INVESTIGATION OF BIOTIC STRESS RESPONSES IN FRUIT TREE CROPS USING META-ANALYTICAL TECHNIQUES.

In recent years, RNA sequencing and analysis using Next Generation Sequencing (NGS) methods have enabled to understand the gene expression pertaining to plant biotic and abiotic stress conditions in both quantitative and qualitative manner. The large number of transcriptomic works published in plants requires more meta-analysis studies that would identify common and specific features in relation of the high number of objective studies performed at different developmental and environmental conditions. Meta-analysis of transcriptomic data will identify commonalities and differences between differentially regulated gene lists and will allow screen which genes are key players in gene-gene and protein-protein interaction networks. These analyses will allow delivering important information on how a specific environmental factor affects plant molecular responses and how plants activate general stress responses to environmental stresses. The identification of common genes between different biotic stress will allow to gain insight into these general responses and help the diagnosis of an early “stress state” of the plants. These analyses help in monitoring stressed plants to start early specific management procedures for each disease or disorder. In this meta-analysis study, I considered all transcriptomic data related to biotic stresses in fruit tree crops, which are already published. The aim was to determine which genes, pathways, gene set categories and predicted protein-protein interaction networks may play key roles in specific responses to pathogen infections

CheriOS: Designing an untrusted single-address-space capability operating system utilising capability hardware and a minimal hypervisor

This thesis presents the design, implementation, and evaluation of a novel capability operating system: CheriOS. The guiding motivation behind CheriOS is to provide strong security guarantees to programmers, even allowing them to continue to program in fast, but typically unsafe, languages such as C. Furthermore, it does this in the presence of an extremely strong adversarial model: in CheriOS, every compartment -- and even the operating system itself -- is considered actively malicious. Building on top of the architecturally enforced capabilities offered by the CHERI microprocessor, I show that only a few more capability types and enforcement checks are required to provide a strong compartmentalisation model that can facilitate mutual distrust. I implement these new primitives in software, in a new abstraction layer I dub the nanokernel. Among the new OS primitives I introduce are one for integrity and confidentiality called a Reservation (which allows allocating private memory without trusting the allocator), as well as another that can provide attestation about the state of the system, a Foundation (which provides a key to sign and protect capabilities based on a signature of the starting state of a program). I show that, using these new facilities, it is possible to design an operating system without having to trust the implementation is correct. CheriOS is fundamentally fail-safe; there are no assumptions about the behaviour of the system, apart from the CHERI processor and the nanokernel, to be broken. Using CHERI and the new nanokernel primitives, programmers can expect full isolation at scopes ranging from a whole program to a single function, and not just with respect to other programs but the system itself. Programs compiled for and run on CheriOS offer full memory safety, both spatial and temporal, enforced control flow integrity between compartments and protection against common vulnerabilities such as buffer overflows, code injection and Return-Oriented-Programming attacks. I achieve this by designing a new CHERI-based ABI (Application Binary Interface) which includes a novel stack structure that offers temporal safety. I evaluate how practical the new designs are by prototyping them and offering a detailed performance evaluation. I also contrast with existing offerings from both industry and academia. CHERI capabilities can be used to restrict access to system resources, such as memory, with the required dynamic checks being performed by hardware in parallel with normal operation. Using the accelerating features of CHERI, I show that many of the security guarantees that CheriOS offers can come at little to no cost. I present a novel and secure IO/IPC layer that allows secure marshalling of multiple data streams through mutually distrusting compartments, with fine-grained authenticated access control for end-points, and without either copying or encryption. For example, CheriOS can restrict its TCP stack from having access to packet contents, or restrict an open socket to ensure data sent on it to arrives at an endpoint signed as a TLS implementation. Even with added security requirements, CheriOS can perform well on real workloads. I showcase this by running a state-of-the-art webserver, NGINX, atop both CheriOS and FreeBSD and show improvements in performance ranging from 3x to 6x when running on a small-scale low-power FPGA implementation of CHERI-MIPS

Transcriptome-based Gene Networks for Systems-level Analysis of Plant Gene Functions

