Water management reforms in the Yellow River Basin: implications for water savings, farm incomes and poverty

River basins / Water management / Governance / Water use / Crop production / Models / Farm income / Poverty / Water users’ associations / China / Yellow River Basin

PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers

BACKGROUND: Long thought "relics" of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene-parent gene relationships without leveraging other homologous genes/pseudogenes. RESULTS: We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and >40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four "flavors" of CUDAlign-based databases (>462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15-PPP4R1L) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a "one stop shop" for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers. CONCLUSIONS: Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike

The Effect of Plant Water Storage on Water Fluxes within the Coupled Soil–Plant System

In addition to buffering plants from water stress during severe droughts, plant water storage (PWS) alters many features of the spatio-temporal dynamics of water movement in the soil–plant system. How PWS impacts water dynamics and drought resilience is explored using a multi-layer porous media model

Adaptive locomotion of artificial microswimmers

Bacteria can exploit mechanics to display remarkable plasticity in response to locally changing physical and chemical conditions. Compliant structures play a striking role in their taxis behavior, specifically for navigation inside complex and structured environments. Bioinspired mechanisms with rationally designed architectures capable of large, nonlinear deformation present opportunities for introducing autonomy into engineered small-scale devices. This work analyzes the effect of hydrodynamic forces and rheology of local surroundings on swimming at low Reynolds number, identifies the challenges and benefits of utilizing elastohydrodynamic coupling in locomotion, and further develops a suite of machinery for building untethered microrobots with self-regulated mobility. We demonstrate that coupling the structural and magnetic properties of artificial microswimmers with the dynamic properties of the fluid leads to adaptive locomotion in the absence of on-board sensors

Multiple Scattering Theory for Two-dimensional Electron Gases in the Presence of Spin-Orbit Coupling

In order to model the phase-coherent scattering of electrons in two-dimensional electron gases in the presence of Rashba spin-orbit coupling, a general partial-wave expansion is developed for scattering from a cylindrically symmetric potential. The theory is applied to possible electron flow imaging experiments using a moveable scanning probe microscope tip. In such experiments, it is demonstrated theoretically that the Rashba spin-orbit coupling can give rise to spin interference effects, even for unpolarized electrons at nonzero temperature and no magnetic field.Comment: 34 pages, 7 figure

EST analysis of gene expression in early cleavage-stage sea urchin embryos

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts

Imaging a Single-Electron Quantum Dot

Images of a single-electron quantum dot were obtained in the Coulomb blockade regime at liquid He temperatures using a cooled scanning probe microscope (SPM). The charged SPM tip shifts the lowest energy level in the dot and creates a ring in the image corresponding to a peak in the Coulomb-blockade conductance. Fits to the lineshape of the ring determine the tip-induced shift of the electron energy state in the dot. SPM manipulation of electrons in quantum dots promises to be useful in understanding, building and manipulating circuits for quantum information processing.Comment: 14 pages including 3 figure

Toward Tuning the Surface Functionalization of Small Ceria Nanoparticles

Understanding and controlling the performance of ceria nanoparticle (CNP) catalysts requires knowledge of the detailed structure and property of CNP surfaces and any attached functional groups. Here we report thermogravimetric analysis results showing that hydrothermally synthesized ∼30 nm CNPs are decorated with 12.9 hydroxyl groups per nm2 of CNP surface.Quantum mechanical calculations of the density and distribution of bound surface groups imply a scaling relationship for surface group density that balances formal charges in the functionalized CNP system. Computational results for CNPs with only hydroxyl surface groups yield a predicted density of bound hydroxyl groups for ∼30 nm CNPs that is ∼33% higher than measured densities. Quantitative agreement between predicted and measured hydroxylsurface densities is achieved when calculations consider CNPs with both –OH and –Ox surface groups. For this more general treatment of CNP surface functionalizations, quantum mechanical calculations predict a range of stable surface group configurations that depend on the chemical potentials of O and H, and demonstrate the potential to tune CNP surfacefunctionalizations by varying temperature and/or partial pressures of O2 and H2O