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At least 703 records · Page 39Linked to original sources
PubMed2002

The 3prime prime or minute-terminal structure required for replication of Barley yellow dwarf virus RNA contains an embedded 3prime prime or minute end.

We determined the 3prime prime or minute-terminal primary and secondary structures required for replication of Barley yellow dwarf virus (BYDV) RNA in oat protoplasts. Computer predictions, nuclease probing, phylogenetic comparisons, and replication assays of specific mutants and chimeras revealed that the 3prime prime or minute-terminal 109 nucleotides (nt) form a structure with three to four stem-loops followed by a coaxially stacked helix incorporating the last four nt [(A/U)CCC]. Sequences upstream of the 109-nt region also contributed to RNA accumulation. The base-pairing but not the sequences or bulges in the stems were essential for replication, but any changes to the 3prime prime or minute-terminal helix destroyed replication. The two 3prime prime or minute-proximal tetraloops tolerated all changes, but the two 3prime prime or minute-distal tetraloops gave most efficient replication if they fit the GNRA consensus. A mutant lacking the 3prime prime or minute-proximal stem-loop produced elevated levels of less-than-full-length minus strands, and no (+) strand. We propose that a "pocket" structure is the origin of (minus sign)-strand synthesis, which is negatively regulated by the inaccessible conformation of the 3prime prime or minute terminus, thus favoring a high (+)/(minus sign) ratio. This 3prime prime or minute structure and the polymerase homologies suggest that genus Luteovirus is more closely related to the Tombusviridae family than to other Luteoviridae genera.

Avena↗
PubMed2002

Mutational analysis of the replication signals in the 3'-nontranslated region of citrus tristeza virus.

Citrus tristeza virus (CTV), a member of the Closteroviridae, has a 19.3-kb messenger-sense RNA genome consisting of 12 open reading frames with nontranslated regions (NTR) at the 5' and 3' termini. The 273 nucleotide (nt) 3'-NTR is highly conserved ( approximately 95%) among the sequenced CTV isolates in contrast to the highly diverse 5'-NTR sequences. The 3' replication signals were mapped to the 3' 234 nts within the NTR. This region of CTV does not contain a poly-A tract nor does it appear to fold as a tRNA-mimic. Instead, a computer-predicted thermodynamically stable secondary structure comprised of 10 stem-and-loop (SL) structures, referred to as SL1 to SL10 (5' to 3'), was common to all CTV isolates. This putative structure was used as a guide to examine the 3' requirements for replication in vivo. The resulting data suggest that a complex 3' structure is required for those functions that provide for efficient replication of CTV in vivo such as minus-strand initiation, regulation of strand asymmetry, effective translation of the myriad of viral mRNAs, or stability of RNAs. Deletions into the 3'-NTR, up to 66 nts from the 5' direction and 11 nts from the 3' direction, deleting or disrupting putative SL1, SL2 and SL3, or SL10, resulted in continued replication, suggesting that these sequences are not essential for basal-level replication, but are required for efficient replication. Predicted stem loops 3 through 10 were examined by mutations designed to alter the primary structures while preserving the secondary structures. Mutations designed to disrupt the predicted stems of SL3, SL5, SL7, SL9, or SL10 resulted in substantially reduced levels of replication, while compensatory mutations resulted in partial restorations of replication, suggesting that these predicted secondary structures are involved in replication. Also, the putative loop sequences of SL5, SL6, SL7, and SL9 tolerated mutagenesis with continued but reduced levels of replication. In contrast, all mutations introduced into putative SL4, SL8, and the stem of SL6 prevented replication, suggesting that the primary structure of these regions make up the core of the 3' replication signal. The 3' triplet, CCA, was shown to be necessary for efficient replication, but deletion of eleven nts to expose an internal CCA resulted in continued replication.

3' Untranslated Regions↗
PubMed1998

Sequence determination and genetic analysis of the leader region of various equine arteritis virus isolates.

