Targeting the Plasmodium falciparum UCHL3 ubiquitin hydrolase using chemically constrained peptides.

The ubiquitin-proteasome system is essential to all eukaryotes and has been shown to be critical to parasite survival as well, including Plasmodium falciparum, the causative agent of the deadliest form of malarial disease. Despite the central role of the ubiquitin-proteasome pathway to parasite viability across its entire life-cycle, specific inhibitors targeting the individual enzymes mediating ubiquitin attachment and removal do not currently exist. The ability to disrupt P. falciparum growth at multiple developmental stages is particularly attractive as this could potentially prevent both disease pathology, caused by asexually dividing parasites, as well as transmission which is mediated by sexually differentiated parasites. The deubiquitinating enzyme PfUCHL3 is an essential protein, transcribed across both human and mosquito developmental stages. PfUCHL3 is considered hard to drug by conventional methods given the high level of homology of its active site to human UCHL3 as well as to other UCH domain enzymes. Here, we apply the RaPID mRNA display technology and identify constrained peptides capable of binding to PfUCHL3 with nanomolar affinities. The two lead peptides were found to selectively inhibit the deubiquitinase activity of PfUCHL3 versus HsUCHL3. NMR spectroscopy revealed that the peptides do not act by binding to the active site but instead block binding of the ubiquitin substrate. We demonstrate that this approach can be used to target essential protein-protein interactions within the Plasmodium ubiquitin pathway, enabling the application of chemically constrained peptides as a novel class of antimalarial therapeutics.

Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation.

BACKGROUND: Despite sexual development being ubiquitous to vertebrates, the molecular mechanisms underpinning this fundamental transition remain largely undocumented in many organisms. We designed a time course experiment that successfully sampled the period when Atlantic salmon commence their trajectory towards sexual maturation. RESULTS: Through deep RNA sequencing, we discovered key genes and pathways associated with maturation in the pituitary-ovarian axis. Analyzing DNA methylomes revealed a bias towards hypermethylation in ovary that implicated maturation-related genes. Co-analysis of DNA methylome and gene expression changes revealed chromatin remodeling genes and key transcription factors were both significantly hypermethylated and upregulated in the ovary during the onset of maturation. We also observed changes in chromatin state landscapes that were strongly correlated with fundamental remodeling of gene expression in liver. Finally, a multiomic integrated analysis revealed regulatory networks and identified hub genes including TRIM25 gene (encoding the estrogen-responsive finger protein) as a putative key regulator in the pituitary that underwent a 60-fold change in connectivity during the transition to maturation. CONCLUSION: The study successfully documented transcriptome and epigenome changes that involved key genes and pathways acting in the pituitary - ovarian axis. Using a Systems Biology approach, we identified hub genes and their associated networks deemed crucial for onset of maturation. The results provide a comprehensive view of the spatiotemporal changes involved in a complex trait and opens the door to future efforts aiming to manipulate puberty in an economically important aquaculture species.

Greenlip Abalone (Haliotis laevigata) Genome and Protein Analysis Provides Insights into Maturation and Spawning.

Wild abalone (Family Haliotidae) populations have been severely affected by commercial fishing, poaching, anthropogenic pollution, environment and climate changes. These issues have stimulated an increase in aquaculture production; however production growth has been slow due to a lack of genetic knowledge and resources. We have sequenced a draft genome for the commercially important temperate Australian 'greenlip' abalone (Haliotis laevigata, Donovan 1808) and generated 11 tissue transcriptomes from a female adult abalone. Phylogenetic analysis of the greenlip abalone with reference to the Pacific abalone (Haliotis discus hannai) indicates that these abalone species diverged approximately 71 million years ago. This study presents an in-depth analysis into the features of reproductive dysfunction, where we provide the putative biochemical messenger components (neuropeptides) that may regulate reproduction including gonad maturation and spawning. Indeed, we isolate the egg-laying hormone neuropeptide and under trial conditions induce spawning at 80% efficiency. Altogether, we provide a solid platform for further studies aimed at stimulating advances in abalone aquaculture production. The H. laevigata genome and resources are made available to the public on the abalone 'omics website, http://abalonedb.org.

