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At least 811 records · Page 45Linked to original sources
PubMed1986

Evidence for a particular mode of transcription in globular loops of lampbrush chromosomes of the newt Pleurodeles waltlii.

In amphibian lampbrush chromosomes, many loops have a specific morphology; this is the case for globular loops in the newt Pleurodeles. We have previously shown that the specific morphology of these loops is linked to an extreme compactness of the transcription products which make up their matrix. We investigated RNA synthesis in this type of loop by carrying out autoradiographic and transcription inhibition studies. We also analysed the organization of transcriptional complexes in these loops in the electron microscope using spread preparations. These studies revealed the presence of several transcription units in the same loop and asynchronous variations in RNA synthesis in these transcription units. We propose and discuss several hypotheses in order to explain this asynchronous RNA synthesis. We also discuss these results in the context of loop morphology and transcription mode.

Amanitins↗
PubMed1991

The superior laryngeal nerve loop and its surgical implications.

Based upon findings from 60 cadavers (120 sides), the incidence of superior laryngeal nerve loop, connecting the cervical sympathetic chain and the superior laryngeal nerve and its branches, the external and internal laryngeal nerve, was 98.3% (118 out of 120 sides). In most cases the loop connected the sympathetic chain and the external laryngeal nerve. The external laryngeal nerve was looped, and not linear as traditionally thought. The loop could be divided into three categories, V-shaped, U-shaped and mixed, and subdivided into 5 types and 17 subtypes according to morphological variation. The loop without exception innervated not only the cricothyroid muscle, but also the thyroid gland. The loop is one of the origins of the thyroid nerve. It seems that for thyroid surgery the loop, when lower in position, should be carefully separated from the superior thyroid vessels before the latter are ligated, in order to preserve a normal nerve supply to the muscle as well as to the part of the gland that remains after surgery.

Adult↗
PubMed1996

Sensitivity of HIV-1 to neutralization by antibodies against O-linked carbohydrate epitopes despite deletion of O-glycosylation signals in the V3 loop.

It has been suggested that threonine or serine residues in the V3 loop of HIV-1 gp120 are glycosylated with the short-chain O-linked oligosaccharides Tn or sialosyl-Tn that function as epitopes for broadly neutralizing carbohydrate specific antibodies. In this study we examined whether mutation of such threonine or serine residues could decrease the sensitivity to infectivity inhibition by Tn or sialosyl-Tn specific antibodies. All potentially O-glycosylated threonine and serine residues in the V3 loop of cloned HIV-1 BRU were mutagenized to alanine thus abrogating any O-glycosylation at these sites. Additionally, one of these T-A mutants (T308A) also abrogated the signal for N-glycosylation at N306 inside the V3-loop. The mutant clones were compared with the wild type virus as to sensitivity to neutralization with monoclonal and polyclonal antibodies specific for the tip of the V3 loop of BRU or for the O-linked oligosaccharides Tn or sialosyl-Tn. Deletion of the N-linked oligosaccharide at N306 increased the neutralization sensitivity to antibodies specific for the tip of the loop, which indicates that N-linked glycosylation modulates the accessibility to this immunodominant epitope. However, none of the mutants with deletions of O-glycosylation signals in the V3 loop displayed any decrease in sensitivity to anti-Tn or anti-sialosyl-Tn antibody. This indicates that these broadly specific neutralization epitopes are located outside the V3 loop of gp 120.

Amino Acid Sequence↗
PubMed2001

Stapled ileoanal pouches without loop ileostomy: a prospective study in 86 patients.

