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The agonist-induced phosphorylation of the rat follitropin receptor maps to the first and third intracellular loops.

Previous results from this laboratory have shown that the rat FSH receptor (rFSHR) becomes phosphorylated on S/T residues upon stimulation of transfected cells with human (h)FSH and that a truncation of the C-terminal tail that removes 12 of the 25 intracellular S/T residues does not affect phosphorylation. Based on the results of phosphopeptide-mapping experiments we analyzed three new mutants. rFSHR-1L and rFSHR-3L were constructed by mutating the S/T residues in the first intracellular loop or the third intracellular loop, respectively. rFSHR-(3L+CT) was constructed by mutating all the S/T residues in the third loop as well as S624, the only C-terminal tail residue that was not previously eliminated as a potential phosphorylation site. All mutants were biologically active. The agonist-induced phosphorylation of rFSHR-3L and rFSHR-(3L+CT) were partially reduced, while that of rFSHR-1L was almost completely lost. The agonist-induced uncoupling of rFSHR-1L and rFSHR-3L are retarded to about the same extent, while the agonist-induced internalization is retarded only in rFSHR-1L. Four major conclusions can be made from the present studies: 1) the phosphorylated rFSHR is a common molecular intermediate in agonist-induced uncoupling and internalization; 2) agonist-induced phosphorylation of the rFSHR maps to the first and third intracellular loops; 3) the phosphorylation of the third intracellular loop facilitates agonist-induced uncoupling but is not necessary for agonist-induced internalization; 4) agonist-induced internalization is facilitated by phosphorylation but it is not known if only the first loop, only the third loop, or both the first and third loops need to be phosphorylated for this response.

Amino Acid Sequence↗

Classification of loops of lampbrush chromosomes according to the arrangement of transcriptional complexes.

The arrangement of transcriptional units in the loops of lampbrush chromosomes from oocyte nuclei of urodele amphibia and from primary nuclei of the green alga Acetabularia have been studied in the electron microscope using spread preparations. Loops with different patterns of arrangement of matrix units (i.e. to a first approximation, transcriptional units) can be distinguished: (i) loops consisting of one active transcriptional unit; (ii) loops containing one active transcriptional unit plus additional fibril-free, i.e. apparently untranscribed, intercepts that may include 'spacer' regions; (iii) loops containing two or more transcriptional units arranged in identical or changing polarities, with or without interspersed apparent spacer regions. Morphological details of the transcriptional complexes are described. The observations are not compatible with the concept that one loop reflects one and only one transcriptional unit but, rather, lead to a classification of loop types according to the arrangement of their transcriptional units. We propose that the lampbrush chromosome loop can represent a unit for the coordinate transcription of either one gene or a set of several (different) genes.

Acetabularia↗

[Study of temperature rise in RF irradiation during MR imaging: measurement of local temperature using a loop phantom].

Cases have been reported of a local rise in temperature at the patient's skin and of burns occurring during MR imaging. To verify this phenomenon, we created a phantom from agarose, saline, and preservative, and measured the increase in local temperature. In addition, phantoms of limbs of the human body shaped such that a closed loop was formed were also used. The temperature of the phantom was measured for 50 minutes in each state, i.e., where a closed loop was formed and where the loop was incomplete. Moreover, the radio frequency (RF) and gradient fields were set as respectively independent states, and the temperature of the phantom was measured. Results of the experiment showed that temperature changed from approximately 6 degrees to 11.5 degrees in the closed loop part of the phantom, whereas there was no significant change when the loop was incomplete. In addition, with exposure to RF, a significant rise in temperature occurred where the loop was closed, whereas there was no significant increase in temperature in gradient fields. This experiment demonstrated that the increase in temperature as a result of RF irradiation occurred in the closed part of the loop phantom. Consequently, a loop formed in the human body may be subject to burns in the area of contact.

Adolescent↗

[A comparative study of a thick and standard loop in transurethral resection of the prostate].

