Mining genomic regions associated with agronomic and biochemical traits in quinoa through GWAS

Quinoa (Chenopodium quinoa Willd.), an Andean crop, is a facultative halophyte food crop recognized globally for its high nutritional value and plasticity to adapt to harsh conditions. We conducted a genome-wide association study on a diverse set of quinoa germplasm accessions. These accessions were evaluated for the following agronomic and biochemical traits: days to 50% flowering (DTF), plant height (PH), panicle length (PL), stem diameter (SD), seed yield (SY), grain diameter (GD), and thousand-grain weight (TGW). These accessions underwent genotyping-by-sequencing using the DNBSeq-G400R platform. Among all evaluated traits, TGW represented maximum broad-sense heritability. Our study revealed average SNP density of ≈ 3.11 SNPs/10 kb for the whole genome, with the lowest and highest on chromosomes Cq1B and Cq9A, respectively. Principal component analysis clustered the quinoa population in three main clusters, one clearly representing lowland Chilean accessions, whereas the other two groups corresponded to germplasm from the highlands of Peru and Bolivia. In our germplasm set, we estimated linkage disequilibrium decay to be ≈ 118.5 kb. Marker-trait analyses revealed major and consistent effect associations for DTF on chromosomes 3A, 4B, 5B, 6A, 7A, 7B and 8B, with phenotypic variance explained (PVE) as high as 19.15%. Nine associations across eight chromosomes were also found for saponin content with 20% PVE by qSPN5A.1. More QTLs were identified for PL and TGW on multiple chromosomal locations. We identified putative candidate genes in the genomic regions associated with DTF and saponin content. The consistent and major-effect genomic associations can be used in fast-tracking quinoa breeding for wider adaptation across marginal environments.

Advantages of a synchrotron light source for fluorescence-detected linear dichroism

Fluorescence-detected linear dichroism (FD-LD) enables one to collect linear dichroism spectra for oriented fluorophores in the presence of other absorbing species and light scattering. The experiment proceeds by scanning the excitation wavelength and using a filter to collect only emitted photons from the fluorophore. Thus, it has the potential to give data with enhanced selectivity and quality. By using a synchrotron radiation light source and fluorescence-detection, we show data for a range of fluorophores in different orienting environments. Film and flow-oriented FD-LD spectra were collected down to 170 nm. Even for flow-oriented liposomes, we have data collected down to 210 nm. For strongly scattering samples, for example, liposomes, FD-LD has the clear advantage that scattering is absent for the longer wavelength fluorescence photons. The collimated and smaller beam size of the synchrotron radiation also gives rise to sharper and more well-defined features in the spectra.

Genome-wide association mapping highlights candidate genes and immune genotypes for net blotch and powdery mildew resistance in barley

Net blotch (NB) and powdery mildew (PM) are major barley diseases with the potential to cause a dramatic loss in grain yield. Breeding for resistant barley genotypes in combination with identifying candidate resistant genes will accelerate the genetic improvement for resistance to NB and PM. To address this challenge, a set of 122 highly diverse barley genotypes from 34 countries were evaluated for NB and PM resistance under natural infection for in two growing seasons. Moreover, four yield traits; plant height (Ph), spike length (SL), spike weight (SW), and the number of spikelets per spike (NOS) were recorded. High genetic variation was found among genotypes in all traits scored in this study. No significant phenotypic correlation was found in the resistance between PM and NB. Immune genotypes for NB and PM were identified. A total of 21 genotypes were immune to both diseases. Of the 21 genotypes, the German genotype HOR_9570 was selected as the most promising genotype that can be used for future breeding programs. Furthermore, a genome-wide association study (GWAS) was used to identify resistant alleles to PM and NB. The results of GWAS revealed a set of 14 and 25 significant SNPs that were associated with increased resistance to PM and NB, respectively. This study provided very important genetic resources that are highly resistant to the Egyptian PM and NB pathotypes and revealed SNP markers that can be utilized to genetically improve resistance to PM and NB.

Model Comparison of Heritability Enrichment Analysis in Livestock Population

Heritability enrichment analysis is an important means of exploring the genetic architecture of complex traits in human genetics. Heritability enrichment is typically defined as the proportion of an SNP subset explained heritability, divided by the proportion of SNPs. Heritability enrichment enables better study of underlying complex traits, such as functional variant/gene subsets, biological networks and metabolic pathways detected through integrating explosively increased omics data. This would be beneficial for genomic prediction of disease risk in humans and genetic values estimation of important economical traits in livestock and plant species. However, in livestock, factors affecting the heritability enrichment estimation of complex traits have not been examined. Previous studies on humans reported that the frequencies, effect sizes, and levels of linkage disequilibrium (LD) of underlying causal variants (CVs) would affect the heritability enrichment estimation. Therefore, the distribution of heritability across the genome should be fully considered to obtain the unbiased estimation of heritability enrichment. To explore the performance of different heritability enrichment models in livestock populations, we used the VanRaden, GCTA and α models, assuming different α values, and the LDAK model, considering LD weight. We simulated three types of phenotypes, with CVs from various minor allele frequency (MAF) ranges: genome-wide (0.005 ≤ MAF ≤ 0.5), common (0.05 ≤ MAF ≤ 0.5), and uncommon (0.01 ≤ MAF < 0.05). The performances of the models with two different subsets (one of which contained known CVs and the other consisting of randomly selected markers) were compared to verify the accuracy of heritability enrichment estimation of functional variant sets. Our results showed that models with known CV subsets provided more robust enrichment estimation. Models with different α values tended to provide stable and accurate estimates for common and genome-wide CVs (relative deviation 0.5−2.2%), while tending to underestimate the enrichment of uncommon CVs. As the α value increased, enrichments from 15.73% higher than true value (i.e., 3.00) to 48.93% lower than true value for uncommon CVs were observed. In addition, the long-range LD windows (e.g., 5000 kb) led to large bias of the enrichment estimations for both common and uncommon CVs. Overall, heritability enrichment estimations were sensitive for the α value assumption and LD weight consideration of different models. Accuracy would be greatly improved by using a suitable model. This study would be helpful in understanding the genetic architecture of complex traits and provides a reference for genetic analysis in the livestock population.

Inter- and intra-chromosomal modulators of the APOE ɛ2 and ɛ4 effects on the Alzheimer's disease risk

The mechanisms of incomplete penetrance of risk-modifying impacts of apolipoprotein E (APOE) ε2 and ε4 alleles on Alzheimer's disease (AD) have not been fully understood. We performed genome-wide analysis of differences in linkage disequilibrium (LD) patterns between 6,136 AD-affected and 10,555 AD-unaffected subjects from five independent studies to explore whether the association of the APOE ε2 allele (encoded by rs7412 polymorphism) and ε4 allele (encoded by rs429358 polymorphism) with AD was modulated by autosomal polymorphisms. The LD analysis identified 24 (mostly inter-chromosomal) and 57 (primarily intra-chromosomal) autosomal polymorphisms with significant differences in LD with either rs7412 or rs429358, respectively, between AD-affected and AD-unaffected subjects, indicating their potential modulatory roles. Our Cox regression analysis showed that minor alleles of four inter-chromosomal and ten intra-chromosomal polymorphisms exerted significant modulating effects on the ε2- and ε4-associated AD risks, respectively, and identified ε2-independent (rs2884183 polymorphism, 11q22.3) and ε4-independent (rs483082 polymorphism, 19q13.32) associations with AD. Our functional analysis highlighted ε2- and/or ε4-linked processes affecting the lipid and lipoprotein metabolism and cell junction organization which may contribute to AD pathogenesis. These findings provide insights into the ε2- and ε4-associated mechanisms of AD pathogenesis, underlying their incomplete penetrance.

Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip

Genotyping platforms, as critical supports for genomics, genetics, and molecular breeding, have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput, automatic, large-scale, and shared facilities. In this study, we integrated an improved genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology to develop a multiple single-nucleotide polymorphism (mSNP) approach in which mSNPs can be captured from a single amplicon. From one 40K maize mSNP panel, we developed three types of markers (40K mSNPs, 251K SNPs, and 690K haplotypes), and generated multiple panels with various marker densities (1K-40K mSNPs) by sequencing at different depths. Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs. Compared with the one-amplicon-one-SNP system, mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection, linkage disequilibrium decay analysis, and genome-wide association studies. The technologies, protocols, and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals, plants, and microorganisms.

