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PubMed1994

Upstream introns influence the efficiency of final intron removal and RNA 3'-end formation.

For all intron-containing pre-mRNAs of higher eukaryotes that have been examined using either living cells or cell-free extracts, a functional 3' splice site within the 3'-terminal intron is required for efficient RNA 3'-end formation. The mechanism by which intron sequences facilitate RNA 3'-end formation, which is achieved by endonucleolytic cleavage and polyadenylation, is not understood. We report here that in intact cells the efficiency of RNA 3'-end formation correlates with the efficiency of final intron removal, even when the intron is normally a 5'-terminal or internal intron. Therefore, the influence of the 3'-terminal intron on 3'-end formation is likely to be attributable to the determinants of splicing efficiency, which include but are not limited to the 3' splice site. Quantitative RNase mapping and methods that couple reverse transcription and the polymerase chain reaction were used to assess the consequence to RNA 3'-end formation of intron deletions within the human gene for triosephosphate isomerase (TPI). Results indicate that the formation of TPI RNA 3' ends requires TPI gene introns in addition to the last intron, intron 6, to proceed efficiently. These additional TPI gene introns are also required for the efficient removal of intron 6. When introns 1 and 5 were engineered to be the final intron, they were found, as was intron 6, to function in RNA 3'-end formation with an efficiency that correlated with their efficiency of removal. The simultaneous deletion of the 5' and 3' splice sites of intron 6 reduced the efficiencies of both RNA 3'-end formation and the removal of intron 5, which constituted the 3'-most functional intron. Deletion of only the 3' splice site of intron 6 precluded RNA 3'-end formation but had no effect on the efficiency of intron 5 removal. Deletion of only the 5' splice site of intron 6, which resulted in exon 6 skipping (i.e., the removal of intron 5, exon 6, and intron 6 as a single unit), had no effect on the efficiencies of either RNA 3'-end formation or the removal of intron 5-exon 6-intron 6. These results indicate that sequences within the 3'-terminal intron are functionally coupled to both RNA 3'-end formation and removal of the penultimate intron via a network of interactions that form across the last two exons and, most likely, between RNA processing factors.

Base Sequence↗

PubMed1997

Attitudes of physical therapists who possess sports specialist certification.

Physical therapists contemplating sports specialist certification need research-based information to facilitate their decision-making process. The purpose of this study was to investigate the attitudes of physical therapists who have received sports specialist certification. These attitudes encompass the physical therapists' sense of fulfillment and their feelings of satisfaction or dissatisfaction with the certification process. Factors contributing to the therapist's decision to become sports specialist certified have also been investigated. Physical therapists who are sports certified specialists (N = 110) participated in this study. Questionnaires were mailed to the entire population of physical therapists who are sports certified specialists (N = 148). Frequency distributions and percentages were used on qualitative data, and mode was calculated for quantitative data. One hundred ten surveys were returned, for a response rate of 74.3%. Analysis of responses from the subject group suggests that physical therapists feel a high level of satisfaction with their decision to specialize, and that continued professional growth, development, and personal achievement are the major contributing factors in their decision to specialize. Based on these findings, physical therapists appeared to display overall satisfaction in their attitudes toward sports specialist certification. Further research may be warranted to further examine sports certified therapists' attitudes toward the specialization process.

Adult↗

PubMed1997

The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I.

Bacteriophage T7 DNA polymerase shares extensive sequence homology with Escherichia coli DNA polymerase I. However, in vivo, E. coli DNA polymerase I is involved primarily in the repair of DNA whereas T7 DNA polymerase is responsible for the replication of the viral genome. In accord with these roles, T7 DNA polymerase is highly processive while E. coli DNA polymerase I has low processivity. The high processivity of T7 DNA polymerase is achieved through tight binding to its processivity factor, E. coli thioredoxin. We have identified a unique 76-residue domain in T7 DNA polymerase responsible for this interaction. Insertion of this domain into the homologous site in E. coli DNA polymerase I results in a dramatic increase in the processivity of the chimeric DNA polymerase, a phenomenon that is dependent upon its binding to thioredoxin.

Bacteriophage T7↗

PubMed1991

Fish meal as a protein supplement in ruminant diets: a review.

