Molecular Modeling of the NPY Binding Site on the Y1 Receptor

A three-dimensional model of the neuropeptide Y (NPY) - rat Y₁ (rY₁) receptor complex and of the NPY _13-36 - rY₁ receptor complex was constructed by molecular modeling based on the electron density projection map of rhodopsin and on site-directed mutagenesis studies of neuropeptide receptors. In order to further guide the modeling, the nucleotide sequences encoding Trp287, Cys295 and His297 in the third extracellular loop of the rY₁ receptor, were altered by site-directed mutagenesis experiments. Single-point mutated receptors were expressed in COS-7 cells, and tested for their ability to bind radio labelled NPY (³H-NPY). Mutations of Trp287 and His297 completely abolished binding of ³H-NPY. The Cys295Ser mutation only slightly decreased the binding of ³H-NPY, suggesting that the involvement of Cys295 in a disulphide bond is not essential for maintaining the correct three-dimensional structure of the binding site for NPY. Molecular dynamics simulations of NPY-rY₁ receptor interactions suggested that Asp199, Asp103 and Asp286 in the receptor interact, respectively, with Lys4, Arg33 and Arg35 of NPY. The simulations also suggested that His297 acts as a hydrogen acceptor from Arg35 in NPY, and that Tyr1 of NPY interacts with a binding pocket on the receptor formed by Asn115, Asp286, Trp287 and His297. Tyr36 in NPY interacted both with Thr41 and Tyr99 via hydrogen bonds, and also with Asn296, His297 and Phe301. The present study suggests that amino acid residues at the extracellular end of the transmembrane helices and in the extracellular loops are strongly involved in binding to NPY and NPY_13-36.Electronic Supplementary Material available.     

Evidence of molybdenum association with particulate organic matter under sulfidic conditions

The geochemical behavior of molybdenum (Mo) in the oceans is closely linked to the presence of sulfide species in anoxic environments, where Fe availability may play a key role in the Mo scavenging. Here, we show that Mo(VI) is reduced in the presence of particulate organic matter (represented by sulfate‐reducing bacteria). Molybdenum was immobilized at the surface of both living cells and dead/lysed cells, but not in cell‐free control experiments. Experiments were carried out at four different Mo concentrations (0.1 to 2 mm ) to yield cell‐associated Mo precipitates with little or no Fe, consisting of mainly Mo(IV)‐sulfide compounds with molecular structures similar to Mo enzymes and to those found in natural euxinic sediments. Therefore, we propose that Mo removal in natural sulfidic waters can proceed via a non‐Fe‐assisted pathway that requires particulate organic matter (dead or living sulfate‐reducing bacteria). This pathway has implications for global marine Mo cycling and the current use of Mo‐based proxies for paleo‐environmental investigations.     

Taurine in plasma and CSF: a study in healthy male volunteers

In order to explore the interrelationship between plasma and cerebrospinal fluid taurine concentrations, three consecutive 6-ml fractions of cerebrospinal fluid were drawn from 30 healthy male volunteers in the early morning after 8 h in the fasting condition. Repeated plasma samples were drawn over 24 h the day before lumbar puncture. Taurine in plasma and cerebrospinal fluid was determined by high performance liquid chromatography. The subjects were categorized as extensive or poor metabolizers with respect to the cytochrome P450 2D6 genotype. The taurine cerebrospinal fluid/plasma ratio at 8 a.m. was negatively influenced by the plasma taurine concentration at 4 p.m. the previous day. It was also negatively influenced by body mass index and positively by the intraspinal pressure. Three poor metabolizers of cytochrome P450 2D6 had higher plasma taurine areas under the curve than 27 extensive metabolizers. Hypothetically, cytochrome P450 2D6 influences the transport of taurine across the blood–brain barrier.     

X-linked progressive mixed deafness: a new microdeletion that involves a more proximal region in Xq21.

We report a large two-generation pedigree with seven affected males segregating for an X-linked mixed conductive sensorineural deafness. The patients present with atypical Mondini-like dysplasia, dilated petrous facial canal, dilatation of the internal auditory meatus fully connected with enlarged cochlear canals, and, in one patient, a wide bulbous posterior labyrinth. Obligatory carrier females are mildly affected. Molecular characterization of this family revealed a deletion of locus DXS169, in Xq21.1. Loci DXS72 and DXS26, which, respectively, flank DXS169 proximally and distally, were intact. Since a gene responsible for X-linked progressive mixed deafness with perilymphatic gusher (DFN3) has previously been assigned by deletion mapping to a slightly more distal interval between DXS26 and DXS121, this study indicates either two different deafness genes or the involvement of a very large region in Xq21.     

