MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.     

BATVI: Fast,sensitive and accurate detection of virus integrations

Background

The study of virus integrations in human genome is important since virus integrations were shown to be associated with diseases. In the literature, few methods have been proposed that predict virus integrations using next generation sequencing datasets. Although they work, they are slow and are not very sensitive.

Results and discussion

This paper introduces a new method BatVI to predict viral integrations. Our method uses a fast screening method to filter out chimeric reads containing possible viral integrations. Next, sensitive alignments of these candidate chimeric reads are called by BLAST. Chimeric reads that are co-localized in the human genome are clustered. Finally, by assembling the chimeric reads in each cluster, high confident virus integration sites are extracted.

Conclusion

We compared the performance of BatVI with existing methods VirusFinder and VirusSeq using both simulated and real-life datasets of liver cancer patients. BatVI ran an order of magnitude faster and was able to predict almost twice the number of true positives compared to other methods while maintaining a false positive rate less than 1%. For the liver cancer datasets, BatVI uncovered novel integrations to two important genes TERT and MLL4, which were missed by previous studies. Through gene expression data, we verified the correctness of these additional integrations.BatVI can be downloaded from http://biogpu.ddns.comp.nus.edu.sg/~ksung/batvi/index.html.

     

Urea‐Modified Carbon Nitrides: Enhancing Photocatalytic Hydrogen Evolution by Rational Defect Engineering

The primary amine groups on the heptazine‐based polymer melon, also known as graphitic carbon nitride (g‐C₃N₄), can be replaced by urea groups using a two‐step postsynthetic functionalization. Under simulated sunlight and optimum Pt loading, this urea‐functionalized carbon nitride has one of the highest activities among organic and polymeric photocatalysts for hydrogen evolution with methanol as sacrificial donor, reaching an apparent quantum efficiency of 18% and nearly 30 times the hydrogen evolution rate compared to the nonfunctionalized counterpart. In the absence of Pt, the urea‐derivatized material evolves hydrogen at a rate over four times that of the nonfunctionalized one. Since “defects” are conventionally accepted to be the active sites in graphitic carbon nitride for photocatalysis, the work here is a demonstrated example of “defect engineering,” where the catalytically relevant defect is inserted rationally for improving the intrinsic, rather than extrinsic, photocatalytic performance. Furthermore, the work provides a retrodictive explanation for the general observation that g‐C₃N₄ prepared from urea performs better than those prepared from dicyandiamide and melamine. In‐depth analyses of the spent photocatalysts and computational modeling suggest that inserting the urea group causes a metal‐support interaction with the Pt cocatalyst, thus facilitating interfacial charge transfer to the hydrogen evolving centers.     

Shifting paradigms in restoration of the world's coral reefs

Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine‐protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required. We have recently discussed options for using assisted evolution (i.e., selective breeding, assisted gene flow, conditioning or epigenetic programming, and the manipulation of the coral microbiome) as a means to enhance environmental stress tolerance of corals and the success of coral reef restoration efforts. The 2014–2016 global coral bleaching event has sharpened the focus on such interventionist approaches. We highlight the necessity for consideration of alternative (e.g., hybrid) ecosystem states, discuss traits of resilient corals and coral reef ecosystems, and propose a decision tree for incorporating assisted evolution into restoration initiatives to enhance climate resilience of coral reefs.     

Stimulatory effects of purified macrophage colony-stimulating factor on murine resident peritoneal macrophages

A purified preparation of macrophage colony-stimulating factor (M-CSF) free of interferon and endotoxin activity was studied for its effects on resident murine peritoneal macrophages. M-CSF was found to induce profound morphologic alterations in resident macrophages. These changes included a marked increase in cell size, membrane ruffling, and cytoplasmic vacuolization. Further, after 72 hr of incubation with 1000 U/ml of M-CSF, there were significant increases in macrophage DNA synthesis as measured by autoradiography (P less than 0.001), and in macrophage monolayer protein content (P less than 0.01). None of these changes was seen in control macrophages or those exposed to recombinant interferon-gamma (IFN). Low activity levels of the ectoenzymes 5'-nucleotidase (5'NTD) and alkaline phosphodiesterase I (APD) have been associated with certain macrophage functions, particularly the expression of tumor cytotoxicity. Macrophage monolayers exposed to M-CSF demonstrated an unaltered level of 5'NTD activity from controls and a significantly increased level of APD activity (P less than 0.01) and did not demonstrate an increased ability to kill tumor cells, as measured by the 51Cr-release assay. On the other hand, IFN caused significant decreases in both 5'NTD (P less than 0.05) and APD (P less than 0.01) and also induced marked tumoricidal activity in macrophage monolayers. These results indicate that purified M-CSF induces highly specific alterations in the functional activity and morphologic appearance of resident macrophages and these changes are distinct from those induced by IFN.     