We compared the safety and efficacy of transurethral resection of the prostate (TURP) with a thick loop and with a standard loop. We compared 36 consecutive men (median age, 70 years) with symptomatic benign prostatic hyperlasia (BPH) treated by TURP with a thick loop to a cohort of 36 men (median age, 72 years) treated by TURP with a standard loop. The safety parameters of evaluation included the operative time, blood loss, chronological changes in serum sodium, and complications. The efficacy parameters of evaluation included International Prostate Symptom Score, quality of life assessment, peak urinary flow rate, and post-void residual urine volume. The operative time (median, 49.5 versus 43.5 minutes), blood loss (median, 179 versus 127 ml), and change in serum sodium (median, -4.0 versus -6.0 mEq/L) were not significantly greater in the thick loop group than in the standard loop group, respectively. There were no major complications in either group. Clinically significant improvement was observed in all efficacy parameters in both groups, with no difference between the two groups. These results suggest that TURP with a thick loop is not necessarily superior to TURP with a standard loop in terms of decreasing the blood loss and decreasing the operative time.

Aged↗

An avian basal ganglia pathway essential for vocal learning forms a closed topographic loop.

The mammalian basal ganglia-thalamocortical pathway is important for motor control, motor learning, and cognitive functions. It contains parallel, closed loops, at least some of which are organized topographically and in a modular manner. Songbirds have a circuit specialized for vocal learning, the anterior forebrain pathway (AFP), forming a basal ganglia loop with only three stations: the pallial ("cortex-like") lateral magnocellular nucleus of the anterior neostriatum (lMAN), the basal ganglia structure area X, and the medial portion of the dorsolateral thalamic nucleus (DLM). Several properties of this pathway resemble those of its mammalian counterpart, but it is unknown whether all projections in the loop are topographically organized, and if so, whether topography is maintained through the entire loop. After small single- or dual-tracer injections into area X and/or the lMAN of adult zebra finches, we found that the area X to DLM projection is topographically organized, and we confirmed the topography for all other AFP projections. Quantitative analysis suggests maintained topography throughout the loop. To test this directly, we injected different tracers into corresponding areas in lMAN and area X. We found somata retrogradely labeled from lMAN and terminals anterogradely labeled from area X occupying the same region of DLM. Many labeled somata were tightly surrounded by tracer-labeled terminals, indicating the microscopically closed nature of the AFP loop. Thus, like mammals, birds have at least one closed, topographic loop traversing the basal ganglia, thalamus, and pallium. Each such loop could serve as a computational unit for motor or cognitive functions.

Animals↗

Bitewing film quality: a clinical comparison of the loop vs. holder techniques.

OBJECTIVE: To compare in vivo bitewing film quality using the holder versus the paper loop technique. METHOD AND MATERIALS: Four bitewing films were taken from the right and left premolar and molar regions of 45 dental students using both the bitewing holder and paper loop techniques. A total of 360 films were taken and assessed by an experienced practitioner not apprised of the bitewing technique used. Of interest were: (1) the number of overlaps and the percentage of teeth showing the alveolar crest; (2) proper film positioning; and (3) the percentage of cone cutting. A Poisson regression using generalized estimating equations (GEEs) was used to estimate the difference in overlap between the two techniques. For proper positioning and cone cutting, logistic regressions using GEEs were used. RESULTS: The average number of horizontal overlaps for the loop and holder techniques at the right premolar, right molar, left premolar, and left molar were 1.64, 2.11, 2.16, 2.78, and 1.64, 2.00, 2.00, 2.18, respectively. The loop technique was 1.11 times more likely to cause overlapping than the holder technique. The highest percentage of teeth showing the alveolar crest by the loop technique was 97.8% in the mandibular second premolar and first molar. With respect to film positioning, the loop technique was 1.12 times more likely to cause improper positioning than the holder technique. Both techniques demonstrated minimal cone cutting (1 in the loop versus 0 in the holder). CONCLUSION: The quality of bitewing films taken by the loop and holder techniques was not significantly different.

Alveolar Process↗

[Mutations in the D-loop region of mitochondrial DNA and the ROS level in the tissue of hepatocellular carcinoma].

