DISSECTION OF STRESS RESPONSE NETWORKS REGULATING MULTIPLE STRESSES IN RICE

Important food crops like rice are constantly exposed to various stresses that can have devastating effect on their survival and productivity. Being sessile, these highly evolved organisms have developed elaborate molecular machineries to sense a mixture of stress signals and elicit a precise response to minimize the damage. However, recent discoveries revealed that the interplay of these stress regulatory and signaling molecules is highly complex and remains largely unknown. In this work, we conducted large scale analysis of differential gene expression using advanced computational methods to dissect regulation of stress response which is at the heart of all molecular changes leading to the observed phenotypic susceptibility. One of the most important stress conditions in terms of loss of productivity is drought. We performed genomic and proteomic analysis of epigenetic and miRNA mechanisms in regulation of drought responsive genes in rice and found subsets of genes with striking properties. Overexpressed genesets included higher number of epigenetic marks, miRNA targets and transcription factors which regulate drought tolerance. On the other hand, underexpressed genesets were poor in above features but were rich in number of metabolic genes with multiple co-expression partners contributing majorly towards drought resistance. Identification and characterization of the patterns exhibited by differentially expressed genes hold key to uncover the synergistic and antagonistic components of the cross talk between stress response mechanisms. We performed meta-analysis on drought and bacterial stresses in rice and Arabidopsis, and identified hundreds of shared genes. We found high level of conservation of gene expression between these stresses. Weighted co-expression network analysis detected two tight clusters of genes made up of master transcription factors and signaling genes showing strikingly opposite expression status. To comprehensively identify the shared stress responsive genes between multiple abiotic and biotic stresses in rice, we performed meta-analyses of microarray studies from seven different abiotic and six biotic stresses separately and found more than thirteen hundred shared stress responsive genes. Various machine learning techniques utilizing these genes classified the stresses into two major classes' namely abiotic and biotic stresses and multiple classes of individual stresses with high accuracy and identified the top genes showing distinct patterns of expression. Functional enrichment and co-expression network analysis revealed the different roles of plant hormones, transcription factors in conserved and non-conserved genesets in regulation of stress response.

Not for Designers: On the Inadequacies of EU Design Law and How to Fix It

Design rights represent an interesting example of how the EU legislature has successfully regulated an otherwise heterogeneous field of law. Yet this type of protection is not for all. The tools created by EU intervention have been drafted paying much more attention to the industry sector rather than to designers themselves. In particular, modern, digitally based, individual or small-sized, 3D printing, open designers and their needs are largely neglected by such legislation. There is obviously nothing wrong in drafting legal tools around the needs of an industrial sector with an important role in the EU economy, on the contrary, this is a legitimate and good decision of industrial policy. However, good legislation should be fair, balanced, and (technologically) neutral in order to offer suitable solutions to all the players in the market, and all the citizens in the society, without discriminating the smallest or the newest: the cost would be to stifle innovation. The use of printing machinery to manufacture physical objects created digitally thanks to computer programs such as Computer-Aided Design (CAD) software has been in place for quite a few years, and it is actually the standard in many industrial fields, from aeronautics to home furniture. The change in recent years that has the potential to be a paradigm-shifting factor is a combination between the opularization of such technologies (price, size, usability, quality) and the diffusion of a culture based on access to and reuse of knowledge. We will call this blend Open Design. It is probably still too early, however, to say whether 3D printing will be used in the future to refer to a major event in human history, or instead will be relegated to a lonely Wikipedia entry similarly to ³Betamax² (copyright scholars are familiar with it for other reasons). It is not too early, however, to develop a legal analysis that will hopefully contribute to clarifying the major issues found in current EU design law structure, why many modern open designers will probably find better protection in copyright, and whether they can successfully rely on open licenses to achieve their goals. With regard to the latter point, we will use Creative Commons (CC) licenses to test our hypothesis due to their unique characteristic to be modular, i.e. to have different license elements (clauses) that licensors can choose in order to adapt the license to their own needs.”

