The PROSITE database, its status in 1995.

The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of proteins (if any) a new sequence belongs or which known domain(s) it contains.     

The PROSITE database, its status in 1997.

The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein (if any) a new sequence belongs, or which known domain(s) it contains.     

Isolation and characterization of a novel gene containing WD40 repeats from the region deleted in velo-cardio-facial/DiGeorge syndrome on chromosome 22q11

Three congenital disorders, cat-eye syndrome (CES), der(22) syndrome, and velo-cardio-facial syndrome/DiGeorge syndrome (VCFS/DGS), result from tetrasomy, trisomy, and monosomy, respectively, of part of 22q11. They share a 1.5-Mb region of overlap, which contains 24 known genes. Although the region has been sequenced and extensively analyzed, it is expected to contain additional genes, which have thus far escaped identification. To understand completely the molecular etiology of VCFS/DGS, der(22) syndrome, and CES, it is essential to isolate all genes in the interval. We have identified and characterized a novel human gene, located within the 1.5-Mb region deleted in VCFS/DGS, trisomic in der(22) syndrome and tetrasomic in CES. The deduced amino acid sequence of the human gene and its mouse homologue contain several WD40 repeats, but lack homology to known proteins. We termed this gene WDR14 (WD40 repeat-containing gene deleted in VCFS). It is expressed in a variety of human and mouse adult and fetal tissues with substantial expression levels in the adult thymus, an organ hypoplastic in VCFS/DGS.     

Recessive yellow in the Mongolian gerbil (Meriones unguiculatus)

A new autosomal recessive coat color mutant in the Mongolian gerbil (Meriones unguiculatus) is described: recessive yellow. On the dorsal side the mutant has a rich yellow to ginger color. Ventrally it shows the typical creamy white belly of a wild-type Mongolian gerbil. The dorsal yellow hairs have short black tips, and a light olive green base. A clear demarcation line between dorsal and ventral color is present. Crosses between recessive yellow animals and multiple homozygous recessive tester animals (a/a; c^chm/c^chm; g/g; p/p) resulted only in animals of an agouti (wild-type) phenotype, showing that the new allele is not allelic with any of the known coat color mutations in the Mongolian gerbil. Molecular studies showed that the new mutant is caused by a missence mutation at the extension (E) locus. On a non-agouti background (a/a; e/e) mutant animals look like a dark wild-type agouti. In contrast to wild-type agouti it shows yellow pigmentation and dark ticking at the ventral side, resulting in the absence of a demarcation line. Since black pigment is present in both the agouti and non-agouti variant (A/A; e/e and a/a; e/e), we conclude that recessive yellow in the Mongolian gerbil is non-epistatic to agouti. Additionally we describe a second mutation at the same locus leading to a similar phenotype, however without black pigment and diminishing yellow pigment during life. Fertility and viability of both new mutants are within normal range. The extension (E) gene is known to encode the melanocortin 1 receptor (MC1R). Interestingly, this is the only gene that is known to account for substantial variation in skin and hair color in humans. Many different mutations are known of which some are associated with higher skin cancer incidence.     

The PROSITE database, its status in 2002

PROSITE [Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583–3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215–219] is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http://www.expasy.org/prosite/) consists of biologically significant patterns and profiles designed in such a way that with appropriate computational tools it can rapidly and reliably help to determine to which known family of proteins (if any) a new sequence belongs, or which known domain(s) it contains.     

An assessment of the resistance gene analogues of Oryza sativa ssp. japonica: their presence and structure

Rice is the first cereal genome of known draft sequence, and the finished sequence for it is now nearly complete. In this paper, we describe a preliminary analysis of known rice genes aimed to detect resistance gene analogues of known structural classes. Putative resistance genes were identified in a dual approach--by using BLASTP searches to identify candidate sequences and by using Hidden Markov Models to predict domain presence in the candidates. The set of proteins examined was obtained from the publicly available data of TIGR (The Institute for Genomic Research). 1744 distinct RGAs were identified, 597 of which belonged to the NBS-LRR class. Supplementary data (sequences and annotations) is available on the web site http:/gkoczyk.bioinfo.pl/CMBL.     