To explore the relationship between ROS level and mutations in D-Loop region of mtDNA, mutations in the D-Loop region of mtDNA and the ROS level in primary hepatocarcinoma tissues were studied. We amplified the D-Loop region of mtDNA of 20 hepatocarcinomas and their adjacent tissue by PCR and then sequencing. ROS in tissue was measured by flow cytometry. mtDNA mutations were detected in 40% (8 of 20) tumor samples. 53 point mutations were detected in eight tumour samples, including 2 insertions, 11 deletions and 40 point mutations. 75% point mutations were T-C and C-T transition. They were four microsatellites among the mutations. Mutations in the adjacent tissues were always companied with mutations in tumour tissues. The mutation frequency in tumour tissues was higher than that in adjacent tissue. There was a larger unidentified deletion. The ROS level in hepatocarcinoma tissue was much higher than control (P<0.01). Meanwhile, we found the ROS level in hepatocarcinoma tissues with mutated mtDNA D-Loop was higher than that hepatocarcinoma tissue normal mtDNA D-Loop, and the ROS level in hepatocarcinoma adjacent tissue with mutated mtDNA D-Loop was higher than that in hepatocarcinoma adjacent tissue with normal mtDNA D-Loop. It was concluded that the D-Loop region of mitochondrial DNA was a highly polymorphoric and mutable region and mutation rate was relatively high in patients with hepaticellular carcinoma, and the abnormal ROS level might be the point mutation in the mitochondrial DNA and hepatocarcinogenesis related to ROS.

Adult↗

Loop electrosurgical excision procedure for CIN.

The loop electrosurgical excision procedure, also referred to as large loop excision of the transformation zone, is gaining acceptance in the United States as a method for treating cervical intraepithelial neoplasia. Loop excision of cervical tissue is accomplished using a high-frequency alternating current (radiofrequency) and thin wire loop electrodes. Loop excision may be in the form of simple excision of the transformation zone or electrosurgical loop conization. The specimens obtained using this technique are suitable for histologic evaluation. Loop excision, which is usually performed under local anesthesia, is associated with minimal short-term and long-term morbidity. Patient acceptance is high. Family physicians who perform colposcopy should consider using loop electrosurgical excision to treat cervical intraepithelial neoplasia in the outpatient setting.

Ambulatory Surgical Procedures↗

Closed-loop control of movement of skeletal muscle.

Closed-loop (feedback) control of skeletal muscle is critically reviewed. The introductory section examines the advantages and disadvantages of open-loop as compared to closed-loop control in general, defines the problem, and outlines our approach. In the biological systems section, muscle structure and function are defined at the level of the motor nerve, neuromuscular junction, and sarcomere. Time delays, power and efficiency, fatigue, and other effects are also discussed in relation to the development of closed-loop control. This section then proceeds to review biological sensors and finally integrates this information by reviewing the body's own closed-loop control system. The third section critically reviews various approaches to the mathematical modeling of muscle. The control problem (in general) is reviewed with particular emphasis on contemporary control systems engineering. Essential to closed-loop control of paralyzed skeletal muscle is sensor technology. Therefore, the fourth section reviews external mechanical sensors. Specifically, potentiometers and Hall effect sensors, capacitive force transducers, inductive displacement transducers (LVDTs), and various position resolvers are discussed. Finally, the fifth section reviews the application of closed-loop control of skeletal muscle to the human being. The focus of this section is the paralyzed individual: past progress and future directions. An extensive bibliography of cited references is then provided so that the interested reader may pursue his/her particular area of interest in more detail. The authors acknowledge that such an extensive review of so many relevant areas is necessarily not complete and often overly simplistic, but our goal is a "first approach" to a comprehensive understanding of the closed-loop (feedback) control problem for achieving movement in paralyzed skeletal muscle.

Animals↗

Scanning electron microscopy of porcine jejunal loops infused with Escherichia coli endotoxin.