Identification and Validation of High LD Hotspot Genomic Regions Harboring Stem Rust Resistant Genes on 1B, 2A (Sr38), and 7B Chromosomes in Wheat

Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is an important disease of common wheat globally. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F_3:6 lines. The results indicated that 184 genotypes (86.8%) had different degrees of resistance to this common race. While 28 genotypes (13.2%) were susceptible to stem rust. A set of 11,911 single-nucleotide polymorphism (SNP) markers was used to perform GWAS which detected 84 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1B, 2A, 2B, 7B and an unknown chromosome. Promising high linkage disequilibrium (LD) genomic regions were found in all chromosomes except 2B which suggested they include candidate genes controlling stem rust resistance. Highly significant LD was found among these 59 significant SNPs on chromosome 2A and 12 significant SNPs with an unknown chromosomal position. The LD analysis between SNPs located on 2A and Sr38 gene reveal high significant LD genomic regions which was previously reported. To select the most promising stem rust resistant genotypes, a new approach was suggested based on four criteria including, phenotypic selection, number of resistant allele(s), the genetic distance among the selected parents, and number of the different resistant allele(s) in the candidate crosses. As a result, 23 genotypes were considered as the most suitable parents for crossing to produce highly resistant stem rust genotypes against the QFCSC.

Autologous reconstructions are associated with greater overall medium-term care costs than implant-based reconstructions in the Finnish healthcare system: A retrospective interim case-control cohort study

PURPOSE

Previous studies have mainly reported the short-term costs of different reconstruction techniques. Revision operations may increase costs in longer follow-up. Authors report medium-term data on different reconstruction methods. We hypothesised that the reconstruction method would affect not only the duration of reconstruction process but also total costs.

METHODS

The reconstruction database was reviewed from 2008 to 2019. Women with autologous (deep inferior epigastric perforator, transverse musculocutaneous gracilis and latissimus dorsi [LD] without implant) and implant-based (implant and LD with implant) reconstructions were included. Variables evaluated included age, body mass index, smoking, comorbidities, radiotherapy, complications and readmissions. Risk factors for multiple revision surgeries were analysed. Time to definitive reconstruction and related costs were also calculated.

RESULTS

In total, 591 patients with autologous reconstructions and 202 with implant-based reconstructions were included. The median follow-up time was 73 months. Definitive reconstruction was obtained in 443 days in implant-based reconstructions and in 403 days in autologous reconstructions (P = 0.050). Independent risk factors for multiple surgeries were younger age (P < 0.001) and comorbidity (P = 0.008). No statistically significant difference was observed in the rate of overall surgical procedures (P = 0.098), but implant-based reconstructions were more commonly associated with two or more planned operations (P = 0.008). Autologous reconstructions were associated with greater total cost ($22 052 vs. $18 329, P < 0.001).

CONCLUSIONS

This review of reconstructions over a 12-year study period revealed that autologous reconstructions are associated with greater overall costs, but there is no statistically significant difference in reconstruction time or rate of surgical procedures. However, a full cost assessment between reconstructive techniques requires a much longer follow-up period.

Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle

A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle. The accuracies of GP using the entire imputed WGS data were lower than those using the HD chip data in all cases. For DP and MP, the accuracy of GP using haploblock approaches outperformed the individual single nucleotide polymorphism (SNP) approach (GBLUP_In_Block) at specific LD levels. Hotelling’s test confirmed that GP using LD-based haplotypes from WGS data can significantly increase the accuracies of GP for RERW, compared with the individual SNP approach (∼1.4 and 1.9% for G_HBLUP and G_HBLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r² ≥ 0.5) were optimal for most scenarios. Our results suggested that LD-based haploblock approach can improve accuracy of genomic prediction for carcass traits using both HD chip and imputed WGS data under the optimal LD thresholds in Chinese Simmental beef cattle.

The Influence of Sex on Clinical Outcomes in Minimally Invasive Lumbar Decompression

BACKGROUND

Research focused on postoperative outcomes among men and women undergoing minimally invasive lumbar decompression (MIS LD) spine surgery is sparse. This study aims to assess the influence of sex on postoperative patient-reported outcome measure (PROM) evaluations and achievement of a minimum clinically important difference (MCID).

METHODS

A prospectively maintained surgical database was retrospectively queried for patients undergoing primary or revision, single or multilevel LD procedures from 2011 to 2019. Patients with incomplete visual analog scale (VAS) leg or back surveys were excluded. Demographic and operative variables were recorded, and a chi-squared analysis or t tests were used to compare by sex. PROMs were evaluated from preoperative to postoperative time points. PROM score differences and postoperative improvement were evaluated between sexes by a t test. Achievement of MCID by sex was compared using chi-squared analysis.

RESULTS

The study cohort (n = 572) was 70% male (n = 398), had an average age of 47 years, and 42% were obese. Sexes differed in preoperative VAS leg, Oswestry Disability Index (ODI), and 12-item short form (SF-12)-physical composite score (PCS) scores (all P < .05) and in ODI at 6 and 12 weeks (P = .048; P = .001) and VAS back and leg scores at 6 months (P = .039; P = .019). Both sexes significantly improved (P < .050) all PROMs at all time points except for VAS back at 1 year for women and ODI at 6 weeks and 6 months for men. The only significant difference in achievement of MCID was for ODI at 6 months (P = .008).

CONCLUSIONS

Significant preoperative differences were observed among sexes with ODI, SF-12-PCS, and VAS leg scores. By 1 year, there were no significant sex differences for any PROM or for achievement of MCID. MIS LD has an equivalent role for both sexes in achieving MCID.

LEVEL OF EVIDENCE

3.

CLINICAL RELEVANCE

Results demonstrate no sex difference in PROMs following LD.

New Amorphous Oxy-Sulfide Solid Electrolyte Material: Anion Exchange, Electrochemical Properties, and Lithium Dendrite Suppression via In Situ Interfacial Modification

Glassy sulfide materials have been considered as promising candidates for solid-state electrolytes (SSEs) in lithium and sodium metal (LM and SM) batteries. While much of the current research on lithium glassy SSEs (GSSEs) has focused on the pure sulfide binary Li₂S + P₂S₅ system, we have expanded these efforts by examining mixed-glass-former (MGF) compositions which have mixtures of glass formers, such as P and Si, which allow melt-quenching synthesis under ambient pressure and therefore the use of grain-boundary-free SSEs. We have doped these MGF compositions with oxygen to improve the chemical, electrochemical, and thermal properties of these glasses. In this work, we report on the short-range order (SRO), namely atomic-level, structures of Li₂S + SiS₂ + P₂O₅ MGF mixed oxy-sulfide glasses and, for the first time, study the critical current density (CCD) of these Si-doped oxy-sulfide GSSEs in LM symmetric cells. The samples were synthesized by planetary ball milling (PBM), and it was observed that a certain minimum milling time was necessary to achieve a final SRO structure. To address the short-circuiting lithium dendrite (LD) problems that were observed in these GSSEs, we demonstrate a simple and novel strategy for these Si-doped oxy-sulfide GSSEs to engineer the LM-GSSE interface by forming an in situ interlayer via heat treatment. Stable cycling to ∼1200 h at a capacity of 2 mAh·cm^-2 per discharge/charge cycle under a current density of 1 mA·cm^-2 is achieved. These results indicate that these MGF oxy-sulfide GSSEs combined with an optimized interfacial modification may find use in LM, and by extrapolation, SM, batteries.

Pairwise linkage disequilibrium estimation for polyploids

Many tasks in statistical genetics involve pairwise estimation of linkage disequilibrium (LD). The study of LD in diploids is mature. However, in polyploids, the field lacks a comprehensive characterization of LD. Polyploids also exhibit greater levels of genotype uncertainty than diploids, yet no methods currently exist to estimate LD in polyploids in the presence of such genotype uncertainty. Furthermore, most LD estimation methods do not quantify the level of uncertainty in their LD estimates. Our study contains three major contributions. (i) We characterize haplotypic and composite measures of LD in polyploids. These composite measures of LD turn out to be functions of common statistical measures of association. (ii) We derive procedures to estimate haplotypic and composite LD in polyploids in the presence of genotype uncertainty. We do this by estimating LD directly from genotype likelihoods, which may be obtained from many genotyping platforms. (iii) We derive standard errors of all LD estimators that we discuss. We validate our methods on both real and simulated data. Our methods are implemented in the R package ldsep, available on the Comprehensive R Archive Network https://cran.r-project.org/package=ldsep.