Isolation and expression pattern of RGS21 gene, a novel RGS member

Regulators of G-protein signaling (RGS) proteins are known for the RGS domain that is composed of a conserved stretch of 120 amino acids, which binds directly to activated G-protein alpha subunits and acts as a GTPase-activating protein (GAP), leading to their deactivation and termination of downstream signals. In this study, a novel human RGS cDNA (RGS21), 1795 bp long and encoding a 152-amino acid polypeptide, was isolated by large-scale sequencing analysis of a human fetal brain cDNA library. Unlike other RGS family members, RGS21 gene has no additional domain/motif and may represent the smallest known member of RGS family. It may belong to the B/R4 subfamily, which suggests that it may serve exclusively as a negative regulator of alphai/o family members and/or alphaq/11. PCR analysis showed that RGS21 mRNA was expressed ubiquitously in the 16 tissues examined, implying general physiological roles.     

Reactions of Hemoglobiniferous Cells to Aced and Basic Dyes under Varying Conditions of H-Ion Activity

1. An attempt has been made to apply Loeb's concept of the amphoteric nature of proteins for the discrimination of suspected hemoglobiniferous substances from known hemoglobiniferous substances according to their reactions to acid and basic dyes with reference to the isoelectric point of hemoglobin (pH 6.8).

2. The substances in the cytoplasm of known hemoglobiniferous cells (red blood corpuscles, normoblasts and erythroblasts) of the lymph nodes, spleen and bone marrow of the albino rat, when suspended in buffered dye-sucrose solutions, retain eosin on the acid side of pH 7.0, but the substances of the Russell bodies, suspected of being hemoglobiniferous, do not retain eosin at all; and the cytoplasm of the plasma cells, also alleged to be slightly hemoglobiniferous, only retains eosin on the acid side of pH 6.4.

3. The only basic dye used which did not precipitate in buffer solutions was methylene blue. This did not react with hemoglobin in accordance with Loeb's concept, because it did not penetrate mature red blood corpuscles and in those immature erythrocytes which it did penetrate it was precipitated by the reticulum.

4. Therefore, from the results obtained with the acid dye, it is tentatively concluded that the substance in the Russell bodies and in the cytoplasm of the plasma cells are not hemoglobiniferous because they do not react as do the substances in known hemoglobiniferous cells with reference to the isoelectric point of hemoglobin.

5. More investigation, however, must be carried out on both fresh and fixed material before a final unequivocal answer can be made to this problem.     

Contribution of invasive species Spartina alterniflora to soil organic carbon pool in coastal wetland: Stable isotope approach

Spartina alterniflora was introduced into China because of its strong sedimentation promotion ability, currently, it became one of the most invasive species along coastal areas. Most researches focused on its high productivity which directly increased soil carbon (C) input. However, little is known about its indirect contribution to soil carbon via increased sedimentation.     

A new role for ATM in selective autophagy of peroxisomes (pexophagy)

Peroxisomes are autonomously replicating and highly metabolic organelles necessary for β-oxidation of fatty acids, a process that generates large amounts of reactive oxygen species (ROS). Maintaining a balance between biogenesis and degradation of peroxisomes is essential to maintain cellular redox balance, but how cells do this has remained somewhat of a mystery. While it is known that peroxisomes can be degraded via selective autophagy (pexophagy), little is known about how mammalian cells regulate pexophagy to maintain peroxisome homeostasis. We have uncovered a mechanism for regulating pexophagy in mammalian cells that defines a new role for ATM (ATM serine/threonine kinase) kinase as a “first responder” to peroxisomal ROS. ATM is delivered to the peroxisome by the PEX5 import receptor, which recognizes an SRL sequence located at the C terminus of ATM to localize this kinase to peroxisomes. In response to ROS, the ATM kinase is activated and performs 2 functions: i) it signals to AMPK, which activates TSC2 to suppresses MTORC1 and phosphorylates ULK1 to induce autophagy, and ii) targets specific peroxisomes for pexophagy by phosphorylating PEX5 at Ser141, which triggers ubiquitnation of PEX5 at Lys209 and binding of the autophagy receptor protein SQSTM1/p62 to induce pexophagy.     

