Improved degradation of lignocellulosic biomass pretreated by Fenton-like reaction using Fe<Subscript>3</Subscript>O<Subscript>4</Subscript> magnetic nanoparticles

The ability of Fe₃O₄ Fenton-like reaction to produce glucose from lignocellulosic biomass was investigated. Fe₃O₄ magnetite nanoparticles were chemically synthesized from iron salts (a mixture of 1 M FeCl₂ and 2M FeCl₃) using an ammonia solution (30% NH₄OH). The synthesized Fe₃O₄ nanoparticles were further characterized by X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy, scanning electron microscopy, and transmission electron microscopy. Reed stems and rice straw biomasses pretreated with optimized Fenton-like reagents (Fe₃O₄ and H₂O₂) increased glucose production by 177 and 87%, respectively, compared to the control without the catalysts.     

Enhancement of 2,3-butanediol production from Jerusalem artichoke tuber extract by a recombinant <Emphasis Type="Italic">Bacillus</Emphasis> sp. strain BRC1 with increased inulinase activity

A Bacillus sp. strain named BRC1 is capable of producing 2,3-butanediol (2,3-BD) using hydrolysates of the Jerusalem artichoke tuber (JAT), a rich source of the fructose polymer inulin. To enhance 2,3-BD production, we undertook an extensive analysis of the Bacillus sp. BRC1 genome, identifying a putative gene (sacC) encoding a fructan hydrolysis enzyme and characterizing the activity of the resulting recombinant protein expressed in and purified from Escherichia coli. Introduction of the sacC gene into Bacillus sp. BRC1 using an expression vector increased enzymatic activity more than twofold. Consistent with this increased enzyme expression, 2,3-BD production from JAT was also increased from 3.98 to 8.10 g L^?1. Fed-batch fermentation of the recombinant strain produced a maximal level of 2,3-BD production of 28.6 g L^?1, showing a high theoretical yield of 92.3%.     

Combination of newly developed SNP and InDel markers for genotyping the <Emphasis Type="Italic">Cf-9</Emphasis> locus conferring disease resistance to leaf mold disease in the tomato

The Cf-9 gene in the tomato is known to confer resistance against leaf mold disease caused by Cladosporium fulvum, and a gene-based marker targeted to the Cf-9 allele has been widely used as a crop protection approach. However, we found this marker to be misleading in genotyping. Therefore, we developed new single-nucleotide polymorphism (SNP) and insertion and deletion (InDel) markers targeted to the Cf-9 allele in order to increase genotyping accuracy and facilitate high-throughput screening. The DNA sequences of reported Cf-9, cf-9, Cf-0, and closely related Cf-4 alleles were compared, and two functional and non-synonymous SNPs were found to distinguish the Cf-9 resistance allele from the cf-9, Cf-0, and Cf-4 alleles. An SNP marker including these two SNPs was developed and applied to the genotyping of 33 tomato cultivars by high-resolution melting analysis. Our SNP marker was able to select all three Cf-9 genotypes (resistant, heterozygous, and susceptible alleles). Interestingly, two cultivars were grouped separately from these three genotypes. To further examine this outgroup, we preformed polymerase chain reaction (PCR) on two InDel regions identified by sequence comparison of the Cf-9 and Cf-4 genes. The band patterns revealed that these two cultivars carried Cf-4 rather than Cf-9 alleles and that three cultivars classified in the Cf-9 resistance group actually carried both Cf-9 and Cf-4 genes. To determine whether these genotyping results were consistent with disease resistance phenotypes, we examined the induction of a hypersensitive response by transiently expressing the corresponding effector genes, and found that the results matched perfectly with the genotyping results. These findings indicate that the combination of our SNP and InDel markers allows resistant Cf-9 alleles to be distinguished from cf-9 and Cf-4 alleles, which will be useful for marker-assisted selection of tomato cultivars resistant to C. fulvum.     

High-performance data mining with intelligent SSD

An intuitive way to process the big data efficiently is to reduce the volume of data transferred over the storage interface to a host system. This is the reason that the notion of intelligent SSD (iSSD) was proposed to give processing power to SSD. There is rich literature on iSSD, however, its real implementation has not been provided to the public yet. Most prior work aims to quantify the benefits of iSSD with analytical modeling. In this paper, we first develop on iSSD simulator and present the potential of iSSD in data mining through the iSSD simulator. Our iSSD simulator performs on top of the gem 5 simulator and fully simulates all the processes of data mining algorithms running in iSSD with cycle-level accuracy. Then, we further addresse how to exploit all the computing resources for efficient processing of data mining algorithms. These days, CPU, GPU, and SSD are recently equipped together in most computing environment. If SSD is replaced with iSSD later on, we have a new computing environment where the three computing resources collaborate one another to process big data quite effectively. For this, scheduling is required to decide which computing resource is going to run for which function at which time. In our heterogeneous scheduling, types of computing resources, memory sizes in computing resources, and inter-processor communication times including IO time in SSD are considered. Our scheduling results show that processing in the collaborative environment outperforms that in the traditional one by up to about 10 times.     

Comparative proteomic analysis between nitrogen supplemented and starved conditions in <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis>

Background

Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen Magnaporthe oryzae copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed.

