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PubMed2026

Two Saccharopolyspora isolates from archaeological excavation sites: polyphasic taxonomy, biosynthetic potential, bioactivity profiling and description of Saccharopolyspora antiqui sp. nov.

Archaeological excavation sites represent underexplored microbial habitats with the potential to recover taxonomically and biotechnologically valuable actinomycetes. In this study, two Saccharopolyspora strains, 5N708T and 5N102, were isolated from soil samples collected from the Gaziantep-Doliche-Dülük and Bitlis-Ahlat-Selçuklu Cemetery archaeological excavation sites in Türkiye. A polyphasic taxonomic approach, including 16S rRNA gene sequencing, phylogenetic and phylogenomic analyses, average nucleotide identity, digital DNA-DNA hybridization, phenotypic characterization, and chemotaxonomic analyses, showed that strain 5N708T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora antiqui sp. nov. is proposed, whereas strain 5N102 was assigned to Saccharopolyspora elongata. Both isolates were further evaluated for their antimicrobial, antioxidant, and cytotoxic activities, and their biosynthetic potential was investigated by genome mining. Both strains showed activity against Staphylococcus aureus, with strain 5N708T producing the larger inhibition zone. Strain 5N102 exhibited markedly stronger antioxidant activity than strain 5N708T in radical scavenging, ferric reducing antioxidant power, and reducing power assays. In contrast, strain 5N708T showed more promising cytotoxic activity, with relative selectivity toward MIA PaCa-2 pancreatic cancer cells compared with HEK293 cells after prolonged incubation. Genome mining revealed multiple biosynthetic gene clusters in both isolates, supporting their capacity to produce secondary metabolites. These findings indicate that archaeological soils are promising reservoirs of taxonomically novel and biologically active Saccharopolyspora strains.

Saccharopolyspora↗
PubMed2001

Cardiac surgery report cards: comprehensive review and statistical critique.

Public report cards and confidential, collaborative peer education represent distinctly different approaches to cardiac surgery quality assessment and improvement. This review discusses the controversies regarding their methodology and relative effectiveness. Report cards have been the more commonly used approach, typically as a result of state legislation. They are based on the presumption that publication of outcomes effectively motivates providers, and that market forces will reward higher quality. Numerous studies have challenged the validity of these hypotheses. Furthermore, although states with report cards have reported significant decreases in risk-adjusted mortality, it is unclear whether this improvement resulted from public disclosure or, rather, from the development of internal quality programs by hospitals. An additional confounding factor is the nationwide decline in heart surgery mortality, including states without quality monitoring. Finally, report cards may engender negative behaviors such as high-risk case avoidance and "gaming" of the reporting system, especially if individual surgeon results are published. The alternative approach, continuous quality improvement, may provide an opportunity to enhance performance and reduce interprovider variability while avoiding the unintended negative consequences of report cards. This collaborative method, which uses exchange visits between programs and determination of best practice, has been highly effective in northern New England and in the Veterans Affairs Administration. However, despite their potential advantages, quality programs based solely on confidential continuous quality improvement do not address the issue of public accountability. For this reason, some states may continue to mandate report cards. In such instances, it is imperative that appropriate statistical techniques and report formats are used, and that professional organizations simultaneously implement continuous quality improvement programs. The statistical methodology underlying current report cards is flawed, and does not justify the degree of accuracy presented to the public. All existing risk-adjustment methods have substantial inherent imprecision, and this is compounded when the results of such patient-level models are aggregated and used inappropriately to assess provider performance. Specific problems include sample size differences, clustering of observations, multiple comparisons, and failure to account for the random component of interprovider variability. We advocate the use of hierarchical or multilevel statistical models to address these concerns, as well as report formats that emphasize the statistical uncertainty of the results.

Bias↗
PubMed2003

A biomonitoring study: trace metals in algae and molluscs from Tyrrhenian coastal areas.

