Long-Term Results and Risk Factors of Treatment for Post-Infarction Ventricular Septal Rupture: A Single-Center Experience.

BACKGROUND: Ventricular septal rupture (VSR) following myocardial infarction (MI) is a rare but lethal complication. We analyzed the long-term results and risk factors for survival in the treatment of VSR. METHODS: From January 2012 to December 2021, 115 consecutive patients with post-MI VSR were admitted to our hospital. Depending on different treatment methods patients were divided into following three groups: medical, transcatheter intervention, and surgical repair. During the study, relevant clinical data, operation-related conditions, and follow-up data were analyzed. The Kaplan-Meier method and log-rank test were used to determine the cumulative incidence of mortality. The independent risk factors for patient mortality were evaluated by multivariate logistic regression. RESULTS: The mean follow-up time was 43.4 ± 34.7 months. The overall in-hospital, 30-day, and long-term mortality rates were 24.3%, 38.3%, and 51.3%, respectively. In the medical group, the in-hospital and 30-day mortality rates were 46.7 % (21/45) and 82.2 % (37/45), respectively, with only three patients alive at follow-up. In the transcatheter intervention group, 30-day and long-term mortality rates were 12% and 28%, respectively. In the surgical repair group, 30-day and long-term mortality rates were 8.9% and 22.2%, respectively. Compared with the surgery-group patients, patients with transcatheter intervention had a longer time from VSR to intervention. Logistic regression analysis revealed that age, previous infarction, Killip class, serum creatinine, Troponin T, N-terminal pro-B-type natriuretic peptide, and medical strategy were risk factors for all-cause mortality. CONCLUSIONS: The 30-day and long-term outcomes of patients treated with surgical repair and transcatheter intervention were significantly better than medically treated patients.

Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.

PURPOSE: Despite the successful progress next-generation sequencing technologies has achieved in diagnosing the genetic cause of rare Mendelian diseases, the current diagnostic rate is still far from satisfactory because of heterogeneity, imprecision, and noise in disease phenotype descriptions and insufficient utilization of expert knowledge in clinical genetics. To overcome these difficulties, we present a novel method called Xrare for the prioritization of causative gene variants in rare disease diagnosis. METHODS: We propose a new phenotype similarity scoring method called Emission-Reception Information Content (ERIC), which is highly tolerant of noise and imprecision in clinical phenotypes. We utilize medical genetic domain knowledge by designing genetic features implementing American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS: ERIC score ranked consistently higher for disease genes than other phenotypic similarity scores in the presence of imprecise and noisy phenotypes. Extensive simulations and real clinical data demonstrated that Xrare outperforms existing alternative methods by 10-40% at various genetic diagnosis scenarios. CONCLUSION: The Xrare model is learned from a large database of clinical variants, and derives its strength from the tight integration of medical genetics features and phenotypic features similarity scores. Xrare provides the clinical community with a robust and powerful tool for variant prioritization.

Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping.

Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype-genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and demonstrates the fundamental importance of subpopulation in interpreting and manipulating the genetics of complex traits in rice.

High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development.

High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large-scale phenotyping studies. To demonstrate the unique capabilities and high-throughput capacity of this phenotyping platform for studying root systems, genome-wide association studies on rice (Oryza sativa) and maize (Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population.

A simple genetic architecture underlies morphological variation in dogs.

Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (< or = 3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping.

The model plant Arabidopsis thaliana exhibits extensive natural variation in resistance to parasites. Immunity is often conferred by resistance (R) genes that permit recognition of specific races of a disease. The number of such R genes and their distribution are poorly understood. In this study, we investigated the basis for resistance to the downy mildew agent Hyaloperonospora arabidopsidis ex parasitica (Hpa) in a global sample of A. thaliana. We implemented a combined genome-wide mapping of resistance using populations of recombinant inbred lines and a collection of wild A. thaliana accessions. We tested the interaction between 96 host genotypes collected worldwide and five strains of Hpa. Then, a fraction of the species-wide resistance was genetically dissected using six recently constructed populations of recombinant inbred lines. We found that resistance is usually governed by single dominant R genes that are concentrated in four genomic regions only. We show that association genetics of resistance to diseases such as downy mildew enables increased mapping resolution from quantitative trait loci interval to candidate gene level. Association patterns in quantitative trait loci intervals indicate that the pool of A. thaliana resistance sources against the tested Hpa isolates may be predominantly confined to six RPP (Resistance to Hpa) loci isolated in previous studies. Our results suggest that combining association and linkage mapping could accelerate resistance gene discovery in plants.

