Genome Sequence Resource for Pathogen Bipolaris sorokiniana Shoemaker GN1 Causing Spot Blotch of Barley (Hordeum vulgare L.)

Spot blotch, caused by fungal pathogen Bipolaris sorokiniana Shoemaker, is one of the most frequent diseases affecting barley-growing regions worldwide. In this study, we reported the genome sequence of the highly virulent B. sorokiniana strain GN1 using the Illumina HiSeq 4000 platform. In total, 57 million 150-nucleotide paired-end clean reads were obtained and assembled into 96 scaffolds with an estimated genome size of 34.33 Mb. Furthermore, we identified genes that may be associated with strain-specific virulence and performed phylogenetic analysis of GN1 with five other Bipolaris spp. These results for GN1 will provide important information in understanding its molecular underpinning of pathogenicity and help identify novel sources of genetic resistance for improving disease resistance in barley.

Genome Resource for Barley Leaf Stripe Pathogen Pyrenophora graminea

Pyrenophora graminea is the causative agent of barley leaf stripe disease. In this study, the strong pathogenic isolate QWC was used to generate DNA for Illumina sequencing. After assembly, its genome size was 42.5 Mb, consisting of 264 scaffolds, and a total of 10,376 genes was predicted. This is the first genome resource available for P. graminea. The genome sequences of P. graminea will accelerate the understanding interaction of P. graminea and barley.

Lidar Observations of Birch and Spruce Pollen in Finland

Pollen has various effects on human health and the environment. To understand phenomena behind atmospheric pollen transport and hence improve pollen forecasts, vertically resolved optical properties and geometrical characteristics of the pollen distribution need to be studied. Lidar measurements and especially the particle depolarization ratio have been found to be an excellent tool to track pollen grains. In this study we present first results of atmospheric pollen characterization based on a 11 days period of birch and spruce pollination events.

[Risk factors for visual field loss progression in patients with primary open-angle glaucoma in Wenzhou area]

Objective: To evaluate risk factors for visual field (VF) loss progression in primary open-angle glaucoma patients. Methods: A prospective nested case-control study. Patients were collected from the Wenzhou glaucoma progression study in the Eye Hospital of Wenzhou Medical University during March 2014 and April 2018. In this study, the eyes were divided into a progression group and a non-progression group using the glaucoma progression analysis methods to analyze the risk factors for glaucomatous VF loss progression. Axial length (AL) and central corneal thickness (CCT) were measured using the Lenstar LS900. The baseline, fluctuation (standard deviation), mean, maximum, minimum and range of intraocular pressure (IOP) during the follow-up period were determined based on IOP measured at each follow-up. The IOP measurements were included from the baseline to the last visit (for the non-progression group), or to the visit at which VF loss progression was determined (for the progression group). The independent sample t-test, Mann-Whitney U inspection and Cox proportional hazards models were used for statistical analysis. Results: A total of 140 patients (140 eyes) were enrolled, including 67 males and 73 females. There were 19.3% of the eyes (27 of 140 eyes) showing VF loss progression. The median time to the endpoint for progression was 24.0 (16.0, 40.0) months. The AL in the progression group and non-progression group were 23.58 (23.05, 24.24) mm and 23.91 (23.10, 24.91) mm (P=0.111). The CCT in the two groups were 531.0 (512.0, 565.0) μm and 535.0 (518.5, 552.0) μm, respectively (P=0.897). The baseline age in the progression group and non-progression group was 71.0 (68.0, 74.0) years and 68.0 (58.0, 72.0) years, respectively (Z=-2.872, P=0.004). The slope of visual field index in the two groups was -3.50 (-7.10, -1.80)%/year and 0.40 (-0.60, 1.40)%/year, respectively (Z=-6.823, P<0.01). The mean IOP during the follow-up was (16.2±2.7) mmHg (1 mmHg=0.133 kPa) in the progression group and (15.1±2.4) mmHg in the non-progression group (t=-2.215, P=0.028). The IOP fluctuation in the progression group and non-progression group was (2.6±1.3) mmHg and (2.0±0.7) mmHg, respectively (t=-2.175, P=0.038). In the multivariate model, older baseline age (HR=1.080; 95%CI:1.019-1.143), higher baseline IOP (HR=1.120; 95%CI:1.016-1.236), higher mean IOP (HR=1.145; 95%CI:1.001-1.309) and higher IOP fluctuation (HR=1.750; 95%CI:1.193-2.566) were all significantly predictive risk factors for glaucomatous VF loss progression. Longer AL (HR=0.725; 95%CI:0.532-0.988) was a protective factor against VF loss progression. However, CCT was found to be not associated with VF loss progression. Conclusion: Baseline age, baseline IOP, mean IOP, IOP fluctuation and shorter AL are found to be risk factors for glaucomatous VF loss progression among eyes with primary open-angle glaucoma in Wenzhou. (Chin J Ophthalmol, 2019, 55: 777-784).