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon.

BACKGROUND: A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts. RESULTS: We report genome wide association studies (GWAS) using fish measured for sexual maturation in freshwater or the marine environment. Genotypic data from a custom 50 K single nucleotide polymorphism (SNP) array was used to identify 13 significantly associated SNP for freshwater maturation with the most strongly associated on chromosomes 10 and 11. A higher number of associations (48) were detected for marine maturation, and the two peak loci were found to be the same for both traits. The number and broad distribution of GWAS hits confirmed a highly polygenetic nature, and GWAS performed separately within males and females revealed sex specific genetic behaviour for loci co-located with positional candidate genes phosphatidylinositol-binding clathrin assembly protein-like (picalm) and membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (magi2). CONCLUSIONS: The results extend earlier work and have implications for future applied breeding strategies to delay maturation in this important aquaculture species.

Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon.

The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing are enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analyzed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from pituitary gland, brain, ovary, and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting, and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. We identified a cluster of 508 tissue specific genes for pituitary gland, 3395 for brain, 2939 for ovary, and 539 for liver. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors (TFs) present in each tissue-specific gene cluster were identified. TFs belonging to homeobox and bhlh families were identified for pituitary gland, pou and zf-c2h2 families for brain, arid, and zf-c2h2 for ovary and rxr-like family for liver. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.

Evolution of Sex Determination Loci in Atlantic Salmon.

Teleost fish exhibit a remarkable diversity in the control of sex determination, offering the opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 fish and 46,501 SNP to map sex determination to three separate genomic locations in Atlantic salmon (Salmo salar). To characterize each, whole genome sequencing was performed to 30-fold depth of coverage using 20 fish representing each of three identified sex lineages. SNP polymorphism reveals male fish carry a single copy of the male specific region, consistent with an XX/XY or male heterogametric sex system. Haplotype analysis revealed deep divergence between the putatively ancestral locus on chromosome 2, compared with loci on chromosomes 3 and 6. Haplotypes in fish carrying either the chromosome 3 or 6 loci were nearly indistinguishable, indicating a founding event that occurred following the speciation event that defined Salmo salar from other salmonids. These findings highlight the evolutionarily fluid state of sex determination systems in salmonids, and resolve to the sequence level differences in animals with divergent sex lineages.

Genome Sequencing of Blacklip and Greenlip Abalone for Development and Validation of a SNP Based Genotyping Tool.

Abalone breeding in southern Australia often involves the production of interspecies hybrids through crossing blacklip (Haliotos rubra) and greenlip (H. laevigata) parental populations. To assist applied breeding and investigate genetic divergence, this study applied genome sequencing and variant detection to develop and validate a SNP genotyping tool. Skim short read Illumina sequencing was performed using 24 individuals from each of the two parental species and a hybrid population. Raw reads were assembled into three population specific pools (each 12-15 fold coverage), before mapping was performed against a draft greenlip abalone reference genome. Variant detection identified 22.4 M raw variants across the three populations (SNP and indels), suggesting they are highly heterozygous. First stage filtering defined a high quality SNP collection of 2.2 M variants independently called in each of the three populations. Second stage filtering identified a much smaller set of variants for assay design and genotyping using a validation set of 191 abalone of known population and pedigree. Comparison of allele frequency data revealed a high proportion of SNP (43%) had divergent allele frequency (< 0.2) between the two parental populations, suggesting they should have utility for parentage assignment. A maximum likelihood approach was used to successfully assign 105 of 105 progeny to their known true parent amongst a set of 86 candidate parents, confirming the genotyping tool has utility for applied breeding. Analysis of pairwise allele sharing successfully discriminated animals into populations, and PCA of genetic distance grouped the hybrid animals with intermediate values between the two parental populations. The findings present a library of DNA polymorphism of utility to breeding and ecological application, and begins to characterize the divergence separating two economically important aquaculture species.

Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar).

In female Atlantic salmon (Salmo salar), exposure to warm summer temperatures causes a reduction in plasma 17ß-estradiol (E2), which impairs downstream vitellogenesis and zonagenesis, and reduces egg fertility and embryo survival. The aim of the present study was to determine whether E2-treatment could offset thermal impairment of endocrine function and maintain egg quality in maiden (first-time-spawning) S. salar reared at 22 °C. Treatment with E2 at 22 °C stimulated vitellogenin (vtg) gene expression and subsequent protein synthesis which promoted oocyte growth and increased egg size relative to untreated fish at 14 and 22 °C. However, E2-treatment at 22 °C was not associated with an increase in egg fertility and embryo survival relative to untreated fish at 22 °C, despite the positive effects of E2-treatment on vitellogenesis and oocyte growth. As there was no evidence to suggest that the estrogen receptor alpha expression was suppressed by high temperature, this could be due to the lack of stimulation on zonagenesis by E2-treatment observed at high temperature during oocyte development. Our results demonstrate that treatment with E2 is not able to maintain zonagenesis or egg quality in maiden S. salar at high temperature, even when vtg gene expression, protein synthesis and subsequent oocyte growth is promoted. This implies that the mechanisms regulating zonagenesis, but not vitellogenesis are impaired at elevated temperature in female S. salar broodstock, and highlights the remarkable complexity of thermally induced endocrine disruption in fish.

Effects of GnRHa treatment during vitellogenesis on the reproductive physiology of thermally challenged female Atlantic salmon (Salmo salar).

Tasmanian Atlantic salmon (S. salar) broodstock can experience temperatures above 20 °C, which impairs reproductive development and inhibits ovulation. The present study investigated the prolonged use of gonadotropin releasing hormone analogue (GnRHa) during vitellogenesis as a means of maintaining endocrine function and promoting egg quality at elevated temperature in maiden and repeat spawning S. salar. GnRHa-treatment during vitellogenesis did not compensate for the negative effects of thermal challenge on the timing of ovulation, egg size, egg fertility or embryo survival in any fish maintained at 22 °C relative to 14 °C. The lack of effectiveness was reflected by the endocrine data, as plasma follicle stimulating hormone and luteinising hormone levels were not different between treated and untreated groups at 22 °C. Furthermore, plasma testosterone and E2 levels were unchanged in GnRHa-treated fish at 22 °C, and plasma levels were generally lower in both groups maintained at 22 °C relative to 14 °C. Transcription of vitellogenin, and zona pellucida B and C was not enhanced in GnRHa-treated fish relative to untreated fish at 22 °C, presumably due to observed suppression of plasma E2. These results indicate that thermal impairment of reproduction is likely to occur on multiple levels, and is difficult to overcome via hormonal manipulation.

Non-physician Clinicians - A Gain for Physicians' Working in Sub-Saharan Africa Comment on "Non-physician Clinicians in Sub-Saharan Africa and the Evolving Role of Physicians".

The changing demands on the health sectors in low- and middle-income countries especially sub-Saharan African countries continue to challenge efforts to address critical shortages of the health workforce. Addressing these challenges have led to the evolution of "non-physician clinicians" (NPCs), that assume some physician roles and thus mitigate the continuing shortage of doctors in these countries. While it is agreed that changes are needed in physicians' roles and their training as part of the new continuum of care that includes NPCs, we disagree that such training should be geared solely at ensuring physicians dominated health systems. Discussions on the workforce models to suit low-income countries must avoid an endorsement of a culture of physician focused health systems as the only model for sub-Saharan Africa (SSA). It is also essential that training for NPCs be harmonized with that of physicians to clarify the technical roles of both.

RAD51 Is a Selective DNA Repair Target to Radiosensitize Glioma Stem Cells.

