Restoration of Koggala lagoon: modelling approach in evaluating lagoon water budget and flow characteristics.

Groyne system modification is described related to restoration efforts to Koggala lagoon, Sri Lanka.The large-scale unplanned sand removal at the lagoon mouth shifted the formation of sand bar towards the lagoon and made adverse effects on its ecosystem. After the removal of the natural sand bar, groyne system was constructed to avoid sand deposition in the lagoon and to protect the highway bridge (across the lagoon outlet channel) from the wave attack.

Large-scale integration of MicroRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems.

The discovery of microRNAs (miRNAs) revealed a hidden layer of gene regulation that is able to integrate multiple genes into biologically meaningful networks. A number of computational prediction programs have been developed to identify putative miRNA targets. Collectively, the miRNAs that have been discovered so far have the potential to target over 60% of genes in our genome.

Ischemic stroke in young Asian women: risk factors, subtypes and outcome.

Background And Objective: The objective of our study was to describe risk factors, mechanisms and outcome of young Asian women with ischemic stroke.

Methods: Twelve tertiary-care centers in 8 Asian countries participated. Women aged 15-45 years were included if they had an ischemic stroke supported by neuroimaging.

Quantitative phosphoproteomic analysis reveals cAMP/vasopressin-dependent signaling pathways in native renal thick ascending limb cells.

Quantitative mass spectrometry was used to identify hormone-dependent signaling pathways in renal medullary thick ascending limb (mTAL) cells via phosphoproteomic analysis. Active transport of NaCl across the mTAL epithelium is accelerated by hormones that increase cAMP levels (vasopressin, glucagon, parathyroid hormone, and calcitonin). mTAL suspensions from rat kidneys were exposed (15 min) to a mixture of these four hormones.

Proinflammatory role for let-7 microRNAS in experimental asthma.

MicroRNAs (miRNAs) are short, non-coding RNAs that target and silence protein coding genes through 3'-UTR elements. Evidence increasingly assigns an immunosuppressive role for miRNAs in immunity, but relatively few miRNAs have been studied, and an overall understanding of the importance of these regulatory transcripts in complex in vivo systems is lacking. Here we have applied multiple technologies to globally analyze miRNA expression and function in allergic lung disease, an experimental model of asthma.

c-Abl mediates high NaCl-induced phosphorylation and activation of the transcription factor TonEBP/OREBP.

The transcription factor TonEBP/OREBP promotes cell survival during osmotic stress. High NaCl-induced phosphorylation of TonEBP/OREBP at tyrosine-143 was known to be an important factor in increasing its activity in cell culture. We now find that TonEBP/OREBP also is phosphorylated at tyrosine-143 in rat renal inner medulla, dependent on the interstitial osmolality.

Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells.

Self-renewing embryonic stem (ES) cells have an exceptional need for timely biomass production, yet the transcriptional control mechanisms responsible for meeting this requirement are largely unknown. We report here that Ronin (Thap11), which is essential for the self-renewal of ES cells, binds with its transcriptional coregulator, Hcf-1, to a highly conserved enhancer element that previously lacked a recognized binding factor. The subset of genes bound by Ronin/Hcf-1 function primarily in transcription initiation, mRNA splicing, and cell metabolism; genes involved in cell signaling and cell development are conspicuously underrepresented in this target gene repertoire.

Vasopressin increases phosphorylation of Ser84 and Ser486 in Slc14a2 collecting duct urea transporters.

Vasopressin-regulated urea transport in the renal inner medullary collecting duct (IMCD) is mediated by two urea channel proteins, UT-A1 and UT-A3, derived from the same gene (Slc14a2) by alternative splicing. The NH(2)-terminal 459 amino acids are the same in both proteins. To study UT-A1/3 phosphorylation, we made phospho-specific antibodies to UT-A sequences targeting phospho-serines at positions 84 and 486, sites identified previously by protein mass spectrometry.

Systematic genetic analysis of the Plasmodium falciparum MSP7-like family reveals differences in protein expression, location, and importance in asexual growth of the blood-stage parasite.

Proteins located on Plasmodium falciparum merozoites, the invasive form of the parasite's asexual blood stage, are of considerable interest in vaccine research. Merozoite surface protein 7 (MSP7) forms a complex with MSP1 and is encoded by a member of a multigene family located on chromosome 13. The family codes for MSP7 and five MSP7-related proteins (MSRPs).

1-Alkyl-3-methylimidazolium alkanesulfonate ionic liquids, [C(n)H(2)(n)(+1)mim][C(k)H(2)(k)(+1)SO(3)]: synthesis and physicochemical properties.

A set of 1-alkyl-3-methylimidazolium alkanesulfonate ionic liquids, [C(n)mim][C(k)SO(3)], formed by the variation of the alkyl chain lengths both in the cation and the anion (n = 1-6, 8, or 10; k = 1-4, or 6), was synthesised, with sixteen of them being novel. The ionic liquids were characterised by (1)H and (13)C NMR spectroscopy, and mass spectrometry. Their viscosities and densities as a function of temperature, as well as melting points and decomposition temperatures, were determined.

A theory for the arrangement of sensory organs in Drosophila.

