaga (Diptera: Sciaridae).

The chive gnat, Bradysia odoriphaga, is a notorious pest of Allium species in China. Colour trapping is an established method for monitoring and control of Bradysia species. In order to clarify the effect of colour preference of B. odoriphaga for the perched substrate, multiple-choice tests were used to assess the response of the chive gnat to different colour hues and brightness levels under different intensities of white illumination and two spectrally different illuminations. Given the choice among four colours differing in hue under different intensities of white illumination and two spectrally different illuminations, chive gnat adults significant preferred the black substrate, a lesser preference to brown and green substrates, and the least preference to orange substrate irrespective of illumination. Given the choice among four levels of brightness under the same illumination conditions as those in the previous experiment (different intensities of white illumination and two spectrally different illuminations), chive gnats preferred black substrate over dark grey, light grey and white substrates. Meanwhile, both virgin and mated adults significantly preferred black over other colour hues and brightness. Based on our results, we conclude that the chive gnat adults significantly prefer black substrates irrespective of colour hues and brightness. This behaviour does not alter with ambient light condition changes. No difference observed between choices of female and male adults. Our results provide new insight for understanding the colour choice behaviour in chive gnat and pave a way to improve monitoring and control of chive gnats and management

The Efficacy and Safety of Acellular Matrix Therapy for Diabetic Foot Ulcers: A Meta-Analysis of Randomized Clinical Trials

Background. Acellular matrix (AM) therapy has shown promise in the treatment of diabetic foot ulcers (DFUs) in several studies. The clinical effects of AM therapy were not well established. Therefore, we conducted a meta-analysis of randomized clinical trials (RCTs) to examine the efficacy and safety of AM therapy for patients with DFUs. Methods. A literature search of 5 databases was performed to identify RCTs comparing AM therapy to standard therapy (ST) in patients with DFUs. The primary outcome was the complete healing rate and the secondary outcomes mainly included time to complete healing and adverse events. Results. Nine RCTs involving 897 patients were included. Compared with ST group, patients allocated to AM group had a higher complete healing rate both at 12 weeks (risk ratio RR=1.73, 95% confidence interval (CI): 1.31 to 2.30) and 16 weeks (RR=1.56, 95% CI: 1.28 to 1.91), a shorter time to complete healing (mean difference MD=−2.41; 95% CI: -3.49 to -1.32), and fewer adverse events (RR=0.64, 95% CI: 0.44 to 0.93). Conclusion. The present study suggests that AM therapy as an adjuvant treatment could further promote the healing of full-thickness, noninfected, and nonischemia DFUs. AM therapy also has a safety profile. More large well-designed randomized clinical trials with long follow-up duration are needed to further explore the efficacy and safety of AM therapy for DFUs

Global molecular evolution and phylogeographic analysis of barley yellow dwarf virus based on the cp and mp genes

Abstract Barley yellow dwarf virus (BYDV) has caused considerable losses in the global production of grain crops such as wheat, barley and maize. We investigated the phylodynamics of the virus by analysing 379 and 485 nucleotide sequences of the genes encoding the coat protein and movement protein, respectively. The maximum clade credibility tree indicated that BYDV-GAV and BYDV-MAV, BYDV-PAV and BYDV-PAS share the same evolutionary lineage, respectively. The diversification of BYDV arises from its adaptability to vector insects and geography. Bayesian phylogenetic analyses showed that the mean substitution rates of the coat and movement proteins of BYDV ranged from 8.327 × 10− 4 (4.700 × 10− 4–1.228 × 10− 3) and 8.671 × 10− 4 (6.143 × 10− 4–1.130 × 10− 3) substitutions/site/year, respectively. The time since the most recent common BYDV ancestor was 1434 (1040–1766) CE (Common Era). The Bayesian skyline plot (BSP) showed that the BYDV population experienced dramatic expansions approximately 8 years into the 21st century, followed by a dramatic decline in less than 15 years. Our phylogeographic analysis showed that the BYDV population originating in the United States was subsequently introduced to Europe, South America, Australia and Asia. The migration pathways of BYDV suggest that the global spread of BYDV is associated with human activities

Etiology and Symptoms of Maize Leaf Spot Caused by Bipolaris spp. in Sichuan, China

Many species of the genus Bipolaris are important plant pathogens and often cause leaf spot, root rot, and seedling blight in an extremely wide range of hosts around the world. In recent years, maize leaf spot caused by Bipolaris species has frequently occurred with complex symptoms and is becoming increasingly serious in Sichuan Province of China. To investigate the population diversity of Bipolaris spp. and their corresponding symptoms in maize, 747 samples of maize leaf spot were collected from 132 sampling sites in 19 administrative districts of Sichuan Province from 2011 to 2018. Based on morphological characteristics, pathogenicity testing, and phylogenetic analysis of the rDNA internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes, a total of 1186 Bipolaris isolates were identified as B. maydis, B. zeicola, B. cynodontis, B. oryzae, B. setariae, and B. saccharicola, among which B. maydis and B. zeicola were the dominant pathogenic species, accounting for 57.34% and 42.07% of the isolates, respectively. We found that B. zeicola isolates were mainly distributed in high altitude and cool mountainous areas, while B. maydis was more widely distributed in Sichuan Province. The typical symptoms caused by the Bipolaris species were clearly distinct in maize. The typical symptoms caused by B. maydis were elongated strip lesions, or fusiform, elliptical lesions, and those caused by B. zeicola were narrow linear lesions. Herein, B. saccharicola was first reported on maize and caused subrotund lesions. This study provides useful information for disease diagnosis and management for Bipolaris leaf spot in maize

Image_2_Molecular evolution and phylogeographic analysis of wheat dwarf virus.JPEG

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10−4 substitutions/site/year (95% credibility interval, 2.828 × 10−4–5.723 × 10−4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517–1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China.</p

Image_1_Molecular evolution and phylogeographic analysis of wheat dwarf virus.JPEG

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10−4 substitutions/site/year (95% credibility interval, 2.828 × 10−4–5.723 × 10−4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517–1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China.</p

Image_3_Molecular evolution and phylogeographic analysis of wheat dwarf virus.JPEG

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10−4 substitutions/site/year (95% credibility interval, 2.828 × 10−4–5.723 × 10−4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517–1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China.</p