Controls on calcium ion fluxes in injured or shocked corn root cells: Importance of proton pumping and cell membrane potential

Passive influx of ⁴⁵Ca²⁺ into non-growing corn root tissue ( Zea mays L.) was increased as a result of actions (cutting, rubbing, chilling, heating, acidifying) or agents (cyanide, uncouplers) known to depolarize the cell membrane, and was decreased by actions (washing) or agents (fusicoccin) known to hyperpolarize it. These responses indicate the presence of Ca²⁺ channels which are voltage controlled. If the injuries were extensive, however, voltage control was lost and hyperpolarization with fusicoccin was expressed by increased ⁴⁵Ca²⁺ influx. Control could be regained by tissue washing, and millimolar levels of external Ca²⁺ would protect against loss of control. Influx of Ca²⁺ was strongly inhibited by La³⁺, but only weakly by verapamil. Intact roots showed greater cold shock sensitivity in maturing cells than in growing cells. We conclude that corn roots normally restrict Ca²⁺ influx by a mechanism linked to hyper-polarization of the plasmalemma.
Calcium ions which enter cold-shocked tissue are partially extruded during the early phase of recovery by a process stimulated by fusicoccin and subject to uncoupling.     

The effect of neurotensin and secretin on gastric acid secretion and mucosal blood flow in man

Neurotensin stimulates pancreatic secretion directly and by potentiating the effect of secretin. Neurotensin also inhibits gastric secretion. Secretin inhibits gastric secretion as well, but whether it also interacts with neurotensin is not known. Secretin is known to inhibit gastric mucosal blood flow (GMBF). The effect of neurotensin on GMBF is not known. Acid secretion (triple lumen perfused orogastric tube) and GMBF ([14C]aminopyrine clearance) were therefore measured in 6 subjects during neurotensin, secretin and neurotensin plus secretin infusions. Neurotensin plus secretin reduced acid secretion by a median 130 (range 34-394) mumol/min which was significantly greater than either neurotensin at 36 (7-67) mumol/min or secretin 54 (20-347) mumol/min alone (P less than 0.05). This effect appeared independent of GMBF. Neurotensin plus secretin reduced GMBF by 14 (12-27) ml/min but not significantly more than neurotensin at 11 (3-20) ml/min or secretin 18 (2-27) ml/min alone. Further, there was no correlation between changes in acid output and GMBF during infusion of the peptides. We conclude that the inhibitory effects of neurotensin and secretin on gastric secretion are at least additive and together they may function as an 'enterogastrone'.     

History of safe exposure and bioinformatic assessment of phosphomannose-isomerase (PMI) for allergenic risk

Newly expressed proteins in genetically engineered crops are evaluated for potential cross reactivity to known allergens as part of their safety assessment. This assessment uses a weight-of-evidence approach. Two key components of this allergenicity assessment include any history of safe human exposure to the protein and/or the source organism from which it was originally derived, and bioinformatic analysis identifying amino acid sequence relatedness to known allergens. Phosphomannose-isomerase (PMI) has been expressed in commercialized genetically engineered (GE) crops as a selectable marker since 2010 with no known reports of allergy, which supports a history of safe exposure, and GE events expressing the PMI protein have been approved globally based on expert safety analysis. Bioinformatic analyses identified an eight-amino-acid contiguous match between PMI and a frog parvalbumin allergen (CAC83047.1). While short amino acid matches have been shown to be a poor predictor of allergen cross reactivity, most regulatory bodies require such matches be assessed in support of the allergenicity risk assessment. Here, this match is shown to be of negligible risk of conferring cross reactivity with known allergens.

