Robusta: Taming the Native Beast of the JVM

Java applications often need to incorporate native-code components for efficiency and for reusing legacy code. However, it is well known that the use of native code defeats Java's security model. We describe the design and implementation of Robusta, a complete framework that provides safety and security to native code in Java applications. Starting from software-based fault isolation (SFI), Robusta isolates native code into a sandbox where dynamic linking/loading of libraries is supported and unsafe system modification and confidentiality violations are prevented. It also mediates native system calls according to a security policy by connecting to Java's security manager. Our prototype implementation of Robusta is based on Native Client and OpenJDK. Experiments in this prototype demonstrate Robusta is effective and efficient, with modest runtime overhead on a set of JNI benchmark programs. Robusta can be used to sandbox native libraries used in Java's system classes to prevent attackers from exploiting bugs in the libraries. It can also enable trustworthy execution of mobile Java programs with native libraries. The design of Robusta should also be applicable when other type-safe languages (e.g., C#, Python) want to ensure safe interoperation with native libraries.Engineering and Applied Science

Silage Management: important practices often overlooked

Four important silage management practices that are in the control of livestock producers and that are sometimes poorly implemented or overlooked entirely include: inoculating, packing, sealing, and managing the feedout face.; Dairy Day, 2000, Kansas State University, Manhattan, KS, 2000

Improving silage quality

Results at Kansas State University from over 200 laboratory-scale trials and 28 farm-scale trials showed that bacterial inoculants consistently improved preservation efficiency and nutritive value of the ensiled material. In contrast, anhydrous ammonia or urea decreased dry matter recovery and production per ton of crop ensiled. Economic analysis also favored the use of bacterial inoculants over nonprotein nitrogen additives. Research conducted using corn, sorghum, and alfalfa silages showed that sealing the exposed surface dramatically reduced top spoilage losses in bunker, trench, or stack silos

Agronomic and silage quality traits of forage sorghum cultivars in 1995

Agronomic and silage quality traits were measure d for 37 forage sorghum cultivars and three grain sorghum hybrids. The 1995 growing season was characterized by above average rainfall in the spring and early summer, and a hard freeze on September 22. At the time of the freeze, 20 cultivars had reached the early-milk to early-dough stage, 12 were in the bloom stage, and the remaining eight were still in the early- to late-boot stage . The late planting date and low plant populations resulted in below-normal whole-plant D M and grain yields. Plant height s for the grain sorghums were near normal, but the forage sorghums were well below expected plant heights. The preensiled, whole-plan t DM contents of the 37 forage sorghums ranged from 23.0 to 39.9%. As expected , the silage nutritive value traits of CP, NDF, and ADF were most favorable for the three grain sorghum hybrids and least favorable for the eight forage sorghum hybrids that were still in the boot stage when the freeze occurred

Effect of Level of Surface Spoilage on the Nutritive Value of Maize Silage Diets

This study determined the effect of surface spoilage in the diet on feed intake and nutrient digestibilities using growing steers fed whole-plant maize silage-based diets. A bunker silo, 0.9 m in depth, and a 2.7 m diameter AgBag were filled with alternating loads of chopped forage. After 90 days, the bunker was sealed with a sheet of polyethylene, and this silage was designated “spoiled”. The silage in the AgBag was designated “normal”. The four diets contained 90% silage and 10% supplement (dry matter basis), and the proportions of silage in the diets were A) 100% normal, B) 75% normal: 25% spoiled; C) 50% normal: 50% spoiled; and D) 25% normal: 75% spoiled. Feed intake decreased linearly as the proportion of spoiled silage increased from 0 to 75%. Steers consuming the normal silage diet had the highest nutrient digestibilities. Spoiled silage also had negative associative effects on nutrient digestibilities, and the integrity of the forage mat in the rumen was partially destroyed

NUCLEAR FACTOR Y Transcription Factors Have Both Opposing and Additive Roles in ABA-Mediated Seed Germination

The authors thank Bing Zhang and Taylor Fore for use of the Zeiss AxioImager microscope and technical assistance. We additionally thank Krishna Suthar and Ashley Robbins for technical support in the lab.Conceived and designed the experiments: BFH RWK. Performed the experiments: RWK CLS KKG JRR NS. Analyzed the data: RWK BFH. Wrote the paper: RWK BFH.In the model organism Arabidopsis thaliana the heterotrimeric transcription factor NUCLEAR FACTOR Y (NF-Y) has been shown to play multiple roles in facilitating plant growth and development. Although NF-Y itself represents a multi-protein transcriptional complex, recent studies have shown important interactions with other transcription factors, especially those in the bZIP family. Here we add to the growing evidence that NF-Y and bZIP form common complexes to affect many processes. We carried out transcriptional profiling on nf-yc mutants and through subsequent analyses found an enrichment of bZIP binding sites in the promoter elements of misregulated genes. Using NF-Y as bait, yeast two hybrid assays yielded interactions with bZIP proteins that are known to control ABA signaling. Accordingly, we find that plants mutant for several NF-Y subunits show characteristic phenotypes associated with the disruption of ABA signaling. While previous reports have shown additive roles for NF-YC family members in photoperiodic flowering, we found that they can have opposing roles in ABA signaling. Collectively, these results demonstrated the importance and complexity of NF-Y in the integration of environmental and hormone signals.Yeshttp://www.plosone.org/static/editorial#pee

