The function and regulation of the U11-48K protein in U12-dependent splicing

The removal of noncoding sequences, or introns, from the eukaryotic messenger RNA precursors is catalyzed by a ribonucleoprotein complex known as the spliceosome. In most eukaryotes, two distinct classes of introns exist, each removed by a specific type of spliceosome. The major, U2-type introns account for over 99 % of all introns, and are almost ubiquitous. The minor, U12-type introns are found in most but not all eukaryotes, and reside in conserved locations in a specific set of genes. Due to their slow excision rates, the U12-type introns are expected to be involved in the regulation of the genes containing them by inhibiting the maturation of the messenger RNAs. However, little information is currently available on how the activity of the U12-dependent spliceosome itself is regulated. The levels of many known splicing factors are regulated through unproductive alternative splicing events, which lead to inclusion of premature STOP codons, targeting the transcripts for destruction by the nonsense-mediated decay pathway. These alternative splice sites are typically found in highly conserved sequence elements, which also contain binding sites for factors regulating the activation of the splice sites. Often, the activation is achieved by binding of products of the gene in question, resulting in negative feedback loops. In this study, I show that U11-48K, a protein factor specific to the minor spliceosome, specifically recognizes the U12-type 5' splice site sequence, and is essential for proper function of the minor spliceosome. Furthermore, the expression of U11-48K is regulated through a feedback mechanism, which functions through conserved sequence elements that activate alternative splicing and nonsense-mediated decay. This mechanism is conserved from plants to animals, highlighting both the importance and early origin of this mechanism in regulating splicing factors. I also show that the feedback regulation of U11-48K is counteracted by a component of the major spliceosome, the U1 small nuclear ribonucleoprotein particle, as well as members of the hnRNP F/H protein family. These results thus suggest that the feedback mechanism is finely tuned by multiple factors to achieve precise control of the activity of the U12-dependent spliceosome.

Integrated modelling approaches to analysis of climate change impacts on forests and forest management

This paper reviews integrated economic and ecological models that address impacts and adaptation to climate change in the forest sector. Early economic model studies considered forests as one out of many possible impacts of climate change, while ecological model studies tended to limit the economic impacts to fixed price-assumptions. More recent studies include broader representations of both systems, but there are still few studies which can be regarded fully integrated. Full integration of ecological and economic models is needed to address forest management under climate change appropriately. The conclusion so far is that there are vast uncertainties about how climate change affects forests. This is partly due to the limited knowledge about the global implications of the social and economical adaptation to the effects of climate change on forests.

Precarious Pregnancies : Alcohol, drugs and the regulation of risks

Since the 1970s alcohol and drug use by pregnant women has become a target of political, professional and personal concern. The present study focuses on prenatal substance use and the regulation of risks by examining different kinds of societal responses to prenatal alcohol and drug use. The study analyses face-to-face encounters between professionals and service users at a specialised maternity clinic for pregnant women with substance abuse problems, medical and political discourses on the compulsory treatment of pregnant women as a means of FAS prevention and official recommendations on alcohol intake during pregnancy. Moreover, the study addresses the women s perspective by asking how women who have used illicit drugs during pregnancy perceive and rank the dangers linked to drug use. The study consists of five empirical sub-studies and a summary article. Sub-study I was written in collaboration with Dorte Hecksher and Sub-study IV with Riikka Perälä. Theoretically the study builds on the one hand, on the socio-cultural approach to the selection and perception of risks and on the other on governmentality studies which focus on the use of power in contemporary Western societies. The study is based on an ethnographic approach and makes use of the principles of multi-sited ethnography. The empirical sub-studies are based on three different types of qualitative data: ethnographic field notes from a maternity clinic from a period of 7 months, documentary material (medical journals, political documents, health education materials, government reports) and 3) interviews from maternity clinics with clients and members of staff. The study demonstrates that the logic of the regulation of prenatal alcohol use in Finland is characterised by the rise of the foetus , a process in which the urgency of protecting the foetus has gradually gained a more prominent role in the discourses on alcohol-related foetal damage. An increasing unwillingness to accept any kinds of risks when foetal health is at stake is manifested in the public debate on the compulsory treatment of pregnant women with alcohol problems and in the health authorities decision to advise pregnant women to refrain from alcohol use during pregnancy (Sub-studies I and II). Secondly, the study suggests that maternity care professionals have an ambivalent role in their mundane encounters with their pregnant clients: on the one hand professionals focus on the well-being of the foetus, but on the other, they need to take into account the women s needs and agency. The professionals daily encounters with their clients are thus characterised by hybridisation: the simultaneous use of technologies of domination and technologies of agency (Sub-studies III and IV). Finally, the study draws attention to the women s understanding of the risks of illicit drug during pregnancy, and shows that the women s understanding of risk differs from the bio-medical view. The study suggests that when drug-using pregnant women seek professional help they can feel that their moral worth is threatened by professionals negative attitudes which can make service-use challenging.