Recombination-deficient Mutant of Salmonella typhimurium

A recombination-deficient (Rec(-)) ultraviolet-sensitive mutant of Salmonella typhimurium was isolated. The mutant grows more slowly than the wild-type strain and degrades its deoxyribonucleic acid extensively both during normal growth and after ultraviolet irradiation. Evidence is presented that a growing Rec(-) population consists of two types of cells, one which can divide and one which cannot.     

The paradoxical relationship between ligamentum flavum hypertrophy and developmental lumbar spinal stenosis

Background

Ligamentum flavum (LF) hypertrophy is a common cause of lumbar spinal stenosis and is thought to be degeneration-driven. Developmental spinal stenosis (DSS) is characterized by pre-existing narrowed spinal canals and is likely a developmental problem that occurs in childhood. In these cases, the LF may demonstrate different characteristics as compared to degeneration-driven stenosis. Thus, this study aimed to investigate the relationship between histological changes of LF and canal size.

Methods

Patients who had surgical decompression for lumbar spinal stenosis were prospectively recruited and divided into three groups (critical DSS, relative DSS and non-DSS) based on previously defined anteroposterior bony spinal canal diameter measurements on MRI. The degree of disc degeneration and LF thickness were also measured from L1 to S1. Surgical LF specimens were retrieved for histological assessment of fibrotic grade and area of fibrosis.

Results

A total of 19 females and 15 males (110 LF specimens) with an overall mean age of 65.9 years (SD?±?9.8 years) were recruited. DSS was found to have a significant negative correlation (p?<?0.001) with LF thickness, its fibrotic grade and area of fibrosis (%). Non-DSS exhibited a significant positive relationship with the degree of LF fibrosis. Disc degeneration and LF thickness had no correlation with LF histology.

Conclusions

Our study is the first to definitively note that degeneration is the cause of LF fibrosis in non-DSS patients; however, in contrast, an inverse relationship exists between canal size and LF fibrosis in DSS patients, suggesting a different pathomechanism. Hence, despite a similar degree of LF thickness, DSS patients have LF with less fibrosis compared with non-DSS patients. Further investigation of the cause of LF changes in DSS is necessary to understand this relationship.

     

Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species

Whole genome duplication (WGD) and subsequent evolution of gene pairs have been shown to have shaped the present day genomes of most, if not all, plants and to have played an essential role in the evolution of many eukaryotic genomes. Analysis of the rice (Oryza sativa ssp. japonica) genome sequence suggested an ancestral WGD ～50-70 Ma common to all cereals and a segmental duplication between chromosomes 11 and 12 as recently as 5 Ma. More recent studies based on coding sequences have demonstrated that gene conversion is responsible for the high sequence conservation which suggested such a recent duplication. We previously showed that gene conversion has been a recurrent process throughout the Oryza genus and in closely related species and that orthologous duplicated regions are also highly conserved in other cereal genomes. We have extended these studies to compare megabase regions of genomic (coding and noncoding) sequences between two cultivated (O. sativa, Oryza glaberrima) and one wild (Oryza brachyantha) rice species using a novel approach of topological incongruency. The high levels of intraspecies conservation of both gene and nongene sequences, particularly in O. brachyantha, indicate long-range conversion events less than 4 Ma in all three species. These observations demonstrate megabase-scale conversion initiated within a highly rearranged region located at ～2.1 Mb from the chromosome termini and emphasize the importance of gene conversion in cereal genome evolution.     

Lifestyle Interventions Limit Gestational Weight Gain in Women with Overweight or Obesity: LIFE‐Moms Prospective Meta‐Analysis

Objective

This study aimed to evaluate the effects of varied lifestyle intervention programs designed to ameliorate excess gestational weight gain (GWG) in pregnant women with overweight or obesity compared with standard care, including effects on pregnancy outcomes.

Methods

Seven clinical centers conducted separate randomized clinical trials to test different lifestyle intervention strategies to modify GWG in diverse populations. Eligibility criteria, specific outcome measures, and assessment procedures were standardized across trials. The results of the separate trials were combined using an individual‐participant data meta‐analysis.

Results

For the 1,150 women randomized, the percent with excess GWG per week was significantly lower in the intervention group compared with the standard care group (61.8% vs. 75.0%; odds ratio [95% CI]: 0.52 [0.40 to 0.67]). Total GWG from enrollment to 36 weeks' gestation was also lower in the intervention group (8.1 ± 5.2 vs. 9.7 ± 5.4 kg; mean difference: ?1.59 kg [95% CI:?2.18 to ?0.99 kg]). The results from the individual trials were similar. The intervention and standard care groups did not differ in preeclampsia, gestational diabetes, cesarean delivery, or birth weight.

Conclusions

Behavioral lifestyle interventions focusing primarily on diet and physical activity among women with overweight and obesity resulted in a significantly lower proportion of women with excess GWG. This modest beneficial effect was consistent across diverse intervention modalities in a large, racially and socioeconomically diverse US population of pregnant women.