Cluster randomized clinical trials in orthodontics: design, analysis and reporting issues

Cluster randomized trials (CRTs) use as the unit of randomization clusters, which are usually defined as a collection of individuals sharing some common characteristics. Common examples of clusters include entire dental practices, hospitals, schools, school classes, villages, and towns. Additionally, several measurements (repeated measurements) taken on the same individual at different time points are also considered to be clusters. In dentistry, CRTs are applicable as patients may be treated as clusters containing several individual teeth. CRTs require certain methodological procedures during sample calculation, randomization, data analysis, and reporting, which are often ignored in dental research publications. In general, due to similarity of the observations within clusters, each individual within a cluster provides less information compared with an individual in a non-clustered trial. Therefore, clustered designs require larger sample sizes compared with non-clustered randomized designs, and special statistical analyses that account for the fact that observations within clusters are correlated. It is the purpose of this article to highlight with relevant examples the important methodological characteristics of cluster randomized designs as they may be applied in orthodontics and to explain the problems that may arise if clustered observations are erroneously treated and analysed as independent (non-clustered).

Using spatial linear models with SAR and CAR structure to examine Texas lung cancer incidence rates

Scholars have found that socioeconomic status was one of the key factors that influenced early-stage lung cancer incidence rates in a variety of regions. This thesis examined the association between median household income and lung cancer incidence rates in Texas counties. A total of 254 individual counties in Texas with corresponding lung cancer incidence rates from 2004 to 2008 and median household incomes in 2006 were collected from the National Cancer Institute Surveillance System. A simple linear model and spatial linear models with two structures, Simultaneous Autoregressive Structure (SAR) and Conditional Autoregressive Structure (CAR), were used to link median household income and lung cancer incidence rates in Texas. The residuals of the spatial linear models were analyzed with Moran's I and Geary's C statistics, and the statistical results were used to detect similar lung cancer incidence rate clusters and disease patterns in Texas.^

Pollen records of the Bykovsky Peninsula

New pollen and radiocarbon data from the Bykovsky Peninsula document the Late Pleistocene and Holocene environmental history of the Laptev Sea coast. More than 60 AMS-14C and conventional 14C dates indicate that the deposits accumulated during the last 60,000 radiocarbon yr BP. High concentration of green alga colonies (Pediustrum and Botryococcus) in the investigated sediment show that sedimentation was mostly in shallow water environments. Scarce grass and sedge communities dominated the vegetation 53-60 kyr BP. Climate was cold and dry. Open Poaceae and Cypcraccae associations with Asteraceae, Ranunculaceae, and Cichoriaceac, dominated in the area about 48-42.5 kyr BP. Steppic communities with Artemisia and shrubby tundra communities with Salix and Betula sect. Nanae were also present. Climate was dry, but relatively warm. Vegetation cover became denser about 42.5-33.5 kyr BP, reflecting more favorable climate conditions. Scarce Poaceae communities with some Caryophyllaceae, Asteraceae, Cichoriaceae, and Selaginella rupestris covered the Bykovsky Peninsula area during the Sartan (Late Weichselian) stage about 26-16 kyr BP. Disturbed, uncovered soils were very common in the area. Climate was extremely cold and dry. Poaceae and Cyperaceae associations with Caryophyllaceae, Asteraceae, Cichoriaceae dominated the vegetation in the late Sartan, ca 16-12.2 kyr BP. Climate was significantly warmer than in the early Sartan time. The lee Complex sedimentation was interrupted about 12 kyr BP; most likely it was connected with the beginning of the Allerod warnring. Shrubby (Betula sect. Nanae, Alnusfnuicosa, Salix, Ericales) tundra was widely distributed on the Bykovsky Peninsula during the early-middle Holacene. Climate was most favorable between 8200 and 4500 yr BP. Vegetation became similar to modern after 4500 yr BP, suggesting a deterioration of climate.

Growth increments of the recent brachiopod Magellania venosa mechanically marked in Paso Comau and Comau Fjord, Chile, 2011/2012

Magellania venosa, the largest recent brachiopod, occurs in clusters and banks in population densities of up to 416 ind/m**2 in Comau Fjord, Northern Chilean fjord region. Below 15 m, it co-occurs with the mytilid Aulacomya atra and it dominates the benthic community below 20 m. To determine the question of why M. venosa is a successful competitor, the in situ growth rate of the brachiopod was studied and its overall growth performance compared with that of other brachiopods and mussels. The growth in length was measured between February 2011 and March 2012 after mechanical tagging and calcein staining. Settlement and juvenile growth were determined from recruitment tiles installed in 2009 and from subsequent photocensus. Growth of M. venosa is best described by the general von Bertalanffy growth function, with a maximum shell length (Linf) of 71.53 mm and a Brody growth constant (K) of 0.336/year. The overall growth performance (OGP index = 5.1) is the highest recorded for a rynchonelliform brachiopod and in the range of that for Mytilus chilensis (4.8-5.27), but lower than that of A. atra (5.74). The maximal individual production (PInd) is 0.29 g AFDM/ind/year at 42 mm shell length and annual production ranges from 1.28 to 89.25 g AFDM/year/m**2 (1-57% of that of A. atra in the respective fjords). The high shell growth rate of M. venosa, together with its high overall growth performance may explain the locally high population density of this brachiopod in Comau Fjord. However, the production per biomass of the population (P/B-ratio) is low (0.535) and M. venosa may play only a minor role in the food chain. Settling dynamics indicates that M. venosa is a pioneer species with low juvenile mortality. The coexistence of the brachiopod and bivalve suggests that brachiopod survival is affected by neither the presence of potential brachiopod predators nor that of space competitors (i.e. mytilids).