In restorative proctocolectomy the use of a stapling technique to construct an ileal pouch with anal anastomosis offers an alternative to the hand-sewn technique following mucosectomy; a temporary defunctioning loop ileostomy may reduce the consequences of an anastomotic leakage, however it may entail discomfort for the patient, an additional operation, possible complications, and longer total hospital stay. This prospective study evaluated the peri- and postoperative courses in 86 consecutive, referred patients receiving ileal pouch-anal anastomosis using the stapling technique to construct the ileal pouch and ileoanal anastomosis, omitting the defunctioning loop ileostomy except in cases of increased risk of ileoanal anastomotic insufficiency according to defined criteria. Follow-up time was 36-96 months. Patients undergoing primary loop ileostomy stayed a median of 19 days in hospital, as opposed to a median of 9 days in those who did not. Eight patients developed pelvic sepsis that demanded a secondary defunctioning loop ileostomy, and five showed symptoms arising from relapsing inflammation in residual rectal mucosa; in three of these, a secondary transanal mucosectomy covered by a loop ileostomy was necessary. During the follow-up period ten patients had bowel obstructions that demanded surgery; two developed late pouch-vaginal fistulas, and one a fistula from the J-limb to the abdominal scar. There was one case of pouch procidentia. At 12-month follow-up the median evacuation frequency was 6 per 24 h, the incidence of minor incontinence was about 10%, and urgency to evacuate occurred in about 10%. None of the patients experienced any major incontinence. The stapling technique and omission of the defunctioning loop ileostomy in restorative proctocolectomy were thus a comparatively reliable and time-saving method with short total hospital stay. In patients at increased risk of anastomotic complications, however, a defunctioning loop ileostomy is recommended. We believe it is important to perform an exact dissection into the anal canal to avoid a residual rectal mucosa that may be inflamed or even become dysplastic.

Adolescent↗
PubMed2003

Stem-loop structures II-IV of the 5' untranslated sequences are required for the expression of the full-length hepatitis C virus genome.

The 5' and 3' untranslated regions (UTR) of the hepatitis C virus (HCV) genome contain stem-loop structures, which are important in viral gene expression and replication. In this study, the functional roles of the predicted stem-loop structures of HCV 5' UTR and 3' UTR in viral gene expression were examined using a chimeric clone of full-length HCV genomic cDNA clone and the gene for green fluorescent protein (GFP). High level expression of the HCV-GFP chimera in Huh-7 cells was accomplished by using a replication defective adenovirus that expresses T7 RNA polymerase and transcription plasmid containing full-length HCV-GFP chimera under the control of a T7 promoter. The HCV-GFP clone, with deletion of stem-loop I, expressed proteins in transfected Huh-7 cells at comparable levels to the wild type HCV clone. Other mutations of the 5' UTR, which either deleted or altered the base pairing of stem-loops II to IV, completely abolished the expression of HCV-GFP chimera. In contrast, deletion of 3' UTR sequences had no effect on HCV protein expression. These findings suggest that the stem-loop structures II to IV of HCV 5' UTR are necessary for protein expression, but that stem loop I is dispensable for protein translation. The stem-loop structures of 3' UTR of HCV genome appear to have no direct role in viral gene expression.

3' Untranslated Regions↗
PubMed1978

S1 nuclease-specific nicking of mitochondrial DNA containing displacement loops.

Conditions are described in which the single strand-specific nuclease S1 selectively nicks mitochondrial DNA containing displacement loops without nicking supercoiled mitochondrial DNA. Using these conditions, the percentage of molecules containing displacement loops can be easily and accurately determined. This method is superior to the traditional electron microscopic examination for assessing the frequency of displacement loop-containing molecules. In addition, this method permits the determination of the relative specific activities of displacement loop and nondisplacement loop-containing mitochondrial DNA after various radioactive labeling protocols. S1 nuclease is shown to cleave the displaced strand of the displacement loop, to partially degrade the 7S-initiation strand, but not to cleave the parental template strand complementary to the 7S-initiation strand. The final product is a nicked circular molecule with at least two breaks localized within the displacement loop region in only one of the two parental strands.

Animals↗
PubMed1991

The effect of adding copper onto Lippes Loop IUDs: results from a ten-year study in Yugoslavia.