Analysis of the effects of amino-acid-sequence on the structure of proteins

The conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues.

Self-assembly of neutral and cationic Pd-II organometallic molecular rectangles: synthesis, characterization and nitroaromatic sensing

Design and synthesis of three novel 2 + 2] self-assembled molecular rectangles 1-3 via coordination driven self-assembly of predesigned Pd(II) ligands is reported. 1,8-Diethynylanthracene was assembled with trans-Pd(PEt3)(2)Cl-2 in the presence of CuCl catalyst to yield a neutral rectangle 1 via Pd-C bond formation. Complex 1 represents the first example of a neutral molecular rectangle obtained via C-Pd coordination driven self-assembly. A new Pd-2(II) organometallic building block with 180 degrees bite-angle 1,4-bistrans-(ethynyl)Pd(PEt3)(2)(NO3)] benzene (M-2) containing ethynyl functionality was synthesized in reasonable yield by employing Sonagashira coupling reaction. Self-assembly of M-2 with two organic clip-type donors (L-2-L-3) afforded 2 + 2] self-assembled molecular rectangles 2 and 3, respectively L-2 = 1,8-bis(4-pyridylethynyl) anthracene; L-3 = 1,3-bis(3-pyridyl) isophthalamide]. The macrocycles 1-3 were fully characterized by multinuclear NMR and ESI-MS spectroscopic techniques, and in case of 1 the structure was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of Pd-ethynyl bonds helped to make the assemblies p-electron rich and fluorescent in nature. Complexes 1-2 showed quenching of fluorescence intensity in solution in presence of nitroaromatics, which are the chemical signatures of many commercially available explosives.

Rudiments of complexity theory for scientists and engineers

Complexity theory is an important and growing area in computer science that has caught the imagination of many researchers in mathematics, physics and biology. In order to reach out to a large section of scientists and engineers, the paper introduces elementary concepts in complexity theory in a informal manner, motivating the reader with many examples.

Molecular organization of the gene encoding Xenopus laevis transforming growth factor-beta 5

Transforming growth factor-beta s (TGF-beta 5) are multifunctional polypeptides, known to influence proliferation and differentiation of many cell types. TGF-beta 5 cDNA was cloned from Xenopus laevis and this isoform is unique to the amphibians. Here, we report the isolation and characterization of the TGF-beta 5 genomic clones to determine the structure of TGF-beta 5 gene. The gene consists of seven exons and all intron-exon boundaries follow the GT-AG consensus. The organization of TGF-beta 5 gene was identical to that of the mammalian TGF-beta isoforms, with the exception of position of the first splice junction. We determined the size of TGF-beta 5 gene to be approximately 20 kb.

Gene Expression Profiling of Preovulatory Follicle in the Buffalo Cow: Effects of Increased IGF-I Concentration on Periovulatory Events

The preovulatory follicle in response to gonadotropin surge undergoes dramatic biochemical, and morphological changes orchestrated by expression changes in hundreds of genes. Employing well characterized bovine preovulatory follicle model, granulosa cells (GCs) and follicle wall were collected from the preovulatory follicle before, 1, 10 and 22 h post peak LH surge. Microarray analysis performed on GCs revealed that 450 and 111 genes were differentially expressed at 1 and 22 h post peak LH surge, respectively. For validation, qPCR and immunocytochemistry analyses were carried out for some of the differentially expressed genes. Expression analysis of many of these genes showed distinct expression patterns in GCs and the follicle wall. To study molecular functions and genetic networks, microarray data was analyzed using Ingenuity Pathway Analysis which revealed majority of the differentially expressed genes to cluster within processes like steroidogenesis, cell survival and cell differentiation. In the ovarian follicle, IGF-I is established to be an important regulator of the above mentioned molecular functions. Thus, further experiments were conducted to verify the effects of increased intrafollicular IGF-I levels on the expression of genes associated with the above mentioned processes. For this purpose, buffalo cows were administered with exogenous bGH to transiently increase circulating and intrafollicular concentrations of IGF-I. The results indicated that increased intrafollicular concentrations of IGF-I caused changes in expression of genes associated with steroidogenesis (StAR, SRF) and apoptosis (BCL-2, FKHR, PAWR). These results taken together suggest that onset of gonadotropin surge triggers activation of various biological pathways and that the effects of growth factors and peptides on gonadotropin actions could be examined during preovulatory follicle development.

