An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.

Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org).

Diverse molecular functions of Hu proteins.

Hu proteins are RNA-binding proteins involved in diverse biological processes. The neuronal members of the Hu family, HuB, HuC, and HuD play important roles in neuronal differentiation and plasticity, while the ubiquitously expressed family member, HuR, has numerous functions mostly related to cellular stress response. The pivotal roles of Hu proteins are dictated by their molecular functions affecting a large number of target genes. Hu proteins affect many post-transcriptional aspects of RNA metabolism, from splicing to translation. In this communication, we will focus on these molecular events and review our current understanding of how Hu proteins mediate them. In particular, emphasis will be put on the nuclear functions of these proteins, which were recently discovered. Three examples including calcitonin/calcitonin gene-related peptide, neurofibromatosis type 1, and Ikaros will be discussed in detail. In addition, an intriguing theme of antagonism between Hu proteins and other AU-rich sequence binding proteins will be discussed.

Pharmacokinetic and pharmacodynamic interaction for a binary mixture of chlorpyrifos and diazinon in the rat.

Chlorpyrifos (CPF) and diazinon (DZN) are two commonly used organophosphorus (OP) insecticides and a potential exists for concurrent exposures. The primary neurotoxic effects from OP pesticide exposures result from the inhibition of acetylcholinesterase (AChE). The pharmacokinetic and pharmacodynamic impact of acute binary exposures of rats to CPF and DZN was evaluated in this study. Rats were orally administered CPF, DZN, or a CPF/DZN mixture (0, 15, 30, or 60 mg/kg) and blood (plasma and RBC), and brain were collected at 0, 3, 6, 12, and 24 h postdosing, urine was also collected at 24 h. Chlorpyrifos, DZN, and their respective metabolites, 3,5,6-trichloro-2-pyridinol (TCP) and 2-isopropyl-4-methyl-6-hydroxypyrimidine (IMHP), were quantified in blood and/or urine and cholinesterase (ChE) inhibition was measured in brain, RBC, and plasma. Coexposure to CPF/DZN at the low dose of 15/15 mg/kg did not alter the pharmacokinetics of CPF, DZN, or their metabolites in blood. A high binary dose of 60/60 mg/kg increased the C(max) and AUC and decreased the clearance for both parent compounds, likely due to competition between CPF and DZN for CYP450 metabolism. At lower doses, most likely to be encountered in occupational or environmental exposures, the pharmacokinetics were linear. A dose-dependent inhibition of ChE was noted in tissues for both the single and coexposures, and the extent of inhibition was plasma > RBC > or = brain. The overall relative potency for ChE inhibition was CPF/DZN > CPF > DZN. A comparison of the ChE response at the low binary dose (15/15 mg/kg), where there were no apparent pharmacokinetic interactions, suggested that the overall ChE response was additive. These experiments represent important data concerning the potential pharmacokinetic and pharmacodynamic interactions for pesticide mixtures and will provide needed insight for assessing the potential cumulative risk associated with occupational or environmental exposures to these insecticides.

A synthetic approach to the Stemona alkaloids.

This paper describes our work developing a strategy for the construction of the typical core structure of the Stemona alkaloids. The approach is to control the relative stereochemistry of the groups on the core 1-azabicyclo[5.3.0]decane ring system by a [3,3] sigmatropic rearrangement of an acylimmonium ion followed by selective reduction. After optimization, this reaction sequence afforded the desired diastereomer in 62% yield. Further efforts were directed toward elaboration of the characteristic butyrolactone substituent.

Synthetic spider silk: a modular fiber.

Spiders make their webs and perform a wide range of tasks with up to seven different types of silk fiber. These different fibers allow a comparison of structure with function, because each silk has distinct mechanical properties and is composed of peptide modules that confer those properties. By using genetic engineering to mix the modules in specific proportions, proteins with defined strength and elasticity can be designed, which have many potential medical and engineering uses.

Comparison of test methods and early toxicity characterization for five dispersants.

The acute toxicities of a commercial dispersant (Corexit 9527) and four experimental dispersant formulations were evaluated using the 96-h mysid (Mysidopsis bahia) test and two rapid screening tests, Microtox and the Mysid IQ Toxicity Test. During 96-h toxicity tests, survival observations were recorded at 3, 6, 9, 12, and 24 h to document mortalities from short-term exposures more consistent with field exposure times and more approximate to exposure times used in Microtox and the Mysid IQ Toxicity Test. At nominal concentrations (6.25 and 12.5 mg/liter) and exposure times (3-24 h) near the upper range of predicted field conditions, mysid mortalities were

Expression and purification of a spider silk protein: a new strategy for producing repetitive proteins.