The present study is the first randomized ten-year comparison of the standard, non-medicated Lippes Loop D and the same device with the addition of 200 mm2 of copper in the form of copper sleeves. The devices were randomly inserted immediately after first trimester medical termination of pregnancy. Out of 400 postabortal IUD insertions, 371 were followed for up to ten years. Gross cumulative life-table accidental pregnancy rates after one year of use were 0.56 for the copper-bearing Lippes Loop and 4.63 for the standard Lippes Loop. After two, four and ten years, these rates were 1.24, 2.70 and 3.62 and 6.03, 7.58 and 14.94, respectively (in all comparisons, rates were significantly different at the 0.05 level or lower). At each time interval, expulsion/displacement rates were 4.49, 4.49, 5.23 and 6.32 for the copper-bearing Lippes Loop and 12.61, 13.29, 15.46 and 19.79 for the standard Lippes Loop (rates were significantly different at the 0.01 level or lower). Differences in removal rates for bleeding and/or pain were not significantly different at any of the follow-up intervals. The lower event rates for copper-bearing Lippes Loop D users indicates that the addition of copper to the Lippes Loop IUD may result in better long-term efficacy profiles for this device among postabortal women. The results also suggest that large, medicated IUDs may be more efficacious for women with larger uteri who often experience higher failure rates due to expulsion or displacement of smaller IUDs into the lower uterine segment.

Adolescent↗
PubMed1992

Three-dimensional structure of apotransketolase. Flexible loops at the active site enable cofactor binding.

The structure determination of apotransketolase and the comparison of its three-dimensional structure with that of the holoenzyme has revealed that no large conformational changes are associated with cofactor binding. Two loops at the active site are flexible in the apoenzyme which enables ThDP to reach its binding site. Binding of the cofactor induces defined conformations for these two loops at the active site. One of these loops is directly involving in binding of the cofactors, Ca2+ and ThDP. This loop acts like a flap which closes off the diphosphate binding site. After binding of the cofactor, residues of this loop form interactions to residues of loop 383-398 from the second subunit. These interactions stabilize the conformation of the two loops from a flexible to a 'closed' conformation.

Apoproteins↗
PubMed1983

Ten-year experience with looped catheter manipulation of ureteral calculi.

Six hundred sixteen procedures for management of ureteral calculi were reviewed. Five hundred six (82%) were endoscopic procedures; 207 were looped catheter manipulations and 299 were stone basket extractions. The retrieval efficiency for ureterolithotomy, looped catheter manipulation, and basket extraction was 100, 46, and 71 per cent, respectively. The average size of calculus was 7.9 mm (lithotomy), 6.9 mm (looped catheter), and 4.2 mm (basket). Looped catheters were used for larger stones, for stones higher in the ureter, and for stones that could not be extracted with a basket. The looped catheter can be utilized for stones at any level of the ureter. There was no significant difference in the complications from use of the looped catheter or stone basket, except for a longer hospital stay for patients who had manipulation with looped catheters than with stone baskets.

Adolescent↗
PubMed2004

Studies of the mechanism of the in-loop synthesis of radiopharmaceuticals.

A series of experiments were performed to better understand the mechanism of the In-loop [11C]CH3I-methylation. The timing of [11C]CH3I delivery is critical for the high yield of radiolabeling since in-loop radioactivity trapping is reversible. Trapped radioactivity escapes faster from a Tefzel loop compared to a PEEK- or stainless steel loop. Up to 50% of delivered radioactivity may be concentrated at the loop origin (representing 8.1% of the total loop volume). A five-fold reduction of the reaction solvent volume and/or precursor amount may lead to a decrease of the product radiochemical yield either by lowering the in-loop radioactivity trapping or by diminishing conversion of [11C]CH3I into the product.

Carbon Radioisotopes↗
PubMed2003

"Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy.