Present day genomic technologies are evolving at an unprecedented rate, allowing interrogation of cellular activities with increasing breadth and depth. However, we know very little about how the genome functions and what the identified genes do. The lack of functional annotations of genes greatly limits the post-analytical interpretation of new high throughput genomic datasets. For plant biologists, the problem is much severe. Less than 50% of all the identified genes in the model plant Arabidopsis thaliana, and only about 20% of all genes in the crop model Oryza sativa have some aspects of their functions assigned. Therefore, there is an urgent need to develop innovative methods to predict and expand on the currently available functional annotations of plant genes. With open-access catching the ‘pulse’ of modern day molecular research, an integration of the copious amount of transcriptome datasets allows rapid prediction of gene functions in specific biological contexts, which provide added evidence over traditional homology-based functional inference. The main goal of this dissertation was to develop data analysis strategies and tools broadly applicable in systems biology research. Two user friendly interactive web applications are presented: The Rice Regulatory Network (RRN) captures an abiotic-stress conditioned gene regulatory network designed to facilitate the identification of transcription factor targets during induction of various environmental stresses. The Arabidopsis Seed Active Network (SANe) is a transcriptional regulatory network that encapsulates various aspects of seed formation, including embryogenesis, endosperm development and seed-coat formation. Further, an edge-set enrichment analysis algorithm is proposed that uses network density as a parameter to estimate the gain or loss in correlation of pathways between two conditionally independent coexpression networks

NASA Tech Briefs, September 2010

Topics covered include: Instrument for Measuring Thermal Conductivity of Materials at Low Temperatures; Multi-Axis Accelerometer Calibration System; Pupil Alignment Measuring Technique and Alignment Reference for Instruments or Optical Systems; Autonomous System for Monitoring the Integrity of Composite Fan Housings; A Safe, Self-Calibrating, Wireless System for Measuring Volume of Any Fuel at Non-Horizontal Orientation; Adaptation of the Camera Link Interface for Flight-Instrument Applications; High-Performance CCSDS Encapsulation Service Implementation in FPGA; High-Performance CCSDS AOS Protocol Implementation in FPGA; Advanced Flip Chips in Extreme Temperature Environments; Diffuse-Illumination Systems for Growing Plants; Microwave Plasma Hydrogen Recovery System; Producing Hydrogen by Plasma Pyrolysis of Methane; Self-Deployable Membrane Structures; Reactivation of a Tin-Oxide-Containing Catalys; Functionalization of Single-Wall Carbon Nanotubes by Photo-Oxidation; Miniature Piezoelectric Macro-Mass Balance; Acoustic Liner for Turbomachinery Applications; Metering Gas Strut for Separating Rocket Stages; Large-Flow-Area Flow-Selective Liquid/Gas Separator; Counterflowing Jet Subsystem Design; Water Tank with Capillary Air/Liquid Separation; True Shear Parallel Plate Viscometer; Focusing Diffraction Grating Element with Aberration Control; Universal Millimeter-Wave Radar Front End; Mode Selection for a Single-Frequency Fiber Laser; Qualification and Selection of Flight Diode Lasers for Space Applications; Plenoptic Imager for Automated Surface Navigation; Maglev Facility for Simulating Variable Gravity; Hybrid AlGaN-SiC Avalanche Photodiode for Deep-UV Photon Detection; High-Speed Operation of Interband Cascade Lasers; 3D GeoWall Analysis System for Shuttle External Tank Foreign Object Debris Events; Charge-Spot Model for Electrostatic Forces in Simulation of Fine Particulates; Hidden Statistics Approach to Quantum Simulations; Reconstituted Three-Dimensional Interactive Imaging; Determining Atmospheric-Density Profile of Titan; Digital Microfluidics Sample Analyzer; Radiation Protection Using Carbon Nanotube Derivatives; Process to Selectively Distinguish Viable from Non-Viable Bacterial Cells; and TEAMS Model Analyzer