Patients with glioblastoma die from local relapse despite surgery and high-dose radiotherapy. Resistance to radiotherapy is thought to be due to efficient DNA double-strand break (DSB) repair in stem-like cells able to survive DNA damage and repopulate the tumor. We used clinical samples and patient-derived glioblastoma stem cells (GSCs) to confirm that the DSB repair protein RAD51 is highly expressed in GSCs, which are reliant on RAD51-dependent DSB repair after radiation. RAD51 expression and RAD51 foci numbers fall when these cells move toward astrocytic differentiation. In GSCs, the small-molecule RAD51 inhibitors RI-1 and B02 prevent RAD51 focus formation, reduce DNA DSB repair, and cause significant radiosensitization. We further demonstrate that treatment with these agents combined with radiation promotes loss of stem cells defined by SOX2 expression. This indicates that RAD51-dependent repair represents an effective and specific target in GSCs.

Strategies for Evaluation of Rys Roots and Weights.

The Rys quadrature method for evaluating molecular integrals requires accurate numerical values of the nodes of a Rys polynomial and associated weight factors. The numerical value of a Rys polynomial for a specified value of its argument can be evaluated by three-term recursion using α and ß coefficients. We review existing integration schemes for computing these recurrence parameters, discuss issues related to computational efficiency and numerical precision, and propose a slightly new integration method using Gauss-Rys quadrature. We discuss the advantages and disadvantages of using Golub's matrix method for the computation of roots and weights.

Human cytomegalovirus miR-UL112-1 promotes the down-regulation of viral immediate early-gene expression during latency to prevent T-cell recognition of latently infected cells.

Human cytomegalovirus, a member of the herpesvirus family, can cause significant morbidity and mortality in immune compromised patients resulting from either primary lytic infection or reactivation from latency. Latent infection is associated with a restricted viral transcription programme compared to lytic infection which consists of defined protein coding RNAs but also includes a number of virally encoded microRNAs (miRNAs). One of these, miR-UL112-1, is known to target the major lytic IE72 transcript but, to date, a functional role for miR-UL112-1 during latent infection has not been shown. To address this, we have analysed latent infection in myeloid cells using a virus in which the target site for miR-UL112-1 in the 3' UTR of IE72 was removed such that any IE72 RNA present during latent infection would no longer be subject to regulation by miR-UL112-1 through the RNAi pathway. Our data show that removal of the miR-UL112-1 target site in IE72 results in increased levels of IE72 RNA in experimentally latent primary monocytes. Furthermore, this resulted in induction of immediate early (IE) gene expression that is detectable by IE-specific cytotoxic T-cells (CTLs); no such CTL recognition of monocytes latently infected with wild-type virus was observed. We also recapitulated these findings in the more tractable THP-1 cell line model of latency. These observations argue that an important role for miR-UL112-1 during latency is to ensure tight control of lytic viral immediate early (IE) gene expression thereby preventing recognition of latently infected cells by the host's potent pre-existing anti-viral CTL response.

Epithelial cell ADAM17 activation by Helicobacter pylori: role of ADAM17 C-terminus and Threonine-735 phosphorylation.

Helicobacter pylori transactivates the epidermal growth factor receptor (EGFR) on gastric epithelial cells via a signalling cascade involving a disintegrin and metalloprotease 17 (ADAM17) cleavage of membrane bound heparin binding-epidermal growth factor (HB-EGF). The effects of H. pylori on ADAM17 C-terminus in epithelial cells have been examined. Total cellular ADAM17 and surface expression of ADAM17 were significantly increased by H. pylori in AGS gastric epithelial cells. These changes were associated with ADAM17 C-terminal phosphorylation at T375 and S791. AGS cells lacking the ADAM17 C-terminal domain induced significantly attenuated cleavage of HB-EGF and were also unable to upregulate HB-EGF and EGFR transcripts to the same extent as cells expressing full length ADAM17. In mitotic unstimulated AGS and ADAM17 over-expressing AGS cells, ADAM17 was highly T735 phosphorylated indicating ADAM17 T735 phosphorylation is modified during the cell cycle. In conclusion, H. pylori induced ADAM17 C-terminal T735 and/or S791 phosphorylation in gastric epithelial cells are likely to be an important trigger inducing ADAM17 activation and shedding of HB-EGF leading to EGFR transactivation. ADAM17 over-expression in gastric cancer represents a potential target for therapeutic intervention.