Gut Microbiota in Patients with Postoperative Atrial Fibrillation Undergoing Off-Pump Coronary Bypass Graft Surgery.

BACKGROUND: Post-operative atrial fibrillation (POAF) is one of the most common complications of cardiac surgery. However, the underlying mechanism is not well understood. Alterations in the gut microbiota are associated with the development of atrial fibrillation (AF). The aim of this study was to explore the relationship between gut microbiota and POAF. METHODS: Fecal samples were collected before surgery from 45 patients who underwent coronary artery bypass grafting with POAF and 90 matched patients without POAF (1:2). 16S rRNA sequencing was used to detect the microbiome profiles of 45 POAF patients and 89 matched patients (one sample in the no-POAF group was deleted owing to low quality after sequencing). Plasma 25-hydroxy vitamin D level was measured by ELISA. RESULTS: Compared to the patients without POAF, gut microbiota composition was remarkably changed in the patients with POAF, with an increase in Lachnospira, Acinetobacter, Veillonella and Aeromonas, and a decrease in Escherichia-Shigella, Klebsiella, Streptococcus, Brevundimonas and Citrobacter. Furthermore, plasma 25-hydroxy vitamin D levels were decreased in POAF patients and negatively correlated with an abundance of Lachnospira. CONCLUSIONS: The gut microbiota composition between patients with and without POAF is significantly different, implying that gut microbiota may play a role in the pathogenesis of POAF. Further studies are needed to fully clarify the role of gut microbiota in the initiation of AF.

Transcriptome landscape of the human placenta.

BACKGROUND: The placenta is a key component in understanding the physiological processes involved in pregnancy. Characterizing genes critical for placental function can serve as a basis for identifying mechanisms underlying both normal and pathologic pregnancies. Detailing the placental tissue transcriptome could provide a valuable resource for genomic studies related to placental disease. RESULTS: We have conducted a deep RNA sequencing (RNA-Seq) study on three tissue components (amnion, chorion, and decidua) of 5 human placentas from normal term pregnancies. We compared the placental RNA-Seq data to that of 16 other human tissues and observed a wide spectrum of transcriptome differences both between placenta and other human tissues and between distinct compartments of the placenta. Exon-level analysis of the RNA-Seq data revealed a large number of exons with differential splicing activities between placenta and other tissues, and 79% (27 out of 34) of the events selected for RT-PCR test were validated. The master splicing regulator ESRP1 is expressed at a proportionately higher level in amnion compared to all other analyzed human tissues, and there is a significant enrichment of ESRP1-regulated exons with tissue-specific splicing activities in amnion. This suggests an important role of alternative splicing in regulating gene function and activity in specific placental compartments. Importantly, genes with differential expression or splicing in the placenta are significantly enriched for genes implicated in placental abnormalities and preterm birth. In addition, we identified 604-1007 novel transcripts and 494-585 novel exons expressed in each of the three placental compartments. CONCLUSIONS: Our data demonstrate unique aspects of gene expression and splicing in placental tissues that provide a basis for disease investigation related to disruption of these mechanisms. These data are publicly available providing the community with a rich resource for placental physiology and disease-related studies.

Preventing intimal thickening of vein grafts in vein artery bypass using STAT-3 siRNA.