Fish meal (FM) as a protein supplement in ruminant diets is presented to illustrate production responses to FM supplementation and to explain the possible factors that may affect the magnitude of these responses. Positive responses are consistently detected when FM is fed to nonruminants, but the responses when fed to ruminants have lacked consistency. Research indicates that ruminal protein degradation of FM is affected by processing factors including type and freshness of fish, addition of preservatives, stabilization of fat, type of dryer used, temperature and duration of heating, and the amount of fish solubles added back to the meal. Performance data published in the last two decades have been categorized into body weight gain and milk yield and composition. Fish meal was more effective in improving body weight gain in young than in finishing ruminants and in males than in females or castrated males. Daily gains and feed efficiencies were higher when FM supplemented medium- or poor-quality silages than when it was added to high-quality silages. No significant advantage was found for replacing protein sources that were highly ruminally degradable with FM in high-corn diets fed to growing ruminants. Milk yield and milk protein concentration were improved by FM supplementation of low-concentrate diets fed to cows in early lactation. However, milk fat percentage was negatively affected by FM supplementation. Reproduction data indicated that body gain and conception rates of high-producing cows were improved by supplementing their diets with FM during early lactation. Results suggest a significant advantage of FM supplementation to ruminant diets if the physiological status of the animal and the quality of the dietary ingredients are taken into account.

Animal Feed↗

PubMed1997

Regulation of tRNA suppressor activity by an intron-encoded polyadenylation signal.

A 26-nt sequence from the 3' UTR of the yeast GAL7 mRNA directs accurate and efficient cleavage and polyadenylation to form the 3' end of the GAL7 mRNA in vivo and in vitro. Here we asked whether this polyadenylation signal can function within the context of a tRNA. Insertion of the GAL7 signal into the intron of the dominant SUP4 nonsense suppressor allowed us to judge the effect of the insert on SUP4 function by observation of nonsense suppression efficiency in vivo. The GAL7 signal impairs the function of SUP4 in an orientation-dependent manner in vivo, consistent with its ability to specify cleavage and polyadenylation in this context in vitro. Mutation of a UA repeat within the GAL7 signal restores SUP4 function partially, consistent with the role of this repeat as an efficiency element in polyadenylation. Mutations that impair the mRNA 3' end-processing factors Rna14p and Rna15p restore suppressor function partially. Northern blot analysis, PCR amplification, and DNA sequence analysis show that the GAL7 signal directs polyadenylation within the body of pre-SUP4 and within the terminator, suggesting that polyadenylation inhibits 5' and 3' end processing, as well as removal of the pre-tRNA intron. These findings indicate that the GAL7 polyadenylation signal is capable of targeting a pre-tRNA to the mRNA processing pathway.

Base Sequence↗

PubMed1994

Organization of small nucleolar ribonucleoproteins (snoRNPs) by fluorescence in situ hybridization and immunocytochemistry.

The organization of the U3, U8, and U13 small nucleolar ribonucleoproteins (snoRNPs) has been investigated in HeLa cells using antisense DNA and 2'-OMe RNA oligonucleotides. Oligomers corresponding to deoxynucleotides that target RNase H degradation of intact RNP particles were synthesized and used for fluorescence in situ hybridization. U3 and U13 are distributed throughout the nucleolus and colocalize with anti-fibrillarin antibodies. U8, however, is organized in discrete ring-like structures near the center of the nucleolus and surround bright punctate regions visualized with anti-RNA polymerase I and anti-UBF/NOR-90 antibodies. In decondensed nucleoli, a necklace of smaller ring-like structures of U8 RNA appear. A model for the recruitment of U8 (and presumably other processing factors) to the sites of rRNA transcription is discussed. Hybridization to mitotic cells showed that unlike pol I and NOR-90, U8 is dispersed into the cytoplasm during mitosis. The subnucleolar organization of U8 is consistent with its demonstrated participation in early intermediate steps in pre-rRNA processing. In contrast, the more dispersed intranucleolar distribution of U3 agrees with its putative involvement in both early and late steps of rRNA maturation. These studies illustrate the feasibility of mapping functional domains within the nucleolus by correlating the in vitro activities of small nuclear RNPs with their in situ locations.

Base Sequence↗

PubMed1994

A second look at second-order belief attribution in autism.

Compared the performance of autistic and mentally retarded subjects, all of whom had passed a standard first-order test of false belief, on a new second-order belief task. 12 autistic and 12 mentally retarded subjects, matched on verbal mental age (assessed by PPVT and a sentence comprehension subtest of the CELF) and full-scale IQ were given two trials of a second-order reasoning task which was significantly shorter and less complex than the standard task used in all previous research. The majority of subjects in both groups passed the new task, and were able to give appropriate justifications to their responses. No group differences were found in performance on the control or test questions. Findings are interpreted as evidence for the role of information processing factors rather than conceptual factors in performance on higher order theory of mind tasks.