Marine organisms were evaluated as possible biomonitors of heavy metal contamination in marine coastal areas. Concentrations of Cd, Cr, Cu, Pb, and Zn were measured in the green algae Ulva lactuca L., the brown algae Padina pavonica (L.) Thivy, the bivalve mollusc Mytilus galloprovincialis Lamarck, and the two gastropod molluscs Monodonta turbinata Born and Patella cerulea L. collected at six coastal stations in the area of the Gulf of Gaeta (Tyrrhenian Sea, central Italy). The coastal area of the Regional Park of Gianola and Monte di Scauri (a "Protected Sea Park" area) was chosen as a control site. Seawater samples were also collected in each site to assess soluble and total metal concentrations and to gain additional information on both the environmental conditions of the area and possible bioaccumulation patterns. Metal concentrations detected in algae and molluscs did not show significant differences among all stations studied. Moreover, statistical analyses (ANOVA, multiple comparison tests, cluster analysis) showed that the Sea Park station was not significantly different from the others. The hypothesis that the Protected Sea Park would be cleaner than the others must therefore be reconsidered. Data from this study were also compared with those previously obtained from uncontaminated sites in the Sicilian Sea, Italy. The results show clearly differences between these two marine ecosystems. The species examined showed great accumulations of metals, with concentration factors (CFs) higher than 10,000 with respect to the concentrations (soluble fractions) in marine waters. Metal concentrations recorded in this area may be used for background levels for intraspecific comparison within the Tyrrhenian area, a body of water about which information is still very scarce.

Animals↗
PubMed2001

Germline diversity of the expressed BALB/c VhJ558 gene family.

Although the mouse immunoglobulin heavy chain (Igh) locus contains 15 heavy chain V (Vh) gene families, at least half of the Vh gene segments are members of the VhJ558 family. This large Vh gene family represents the least characterized germline coding regions of any of the mouse antigen receptor loci and the contribution of individual VhJ558 genes to the preimmune repertoire is poorly understood. In fact, relatively few germline VhJ558 sequences have been reported for BALB/c, the foundation strain for mouse immunoglobulin genetics and the prototypic strain of the Igh(a) haplotype. Here we present a database consisting of 66 sequences estimated to represent one-half of the total number of functional BALB/c VhJ558 genes. Our results indicate that a subset of the VhJ558 genes is highly expressed in the preimmune repertoire, with just nine Vh sequences accounting for nearly 50% of the VhJ558 heavy chains expressed by splenic B cells. We show that this disparity in the expressed Vh gene repertoire is not due to the position of the Vh genes relative to the Dh cluster or to multiple germline copies of the highly expressed VhJ558 genes. Together, these data constitute the first detailed analysis of functional BALB/c VhJ558 genes, demonstrate a striking bias in the use of particular VhJ558 genes in the preimmune repertoire, and provide sufficient information to study the regulation of the Dh-distal region of the Igh-V locus at the level of individual genes.

Amino Acid Sequence↗
PubMed2003

Characterization of PfRhop148, a novel rhoptry protein of Plasmodium falciparum.

Rhoptries are apical organelles which play an important role in erythrocytic invasion. A Plasmodium falciparum cDNA clone, coding for a novel rhoptry protein PfRhop148, was obtained by antibody screening of a library. The deduced amino acid sequence consists of 1262 amino acids and is highly rich in Asn (22%). The Asn residues are distributed in clusters and in multiple units of repeats. Analysis of specific RNA transcript and protein showed that PfRhop148 was synthesized at around 21 h post-invasion. IFA and immunoelectron microscopic analyses revealed a rhoptry localization for the protein. The role of this protein in invasion and its relationship to the RhopH complex is now under further investigation.

Amino Acid Sequence↗
PubMed1996

Identification and localization of rab6, separation of rab6 from ERD2 and implications for an 'unstacked' Golgi, in Plasmodium falciparum.

The rab6 gene product in mammalian cells and yeast is localized to and regulates protein transport in the medial and trans Golgi cisternae, as well as the trans Golgi network. We have identified a homologue in the malaria parasite Plasmodium falciparum which displays a rab-like sequence that is 62.4% identical to mammalian rab6. In addition the parasite gene (Pfrab6 gene) contains an N-terminal hydrophobic domain, unique to P. falciparum. Antibodies developed to Pfrab6 localize protein in 4-7 well-resolved sites in a ring-stage parasite, as detected by high resolution fluorescence microscopy. This suggests that there are multiple, distinct foci of medial/trans Golgi membranes in a ring. ERD2 is a cis Golgi marker in mammalian cells. The plasmodial homologue of ERD2 (PfERD2) is concentrated in a single perinuclear region in a ring-stage parasite. This site is distinct from the Pfrab6 membranes, indicating that early and late Golgi markers can be segregated in P. falciparum. Mammalian cells contain a single Golgi complex where cis medial and trans markers are tightly stacked in closely apposed cisternae. In P. falciparum-rings however, rab6-associated membranes are not invariably 'stacked' with an ERD2 structure. In immunoelectron microscopy studies, both the PfERD2- and Pfrab6-associated membranes appear tubulovesicular in nature, devoid of cisternal morphology. Hence the Golgi of ring stage parasites may comprise of multiple, 'unstacked' tubulovesicular clusters, suggesting a primitive organization of the organelle in Plasmodia.