Phenobarbitone-mediated translocation of the cytosolic proteins interacting with the 5 '-proximal region of rat liver CYP2B1/B2 gene into the nucleus

The positive element (PE) (-69 to -98 bp) within the 5'-proximal region of the CYP2B1B2 gene (+1 to -179 bp) of rat liver is essential for phenobarbitone (PB) response and gives a single major complex with the rat liver cytosol in gel shift analysis. This complex corresponds to complex I (top) of the three complexes given by the nuclear extracts. PB treatment of rats leads to a decrease in complex I formation with the cytosol and PE and an increase in the same with the nuclear extract in gel shift analysis. Both the changes are counteracted by simultaneous okadaic acid administration. The nuclear protein giving rise to complex I has been isolated and has an M-r of 26 kDa. The cytosolic counterpart consists of two species, 26 and 28 kDa, as revealed by Southwestern blot analysis using labeled PE. It is concluded that PB treatment leads to the translocation accompanied by processing of the cytosolic protein species into the nucleus that requires protein dephosphorylation. It is suggested that PB may exert a global regulation on the transcription of many genes by modulating the phosphorylation status of different protein factors involved in transcriptional regulation. (C) 2002 Elsevier Science (USA).

The origin of degeneracies and crossings in the 1d Hubbard model

The paper is devoted to the connection between integrability of a finite quantum system and degeneracies of its energy levels. In particular, we analyse in detail the energy spectra of finite Hubbard chains. Heilmann and Lieb demonstrated that in these systems there are crossings of levels of the same parameter-independent symmetry. We show that this apparent violation of the Wigner-von Neumann noncrossing rule follows directly from the existence of nontrivial conservation laws and is a characteristic signature of quantum integrability. The energy spectra of Hubbard chains display many instances of permanent (at all values of the coupling) twofold degeneracies that cannot be explained by parameter-independent symmetries. We relate these degeneracies to the different transformation properties of the conserved currents under spatial reflections and the particle-hole transformation and estimate the fraction of doubly degenerate states. We also discuss multiply degenerate eigenstates of the Hubbard Hamiltonian. The wavefunctions of many of these states do not depend on the coupling, which suggests the existence of an additional parameter-independent symmetry.

Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large [Delta]Cp's

Maltose binding protein (MBP) is a large, monomeric two domain protein containing 370 amino acids. In the absence of denaturant at neutral pH, the protein is in the native state, while at pH 3.0 it forms a molten globule. The molten globule lacks a tertiary circular dichroism signal but has secondary structure similar to that of the native state. The molten globule binds 8-anilino-1-naphthalene sulfonate (ANS). The unfolding thermodynamics of MBP at both pHs were measured by carrying out a series of isothermal urea melts at temperatures ranging from 274–329 K. At 298 K, values of [Delta]G°, [Delta]Cp, and Cm were 3.1 ± 0.2 kcal mol−1, 5.9 ± 0.8 kcal mol−1 K−1 (15.9 cal (mol-residue)−1 K−1), and 0.8 M, respectively, at pH 3.0 and 14.5 ± 0.4 kcal mol−1, 8.3 ± 0.7 kcal mol−1 K−1 (22.4 kcal (mol-residue)−1 K−1), and 3.3 M, respectively, at pH 7.1. Guanidine hydrochloride denaturation at pH 7.1 gave values of [Delta]G° and [Delta]Cp similar to those obtained with urea. The m values for denaturation are strongly temperature dependent, in contrast to what has been previously observed for small globular proteins. The value of [Delta]Cp per mol-residue for the molten globule is comparable to corresponding values of [Delta]Cp for the unfolding of typical globular proteins and suggests that it is a highly ordered structure, unlike molten globules of many small proteins. The value of [Delta]Cp per mol-residue for the unfolding of the native state is among the highest currently known for any protein.

Compiler Assisted Leakage Energy Optimization for Clustered VLIW Architectures

Miniaturization of devices and the ensuing decrease in the threshold voltage has led to a substantial increase in the leakage component of the total processor energy consumption. Relatively simpler issue logic and the presence of a large number of function units in the VLIW and the clustered VLIW architectures attribute a large fraction of this leakage energy consumption in the functional units. However, functional units are not fully utilized in the VLIW architectures because of the inherent variations in the ILP of the programs. This underutilization is even more pronounced in the context of clustered VLIW architectures because of the contentions for the limited number of slow intercluster communication channels which lead to many short idle cycles.In the past, some architectural schemes have been proposed to obtain leakage energy bene .ts by aggressively exploiting the idleness of functional units. However, presence of many short idle cycles cause frequent transitions from the active mode to the sleep mode and vice-versa and adversely a ffects the energy benefits of a purely hardware based scheme. In this paper, we propose and evaluate a compiler instruction scheduling algorithm that assist such a hardware based scheme in the context of VLIW and clustered VLIW architectures. The proposed scheme exploits the scheduling slacks of instructions to orchestrate the functional unit mapping with the objective of reducing the number of transitions in functional units thereby keeping them off for a longer duration. The proposed compiler-assisted scheme obtains a further 12% reduction of energy consumption of functional units with negligible performance degradation over a hardware-only scheme for a VLIW architecture. The benefits are 15% and 17% in the context of a 2-clustered and a 4-clustered VLIW architecture respectively. Our test bed uses the Trimaran compiler infrastructure.