How Well Can Multivariate and Univariate GWAS Distinguish Between True and Spurious Pleiotropy?

Quantification of the simultaneous contributions of loci to multiple traits, a phenomenon called pleiotropy, is facilitated by the increased availability of high-throughput genotypic and phenotypic data. To understand the prevalence and nature of pleiotropy, the ability of multivariate and univariate genome-wide association study (GWAS) models to distinguish between pleiotropic and non-pleiotropic loci in linkage disequilibrium (LD) first needs to be evaluated. Therefore, we used publicly available maize and soybean genotypic data to simulate multiple pairs of traits that were either (i) controlled by quantitative trait nucleotides (QTNs) on separate chromosomes, (ii) controlled by QTNs in various degrees of LD with each other, or (iii) controlled by a single pleiotropic QTN. We showed that multivariate GWAS could not distinguish between QTNs in LD and a single pleiotropic QTN. In contrast, a unique QTN detection rate pattern was observed for univariate GWAS whenever the simulated QTNs were in high LD or pleiotropic. Collectively, these results suggest that multivariate and univariate GWAS should both be used to infer whether or not causal mutations underlying peak GWAS associations are pleiotropic. Therefore, we recommend that future studies use a combination of multivariate and univariate GWAS models, as both models could be useful for identifying and narrowing down candidate loci with potential pleiotropic effects for downstream biological experiments.

GWAS revealed effect of genotype × environment interactions for grain yield of Nebraska winter wheat

Background

Improving grain yield in cereals especially in wheat is a main objective for plant breeders. One of the main constrains for improving this trait is the G × E interaction (GEI) which affects the performance of wheat genotypes in different environments. Selecting high yielding genotypes that can be used for a target set of environments is needed. Phenotypic selection can be misleading due to the environmental conditions. Incorporating information from phenotypic and genomic analyses can be useful in selecting the higher yielding genotypes for a group of environments.

Results

A set of 270 F_3:6 wheat genotypes in the Nebraska winter wheat breeding program was tested for grain yield in nine environments. High genetic variation for grain yield was found among the genotypes. G × E interaction was also highly significant. The highest yielding genotype differed in each environment. The correlation for grain yield among the nine environments was low (0 to 0.43). Genome-wide association study revealed 70 marker traits association (MTAs) associated with increased grain yield. The analysis of linkage disequilibrium revealed 16 genomic regions with a highly significant linkage disequilibrium (LD). The candidate parents’ genotypes for improving grain yield in a group of environments were selected based on three criteria; number of alleles associated with increased grain yield in each selected genotype, genetic distance among the selected genotypes, and number of different alleles between each two selected parents.

Conclusion

Although G × E interaction was present, the advances in DNA technology provided very useful tools and analyzes. Such features helped to genetically select the highest yielding genotypes that can be used to cross grain production in a group of environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07308-0.

Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of External Ventricular and Lumbar Drainage-Associated Ventriculitis and Meningitis

Metagenomic next-generation sequencing (mNGS) has become a widely used technology that can accurately detect individual pathogens. This prospective study was performed between February 2019 and September 2019 in one of the largest clinical neurosurgery centers in China. The study aimed to evaluate the performance of mNGS on cerebrospinal fluid (CSF) from neurosurgical patients for the diagnosis of external ventricular and lumbar drainage (EVD/LD)-associated ventriculitis and meningitis (VM). We collected CSF specimens from neurosurgical patients with EVD/LD for more than 24 h to perform conventional microbiological studies and mNGS analyses in a pairwise manner. We also investigated the usefulness of mNGS of CSF for the diagnosis of EVD/LD-associated VM. In total, 102 patients were enrolled in this study and divided into three groups, including confirmed VM (cVM) (39), suspected VM (sVM) (49), and non-VM (nVM) (14) groups. Of all the patients, mNGS detected 21 Gram-positive bacteria, 20 Gram-negative bacteria, and five fungi. The three primary bacteria detected were Staphylococcus epidermidis (9), Acinetobacter baumannii (5), and Staphylococcus aureus (3). The mNGS-positive coincidence rate of confirmed EVD/LD-associated VM was 61.54% (24/39), and the negative coincidence rate of the nVM group was 100% (14/14). Of 15 VM pathogens not identified by mNGS in the cVM group, eight were negative with mNGS and seven were inconsistent with the conventional microbiological identification results. In addition, mNGS identified pathogens in 22 cases that were negative using conventional methods; of them, 10 patients received a favorable clinical treatment; thus, showing the benefit of mNGS-guided therapy.

Nutrient Signaling, Stress Response, and Inter-organelle Communication Are Non-canonical Determinants of Cell Fate

Isogenic cells manifest distinct cellular fates for a single stress; however, the nongenetic mechanisms driving such fates remain poorly understood. Here, we implement a robust multi-channel live-cell imaging approach to uncover noncanonical factors governing cell fate. We show that in response to acute glucose removal (AGR), budding yeast undergoes distinct fates, becoming either quiescent or senescent. Senescent cells fail to resume mitotic cycles following glucose replenishment but remain responsive to nutrient stimuli. Whereas quiescent cells manifest starvation-induced adaptation, senescent cells display perturbed endomembrane trafficking and defective nucleus-vacuole junction (NVJ) expansion. Surprisingly, senescence occurs even in the absence of lipid droplets. Importantly, we identify the nutrient-sensing kinase Rim15 as a key biomarker predicting cell fates before AGR stress. We propose that isogenic yeast challenged with acute nutrient shortage contains determinants influencing post-stress fate and demonstrate that specific nutrient signaling, stress response, trafficking, and inter-organelle biomarkers are early indicators for long-term fate outcomes.

The Utility of Elevated Serum Lactate Dehydrogenase in Current Clinical Practice

OBJECTIVE

Because of its wide tissue distribution, elevation of serum lactate dehydrogenase (LD) is a nonspecific finding. Although serum LD is still included in the prognosis and staging of metastatic melanoma and germ cell tumors, its nonspecificity has led to decreased usefulness.

METHODS

In this study, we analyzed the serum LD assays performed in a 726-bed hospital during a 1-year period and reviewed charts of patients with serum LD of >3 standard deviations (SD).

RESULTS

Of 312 patients with elevated serum LD, only 9 were patients with melanoma and germ cell tumors. The other 303 patients had other malignancies, chronic conditions, and sepsis.

CONCLUSION

Elevated serum LD (even >3 SD) is an extremely nonspecific finding that does not contribute to clinical management in a majority of patients. As such, serum LD testing should be retired from routine clinical order sets and restricted in use.

Association analysis of polymorphisms in LEP (rs7799039 and rs2167270) and LEPR (rs1137101) gene towards the development of type 2 diabetes in North Indian Punjabi population

OBJECTIVES

Obesity is a major risk factor in aetiology of type 2 diabetes mellitus (T2DM). Leptin (LEP) is an anti-obesity hormone which regulates food intake, energy expenditure and glucose metabolism. The genetic variants in leptin and leptin receptor gene (LEPR) may play major role in the pathogenesis of T2DM and obesity. The current study aimed to investigate the association of polymorphisms in LEP (rs7799039, -2548G/A and rs2167270, 19G/A) and LEPR (rs1137101, 668A/G) gene with type 2 diabetes in North Indian Punjabi population.

METHODS

A total of 817 subjects were included for the present case-control study, consisting of 417 T2DM patients and 400 healthy controls. The anthropometric, physiometric and biochemical measurements were taken from all the subjects. The genotyping of LEP and LEPR gene variants were carried out by polymerase chain reaction based restriction fragment length polymorphism method (PCR-RFLP), followed by genotyping of 10% of the samples for each polymorphism by Sanger sequencing method for quality control measurement.

