A comparison of numerical approaches to the solution of the time-dependent Schrödinger equation in one dimension.

We present a simple, one-dimensional model of an atom exposed to a time-dependent intense, short-pulse EM field with the objective of teaching undergraduates how to apply various numerical methods to study the behavior of this system as it evolves in time using several time propagation schemes.In this model, the exact Coulomb potential is replaced by a soft-core interaction to avoid the singularity at the origin. While the model has some drawbacks, it has been shown to be a reasonable representation of what occurs in the fully three-dimensional hydrogen atom.The model can be used as a tool to train undergraduate physics majors in the art of computation and software development. PROGRAM SUMMARY: Program Title:: 1d hydrogen light interactionProgram Files doi:: http://dx.doi.org/10.17632/2275fmvdzc.1Code Ocean Capsule:: https://doi.org/10.24433/CO.1476487.v1Licensing provisions:: MIT licenseProgramming language:: FORTRAN90Nature of problem:: The one dimensional time dependent Schrödinger equation has been shown to be quite useful as a model to study the Hydrogen atom exposed to an intense, short pulse, electromagnetic field. We use a model potential that is cut-off near x = 0 and avoids the singularity of the true 1-D potential, but retains the characteristic Rydberg series and continuum to study excitation and ionization of the true H atom. The code employs a number of numerical methods to understand and compare the efficacy and accuracy when applied to this model problem.Solution method:: The program uses and contrasts a number of approaches; the Crank-Nicolson, Short Iterative Lanczos, various incarnations of the split-operator and the Chebychev method have been programmed. These methods have been compared using a 3-point finite difference (FD) discretization of the space coordinate. For completeness, some attention has also been given to using 5-9 FD formulas in order to show how higher order discretization affects the accuracy and efficiency of the methods but the primary focus of the method is the time propagation.Additional comments including restrictions and unusual features:: The main purpose of this code is as a teaching tool for undergraduates interested in acquiring knowledge of numerical methods and programming skills useful to a practicing computational physicist.

Molecular cloning and characterisation of DESC4, a new transmembrane serine protease.

Type II transmembrane serine proteases (TTSPs) are a growing family of multidomain proteins. Among the TTSPs, a new subfamily of HAT/DESC1-like ( human airway trypsin-like protease/ differentially expressed in squamous cell carcinoma gene 1) proteases is emerging consisting so far of four members: DESC1-3 and HAT. The cDNA of a new member of this subfamily, named DESC4, was isolated from rat tongue tissue and characterised. Analysis of selected tissues by RT-PCR demonstrated expression of DESC4 in brain, colon, heart, liver, lung and tongue. At the cellular level, DESC4 expression is confined to epithelial cells within the cleft of the circumvallate papillae extending into the ducts of minor salivary glands, the respiratory epithelium of the nasal cavity and tear gland ducts of the eyes as analysed by in situ hybridisation of sensory organ tissues. In transfected mammalian cells, DESC4 is localised to the plasma membrane as shown by immunocytochemistry and subcellular fractionation experiments. Our results suggest that we have identified a protease that is an important constituent of sensory systems and other organs.

Identification and tissue distribution of novel KET/p63 splice variants.

The human p53 protein family comprises three members - p53, p63 and p73. Whereas only one p53 variant is known multiple isoforms of p63 and p73 have been described. Depending on the isoform p63 influences p53-responsive genes in a p53-like or -distinct manner. We have cloned multiple splice variants of keratinocyte transcription factor (KET), the rat ortholog of human p63. Several tissue specific variations of exon 1 resulting in different amino-terminal ends were identified. Transactivation properties of the splice variants inversely correlated with the length of the N-termini as determined by activation of the p53-responsive p21 promotor. Multiple KET isoforms are colocalized in different rat tissues. The amino-terminal truncated form DeltaNKETalpha is expressed in epithelial tissues, while expression of the most p53-like KET isotype TAKETgamma was detected in skeletal muscle. Expression of a major KET variant appears to be a cell-type specific rather than a differentiation specific phenomenon.

Induction of membrane chloride currents in Xenopus laevis oocytes by the sulfonyl amide sweeteners acesulfame K and saccharin.

Sweet receptors have remained elusive. In Xenopus oocytes sulfonyl amide sweeteners but not sweet compounds belonging to other chemical classes dose dependently induced membrane chloride currents via the inositol trisphosphate/calcium pathway. Induction of membrane currents was exclusively observed following extracellular application of sulfonyl amides but not by intracellular pressure injection, suggesting the involvement of a plasma membrane receptor. The presence of this receptor in oocytes and the observed seasonal variation of the sweet response offers an opportunity for a molecular cloning approach.