Synthetic genes were constructed based on the known sequence of the spider dragline silk protein MaSp 2. The genes had 8, 16, or 32 contiguous units of the consensus repeat sequence of the protein. These artificial genes were constructed using a strategy involving compatible but nonregenerable restriction sites, which allowed construction of very large inserts in a precisely controlled manner. This strategy should have general utility in the controlled construction of repetitive proteins composed of identical or different repeat units. The protein from the 16-unit repeat was produced in Escherichia coli at levels up to 10 mg/g wet wt of cells although yields of 1-2 mg/g were more typical. The protein was easily purified with high recovery using an affinity column. The purified protein had the predicted amino acid composition and N-terminal sequence after cleavage of a leader sequence. The methodology described will allow production of sufficient quantities of protein for basic structure/function studies including production of synthetic fibers.

Isolation of a clone encoding a second dragline silk fibroin. Nephila clavipes dragline silk is a two-protein fiber.

Spider dragline silk is a unique protein fiber possessing both high tensile strength and high elasticity. A partial cDNA clone for one dragline silk protein (Spidroin 1) was previously isolated. However, the predicted amino acid sequence could not account for the amino acid composition of dragline silk. We have isolated a partial cDNA clone for another dragline silk protein (Spidroin 2), demonstrating that dragline silk is composed of multiple proteins. The amino acid sequence exhibits an entirely different repetitive motif than Spidroin 1. Spidroin 2 is predicted to consist of linked beta-turns in proline-rich regions which alternate with beta-sheet regions composed of polyalanine segments. This structure for Spidroin 2 provides a model for dragline silk structure and function.

Polymyositis with hypokalemia: correction with potassium replacement in the absence of steroids.

A patient presented with typical polymyositis, but also with hypokalemia. Correction of potassium deficit without corticosteroids led to complete resolution of symptoms and laboratory abnormalities. Muscle biopsy performed after correction of the hypokalemia revealed focal fiber necrosis with regeneration and inflammatory infiltrate that contained, among others, many eosinophils. Hypokalemia should be considered in the differential diagnosis of polymyositis even in the face of an inflammatory muscle infiltrate.

Compartmentalization and persistence of endothall in experimental pools.

The compartmentalization and persistence of endothall, an aquatic herbicide, was studied using static greenhouse experimental pools. An overall aqueous pseudo-first-order decay rate coefficient of 0.173 day-1 and a half-life of 4.01 days were observed at endothall treatment levels of 0.03, 1.6, and 4.5 mg liter-1. Instantaneous sediment partition coefficients (Kp) were calculated at maximum endothall concentrations in sediments and ranged from 51.4 to 127.7. Bioconcentration factors (BCF) for the submerged aquatic macrophyte, Myriophyllum spicatum, ranged from 3.9 to 768.9. These instantaneous BCF values were calculated at the maximum M. spicatum endothall concentrations. The short aqueous half-life for endothall compares well with previous studies; however, both the Kp and BCF were one to three orders of magnitude higher than observed in a previous laboratory study and calculated from regression equations based on endothall solubility. Experimental pool studies can be important steps in translation of data from the laboratory to field and in the development of field sampling protocols that require understanding of expected behavior of a chemical in aquatic systems.

Glucocorticoids regulate proopiomelanocortin gene expression in vivo at the levels of transcription and secretion.

After adrenalectomy, the plasma levels of adrenocorticotropic hormone (corticotropin, ACTH)/endorphin peptides in rats rise dramatically in the first 4 hr while pituitary peptide levels fall sharply. Eight hours after adrenalectomy, plasma levels are near control values again but they then increase continuously over the next 8 days. Proopiomelanocortin (POMC) mRNA levels in the anterior pituitary (quantitated by hybridization with cloned POMC cDNA) increase 2-fold in the first 24 hours, reaching 15- to 20-fold the control level 18 days after adrenalectomy. When dexamethasone is administered to rats 8 days after adrenalectomy, the above events are reversed. Plasma ACTH falls to control levels within 2 hr whereas anterior pituitary POMC mRNA requires 5 days of treatment for return to control levels. The levels of POMC mRNA in the neurointermediate lobe and the hypothalamus are not altered by either treatment. Adrenalectomy increases transcription of the POMC gene in the anterior pituitary approximately 20-fold and halves transcription of the growth hormone gene within 1 hr of operation. Administration of dexamethasone immediately after adrenalectomy suppresses the increase in transcription of the POMC gene and increases the transcription of the growth hormone gene. Transcription of the POMC gene(s) in the neurointermediate lobe is not altered by either of these treatments.