Methods

M. oryzae strain 70–15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source. Proteins were isolated and subjected to unfractionated gel-free based liquid chromatography-tandem mass spectrometry (LC-MS/MS). The subcellular localization and function of the identified proteins were predicted using bioinformatics tools.

Results

A total of 5498 M. oryzae proteins were identified. Comparative analysis of protein expression showed 363 proteins and 266 proteins significantly induced or uniquely expressed under nitrogen starved or nitrogen supplemented conditions, respectively. A functional analysis of differentially expressed proteins revealed that during nitrogen starvation nitrogen catabolite repression, melanin biosynthesis, protein degradation and protein translation pathways underwent extensive alterations. In addition, nitrogen starvation induced accumulation of various extracellular proteins including small extracellular proteins consistent with observations of a link between nitrogen starvation and the development of pathogenicity in M. oryzae.

Conclusion

The results from this study provide a comprehensive understanding of fungal responses to nitrogen availability.

     

Evaluating the impact of the nationwide public–private mix (PPM) program for tuberculosis under National Health Insurance in South Korea: A difference in differences analysis

BackgroundPublic–private mix (PPM) programs on tuberculosis (TB) have a critical role in engaging and integrating the private sector into the national TB control efforts in order to meet the End TB Strategy targets. South Korea’s PPM program can provide important insights on the long-term impact and policy gaps in the development and expansion of PPM as a nationwide program.Methods and findingsHealthcare is privatized in South Korea, and a majority (80.3% in 2009) of TB patients sought care in the private sector. Since 2009, South Korea has rapidly expanded its PPM program coverage under the National Health Insurance (NHI) scheme as a formal national program with dedicated PPM nurses managing TB patients in both the private and public sectors. Using the difference in differences (DID) analytic framework, we compared relative changes in TB treatment outcomes—treatment success (TS) and loss to follow-up (LTFU)—in the private and public sector between the 2009 and 2014 TB patient cohorts. Propensity score matching (PSM) using the kernel method was done to adjust for imbalances in the covariates between the 2 population cohorts. The 2009 cohort included 6,195 (63.0% male, 37.0% female; mean age: 42.1) and 27,396 (56.1% male, 43.9% female; mean age: 45.7) TB patients in the public and private sectors, respectively. The 2014 cohort included 2,803 (63.2% male, 36.8% female; mean age: 50.1) and 29,988 (56.5% male, 43.5% female; mean age: 54.7) patients. In both the private and public sectors, the proportion of patients with transfer history decreased (public: 23.8% to 21.7% and private: 20.8% to 17.6%), and bacteriological confirmed disease increased (public: 48.9% to 62.3% and private: 48.8% to 58.1%) in 2014 compared to 2009. After expanding nationwide PPM, absolute TS rates improved by 9.10% (87.5% to 93.4%) and by 13.6% (from 70.3% to 83.9%) in the public and private sectors. Relative to the public, the private saw 4.1% (95% confidence interval [CI] 2.9% to 5.3%, p-value < 0.001) and −8.7% (95% CI −9.7% to −7.7%, p-value <0.001) higher rates of improvement in TS and reduction in LTFU. Treatment outcomes did not improve in patients who experienced at least 1 transfer during their TB treatment. Study limitations include non-longitudinal nature of our original dataset, inability to assess the regional disparities, and verify PPM program’s impact on TB mortality.ConclusionsWe found that the nationwide scale-up of the PPM program was associated with improvements in TB treatment outcomes in the private sector in South Korea. Centralized financial governance and regulatory mechanisms were integral in facilitating the integration of highly diverse South Korean private sector into the national TB control program and scaling up of the PPM intervention nationwide. However, TB care gaps continued to exist for patients who transferred at least once during their treatment. These programmatic gaps may be improved through reducing administrative hurdles and making programmatic amendments that can help facilitate management TB patients between institutions and healthcare sectors, as well as across administrative regions.

Sarah Yu and co-workers study population-level provision of tuberculosis care and outcomes in South Korea.     

Kinesin-1-dependent transport of the βPIX/GIT complex in neuronal cells

Proper targeting of the βPAK-interacting exchange factor (βPIX)/G protein-coupled receptor kinase-interacting target protein (GIT) complex into distinct cellular compartments is essential for its diverse functions including neurite extension and synaptogenesis. However, the mechanism for translocation of this complex is still unknown. In the present study, we reported that the conventional kinesin, called kinesin-1, can transport the βPIX/GIT complex. Additionally, βPIX bind to KIF5A, a neuronal isoform of kinesin-1 heavy chain, but not KIF1 and KIF3. Mapping analysis revealed that the tail of KIF5s and LZ domain of βPIX were the respective binding domains. Silencing KIF5A or the expression of a variety of mutant forms of KIF5A inhibited βPIX targeting the neurite tips in PC12 cells. Fur-thermore, truncated mutants of βPIX without LZ domain did not interact with KIF5A, and were unable to target the neurite tips in PC12 cells. These results defined kinesin-1 as a motor protein of βPIX, and may provide new insights into βPIX/GIT complex-dependent neuronal pathophysiology.