     

Effect of various environmental illumination modalities on the muricidal behavior of male Wistar rats

The aim of this research is to study the effects of different modalities of environment lighting on the appearance of the muricide behaviour in the Wistar male Rat. Indeed it is known that the exposition of Rats in environment to continuous light determine a reduction of the cerebral content of serotonin, which is known to unchain the muricide behaviour in naturally not muricide Rats. The animals are kept in different situations of environment lighting: 1) L/D = the natural light of the day alternated with the dark of the night; 2) L/L sodium = continuous light emitted by a sodium steam lamp; 3) L/L neon = continuous light issued from fluorescent neon tubes. The muricide behaviour is studied by comparison Rat-Mouse. The results obtained show that the continuous sodium steam light (L/L, sodium) remarkably increase the percentage of the animals which become muricide compared to the control animals bred in natural environment with a normal succession day-night (L/D). On the contrary the percentage is remarkably reduced compared to the control animals in Rats of the same group when these animals are exposed to continuous light issued from fluorescent neon tubes (L/L, neon).     

Molecular cloning and characterization of two novel pro-apoptotic isoforms of caspase-10

Caspase-10/a (Mch4) and caspase-10/b (FLICE2) are related death effector domain-containing cysteine aspartases presumed to be at or near the apex of apoptotic signaling pathways. We report the cloning and characterization of two novel proteins that are splice isoforms of the caspase-10 family. Caspase-10/c is a truncated protein that is essentially a prodomain-only form of the caspase that lacks proteolytic activity in vitro but efficiently induces the formation of perinuclear filamentous structures and cell death in vivo. Caspase-10/c mRNA is specifically up-regulated upon TNF stimulation, suggesting a potential role of this isoform in amplifying the apoptotic response to extracellular stimuli such as cytokines. Caspase-10/d is a hybrid of the known caspases Mch4 and FLICE2, as it is identical to FLICE2 except for the small (p12) catalytic subunit, which is identical to Mch4. Caspase-10/d is proteolytically active in vitro and also induces cell death in vivo, although it is less active than Mch4. The mRNAs for all known isoforms of caspase-10 are abundantly expressed in fetal lung, kidney, and skeletal muscle but are very poorly expressed or absent in these tissues in the adult, implying a possible role for the caspase-10 family in fetal development.     

Some peculiar synaptic complexes in the first visual ganglion of the fly,Musca domestica

Summary In the lamina ganglionaris, the first optic ganglion of the fly, the inventory of cell types as well as the patterns of their connections are well known from light microscopic investigations. Even the synaptic contacts are known with relative completeness. However, the structural details visible on electron micrographs are very difficult to interpret in functional terms. This paper concentrates on two aspects: 1) the synaptic complex between a retinula cell axon and four postsynaptic elements, arranged in a constant elongated array (it is suggested that all synapses in which the retinula cell is presynaptic are of this kind), and 2) the gnarl complex in which a presynaptic specialization in one neuron is separated from another neuron by a complicated glial invagination. The participation of glia at postsynaptic sites seems to be quite common in this ganglion. Occasionally it seems that a glia cell is the only postsynaptic partner facing a presynaptic specialization within a neuron.     

Autotaxin (ATX): a multi-functional and multi-modular protein possessing enzymatic lysoPLD activity and matricellular properties

Recent studies have established that autotaxin (ATX), also known as phosphodiesterase Ialpha/autotaxin (PD-Ialpha/ATX) or (ecto)nucleotide pyrophosphatase/phosphodiesterase 2 [(E)NPP2], represents a multi-functional and multi-modular protein. ATX was initially thought to function exclusively as a phosphodiesterase/pyrophosphatase. However, it has become apparent that this enzymatically active site, which is ultimately responsible for ATX's originally discovered property of tumor cell motility stimulation, mediates the conversion of lysophosphatidylcholine (LPC) to lysophosphatidic acid (LPA). In addition, a separate functionally active domain, here referred to as the Modulator of Oligodendrocyte Remodeling and Focal adhesion Organization (MORFO) domain, was discovered in studies analyzing the role of ATX during the differentiation of myelinating cells of the central nervous system (CNS), namely oligodendrocytes. This novel domain was found to mediate anti-adhesive, i.e. matricellular, properties and to promote morphological maturation of oligodendrocytes. In this review, we summarize our current understanding of ATX's structure-function domains and discuss their contribution to the presently known main functional roles of ATX.