BACKGROUND: Proliferation and migration of vascular smooth muscle cells (VSMCs) play a key role in neointimal formation which leads to restenosis of vein graft in venous bypass. STAT-3 is a transcription factor associated with cell proliferation. We hypothesized that silencing of STAT-3 by siRNA will inhibit proliferation of VSMCs and attenuate intimal thickening. METHODS: Rat VSMCs were isolated and cultured in vitro by applying tissue piece inoculation methods. VSMCs were transfected with STAT 3 siRNA using lipofectamine 2000. In vitro proliferation of VSMC was quantified by the MTT assay, while in vivo assessment was performed in a venous transplantation model. In vivo delivery of STAT-3 siRNA plasmid or scramble plasmid was performed by admixing with liposomes 2000 and transfected into the vein graft by bioprotein gel applied onto the adventitia. Rat jugular vein-carotid artery bypass was performed. On day 3 and7 after grafting, the vein grafts were extracted, and analyzed morphologically by haematoxylin eosin (H&E), and assessed by immunohistochemistry for expression of Ki-67 and proliferating cell nuclear antigen (PCNA). Western-blot and reverse transcriptase polymerase chain reaction (RT-PCR) were used to detect the protein and mRNA expression in vivo and in vitro. Cell apoptosis in vein grafts was detected by TUNEL assay. RESULTS: MTT assay shows that the proliferation of VSMCs in the STAT-3 siRNA treated group was inhibited. On day 7 after operation, a reduced number of Ki-67 and PCNA positive cells were observed in the neointima of the vein graft in the STAT-3 siRNA treated group as compared to the scramble control. The PCNA index in the control group (31.3 ± 4.7) was higher than that in the STAT-3 siRNA treated group (23.3 ± 2.8) (P < 0.05) on 7d. The neointima in the experimental group(0.45 ± 0.04 µm) was thinner than that in the control group(0.86 ± 0.05 µm) (P < 0.05).Compared with the control group, the protein and mRNA levels in the experimental group in vivo and in vitro decreased significantly. Down regulation of STAT-3 with siRNA resulted in a reduced expression of Bcl-2 and cyclin D1. However, apoptotic cells were not obviously found in all grafts on day 3 and 7 post surgery. CONCLUSIONS: The STAT-3 siRNA can inhibit the proliferation of VSMCs in vivo and in vitro and attenuate neointimal formation.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.

Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.

Staged procedures versus primary repair for tetralogy of Fallot and small left ventricle.

INTRODUCTION: This study was conducted to address whether staged surgical intervention or primary repair would be preferred for treating patients with tetralogy of Fallot and small left ventricle. METHODS: We retrospectively assessed 28 patients with tetralogy of Fallot and small left ventricle at the Chinese PLA 208th Hospital, Changchun, between January 2005 and December 2008. Of this cohort, 11 patients had undergone a systemic-to-pulmonary arterial shunt with a polytetrafluoroethylene interposition graft (off pump), followed by ancillary repair procedures as a surgically staged group; the remaining 17 patients underwent primary intracardiac repair via cardiopulmonary bypass. The oxygen level as measured by pulse oximetry (SpO2), the McGoon ratio, and the left ventricular end-diastolic volume index (LVEDVI) were measured before shunt procedures and at 6 to 18 months afterwards. All data were analyzed statistically with the paired Student t test. The 2 groups were compared with respect to LVEDVI values and McGoon indices at baseline by the independent t test. RESULTS: None of the patients died as a direct result of the surgery, but 1 fatality due to pneumonia occurred 4 months after shunting. Mean postshunt values for SpO2, the McGoon ratio, and the LVEDVI increased significantly from 76.8% ± 9.0% to 87.5% ± 2.4% (P < .01), from 1.42 ± 0.27 to 1.62 ± 0.32 (P < .05), and from 20.1 ± 7.0 mL/m2 to 34.3 ± 7.4 mL/m2 (P < .01), respectively. Nine patients were fully repaired within the 6- to 18-month time frame after shunting, while 1 patient awaited definitive surgery for pulmonary hypoplasia. In the primary-repair group, in which the increases the LVEDVI and McGoon ratio were comparatively higher, 1 patient died of hypoxemia. CONCLUSION: A LVEDVI 20 mL/m2 may be an indication for primary repair in patients with tetralogy of Fallot. With values <20 mL/m2, staged procedures (i.e., shunt with a polytetrafluoroethylene interposition graft) can promote left ventricle development and allow safe transition to the final repair.

Chilling injury of tomato fruit was alleviated under low-temperature storage by silencing Sly-miR171e with short tandem target mimic technology.