Homologous NF-YC2 Subunit from Arabidopsis and Tobacco Is Activated by Photooxidative Stress and Induces Flowering

The transcription factor NF-Y consists of the three subunits A, B and C, which are encoded in Arabidopsis in large gene families. The multiplicity of the genes implies that NF-Y may act in diverse combinations of each subunit for the transcriptional control. We aimed to assign a function in stress response and plant development to NF-YC subunits by analyzing the expression of NF-Y genes and exploitation of nf-y mutants. Among the subunit family, NF-YC2 showed the strongest inducibility towards oxidative stress, e.g. photodynamic, light, oxidative, heat and drought stress. A tobacco NF-YC homologous gene was found to be inducible by photooxidative stress generated by an accumulation of the tetrapyrrole metabolite, coproporphyrin. Despite the stress induction, an Arabidopsis nf-yc2 mutant and NF-YC2 overexpressors did not show phenotypical differences compared to wild-type seedlings in response to photooxidative stress. This can be explained by the compensatory potential of other members of the NF-YC family. However, NF-YC2 overexpression leads to an early flowering phenotype that is correlated with increased FLOWERING LOCUS T-transcript levels. It is proposed that NF-YC2 functions in floral induction and is a candidate gene among the NF-Y family for the transcriptional activation upon oxidative stress

MicroRNA Transcriptomic Analysis of Heterosis during Maize Seed Germination

Heterosis has been utilized widely in the breeding of maize and other crops, and plays an important role in increasing yield, improving quality and enhancing stresses resistance, but the molecular mechanism responsible for heterosis is far from clear. To illustrate whether miRNA-dependent gene regulation is responsible for heterosis during maize germination, a deep-sequencing technique was applied to germinating embryos of a maize hybrid, Yuyu22, which is cultivated widely in China and its parental inbred lines, Yu87-1 and Zong3. The target genes of several miRNAs showing significant expression in the hybrid and parental lines were predicted and tested using real-time PCR. A total of 107 conserved maize miRNAs were co-detected in the hybrid and parental lines. Most of these miRNAs were expressed non-additively in the hybrid compared to its parental lines. These results indicated that miRNAs might participate in heterosis during maize germination and exert an influence via the decay of their target genes. Novel miRNAs were predicted follow a rigorous criterion and only the miRNAs detected in all three samples were treated as a novel maize miRNA. In total, 34 miRNAs belonged to 20 miRNA families were predicted in germinating maize seeds. Global repression of miRNAs in the hybrid, which might result in enhanced gene expression, might be one reason why the hybrid showed higher embryo germination vigor compared to its parental lines

Identification and Characterization of NF-Y Transcription Factor Families in the Monocot Model Plant Brachypodium distachyon

BACKGROUND: Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor composed of NF-YA, NF-YB and NF-YC proteins. Using the dicot plant model system Arabidopsis thaliana (Arabidopsis), NF-Y were previously shown to control a variety of agronomically important traits, including drought tolerance, flowering time, and seed development. The aim of the current research was to identify and characterize NF-Y families in the emerging monocot model plant Brachypodium distachyon (Brachypodium) with the long term goal of assisting in the translation of known dicot NF-Y functions to the grasses. METHODOLOGY/PRINCIPAL FINDINGS: We identified, annotated, and further characterized 7 NF-YA, 17 NF-YB, and 12 NF-YC proteins in Brachypodium (BdNF-Y). By examining phylogenetic relationships, orthology predictions, and tissue-specific expression patterns for all 36 BdNF-Y, we proposed numerous examples of likely functional conservation between dicots and monocots. To test one of these orthology predictions, we demonstrated that a BdNF-YB with predicted orthology to Arabidopsis floral-promoting NF-Y proteins can rescue a late flowering Arabidopsis mutant. CONCLUSIONS/SIGNIFICANCE: The Brachypodium genome encodes a similar complement of NF-Y to other sequenced angiosperms. Information regarding NF-Y phylogenetic relationships, predicted orthologies, and expression patterns can facilitate their study in the grasses. The current data serves as an entry point for translating many NF-Y functions from dicots to the genetically tractable monocot model system Brachypodium. In turn, studies of NF-Y function in Brachypodium promise to be more readily translatable to the agriculturally important grasses