A general formulation for the efficient evaluation of n-electron integrals over products of Gaussian charge distributions with Gaussian geminal functions.

In this work, we present a general formulation for the evaluation of many-electron integrals which arise when traditional one particle expansions are augmented with explicitly correlated Gaussian geminal functions. The integrand is expressed as a product of charge distributions, one for each electron, multiplied by one or more Gaussian geminal factors. Our formulation begins by focusing on the quadratic form that arises in the general n-electron integral. Using the Rys polynomial method for the evaluation of potential energy integrals, we derive a general formula for the evaluation of any n-electron integral. This general expression contains four parameters ω, θ, v, and h, which can be evaluated by an examination of the general quadratic form. Our analysis contains general expressions for any n-electron integral over s-type functions as well as the recursion needed to build up arbitrary angular momentum. The general recursion relation requires at most n + 1 terms for any n-electron integral. To illustrate the general method, we develop explicit expressions for the evaluation of two, three, and four particle electron repulsion integrals as well as two and three particle overlap and nuclear attraction integrals. We conclude our exposition with a discussion of a preliminary computational implementation as well as general computational requirements. Implementation on parallel computers is briefly discussed.

Analyzing molecular static linear response properties with perturbed localized orbitals.

Perturbed localized molecular orbitals (LMOs), correct to first order in an applied static perturbation and consistent with a chosen localization functional, are calculated using analytic derivative techniques. The formalism is outlined for a general static perturbation and variational localization functionals. Iterative and (formally) single-step approaches are compared. The implementation employs an iterative sequence of 2x2 orbital rotations. The procedure is verified by calculations of molecular electric-field perturbations. Boys LMO contributions to the electronic static polarizability and the electric-field perturbation of the r(2) expectation value are calculated and analyzed for ethene, ethyne, and fluoroethene (H(2)C=CHF). For ethene, a comparison is made with results from a Pipek-Mezey localization. The calculations show that a chemically intuitive decomposition of the calculated properties is possible with the help of the LMO contributions and that the polarizability contributions in similar molecules are approximately transferable.

On the basis-set dependence of local and integrated electron density properties: Application of a new computer program for quantum-chemical density analysis.

A new computer program for post-processing analysis of quantum-chemical electron densities is described. The code can work with Slater- and Gaussian-type basis functions of arbitrary angular momentum. It has been applied to explore the basis-set dependence of the electron density and its Laplacian in terms of local and integrated topological properties. Our analysis, including Gaussian/Slater basis sets up to sextuple/quadruple-zeta order, shows that these properties considerably depend on the choice of type and number of primitives utilized in the wavefunction expansion. Basis sets with high angular momentum (l = 5 or l = 6) are necessary to achieve convergence for local properties of the density and the Laplacian. In agreement with previous studies, atomic charges defined within Bader's Quantum Theory of Atoms in Molecules appear to be much more basis-set dependent than the Hirshfeld's stockholder charges. The former ones converge only at the quadruple-zeta/higher level with Gaussian/Slater functions.

On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model.

