nGASP – the nematode genome annotation assessment project

Background  

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase.     

The small genome of an abundant coastal ocean methylotroph

OM43 is a clade of uncultured β-proteobacteria that is commonly found in environmental nucleic acid sequences from productive coastal ocean ecosystems, and some freshwater environments, but is rarely detected in ocean gyres. Ecological studies associate OM43 with phytoplankton blooms, and evolutionary relationships indicate that they might be methylotrophs. Here we report on the genome sequence and metabolic properties of the first axenic isolate of the OM43 clade, strain HTCC2181, which was obtained using new procedures for culturing cells in natural seawater. We found that this strain is an obligate methylotroph that cannot oxidize methane but can use the oxidized C1 compounds methanol and formaldehyde as sources of carbon and energy. Its complete genome is 1304 428 bp in length, the smallest yet reported for a free-living cell. The HTCC2181 genome includes genes for xanthorhodopsin and retinal biosynthesis, an auxiliary system for producing transmembrane electrochemical potentials from light. The discovery that HTCC2181 is an extremely simple specialist in C1 metabolism suggests an unanticipated, important role for oxidized C1 compounds as substrates for bacterioplankton productivity in coastal ecosystems.     

Reproductive endocrine responses to photoperiod and exogenous gonadotropins in the pallas' cat (Otocolobus manul)

Fecal samples were collected for 14–26 months from three male and six female Pallas' cats (Otocolobus manul) to examine gonadal steroidogenic activity in response to changes in photoperiod and treatment with exogenous gonadotropins. Females exhibited a seasonal anestrus from May–December, excreting consistently low concentrations of fecal estrogens (overall mean, 50.2±8.5 ng/g). During the breeding season (January–April), baseline fecal estrogen concentrations were higher, averaging 128.4±18.9 ng/g, with peak concentrations ranging from 455.8–909.6 ng/g. Interpeak intervals in estrogen excretion ranged between 7 and 21 days, with an average estrous cycle length of 14.3±1.7 days. Two females became pregnant after natural mating, with overall luteal progestogen concentrations averaging ～40 μg/g throughout gestation. Fecal estrogens increased in mid‐gestation, peaking just before birth. Induction of follicular development with eCG (100–300 IU, i.m.) resulted in an increase in fecal estrogens (peak range, 263.1–1198.1 ng/g), followed by a postovulatory increase in fecal progestogens (overall mean, 41.1±11.9 μg/g) after hCG (75–150 IU, i.m.). Despite apparently normal ovarian responses, none of the females conceived after artificial insemination (AI). The gonadotropin‐induced nonpregnant luteal phase lasted 49.8±5.3 days (range, 30–60 days), whereas gestation lasted ～70 days. In the male Pallas' cat, fecal androgens were elevated from November–April (overall mean, 352.3±30.3 ng/g) compared with nadir concentrations during the rest of the year (82.1±3.3 ng/g). Entrainment of seasonality to photoperiod was demonstrated by stimulation of gonadal steroidogenic activity in cats exposed to increasing artificial light during natural (nonbreeding season) and artificially induced short‐day photoperiods. In summary, reproduction in Pallas' cats is highly seasonal and photoperiod‐dependent. Females exhibit elevated baseline and peak fecal estrogen concentrations for 3–4 months during late winter/early spring. Testicular steroidogenic activity precedes the rise in female estrogen excretion by about 2 months, presumably to ensure maximal sperm production during the breeding season. Zoo Biol 21:347–364, 2002. Published 2002 Wiley‐Liss, Inc.     

Mechanical ventilation results in progressive contractile dysfunction in the diaphragm.

