A high-density differential screening strategy for identification of fovea genes with altered expression in the retina during aging

A human fovea cDNA library was arrayed at high-density and reacted with age-specific (4 yr & 80 yr) retinal probes to identify genes with altered expression during aging. Using this approach, we screened 55,368 genes by Southern analysis and determined that 0.7% are differentially expressed in young and old tissues. Northern analysis of total RNA from retina of humans aged 2–94 yr show that expression of one of the clones identified (clone dd₁₁₂) decreases with aging.     

Specific myosin heavy chain mutations suppress troponin I defects in Drosophila muscles

We show that specific mutations in the head of the thick filament molecule myosin heavy chain prevent a degenerative muscle syndrome resulting from the hdp2 mutation in the thin filament protein troponin I. One mutation deletes eight residues from the actin binding loop of myosin, while a second affects a residue at the base of this loop. Two other mutations affect amino acids near the site of nucleotide entry and exit in the motor domain. We document the degree of phenotypic rescue each suppressor permits and show that other point mutations in myosin, as well as null mutations, fail to suppress the hdp2 phenotype. We discuss mechanisms by which the hdp2 phenotypes are suppressed and conclude that the specific residues we identified in myosin are important in regulating thick and thin filament interactions. This in vivo approach to dissecting the contractile cycle defines novel molecular processes that may be difficult to uncover by biochemical and structural analysis. Our study illustrates how expression of genetic defects are dependent upon genetic background, and therefore could have implications for understanding gene interactions in human disease.     

Evaluating a new graphical ordinal logit method (GOLDminer) in the diagnosis of myocardial infarction utilizing clinical features and laboratory data

OBJECTIVE: We used a new graphical ordinal logit method (GOLDminer) to assess a single cardiac troponin T (cTnT) analysis at the time of admission (first generation monoclonal; Roche BMC Corp., Indianapolis, Indiana), the character of chest pain, and electrocardiographic (ECG)findings in predicting the likelihood of acute myocardial infarction (AMI) in patients presenting with suspected myocardial ischemia. The final diagnosis of AMI was based on serial ECG findings and evolution of CKMB isoenzyme levels in conjunction with clinical findings. SUBJECTS: The study population consisted of 293 consecutive patients who presented at a mean of six hours after onset of chest pain or associated symptoms warranting a "rule-out" for AMI assessment to a university-affiliated community hospital. RESULTS: The odds-ratio for an elevated cTnT (> 0. 1 ng/ml) in AMI was 22.2:1. There was an association between typical chest pain and cTnT (chi square = 78.23, p < .0001) and between abnormal ECG findings and cTnT (chi square = 108, p < .0001). The cTnT yielded diagnostic benefit in addition to chest pain characteristics and ECG findings in AMI. We present the odds-ratios for the combined features in GOLDminer plots. CONCLUSION: We demonstrate how the odds-ratios for AMI are obtained after scaling continuous to ordinal the values for a single cTnT determination alone and with other features in patients presenting with chest pain.     

Diagnosis of myocardial infarction: integration of serum markers and clinical descriptors using information theory

OBJECTIVE: We examine the use of information theory applied to a single cardiac troponin T (cTnT) (first generation monoclonal; Boehringer Mannheim Corp., Indianapolis, Indiana) used with the character of chest pain, electrocardiography (ECG) and serial ECG changes in the evaluation of acute myocardial infarction (AMI). We combined a single measure of cTnT (blinded to the investigators) with a creatine kinase MB isoenzyme (CK-MB) measurement to discover the best decision value for this test in a study of 293 consecutive patients presenting to the emergency department with symptoms warranting exclusion of AMI. METHODS: The decision value for determining whether cTnT is positive or negative was determined independently of the final diagnosis by examining the information in the cTnT and CKMB data. Using information theory, an autocorrelation matrix with a one-to-one pairing of the CKMB and troponin T was constructed. The effective information, also known as Kullback entropy, assigned the values for troponin T and for CKMB that have the lowest frequency of misclassification error. The Kullback entropy is determined by subtracting the data entropy from the maximum entropy of the data set in which the information has been destroyed. The assignment of the optimum decision values was made independently of the clinical diagnoses without the construction of a receiver-operator characteristic curve (ROC). The final diagnosis of AMI was independently determined by the clinicians and entered into the medical record. RESULTS: The decision value for cTnT was 0.1 ng/ml as determined by the the information in the data. The method was validated within the same study by mapping the results so obtained into the diagnoses obtained independently by the clinicians using all of the methods at their disposal. The cTnT was different in AMI (n = 60) compared with non-AMI patients (n = 233) (2.08 +/- 0.21 vs. 0.07 +/- 0.10; p < .0001). CONCLUSION: Information theory provides a strong framework and methodology for determining the decision value for cTnT which minimizes misclassification errors at 0.1 ng/ml. The result has a strong correlation with other features in detecting AMI in patients presenting with chest pain.     