RESULTS

The risk genotype frequencies were found to be significantly higher in T2DM cases than control subjects (rs7799039, p = 0.001; rs2167270, p = 0.019 and rs1137101, p = 0.003). Under recessive genetic model LEPrs7799039 and LEPRrs1137101 polymorphism conferred 3.4 and 2.1 fold risk towards the development of T2DM after adjustment of various covariates (OR = 3.44, 95%CI: 1.768-6.681, p = 0.001 and OR: 2.12, 95%CI: 1.256-3.569, p = 0.005, respectively). In the stratified analysis of LEP variant rs7799039 by age, gender, BMI and alcohol use, a significantly increased risk of T2DM was found in female, BMI ≥ 23 and never drinking subgroups. However, in the LEPR variant rs1137101, significantly increased risk of T2DM was observed in age <50, male, BMI ≥ 23 and never drinking subgroup. The A-G haplotype combination of rs7799039A and rs2167270G conferred significant 2 fold risk towards T2DM (OR = 2.35, 95%CI: 1.34-4.12, p = 0.002). In control group, the genetic variants rs7799039 and rs1137101 were significantly associated with levels of random blood sugar and low density lipoprotein cholesterol levels.

CONCLUSION

The present study revealed the association of LEP rs7799039 and LEPR rs1137101 with type 2 diabetes mellitus, which suggest its predominant role in the estimation of type 2 diabetes mellitus in North Indian Punjabi population.

Predictive risk factors of complications in different breast reconstruction methods

PURPOSE

Women with different BMI, age and comorbidities seek for breast reconstruction. It is critical to understand the risk associated with each technique to ensure the most appropriate method and timing is used. Outcome after reconstructions have been studied, but consensus is lacking regarding predictive risk factors of complications. The authors present their experience of different autologous and alloplastic reconstructions with an emphasis on predictors of complications.

METHODS

Prospectively maintained reconstruction database from 2008 to 2019 was reviewed. Factors associated with complications were identified using logistic regression, multinomial logistic regression and risk factor score to determine predictors of complications.

RESULTS

A total of 850 breast reconstructions were performed in 793 women, including 447 DIEP, 283 LD, 12 TMG and 51 implant reconstructions. Complications included minor (n = 231, 29%), re-surgery requiring (n = 142, 18%) and medical complications (n = 7, 1%). Multivariable analysis showed that complications were associated independently with BMI > 30 (OR 1.59; 95% CI 1.05-2.39, p = 0.027), LD technique (OR 4.05; 95% CI 2.10-7.81, p < 0.001), asthma or chronic obstructive pulmonary disease (OR 2.77; 95% CI 1.50-5.12, p = 0.001) and immediate operation (OR 0.69; 95% CI 0.44-1.07, p = 0.099). Each factor contributed 1 point in the creation of a risk-scoring system. The overall complication rate was increased as the risk score increased (35%, 61%, 76% and 100% for 1, 2, 3 and 4 risk scores, respectively, p < 0.001).

CONCLUSIONS

The rate of complication can be predicted by a risk-scoring system. In increasing trend of patients with medical problems undergoing breast reconstruction, tailoring of preventive measures to patients' risk factors and careful consideration of the best timing of reconstruction is mandatory to prevent complications and costs.

IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix

Genome-wide association study (GWAS), exploring the historical and evolutionary recombinations at the population level, is a major method adopted to identify quantitative trait loci (QTL) for complex traits. However, to summarize GWAS results, gene structure, and linkage disequilibrium (LD) in a single view, multiple tools are required. It is tedious to generate these three results and manually put them together; moreover, it may eventually lead to inaccuracies. On the other hand, genotype markers are usually detected by DNA- and/or RNA-Seq. For GWAS analysis based on RNA-Seq, markers from DNA-Seq provide more genetic information when displaying LD. The currently released software package does not have this function for an integrated analysis of LD, using genotypic markers different from that in association analysis. Here, we present an R package, IntAssoPlot, which provides an integrated visual display of GWAS results, along with LD and gene structure information, in a publication-ready format. The main panel of an IntAssoPlot plot has a connecting line linking the genome-wide association P-values on the -log10 scale with the gene structure and LD matrix. Importantly, IntAssoPlot is designed to plot GWAS results with LD calculated from genotypes different from those in GWAS analysis. IntAssoPlot provides a powerful visualization tool to gain an integrated insight into GWAS results. The functions provided by IntAssoPlot increase the efficiency by revealing GWAS results in a publication-ready format. Inspection of the output image can provide important biological information, including the loci that passed the genome-wide significance threshold, genes located at or near the significant loci, and the extent of LD within the selected region.

Concerted variation of the 3' regulatory region of Ig heavy chain and Gm haplotypes across human continental populations

OBJECTIVES

The 3' regulatory region of the immunoglobulin heavy chain gene (IGH) includes the HS1.2 enhancer displaying length polymorphism with four known variants. The goal of the research was to provide an overview of this variability and of its evolutionary significance across human populations.

MATERIALS AND METHODS

We compiled published and original data on HS1.2 polymorphism in 3,100 subjects from 26 human populations. Moreover, we imputed the haplotypic arrangement of the HS1.2 region in the 1000 Genomes Project (1KGP). In this dataset, imputation could also be obtained for the G1m-G3m allotype by virtue of the precise correspondence between serological types and amino acid (and DNA) substitutions in IGHG1 and IGHG3.

RESULTS

HS1.2 variant frequencies displayed similar patterns of continental partitioning as those reported in the literature for the physically neighboring IGHG1-IGHG3 system. The 1KGP data revealed that linkage disequilibrium (LD) can explain the spread of joint HS1.2-IGHG1-IGHG3 associations across continents and within continental populations, with stronger LD out of Africa and the features of an evolutionarily stable genomic block with differential expression in lymphoblastoid cell lines.

DISCUSSION

Strong population structuring involves at least the entire 70 kb genomic region here considered, due to the tight LD which maintained HS1.2, IGHG1, and IGHG3 in nonrandom arrangements. This might be key to better understand the evolutionary path of the entire genomic region driven by immune response capabilities, during the formation of continental gene pools.

Genetic Dissection of Nitrogen Use Efficiency in Tropical Maize Through Genome-Wide Association and Genomic Prediction

In sub-Saharan Africa, one of the major challenges to smallholder farmers is soil with low fertility and inability to apply nitrogen fertilizer externally due to the cost. Development of maize hybrids, which perform better in nitrogen depleted soils, is one of the promising solutions. However, breeding maize for nitrogen use efficiency (NUE) is hindered by expensive phenotypic evaluations and trait complexity under low N stress. Genome-wide association study (GWAS) and genomic prediction (GP) are promising tools to circumvent this interference. Here, we evaluated a mapping panel in diverse environments both under optimum and low N management. The objective of this study was to identify SNPs significantly associated with grain yield (GY) and other traits through GWAS and assess the potential of GP under low N and optimum conditions. Testcross progenies of 411 inbred lines were planted under optimum and low N conditions in several locations in Africa and Latin America. In all locations, low N fields were previously depleted over several seasons, and no N fertilizer was applied throughout the growing season. All inbred lines were genotyped with genotyping by sequencing. Genotypic and GxE interaction variances were significant, and heritability estimates were moderate to high for all traits under both optimum and low N conditions. Genome-wide LD decay at r ² = 0.2 and r ² = 0.34 were 0.24 and 0.19 Mbp, respectively. Chromosome-specific LD decays ranged from 0.13 to 0.34 Mbps with an average of 0.22 Mbp at r ² = 0.2. GWAS analyses revealed 38 and 45 significant SNPs under optimum and low N conditions, respectively. Out of these 83 significant SNPs, 3 SNPs on chromosomes 1, 2, and 6 were associated either with different traits or the same trait under different management conditions, suggesting pleiotropic effects of genes. A total of 136 putative candidate genes were associated with the significant SNPs, of which seven SNPs were linked with four known genes. Prediction accuracies were moderate to high for all traits under both optimum and low N conditions. These results can be used as useful resources for further applications to develop hybrids or lines with better performance under low N conditions.