MediaSync: Handbook on Multimedia Synchronization

This book provides an approachable overview of the most recent advances in the fascinating field of media synchronization (mediasync), gathering contributions from the most representative and influential experts. Understanding the challenges of this field in the current multi-sensory, multi-device, and multi-protocol world is not an easy task. The book revisits the foundations of mediasync, including theoretical frameworks and models, highlights ongoing research efforts, like hybrid broadband broadcast (HBB) delivery and users' perception modeling (i.e., Quality of Experience or QoE), and paves the way for the future (e.g., towards the deployment of multi-sensory and ultra-realistic experiences). Although many advances around mediasync have been devised and deployed, this area of research is getting renewed attention to overcome remaining challenges in the next-generation (heterogeneous and ubiquitous) media ecosystem. Given the significant advances in this research area, its current relevance and the multiple disciplines it involves, the availability of a reference book on mediasync becomes necessary. This book fills the gap in this context. In particular, it addresses key aspects and reviews the most relevant contributions within the mediasync research space, from different perspectives. Mediasync: Handbook on Multimedia Synchronization is the perfect companion for scholars and practitioners that want to acquire strong knowledge about this research area, and also approach the challenges behind ensuring the best mediated experiences, by providing the adequate synchronization between the media elements that constitute these experiences

Proteome characterizations of microbial systems using MS-based experimental and informatics approaches to examine key metabolic pathways, proteins of unknown function, and phenotypic adaptation

Microbes express complex phenotypes and coordinate activities to build microbial communities. Recent work has focused on understanding the ability of microbial systems to efficiently utilize cellulosic biomass to produce bioenergy-related products. In order to maximize the yield of these bioenergy-related products from a microbial system, it is necessary to understand the molecular mechanisms.The ability of mass spectrometry to precisely identify thousands of proteins from a bacterial source has established mass spectrometry-based proteomics as an indispensable tool for various biological disciplines. This dissertation developed and optimized various proteomics experimental and informatic protocols, and integrated the resulting data with metabolomics, transcriptomics, and genomics in order to understand the systems biology of bio-energy relevant organisms. Integration of these various omics technologies led to an improved understanding of microbial cell-to-cell communication in response to external stimuli, microbial adaptation during deconstruction of lignocellulosic biomass and proteome diversity when an organism is subjected to different growth conditions.Integrated omics revealed Clostridium thermocellum\u27s accumulate long-chain, branched fatty acids over time in response to cytotoxic inhibitors released during the deconstruction and utilization of switchgrass. A striking feature implies a restructuring of C. thermocellum\u27s cellular membrane as the culture progresses. The membrane remodulation was further examined in a study involving the swarming and swimming phenotypes of Paenibacillus polymyxa. The possible roles of phospholipids, hydrolytic enzymes, surfactin, flagellar assembly, chemotaxis and glycerol metabolism in swarming motility were investigated by integrating lipidomics with proteomics.Extracellular proteome analysis of Caldicellulosiruptor bescii revealed secretome plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. This study further opened the avenue for research to characterize proteins of unknown function (PUFs) specific to growth conditions.To gain a better understanding of the possible functions of PUFs in C. thermocellum, a time course analysis of C. thermocellum was conducted. Based on the concept of guilt-by-association, protein intensities and their co-expressions were used to tease out the functional aspect of PUFs. Clustering trends and network analysis were used to infer potential functions of PUFs. Selected PUFs were further interrogated by the use of phylogeny and structural modeling

Advances in Public Transport Platform for the Development of Sustainability Cities

Modern societies demand high and varied mobility, which in turn requires a complex transport system adapted to social needs that guarantees the movement of people and goods in an economically efficient and safe way, but all are subject to a new environmental rationality and the new logic of the paradigm of sustainability. From this perspective, an efficient and flexible transport system that provides intelligent and sustainable mobility patterns is essential to our economy and our quality of life. The current transport system poses growing and significant challenges for the environment, human health, and sustainability, while current mobility schemes have focused much more on the private vehicle that has conditioned both the lifestyles of citizens and cities, as well as urban and territorial sustainability. Transport has a very considerable weight in the framework of sustainable development due to environmental pressures, associated social and economic effects, and interrelations with other sectors. The continuous growth that this sector has experienced over the last few years and its foreseeable increase, even considering the change in trends due to the current situation of generalized crisis, make the challenge of sustainable transport a strategic priority at local, national, European, and global levels. This Special Issue will pay attention to all those research approaches focused on the relationship between evolution in the area of transport with a high incidence in the environment from the perspective of efficiency