Assembly of thick filaments and myofibrils occurs in the absence of the myosin head

We investigated the importance of the myosin head in thick filament formation and myofibrillogenesis by generating transgenic Drosophila lines expressing either an embryonic or an adult isoform of the myosin rod in their indirect flight muscles. The headless myosin molecules retain the regulatory light-chain binding site, the alpha-helical rod and the C-terminal tailpiece. Both isoforms of headless myosin co-assemble with endogenous full-length myosin in wild-type muscle cells. However, rod polypeptides interfere with muscle function and cause a flightless phenotype. Electron microscopy demonstrates that this results from an antimorphic effect upon myofibril assembly. Thick filaments assemble when the myosin rod is expressed in mutant indirect flight muscles where no full-length myosin heavy chain is produced. These filaments show the characteristic hollow cross-section observed in wild type. The headless thick filaments can assemble with thin filaments into hexagonally packed arrays resembling normal myofibrils. However, thick filament length as well as sarcomere length and myofibril shape are abnormal. Therefore, thick filament assembly and many aspects of myofibrillogenesis are independent of the myosin head and these processes are regulated by the myosin rod and tailpiece. However, interaction of the myosin head with other myofibrillar components is necessary for defining filament length and myofibril dimensions.     

Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain

Proper folding of the RNA is an essential step in the assembly of functional ribonucleoprotein complexes. We examined the role of conserved base pairs formed between two distant loops in the Alu portion of the mammalian signal recognition particle RNA (SRP RNA) in SRP assembly and functions. Mutations disrupting base pairing interfere with folding of the Alu portion of the SRP RNA as monitored by probing the RNA structure and the binding of the protein SRP9/14. Complementary mutations rescue the defect establishing a role of the tertiary loop–loop interaction in RNA folding. The same mutations in the Alu domain have no major effect on binding of proteins to the S domain suggesting that the S domain can fold independently. Once assembled into a complete SRP, even particles that contain mutant RNA are active in arresting nascent chain elongation and translocation into microsomes, and, therefore, tertiary base pairing does not appear to be essential for these activities. Our results suggest a model in which the loop–loop interaction and binding of the protein SRP9/14 play an important role in the early steps of SRP RNA folding and assembly.     

Cloning and characterization of Kin5, a novel Tetrahymena ciliary kinesin II

Two Tetrahymena kinesin-like proteins (klps) of the kinesin II subfamily, Kin1 and Kin2, were first identified by Brown et al. [1999: Mol Biol Cell 10: 3081-3096] and shown to be involved in ciliary morphogenesis probably as molecular motors in intraciliary transport (ICT). Using Tetrahymena genomic DNA as a template, we cloned Kin5, another kinesin II subfamily member. Kin5 is upregulated upon deciliation, suggesting that Kin5 is a ciliary protein. Kin5 is most closely related to Osm3, a Caenorhabditis elegans kinesin II; Osm3 and Kin5 have a 56% identity, which rises to 60.4% in the motor domain and a 45% identity in a 60 amino acid region of the C-terminal FERM (4.1, Ezrin, Radixin, Moesin) domain, not present in Kin1 or Kin2, which we hypothesize to be a critical domain either for dimerization or for cargo recognition in ICT. An antibody to a peptide sequence from the tail region of Kin5 localizes in a punctate pattern along the ciliary axoneme, colocalizing with an antibody to the raft protein IFT139. These findings suggest that Kin5 is an ICT motor like Osm3. Osm3 orthologs apparently transport membrane proteins and Kin5 may be the homodimeric kinesin II that performs this function in Tetrahymena cilia.     

(2-amino-phenyl)-amides of omega-substituted alkanoic acids as new histone deacetylase inhibitors

A variety of omega-substituted alkanoic acid (2-amino-phenyl)-amides were designed and synthesized. These compounds were shown to inhibit recombinant human histone deacetylases (HDACs) with IC(50) values in the low micromolar range and induce hyperacetylation of histones in whole cells. They induced expression of p21WAF1/Cip1 and caused cell-cycle arrest in human cancer cells. Compounds in this class showed efficacy in human tumor xenograft models.