Cloning and chromosomal mapping of the human p53-related KET gene to chromosome 3q27 and its murine homolog Ket to mouse chromosome 16.

KET is a member of the newly discovered family of proteins that is related to the tumor suppressor p53. Here we describe the molecular cloning of a human cDNA of 4846 bp encoding a protein of 680 amino acids. The human KET protein shares 98% identity with the previously characterized rat homolog. The remarkably high degree of conservation lends support to the notion that KET proteins have important basic functions in development and differentiation. Using the GeneBridge 4 radiation hybrid panel, we have mapped KET to human Chromosome (Chr) 3q27. KET is located between the somatostatin gene SST (proximal) and the apolipoprotein D gene APOD (distal) in a region of conserved synteny to mouse Chr 16. This chromosomal region is deleted in early stages of tumorigenesis of mouse islet cell carcinomas and contains the hitherto unidentified Loh2 gene, a putative suppressor of angiogenesis. The murine homolog Ket was mapped in an interspecific backcross panel and falls into this region of loss of heterozygosity. From our mapping data we infer that KET might act as a tumor suppressor and is considered as a candidate for Loh2.

Cloning of the alphaA-crystallin genes of a blind cave form and the epigean form of Astyanax fasciatus: a comparative analysis of structure, expression and evolutionary conservation.

In the present study we have analyzed the integrity and expression of the alphaA-crystallin gene, that codes for a major structural component of the lens, in a blind cave form of the teleostean fish, Astyanax fasciatus. This is the first alphaA-crystallin gene cloned from a teleostean fish. Sequence comparison of this cave-form gene with its epigean conspecific and with homologs of distantly related taxa has illustrated conservation of regulatory and coding regions. Although no crystallin proteins are produced in the lens of the cave form, and the mRNA of this gene could not be detected by in situ hybridization of different developmental stages, the promoter region of cave-fish alphaA-crystallin is functionally intact. The deduced amino-acid sequence of the alphaA-crystallin gene of the cave form differs from that of its epigean conspecific at only one position (139). This is within an important, small heat-shock protein-related region, HCR2. A comparison of the 5'-flanking regions of the A. fasciatus alphaA-crystallin gene with the chicken homolog revealed the high conservation of lens-specific regulatory sequences and further demonstrates the evolutionary conservation of this gene. 1988 Elsevier Science B.V.

A novel protein with strong homology to the tumor suppressor p53.

The p53 tumor suppressor orchestrates a number of important genes involved in cell-cycle control and apoptosis. Mice deficient for p53 show a high incidence of cancer but are developmentally normal suggesting that compensatory mechanisms exist in embryogenesis and differentiation. The new KET protein is the first mammalian protein with strong homology to p53 in all evolutionary conserved regions. This conservation makes a functional redundancy of the two proteins in cell-cycle control possible. KET is expressed during embryonic development and in certain adult tissues. Among all of the known p53 proteins of different species KET is most closely related to that found in squid. The relationship between KET and the invertebrate p53 protein sheds light on the evolutionary origin of p53. KET appears to be an ancestral p53-related protein in vertebrates with a possible role in development and differentiation while the ubiquitously expressed p53 protein attained its general role as 'guardian of the genome' during evolution.

Comparative analysis of Pax-6 sequence and expression in the eye development of the blind cave fish Astyanax fasciatus and its epigean conspecific.

The Pax-6 gene encodes a transcription factor essential for eye development in a wide range of animal phyla. In order to elucidate a possible role of Pax-6 in the eye regression of a blind cave form of the freshwater fish Astyanax fasciatus (Characidae, Teleostei) we investigated the expression of Pax-6 in eyes and brains of different larval stages by in situ hybridization. Pattern, strength, and time course of Pax-6 expression were not altered in the tissues of the cave form when compared to the epigean form. Pax-6 was even expressed in the highly degenerated eyes of late larval stages of the cave form. Comparative sequence analysis of Pax-6 cDNA clones of both forms of Astyanax fasciatus showed the complete integrity of cave fish Pax-6 mRNA. These results suggest that Pax-6 is not involved in the evolutionary process of eye degeneration in this model system of cave-living fishes. Comparison of the Astyanax Pax-6 cDNA with the other available fish Pax-6 sequence from zebrafish revealed putative fish-specific regions of homology. A stretch of 19 N-terminal amino acids is nearly identical on the nucleotide and amino acid levels in both fish species but not present in all other known Pax-6 sequences.

Heterologous expression of human vasopressin-neurophysin precursors in a pituitary cell line: defective transport of a mutant protein from patients with familial diabetes insipidus.