Phenol-extracted Escherichia coli endotoxin was infused into ligated jejunal loops in 3 pigs. Tissue samples were collected from the center of each loop 6 hours later and examined with scanning electron microscopy. Control loops infused with pyrogen-free water were examined, as well as nonligated biopsy and blind-loop samples. Loops infused with endotoxin had predominantly ridge-shaped villi, many actively secreting goblet cells, and numerous large epithelial ulcerations involving the tips and sides of villi. Tight junction disruption between epithelial cells was observed in 1 pig. In contrast, small ulcers were rarely seen in ligated control loops. Villi were predominantly tongue-shaped, and goblet cell activity was moderate. Pathologic changes were greater in endotoxin-infused loops than in water-infused loops at 6 hours after infusion.

Animals↗

The majority of neutralizing Abs in HIV-1-infected patients recognize linear V3 loop sequences. Studies using HIV-1MN multiple antigenic peptides.

Multiple antigenic peptides (MAP) comprising eight synthetic peptides corresponding to the V3 loop of HIV-1MN or HIV-1IIIB linked to a lysine core were used to characterize the humoral Ab response of HIV-1-infected patients against this domain. One hundred percent of the tested sera from HIV-1-infected European patients reacted significantly with the HIV-1MN V3 loop MAP. Most, but not all, sera also reacted against the HIV-1IIIB V3 loop MAP, albeit with low titers. The in vitro neutralization capacity of the patients' sera against HIV-1MN or HIV-1IIIB infection were tested. All sera showed significant neutralizing titers against HIV-1MN, in comparison with the low (when detectable) neutralizing titers against HIV-1IIIB. Competition assays revealed that the majority of HIV-1MN-neutralizing Abs in patients' sera react with the V3 loop peptides. Only a small fraction of the total neutralizing capacity, presumably specific for other neutralizing epitopes, could not be adsorbed with HIV-1MN V3 loop peptides. The V3 loop peptides could also compete for the binding of Abs in patients' sera mediating Ab-dependent cellular cytotoxicity (ADCC) of HIV-1MN infected cells, inhibiting 30 to 80% of the ADCC activity. Finally, the HIV-1MN V3 loop MAP, when used as immunogen in the presence of RIBI adjuvant without a carrier protein, elicited Abs able to neutralize HIV-1MN (but not HIV-1IIIB) and to initiate ADCC of HIV-1MN-infected cells. This neutralizing and ADCC activity, mediated by V3MN-specific rabbit Abs, could be totally absorbed by V3MN loop peptides.

Amino Acid Sequence↗

Lack of association between anti-V3 loop antibody and perinatal HIV-1 transmission in Kinshasa, Zaire, despite use of assays based on local HIV-1 strains.

Maternal antibodies against the V3 loop principal neutralizing domain (PND) have been reported to protect against perinatal HIV-1 transmission. To study this association in an African city with a long-standing HIV epidemic and no established "consensus sequence" for the V3 loop region of gp120, we determined the DNA sequence for the V3 region of HIV-1 from 13 HIV-1-infected residents of Kinshasa, Zaire, and developed peptide enzyme immunoassays (EIAs) reflecting the V3 loop PND for those HIV-1 strains. Using the most broadly reactive locally derived V3 loop peptide in a limited-antigen EIA, there was no significant difference in the perinatal HIV-1 transmission risk between 64 women with anti-V3 loop antibody (transmission risk, 30%) and 104 women without anti-V3 loop antibody (transmission risk, 25%; p = 0.5); this finding was unchanged after we controlled for maternal AIDS and low birth weight. Although we used assays for V3 loop antibody based on local HIV-1 strains and evaluated a large number of mother-child pairs, we found no evidence that maternal anti-V3 loop PND antibody protects against perinatal HIV-1 transmission.

Amino Acid Sequence↗

Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA.