These experiments tested the hypothesis that a relatively short duration of controlled mechanical ventilation (MV) will impair diaphragmatic maximal specific force generation (specific P(o)) and that this force deficit will be exacerbated with increased time on the ventilator. To test this postulate, adult Sprague-Dawley rats were randomly divided into one of six experimental groups: 1) control (n = 12); 2) 12 h of MV (n = 4); 3) 18 h of MV (n = 4); 4) 18 h of anesthesia and spontaneous breathing (n = 4); 5) 24 h of MV (n = 7); and 6) 24 h of anesthesia and spontaneous breathing (n = 4). MV animals were anesthetized, tracheostomized, and ventilated with room air. Animals in the control group were acutely anesthetized but were not exposed to MV. Animals in two spontaneous breathing groups were anesthetized and breathed spontaneously for either 18 or 24 h. No differences (P > 0.05) existed in diaphragmatic specific P(o) between control and the two spontaneous breathing groups. In contrast, compared with control, all durations of MV resulted in a reduction (P < 0.05) in diaphragmatic specific tension at stimulation frequencies ranging from 15 to 160 Hz. Furthermore, the MV-induced decrease in diaphragmatic specific P(o) was time dependent, with specific P(o) being approximately 18 and approximately 46% lower (P < 0.05) in animals mechanically ventilated for 12 and 24 h, respectively. These data support the hypothesis that relatively short-term MV impairs diaphragmatic contractile function and that the magnitude of MV-induced force deficit increases with time on the ventilator.     

Identification of residues essential for carbohydrate recognition by the insulin-like growth factor II/mannose 6-phosphate receptor.

Two distinct mannose 6-phosphate (Man-6-P) receptors (MPRs), the cation-dependent MPR (CD-MPR) and the insulin-like growth factor II/MPR (IGF-II/MPR), recognize a diverse population of Man-6-P-containing ligands. The IGF-II/MPR is a type I transmembrane glycoprotein with a large extracytoplasmic region composed of 15 repeating domains that display sequence identity to each other and to the single extracytoplasmic domain of the CD-MPR. A structure-based sequence alignment of the two distinct Man-6-P-binding sites of the IGF-II/MPR with the CD-MPR implicates several residues of IGF-II/MPR domains 3 and 9 as essential for Man-6-P binding. To test this hypothesis single amino acid substitutions were made in constructs encoding either the N- or the C-terminal Man-6-P-binding sites of the bovine IGF-II/MPR. The mutant IGF-II/MPRs secreted from COS-1 cells were analyzed by pentamannosyl phosphate-agarose affinity chromatography, identifying four residues (Gln-392, Ser-431, Glu-460, and Tyr-465) in domain 3 and four residues (Gln-1292, His-1329, Glu-1354, and Tyr-1360) in domain 9 as essential for Man-6-P recognition. Binding affinity studies using the lysosomal enzyme, beta-glucuronidase, confirmed these results. Together these analyses provide strong evidence that the two Man-6-P-binding sites of the IGF-II/MPR are structurally similar to each other and to the CD-MPR and utilize a similar carbohydrate recognition mechanism.     

The relationships between active extensibility, and passive and active stiffness of the knee flexors

Insufficient active knee flexor stiffness may predispose the anterior cruciate ligament to injury. Insufficient passive stiffness may result in insufficient active stiffness. Similarly, higher levels of musculotendinous extensibility may inhibit active and passive muscle stiffness, potentially contributing to an increased risk of injury. The literature is both limited and inconsistent concerning relationships between extensibility, passive stiffness, and active stiffness. Extensibility was measured as the maximal active knee extension angle from a supine position with the hip flexed to 90°. Passive stiffness was calculated as the slope of the moment–angle curve resulting from passive knee extension. Active stiffness was assessed via acceleration associated with damped oscillatory motion about the knee. Stepwise multiple regression indicated that passive stiffness accounted for 25% of active muscle stiffness variance. The linear combination of extensibility and passive stiffness explained only 2% more variance compared to passive stiffness alone. Musculotendinous extensibility was moderately related to passive muscle stiffness, and weakly related to active muscle stiffness. The moderate relationship observed between active and passive stiffness emphasizes the dependence of active muscle stiffness on cross-bridge formation, and the relatively smaller contribution from parallel elastic tissues. Additionally, heightened extensibility does not appear to be a predisposing factor for reduced muscle stiffness.     