PGPBS, a mitogen-activated protein kinase kinase, is required for vegetative differentiation, cell wall integrity, and pathogenicity of the barley leaf stripe fungus Pyrenophora graminea

The high-osmolarity glycerol (HOG) signaling pathway regulates the adaptation of fungi to environmental stressors. The mitogen-activated protein kinase kinase (MAPKK) PBS2 of Saccharomyces cerevisiae serves as a scaffold protein in the HOG pathway. We characterized the pgpbs gene of Pyrenophora graminea, which encodes a MAPKK that is 56% orthologous to PBS2 of S. cerevisiae. A cloning technique based on homology was applied to amplify the pgpbs gene. Specific silent mutations then were generated in pgpbs. We evaluated the potential roles of PGPBS in the osmotic response, vegetative differentiation, cell wall integrity, drug resistance, and pathogenicity. Our findings indicated that the pgpbs coding region comprises 2075 base pairs and encodes a protein of 676 amino acids. Mutants deficient in pgpbs expression had significant reductions in vegetative growth and were sensitive to calcofluor white (CFW), an inhibitor of cell wall synthesis. Mutants also lost pathogenicity and were sensitive to an osmotic stress-inducing medium containing NaCl and sorbitol. Moreover, mutants had increased resistance to the dicarboximide fungicide iprodione and the triazole fungicide tebuconazole. These findings suggest that pgpbs is involved in the osmotic and ionic stress responses, vegetative differentiation, cell wall integrity, virulence, and tolerance to iprodione and tebuconazole. We expect that our findings will help elucidate the pathogenesis of barley leaf stripe and will inform strategies for breeding resistance to this disease.

[An in vivo biomechanical study of Chinese female with uterosacral ligament suspension]

Objective: To measure in vivo biomechanical properties of pelvic support structures associated with uterosacral ligament suspension (ULS) . Methods: Ten Chinese female cadavers (death within 48 hours) without embalming were carefully dissected to expose the ligament. After dissection, ligaments were sewn according to standard ULS surgical technique. They were stretched at a steady rate to breakage during constant electronic registration of load and displacement. In vivo biomechanical properties were evaluated by a load-displacement curve. Results: Ultimate load of uterosacral ligament, ring around cervix were (37.3±23.5) , (49.3±28.4) N, respectively. The differences between the two groups was not significant (P>0.05) . Ligament stiffness were (1.26±1.22) , (1.45±0.92) N/mm, respectively. There was no significant difference between groups (P>0.05) . Conclusions: The uterosacral ligament, ring around cervix with sufficient strength are not easy to deform. ULS is an effective procedure for treating middle pelvic defects from a biomechanics perspective.

Comparative transcriptome analysis of genes involved in Na+ transport in the leaves of halophyte Halogeton glomeratus

Compartmentalization of Na⁺ into vacuoles is considered to be the most critical aspect of salt tolerance in H. glomeratus, an annual, succulent halophyte. Previous analysis of transcriptome involved in the H. glomeratus salt stress response relied on next-generation sequencing technologies that limit the capture of accurately spliced, full-length isoforms. To gain deeper insights into its salt stress response, we used the H. glomeratus Iso-Seq transcriptome database as a reference, and subsequent next-generation sequencing was subjected to various NaCl concentrations of leaves from plants revealed 115 upregulated and 87 downregulated differentially expressed isoforms (core DEIs). The majority of the core DEIs were involved in carbohydrate metabolism and energy production and conversion. In contrast, levels of known isoforms encoding Na⁺ transporters did not change significantly under salt stress. However, 16 core DEIs of unknown function were predicted to possess transmembrane domains, suggesting that these candidate isoforms could be involved in Na⁺ transport in H. glomeratus. These results suggest a potential means for identification of novel Na⁺ transporters, in addition to providing a foundation for further investigation of Na⁺ transport networks in halophytes.

Clinical Outcomes of Endovascular Treatment within 24 Hours in Patients with Mild Ischemic Stroke and Perfusion Imaging Selection

BACKGROUND AND PURPOSE

Endovascular thrombectomy has been accepted as the standard of care for patients with acute ischemic stroke. Our aim was to investigate the clinical outcomes of patients with mild ischemic stroke with acute proximal large-vessel occlusion after endovascular treatment within 24 hours of symptom onset.