The initiation of translation on the positive-sense RNA genome of hepatitis C virus (HCV) is directed by an internal ribosomal entry site (IRES) that occupies most of the 341-nt 5' nontranslated RNA (5'NTR). Previous studies indicate that this IRES differs from picornaviral IRESs in that its activity is dependent upon RNA sequence downstream of the initiator AUG. Here, we demonstrate that the initiator AUG of HCV is located within a stem-loop (stem-loop IV) involving nt -12 to +12 (with reference to the AUG). This structure is conserved among HCV strains, and is present in the 5'NTR of the phylogenetically distant GB virus B. Mutant, nearly genome-length RNAs containing nucleotide substitutions predicted to enhance the stability of stem-loop IV were generally deficient in cap-independent translation both in vitro and in vivo. Additional mutations that destabilize the stem-loop restored translation to normal. Thus, the stability of the stem-loop is strongly but inversely correlated with the efficiency of internal initiation of translation. In contrast, mutations that stabilize this stem-loop had comparatively little effect on translation of 5' truncated RNAs by scanning ribosomes, suggesting that internal initiation of translation follows binding of the 40S ribosome directly at the site of stem-loop IV. Because stem-loop IV is not required for internal entry of ribosomes but is able to regulate this process, we speculate that it may be stabilized by interactions with a viral protein, providing a mechanism for feedback regulation of translation, which may be important for viral persistence.

Antigens, Viral↗

Use of circular permutation to assess six bulges and four loops of DNA-packaging pRNA of bacteriophage phi29.

A 120-base phage phi29 encoded RNA (pRNA) has a novel role in DNA packaging. This pRNA possesses five single-base bulges, one three-base bulge, one bifurcation bulge, one bulge loop, and two stem loops. Circularly permuted pRNAs (cpRNA) were constructed to examine the function of these bulges and loops as well as their adjacent sequences. Each of the five single-base bulges was nonessential. The bifurcation bulge could be deleted and replaced with a new opening to provide flexibility for maintaining an overall correct folding in three-way junction. All of these nonessential bulges or their adjacent bases could be used as new termini for cpRNAs. The three-base (C18C19A20) bulge was dispensable for procapsid binding, but was indispensable for DNA packaging. The secondary structure around this CCA bulge and the phylogenetically conserved bases within or around it were investigated. Bases A14C15U16 were confirmed, by compensatory modification, to pair with U103G102A101. A99 was needed only to allow the proper folding of CCA bulge in the appropriate sequence order and distance constraints. Beyond these, the seemingly phylogenetic conservation of other bases has little role in pRNA activity. Each of the three stem loops was essential for procapsid binding, DNA packaging, and phage assembly. Disruption of the middle of any one of the loops resulted in dramatic reductions in procapsid binding, subsequent DNA packaging, and phage assembly activities. However, disruption of the loops at sequences that were close to double-stranded regions of the RNA did not interfere with pRNA activity significantly. Our results suggest that double-stranded helical regions near these loops were most likely not involved in interactions with components of the DNA-packaging machinery. Instead, these regions appear to be merely present to serve as a scaffolding to display the single-stranded loops that are important for pRNA tertiary structure or for interaction with the procapsid or other packaging components.

Bacillus Phages↗

The effect of pseudouridine and pH on the structure and dynamics of the anticodon stem-loop of tRNA(Lys,3).

The anticodon stem-loop hairpin of tRNA(Lys,3) was synthesized and the solution structure determined by NMR spectroscopy. The hairpin is thermodynamically stabilized by pseudouridine as determined by UV Tm measurements, and the local loop structure is stabilized with base-stacking of the nucleosides in the anticodon loop 5' of the psi 39 nucleoside modification. The tRNA(Lys,3) hairpin also contains an A(+)-C base-pair that effectively reduces the size of the normal 7 nucleotide anticodon loop to 5 nucleotides and induces a change in the loop backbone conformation. The stabilizing effects of the A(+)-C base-pair and pseudouridine are only partially additive, suggesting that the conformational changes caused by each modification are not completely compatible. The structure of the anticodon loop is distinctly different from that seen for other tRNAs exemplified by tRNA(Phe), suggesting that the full complement of modified nucleosides present in tRNA(Lys,3) should significantly change the structure compared to the unmodified tRNA anticodon loop. The conformation of the loop has important implications for the role of nucleoside modification in codon-anticodon recognition and for utilization of tRNA(Lys,3) by HIV-1 as the natural reverse transcriptase primer.