A long-acting, highly potent interferon alpha-2 conjugate created using site-specific PEGylation

Recombinant interferon alpha-2 (IFN-alpha2) is used clinically to treat a variety of viral diseases and cancers. IFN-alpha2 has a short circulating half-life, which necessitates frequent administration to patients. Previous studies showed that it is possible to extend the circulating half-life of IFN-alpha2 by modifying lysine residues of the protein with amine-reactive poly(ethylene glycol) (PEG) reagents. However, amine-PEGylated IFN-alpha2 comprises a heterogeneous product mixture with low specific activity due to the large number and critical locations of lysine residues in IFN-alpha2. In an effort to overcome these problems we determined the feasibility of creating site-specific, mono-PEGylated IFN-alpha2 analogues by introducing a free (unpaired) cysteine residue into the protein, followed by modification of the added cysteine residue with a maleimide-PEG reagent. IFN-alpha2 cysteine analogues were expressed in Escherichia coli and purified, and their in vitro bioactivities were measured in the human Daudi cell line growth inhibition assay. Several cysteine analogues were identified that do not significantly affect in vitro biological activity of IFN-alpha2. Certain of the cysteine analogues, but not wild-type IFN-alpha2, reacted with maleimide-PEG to produce mono-PEGylated proteins. The PEG-Q5C analogue retained high in vitro bioactivity (within 3- to 4-fold of wild-type IFN-alpha2) even when modified with 20- and 40-kDa PEGs. Pharmacokinetic experiments indicated that the 20-kDa PEG-Q5C and 40-kDa PEG-Q5C proteins have 20-fold and 40-fold longer half-lives, respectively, than IFN-alpha2 following subcutaneous administration to rats. These studies demonstrate the feasibility of using site-specific PEGylation technology to create a long-acting, mono-PEGylated IFN-alpha2 protein with high specific activity.     

Crystal structure of human ABAD/HSD10 with a bound inhibitor: implications for design of Alzheimer's disease therapeutics

The enzyme 17beta-hydroxysteroid dehydrogenase type 10 (HSD10), also known as amyloid beta-peptide-binding alcohol dehydrogenase (ABAD), has been implicated in the development of Alzheimer's disease. This protein, a member of the short-chain dehydrogenase/reductase family of enzymes, has been shown to bind beta-amyloid and to participate in beta-amyloid neurotoxicity. We have determined the crystal structure of human ABAD/HSD10 complexed with NAD(+) and an inhibitory small molecule. The inhibitor occupies the substrate-binding site and forms a covalent adduct with the NAD(+) cofactor. The crystal structure provides a basis for the design of potent, highly specific ABAD/HSD10 inhibitors with potential application in the treatment of Alzheimer's disease.     

The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster

We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p[RS3] and p[RS5], to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The entire collection, along with a computational and genetic toolbox for designing and generating custom deletions, is publicly available. Using the collection it is theoretically possible to generate >12,000 deletions between 1 bp and 1 Mb in size by simple eye color selection. In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence.     

RNA interference-mediated silencing of the S100A10 gene attenuates plasmin generation and invasiveness of Colo 222 colorectal cancer cells

S100A10 is a key plasminogen receptor of the extracellular cell surface that is overexpressed in many cancer cells. Typically, S100A10 is thought to be anchored to the plasma membrane via the phospholipid-binding sites of its binding partner, annexin A2. Here, using the potent and highly sequence-specific mechanism of RNA interference (RNAi), we have stably silenced the expression of the S100A10 gene in colorectal (CCL-222) cancer cells. We show that siRNA expression mediated by the pSUPER vector causes efficient, stable, and specific down-regulation of S100A10 gene expression. The siRNA-mediated down-regulation of S100A10 gene expression resulted in a major decrease in the appearance of extracellular S100A10 protein and correlated with a 45% loss of plasminogen binding, a 65% loss in cellular plasmin generation and a complete loss in plasminogen-dependent cellular invasiveness. We also observed that the CCL-222 cells do not express annexin A2 on their extracellular surface. Thus, the data show that annexin A2 is not required by S100A10 for its association with the plasma membrane, for its colocalization with uPAR, or for its binding and activation of plasminogen.