MATERIALS AND METHODS

Between January 2014 and August 2017, ninety-three Chinese patients with mild ischemic stroke (NIHSS scores, 0-8) and large-vessel occlusion with endovascular treatment were retrospectively enrolled from 7 comprehensive stroke centers. They were divided into 2 groups: ≤6 hours and 6-24 hours from symptom onset to groin puncture. We analyzed their modified Rankin Scale scores at 90 days, symptomatic intracranial hemorrhage at 48 hours, and mortality during 90 days. Multivariable linear regression analysis was used to identify predictors for NIHSS shift after discharge.

RESULTS

Twenty-nine patients received endovascular treatment within 6-24 hours after symptom onset and had an imaging mismatch based on perfusion CT or diffusion-weighted MR imaging. There were no substantial differences between the 2 groups in 90-day functional independence (P = .54) and the risks of the combination of symptomatic intracranial hemorrhage and death (P = .72). Two significant indicators of NIHSS shift were 48-hour symptomatic intracranial hemorrhage (unstandardized β = 7.28; 95% CI, 3.48-11.1; P < .001) and baseline systolic blood pressure (unstandardized β = 0.08; 95% CI, 0.03-0.14; P = .005).

CONCLUSIONS

Patients with mild ischemic stroke and large-vessel occlusion in the anterior circulation, an imaging mismatch, and endovascular treatment within 6-24 hours of initial symptoms showed no heterogeneity in the efficacy and safety outcome compared with those treated ≤6 hours from symptom onset.

The Griffiths Development Scales-Chinese (GDS-C): A cross-cultural comparison of developmental trajectories between Chinese and British children

BACKGROUND

The Griffiths Mental Development Scales (GMDS) are used in many countries to assess the development of children from birth to 8 years. There is a need for accurate and culturally appropriate developmental assessment tools for Chinese children. Here, we adapted the GMDS for use in Chinese children and compare the developmental trajectories between Chinese and British children.

METHODS

Children with typical development were recruited from 7 urban cities in China between 2009 and 2013. The Griffiths Mental Development Scales-Chinese (GDS-C) were adapted and used to assess the development of urban Chinese children. Developmental curves were computed for 6 subscales using learning management system methods and compare against the British curves from the Griffiths Mental Development Scales-Extended Revised (GMDS-ER).

RESULTS

The GDS-C were used to assess the developmental status of 815 Chinese children. Plots of the 1st, 5th, 10th, 25th, 50th, 75th, 90th, 95th, and 99th percentiles, and full percentile tables were obtained, which showed similar trends to data from the British GMDS-ER.

CONCLUSIONS

The Chinese developmental curves obtained from the GDS-C showed similarities and differences to the developmental curves from the British GMDS-ER. The development of urban Chinese children should be assessed with the culturally appropriate GDS-C.

Oxidation-induced generation of a mild electrophile for proximity-enhanced protein-protein crosslinking

We report a strategy to introduce a reactive electrophile into proteins through the conversion of a chemically inert group into a bioreactive group in response to an inducer molecule. This strategy was demonstrated by oxidation-induced and proximity-enhanced protein-protein crosslinking in the presence of a large excess of free nucleophile.

Molecular Mechanisms of Acclimatization to Phosphorus Starvation and Recovery Underlying Full-Length Transcriptome Profiling in Barley (Hordeum vulgare L.)

A lack of phosphorus (P) in plants can severely constrain growth and development. Barley, one of the earliest domesticated crops, is extensively planted in poor soil around the world. To date, the molecular mechanisms of enduring low phosphorus, at the transcriptional level, in barley are still unclear. In the present study, two different barley genotypes (GN121 and GN42)-with contrasting phosphorus efficiency-were used to reveal adaptations to low phosphorus stress, at three time points, at the morphological, physiological, biochemical, and transcriptome level. GN121 growth was less affected by phosphorus starvation and recovery than that of GN42. The biomass and inorganic phosphorus concentration of GN121 and GN42 declined under the low phosphorus-induced stress and increased after recovery with normal phosphorus. However, the range of these parameters was higher in GN42 than in GN121. Subsequently, a more complete genome annotation was obtained by correcting with the data sequenced on Illumina HiSeq X 10 and PacBio RSII SMRT platform. A total of 6,182 and 5,270 differentially expressed genes (DEGs) were identified in GN121 and GN42, respectively. The majority of these DEGs were involved in phosphorus metabolism such as phospholipid degradation, hydrolysis of phosphoric enzymes, sucrose synthesis, phosphorylation/dephosphorylation and post-transcriptional regulation; expression of these genes was significantly different between GN121 and GN42. Specifically, six and seven DEGs were annotated as phosphorus transporters in roots and leaves, respectively. Furthermore, a putative model was constructed relying on key metabolic pathways related to phosphorus to illustrate the higher phosphorus efficiency of GN121 compared to GN42 under low phosphorus conditions. Results from this study provide a multi-transcriptome database and candidate genes for further study on phosphorus use efficiency (PUE).