Adolescent↗

PubMed1995

[The role of neurotrophic factors in adaptational processes in the nervous system].

Many of neurotrophic factors (NTF) promote the survival during development, growth and neurite differentiation of neurons. The most known NTF are nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophins-3,4,5. These factors increase the survival of peripheral sensory neurons and some central neurons. The NTF are produced by the target of neuronal proections including brain tissues. So the process of adaptation in the nervous system may be also connected with level of the NTF. Recently it is shown that the NTF level in the brain is changed by central nervous system deseases--epilepsy, Parcinson and Alcgeimer deseases. In this conditions NGF and BDNF mRNC expression and their receptors mRNC are increased. So NTF diffusion in intracellular space can provide the brain function regulation in normal and pathological conditions. Model of chronic epileptogenesis was in vitro. The organotypic coculture was used--the rat newborn hippocampus and chick embryo dorsal root ganglia. Veratridine (30 nM) added in culture media induced neuronal activity in hippocampus explants and the level of NTF in media cosequently rised. It was shown that neurite-stimulating effect was mediated by veratridine. This action was blocked by NGF-antybody treatment and due to NGF activity.

Adaptation, Physiological↗

PubMed1991

Complex factors in hydrocarbon/water, soil/water and fish/water partitioning.

Many partitioning and toxicological events that appear to correlate simply with log P (octanol/water) can be resolved into greater detail by a factoring process. Log P can be separated into lipophilic (PL) and hydrophilic (PH) contributions that combine well with polarizability (MR) and hydrogen-bonding (HB) to describe partitioning and non-specific binding in phases that differ greatly from n-octanol. In addition, hydrogen-bonding can be factored into donor groups (HBD) and acceptor groups (HBA) for stronger correlations and greater mechanistic insight. These descriptors are applied to a variety of problems in simple partitioning, soil organic matter binding, bioaccumulation in fish, and aquatic narcosis and toxicity.

Animals↗

PubMed1991

Proper and improper folding of proteins in the cellular environment.

Protein folding in the cellular environment involves an interplay between the intrinsic biophysical properties of a protein, in both its folded and unfolded states, and various accessory proteins that aid the process. Factors such as peptidyl prolyl isomerase, protein disulfide isomerase, thioredoxin, and SecB may interact with the unfolded forms of specific classes of proteins, while members of the hsp70/DnaK and hsp60/GroEL molecular chaperone families may play a more general role in folding. Secretion, proteolysis, and aggregation are other in vivo processes that depend greatly on the folding behavior of a given protein. Intrinsic folding rates, or even translation rates, of nascent proteins may be optimized by natural selection to ensure smooth coordination with all the cellular components required for a successful folding reaction.

Bacterial Proteins↗

PubMed1996

Improving pain management in critical care.

BACKGROUND: In April 1994 at the University of California at Los Angeles Medical Center the Surgical Intensive Care Unit's (SICU's) Quality Improvement Council unanimously agreed on pain management as one of the major factors that negatively affect outcomes for their patient population. Using the FOCUS-PDCA (plan-do-check-act) model for quality improvement (QI), the council chartered a subcommittee to improve the pain management in their ICUs. METHODOLOGY: The subcommittee first measured the pain assessment scores of patients at transfer from the ICU. After ascertaining that these scores were greater than the goal of 2, the process of providing pain relief was examined with the assistance of process control statistics, which showed a process barely capable of meeting the goal of pain score of 2 or less on a 0-5 scale. The process factors that affected this outcome were examined and changes were made where appropriate. One of these changes was development of a guideline for acute pain management based on the Agency for Health Care Policy Research's Acute Pain Management Clinical Practice Guideline. Reassessment of the pain scores and the process was then conducted. RESULTS: The pain assessment scores at transfer from the ICU decreased significantly. Thirty-five percent of patients in the preguideline survey rated their scores as greater than 2, compared with only 21% at the postguideline survey. Pain assessment and documentation also improved significantly. CONCLUSION: The Quality Improvement Council felt that improvements in pain management were due largely to their having provided staff with the right tools to use in assessing, documenting, and controlling pain. Gains in pain management continue to be made.

Hospitals, University↗

PubMed1988

[Effect of nerve growth factor on synaptic processes in the sympathetic ganglion].