DNA looping is often involved in positive and negative regulation of gene transcription in both prokaryotes and eukaryotes. The transcription of the gal operon of Escherichia coli from two overlapping promoters P1 and P2 is negatively regulated via Gal repressosome assembly. It involves binding of two dimeric Gal repressor proteins (GalR) to two operators, O(E) and O(I), flanking the two promoters, and formation of 113 bp DNA loop due to tetramerization of the two bound GalR dimers. The process requires negatively supercoiled DNA and the presence of the histone-like protein HU. Previous modeling of the repressosome based on evaluation of DNA elastic energy suggested a mutual antiparallel, rather than parallel, orientation of the two gal operators in an under-twisted DNA loop. To visualize the Gal loop by atomic force microscopy (AFM), plasmid DNA molecules were constructed with increased distance between the two operators. The AFM results demonstrated the formation of an antiparallel DNA loop in the Gal repressosome consistent with our earlier hypothesis. Importantly, the overall shape of the GalR mediated loop proved to be indistinguishable from that in the chimerical loop of the same size containing two lac operators (instead of two gal operators) and formed by LacI. In addition, a possibility of the gal operon repression mediated by GalR in the absence of HU was shown in the new DNA constructs. Implications of these findings for the DNA structural organization in bacterial nucleoid are discussed.

Bacterial Proteins↗
PubMed2004

Somatic mutations in the D-loop and decrease in the copy number of mitochondrial DNA in human hepatocellular carcinoma.

Somatic mutations in mitochondrial DNA (mtDNA) have been detected in many human cancers, including hepatocellular carcinoma (HCC). The D-loop region was found to be a "hot spot" for mutation in mtDNA of the tumors. However, effects of the D-loop mutations on the copy number of mtDNA in tumor tissues are poorly understood. Using direct sequencing, we examined mutations in the D-loop region of mtDNA in 61 HCCs and the corresponding non-tumor liver tissues. The results revealed that 39.3% of the HCCs carried somatic mutation(s) in the D-loop of mtDNA, and most of these mutations were homoplasmic. Moreover, 37.0% (10/27) of these mutations were T-to-C and G-to-A transitions and 40.7% (11/27) of them were located in the polycytidine stretch between nucleotide position (np) 303 and 309 of mtDNA. In addition, we found that mtDNA copy number of HCC was significantly decreased in 60.5% of the patients with hepatoma, especially in those with somatic mutation(s) in the D-loop of mtDNA (17/24). This decrease in mtDNA copy number was highly associated with the occurrence of point mutations near the replication origin of the heavy-strand of mtDNA. Interestingly, we found that 42.9% (6/14) of the HCCs without mutation in the D-loop had a reduced copy number of mtDNA, indicating that other unidentified factors involved in mitochondrial biogenesis might be defective in the tumor. The results obtained in this study strongly suggest that somatic mutations in the D-loop together with the decrease in the copy number of mtDNA may be an important event during the early phase of liver carcinogenesis.

Base Sequence↗
PubMed2006

The G490E mutation in reverse transcriptase does not impact tRNA primer selection by HIV-1 with altered PBS and A-loop.

The initiation of HIV-1 reverse transcription utilizes a cellular tRNA(Lys,3) as a primer. The 3' terminal 18-nucleotides of the cellular tRNA(Lys,3) are complementary to a region on the viral genome, designated as the primer binding site (PBS). Previous studies have shown that forcing HIV-1 to utilize alternative tRNA primers through alteration of the PBS results in viruses that revert to utilize tRNA(Lys,3) following in vitro replication. In some instances though, HIV-1 has been shown to select alternative tRNAs for initiation of reverse transcription if additional mutations upstream in the U5 region (A-loop) were made to be complementary to these alternative tRNAs. Recently, an HIV-1 has been described in which the U5 region distinct from the A-loop, designated as the primer activation site (PAS), was mutated in conjunction with the PBS to force the virus to use tRNA(Lys1,2) as a primer. An additional mutation in reverse transcriptase (RT), G490E, was found to facilitate the forced use of tRNA(Lys1,2) as the primer. In the current study, we have investigated the impact of the G490E mutation in RT on the selection and use of alternative primers by HIV-1. Viruses were first constructed in which the PBS and A-loop region were made complementary to tRNA(Trp). Previous studies from our laboratory have shown that these viruses are unstable and mutate to select tRNA(Met) or tRNA(Lys1,2). Analysis of the replication of viruses with the U5 and PBS complementary to tRNA(Trp) with or without the G490E mutation revealed no significant differences with respect to infectivity and viral growth in SupT1 or peripheral blood mononuclear cells (PBMC). In addition, the presence of the G490E mutation did not influence the capacity of this virus to revert to utilize tRNA(Met) as the primer for initiation of reverse transcription. In a previous study, we have described an HIV-1 that has been forced to utilize tRNA(Lys1,2) through mutations in the A-loop and PBS. The G490E RT mutation in this virus did not impact on the virus infectivity or growth in SupT1 or PBMC. We did not find a significant fitness advantage to viruses in which the A-loop and PBS were made complementary to tRNA(Lys1,2) that also contained the G490E mutation in RT. The results of these studies then establish that HIV-1 can be forced to use alternative primers through mutations in the U5 (PAS or A-loop) for certain tRNAs. Furthermore, for mutations in the A-loop and PBS, the RT does not play an important role in dictating the selection of the alternative primers to be used for initiation of reverse transcription.

Amino Acid Substitution↗
PubMed2003

Determination of the membrane contact residues and solution structure of the helix F/G loop of prostaglandin I2 synthase.

From our topological arrangement model of prostaglandin I(2) synthase (PGIS) created by homology modeling and topology studies, we hypothesized that the helix F/G loop of PGIS contains a membrane contact region distinct from the N-terminal membrane anchor domain. To provide direct experimental data we have explored the relationship between the endoplasmic reticulum (ER) membrane and the PGIS F/G loop using a constrained synthetic peptide to mimic PGIS residues 208-230 cyclized on both ends through a disulfide bond with added Cys residues. The solution structure and the residues important for membrane contact of the constrained PGIS F/G loop peptide were investigated by high-resolution 1H two-dimensional nuclear magnetic resonance (2D NMR) experiments and a spin label incorporation technique. Through the combination of 2D NMR experiments in the presence of dodecylphosphocholine (DPC) micelles used to mimic the membrane environment, complete 1H NMR assignments of the F/G loop segment have been obtained and the solution structure of the peptide has been determined. The PGIS F/G loop segment shows a defined helix turn helix conformation, which is similar to the three-dimensional crystallography structure of P450BM3 in the corresponding region. The orientation and the residues contacted with the membrane of the PGIS F/G loop were evaluated from the effect of incorporation of a spin-labeled 12-doxylstearate into the DPC micelles with the peptide. Three residues in the peptide corresponding to the PGIS residues L217 (L11), L222 (L16), and V224 (V18) have been demonstrated to contact the DPC micelles, which implies that the residues are involved in contact with the ER membrane in the native membrane-bound PGIS. These results provided the first experimental evidence to localize the membrane contact residues in the F/G loop region of microsomal P450 and are valuable to further define and understand the membrane topology of PGIS and those of other microsomal P450s in the native membrane environment.

Amino Acid Sequence↗
PubMed2002

Role of the C-terminus and the long cytoplasmic loop in reduced folate carrier expression and function.

The reduced folate carrier (RFC1), a member of the major facilitative superfamily, generates uphill transport of folates into cells through an exchange mechanism with intracellular organic anions. RFC1 has twelve transmembrane domains with N- and C-termini, and the long loop connecting the 6th and 7th transmembrane domains, directed to the cytoplasm. To elucidate the role of the C-terminus and the long cytoplasmic loop in carrier function, mutants with deletion of the entire C-terminus or with progressive deletions of the loop region were constructed and stably transfected into the murine MTX(r)A cell line, which lacks functional RFC1. While expression of the C-terminus-deleted RFC1 protein could not be detected in the cell lysate, the RFC1 mutant lacking 57 of 66 amino acid residues of the long cytoplasmic loop appeared to be inserted into the cytoplasmic membrane but was not functional. In cell lines in which 17 or 31 amino acids were deleted from the carboxyl half of the loop, there was partial preservation of methotrexate, 5-formyltetrahydrofolate, and 5-methyltetrahydrofolate transport. The loss of 5-formyltetrahydrofolate transport activity in the delta31 and delta17 mutants was due primarily to a decrease in substrate binding to the carrier. Mutants with partially truncated internal loops demonstrated an anion responsiveness similar to that of wild-type RFC1, indicating that this region of the carrier does not contain a site(s) that plays a role in anion exchange. This is the first study to describe the important role of the long cytoplasmic loop in substrate binding and the crucial role of the C-terminus in maintaining stability of RFC1.

Amino Acid Sequence↗
PubMed2000

Closed loops of nearly standard size: common basic element of protein structure.

By screening the crystal protein structure database for close Calpha-Calpha contacts, a size distribution of the closed loops is generated. The distribution reveals a maximum at 27+/-5 residues, the same for eukaryotic and prokaryotic proteins. This is apparently a consequence of polymer statistic properties of protein chain trajectory. That is, closure into the loops depends on the flexibility (persistence length) of the chain. The observed preferential loop size is consistent with the theoretical optimal loop closure size. The mapping of the detected unit-size loops on the sequences of major typical folds reveals an almost regular compact consecutive arrangement of the loops. Thus, a novel basic element of protein architecture is discovered; structurally diverse closed loops of the particular size.

Protein Structure, Secondary↗
PubMed2000

Properties of an insulin receptor with an IGF-1 receptor loop exchange in the cysteine-rich region.

The insulin receptor (IR) and the insulin-like growth factor-I receptor (IGF-1R) show differential binding of insulin and IGFs. The specificity determinants for IGF-1 binding are known to be located in the cysteine-rich (Cys-rich) region between residues 223 and 274 of human IGF-1R, which includes a loop that protrudes into the putative ligand binding site. In this report we have replaced residues 260-277 of human IR with residues 253-266 of the human IGF-1R to produce an IR-based, cysteine loop exchange chimaera, termed hIR-Cys loop exchange (CLX), in which all 14 amino acid residues in the exchanged loop differ from wild-type insulin receptor. This loop exchange had a detrimental effect on the efficiency of pro-receptor processing and on the binding of the mouse monoclonal antibody 83-7. However, this antibody, which binds hIR but not hIGF-1R, was still capable of immunoprecipitating the mature chimaeric receptor, indicating that the conformational epitope recognised by this antibody is not primarily determined by the loop region exchanged. The loop exchange did not significantly affect the ability of insulin to displace bound radiolabelled insulin, but increased the capacity of IGF-1 to competitively displace labelled insulin by at least 10 fold.

Amino Acid Sequence↗
PubMed2002

Evolutionary relationship between the bacterial HPr kinase and the ubiquitous PEP-carboxykinase: expanding the P-loop nucleotidyl transferase superfamily.

Similarities between protein three-dimensional structures can reveal evolutionary and functional relationships not apparent from sequence comparison alone. Here we report such a similarity between the metabolic enzymes histidine phosphocarrier protein kinase (HPrK) and phosphoenolpyruvate carboxykinase (PCK), suggesting that they are evolutionarily related. Current structure classifications place PCK and other P-loop containing nucleotidyl-transferases into different folds. Our comparison of both HPrK and PCK to other P-loop containing proteins reveals that all share a common structural motif consisting of an alphabeta segment containing the P-loop flanked by an additional beta-strand that is adjacent in space, but far apart along the sequence. Analysis also shows that HPrK/PCK differ from other P-loop containing structures no more than they differ from each other. We thus suggest that HPrK and PCK should be classified with other P-loop containing proteins, and that all probably share a common ancestor that probably contained a simple P-loop motif with different protein segments being added or lost over the course of evolution. We used the structure-based sequence alignment containing residues specific to HPrK/PCK to identify additional members of this P-loop containing family.

Amino Acid Motifs↗