Birthweight and cardiometabolic risk patterns in multiracial children

BACKGROUND/OBJECTIVES

Prenatal growth, which is widely marked by birthweight, may have a pivotal role in affecting the lifelong risk of cardiometabolic disorders; however, comprehensive evaluation of its relations with childhood cardiometabolic risk patterns and the ethnic and gender disparities in national representative populations is still lacking. The aim of this study was to evaluate the associations between birthweight and comprehensive patterns of cardiometabolic risk in a nationally representative sample of children and adolescents.

SUBJECTS/METHODS

Prospective analyses were performed using data from 28 153 children 0 to 15 years in the National Health and Nutrition Examination Survey from 1999 through 2014. We defined childhood cardiometabolic disorders using standard definitions for obesity, high blood pressure, hyperglycemia and dyslipidemia.

RESULTS

Five birthweight categories <2.5, 2.5-3.0, 3.0-3.5, 3.5-4.2 and ⩾4.2 kg accounted for 8.2%, 17.9%, 35.7%, 27.9% and 10.4% of the population, respectively. In all children, with increasing birthweight, we observed significantly increasing trends of the risk of general and central obesity (P for trend <0.01) and significantly decreasing trends of the risk of high systolic blood pressure (SBP), high HbA1c and low high-density lipoprotein cholesterol (HDL-C) (P for trend <0.05). The associations were independent of current body mass index (BMI). In addition, we found that the relations of birthweight with high waist circumference in Black children showed U-shape, as well as high SBP in Mexican and Hispanic children. Moreover, we found that the associations of low birthweight with high SBP and low HDL-C appeared to more prominent significant in boys, whereas the inverse association with high HbA1c was more evident in girls.

CONCLUSIONS

Our data indicate that birthweight is significantly related to childhood cardiometabolic risk, independent of current BMI, and the associations exhibit race and gender-specific patterns.

Transcriptome sequencing and comparative analysis of differentially-expressed isoforms in the roots of Halogeton glomeratus under salt stress

Although Halogeton glomeratus (H. glomeratus) has been confirmed to have a unique mechanism to regulate Na⁺ efflux from the cytoplasm and compartmentalize Na⁺ into leaf vacuoles, little is known about the salt tolerance mechanisms of roots under salinity stress. In the present study, transcripts were sequenced using the BGISEQ-500 sequencing platform (BGI, Wuhan, China). After quality control, approximately 24.08 million clean reads were obtained and the average mapping ratio to the reference gene was 70.00%. When comparing salt-treated samples with the control, a total of 550, 590, 1411 and 2063 DEIs were identified at 2, 6, 24 and 72h, respectively. Numerous differentially-expressed isoforms that play important roles in response and adaptation to salt condition are related to metabolic processes, cellular processes, single-organism processes, localization, biological regulation, responses to stimulus, binding, catalytic activity and transporter activity. Fifty-eight salt-induced isoforms were common to different stages of salt stress; most of these DEIs were related to signal transduction and transporters, which maybe the core isoforms regulating Na⁺ uptake and transport in the roots of H. glomeratus. The expression patterns of 18 DEIs that were detected by quantitative real-time polymerase chain reaction were consistent with their respective changes in transcript abundance as identified by RNA-Seq technology. The present study thoroughly explored potential isoforms involved in salt tolerance on H. glomeratus roots at five time points. Our results may serve as an important resource for the H. glomeratus research community, improving our understanding of salt tolerance in halophyte survival under high salinity stress.

A genetically encoded cyclobutene probe for labelling of live cells

We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a cyclobutene-containing amino acid into proteins in response to an amber nonsense codon. Fast and fluorescent labeling of purified proteins and intact proteins in live cells was demonstrated using the inverse electron demand Diels-Alder reaction with a tetrazine.

Dietary Quality Is Associated with Abdominal Aortic Calcification: A Mean of 18-Year Longitudinal Study in Community-Dwelling Older Adults

OBJECTIVE

This study aimed to examine the association between baseline and changes in dietary quality assessed by the Alternative Healthy Eating Index-2010 (AHEI-2010) and abdominal aortic calcification (AAC) among community-dwelling older adults.