Amino Acid Sequence↗
PubMed1996

Study of the amidase signature group.

Computer methods for database search, multiple alignment and cluster analysis indicated significant homology between amino-acid sequences of 21 amidases or amidohydrolases (EC 3.5). All of them were found to be involved in the reduction of organic nitrogen compounds and ammonia production. A conserved motif was found which may be important in amide binding and in catalytic mechanisms. Homology studies between these amidases and some ureases, nitrilases and acyl-transferases or enzymes with unknown functions provided new insight into the evolution of these proteins. Dissemination of these genes seemed to be facilitated by transfer of genetic elements such as transposons and plasmids.

Amidohydrolases↗
PubMed1999

Protein modules as organizers of membrane structure.

Investigations conducted over the past 18 months have shed new light on how modular protein-binding domains, in particular PDZ domains, co-ordinate the assembly of functional plasma membrane domains. Members of the MAGUK (membrane-associated guanylate kinase) protein family, like PSD-95, use multiple domains to cluster ion channels, receptors, adhesion molecules and cytosolic signaling proteins at synapses, cellular junctions, and polarized membrane domains. Other PDZ proteins, like the Drosophila protein INAD and the epithelial Na(+)/H(+) regulatory factor (NHERF), organize cellular signaling by localizing transmembrane and cytosolic components to specific membrane domains and assembling these components into functional complexes. The organization of these proteins into discreet structures has functional consequences for downstream signaling.

Animals↗
PubMed1987

Recurrent pseudobacteremias traced to a radiometric blood culture device.

Five clusters of pseudobacteremias over a seven-month period were traced to a BACTEC radiometric device. Four episodes were due to enterococcus and one involved Staphylococcus aureus. Each cluster began with multiple positive blood cultures from a patient with clinical evidence of bacteremia. On subsequent days each bottle in sequence yielded growth of the identical organism, as shown by phage typing and antibiograms. Cultures from patients believed to be infected with the organisms tested positive earlier (mean = 1.4 days) than those patients believed to be pseudobacteremic (mean = 4.8 days). Investigation pointed toward the BACTEC device as the most likely source. Resin beads were found in the needle on several occasions and were shown to be transferred from bottle to bottle. We postulated that contaminated resin beads or liquid from a positive bottle remained in the needle above the portion that was heat-sterilized, contaminating the next bottle when it was sampled.

Bacteriological Techniques↗
PubMed2006

Early events in node of Ranvier formation during myelination and remyelination in the PNS.

Action potential conduction velocity increases dramatically during early development as axons become myelinated. Integral to this process is the clustering of voltage-gated Na(+) (Nav) channels at regularly spaced gaps in the myelin sheath called nodes of Ranvier. We show here that some aspects of peripheral node of Ranvier formation are distinct from node formation in the CNS. For example, at CNS nodes, Nav1.2 channels are detected first, but are then replaced by Nav1.6. Similarly, during remyelination in the CNS, Nav1.2 channels are detected at newly forming nodes. By contrast, the earliest Nav-channel clusters detected during developmental myelination in the PNS have Nav1.6. Further, during PNS remyelination, Nav1.6 is detected at new nodes. Finally, we show that accumulation of the cell adhesion molecule neurofascin always precedes Nav channel clustering in the PNS. In most cases axonal neurofascin (NF-186) accumulates first, but occasionally paranodal neurofascin is detected first. We suggest there is heterogeneity in the events leading to Nav channel clustering, indicating that multiple mechanisms might contribute to node of Ranvier formation in the PNS.

Journal Article↗
PubMed1979

Neuronal unit activity in the abducens nucleus during classical conditioning of the nictitating membrane response in the rabbit (Oryctolagus cuniculus).

Neuronal unit activity was recorded from the abducens (6th nerve) nucleus, the "final common path," during classical conditioning of the nictitating membrane (NM) response in the rabbit, with the use of a tone conditioned stimulus, an air puff unconditioned stimulus (UCS), 250-msec interstimulus interval, and 60-sec intertrial interval. Animals were given 2 days of conditioning training (104 trials in eight blocks per day) and 1 day of extinction. Control animals were given comparable periods of stimulus presentations, explicitly unpaired. Activity of small clusters of units--"multiple unit" recording--was compared with the amplitude-time course of the NM response. Between-blocks comparisons of neural and behavioral responses indicated an essentially perfect correlation during acquisition of the conditioned response (Day 1, r = .99; Day 2, r = .98) and a slightly lower correlation during extinction (r = .93) for the conditioning animals. Within-blocks comparisons indicated a close correspondence between the histograms of unit activity and the amplitude-time course of the NM response for the conditioning animals in all phase of training and for the control animals in the UCS trial blocks.