Familial hypothalamic diabetes insipidus is an autosomal dominant disorder characterized by deficient vasopressin synthesis. Different point mutations in the vasopressin-neurophysin (VP-NP) precursor gene have been found in affected families. In a Dutch kindred, a single G to T transversion in the NP-encoding exon B of one allele converts the highly conserved glycine 17 to a valine residue. In order to examine whether this point mutation affects the processing and transport of the VP-NP precursor, the normal (HV2) and mutant (MT6) vasopressin cDNAs were stably expressed in the mouse pituitary cell line AtT20. The normal precursor was correctly glycosylated and processed, and NP was detected in the culture medium. Secretion of NP was stimulated by 8-bromo-cAMP, indicating that the normal precursor was targeted to the regulated secretory pathway. In contrast, the mutant precursor was synthesized, but processing and secretion were dramatically reduced. The mutant precursor was core-glycosylated but remained endoglycosidase H-sensitive, suggesting that the protein did not reach the trans-Golgi network. These results were supported by immunocytochemical studies. In HV2 cells, NP derived from the precursor was concentrated in the tips of the cell processes where secretory granules accumulate. In MT6 cells, NP staining was restricted to the endoplasmic reticulum (ER) as determined by colocalization with an ER-resident protein, BiP. These results suggest that the mutation within the conserved part of NP alters the conformation of the precursor and thus triggers its retention in the ER.

Porcine VEG proteins and tear prealbumins.

Small soluble proteins, belonging to the lipocalin family are secreted in large amounts by tongue von Ebner's glands and lachrymal glands. In humans, the lingual protein, called VEG, and the lachrymal protein, called tear prealbumin, have shown identical cDNA sequences. In the pig, we have purified homodimeric proteins with subunits of 17 kDa, both from von Ebner's glands and from lachrymal glands. In both cases, the proteins can be resolved into two isoforms on a chromatofocusing column. Partial aminoacid sequences and full cDNA sequences have been obtained for the more abundant forms purified from both tissues. The two proteins appear to be identical, as in humans. The reason why the same protein is expressed in different tissues, as well as its physiological function, still remain to be clarified.

Denatonium bitter tasting among transgenic mice expressing rat von Ebner's gland protein.

Von Ebner's gland protein (VEGP) is a secretory protein, which is abundantly expressed in the small von Ebner's salivary glands of the tongue. VEGP as component of the perireceptor environment around taste papillae might function as transporter of hydrophobic molecules, for example bitter substances. Here we report a new approach to investigate the physiological role of VEGP by expression of the cloned rat VEGP gene in transgenic mice. Taste papillae of mice, in contrast to rats, do not contain VEGP. The founder mouse 4345 and three offspring carry the transgene as shown by PCR analysis and saliva of the transgenic mice contains high amounts of VEGP. In two-bottle preference tests, transgenic and nontransgenic siblings show significantly different capabilities to taste the bitter compound denatonium benzoate at 10 microM. The reduced sensitivity of transgenic mice to denatonium benzoate points to a clearance function of VEGP the specificity of which for taste compounds and other molecules remains to be seen.

Structural organization of the genes for rat von Ebner's gland proteins 1 and 2 reveals their close relationship to lipocalins.

The rat von Ebner's gland protein 1 (VEGP 1) is a secretory protein, which is abundantly expressed in the small acinar von Ebner's salivary glands of the tongue. Based on the primary structure of this protein we have previously suggested that it is a member of the lipocalin superfamily of lipophilic-ligand carrier proteins. Although the physiological role of VEGP 1 is not clear, it might be involved in sensory or protective functions in the taste epithelium. Here, we report the purification of VEGP 1 and of a closely related secretory polypeptide, VEGP 2, the isolation of a cDNA clone encoding VEGP 2, and the isolation and structural characterization of the genes for both proteins. Protein purification by gel-filtration and anion-exchange chromatography using Mono Q revealed the presence of two different immunoreactive VEGP species. N-terminal sequence determination of peptide fragments isolated after protease Asp-N digestion allowed the identification of a new VEGP, named VEGP 2, in addition to the previously characterized VEGP 1. The complete VEGP 2 sequence was deduced from a cDNA clone isolated from a von Ebner's gland cDNA library. The VEGP 2 cDNA encodes a protein of 177 amino acids and is 94% identical to VEGP 1. DNA sequence analysis of the rat VEGP 1 and 2 genes isolated from rat genomic libraries revealed that both span about 4.5 kb and contain seven exons. The VEGP 1 and 2 genes are non-allelic distinct genes in the rat genome and probably arose by gene duplication. The high degree of nucleotide sequence identity in introns A-C (94-100%) points to a recent gene conversion event that included the 5' part of the genes. The genomic organization of the rat VEGP genes closely resembles that found in other lipocalins such as beta-lactoglobulin, mouse urinary proteins (MUPs) and prostaglandin D synthase, and therefore provides clear evidence that VEGPs belong to this superfamily of proteins.