Drosophila Snazarus Regulates a Lipid Droplet Population at Plasma Membrane-Droplet Contacts in Adipocytes

Adipocytes store nutrients as lipid droplets (LDs), but how they organize their LD stores to balance lipid uptake, storage, and mobilization remains poorly understood. Here, using Drosophila fat body (FB) adipocytes, we characterize spatially distinct LD populations that are maintained by different lipid pools. We identify peripheral LDs (pLDs) that make close contact with the plasma membrane (PM) and are maintained by lipophorin-dependent lipid trafficking. pLDs are distinct from larger cytoplasmic medial LDs (mLDs), which are maintained by FASN1-dependent de novo lipogenesis. We find that sorting nexin CG1514 or Snazarus (Snz) associates with pLDs and regulates LD homeostasis at ER-PM contact sites. Loss of SNZ perturbs pLD organization, whereas Snz over-expression drives LD expansion, triacylglyceride production, starvation resistance, and lifespan extension through a DESAT1-dependent pathway. We propose that Drosophila adipocytes maintain spatially distinct LD populations and identify Snz as a regulator of LD organization and inter-organelle crosstalk.

Release of doxorubicin from its liposomal coating via high intensity ultrasound

The present ex vivo study was performed to analyze the impact of high intensity ultrasound (HIUS) on penetration depth and particle stability of liposomal doxorubicin (LD) on the peritoneal surface. Fresh post mortem swine peritoneum was cut into proportional sections and subjected to a previously established ex vivo model of pressurized intraperitoneal aerosol chemotherapy (PIPAC). Samples were treated with 50 ml NaCl (0.9%) containing 3 mg LD via PIPAC or lavage. In both groups, half of the samples received additional HIUS treatment. Samples treated via PIPAC were covered with a 30-mm-thick abdominal muscle wall tissue, fatty tissue and skin, followed by transcutaneous HIUS. Samples administered with LD via lavage received close-range contact HIUS. Doxorubicin tissue penetration was measured using fluorescence microscopy on frozen sections. Liposomal integrity on peritoneal surfaces was measured via electron microscopy (EM). Mean penetration rates of doxorubicin were significantly higher with HIUS in combination with PIPAC or lavage compared with PIPAC alone (P<0.001) or lavage alone (P<0.00001). LD was not detected on the peritoneal surface via EM analysis in either group following HIUS. The present data suggested that HIUS may be a feasible application that can facilitate the release of doxorubicin from its liposomal envelope. HIUS was effective in both close-range, in contact with the samples, and through the abdominal wall. The present approach may be used in the future for both endoscopic and open lavage of the peritoneal cavity with LD in intraperitoneal chemotherapeutic applications such as hyperthermic intraperitoneal chemotherapy or PIPAC.

Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Simple Summary

The pig is one of the most important livestock animals, providing the majority of protein for humans. The population genetics analysis of pigs not only helps humans understand the domestication of the pig but also helps breeders in the genetic improvement of pigs. In this study, the population genetics of 11 pig breeds of South China were analyzed with the help of single nucleotide polymorphism (SNP) chips. The results showed that the genetic diversity of South China indigenous pigs is declining rapidly, and gene introgression from commercial pigs to indigenous pigs was detected. Selection signature analysis showed differences among South China indigenous pig breeds, commercial pig breeds, and wild pig breeds were present for meat quality and growth. Our study deepened understanding of the conservation status and selection mechanisms of Chinese indigenous pigs.

Abstract

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

Promethin Is a Conserved Seipin Partner Protein

Seipin (BSCL2/SPG17) is a key factor in lipid droplet (LD) biology, and its dysfunction results in severe pathologies, including the fat storage disease Berardinelli-Seip congenital lipodystrophy type 2, as well as several neurological seipinopathies. Despite its importance for human health, the molecular role of seipin is still enigmatic. Seipin is evolutionarily conserved from yeast to humans. In yeast, seipin was recently found to cooperate with the lipid droplet organization (LDO) proteins, Ldo16 and Ldo45, two structurally-related proteins involved in LD function and identity that display remote homology to the human protein promethin/TMEM159. In this study, we show that promethin is indeed an LD-associated protein that forms a complex with seipin, and its localization to the LD surface can be modulated by seipin expression levels. We thus identify promethin as a novel seipin partner protein.

Perilipin-2 is critical for efficient lipoprotein and hepatitis C virus particle production

In hepatocytes, PLIN2 is the major protein coating lipid droplets (LDs), an organelle the hepatitis C virus (HCV) hijacks for virion morphogenesis. We investigated the consequences of PLIN2 deficiency on LDs and on HCV infection. Knockdown of PLIN2 did not affect LD homeostasis, likely due to compensation by PLIN3, but severely impaired HCV particle production. PLIN2-knockdown cells had slightly larger LDs with altered protein composition, enhanced local lipase activity and higher β-oxidation capacity. Electron micrographs showed that, after PLIN2 knockdown, LDs and HCV-induced vesicular structures were tightly surrounded by ER-derived double-membrane sacs. Strikingly, the LD access for HCV core and NS5A proteins was restricted in PLIN2-deficient cells, which correlated with reduced formation of intracellular HCV particles that were less infectious and of higher density, indicating defects in maturation. PLIN2 depletion also reduced protein levels and secretion of ApoE due to lysosomal degradation, but did not affect the density of ApoE-containing lipoproteins. However, ApoE overexpression in PLIN2-deficient cells did not restore HCV spreading. Thus, PLIN2 expression is required for trafficking of core and NS5A proteins to LDs, and for formation of functional low-density HCV particles prior to ApoE incorporation.This article has an associated First Person interview with the first author of the paper.

Association of CYBA gene (-930 A/G and 242 C/T) polymorphisms with oxidative stress in breast cancer: a case-control study

Background

Oxidative stress (OS) is a key characteristic feature in cancer initiation and progression. Among multiple cancers, NADPH oxidase (NOX) dependent free radical production is implicated in oxidative stress. P22phox, a subunit of NADPH oxidase encoded by the CYBA gene has functional polymorphisms associated with various complex diseases. The present study was aimed to examine the importance and association of the functional polymorphisms of CYBA gene (-930 A/G and 242 C/T) with the oxidative stress in breast cancer (BC) development and progression.

Materials and Methods

We have performed a case-control study on 300 breast cancer patients and 300 healthy individuals as controls to examine the role of CYBA gene -930 A/G and 242 C/T single nucleotide polymorphisms (SNPs) using As-PCR and PCR-RFLP assays and its association with OS as measured by plasma MDA levels. Linkage disequilibrium (LD) plots were generated using Haploviewtool and Multifactor dimensionality reduction (MDR) analysis was applied to assess high-order interactions between the SNPs. The Insilco analysis has been performed to predict the effect of SNPs on the gene regulation using online tools.

Results

We have found that genotype frequencies of CYBA gene -930 A/G and 242C/T polymorphism were significantly different between controls and BC patients (p < 0.05). The haplotype combination -930G/242C and -930G/242T were associated with 1.44 & 1.56 folds increased risk for breast cancer respectively. Further, the MDA levels were higher in the patients carrying -930G/242C and -930G/242T haplotype (p < 0.001). Our results have been substantiated by Insilco analysis.

Conclusion

Results of the present study suggest that GG genotype of -930 A/G polymorphism, -930G/242C and -930G/242T haplotypes of CYBA gene polymorphisms have shown association with higher MDA levels in breast cancer patients, signify that elevated oxidative stress might aid in increased risk for breast cancer initiation and progression.

One Hundred Years of Linkage Disequilibrium

One hundred years ago, the first population genetic calculations were made for two loci. They indicated that populations should settle down to a state where the frequency of an allele at one locus is independent of the frequency of an allele at a second locus, even if these loci are linked. Fifty years later it was realized what is obvious in retrospect, that these calculations ignored the effect of chance segregation of linked loci, an effect now widely recognized following the association of closely linked markers (SNPs) with rare genetic diseases. Linkage disequilibrium is now accepted as the norm for closely linked loci, leading to powerful applications in the mapping of disease alleles and quantitative trait loci, in the detection of sites of selection in the human genome, in the application of genomic prediction of quantitative traits in animal and plant breeding, in the estimation of population size, and in the dating of population divergence.

Violent incidents in a secure service for individuals with learning disabilities: Incident types, circumstances and staff responses

BACKGROUND

The issue of violence in secure services has long been recognized both in the UK and worldwide. However, there is currently scarce literature available about violence within learning disability (LD) secure settings.

METHODS

Secondary data analysis was conducted on violent incidents, using information routinely collected by the staff over a 1-year period.