The nerves growth factor (7S NGF) from salivary glands of male mice activated the interneuronal relations in the inferior mesenteric plexus of 6-14-day old guinea-pigs. Superfusion of the ganglia with 7S NGF diluted to 1 X 10(-8) M (135 ng/ml) inhibited suppression of the acetylcholine release with hemicholinum or modified solutions. Atropine (1 X 10(-6) M) did not alter, and benzohexonium (1 X 10(-6) M) eliminated the excitatory effect of the 7S NGF Under d-tubocurarine (1 X 10(-6) M) blockade of H-cholinoreceptors, the 7S NGF decreased the MP and increased the duration blockade of synaptic transmission. Reduction of the tested protein effects in presence of potassium (K+ - 0.24 mM) and ouabain (1 X 10(-7) M) suggested the effect of the 7S NGF on processes of active and passive movements of electrogenic cations.

Action Potentials↗

PubMed2025

The RNA splicing factor PRPF8 is required for left-right organiser cilia differentiation and determination of cardiac left-right asymmetry via regulation of Arl13b splicing.

Cilia function in the left-right organizer (LRO) is critical for determining internal organ asymmetry in vertebrates. To further understand the genetics of left-right asymmetry, we isolated a mouse mutant with laterality defects, l11Jus27, from a random mutagenesis screen. l11Jus27 mutants carry a missense mutation in the pre-mRNA processing factor, Prpf8. cephalophŏnus (cph) mutant zebrafish, carrying a protein truncating mutation in prpf8, phenocopy the laterality defects of l11Jus27 mutants. Prpf8 mutant mouse and fish embryos have increased expression of an alternative transcript encoding the cilium-associated protein, ARL13B, that lacks exon 9. In zebrafish, over-expression of the arl13b transcript lacking exon 9 perturbed cilium formation and caused laterality defects. The shorter ARL13B protein isoform lacked interactions with intraflagellar transport proteins. Our data suggest that PRPF8 plays a prominent role in LRO cilia by through the regulation of alternative splicing of ARL13B, thus uncovering a new mechanism for cilia-linked developmental defects.

ARL13B↗

PubMed1997

Novel genes involved in endosomal traffic in yeast revealed by suppression of a targeting-defective plasma membrane ATPase mutant.

A novel genetic selection was used to identify genes regulating traffic in the yeast endosomal system. We took advantage of a temperature-sensitive mutant in PMA1, encoding the plasma membrane ATPase, in which newly synthesized Pma1 is mislocalized to the vacuole via the endosome. Diversion of mutant Pma1 from vacuolar delivery and rerouting to the plasma membrane is a major mechanism of suppression of pma1(ts). 16 independent suppressor of pma1 (sop) mutants were isolated. Identification of the corresponding genes reveals eight that are identical with VPS genes required for delivery of newly synthesized vacuolar proteins. A second group of SOP genes participates in vacuolar delivery of mutant Pma1 but is not essential for delivery of the vacuolar protease carboxypeptidase Y. Because the biosynthetic pathway to the vacuole intersects with the endocytic pathway, internalization of a bulk membrane endocytic marker FM 4-64 was assayed in the sop mutants. By this means, defective endosome-to-vacuole trafficking was revealed in a subset of sop mutants. Another subset of sop mutants displays perturbed trafficking between endosome and Golgi: impaired pro-alpha factor processing in these strains was found to be due to defective recycling of the trans-Golgi protease Kex2. One of these strains defective in Kex2 trafficking carries a mutation in SOP2, encoding a homologue of mammalian synaptojanin (implicated in synaptic vesicle endocytosis and recycling). Thus, cell surface delivery of mutant Pma1 can occur as a consequence of disturbances at several different sites in the endosomal system.

Biological Transport↗

PubMed1996

Requirement of proliferating cell nuclear antigen in RAD6-dependent postreplicational DNA repair.

The proliferating cell nuclear antigen (PCNA) acts as a processivity factor for replicative DNA polymerases and is essential for DNA replication. In vitro studies have suggested a role for PCNA-in the repair synthesis step of nucleotide excision repair, and PCNA interacts with the cyclin-dependent kinase inhibitor p21. However, because of the lack of genetic evidence, it is not clear which of the DNA repair processes are in fact affected by PCNA in vivo. Here, we describe a PCNA mutation, pol30-46, that confers ultraviolet (UV) sensitivity but has no effect on growth or cell cycle progression, and the mutant pcna interacts normally with DNA polymerase delta and epsilon. Genetic studies indicate that the pol30-46 mutation is specifically defective in RAD6-dependent postreplicational repair of UV damaged DNA, and this mutation impairs the error-free mode of bypass repair. These results implicate a role for PCNA as an intermediary between DNA replication and postreplicational DNA repair.