Protein analysis of human von Ebner saliva and a method for its collection from the foliate papillae.

The lingual serous glands of von Ebner are located close to the foliate and circumvallate papillae. Saliva secreted by these glands provides the immediate environment of the taste buds, and it has been hypothesized that it modulates taste perception. The purpose of this study was to develop a technique for collection of unstimulated and stimulated saliva from human von Ebner glands. Saliva was collected under resting conditions and after application of various gustatory stimuli (sweet, sour, salt, and bitter) by insertion of periostrips into the folds of the foliate papillae of healthy human volunteers. Stimulated saliva was also collected in glass microcapillaries or micropipettes. The flow-rates of unstimulated von Ebner saliva were 2.3 +/- 0.6 (S.E.) microL/min and 4.5 +/- 1.2 (S.E.) microL/min with 1% citric acid stimulation. The protein content was 2.5 +/- 0.5 (S.E.) mg/mL. The SDS gel electrophoretic profile of von Ebner saliva revealed two protein bands of Mr 18,000 that were identified on Western blots as von Ebner gland (VEG) proteins. Although lingual lipase activity was detected at very low levels by enzyme assay, this protein was not detected on Western blots. This collection technique should prove useful for analysis of specific functions associated with secretion from von Ebner glands.

Molecular cloning of human von Ebner's gland protein, a member of the lipocalin superfamily highly expressed in lingual salivary glands.

Von Ebner's glands (VEG) are small lingual salivary glands. Their ducts open into trenches of circumvallate and foliate papillae, thus influencing the milieu where the interaction between taste receptor cells and sapid molecules takes place. The major secretions of human VEG is a protein with a molecular mass of 18 kDa. The human VEG protein crossreacts with antibodies raised against the rat VEG protein, indicating sequence similarity between the rat and human VEG proteins. This was subsequently confirmed by N-terminal protein sequencing. A cDNA clone, isolated from a human VEG library, contained an insert of 735 bp including an open reading frame that encodes the human VEG protein of 176 amino acids. Comparison of the human and rat VEG proteins revealed an overall identity of 60%. Immunocytochemistry, in situ hybridization and in vitro translation studies demonstrated the human VEG protein to be highly and exclusively expressed in VEG. The VEG proteins are members of the lipocalin protein superfamily and, together with the rat odorant binding protein II, they constitute a new subfamily. Sequence similarity to proteins such as the retinol binding protein and the odorant binding protein which are lipophilic ligand carriers, suggests a possible function for the human VEG protein in taste perception.

Perireceptor events in taste.

The microenvironment at chemical receptor sites is important for ligand-receptor interaction as it can influence the entry, residence time or exit of odorant and sapid molecules. The perireceptor milieu at apical taste cell microvilli consists of taste pore mucus and secretions from salivary glands. The majority of taste buds are sheltered in epithelial folds of the foliate and circumvallate papillae where saliva is provided predominantly by the lingual von Ebner's glands (VEGs). To investigate possible saliva-tastant interactions, we have characterized a prominent 18 kDa secretory protein expressed in human, rat and pig VEGs. The human and rat VEG proteins share 60% sequence identity and, by virtue of their protein and gene structure, can be assigned to the lipocalin superfamily of lipophilic ligand carrier proteins. VEG proteins might function as transporters of hydrophobic molecules, for example bitter substances, like the nasal odorant-binding proteins that belong to the same protein family. Because binding experiments using various bitter substances have so far failed, and in light of the species-specific expression, other functions for VEG proteins must be considered. These include the protection of taste epithelia, pheromone transport and lipid binding.

Postnatal development of von Ebner's glands: accumulation of a protein of the lipocalin superfamily in taste papillae of rat tongue.

Antibodies produced against rat von Ebner's gland (VEG) protein, a recently characterized member of a lipophilic ligand carrier protein family, detect this protein immunocytochemically in von Ebner's gland acini and show that it is present at high concentrations in the clefts of circumvallate and foliate papillae. During embryonic development, von Ebner's gland anlagen are innervated (as shown immunocytochemically using neuronal specific antibodies) as early as embryonic day 20, before lateral glandular outgrowth and VEG protein can be observed. Expression of the VEG protein as determined by in situ hybridization and immunocytochemistry begins at postnatal day-2 cells in differentiating and branching off from von Ebner's gland ducts, and sharply increases with further enlargement and maturation of the gland. The close temporal correlation of von Ebner's gland innervation and VEG protein expression with papilla innervation and taste-bud development suggests a functional relationship of both structures. VEG protein might control access of lipophilic sapid molecules, such as bitter substances, to the gustatory receptors.