Inhibition of Bfl-1 with N-aryl maleimides

High-throughput screening of 66,000 compounds using competitive binding of peptides comprising the BH3 domain to anti-apoptotic Bfl-1 led to the identification of 14 validated 'hits' as inhibitors of Bfl-1. N-Aryl maleimide 1 was among the validated 'hits'. A chemical library encompassing over 280 analogs of 1 was prepared following a two-step synthesis. Structure-activity studies for inhibition of Bfl-1 by analogs of N-aryl maleimide 1 revealed a preference for electron-withdrawing substituents in the N-aryl ring and hydrophilic amines appended to the maleimide core. Inhibitors of Bfl-1 are potential development candidates for anti-cancer therapeutics.     

Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes

Procedures and reagents are needed to specifically detect all the macromolecules that are being identified in the course of genome projects. We discuss how this challenge may be met using a set of ligation-based reagents termed padlock probes and proximity ligation probes. These probes include elements with affinity for specific nucleic acid and protein molecules, respectively, along with unique identifier DNA sequence elements that encode the identity of the recognized target molecules. The information content of DNA strands that form in the detection reactions are recorded after amplification, allowing the recognized target molecules to be identified. The procedures permit highly specific solution-phase or localized analyses of large sets of target molecules as required in future molecular analyses.     

Ultrasonography in early pregnancy diagnosis and measurements of fetal size in reindeer (Rangifer tarandus tarandus)

Transrectal or transabdominal examinations of 13 pluriparous reindeer (Rangifer tarandus tarandus) by ultrasonography from the start of mating until week 20 of gestation were conducted to find out when pregnancy could first be detected and to describe fetal development in early pregnancy. The examinations (n=35 per animal) were performed with a 5 MHz linear transducer from 7th October until 1st January and with a 3 MHz sector transducer from that time until 24th February. Time of pregnancy diagnosis by ultrasonography, the first fetal heartbeat and measurements of crown-rump length, chest width and chest depth were recorded during the examinations. Pregnancy was diagnosed by transrectal ultrasonography between the weeks 3 and 7 of gestation. The accuracy of the pregnancy diagnosis, defined as the proportion of females correctly detected to be pregnant, was 15% at week 3, 46% at week 4, 77% at week 5, and 92% at week 6 of gestation. Fetal heartbeat was first detected between the weeks 5 and 8 of gestation. The first measurements of crown-rump length were made on week 3 of gestation, of chest width on week 4 and of chest depth on week 5 of gestation. Chest width and depth were detectable until the end of the study at week 20 of gestation. Transrectal ultrasonography is an efficient tool in early pregnancy diagnosis of reindeer. The fetal growth curves obtained by ultrasonography resembled those obtained in previous morphological studies.     

Changes of glial-neuronal interaction and metabolism after a subconvulsive dose of pentylenetetrazole

Pentylenetetrazole (PTZ) injection causes seizures in rodents and this is used in several models of epilepsy. In the present study a low dose (20 mg/kg) was injected into rats in order to analyze metabolic disturbances caused by subconvulsive amounts of PTZ. Intraperitoneal injection of PTZ was followed, 30 min later, by injection of [1-(13C)]glucose plus [1,2-(13C)]acetate and 15 min thereafter decapitation. Analyses of extracts from cerebrum, subcortex and cerebellum were performed using 13C NMRS and HPLC. Whereas convulsive doses of PTZ lead to most pronounced changes in cerebellum [J. Neurochem. 85 (2003) 1200], it could be shown that subconvulsive doses affected mainly amino acid metabolism in cerebrum. In glutamatergic neurons in the cerebrum PTZ affected both the metabolic and releasable pools of glutamate, whereas, in the subcortex and cerebellum only the metabolic pool was affected. This could be deducted from the findings that less [4-(13C)]glutamine, [3,4-(13C)]glutamate and [2-(13C)]aspartate, which are labeled from [1-(13C)]glucose, were detected in this area. Glial metabolism was also changed as evidenced by the decreased pyruvate carboxylation versus pyruvate dehydrogenation ratio both in cerebrum and subcortex. Comparison between convulsive and nonconvulsive doses of PTZ lead to the hypothesis that changes observed in the cerebellum are mainly due to seizures, whereas those in cerebrum and subcortex are coupled to the action of the chemical stimulant.     

POSaM: a fast,flexible, open-source,inkjet oligonucleotide synthesizer and microarrayer

DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo. We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays.