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At least 199 records · Page 11Linked to original sources
PubMed2002

The human-specific Yp11.2/Xq21.3 homology block encodes a potentially functional testis-specific TGIF-like retroposon.

Yp11.2/Xq21.3 is a human-specific homology block that constitutes the largest shared region among the sex chromosomes, spanning some 3.5 Mb. Only two transcribed sequences have been mapped to this segment: the protocadherin genes PCDHX/Y, and the X-linked poly(A)-binding protein PABPC5 gene, whose Y-homolog has been lost during human evolution. This paper reports the genomic structure, expression, and evolutionary conservation of a third (X-Y homologous) transcribed sequence, TGIFLX/Y (TGIF-like X/Y), mapping to this region. TGIFLX/Y has a 2666-bp mRNA encoded by two exons separated by a 96-bp intron. TGIFLX/Y are homeodomain-containing genes related to the TALE superclass gene family. Comparative DNA analysis indicates that TGIFLX originated from retrotransposition of TGIF2, located on 20q11.2-12, onto the X Chromosome. RT-PCR analysis reveals that both X- and Y-linked genes are specifically expressed in adult testis. Cloning and sequencing of TGIFLX homologs in hominoids and Old World monkeys provides evidence for an open reading frame in the eight species studied. Interestingly, a single base pair deletion in the human TGIFLY (as compared with TGIFLX) creates a different reading frame where the C-terminal residues shared by TGIFLX and other TGIF proteins are missing. The conservation, similarity to protein-encoding transcription factors, and specific expression in testis points to a transcriptional role for TGIFLX/Y in this tissue.

Amino Acid Sequence↗
PubMed2002

The naris muscles in tiger salamander. I. Potential functions and innervation as revealed by biocytin tracing.

The naris constrictor muscle, along with naris dilator and naris accessory muscles, controls the opening and closing of the external naris in tiger salamanders. It has been hypothesized that contraction of the naris constrictor muscle also causes the external nasal gland to secrete its contents inside the lateral wall of the external naris opening. This location is just rostral to vomeronasal organ and thus secretion in this region may be important for access of odorous compounds to vomeronasal organ. Little is known about the innervation of the naris muscles. To elucidate the neural control of these muscles, their innervation was examined using retrograde tract tracing with biocytin. Following application of biocytin to the naris constrictor muscle, labeling was observed in a ventral axonal plexus of the palatine nerve and numerous neuronal cell bodies distributed along this peripheral nerve plexus and within the main portion of the palatine ganglion. If the naris accessory and/or dilator muscles were also exposed to the tracer, the lateral-most branch of the palatine nerve and its associated neural cell bodies were labeled. To confirm the functional innervation of the muscles by the palatine nerve, the nerve was cut and the contraction of the muscles was eliminated. These findings demonstrate that the muscles controlling the external naris are under the control of palatine ganglion neurons. We hypothesize that this innervation of the naris constrictor muscle controls both muscle contraction and glandular secretion that may facilitate access of chemosensory substances to the vomeronasal organ.

Ambystoma↗
PubMed2003

Theoretical potential functions and vibrational analysis for halocarbonyl azides CXO-NNN (X=F, Cl and Br).

The structural stability of halocarbonyl azides CXO-NNN (X=F, Cl and Br) was investigated by DFT and MP2 calculations using the 6-311++G** basis set. From the calculations, the molecules were found to have an s-cis<--> s-trans conformational equilibrium with cis being the lower -energy form. Full energy optimizations were carried out for the transition states and the minima at the B3LYP/6 -311++G** and MP2/6 -311++G** levels, from which the rotational barriers were calculated to be of the order 8-10 kcal x mol(-1). The vibrational frequencies were computed at the DFT -B3LYP level and the vibrational assignments for the normal modes of the stable conformers were made on the basis of normal coordinate calculations.

Azides↗
PubMed2026

Integrative Transcriptomic and Proteomic Profiling Identifies S100P as a Potential Functional Biomarker for Sessile Serrated Lesions.

BACKGROUND: Sessile serrated lesions (SSLs) account for 15% of colorectal cancers (CRCs) but detection remains difficult due to flat morphology, mucinous features, and subtle histology. AIMS: This study aimed to identify novel and functionally relevant biomarkers of SSLs using transcriptomic screening and multi-omics validation. METHODS: Paired SSL and normal mucosa specimens (n&#x2009;=&#x2009;6) underwent RNA sequencing. Differentially expressed genes (DEGs) were filtered for membrane or secretory proteins and validated across TCGA and adenoma transcriptomes. Functional significance was assessed using CRISPR dependency profiling, proteotranscriptomic concordance, pharmacogenomic sensitivity, and connectivity map analysis. RESULTS: We identified 216 upregulated genes in SSLs, including 68 encoding secretory/membrane proteins that better discriminated SSLs from controls and were enriched for adhesion and neuronal signaling while suppressing TNF&#x3b1;-NF&#x3ba;B inflammatory pathways. Cross-cohort comparison revealed five overlapping candidates between SSLs and TCGA CMS1 tumors. Among them, S100P emerged as the primary biomarker candidate, showing consistent upregulation in SSLs and CMS1 tumors while remaining low in normal mucosa and conventional adenomas. TFF1 also showed RNA-level upregulation but appeared more context-dependent. S100P demonstrated strong RNA-protein concordance in CRC cell-line profiling, supporting its detectability as a biomarker candidate. Pharmacogenomic profiling of LS411N cells revealed marked sensitivity to SN-38 and fluoropyrimidines, consistent with serrated CRC vulnerabilities. Connectivity map analysis identified perturbations, including MAPK1 and histone acetyltransferase suppression, that may reverse parts of the SSL transcriptional program. CONCLUSION: These findings prioritize S100P as a promising biomarker candidate for SSLs that warrants further validation in larger cohorts and clinically applicable platforms.

Humans↗
PubMed2006

Chemical communication in Chagas disease vectors. Source, identity, and potential function of volatiles released by the metasternal and Brindley's glands of Triatoma infestans adults.

Compounds from the metasternal and Brindley's glands of the blood-sucking bug, Triatoma infestans, were identified by solid phase microextraction (SPME) and gas chromatography-mass spectrometry. Volatile compounds released by adult bugs during copulation or after mechanical disturbance were also characterized. Six compounds were identified and found consistently in all samples from metasternal glands. The most abundant were 3-pentanone, 2-methylbutanol, 3-pentanol, and an unidentified compound. The metasternal gland blends did not differ qualitatively between sexes. Compounds found in Brindley's glands were short chain acids, alcohols, esters, and a ketone with no qualitative differences between sexes. Isobutyric acid was the main component of this blend, and two new confirmed compounds were described as products of these glands: 2-butanone and 2-methylbutyric acid. 3-Pentanone was collected from the headspace over 33% of the copulating pairs of T. infestans. Volatiles found in the headspace of disturbed T. infestans adults included short-chain fatty acids, alcohols, esters, and ketones, with no qualitative differences between sexes. Both types of glands apparently discharge their contents after disturbance. However, most of the volatiles released by bugs after disturbance came from Brindley's glands. The locomotor activity of fourth instars increased significantly after stimulation with the odors emitted by disturbed adults, as compared with larvae stimulated by the odor of undisturbed adults or by clean air. We also studied the directional behavioral response of fifth instars to the disturbance scent in a locomotion compensator. Larvae exposed to volatiles released by disturbed adults walked away from the direction of the odor. The results suggest that this blend or part of it functions as an alarm pheromone for T. infestans. We suggest that the metasternal glands of this species are involved both in the sexual and the alarm contexts, and that the Brindley's glands probably have both alarm and defensive roles.

Animals↗
PubMed1987

Quantitation and potential function of nucleolar phosphoprotein pp 105 in mouse tumor cells, embryonic cells and normal tissues.

1. Nucleolar phosphoprotein pp 105 was determined in various mouse cell and tissue extracts using a highly sensitive ELISA. The results indicate that the highest relative amounts of pp 105 correlate with cells and tissues of high growth rate such as tumor cell lines, solid tumors and embryonic tissues. 2. The specific phosphorylation of pp 105 was compared in a 1 min endogenous phosphorylation assay with native cell and tissue extracts. 3. The mitogenic activity of highly purified pp 105 was demonstrated in cultures of resting mouse embryonic cells and mouse thymocytes.

Animals↗
PubMed1990

Cloning of a full-length cDNA encoding bovine thymus poly(ADP-ribose) synthetase: evolutionarily conserved segments and their potential functions.

The primary structure of bovine thymus poly(ADP-ribose) synthetase, as deduced from the nucleotide sequence of a cloned cDNA, indicated that this enzyme is composed of 1016 amino acids (aa) with an Mr of 113,481. An abundance of Lys and Arg residues was in accord with the known basic nature of this protein. A comparison with reported sequences of human counterparts revealed: (1) three functional domains separated by partial proteolysis, i.e., DNA-binding (N-terminal), automodification (central), and NAD-binding (C-terminal) domains, have, in this order, increasing degrees of homology; (2) the DNA-binding domain is composed of two distinct regions: one, less conserved, containing zinc-binding fingers and the other, more conserved, containing helix-turn-helix motifs; (3) all Glu and Asp residues in the automodification domain are conserved; and (4) a 78-aa stretch encompassing the nucleotide-binding fold in the NAD-binding domain is completely conserved. These results are compatible with specific features of each domain, i.e., complex DNA-enzyme interactions, multiple automodification at acidic aa residues, and a stringent specificity for the substrate, NAD.

Amino Acid Sequence↗
PubMed1994

Isolation of a potentially functional HPRT processed pseudogene from the hill kangaroo Macropus robustus.

A highly conserved hypoxanthine phosphoribosyltransferase processed pseudogene (KPH) has been isolated from a female kangaroo (Macropus robustus) lambda EMBL3 genomic library. The pseudogene contains only transcribed material with all of the introns precisely removed and has possible direct repeats at either end of the message. It has a 654-nucleotide open reading frame (ORF) from the Met start codon to the stop codon that contains no additions, deletions or premature stops relative to expressed HPRT genes and, therefore, the possibility exists that it is expressed in vivo. Possible CAAT and GC boxes are present in the region 5' to the ORF and a polyadenylation signal is present in the region 3' to the ORF. If not expressed, the age of the pseudogene is estimated to be 10.7 million years. We propose that integration into the genome occurred specifically in a homocopolymeric region within a highly repeated region unique to the kangaroo genome.

Amino Acid Sequence↗
PubMed1994

Isolation of a potentially functional Y-box protein (MSY-1) processed pseudogene from mouse: evolutionary relationships within the EF1A/dbpB/YB-1 gene family.

A processed pseudogene from Mus musculus, designated psi MSY-2, was obtained with a MSY-1 cDNA (encoding mouse Y-box factor 1) probe. Mouse psi MSY-2 is intronless and has an ORF with an in-frame translational stop. The pseudogene has repeat sequences at the 5' and 3' boundaries, suggestive of an origin as a retroposon, and exhibits mutagenesis of CpG residues at a frequency at least tenfold higher than predicted from random mutagenesis. This indicates that 'repeat-induced point mutagenesis' or ripping has occurred. We find that the mouse genome contains many DNA sequences with homology to a cDNA encoding the DNA-binding domain of the Y-box proteins. We estimate that there are at least 15 copies per haploid genome.

Animals↗
PubMed2005

Expression analysis and potential functional role of the CXCR4 chemokine receptor in bladder cancer.

OBJECTIVE: Recent analysis gave evidence for the fact that the chemokine receptor CXCR4 is of functional significance in the multistep procedure of metastasis directing tumor cells to their metastatic target organs. In our study we investigated the expression of the CXCR4 receptor on bladder cancer cells and the functional activation of the CXCR4 receptor in bladder cancer cell lines regarding signal transduction pathways, which are involved in metastasis. METHODS: Receptor transcript expression was analysed and quantified by reverse transcription PCR with RNA extracted from different samples of native human bladder cancer tissue, normal urothelium and the bladder cancer cell lines J82 and T24. Measurement of intracellular [Ca(++)](i) and analysis of intracellular stress fiber formation, chemotaxis, Matrigel invasion and proliferation were performed in the bladder cancer cell lines J82 and T24 upon stimulation with the specific agonist SDF-1. RESULTS: Specific CXCR4 receptor transcripts were detected in normal urothelium, the bladder cancer cell lines J82 and T24 and in all bladder carcinoma specimens. We did not observe a quantitative correlation of transcript expression and tumor stage. While SDF-1 did not evoke increases in [Ca(++)](i) in bladder cancer cell lines, we observed a distinct rise in intracellular stress fiber formation, chemotactic activity, invasion through Matrigel coated membranes and cell growth upon stimulation with SDF-1, which was blocked in the presence of a specific CXCR4 receptor antibody. CONCLUSION: Our results support that the chemokine receptor CXCR4 is an interesting candidate for the future investigation of metastasis of bladder cancer in vivo.

Chemokine CXCL12↗
PubMed2006

Levels of G-protein alpha q/11 subunits and of phospholipase C-beta(1-4), -gamma, and -delta1 isoforms in postmortem human brain caudate and cortical membranes: potential functional implications.

The levels of expression of G-protein alpha(q/11) (Galpha(q/11)) subunits and PLC-beta(1-4), -gamma, and -delta(1) isoforms were quantified by Western blot analysis in order to establish their contribution to the patterns of PLC functioning reported here. Quantitative measurements of the levels of Galpha(q/11) subunits in each region were obtained by comparison with known amounts of Escherichia coli expressed recombinant Galpha(q) subunits. Quantitative analysis indicated that Galpha(q/11) subunits are abundant polypeptides in human brain, with values ranging from about 1200 ng/mg in cerebral cortex to close to 900 ng/mg of membrane protein in caudate. In cerebral cortical membranes, the PLC-beta(1) isoform was more abundant than in caudate membranes. The highest levels of PLC-beta(2) expression were detected in caudate membranes. PLC-beta(3) was little expressed, and there were no significant differences in the relative values between both brain regions. Finally, the levels of the PLC-beta(4) isoform were significantly lower in caudate than in cortical membranes. It is concluded that although most of these data represent relative, not absolute, measures of protein levels within these regions, they contribute nonetheless to the significant differences observed in signaling capacities through the PLC system in both human brain regions.

Adult↗
PubMed2006

Novel paralogous gene families with potential function in legume nodules and seeds.

Within the plant kingdom, legumes are unusual in their ability to form nitrogen-fixing nodules in symbiosis with certain bacteria in the family Rhizobiaceae (rhizhobia). Genes that are required for signaling between plant and symbiont, and for the development and maintenance of the nodule, were either created de novo or adopted from other plant pathways. Only in recent years have genome-scale sequence data from legumes made it possible to identify large, novel families of genes probably evolved to function in nodulation. Members of these novel families are expressed in seeds or nodules, and are homologous to defense-related proteins. Perhaps the most striking example is a large family (of more than 340 members) of cysteine cluster proteins that have homology to plant defensins.

Fabaceae↗
PubMed2006

Role of omega-3 fatty acids in brain development and function: potential implications for the pathogenesis and prevention of psychopathology.

The principle omega-3 fatty acid in brain, docosahexaenoic acid (DHA), accumulates in the brain during perinatal cortical expansion and maturation. Animal studies have demonstrated that reductions in perinatal brain DHA accrual are associated with deficits in neuronal arborization, multiple indices of synaptic pathology including deficits in serotonin and mesocorticolimbic dopamine neurotransmission, neurocognitive deficits, and elevated behavioral indices of anxiety, aggression, and depression. In primates and humans, preterm delivery is associated with deficits in fetal cortical DHA accrual, and children/adolescents born preterm exhibit deficits in cortical gray matter maturation, neurocognitive deficits particularly in the realm of attention, and increased risk for attention-deficit/hyperactivity disorder (ADHD) and schizophrenia. Individuals diagnosed with ADHD or schizophrenia exhibit deficits in cortical gray matter maturation, and medications found to be efficacious in the treatment of these disorders increase cortical and striatal dopamine neurotransmission. These associations in conjunction with intervention trials showing enhanced cortical visual acuity and cognitive outcomes in preterm and term infants fed DHA, suggest that perinatal deficits in brain DHA accrual may represent a preventable neurodevelopmental risk factor for the subsequent emergence of psychopathology.