In this study, the role of Sly-miR171e on post-harvest cold tolerance of tomato fruit was researched. The results showed that overexpression of Sly-miR171e (miR171e-OE) promoted postharvest chilling injury (CI) of tomato fruit at the mature red (MR) and mature green (MG) stage. Contrasted with the wild type (WT) and miR171e-OE fruit, the knockdown of Sly-miR171e (miR171e-STTM) showed a lower CI index, lower hydrogen peroxide (H2O2) content, and higher fruit firmness after harvest. In the fruit of miR171e-STTM, the expression level of GRAS24, CBF1, GA2ox1, and COR, and the GA3 content were ascended, while the expression levels of GA20ox1 and GA3ox1 were descended. The research demonstrated that CI in tomato fruit was alleviated at low temperature storage by silencing Sly-miR171e with short tandem target mimic (STTM) technology. Furthermore, it also provided helpful information for genetic modification of miR171e and control of CI in the postharvest fruit.

Survival and risk factors associated with surgical repair of ventricular septal rupture after acute myocardial infarction: A single-center experience.

Objective: To analyze the survival and risk factors associated with the surgical treatment of ventricular septal rupture (VSR) after acute myocardial infarction (AMI). Methods: We retrospectively analyzed 45 consecutive patients with VSR after AMI whose procedures were performed in the Department of Cardiovascular Surgery at the General Hospital of Northern Theater Command between January 2012 and December 2021. Relevant clinical data, surgery-related conditions, and follow-up data of all patients were summarized. Patients were divided into the survival group and the death group. The Kaplan-Meier method and log-rank test were used to determine the cumulative incidence of all-cause mortality. Multivariate logistic regression was used to evaluate the independent risk factors for all-cause mortality. Results: The average postoperative follow-up time was 42.1 ± 34.1 months. The overall mortality rate was 20% (9/45 patients) and the operative mortality rate was 8.9% (4/45 patients). Logistic analysis showed that the death group had higher serum creatinine (127.32 ± 47.82 vs. 82.61 ± 27.80 µmol/L, respectively; P = 0.0238) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) [8,654.00 pg/mL (6,197.00-11,949.00 pg/mL) vs. 4,268.96 pg/mL (1,800.00-7,894.00 pg/mL), respectively; P = 0.0134] levels than the survival group. The cardiopulmonary bypass time (CPB) was longer in the death group than in the survival group [131.00 min (121.00-184.00 min) vs. 119.00 min (103.00-151.50 min), respectively; P = 0.0454]. Significantly more red blood cells were transfused in the death group than in the survival group [11.60 units (6.10-16.50) vs. 3.75 units (0.00-7.00 units), respectively; P = 0.0025]. Intra-aortic balloon pump (IABP) implantation (P = 0.016) and ventilation time (P = 0.0022) were risk factors for mortality. A 1-month landmark analysis showed that compared with patients with VSR to surgical time >14 days, patients who underwent surgery within 14 days had a higher rate of all-cause mortality (25.00 vs. 3.33%; log-rank P = 0.023). Patients with VSR within 14 days also had a higher rate of residual shunts that were higher than moderate. Multivariate analysis showed that transfusion of red blood cells and NT-proBNP level were risk factors for all-cause mortality, as well as major adverse cardiovascular and cerebrovascular events. Conclusions: Surgical repair resulted in good outcomes for patients with VSR after AMI. Patients with VSR to surgical time >14 days had a lower rate of all-cause mortality. Treatment strategies for VSR should be based on the patient's condition and comprehensively determined through real-time evaluation and monitoring.

The association between fetal fraction and pregnancy-related complications among Chinese population.