RESULTS

Physical assaults were the most frequent type of incident, and the distribution in terms of days or months was homogenous and incidents were concentrated in the corridors, lounges and dining rooms of secure facilities. Antipsychotic medication was not regularly prescribed. Generalized linear modelling analyses revealed significant predictors that increased the chances of seclusion and physical restraint, such as being female or directing the violence towards staff.

CONCLUSIONS

These findings can inform staff training on violence prevention and suggest that increased ward-based supervision and enhanced use of psychological formulations may help in reducing violence within this service context.

Linkage disequilibrium and functional analysis of PRE1 insertion together with SNPs in the promoter region of IGFBP7 gene in different pig breeds

Polymorphisms in regions upstream of transcription initiation site may modify the transcriptional activity of target genes by changing promoter activity. This study aims to determine whether or not polymorphisms at porcine IGFBP7 promoter region affect gene expression. In this study, eight SNPs and one PRE1 insertion in this region were first confirmed. The PRE1 insertion was widespread in 20 Chinese indigenous breeds, but was not observed in three commercial breeds. A perfect linkage disequilibrium, consisting of six of those SNPs and a PRE1, was observed with two haplotypes (h1 and h2) in five pig breeds. The h1 haplotype had an overwhelming superiority distribution in Large White, Landrace, and Bama mini-pig; in turn, the h2 only existed in the PRE1 presence breeds. As the haplotypes and PRE1 were located at gene promoter regions, we further investigated the transfection of plasmids with three different fragments of IGFBP-7 promoter region (H1, H2, RF). The CMV promoter of the pEGFP-N1 was substituted by these three different fragments, respectively. Different transcriptional and translational activities of EGFP in PK-15 cells were observed in these three recombinant plasmids by quantitative real-time PCR and flow cytometric analysis. The results indicated that H1 had the higher transcriptional and translational activities of EGFP as compared to the H2 (P < 0.05, P < 0.05). As compared to the RF group, EGFP mRNA expression level was significantly higher in H1 groups (P < 0.05). The IGFBP-7 promoter polymorphisms detected in this study may be important functional variants and potential genetic markers for pig population genetic study.

Amyloids and prions in plants: Facts and perspectives

Amyloids represent protein fibrils that have highly ordered structure with unique physical and chemical properties. Amyloids have long been considered lethal pathogens that cause dozens of incurable diseases in humans and animals. Recent data show that amyloids may not only possess pathogenic properties but are also implicated in the essential biological processes in a variety of prokaryotes and eukaryotes. Functional amyloids have been identified in archaea, bacteria, fungi, and animals, including humans. Plants are one of the most poorly studied groups of organisms in the field of amyloid biology. Although amyloid properties have not been shown under native conditions for any plant protein, studies demonstrating amyloid properties for a set of plant proteins in vitro or in heterologous systems in vivo have been published in recent years. In this review, we systematize the data on the amyloidogenic proteins of plants and their functions and discuss the perspectives of identifying novel amyloids using bioinformatic and proteomic approaches.

Fluorescence detected linear dichroism spectroscopy: A selective and sensitive probe for fluorophores in flow-oriented systems

Fluorescence detection typically enhances sensitivity and selectivity for fluorescent analytes. The potential for combining fluorescence detection with flow orientation of the sample in the normal configuration of linear dichroism experiments is explored in this work by measuring the fluorescence emitted from flow-orientated DNA-bound ligands and M13 bacteriophage. Data for ethidium bromide, Hoechst 33258, and 4,6-diamidino-2-phenyindole are presented. The theoretical basis of the technique is also presented for instruments running in both the fixed direct-current mode, which is the normal operation mode of circular dichroism spectropolarimeters, and also in fixed high-tension voltage mode. The role of the stray light reaching the detector that results in a spectral shape in fixed direct current mode that resembles the shape of a linear dichroism spectrum, rather than the expected reduced linear dichroism, is also explored.

Genomic variance estimates: With or without disequilibrium covariances?

Whole-genome regression methods are often used for estimating genomic heritability: the proportion of phenotypic variance that can be explained by regression on marker genotypes. Recently, there has been an intensive debate on whether and how to account for the contribution of linkage disequilibrium (LD) to genomic variance. Here, we investigate two different methods for genomic variance estimation that differ in their ability to account for LD. By analysing flowering time in a data set on 1,057 fully sequenced Arabidopsis lines with strong evidence for diversifying selection, we observed a large contribution of covariances between quantitative trait loci (QTL) to the genomic variance. The classical estimate of genomic variance that ignores covariances underestimated the genomic variance in the data. The second method accounts for LD explicitly and leads to genomic variance estimates that when added to error variance estimates match the sample variance of phenotypes. This method also allows estimating the covariance between sets of markers when partitioning the genome into subunits. Large covariance estimates between the five Arabidopsis chromosomes indicated that the population structure in the data led to strong LD also between physically unlinked QTL. By consecutively removing population structure from the phenotypic variance using principal component analysis, we show how population structure affects the magnitude of LD contribution and the genomic variance estimates obtained with the two methods.

rs12603332 is associated with male asthma patients specifically in urban areas of Lahore, Pakistan

OBJECTIVE

rs12603332, an important regulatory site variant, is known to alter the regulatory motif E2A that is involved in the maturation of B-lymphocytes. The study was designed to check whether different environmental exposures alter its risk allele association with asthma or not.

METHODS

200 Physician-diagnosed asthma patients and 108 healthy individuals were enrolled from hospitals of Lahore. After quantitation of DNA extracted from peripheral blood, amplification of genomic region with rs12603332, followed by single base extension (SBE), was performed. Allele and genotype frequencies were calculated by SHEsis and Haploview software packages. Statistical analyses on PLINK were also performed, taking different factors as covariates. HaploReg analysis was done to predict the effect of risk allele on different regulatory motifs.

RESULTS

Risk allele for rs12603332 i.e., "C" allele was found to be significantly associated with male patients residing in urban localities.

CONCLUSION

The finding suggests that on exposure with urban environment, risk allele carriers tend to develop asthma symptoms via epigenetic regulation of motif associated with maturation of B-lymphocytes.

The ER-Localized Transmembrane Protein EPG-3/VMP1 Regulates SERCA Activity to Control ER-Isolation Membrane Contacts for Autophagosome Formation

During autophagosome formation in mammalian cells, isolation membranes (IMs; autophagosome precursors) dynamically contact the ER. Here, we demonstrated that the ER-localized metazoan-specific autophagy protein EPG-3/VMP1 controls ER-IM contacts. Loss of VMP1 causes stable association of IMs with the ER, thus blocking autophagosome formation. Interaction of WIPI2 with the ULK1/FIP200 complex and PI(3)P contributes to the formation of ER-IM contacts, and these interactions are enhanced by VMP1 depletion. VMP1 controls contact formation by promoting SERCA (sarco[endo]plasmic reticulum calcium ATPase) activity. VMP1 interacts with SERCA and prevents formation of the SERCA/PLN/SLN inhibitory complex. VMP1 also modulates ER contacts with lipid droplets, mitochondria, and endosomes. These ER contacts are greatly elevated by the SERCA inhibitor thapsigargin. Calmodulin acts as a sensor/effector to modulate the ER contacts mediated by VMP1/SERCA. Our study provides mechanistic insights into the establishment and disassociation of ER-IM contacts and reveals that VMP1 modulates SERCA activity to control ER contacts.

Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

BACKGROUND

Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of linkage disequilibrium (LD) and ancestral effective population size (Ne) through quantifying this diversity and comparison between populations allows for more informed decisions with regards to selective breeding taking population genetic diversity into account. The estimation of N e can be determined via genetic markers and requires knowledge of genetic distances between these markers. Single nucleotide polymorphisms (SNP) data from a sample of 12,597 New Zealand crossbred and purebred sheep genotyped with the Illumina Ovine SNP50 BeadChip was used to perform a genome-wide scan of LD and N e . Three methods to estimate genetic distances were investigated: 1) M1: a ratio fixed across the whole genome of one Megabase per centiMorgan; 2) M2: the ratios of genetic distance (using M3, below) over physical distance fixed for each chromosome; and, 3) M3: a genetic map of inter-SNP distances estimated using CRIMAP software (v2.503).