Molecular weight forms of adrenocorticotropic hormone secreted by primary cultures of mouse anterior pituitary.

Extracts of mouse anterior pituitary cells in monolayer culture were subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis to separate the molecular weight forms of ACTH. The gels were sliced and each segment was eluted. The eluates were assayed for ACTH immunoactivity. Approximately 10% of the immunoactivity in the extracts was found to be present as 20,000--32,000 mol wt ACTH. The remainder of the immunoactivity was equally distributed between two forms of ACTH with apparent molecular weights of 11,800 and 4,500. This distribution is very similar to that found in extracts of mouse anterior pituitary. Mouse anterior pituitary cultures were incubated for 2 h in serum-free tissue culture medium. ACTH was concentrated from the medium and fractionated by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The medium was found to contain predominantly the 4,500 and 11,800 forms of ACTH. When vasopressin was added to these cultures (100 ng/ml), the rate of secretion of ACTH was more than doubled in serum free medium. Analysis of the medium from vasopressin-stimulated cultures showed that the 4,500 and 11,800 mol wt forms of ACTH were again the predominant forms present.

Coordinate control of corticotropin, beta-lipotropin, and beta-endorphin release in mouse pituitary cell cultures.

Hypothalamic extract stimulates the release of corticotropin (ACTH) and endorphins 2.5- to 30-fold in mouse pituitary tumor cell cultures (AtT-20/D(16v) line) and primary cell cultures from mouse anterior pituitary. ACTH and endorphin activities were measured by radioimmunoassay and immunoprecipitation. Pretreatment of tumor cell cultures with 1 muM dexamethasone reduced the stimulatory effect of the extract on release of ACTH and endorphins. Pretreatment of primary cell cultures with 10(-6) M dexamethasone reduced the stimulatory effect of both vasopressin and the extract on the release of ACTH and endorphins. Release of ACTH and endorphin was coupled in both kinds of cultures in the basal, stimulated, and inhibited states. The molecular weight forms of ACTH and endorphin in tumor cell culture medium were analyzed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. Radioimmunoassay and immunoprecipitation show that the 13,000-dalton and 4500-dalton forms of ACTH were present in about equal amounts in medium from cultures incubated with or without hypothalamic extract for 15 min, 30 min, or 2 hr. Smaller amounts of the high molecular weight forms of ACTH (20,000- to 23,000-dalton and 31,000-dalton ACTH) were observed in the culture medium at these times. The predominant forms of endorphin released after 20 min or 3 hr of incubation had molecular weights of 31,000, 11,700 (beta-lipotropic hormone-size material) and 3500 (beta-endorphin-size material). No degradation of the forms of endorphin released into the culture medium was observed after incubating the culture medium for 1.5 hr in the absence of cells. The proportions of the different forms of endorphin and ACTH present in the culture medium resembles that seen in cell extracts.

Glucomannan Biosynthesis Catalyzed by Pisum sativum Enzymes.

The results of molecular weight studies, structural analysis of the [(14)C]polysaccharides, and enzymic properties indicate that the Pisum sativum guanosine diphosphosphate glucose: glucosyltransferase is an enzymic component involved in the biosynthesis of glucomannan chains. The properties of the Pisum sativum particulate enzyme are essentially identical to the glucomannan synthetase obtained from Phaseolus aureus. Also present in the particulate preparation is an enzyme which catalyzes the formation of a [(14)C]mannolipid, using guanosine diphosphate-[(14)C]mannose as a substrate. The [(14)C]mannolipid is hydrolyzed by treatment with 0.012 m HCl, but is stable to treatment with 0.09 m NaOH. The formation of the [(14)C]mannolipid is apparently reversed by guanosine diphosphate, but not by guanosine monophosphate. The chromatographic mobility of the [(14)C]mannolipid is identical to that of a similar mannolipid synthesized by a Phaseolus aureus enzyme.