To examine the association of fetal fraction with a wide spectrum of pregnancy-related complications among Chinese population, we carried out a single-institution retrospective cohort study of women with negative Noninvasive prenatal testing (NIPT) results and singleton pregnancies between May 2018 and May 2020. Indicators of pregnancy-related complications were examined individually, including preterm birth, low birth weight, hypertensive disorders of pregnancy, gestational diabetes, oligohydramnios and intrahepatic cholestasis. We evaluated disease odds ratios (ORs) and 95% confidence intervals (CIs), after controlling for potential confounders including body mass index (BMI), maternal age and gestational week at NIPT. A total of 3534 women were included in our analyses. Women with fetal fraction<15.15% had increased risk of gestational hypertension (OR 4.41, CI [1.65, 12.45]) and oligohydramnios (OR 2.26, CI [1.33, 3.80]) compared to women with fetal fraction≥15.15%. No significant associations with fetal fraction were found for preterm birth, low birth weight, gestational diabetes, and intrahepatic cholestasis. In Summary, fetal fraction is inversely associated with the risk of gestational hypertension and oligohydramnios.

Silencing of Sly-miR171d increased the expression of GRAS24 and enhanced postharvest chilling tolerance of tomato fruit.

The role of Sly-miR171d on tomato fruit chilling injury (CI) was investigated. The results showed that silencing the endogenous Sly-miR171d effectively delayed the increase of CI and electrolyte leakage (EL) in tomato fruit, and maintained fruit firmness and quality. After low temperature storage, the expression of target gene GRAS24 increased in STTM-miR171d tomato fruit, the level of GA3 anabolism and the expression of CBF1, an important regulator of cold resistance, both increased in STTM-miR171d tomato fruit, indicated that silencing the Sly-miR171d can improve the resistance ability of postharvest tomato fruit to chilling tolerance.

Preventive Effect of Berberine on Postoperative Atrial Fibrillation.

BACKGROUND: Postoperative atrial fibrillation (POAF) is one of the most common complications of cardiac surgery, but the underlying factors governing POAF are not well understood. The aim of this study was to investigate the efficacy of berberine administration on POAF. METHODS: We conducted a randomized, double-blind, placebo-controlled trial with patients who underwent isolated coronary artery bypass grafting in China to study the impact of oral berberine on the incidence of POAF. A total of 200 patients who underwent coronary artery bypass grafting were randomized into the berberine group (n=100) and the placebo group (n=100). All patients underwent 7-day continuous telemetry and Holter monitoring. RESULTS: The primary outcome was the incidence of POAF at 7 days. Secondary outcomes included clinical outcomes, POAF burden, intestinal endotoxin, and serum inflammatory biomarker levels. The POAF incidence was reduced from 35% to 20% under berberine treatment (hazard ratio, 0.5 [95% CI, 0.29-0.78]; P=0.0143). Perioperative mortality and morbidity did not differ between the 2 groups. POAF burden and the dose of amiodarone were significantly reduced in the berberine group. Oral berberine significantly decreased lipopolysaccharide, CRP (C-reactive protein), and IL (interleukin)-6 levels. Elevated lipopolysaccharide after surgery has been associated with POAF. CONCLUSIONS: Our results showed that administration of berberine may be effective for reducing the occurrence of POAF after coronary artery bypass grafting. REGISTRATION: URL: https://www.chictr.org.cn; Unique identifier: ChiCTR2000028839.

Selection and Validation of Reference Genes for Pan-Cancer in Platelets Based on RNA-Sequence Data.

Many studies in recent years have demonstrated that some messenger RNA (mRNA) in platelets can be used as biomarkers for the diagnosis of pan-cancer. The quantitative real-time polymerase chain reaction (RT-qPCR) molecular technique is most commonly used to determine mRNA expression changes in platelets. Accurate and reliable relative RT-qPCR is highly dependent on reliable reference genes. However, there is no study to validate the reference gene in platelets for pan-cancer. Given that the expression of some commonly used reference genes is altered in certain conditions, selecting and verifying the most suitable reference gene for pan-cancer in platelets is necessary to diagnose early stage cancer. This study performed bioinformatics and functional analysis from the RNA-seq of platelets data set (GSE68086). We generated 95 candidate reference genes after the primary bioinformatics step. Seven reference genes (YWHAZ, GNAS, GAPDH, OAZ1, PTMA, B2M, and ACTB) were screened out among the 95 candidate reference genes from the data set of the platelets' transcriptome of pan-cancer and 73 commonly known reference genes. These candidate reference genes were verified by another platelets expression data set (GSE89843). Then, we used RT-qPCR to confirm the expression levels of these seven genes in pan-cancer patients and healthy individuals. These RT-qPCR results were analyzed using the internal stability analysis software programs (the comparative Delta CT method, geNorm, NormFinder, and BestKeeper) to rank the candidate genes in the order of decreasing stability. By contrast, the GAPDH gene was stably and constitutively expressed at high levels in all the tested samples. Therefore, GAPDH was recommended as the most suitable reference gene for platelet transcript analysis. In conclusion, our result may play an essential part in establishing a molecular diagnostic platform based on the platelets to diagnose pan-cancer.

ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.

MOTIVATION: The development of new high-throughput genotyping products requires a significant investment in testing and training samples to evaluate and optimize the product before it can be used reliably on new samples. One reason for this is current methods for automated calling of genotypes are based on clustering approaches which require a large number of samples to be analyzed simultaneously, or an extensive training dataset to seed clusters. In systems where inbred samples are of primary interest, current clustering approaches perform poorly due to the inability to clearly identify a heterozygote cluster. RESULTS: As part of the development of two custom single nucleotide polymorphism genotyping products for Oryza sativa (domestic rice), we have developed a new genotype calling algorithm called 'ALCHEMY' based on statistical modeling of the raw intensity data rather than modelless clustering. A novel feature of the model is the ability to estimate and incorporate inbreeding information on a per sample basis allowing accurate genotyping of both inbred and heterozygous samples even when analyzed simultaneously. Since clustering is not used explicitly, ALCHEMY performs well on small sample sizes with accuracy exceeding 99% with as few as 18 samples. AVAILABILITY: ALCHEMY is available for both commercial and academic use free of charge and distributed under the GNU General Public License at http://alchemy.sourceforge.net/ CONTACT: mhw6@cornell.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is controlled by a mitochondrial molybdenum transporter (MOT1).

Molybdenum (Mo) is an essential micronutrient for plants, serving as a cofactor for enzymes involved in nitrate assimilation, sulfite detoxification, abscisic acid biosynthesis, and purine degradation. Here we show that natural variation in shoot Mo content across 92 Arabidopsis thaliana accessions is controlled by variation in a mitochondrially localized transporter (Molybdenum Transporter 1 - MOT1) that belongs to the sulfate transporter superfamily. A deletion in the MOT1 promoter is strongly associated with low shoot Mo, occurring in seven of the accessions with the lowest shoot content of Mo. Consistent with the low Mo phenotype, MOT1 expression in low Mo accessions is reduced. Reciprocal grafting experiments demonstrate that the roots of Ler-0 are responsible for the low Mo accumulation in shoot, and GUS localization demonstrates that MOT1 is expressed strongly in the roots. MOT1 contains an N-terminal mitochondrial targeting sequence and expression of MOT1 tagged with GFP in protoplasts and transgenic plants, establishing the mitochondrial localization of this protein. Furthermore, expression of MOT1 specifically enhances Mo accumulation in yeast by 5-fold, consistent with MOT1 functioning as a molybdate transporter. This work provides the first molecular insight into the processes that regulate Mo accumulation in plants and shows that novel loci can be detected by association mapping.

Hydrothermal preparation of novel rGO-KTaO3 nanocubes with enhanced visible light photocatalytic activity.

In this study, nanocubes KTaO3-reduced graphene oxide (rGO-KTaO3) photocatalysts were synthesized by a facile hydrothermal method. Different technical methods were carried out to characterize the as-prepared compounds. UV-Vis spectra show that the absorption sideband of the complexes red-shift to visible light region, which enhances the light utilization. Meanwhile, X-ray photoelectron spectroscopy (XPS) reveals that the graphene oxide (GO) in the composite has been partially reduced, leading to more effective electron transport and thus improving the photocatalytic efficiency. Furthermore, photocatalytic degradation efficiency of Methylene blue (MB) and Rhodamine B (RhB) in the presence of rGO-KTaO3 reaches 96% and 98%, which is 10 times of that of KTaO3. The synthesized rGO-KTaO3 has good photocatalytic properties. Moreover, the stability of this photocatalyst is particularly excellent. The detailed mechanism of photocatalysis has been carefully discussed in the article.