The role of a firm's absorptive capacity and the technology transfer process in clusters: How effective are technology centres in low-tech clusters?

This paper analyses how the internal resources of small- and medium-sized enterprises determine access (learning processes) to technology centres (TCs) or industrial research institutes (innovation infrastructure) in traditional low-tech clusters. These interactions basically represent traded (market-based) transactions, which constitute important sources of knowledge in clusters. The paper addresses the role of TCs in low-tech clusters, and uses semi-structured interviews with 80 firms in a manufacturing cluster. The results point out that producer–user interactions are the most frequent; thus, the higher the sector knowledge-intensive base, the more likely the utilization of the available research infrastructure becomes. Conversely, the sectors with less knowledge-intensive structures, i.e. less absorptive capacity (AC), present weak linkages to TCs, as they frequently prefer to interact with suppliers, who act as transceivers of knowledge. Therefore, not all the firms in a cluster can fully exploit the available research infrastructure, and their AC moderates this engagement. In addition, the existence of TCs is not sufficient since the active role of a firm's search strategies to undertake interactions and conduct openness to available sources of knowledge is also needed. The study has implications for policymakers and academia.

Accessing and managing open medical resources in Africa over the Internet

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections.

Voltage dependence of the pattern and frequency of discrete Ca2+ release events after brief repriming in frog skeletal muscle

Applying a brief repolarizing pre-pulse to a depolarized frog skeletal muscle fiber restores a small fraction of the transverse tubule membrane voltage sensors from the inactivated state. During a subsequent depolarizing test pulse we detected brief, highly localized elevations of myoplasmic Ca2+ concentration (Ca2+ “sparks”) initiated by restored voltage sensors in individual triads at all test pulse voltages. The latency histogram of these events gives the gating pattern of the sarcoplasmic reticulum (SR) calcium release channels controlled by the restored voltage sensors. Both event frequency and clustering of events near the start of the test pulse increase with test pulse depolarization. The macroscopic SR calcium release waveform, obtained from the spark latency histogram and the estimated open time of the channel or channels underlying a spark, exhibits an early peak and rapid marked decline during large depolarizations. For smaller depolarizations, the release waveform exhibits a smaller peak and a slower decline. However, the mean use time and mean amplitude of the individual sparks are quite similar at all test depolarizations and at all times during a given depolarization, indicating that the channel open times and conductances underlying sparks are essentially independent of voltage. Thus, the voltage dependence of SR Ca2+ release is due to changes in the frequency and pattern of occurrence of individual, voltage-independent, discrete release events.

Synaptic and extrasynaptic γ-aminobutyric acid type A receptor clusters in rat hippocampal cultures during development

We have simultaneously measured the expression of postsynaptic γ-aminobutyric acid type A (GABAA) receptor clusters and of presynaptic boutons in neonatal rat hippocampal cultures between days 1 and 30. GABAA receptors were labeled with antibodies recognizing the extracellular domains of β2/3 and γ2 subunits. Boutons were visualized by activity-dependent uptake of the styryl dye FM4-64, or by antibodies against the presynaptic vesicular protein SV2 or the GABA-synthesizing enzyme glutamic acid decarboxylase (GAD). GABAA receptor clusters could be seen in living neurons already 6 h after culturing, much before presynaptic markers could be identified in nerve terminals. The densities of receptor clusters that contained the β2/3 subunits were constant between days 10 and 30 in culture, whereas γ2 subunit-containing clusters fluctuated and reached a maximum on day 20. SV2 and GAD staining could be measured from day 2 onwards. Clustering of GAD in presynaptic terminals and FM4-64 uptake were observed only at day 5 and afterward. SV2 staining and FM4-64 uptake increased in parallel between days 5 and 20 and remained constant thereafter. GAD-stained boutons were fewer than those labeled with other, less specific, presynaptic stains. They reached a maximum on day 20 and fell again toward day 30. Double labeling of GABAA receptors and of presynaptic boutons in neurons during differentiation showed that, even after 30 days in culture, large fractions of GABAA receptor clusters containing β2/3 and/or γ2 subunits remained extrasynaptic.