Anticodon↗

Diverting loop versus end ileostomy during ileoanal pullthrough procedure for ulcerative colitis.

A two-stage ileoanal pullthrough procedure (IAPP) is often used for patients with ulcerative colitis (UC) requiring proctocolectomy. We analyzed the recent University of California at Los Angeles experience with diverting end and loop ileostomies in patients undergoing a two-stage IAPP. A retrospective analysis of 21 patients with UC undergoing loop ileostomy between March 1992 and March 1995 was performed. Comparison was made with 21 age- and gender-matched patients undergoing end ileostomy between January 1991 and December 1995. There was no mortality or major septic complications. A second laparotomy was required in all patients with end ileostomies, whereas loop ileostomies were closed without abdominal exploration. During ileostomy closure, operative time and mean hospital stay were significantly reduced with the use of loop ileostomy. The time to oral feeding was not significantly different between end and loop ileostomy groups after ileostomy closure. The complication rate after IAPP was similar between groups. However, after ileostomy closure, the complication rate was significantly reduced with the use of loop ileostomy. We conclude that loop ileostomy is a desirable option for UC patients undergoing intestinal diversion during IAPP. Loop ileostomies can be created easily and without an increase in operative time. Subsequent ileostomy closure can be performed as a local procedure, which may shorten operative time and length of hospital stay.

Adolescent↗

AAV-mediated genome editing is influenced by the formation of R-loops.

Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for in&#xa0;vivo gene therapy. However, rAAVs also integrate throughout the genome. Here, we describe DNA-RNA immunoprecipitation sequencing (DRIP-seq) in murine HEPA1-6 hepatoma cells and whole murine liver to establish the similarities and differences in genomic R-loop formation in a transformed cell line and intact tissue. We show enhanced AAV-HR in mice upon genetic and pharmacological upregulation of R-loops. Selecting the highly expressed Albumin gene as a model locus for genome editing in both in&#xa0;vitro and in&#xa0;vivo experiments showed that the R-loop prone 3' end of Albumin was efficiently edited by AAV-HR, whereas the upstream R-loop-deficient region did not result in detectable vector integration. In addition, we found a positive correlation between previously reported off-target rAAV integration sites and R-loop enriched genomic regions. Thus, we conclude that high levels of R-loops, present in highly transcribed genes, may promote rAAV vector genome integration. These findings may shed light on potential mechanisms for improving the safety and efficacy of genome editing by modulating R-loops and may enhance our ability to predict regions most susceptible to off-target insertional mutagenesis by rAAV vectors.

Dependovirus↗

An examination of glutamic acid in the -X chelating position of the helix-loop-helix calcium binding motif.

Poor calcium affinity was exhibited in helix-loop-helix calcium binding motifs with X-axis acid pairs containing aspartic acid in the -X chelating position. In order to increase interaction of the -X chelating residue with the cation, helix-loop-helix calcium binding motifs were synthesized containing three and four acid residues in chelating positions, with a glutamic acid replacing aspartic acid in the -X chelating position. The glutamate-containing motif gave an unexpected 6-fold decrease in cation affinity for the three-acid residue loop motif (KCa = 524 microM vs KCa = 3140 microM) and a 46-fold decrease for the four-acid residue loop motif (KCa = 42.1 microM vs KCa 1950 microM). To improve calcium binding of the glutamate-containing motifs, peptides were synthesized keeping glutamate in the -X position and inserting serine in the +Z position to provide a hydrogen-bonded system stabilizing the glutamate interaction with the cation. The serine residue further reduced calcium affinity in both the three-acid residue loop (KCa = 19.6 mM) and the four-acid residue loop (KCa = 2806 microM). These results indicate that glutamate and serine residues in the -X and +Z positions, respectively, can be detrimental to calcium binding. However, in natural calcium binding proteins, glutamate in the -X chelating position can confer high affinity for calcium in helix-loop-helix calcium binding motifs, but this may be dependent on the environment created by as yet undetermined factors.

Amino Acid Sequence↗