Centrifugation, Density Gradient↗

PubMed1997

Mutational analysis of ectopic factor VIII transcripts from hemophilia A patients: identification of cryptic splice site, exon skipping and novel point mutations.

Mutational analysis of the gene for clotting factor VIII is complicated by its large size, the high frequency of de novo mutations and its tissue-specific expression. In order to facilitate the search for mutations, we have used a combination of reverse transcription-polymerase chain reaction (RT-PCR) of ectopic factor VIII transcripts, PCR of genomic DNA, single-strand conformation polymorphism analysis and direct sequencing. Here we describe the characterization of seven potentially pathogenic mutations: five of them are novel and the reason for the pathogenicity of the sixth could be determined. Here cDNA analysis revealed the absence of the first 47 bp of exon 16 in approximately 80% of the processed factor VIII mRNA, likely due to activation of a cryptic acceptor splice site within exon 16. The other novel mutations reported here include the skipping of exon 19, which predicts the removal of the corresponding 39 amino acids from the A3 domain, and four missense mutations: W14G, Y620C, W1889L, and Q2087R.

DNA Mutational Analysis↗

PubMed1996

Dual role of the 44/62 protein as a matchmaker protein and DNA polymerase chaperone during assembly of the bacteriophage T4 holoenzyme complex.

Processive DNA synthesis in the bacteriophage T4 system requires the formation of a holoenzyme complex composed of the T4 DNA polymerase and the 44/62 and 45 accessory proteins. While ATP hydrolysis by the 44/62 protein is essential for holoenzyme formation, the role of the sliding clamp or processivity factor is attributed to the 45 protein. Beyond the need for ATP hydrolysis, the exact role of the 44/62 protein in complex assembly has not been clearly defined. In this paper, we have investigated the kinetics of complex assembly in the presence of both saturating and substoichiometric concentrations of the 44/62 protein. Under saturating conditions, complex assembly is 100% efficient, with all of the polymerase bound in a processive complex. Under conditions of limiting 44/62 protein, the 44/62 protein can act catalytically to assemble the 45 protein and polymerase into a productive complex. However, kinetic simulations indicate that a significant fraction of polymerase is sequestered in a nonproductive complex with the 45 protein. Thus, a second role for the 44/62 protein during complex assembly is that of a chaperone protein to ensure productive pol.45.DNA complex formation. We have also investigated the stability of the 45 protein on the DNA. The off rate of 0.003 s-1 for the 45 protein closely parallels that of the holoenzyme complex. Therefore, disassembly of the complex appears to involve the coordinated dissociation of both the 45 protein and the polymerase from the DNA.

Bacteriophage T4↗

PubMed1994

Cancer survival and the duration of symptoms. An analysis of possible forms of the risk function. ISDS II Project Investigators.

The time interval between onset of symptoms and the diagnosis of cancer [symptom to diagnosis interval (SDI), or duration of symptoms] is a highly complex variable reflecting patient behaviour, the clinical course, the functioning of the health system and tumour biology. In order to assess possible forms of the risk function of SDI upon cancer survival whilst taking into account the effects of age, sex, tumour site and stage at diagnosis, 1887 symptomatic cases of lung, breast, stomach, colon, rectal, bladder cancer and lymphomas registered in the Tumour Registry of the Hospital del Mar (Barcelona) were analysed by means of survival curves and Cox proportional hazards regression. Subjects (mean age 64 years) were followed for a median length of 15 months after diagnosis (follow-up rate 93.5%). SDI showed a weak relationship with tumour stage at diagnosis and with survival: out of the seven sites studied, only in breast cancer was tumour extension at diagnosis significantly influenced by duration of symptoms, and only lung and rectal cancers showed a detectable form of the risk function of SDI upon survival; neither was linear, and for rectal cancer the relationship was complexly related with tumour stage. Hence, results show that forms of the risk function of duration of symptoms on cancer survival are specific to tumour sites, and that the interval should not be represented as a linear, continuous term. Studies analysing more complex sets of factors, processes and forms of the SDI function are needed.

Age Distribution↗