RESULTS

The estimates obtained with M2 and M3 showed much less variability between autosomes than those with M1, which tended to give lower N e results and higher LD decay. The results suggest that N e has decreased since the development of sheep breeds in Europe and this reduction in Ne has been accelerated in the last three decades. The N e estimated for five generations in the past ranged from 71 to 237 for Texel and Romney breeds, respectively. A low level of genetic kinship and inbreeding was estimated in those breeds suggesting avoidance of mating close relatives.

CONCLUSIONS

M3 was considered the most accurate method to create genetic maps for the estimation of LD and Ne. The findings of this study highlight the history of genetic selection in New Zealand crossbred and purebred sheep and these results will be very useful to understand genetic diversity of the population with respect to genetic selection. In addition, it will help geneticists to identify genomic regions which have been preferentially selected within a variety of breeds and populations.

Infectious Agents and Neurodegenerative Diseases: Exploring the Links

Recent studies have shown that bacterial and viral infections are risk factors for various neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS), Multiple Sclerosis (MS), Alzheimer's disease (AD), and Lyme disease (LD). However, it is still controversial how the infections play a role in neurological diseases progression. Infections in central nervous system may lead multiple damages in infected and neighboring cells. The infection leads to the activation of inflammatory processes and host immune responses, which acts as defense mechanism and also causes damage to the host neuronal functions and viability. Several bacterial and viral pathogens have been reported for neurodegeneration, such as the production and deposit of misfolded protein aggregates, oxidative stress, deficient autophagic processes, synaptopathies and neuronal death. These effects may act in combination with other factors, like aging, metabolic diseases and the genetic makeup of the host. We will focus in this review on the possible link between neurodegeneration and infections particularly Chlamydophila pneumoniae, Borrelia burgdorferi, Mycoplasma etc.

Application of DRIFTS, 13C NMR, and py-MBMS to Characterize the Effects of Soil Science Oxidation Assays on Soil Organic Matter Composition in a Mollic Xerofluvent

Chemical oxidations are routinely employed in soil science to study soil organic matter (SOM), and their interpretation could be improved by characterizing oxidation effects on SOM composition with spectroscopy. We investigated the effects of routinely employed oxidants on SOM composition in a Mollic Xerofluvent representative of intensively managed agricultural soils in the California Central Valley. Soil samples were subjected to oxidation by potassium permanganate (KMnO₄), sodium hypochlorite (NaOCl), and hydrogen peroxide (H₂O₂). Additionally, non-oxidized and oxidized soils were treated with hydrofluoric acid (HF) to evaluate reduction of the mineral component to improve spectroscopy of oxidation effects. Oxidized non-HF and HF-treated soils were characterized by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), ¹³C cross polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, and pyrolysis molecular beam mass spectrometry (py-MBMS), and for particle size distribution (PSD) using laser diffractometry (LD). Across the range of soil organic carbon (OC) removed by oxidations (14-72%), aliphatic C-H stretch at 3000-2800 cm^-1 (DRIFTS) decreased with OC removal, and this trend was enhanced by HF treatment due to significant demineralization in this soil (70%). Analysis by NMR spectroscopy was feasible only after HF treatment, and did not reveal trends between OC removal and C functional groups. Pyrolysis-MBMS did not detect differences among oxidations, even after HF treatment of soils. Hydrofluoric acid entailed OC loss (13-39%), and for H₂O₂ oxidized soils increased C:N and substantially decreased mean particle size. This study demonstrates the feasibility of using HF to improve characterizations of SOM composition following oxidations as practiced in soil science, in particular for DRIFTS. Since OC removal by oxidants, mineral removal by HF, and the interaction of oxidants and HF observed for this soil may differ for soils with different mineralogies, future work should examine additional soil and land use types to optimize characterizations of oxidation effects on SOM composition.

A different kind of love - lipid droplet contact sites

Lipid droplets (LDs) store lipids and hence serve as energy reservoir and as a source for building-blocks for the organelle membrane systems. LD biology therefore depends on tight communication with other organelles. The unique architecture of LDs, consisting of a neutral lipid core shielded by a phospholipid-monolayer, is however an obstacle to bulk-exchange of bilayer-bounded vesicles with other organelles. In recent years, it is emerging that contact sites, places where two organelles are positioned in close proximity allowing vesicle-independent communication, are an important way to integrate LDs into the organellar landscape. However, few LD contact sites have been studied in depth and our understanding of their structure, extent and function is only starting to emerge. Here, we highlight recent findings on the functions of LD contact sites and on the proteins involved in their formation and hypothesize about the unique characteristics of the contact sites formed by these intriguing organelles. This article is part of a Special Issue entitled: Recent Advances in Lipid Droplet Biology edited by Rosalind Coleman and Matthijs Hesselink.

Linkage drag constrains the roots of modern wheat

Roots, the hidden half of crop plants, are essential for resource acquisition. However, knowledge about the genetic control of below-ground plant development in wheat, one of the most important small-grain crops in the world, is very limited. The molecular interactions connecting root and shoot development and growth, and thus modulating the plant's demand for water and nutrients along with its ability to access them, are largely unexplored. Here, we demonstrate that linkage drag in European bread wheat, driven by strong selection for a haplotype variant controlling heading date, has eliminated a specific combination of two flanking, highly conserved haplotype variants whose interaction confers increased root biomass. Reversing this inadvertent consequence of selection could recover root diversity that may prove essential for future food production in fluctuating environments. Highly conserved synteny to rice across this chromosome segment suggests that adaptive selection has shaped the diversity landscape of this locus across different, globally important cereal crops. By mining wheat gene expression data, we identified root-expressed genes within the region of interest that could help breeders to select positive variants adapted to specific target soil environments.

First-Year College Students With ADHD and/or LD

Students with attention-deficit/hyperactivity disorder (ADHD) and/or learning disabilities (LD) experience significant challenges in making the transition from high school to college. This study examined the ways first-year college students with ADHD, LD, ADHD+LD, and comparison peers differ in engagement, core self-evaluation, high school preparation behaviors, and goals/expectations. Participants were from the 2010 Cooperative Institutional Research Program Freshman Survey, including students with ADHD ( n = 5,511), LD ( n = 2,626), ADHD+LD ( n = 1,399), or neither disability ( n = 5,737). Controlling for SAT/ACT scores, family income, and parent education, students with ADHD, LD, or ADHD+LD differed from peers on self-ratings of academic and creative abilities and psychosocial functioning; school disengagement, substance use, and emotional difficulties during their last year of high school; reasons for attending college; and expectations for college activities. Several differences were found between disability groups. Implications for college support services and future research are discussed.

A Synthesis of Reading and Spelling Interventions and Their Effects on Spelling Outcomes for Students With Learning Disabilities

Spelling is one of the most challenging areas for students with learning disabilities (LD), and improving spelling outcomes for these students is of high importance. In this synthesis, we examined the effects of spelling and reading interventions on spelling outcomes for students with LD in Grades K through 12. A systematic search of peer-reviewed literature published between 2004 and 2014 was conducted using electronic databases and hand searches of relevant journals. To be eligible for inclusion, studies had to meet the following criteria: (a) Participants were identified with LD and were in Grades K through 12, (b) designs were either treatment/comparison or single case, (c) a reading or spelling intervention was implemented, (d) at least one spelling outcome was measured, and (e) instruction was in English. Ten studies met criteria for inclusion in the synthesis, and effectiveness ranged from ineffective to highly effective. Findings demonstrated that spelling outcomes for taught words were improved for students with LD with the use of explicit instruction or self-correction strategies.

