Genetic defects in common variable immunodeficiency

Common variable immunodeficiency (CVID) is the most frequent clinically manifested primary immunodeficiency. According to clinical and laboratory findings, CVID is a heterogeneous group of diseases. Recently, the defects of molecules regulating activation and terminal differentiation of B lymphocytes have been described in some patients with CVID. In this study, we show the overview of deficiencies of inducible costimulator, transmembrane activator and calcium-modulator and cytophilin ligand interactor, CD19 molecules, their genetic basis, pathogenesis and clinical manifestations

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs

Stomatal design principles in synthetic and real leaves

Stomata are portals in plant leaves that control gas exchange for photosynthesis, a process fundamental to life on Earth. Gas fluxes and plant productivity depend on external factors such as light, water and CO(2) availability and on the geometrical properties of the stoma pores. The link between stoma geometry and environmental factors has informed a wide range of scientific fields—from agriculture to climate science, where observed variations in stoma size and density are used to infer prehistoric atmospheric CO(2) content. However, the physical mechanisms and design principles responsible for major trends in stomatal patterning are not well understood. Here, we use a combination of biomimetic experiments and theory to rationalize the observed changes in stoma geometry. We show that the observed correlations between stoma size and density are consistent with the hypothesis that plants favour efficient use of space and maximum control of dynamic gas conductivity, and that the capacity for gas exchange in plants has remained constant over at least the last 325 Myr. Our analysis provides a new measure to gauge the relative performance of species based on their stomatal characteristics

Stomatal design principles in synthetic and real leaves

Stomata are portals in plant leaves that control gas exchange for photosynthesis, a process fundamental to life on Earth. Gas fluxes and plant productivity depend on external factors such as light, water and CO2 availability and on the geometrical properties of the stoma pores. The link between stoma geometry and environmental factors has informed a wide range of scientific fields-from agriculture to climate science, where observed variations in stoma size and density are used to infer prehistoric atmospheric CO2 content. However, the physical mechanisms and design principles responsible for major trends in stomatal patterning are not well understood. Here, we use a combination of biomimetic experiments and theory to rationalize the observed changes in stoma geometry. We show that the observed correlations between stoma size and density are consistent with the hypothesis that plants favour efficient use of space and maximum control of dynamic gas conductivity, and that the capacity for gas exchange in plants has remained constant over at least the last 325 Myr. Our analysis provides a new measure to gauge the relative performance of species based on their stomatal characteristics

Separation and pattern formation in hydraulic jumps

We present theory and experiments on the circular hydraulic jump in the stationary regime. The theory can handle the situation in which the fluid flows over an edge far away from the jump. In the experiments the external height is controlled, and a series of transitions in the flow structure appears. First the steepening of the jump causes a transition akin to the breaking of a wave, and subsequently a series of shapes appear, which break the azimuthal symmetry. 1 Introduction One of the most well-known examples of strongly non-linear waves is the river bore, which appears when rivers experience strong tides. The tidal waves created at the mouth of the river appears almost like a step in the water level and can run for several miles upstream with almost no change of form [1]. Considering the strong interest in non-linear phenomena and the enormous progress in the understanding of solitary wave motion, it is quite surprising that no theory yet exists for this phenomenon, describing the..

Supplemental online material from Stomatal design principles in synthetic and real leaves

Stomata are portals in plant leaves that control gas exchange for photosynthesis, a process fundamental to life on the Earth. Gas fluxes and plant productivity depend on external factors such as light, water and CO₂ availability and on geometrical properties of the stomata pores. The link between stomata geometry and environmental factors has informed a wide range of scientific fields - from agriculture to climate science, where observed variations in stomata size and density are used to infer prehistoric atmospheric CO₂ content. However, the physical mechanisms and design principles, responsible for major trends in stomatal patterning, are not well understood. Here, we use a combination of biomimetic experiments and theory to rationalize the observed changes in stomatal geometry. We show that the observed correlations between stomatal size and density are consistent with the hypothesis that plants favour efficient use of space and maximum control of dynamic gas conductivity, and that the capacity for gas exchange in plants has remained constant over at least the last 325 myr. Our analysis provides a new measure to gauge the relative performance of species based on their stomatal characteristics

Branch angle and leaflet shape are associated with canopy coverage in soybean

Abstract Early canopy coverage is a desirable trait that is a major determinant of yield in soybean (Glycine max). Variation in traits comprising shoot architecture can influence canopy coverage, canopy light interception, canopy‐level photosynthesis, and source‐sink partitioning efficiency. However, little is known about the extent of phenotypic diversity of shoot architecture traits and their genetic control in soybean. Thus, we sought to understand the contribution of shoot architecture traits to canopy coverage and to determine the genetic control of these traits. We examined the natural variation for shoot architecture traits in a set of 399 diverse maturity group I soybean (SoyMGI) accessions to identify relationships between traits, and to identify loci that are associated with canopy coverage and shoot architecture traits. Canopy coverage was correlated with branch angle, number of branches, plant height, and leaf shape. Using previously collected 50K single nucleotide polymorphism data, we identified quantitative trait locus (QTL) associated with branch angle, number of branches, branch density, leaflet shape, days to flowering, maturity, plant height, number of nodes, and stem termination. In many cases, QTL intervals overlapped with previously described genes or QTL. We also found QTL associated with branch angle and leaflet shape located on chromosomes 19 and 4, respectively, and these QTL overlapped with QTL associated with canopy coverage, suggesting the importance of branch angle and leaflet shape in determining canopy coverage. Our results highlight the role individual architecture traits play in canopy coverage and contribute information on their genetic control that could help facilitate future efforts in their genetic manipulation

BaRTv2:A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA‐seq data, and enables detailed investigations of transcriptional and post‐transcriptional regulation. Using novel computational methods and a combination of PacBio Iso‐seq and Illumina short‐read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2‐row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high‐resolution reverse transcriptase‐polymerase chain reaction and 5'‐RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high‐quality resource for advanced transcriptomic analyses, including both transcriptional and post‐transcriptional regulation, with exceptional resolution and precision