A missense mutation in the vasopressin-neurophysin precursor gene cosegregates with human autosomal dominant neurohypophyseal diabetes insipidus.

Familial neurohypophyseal diabetes insipidus in humans is a rare disease transmitted as an autosomal dominant trait. Affected individuals have very low or undetectable levels of circulating vasopressin and suffer from polydipsia and polyuria. An obvious candidate gene for the disease is the vasopressin-neurophysin (AVP-NP) precursor gene on human chromosome 20. The 2 kb gene with three exons encodes a composite precursor protein consisting of the neuropeptide vasopressin and two associated proteins, neurophysin and a glycopeptide. Cloning and nucleotide sequence analysis of both alleles of the AVP-NP gene present in a Dutch ADNDI family reveals a point mutation in one allele of the affected family members. Comparison of the nucleotide sequences shows a G----T transversion within the neurophysin-encoding exon B. This missense mutation converts a highly conserved glycine (Gly17 of neurophysin) to a valine residue. RFLP analysis of six related family members indicates cosegregation of the mutant allele with the DI phenotype. The mutation is not present in 96 chromosomes of an unrelated control group. These data suggest that a single amino acid exchange within a highly conserved domain of the human vasopressin-associated neurophysin is the primary cause of one form of ADNDI.

Regulation of vasopressin expression in cultured diencephalic neurons by glucocorticoids.

Glucocorticoids have long been recognized as playing a major role in the regulation of vasopressin synthesis. However, the factors determining cellular specificity and molecular mechanisms of glucocorticoid action on the vasopressin gene are not understood. In the present investigation, we used primary cell cultures derived from 14-day-old fetal rat diencephalon to investigate the regulation of vasopressin expression under controlled conditions. The experimental paradigm used ensured that only magnocellular, but not parvocellular neurons grew in the cultures. The following criteria were used to establish this phenotype. (1) Cultures were derived from fetal brain well before the time parvocellular neurons are generated, and neuronal precursors did not proliferate in vitro. (2) Vasopressinergic neurons measured some 18 x 25 microns, being conspicuously larger than the average neuronal population in vitro, and clearly larger than parvocellular neurons in vivo. (3) Neurons did not express corticotropin releasing factor in vitro. Selective neutralization of glucocorticoids contained in the serum-supplemented culture medium by the drug RU 38 486 resulted in an about 2-fold increase of numbers of vasopressinergic cells and about 4-fold increase in vasopressin mRNA, but did not affect numbers of oxytocinergic neurons or expression of general neuronal marker proteins. The effects of RU 38,486 were not dependent on synaptic communication between cultured cells, as the drug was still effective when cells were synaptically isolated by growth is in 14 mM Mg2+. RU was not mitogenic for vasopressinergic neurons.(ABSTRACT TRUNCATED AT 250 WORDS)

Possible role for salivary gland protein in taste reception indicated by homology to lipophilic-ligand carrier proteins.

Sensory transduction in taste and olfaction, the principal chemical senses, seems to be mediated by membrane-associated proteins on the apical surfaces of the respective receptor cells. The recent isolation and characterization of soluble 'odorant-binding proteins' secreted from the nasal glands of rat, cow and frog, led to the hypothesis that these proteins function as necessary cofactors in olfactory transduction by concentrating and delivering odorants to the receptors. The primary reception of taste stimuli occurs in specialized neuroepithelial receptor cells bundled in taste buds that are clustered in various types of papillae in the lingual epithelium of the tongue. Small tubulo-alveolar salivary glands, the von Ebner's glands, are located beneath the circumvallate and the foliate papillae. Their ducts open exclusively into the trough at the base of the papillae. Taste buds located in the medial and lateral walls of the papillae open with their taste pores into the trough and consequently are in direct contact with the secretions of von Ebner's glands. Here we report the molecular cloning and characterization of a protein of relative molecular mass 18,000 that is highly expressed in von Ebner's glands. Like the odorant-binding proteins, this protein shows similarity to members of a protein superfamily of hydrophobic molecule transporters, indicating that pre-receptor events could also be necessary for the concentration and delivery of sapid molecules in the gustatory system, and emphasizing the close relationship of taste and olfaction.