Abducens Nerve↗
PubMed2003

Psychosocial distress associated with disfiguring eye conditions.

PURPOSE OF STUDY: Visible disfigurement is associated with a range of psychosocial difficulties; however, the problems encountered by patients with eye conditions are under-researched. This study aimed to establish the extent and type of psychosocial distress in this patient population, and to explore the extent to which patients' needs are currently met. METHOD: Standardised measures (anxiety, depression, appearance-related distress, and quality of life) and a semistructured interview (exploring individual experiences and satisfaction with care) were administered to 153 consecutive attenders at outpatient eye clinics in three different hospitals. Responses were analysed using descriptive statistics, multiple regression, and cluster analyses. RESULTS: Between 10 and 49% of the patient sample scored unfavourably on standardised measures in comparison with normative values. Cluster analyses revealed that more distressed patients typically exhibited higher levels of anxiety, depression, social anxiety, self-consciousness, and social avoidance. Quality of life scores were also less favourable. Distressed patients felt less well informed, less involved in their treatment, and less well supported in the clinic setting. Variability within the sample was high; however, the effects of the cause and duration of the condition were not significantly related to distress. Clinic staff identified a variety of constraints to meeting patients' need, including patient numbers, the lack of appropriate training, and the lack of referral possibilities. CONCLUSIONS: A considerable proportion of patients with disfiguring eye conditions experience high levels of psychosocial distress. Several options exist for ways in which patients' needs might more effectively be met within the constraints currently facing care providers.

Adaptation, Psychological↗
PubMed1998

Tumors of DNA mismatch repair-deficient hosts exhibit dramatic increases in genomic instability.

DNA mismatch repair (MMR) deficiency is associated with an increased mutational burden and predisposition to certain malignancies. Relatively little is known, however, about gene-specific mutation frequencies within MMR-deficient primary tumors. Thymic lymphomas from Msh2(-/-) mice were thus analyzed by using a lacI-based transgenic shuttle-phage mutation detection system. All tumors exhibited greatly elevated lacI gene mutation frequencies, ranging from 3.2- to 17.4-fold above the approximately 15-fold elevations present within normal Msh2(-/-) thymi. In addition, lacI genes harboring multiple changes, including clusters of mutations, were found in thymic tumor DNA. The results suggest that an additional mutator activity, such as an error-prone DNA polymerase, leads to increased genomic instability in these MMR-deficient tumors.

Animals↗
PubMed1998

BCL-6 mutations in normal germinal center B cells: evidence of somatic hypermutation acting outside Ig loci.

The molecular mechanism involved in the process of antigen-driven somatic hypermutation of Ig genes is unknown, but it is commonly believed that this mechanism is restricted to the Ig loci. B cell lymphomas commonly display multiple somatic mutations clustering in the 5'-regulatory region of BCL-6, a proto-oncogene encoding for a POZ/Zinc finger transcriptional repressor expressed in germinal center (GC) B cells and required for GC formation. To determine whether BCL-6 mutations represent a tumor-associated phenomenon or reflect a physiologic mechanism, we screened single human tonsillar GC B cells for mutations occurring in the BCL-6 5'-noncoding region and in the Ig variable heavy chain sequences. Thirty percent of GC B cells, but not naive B cells, displayed mutations in the 742 bp region analyzed within the first intron of BCL-6 (overall frequency: 5 x 10(-4)/bp). Accordingly, an expanded survey in lymphoid malignancies showed that BCL-6 mutations are restricted to B cell tumors displaying GC or post-GC phenotype and carrying mutated Ig variable heavy chain sequences. These results indicate that the somatic hypermutation mechanism active in GC B cells physiologically targets non-Ig sequences.

B-Lymphocytes↗
PubMed2003

Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR.

The work presented here is a first step toward a long term goal of systems biology, the complete elucidation of the gene regulatory networks of a living organism. To this end, we have employed DNA microarray technology to identify genes involved in the regulatory networks that facilitate the transition of Escherichia coli cells from an aerobic to an anaerobic growth state. We also report the identification of a subset of these genes that are regulated by a global regulatory protein for anaerobic metabolism, FNR. Analysis of these data demonstrated that the expression of over one-third of the genes expressed during growth under aerobic conditions are altered when E. coli cells transition to an anaerobic growth state, and that the expression of 712 (49%) of these genes are either directly or indirectly modulated by FNR. The results presented here also suggest interactions between the FNR and the leucine-responsive regulatory protein (Lrp) regulatory networks. Because computational methods to analyze and interpret high dimensional DNA microarray data are still at an early stage, and because basic issues of data analysis are still being sorted out, much of the emphasis of this work is directed toward the development of methods to identify differentially expressed genes with a high level of confidence. In particular, we describe an approach for identifying gene expression patterns (clusters) obtained from multiple perturbation experiments based on a subset of genes that exhibit high probability for differential expression values.