We study the arrangements of recurved bristles on the anterior wing margin of wild-type and mutant Drosophila. The epidermal or neural fate of a proneural cell depends on the concentrations of proteins of the achaete-scute complex. At puparium formation, concentrations of proteins are nearly identical in all cells of the anterior wing and each cell has the potential for neural fate.

The genome of a songbird.

The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes.

Discovery of novel microRNAs in female reproductive tract using next generation sequencing.

MicroRNAs (miRNAs) are small non-coding RNAs that mediate post-transcriptional gene silencing. Over 700 human miRNAs have currently been identified, many of which are mutated or de-regulated in diseases. Here we report the identification of novel miRNAs through deep sequencing the small RNAome (<30 nt) of over 100 tissues or cell lines derived from human female reproductive organs in both normal and disease states.

Atmospheric pressure femtosecond laser imaging mass spectrometry.

A novel atmospheric pressure imaging mass spectrometry approach that offers improved lateral resolution (10 microm) using near-infrared femtosecond laser pulses for nonresonant desorption and ionization of sample constituents without the need of a laser-absorbing matrix is demonstrated. As a proof of concept the method was used to image a two-chemical pattern in paper. To demonstrate the ability of the approach to analyze biological tissue, a monolayer of onion epidermis was imaged allowing the chemical visualization of individual cells using mass spectrometry at ambient conditions for the first time.

Molecular profiling uncovers a p53-associated role for microRNA-31 in inhibiting the proliferation of serous ovarian carcinomas and other cancers.

MicroRNAs (miRNA) regulate complex patterns of gene expression, and the relevance of altered miRNA expression to ovarian cancer remains to be elucidated. By comprehensively profiling expression of miRNAs and mRNAs in serous ovarian tumors and cell lines and normal ovarian surface epithelium, we identified hundreds of potential miRNA-mRNA targeting associations underlying cancer. Functional overexpression of miR-31, the most underexpressed miRNA in serous ovarian cancer, repressed predicted miR-31 gene targets including the cell cycle regulator E2F2.

Do toads have a jump on how far they hop? Pre-landing activity timing and intensity in forelimb muscles of hopping Bufo marinus.

During jumping or falling in humans and various other mammals, limb muscles are activated before landing, and the intensity and timing of this pre-landing activity are scaled to the expected impact. In this study, we test whether similarly tuned anticipatory muscle activity is present in hopping cane toads. Toads use their forelimbs for landing, and we analysed pre-landing electromyographic (EMG) timing and intensity in relation to hop distance for the m.

Photoelectron imaging of small silicon cluster anions, Si(n) (-) (n=2-7).

Photoelectron imaging experiments were conducted on small silicon cluster anions, Si(n) (-) (n=2-7), acquired at a photon energy of 3.49 eV (355 nm). Electronic transitions arising from the anion ground states are observed, and the evaluated vertical detachment energies agree well with previous measurements and theoretical calculations.

A putative role for microRNA-205 in mammary epithelial cell progenitors.

In an effort to understand the potential role of microRNAs (miRNAs) in mammary-gland stem or progenitor cells, miRNA microarrays were performed on subpopulations of the mouse mammary epithelial cell (MEC) line COMMA-DbetaGeo. This cell line contains a heterogeneous subpopulation of progenitors characterized by the expression of stem cell antigen 1 (Sca-1; encoded by Ly6a). Microarray analysis indicated that the Sca-1 subpopulations have distinct miRNA expression profiles.

A link between mir-100 and FRAP1/mTOR in clear cell ovarian cancer.

MicroRNAs (miRNAs) are small noncoding RNAs that direct gene regulation through translational repression and degradation of complementary mRNA. Although miRNAs have been implicated as oncogenes and tumor suppressors in a variety of human cancers, functional roles for individual miRNAs have not been described in clear cell ovarian carcinoma, an aggressive and chemoresistant subtype of ovarian cancer. We performed deep sequencing to comprehensively profile miRNA expression in 10 human clear cell ovarian cancer cell lines compared with normal ovarian surface epithelial cultures and discovered 54 miRNAs that were aberrantly expressed.

Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e.

Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach.

Background: MicroRNAs (miRNAs) play critical roles in a wide spectrum of biological processes and have been shown to be important effectors in the intricate host-pathogen interaction networks. Avian influenza virus (AIV) not only causes significant economic losses in poultry production, but also is of great concern to human health. The objective of this study was to identify miRNAs associated with AIV infections in chickens.

Creating perfectly ordered quantum dot arrays via self-assembly.

Several applications involving quantum dots require perfect long-range ordered arrays. Unfortunately, self-assembly (the choice method to fabricate quantum dots) leads to patterns that, although short range ordered, exhibit defects equivalent to grain boundaries and dislocations on a large scale. We note that rotational invariance of film growth is one reason for formation of defects, and hence study an anisotropic model of quantum dot formation.

The completion of the Mammalian Gene Collection (MGC).

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis.

A genome-wide screen for copy number alterations in Aicardi syndrome.

Aicardi syndrome is a severe neurodevelopmental disorder that affects females or rarely males with a 47,XXY karyotype. Therefore, it is thought to be caused by heterozygous defects in an essential X-linked gene or by defects in an autosomal gene with sex-limited expression. Because all reported cases are sporadic with one exception, traditional linkage analysis to identify the mutant gene is not possible, and the de novo mutation rate must be high.