Accurate, yet simple and efficient, formulae are presented for calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) from the aspherical Hansen-Coppens pseudoatom model of electron density [Hansen & Coppens (1978). Acta Cryst. A34, 909-921]. They are based on the expansion of |r' - r|(-1) in spherical harmonics and the incomplete gamma function for a Slater-type function of the form R(l)(r) = r(n) exp(-alpha ). The formulae are valid for 0 < or = r < or = infinity and are easily extended to higher values of l. Special treatment of integrals is needed only for functions with n = l and n = l + 1 at r = 0. The method is tested using theoretical pseudoatom parameters of the formamide molecule obtained via reciprocal-space fitting of PBE/6-31G** densities and experimental X-ray data of Fe(CO)(5). The ESP, EF and EFG values at the nuclear positions in formamide are in very good agreement with those directly evaluated from density-functional PBE calculations with 6-31G**, aug-cc-pVDZ and aug-cc-pVTZ basis sets. The small observed discrepancies are attributed to the different behavior of Gaussian- and Slater-type functions near the nuclei and to imperfections of the reciprocal-space fit. An EF map is displayed which allows useful visualization of the lattice EF effects in the crystal structure of formamide. Analysis of experimental 100 K X-ray data of Fe(CO)(5) yields the value of the nuclear quadrupole moment Q((57)Fe(m)) = 0.12 x 10(-28) m(2) after taking into account Sternheimer shielding/antishielding effects of the core. This value is in excellent agreement with that reported by Su & Coppens [Acta Cryst. (1996), A52, 748-756] but slightly smaller than the generally accepted value of 0.16 +/- 5% x 10(-28) m(2) obtained from combined theoretical/spectroscopic studies [Dufek, Blaha & Schwarz (1995). Phys. Rev. Lett. 25, 3545-3548].

Particle size limits to meet USP content uniformity criteria for tablets and capsules.

Content uniformity (CU) of pharmaceutical dosage units can be affected by active pharmaceutical ingredient (API) particle size and size distribution. Previous authors have estimated this impact but use of different particle size descriptors led to confusion and difficulty in applying the theoretical models developed. We show that when the same descriptors for particle size and distribution are used (i.e., median diameter on a weight basis (d(50)) and geometric standard deviation (sigma(g))), previously published models are consistent. The approach of Yalkowsky and Bolton4 [Pharm Res 7:962-966, 1990] is modified to use these descriptors and updated for current USP28/NF23 CU criteria. A nomograph is provided to allow easy estimation of an acceptable d(50) for a given dose and sigma(g). To test the model's validity, tablets were manufactured over a wide range of doses and assayed for CU. As predicted, %relative standard deviation (RSD) increased as dose decreased. However, for APIs that deviate significantly from the assumed log-normal distribution, sigma(g) is more appropriately described by the upper region of the API size distribution, presumably because large particles have greatest influence on CU. At very low doses, CU values deviate significantly from normality, consistent with the presence of single large API particles causing super-potent dosage units.

Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set.

As electrostatic forces play a prominent role in the process of folding and binding of biological macromolecules, an examination of the method dependence of the electrostatic interaction energy is of great importance. An extensive analysis of the basis set and method dependence of electrostatic interaction energies (Ees) in molecular systems using six test dimers of α-glycine is presented. A number of Hartree-Fock, Kohn-Sham, Møller-Plesset, configuration interaction (CI), quadratic CI, and coupled cluster calculations were performed using several double-, triple-, and quadruple-ζ-quality Gaussian- and Slater-type (Kohn-Sham calculations only) basis sets. The main factor affecting Ees was found to be the inclusion of diffuse functions in the basis set expansions. Møller-Plesset (even at second order), quadratic CI, and coupled cluster calculations produce the most consistent results. Hartree-Fock and CI methods usually overestimate the Ees, while the Kohn-Sham approach tends to underestimate the magnitude of the electrostatic interaction. The combination of the transferable-pseudoatom databank and the exact potential and multipole moment method reproduces Kohn-Sham B3LYP/6-31G** results on which it is based, confirming the excellent transferability of the pseudoatom densities within the systems studied. However, because Kohn-Sham calculations with double-ζ-quality basis sets show considerable deviations from advanced correlated methods, further development of the databank using electron densities from such methods is highly desirable.