Cell Division↗
PubMed1994

The relation between isometric lifting strength and muscular fitness measures.

The purpose of this study was to construct an isometric lift dynamometer and relate isometric lifting strength to dynamic measures of muscular fitness, leg and back strength and muscular power output. Thirty-one male subjects, aged 19-24 years, performed a standing broad jump (for distance), a vertical jump (for flight time), 3 maximal pulls (for peak power) on a rowing ergometer and maximal isometric leg and back extensions on a conventional dynamometer. The results of these tests were correlated with the maximum isometric lifting strength (MILS) obtained on the lift dynamometer using cluster correlation and multiple regression. Significant correlations (p < 0.001) were found between isometric lifting strength and back strength (BS) (r = 0.59), and leg strength (LS) (r = 0.74). A significant correlation was also noted between isometric lifting strength and both standing broad jump (SBJ) (r = 0.58, p < 0.001) and power output (PO) (r = 0.38, (p < 0.05). Multiple regression analysis was used to predict lifting performance from a battery of standard fitness tests. The prediction equation for maximal isometric lifting strength included the terms LS, BS, SBJ and PO (r = 0.80). The relation between isometric lifting strength and other muscular fitness variables suggest that the method used provides an acceptable measure of strength and an indication of the involvement of back and leg musculature in squat lifting.

Adult↗
PubMedDate not supplied

Pathological determinants of the transition to clinical dementia in Alzheimer's disease.

The authors developed multivariate models to examine the association between Clinical Dementia Rating (CDR) scale scores and the spatial distribution of paired helical filament tau (PHF-tau) pathology. Severity of tauopathy was examined in 14 cortical regions of interest (ROIs). Classification trees were used to test the independent hierarchical contributions of each ROI to dementia. Multiple-regression and cluster analyses were performed to determine the relative contributions of select ROIs to dementia. Dementia (CDR > or = 1) was modeled as a dichotomous variable. Autopsy material was obtained from 124 demented and nondemented elderly patients. All ROIs except the hippocampus made significant contributions to dementia. However, they were not independent. In multivariate models, only a single step (Step 7 in a hierarchical progression), which contained four ROIs, contributed significantly to dementia. A classification tree resulted in a single decision split, suggesting that only Step 7 ROIs need be considered. A total of 89.4% of the cases were correctly classified (p < .0001). Twelve discrepant cases all had superimposed vasculopathy that might also have affected the function of Step 7 ROIs. The transition to clinical dementia was associated with the presence of tauopathy in A9/10, A22, A23, and A39. Animal studies suggest that these represent a single distributed cortical network focusing on prefrontal regions that provide "executive control" over complex goal-directed behaviors. A22, A23, and A39 provide major afferents to other frontal systems and have previously been implicated in very early clinical Alzheimer's disease.

Alzheimer Disease↗
PubMed1995

Chromatin structure and radiation-induced DNA strand breaks in human cells: soluble scavengers and DNA-bound proteins offer a better protection against single- than double-strand breaks.

In the present investigation we have studied the formation of DNA double-strand breaks (dsbs) in different chromatin substrates and made a comparison with our previous results on radiation-induced single-strand breaks (ssb). Removal of soluble scavengers increased the number of ssbs by a factor of 2, but increased dsbs only 1.2 times. Decondensation of the chromatin increased ssbs and dsbs to the same extent, by a factor of 3-4. Removal of DNA-bound proteins gave an additional increase in ssbs and dsbs by a factor of 14 and 5 respectively. The increase in both ssbs and dsbs was caused by OH radicals. The differential effect on ssbs and dsbs can be explained by assuming that dsbs are formed mainly by multiple hits from clusters of ionizations close to the DNA. When the DNA-bound proteins are removed, more distant radicals can reach the DNA, which favours ssb formation. Under those conditions dsbs also induced by single OH radicals become important. DNA-bound proteins protect DNA only to a limited extent by acting as scavengers of OH radicals. The largest part of the protection depends on the fact that DNA in the chromatin is made up of large, compact aggregates, where the distance between separate aggregates exceeds the effective range of the OH radicals and the amount of water inside the aggregates is too small to give a maximal contribution of OH radicals compared with when DNA is more evenly distributed in a given volume.

Cells, Cultured↗