Animals↗
PubMed2006

Protein tyrosine and serine-threonine phosphatases in the sea urchin, Strongylocentrotus purpuratus: identification and potential functions.

Protein phosphatases, in coordination with protein kinases, play crucial roles in regulation of signaling pathways. To identify protein tyrosine phosphatases (PTPs) and serine-threonine (ser-thr) phosphatases in the Strongylocentrotus purpuratus genome, 179 annotated sequences were studied (122 PTPs, 57 ser-thr phosphatases). Sequence analysis identified 91 phosphatases (33 conventional PTPs, 31 dual specificity phosphatases, 1 Class III Cysteine-based PTP, 1 Asp-based PTP, and 25 ser-thr phosphatases). Using catalytic sites, levels of conservation and constraint in amino acid sequence were examined. Nine of 25 receptor PTPs (RPTPs) corresponded to human, nematode, or fly homologues. Domain structure revealed that sea urchin-specific RPTPs including two, PTPRLec and PTPRscav, may act in immune defense. Embryonic transcription of each phosphatase was recorded from a high-density oligonucleotide tiling microarray experiment. Most RPTPs are expressed at very low levels, whereas nonreceptor PTPs (NRPTPs) are generally expressed at moderate levels. High expression was detected in MAP kinase phosphatases (MKPs) and numerous ser-thr phosphatases. For several expressed NRPTPs, MKPs, and ser-thr phosphatases, morpholino antisense-mediated knockdowns were performed and phenotypes obtained. Finally, to assess roles of annotated phosphatases in endomesoderm formation, a literature review of phosphatase functions in model organisms was superimposed on sea urchin developmental pathways to predict areas of functional activity.

Animals↗
PubMed2003

dHAND-Cre transgenic mice reveal specific potential functions of dHAND during craniofacial development.

Most of the bone, cartilage, and connective tissue of the craniofacial region arise from cephalic neural crest cells. Presumably, patterning differences in crest cells are a result of regional action of transcription factors within the developing pharyngeal arches. The basic helix-loop-helix transcription factor dHAND/HAND2 is expressed throughout much of the neural crest-derived mesenchyme of the pharyngeal arches, suggesting that it plays a crucial role in craniofacial development. However, targeted inactivation of the dHAND gene results in embryonic lethality by E10.5 due to vascular defects, preventing further analysis of the role of dHAND in cephalic neural crest cell development. In order to examine putative roles of dHAND during later stages of embryogenesis, we have used a transgenic lineage marker approach, in which a portion of the dHAND upstream region containing an enhancer that directs dHAND expression to the pharyngeal arches is used to drive Cre recombinase expression. By crossing these dHAND-Cre transgenic mice with R26R mice, we can follow the fate of cells that expressed dHAND at any time during development by examining beta-galactosidase activity. We show that dHAND is first expressed in postmigratory cephalic neural crest cells within the pharyngeal arches. In older embryos, beta-galactosidase-labeled cells are observed in most of the neural crest-derived lower jaw skeleton and surrounding connective tissues. However, labeled cells only contribute to substructures within the middle ear, indicating that our transgene is not globally expressed in cephalic neural crest cells within the pharyngeal arches. Moreover, dHAND-Cre mice will provide a valuable tool for tissue-specific inactivation of gene expression in multiple tissue types of neural crest origin.

Animals↗
PubMed2002

Estrogen receptor beta. Potential functional significance of a variety of mRNA isoforms.

Recent cloning of estrogen receptor beta (ERbeta) was followed by the discovery of a variety of its isoforms. This review describes the complexity of ERbeta mRNAs in various species for which most data have been gathered so far. The most surprising finding is the great variation in isoform structure among various mammalian species. This may reflect either the fact that only a very limited number of isoforms have been described so far or between-species specificity, especially as common elements in closely related species could still be noted. Isoform variations, as detected mainly at the mRNA sequence level, should result in profound functional differences at the level of proteins as already shown in selected cases. Thus, it is proposed that the diversity of ERbeta isoforms implies a functional role of this phenomenon in cellular physiology and pathology of estrogen response.

Animals↗