DESIGN

Population-based longitudinal study.

SETTING

A subset of the Melbourne Collaborative Cohort Study (MCCS).

PARTICIPANTS

262 community-dwelling adults (60% female) aged 53 ± 5 years at baseline.

MEASUREMENTS

Dietary intake was assessed using validated Food Frequency Questionnaires at baseline (1990-1994) and follow-up (2010-2011). AAC was evaluated by radiography and dual-energy x-ray absorptiometry (DXA) at follow-up.

RESULTS

Higher baseline AHEI-2010 score was associated with lower AAC severity by radiography [OR (95% CI) for Tertile 3 VS Tertile 1: 0.53 (0.29-0.99)] after adjustment for gender, age, physical activity, smoking, BMI, systolic blood pressure, plasma total cholesterol, calcium and energy intake. The association between AHEI-2010 and AAC severity by DXA was also significant in the multivariate-adjusted model [OR (95% CI) for Tertile 3 VS Tertile 1: 0.38 (0.20-0.70)]. Changes in AHEI-2010 over 18 years were not associated with AAC severity.

CONCLUSION

Baseline but not the changes in AHEI-2010 was inversely associated with the risk of AAC severity suggesting that a high quality diet might help prevent or delay the progression of AAC in community-dwelling older adults and the benefits might be manifested over the long-term.

Fluorogenic protein labeling using a genetically encoded unstrained alkene

A new fluorogenic bioorthogonal reaction between styrene (an unstrained alkene) and a tetrazine was developed.

We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels–Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene–tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.

Comparative Proteomic Analysis of Cultured Suspension Cells of the Halophyte Halogeton glomeratus by iTRAQ Provides Insights into Response Mechanisms to Salt Stress

Soil salinity severely threatens land use capability and crop yields worldwide. An analysis of the molecular mechanisms of salt tolerance in halophytes will contribute to the development of salt-tolerant crops. In this study, a combination of physiological characteristics and iTRAQ-based proteomic approaches was conducted to investigate the molecular mechanisms underlying the salt response of suspension cell cultures of halophytic Halogeton glomeratus. These cells showed halophytic growth responses comparable to those of the whole plant. In total, 97 up-regulated proteins and 192 down-regulated proteins were identified as common to both 200 and 400 mM NaCl concentration treatments. Such salinity responsive proteins were mainly involved in energy, carbohydrate metabolism, stress defense, protein metabolism, signal transduction, cell growth, and cytoskeleton metabolism. Effective regulatory protein expression related to energy, stress defense, and carbohydrate metabolism play important roles in the salt-tolerance of H. glomeratus suspension cell cultures. However, known proteins regulating Na(+) efflux from the cytoplasm and its compartmentalization into the vacuole did not change significantly under salinity stress suggesting our existing knowledge concerning Na(+) extrusion and compartmentalization in halophytes needs to be evaluated further. Such data are discussed in the context of our current understandings of the mechanisms involved in the salinity response of the halophyte, H. glomeratus.

A photoactivatable Src homology 2 (SH2) domain

A photoactivatable SH2 domain that can be potentially applied as an optogenetic tool to the photocontrol of phosphotyrosine-associated biological processes.

Population genetic differentiation of the black locust gall midge Obolodiplosis robiniae (Haldeman) (Diptera: Cecidomyiidae): a North American pest invading Asia

Obolodiplosis robiniae is native to North America and is an important introduced insect pest that forms leaf margin roll galls on species of genus Robinia (Fabaceae) in China. It was first detected in China in 2004, but subsequently spread and provoked local outbreaks. An analysis of a 676-bp sequence of the mitochondrial DNA cytochrome oxidase subunit I was conducted in 560 individuals from 28 populations, in order to (1) assess population genetic structuring and (2) explore possible explanations for the rapid spread and invasion success of O. robiniae. Yet, only four haplotypes were identified and the nucleotide diversity was low (π = 0.00005) and among the 560 specimens studied, only ten showed haplotypic variation involving no more than three substitutions. The result showed a low degree of genetic diversity among populations of the successful invasive gall midge, which suggested that the pest experienced a severe genetic bottleneck and a loss of genetic diversity after its introduction. The successful establishment and spread of O. robiniae in China is attributed to the wide distribution of its host plant, thus allowing ample opportunities for gene flow in the pest species, and to the advantageous life history characteristics of O. robiniae.