Haplotype hitchhiking promotes trait coselection in Brassica napus

Local haplotype patterns surrounding densely spaced DNA markers with significant trait associations can reveal information on selective sweeps and genome diversity associated with important crop traits. Relationships between haplotype and phenotype diversity, coupled with analysis of gene content in conserved haplotype blocks, can provide insight into coselection for nonrelated traits. We performed genome-wide analysis of haplotypes associated with the important physiological and agronomic traits leaf chlorophyll and seed glucosinolate content, respectively, in the major oilseed crop species Brassica napus. A locus on chromosome A01 showed opposite effects on leaf chlorophyll content and seed glucosinolate content, attributed to strong linkage disequilibrium (LD) between orthologues of the chlorophyll biosynthesis genes EARLY LIGHT-INDUCED PROTEIN and CHLOROPHYLL SYNTHASE, and the glucosinolate synthesis gene ATP SULFURYLASE 1. Another conserved haplotype block, on chromosome A02, contained a number of chlorophyll-related genes in LD with orthologues of the key glucosinolate biosynthesis genes METHYLTHIOALKYMALATE SYNTHASE-LIKE 1 and 3. Multigene haplogroups were found to have a significantly greater contribution to variation for chlorophyll content than haplotypes for any single gene, suggesting positive effects of additive locus accumulation. Detailed reanalysis of population substructure revealed a clade of ten related accessions exhibiting high leaf chlorophyll and low seed glucosinolate content. These accessions each carried one of the above-mentioned haplotypes from A01 or A02, generally in combination with further chlorophyll-associated haplotypes from chromosomes A05 and/or C05. The phenotypic rather than pleiotropic correlations between leaf chlorophyll content index and seed GSL suggest that LD may have led to inadvertent coselection for these two traits.

Genetic association and stress mediated down-regulation in trabecular meshwork implicates MPP7 as a novel candidate gene in primary open angle glaucoma

Background

Glaucoma is the largest cause of irreversible blindness affecting more than 60 million people globally. The disease is defined as a gradual loss of peripheral vision due to death of Retinal Ganglion Cells (RGC). The RGC death is largely influenced by the rate of aqueous humor production by ciliary processes and its passage through the trabecular meshwork (TM) in the anterior part of the eye. Primary open angle glaucoma (POAG), the most common subtype, is a genetically complex disease. Multiple genes and many loci have been reported to be involved in POAG but taken together they explain less than 10 % of the patients from a genetic perspective warranting more studies in different world populations. The purpose of this study was to perform genome-wide search for common variants associated with POAG in an east-Indian population.

Methods

The study recruited 746 POAG cases and 697 controls distributed into discovery and validation cohorts. In the discovery phase, genome-wide genotype data was generated on Illumina Infinium 660 W-Quad platform and the significant SNPs were genotyped using Illumina GGGT assay in the second phase. Logistic regression was used to test association in the discovery phase to adjust for population sub-structure and chi-square test was used for association analysis in validation phase. Publicly available expression dataset for trabecular meshwork was used to check for expression of the candidate gene under cyclic mechanical stress. Western blot and immunofluorescence experiments were performed in human TM cells and murine eye, respectively to check for expression of the candidate gene.

Results

Meta-analysis of discovery and validation phase data revealed the association of rs7916852 in MPP7 gene (p = 5.7x10⁻⁷) with POAG. We have shown abundant expression of MPP7 in the HTM cells. Expression analysis shows that upon cyclic mechanical stress MPP7 was significantly down-regulated in HTM (Fold change: 2.6; p = 0.018). MPP7 protein expression was also found to be enriched in the ciliary processes of the murine eye.

Conclusion

Using a genome-wide approach we have identified MPP7 as a novel candidate gene for POAG with evidence of its expression in relevant ocular tissues and dysregulation under mechanical stress possibly mimicking the disease scenario.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-016-0177-6) contains supplementary material, which is available to authorized users.

Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity

Targeted sequencing of sixteen SLE risk loci among 1349 Caucasian cases and controls produced a comprehensive dataset of the variations causing susceptibility to systemic lupus erythematosus (SLE). Two independent disease association signals in the HLA-D region identified two regulatory regions containing 3562 polymorphisms that modified thirty-seven transcription factor binding sites. These extensive functional variations are a new and potent facet of HLA polymorphism. Variations modifying the consensus binding motifs of IRF4 and CTCF in the XL9 regulatory complex modified the transcription of HLA-DRB1, HLA-DQA1 and HLA-DQB1 in a chromosome-specific manner, resulting in a 2.5-fold increase in the surface expression of HLA-DR and DQ molecules on dendritic cells with SLE risk genotypes, which increases to over 4-fold after stimulation. Similar analyses of fifteen other SLE risk loci identified 1206 functional variants tightly linked with disease-associated SNPs and demonstrated that common disease alleles contain multiple causal variants modulating multiple immune system genes.

Do the symptoms of language disorder align with treatment goals? An exploratory study of primary-grade students' IEPs

Individual Education Plans (IEPs) are legal documents that guide the treatment of students with language disorder (LD). This exploratory study investigated the extent to which students' symptoms of LD align with goals on their IEPs. A total of 99 kindergarten and first-grade students receiving treatment for LD in the public schools participated. IEPs were collected and coded for each student and norm-referenced measures were used to assess students' grammar, vocabulary, listening comprehension, and literacy skills in the fall of the academic year. Results showed there to be alignment between students' symptoms and IEP goals only in the area of vocabulary, such that students who had an IEP goal for vocabulary had lower scores on a vocabulary assessment than those without a goal. In general, there is limited alignment between observed symptoms of LD and treated symptoms as identified on students' IEPs. The limited alignment found in this study suggests more investigation is needed to understand the extent to which IEP goals, as potential indicators of treatment foci, should map on to students' symptoms.

LEARNING OUTCOMES

Readers will be able to: (1) explain the theoretical and practical relevance of treatment goals aligning to symptoms for children with language impairment; (2) identify three analytic methods used to investigate alignment between treatment goals and symptoms; and (3) describe the extent to which IEP goals align to children's symptoms in a sample of children receiving services in the public schools.

Genetic differentiation and evolutionary adaptation in Cryptomeria japonica

Local adaptation of plant species is a central issue for survival during global climate change, especially for long-lived forest trees, with their lengthy regeneration time and spatially limited gene flow. Identification of loci and/or genomic regions associated with local adaptation is necessary for knowledge of both evolution and molecular breeding for climate change. Cryptomeria japonica is an important species for forestry in Japan; it has a broad natural distribution and can survive in a range of different environments. The genetic structure of 14 natural populations of this species was investigated using 3930 SNP markers. Populations on the Pacific Ocean side of Japan are clearly different from those on the Japan Sea side, as discussed in previous studies. Structure analysis and population network trees show that peripheral populations, including the most northerly and southerly ones, have unique features. We found that the genetic differentiation coefficient is low, F_ST = 0.05, although it must account for the presence of important genes associated with adaptation to specific environments. In total, 208 outlier loci were detected, of which 43 were associated with environmental variables. Four clumped regions of outlier loci were detected in the genome by linkage analysis. Linkage disequilibrium (LD) was quite high in these clumps of outlier loci, which were found in linkage groups (LGs) 2, 7, 10, and 11, especially between populations of two varieties, and when interchromosomal LD was also detected. The LG7 region is characteristic of the Yakushima population, which is a large, isolated, peripheral population occupying a specific environment resulting from isolation combined with volcanic activity in the region. The detected LD may provide strong evidence for selection between varieties.

Utility of measurement of interleukin-1ß and interleukin-8 in the diagnosis of complicated parapneumonic pleural effusions

OBJECTIVES

Thirty percent of patients with pneumonia develop pleural effusion, and of these, 20% have complicated effusion (CPPE), which may require a chest tube or surgery for resolution. The objective of the study is to compare the diagnostic yield of determining interleukin-1β and interleukin-8 in pleural fluid (PF) (PFIL-1β and PFIL-8) with respect to classic criteria (pH <7.2, lactate dehydrogenase [LD] >1,000 IU/mL, and/or glucose <60 mg/dL) in the early diagnosis of CPPE.

METHODS

Of the 559 patients studied, 40 had CPPE. All underwent PF analysis: pH, glucose (PFGLUC), LD (PFLD), PFIL-1β and PFIL-8, and PF/serum ratios (PF/SIL-1β and PF/SIL-8).

RESULTS

The diagnostic criterion that showed the best area under the curve was the combination of PF/SIL-8 and PFIL-1β (0.906), with a statistically significant difference (P < .05) compared with the classic criterion of pH and PFGLUC or PFLD (0.826). The combination of PF/SIL-8 and PFIL-1β (cutoffs >5.73 and >9.14 pg/mL, respectively) was significantly more sensitive (72.7%) and more specific (97.9%) (P < .05) than the rest of the parameters used.

CONCLUSIONS

Measurement of IL-1β and IL-8 in pleural fluid may be useful in the early diagnosis of CPPE, although individually, it may not improve the results obtained with the PFLD. Further studies are needed to more firmly establish what role these new parameters can play in the diagnosis of CPPE.