Effect of shear deformation on interfacial stresses in plated beams subjected to arbitrary loading

Bonding a fibre reinforced polymer (FRP) composite or metallic plate to the soffit of a reinforced concrete (RC), timber or metallic beam can significantly increase its strength and other aspects of structural performance. These hybrid beams are often found to fail due to premature debonding of the plate from the original beam in a brittle manner. This has led to the development of many analytical solutions over the last two decades to quantify the interfacial shear and normal stresses between the adherends. The adherends are subjected to axial, bending and shear deformations. However, most analytical solutions have neglected the influence of shear deformation of the adherends. For the few solutions which consider this effect in an approximate manner, their applicability is limited to one or two specific load cases. This paper presents a general analytical solution for the interfacial stresses in plated beams under an arbitrary loading with the shear deformation of the adherends duly considered. The shear stress distribution is assumed to be parabolic through the depth of the adherends in predicting the interfacial shear stress and Timoshenko's beam theory is adopted in predicting interfacial normal stress to account for the shear deformation. The solution is applicable to a beam of arbitrary prismatic cross-section bonded symmetrically or asymmetrically with a thin or thick plate, both having linear elastic material properties. The effect of shear deformation is illustrated through an example beam. The influence of material and geometric parameters of the adherends and adhesive on the interfacial stress concentrations at the plate end is discussed. (C) 2011 Elsevier Ltd. All rights reserved.

UDP-glucose 4, 6-dehydratase Activity Plays an Important Role in Maintaining Cell Wall Integrity and Virulence of Candida albicans

Candida albicans, a human fungal pathogen, undergoes morphogenetic changes that are associated with virulence. We report here that GAL102 in C. albicans encodes a homolog of dTDP-glucose 4,6-dehydratase, an enzyme that affects cell wall properties as well as virulence of many pathogenic bacteria. We found that GAL102 deletion leads to greater sensitivity to antifungal drugs and cell wall destabilizing agents like Calcofluor white and Congo red. The mutant also formed biofilms consisting mainly of hyphal cells that show less turgor. The NMR analysis of cell wall mannans of gal102 deletion strain revealed that a major constituent of mannan is missing and the phosphomannan component known to affect virulence is greatly reduced. We also observed that there was a substantial reduction in the expression of genes involved in biofilm formation but increase in the expression of genes encoding glycosylphosphatidylinositol-anchored proteins in the mutant. These, along with altered mannosylation of cell wall proteins together might be responsible for multiple phenotypes displayed by the mutant. Finally, the mutant was unable to grow in the presence of resident peritoneal macrophages and elicited a weak pro-inflammatory cytokine response in vitro. Similarly, this mutant elicited a poor serum pro-inflammatory cytokine response as judged by IFN gamma and TNF alpha levels and showed reduced virulence in a mouse model of systemic candidiasis. Importantly, an Ala substitution for a conserved Lys residue in the active site motif YXXXK, that abrogates the enzyme activity also showed reduced virulence and increased filamentation similar to the gal102 deletion strain. Since inactivating the enzyme encoded by GAL102 makes the cells sensitive to antifungal drugs and reduces its virulence, it can serve as a potential drug target in combination therapies for C. albicans and related pathogens.

Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands

The enzyme telomerase synthesizes the G-rich DNA strands of the telomere and its activity is often associated with cancer. The telomerase may be therefore responsible for the ability of a cancer cell-to escape apoptosis. The G-rich DNA sequences often adopt tetra-stranded structure, known as the G-quadruplex DNA (G4-DNA). The stabilization of the telomeric DNA into the G4-DNA structures by small molecules has been the focus of many researchers for the design and development of new anticancer agents. The compounds which stabilize the G-quadruplex in the telomere inhibit the telomerase activity. Besides telomeres, the G4-DNA forming sequences are present in the genomic regions of biological significance including the transcriptional regulatory and promoter regions of several oncogenes. Inducing a G-quadruplex structure within the G-rich promoter sequences is a potential way of achieving selective gene regulation. Several G-quadruplex stabilizing ligands are known. Minor groove binding ligands (MGBLs) interact with the double-helical DNA through the minor grooves sequence-specifically and interfere with several DNA associated processes. These MGBLs when suitably modified switch their preference sometimes from the duplex DNA to G4-DNA and stabilize the G4-DNA as well. Herein, we focus on the recent advances in understanding the G-quadruplex structures, particularly made by the human telomeric ends, and review the results of various investigations of the interaction of designed organic ligands with the G-quadruplex DNA while highlighting the importance of MGBL-G-quadruplex interactions.