Psr1p interacts with SUN/sad1p and EB1/mal3p to establish the bipolar spindle

Regular Abstracts - Sunday Poster Presentations: no. 382During mitosis, interpolar microtubules from two spindle pole bodies (SPBs) interdigitate to create an antiparallel microtubule array for accommodating numerous regulatory proteins. Among these proteins, the kinesin-5 cut7p/Eg5 is the key player responsible for sliding apart antiparallel microtubules and thus helps in establishing the bipolar spindle. At the onset of mitosis, two SPBs are adjacent to one another with most microtubules running nearly parallel toward the nuclear envelope, creating an unfavorable microtubule configuration for the kinesin-5 kinesins. Therefore, how the cell organizes the antiparallel microtubule array in the first place at mitotic onset remains enigmatic. Here, we show that a novel protein psrp1p localizes to the SPB and plays a key role in organizing the antiparallel microtubule array. The absence of psr1+ leads to a transient monopolar spindle and massive chromosome loss. Further functional characterization demonstrates that psr1p is recruited to the SPB through interaction with the conserved SUN protein sad1p and that psr1p physically interacts with the conserved microtubule plus tip protein mal3p/EB1. These results suggest a model that psr1p serves as a linking protein between sad1p/SUN and mal3p/EB1 to allow microtubule plus ends to be coupled to the SPBs for organization of an antiparallel microtubule array. Thus, we conclude that psr1p is involved in organizing the antiparallel microtubule array in the first place at mitosis onset by interaction with SUN/sad1p and EB1/mal3p, thereby establishing the bipolar spindle.postprin

Removal of antagonistic spindle forces can rescue metaphase spindle length and reduce chromosome segregation defects

Regular Abstracts - Tuesday Poster Presentations: no. 1925Metaphase describes a phase of mitosis where chromosomes are attached and oriented on the bipolar spindle for subsequent segregation at anaphase. In diverse cell types, the metaphase spindle is maintained at a relatively constant length. Metaphase spindle length is proposed to be regulated by a balance of pushing and pulling forces generated by distinct sets of spindle microtubules and their interactions with motors and microtubule-associated proteins (MAPs). Spindle length appears important for chromosome segregation fidelity, as cells with shorter or longer than normal metaphase spindles, generated through deletion or inhibition of individual mitotic motors or MAPs, showed chromosome segregation defects. To test the force balance model of spindle length control and its effect on chromosome segregation, we applied fast microfluidic temperature-control with live-cell imaging to monitor the effect of switching off different combinations of antagonistic forces in the fission yeast metaphase spindle. We show that spindle midzone proteins kinesin-5 cut7p and microtubule bundler ase1p contribute to outward pushing forces, and spindle kinetochore proteins kinesin-8 klp5/6p and dam1p contribute to inward pulling forces. Removing these proteins individually led to aberrant metaphase spindle length and chromosome segregation defects. Removing these proteins in antagonistic combination rescued the defective spindle length and, in some combinations, also partially rescued chromosome segregation defects. Our results stress the importance of proper chromosome-to-microtubule attachment over spindle length regulation for proper chromosome segregation.postprin

Grand Celebration: 10th Anniversary of the Human Genome Project

In 1990, scientists began working together on one of the largest biological research projects ever proposed. The project proposed to sequence the three billion nucleotides in the human genome. The Human Genome Project took 13 years and was completed in April 2003, at a cost of approximately three billion dollars. It was a major scientific achievement that forever changed the understanding of our own nature. The sequencing of the human genome was in many ways a triumph for technology as much as it was for science. From the Human Genome Project, powerful technologies have been developed (e.g., microarrays and next generation sequencing) and new branches of science have emerged (e.g., functional genomics and pharmacogenomics), paving new ways for advancing genomic research and medical applications of genomics in the 21st century. The investigations have provided new tests and drug targets, as well as insights into the basis of human development and diagnosis/treatment of cancer and several mysterious humans diseases. This genomic revolution is prompting a new era in medicine, which brings both challenges and opportunities. Parallel to the promising advances over the last decade, the study of the human genome has also revealed how complicated human biology is, and how much remains to be understood. The legacy of the understanding of our genome has just begun. To celebrate the 10th anniversary of the essential completion of the Human Genome Project, in April 2013 Genes launched this Special Issue, which highlights the recent scientific breakthroughs in human genomics, with a collection of papers written by authors who are leading experts in the field