The entire leader sequence of ten equine arteritis virus (EAV) isolates including the Bucyrus reference strain was determined and analyzed at the primary nucleotide and secondary structure levels. The leader sequence of eight EAV isolates was determined to be 206 nucleotides (nt) in length, whereas those of the 86AB-A1 and 86NY-A1 isolates were found to be 205 and 207 nt in length, respectively. The sequence identity of the leader sequences between the different isolates and the Bucyrus reference strain ranged from 94.2 to 98.5%. An AUG start codon found at position 14 in all EAV isolates could initiate an open reading frame (ORF) that could produce a polypeptide of 37 amino acids, except for the 86NY-A1 isolate where the intraleader polypeptide would contain 54 amino acids. Five patterns of computer-predicted RNA secondary structures were identified in the ten EAV leader regions analyzed. All EAV isolates showed three conserved stem-loops (designated A, B and C). An additional conserved stem-loop (D) was observed in six EAV isolates, including the Bucyrus reference strain. Based on the presence or absence of stem-loop D, all EAV isolates analyzed in this study could be tentatively classified into two genogroups (I and II). The significance of the intraleader ORF and the predicted secondary structures has yet to be determined.

5' Untranslated Regions↗
PubMed1990

Spatio-temporal interactions and the spatial phase preferences of visual neurons.

We recorded single neuron responses in the cat's lateral geniculate nucleus (LGN) and visual cortex to compound stimuli composed of two sinusoidal gratings in a 2:1 frequency ratio. To probe visual receptive field symmetry, we varied the relative spatial phase of the two components and measured the effect on neuronal responses. We expected that on-center LGN neurons would respond best to gratings combined in positive cosine (bright bar) phase, while off-center LGN neurons would respond best to gratings combined in negative cosine (dark bar) phase. When drifting stimuli were used, cells' phase preferences were roughly 90 deg away from the expected values; when stationary, contrast-modulated stimuli were used, phase preferences were as originally predicted. Computer simulations showed that this discrepancy could be explained by taking into account the cells' temporal properties. Thus, tests using drifting stimuli confound the spatial structure of visual neural receptive fields with their temporal response characteristics. A small sample of data from cortical neurons reveals the same confound.

Action Potentials↗
PubMed1992

Topological and functional studies on HlyB of Escherichia coli.

The topology of HlyB, a protein located in the inner membrane of Escherichia coli and involved in the secretion of alpha-haemolysin (HlyA), was determined by the generation of HlyB-PhoA and HlyB-LacZ fusion proteins. The data obtained by this biochemical method together with computer predictions suggest that HlyB is inserted in the cytoplasmic membrane by six stable hydrophobic, alpha-helical transmembrane segments. These segments extend from amino acid positions 158 to 432 of HlyB. The cytoplasmic loops between these transmembrane segments are relatively large and carry an excess of positively charged amino acids, while the periplasmic loops are rather small. In addition to these six transmembrane segments, two additional regions in the 78 N-terminal amino acids of HlyB appear to be also inserted in the cytoplasmic membrane. However, the association of these two segments with the cytoplasmic membrane seems to be less tight, since active PhoA and LacZ fusions were obtained by insertion into the same positions of these segments. A LacZ-HlyAs, fusion protein carrying, at the C-terminus of LacZ, the 60-amino acid signal sequence of HlyA was not secreted in the presence of HlyB/HlyD. However, transport of this fusion protein into the cytoplasmic membrane appeared to be initiated, as suggested by the tight association of this protein with the inner membrane. A similar close association of LacZ-HlyAs with the inner membrane was also observed in the presence of HlyB alone but not in its absence. These data suggest that HlyB recognizes the HlyA signal sequence and initiates the transport of HlyA into the membrane.

Alkaline Phosphatase↗
PubMed1995

Expression of nonstructural protein NS3 of African horsesickness virus (AHSV): evidence for a cytotoxic effect of NS3 in insect cells, and characterization of the gene products in AHSV infected Vero cells.

The smallest genome segment of African horsesickness virus (AHSV), segment 10 (S10), encodes two minor nonstructural proteins, NS3 and NS3A. While the cognate bluetongue virus (BTV) proteins have been suggested to play a role in the release of virus particles from infected cells, no function has yet been ascribed to AHSV NS3/NS3A. When the AHSV-3 S10 gene was expressed in a baculovirus system only a single NS3 protein (24 K) was synthesized, at lower levels than expected. It was shown that this could be due to a membrane association of NS3, leading to an alteration in host cell membrane permeability and eventual cell death. Based on computer predictions a general model for the membrane-associated topology of NS3 of five different orbiviruses was proposed. Studies on AHSV-3 infected Vero cells showed that equimolar amounts of NS3 and NS3A were synthesized. No evidence was found for the glycosylation of NS3. The S10 genes and NS3/3A proteins of AHSV-3 and AHSV-7 were shown to be closely related, and clearly distinct from the cognate proteins of the other 7 AHSV serotypes. This distinguishes the AHSV S10 gene product from that of BTV NS3, which appears to be much more conserved.

African Horse Sickness Virus↗
PubMed1994

cDNA cloning and functional characterization of a meiosis-specific protein (MNS1) with apparent nuclear association.

It is well known that cytoskeleton and karyoskeleton proteins are associated with changes in cell shape and with the rearrangement of the dynamic structures involved in cell division and motility. In higher vertebrates, there are three major skeletal protein groups: microfilaments, microtubules and intermediate filaments, each representing a multigene family. Some of these skeletal proteins are expressed in a temporally- and spatially-specific fashion, and they establish cell-specific cytoplasmic and nucleoplasmic organization during development. Here we report the cDNA cloning of a novel 60 kDa skeletal protein from mouse spermatocytes, termed MNS 1 (meiosis-specific nuclear structural protein), whose computer-predicted protein configuration indicates long alpha-helical coiled-coil domains flanked by non-helical terminal domains. Functional characterization of MNS1 by ectopic expression in culture cells indicated that it is a detergent- and high salt-resistant skeletal protein which is involved in organization of the nuclear or perinuclear architecture. The MNS1 protein is specifically expressed at the pachytene stage during spermatogenesis, so that its function may involve the determination and maintenance of the appropriate nuclear morphology during meiotic prophase.

Amino Acid Sequence↗
PubMed1989

Pharmacokinetics of a single dose of ofloxacin in healthy elderly subjects using noncompartmental and compartmental models.

The pharmacokinetics of ofloxacin following a single 200 mg oral dose were studied in twelve healthy elderly volunteers. Relevant pharmacokinetic parameters were analysed by both noncompartmental and compartmental models. In compartmental analysis, the data on plasma concentrations was best described by an open two-compartment model. A zero-order absorption behaviour was found in some volunteers. The terminal half-lives were slightly prolonged and ranged from 6.2-11.6 h. A linear relationship was found between the renal clearance of the drug and the estimated creatinine clearance. Computer predictions of a multiple 200 mg dose regimen showed no important accumulation of ofloxacin. The recommendation of some authors that, in general, ofloxacin dosage may be halved in the elderly could not be confirmed. This has to be determined through further clinical experience in elderly ill subjects.

Aged↗
PubMedDate not supplied

RNAs Selected in vitro by the HIV-2 Tat Protein.

The Tat proteins of human immunodeficiency virus types 1 (HIV-1) and 2 (HIV-2), termed Tat-1 and Tat-2, respectively, are essential for efficient viral replication. Tat proteins activate viral transcription by binding to the TAR RNA stem-loop structure at the 5' end of viral transcripts. We used an in vitro selection procedure to identify RNAs present in a large sequence pool that are able to bind to purified Tat-2 protein. The sequences of the selected RNAs demonstrated a consensus feature: 20 of 27 RNAs contained computer-predicted loop structures that were >50% U or C nucleotides. A selected RNA was characterized for its in vitro binding properties to various Tat-2 proteins. This synthetic RNA was bound by wild-type Tat-2 proteins with an affinity that was only slightly lower than that of the natural HIV-2 TAR RNA. Tat-2 required a wild-type RNA binding domain to bind to this synthetic RNA. This study indicates that in vitro selection techniques can be used to investigate Tat protein-TAR RNA interactions. Copyright 1997 S. Karger AG, Basel

Journal Article↗
PubMedDate not supplied

Instrumental neutron activation analysis of biological samples.

The elemental compositions of 18 biological reference materials have been processed, for 14 stepped combinations of irradiation/decay/counting times, by the INAA Advance Prediction Computer Program. The 18 materials studied include 11 plant materials, 5 animal materials, and 2 other biological materials. Of these 18 materials, 14 are NBS Standard Reference Materials and four are IAEA reference materials. Overall, the results show that a mean of 52% of the input elements can be determined to a relative standard deviation of +/- 10% or better by reactor flux (thermal plus epithermal) INAA.

Animals↗
PubMed1996

Localization of the sequence-determined DNA bending center upstream of the streptokinase gene skc.

DNA sequences upstream of the core promoter region of the streptokinase gene (skc) from Streptococcus equisimilis H46A increase skc transcription more than tenfold in vivo. This promoter upstream region contains a segment of intrinsically bent DNA, the precise location of which was determined experimentally by circular permutation analysis and theoretically by computer prediction. Electrophoretic analysis of circularly permuted upstream DNA fragments placed the bend center approximately at position -100 with respect to the major transcription initiation site of skc. This position was in excellent agreement with the center of maximum curvature predicted theoretically. Knowledge of the precise location of the bend center will be useful for future studies of the possible effect of DNA bending on skc transcription.

Base Sequence↗
PubMed2003

Identification of a new murine lectin-like gene in close proximity to CD94.

The cytolytic activities of natural killer (NK) cells are controlled by immune receptors expressed on the NK cell surface that interact with MHC I molecules on the target cell. In the murine system, the receptors that perform this function are members of the c-type lectin superfamily and are found in a 4 Mbp cluster termed the natural killer gene complex (NKC) on chromosome 6. To date, over 30 receptor genes, which largely exhibit lymphoid-restricted expression, have been cloned from this region. With the completion of genomic sequencing in this region, computer prediction of genes based in part on expressed sequence tag (EST) evidence has allowed the identification of potential new genes in the cluster. In this study, we investigated one of these predicted genes and showed that it is a bona fide gene, which is transcribed in both the mouse and rat but is not present in humans. A phylogenetic comparison also showed that the novel gene, Klre-1, is most closely related to CD94. Strikingly, the Klre-1 gene is located within very close proximity (2.3 kb) to the CD94 gene. Consequently, we examined the expression patterns of Klre-1 by quantitative real-time polymerase chain reaction and found a correlation between expression of CD94 and Klre-1 in primary cells as well as cell lines. This discovery presents further possibilities for characterising transcriptional control of genes in the NKC.

Amino Acid Sequence↗
PubMed2026

Cross-tissue Mendelian randomization prioritizes RAB27B as a brain-derived candidate protein for postpartum depression.

OBJECTIVE: Postpartum depression (PPD) is one of the most common and debilitating complications of childbirth, yet the candidate proteins linking genetic risk to disease remain poorly defined. Building on recent genome-wide association studies (GWAS), we sought to integrate cross-tissue proteogenomic data to identify candidate proteins for PPD and explore therapeutic opportunities. METHODS: We conducted two-sample Mendelian randomization (MR) using genome-wide significant cis-protein QTLs from brain (n = 608 proteins), cerebrospinal fluid (CSF; n = 214), and plasma (n = 612). PPD summary statistics were obtained from FinnGen R8 (13,657 cases, 236,178 controls) and replicated in an independent GWAS. Phenome-wide association (PheWAS) was used to assess pleiotropy. Potential therapeutic targets were evaluated through DSigDB drug repurposing, molecular docking, and molecular dynamics simulations. RESULTS: Among all proteins tested, RAB27B was the only brain-derived protein surpassing Bonferroni correction (OR = 1.60; 95% CI: 1.30-1.96; P = 6.6 × 10⁻⁶), whereas no significant proteins were identified in CSF or plasma. This association was replicated in an independent GWAS (OR = 1.27; 95% CI: 1.02-1.58; P = 0.037). PheWAS identified no pleiotropic associations at genome-wide significance. In silico drug repurposing identified pregnenolone as a candidate ligand with computationally predicted stable binding to RAB27B, providing a starting point for future experimental validation. CONCLUSION: This study provides the first cross-tissue proteogenomic evidence that RAB27B is a brain-derived, reproducible candidate protein genetically associated with PPD. By extending GWAS signals to functional protein-level mechanisms and therapeutic inference, our findings nominate RAB27B and pregnenolone as promising directions for postpartum psychiatric research.

Humans↗
PubMed2004

The complete nucleotide sequence, genome organization, and specific detection of Beet mosaic virus.

Beet mosaic virus (BtMV) was identified almost five decades ago but has not been fully characterized at the molecular level. In this study, we have determined for the first time the complete nucleotide sequence of BtMV genomic RNA and have developed a specific molecular means for its diagnosis. The viral genome of BtMV comprises 9591 nucleotides, excluding the 3' terminal poly (A) sequence, and contains a single open reading frame (ORF) that begins at nt 166 and terminates at nt 9423, encoding a single polyprotein of 3086 amino acid residues. A 3' untranslated region of 168 nucleotides follows the ORF. The deduced genome organization is typical for a member of the family Potyviridae and includes 10 proteins: P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and coat protein (CP). Nine putative protease cleavage sites were predicted computationally and by analogy with genome arrangements of other potyviruses. Conserved sequence motifs of homologous proteins of other potyviruses were found in corresponding positions of BtMV. BtMV is a distinct species of the genus Potyvirus with the most closely related species being Peanut mottle virus ( approximately 55% amino acid identity). Based on the nucleotide sequence obtained, we have developed a virus-specific RT-PCR assay for accurate diagnosis and differentiation of BtMV.

Amino Acid Sequence↗
PubMed2026

Expansion of the allelic and phenotypic spectrum of MED25-related developmental disorder: novel compound heterozygous variants with structural domain implications.

MED25-related developmental disorder (Basel-Vanagaite-Smirin-Yosef syndrome) is a rare autosomal recessive disorder, defined by severe neurodevelopmental delay, corpus callosum abnormalities, ocular involvement, epilepsy, and marked facial appearance. MED25 pathogenic variants interfere with the functioning of the Mediator complex, which is responsible for RNA polymerase II transcription. We report a 9-year-old girl who presents with significant global developmental delay, agenesis of the corpus callosum, congenital cataracts, epilepsy, hypotonia, musculoskeletal abnormalities, and typical craniofacial features. Trio-based whole-exome sequencing revealed compound heterozygous variants in MED25: a maternally transmitted truncating variant (c.1366 C > T; p.Gln456*) and a paternally inherited missense variant (c.430 C > T; p.Leu144Phe). The new classification of the missense variant as potentially pathogenic is supported by a systematic ACMG re-evaluation supported by segregation analysis, phenotypic specificity, computational prediction, and structural localization in the MED25 Activator Interaction Domain (ACID). Comparative phenotypic analyses show strong agreement with reported cases but add more data to fine-tune clinical spectrum. This article broadens the allelic and phenotypic spectrum of MED25-related developmental disorder and highlights the need for comprehensive evaluation across molecular, structural, and phenotypic pathways to elucidate variant signature in rare genetic disease models correctly.

Humans↗
PubMed2006

Use of RNA interference to inhibit integrin subunit alphaV-mediated angiogenesis.

One of the central molecules in capillary formation during angiogenesis is the integrin alphaVbeta3. The aim of this study was to inhibit alphaV-mediated angiogenesis in vitro using RNAs (siRNA) as well as antisense oligodeoxyribonucleotides (asON). Five siRNAs, against the alphaV chain of alphaVbeta3, and three asON, which had the respective sequence of the antisense sequence of three of the siRNAs molecules, were examined. Two of the siRNAs and their respective asON were designed on the basis of computer-predicted secondary structure analysis of alphaV mRNA. The different molecules were transfected into human umbilical vein endothelials cells (HUVEC) using lipofection. Following stimulation by PMA, two siRNAs showed a dose-dependent inhibition of PMA-induced alphaV mRNA and protein upregulation, as assessed by real-time RT-PCR and flow cytometry. At a concentration of 25 nM a complete inhibition of protein upregulation was found using siRNAs while transfection of the respective asON sequences reduced the protein upregulation only by 44%. To evaluate the anti-angiogenic potential a cell culture model of human angiogenesis based on the co-cultivation of endothelial cells and dermal fibroblasts was used. Transfection of the siRNA sequence (50 nM) resulted in an inhibition of the total length of capillary-like tubules by 40.6% in comparison to 21.1% using the respective asON sequence. In conclusion, siRNA-based downregulation of alphaV expression showed a stronger inhibition of capillary tube formation in an angiogenesis in vitro assay, than asON having the same sequence as the antisense strand of the siRNAs. Therefore, siRNAs are useful tools for functional alphaV knock-down experiments and might be a therapeutic alternative for antagonists which bind directly to the integrins alphaVbeta3 or alphaVbeta5.

Apoptosis↗
PubMed2026

Identification and validation of natural dengue virus NS1 inhibitors with promising antiviral potential.

Dengue infection remains a major global public health challenge, with no specific antiviral therapy currently available. The dengue virus non-structural protein 1 (NS1) exists in both intracellular and secreted forms playing a pivotal role in viral replication, immune evasion, and pathogenesis, particularly by contributing to endothelial disruption and vascular leakage during severe disease, thereby making it a promising therapeutic target. In silico screening identified berberine, betulinic acid, and ursolic acid as top candidates, exhibiting high binding affinities and stable interactions within the NS1 binding pocket. These computational predictions were further validated by biophysical assays, which demonstrated strong and specific binding interactions between the purified NS1 protein and the selected compounds. All three compounds significantly reduced viral genome levels, with the highest inhibition observed for berberine (60%), and followed by betulinic acid (40%) and ursolic acid (28%). Consistently, berberine showed the most potent inhibition of both intracellular and extracellular NS1. Overall, these findings highlight the inhibitory potential of natural compounds against DENV NS1 and provide a strong foundation for the development of NS1-targeted antivirals as a novel therapeutic strategy against dengue infection.

Antiviral Agents↗
PubMed2005

Characterization of the mouse myeloid-associated differentiation marker (MYADM) gene: promoter analysis and protein localization.

Hematopoietic differentiation is a complex process involving many genes inducing functional changes and characteristics of different cell lineages. To understand this process, it is important to identify genes involved in lineage commitment and maturation of hematopoietic progenitor cells. Recently we isolated the novel gene MYADM which is strongly up-regulated as multipotent progenitor cells differentiate towards myeloid cells. Because it is not expressed in lymphocytes, understanding the transcriptional control of MYADM could further explain differences in gene expression between myeloid and lymphoid cells. To identify regulatory elements controlling its restricted expression, we have analyzed the 5'-flanking region of the MYADM gene. The proximal promoter was found to lack both TATA and CCAAT boxes, but contained several potential binding sites for both ubiquitous and myeloid-specific transcription factors. Maximal promoter activity was contained within 800 bp from the tentative transcription initiation site, which was reduced as portions of the 5'-end were deleted, and completely abolished when the transcription initiation site was deleted. This promoter sequence had higher activity in myeloid cells compared to B cells, and activity was enhanced during myeloid differentiation, suggesting that we have identified the MYADM core promoter. Computer predictions had suggested MYADM to encode a protein with multiple transmembrane domains. By immunofluorescence and confocal microscopy we demonstrate that the protein is localized to the nuclear envelope and to intracytoplasmic membranes, indicating that MYADM constitutes an integral membrane protein.

5' Flanking Region↗