Physiology, growth and development of larval krill ''Euphausia superba'' in autumn and winter in the Lazarev Sea, Antarctica

The physiological condition of larval Antarctic krill was investigated during austral autumn 2004 and winter 2006 in the Lazarev Sea, to provide better understanding of a critical period of their life cycle. The condition of larvae was quantified in both seasons by determining their body length (BL), dry mass (DM), elemental- and biochemical composition, as well as stomach content analysis, and rates of metabolism and growth. Overall the larvae in autumn were in better condition under the ice than in open water, and for those under the ice there was a decrease in condition from autumn to winter. Thus growth rates of furcilia larvae in open water in autumn were similar to winter values under the ice (mean 0.008 mm/d), whereas autumn, under ice values were higher: 0.015 mm/d. Equivalent larval stages had up to 30% lower BL and 70% lower DM in winter compared to autumn, with mean oxygen consumption 44% lower (0.54 µl O2 DM/h). However, their ammonium excretion rates doubled (from 0.03-0.06 µg NH4 DM/h) so their mean O:N ratio was 46 in autumn and 15 in winter. Thus differing metabolic substrates were used between autumn and winter, suggesting a flexible overwintering strategy, as suggested for adults. The larvae were eating small copepods (Oithona spp.) and/or protozoans as well as autotrophic food under the ice. However, pelagic Chlorophyll a (Chl a) was a good predictor for growth in both seasons. The physics (current speed/ice topography) probably has a critical part to play in whether larval krill can exploit the food that may be associated with sea ice or be advected away from such suitable feeding habitat.

(Appendix) Late Cretaceous calcareous nannofossils of DSDP Holes 80-549 and 80-551

he early late Cretaceous (Cenomanian-early Turonian) is thought to have been one of the warmest periods of the Phanerozoic. This period was characterised by tropical sea surface temperatures of up to 36 °C and a pole-to-equator-gradient of less than 10 °C. The subsequent Turonian-Maastrichtian was characterised by a continuous climatic cooling, peaking in the Maastrichtian. This climatic cooling and the resulting palaeoceanographic changes had an impact on planktic primary producer communities including calcareous nannofossils. In order to gain a better understanding of these Cenomanian-Maastrichtian palaeoceanographic changes, calcareous nannofossils have been studied from the proto North Atlantic (Goban Spur, DSDP Sites 549, 551). In order to see potential differences between open oceanic and shelf dwelling nannofossils, the data from Goban Spur have been compared to findings from the European shelf (northern Germany). A total of 77 samples from Goban Spur were studied for calcareous nannofossils revealing abundant (mean 6.2 billion specimens/g sediment) and highly diverse (mean 63 species/sample) nannofossil assemblages. The dominant taxa are Watznaueria spp. (mean 30.7%), Prediscosphaera spp. (mean 18.3%), Zeugrhabdotus spp. (mean 8.3%), Retecapsa spp. (mean 7.2%) and Biscutum spp. (mean 6.6%). The Cenomanian assemblages of both Goban Spur (open ocean) and Wunstorf (shelf) are characterised by elevated abundances of high fertility taxa like Biscutum spp., Zeugrhabdotus spp. and Tranolithus orionatus. Early Turonian to Maastrichtian calcareous nannofossil assemblages of Goban Spur are, however, quite different to those described from European sections. Oceanic taxa like Watznaueria spp., Retecapsa spp. and Cribrosphearella ehrenbergii dominate in Goban Spur whereas the fertility indicators Biscutum spp. and T. orionatus are more abundant in the European shelf assemblages. This shift from a homogeneous distribution of calcareous nannofossils in the Cenomanian towards a heterogeneous one in the Turonian-Maastrichtian implies a change of the ocean circulation. The "eddy ocean" system of the Cenomanian was replaced by an oceanic circulation similar to the modern one in the Turonian-Maastrichtian, caused by the cooling. The increased pole-to-equator-gradients resulted in an oceanic circulation similar to the modern one.

Waste, fraud, and abuse : hearing before the Committee on Governmental Affairs, United States Senate, One hundredth Congress, first session.

"February 19, 1987"--Pt. 2.