Fabrication of ultralow-loss Si/SiO(2) waveguides by roughness reduction

We demonstrate 0.8-dB/cm transmission loss for a single-mode, strip Si/SiO(2) waveguide with submicrometer cross-sectional dimensions. We compare the conventional waveguide-fabrication method with two smoothing technologies that we have developed, oxidation smoothing and anisotropic etching. We observe significant reduction of sidewall roughness with our smoothing technologies, which directly results in reduced scattering losses. The rapid increase in the scattering losses as the waveguide dimension is miniaturized, as seen in conventionally fabricated waveguides, is effectively suppressed in the waveguides made with our smoothing technologies. In the oxidation smoothing case, the loss is reduced from 32 dB/cm for the conventional fabrication method to 0.8 dB/cm for the single-mode waveguide width of 0.5 microm . This is to our knowledge the smallest reported loss for a high-index-difference system such as a Si/SiO(2) strip waveguide.

Solution structure of p21(Waf1/Cip1/Sdi1) C-terminal domain bound to Cdk4

Cyclin-dependent kinase (Cdk) inhibitor p21(Waf1/Cip1/Sdi1), a multifunctional protein, has a major role as tumor suppressor, mediating G1/S arrest through inhibition of Cdks. Recent biological studies of Cyclin D1/Cdk4 have proposed that p21 C-terminal domain (p21(CT)) plays a key role as a potent Cdk4 inhibitor. We report here solution structures of p21(CT) for both the free and Cdk4-bound forms using 2D transferred NOE spectroscopy and dynamical simulated annealing calculations. Even though p21(CT) peptide is very flexible in the free state, when it bound to Cdk4, the structure becomes well structured in the binding domain. Therefore we propose that p21(CT) experiences an extensive conformational change upon Cdk4 binding. This structural change of p21(CT) may suggest the molecular mechanism of p21 for specificity and inhibition mode to assemble different cyclin-Cdk complexes. Especially, our data suggests that the D(149)FYHSKRR(156) region of p21 is critical for Cdk4 binding, indicating that the major driving force for complex originates from hydrophobic interaction between p21 and Cdk4.

New steroidal alkaloids from an undescribed sponge of the genus Corticium

Two new steroidal alkaloids, along with a previously reported one of the plakinamine class, were isolated from the sponge Corticium sp. collected from Guam. The structures of the new compounds were determined by combined spectroscopic methods. These compounds exhibited moderate cytotoxicity and antifungal activity as well as DNA- and RNA-cleaving activities.

Transient dissociation of polyribosomes and concurrent recruitment of calreticulin and calmodulin transcripts in gravistimulated maize pulvini

The dynamics of polyribosome abundance were studied in gravistimulated maize (Zea mays) stem pulvini. During the initial 15 min of gravistimulation, the amount of large polyribosomes transiently decreased. The transient decrease in polyribosome levels was accompanied by a transient decrease in polyribosome-associated mRNA. After 30 min of gravistimulation, the levels of polyribosomes and the amount of polyribosome-associated mRNA gradually increased over 24 h up to 3- to 4-fold of the initial value. Within 15 min of gravistimulation, total levels of transcripts coding for calreticulin and calmodulin were elevated 5-fold in maize pulvinus total RNA. Transcripts coding for calreticulin and calmodulin were recruited into polyribosomes within 15 min of gravistimulation. Over 4 h of gravistimulation, a gradual increase in the association of calreticulin and calmodulin transcripts with polyribosomes was seen predominantly in the lower one-half of the maize pulvinus; the association of transcripts for vacuolar invertase with polyribosomes did not change over this period. Our results suggest that within 15 min of gravistimulation, the translation of the majority of transcripts associated with polyribosomes decreased, resembling a general stress response. Recruitment of calreticulin and calmodulin transcripts into polyribosomes occurred predominantly in the lower pulvinus one-half during the first 4 h when the presentation time for gravistimulation in the maize pulvinus is not yet complete.

Transient dissociation of polyribosomes and concurrent recruitment of calreticulin and calmodulin transcripts in gravistimulated maize pulvini

The dynamics of polyribosome abundance were studied in gravistimulated maize (Zea mays) stem pulvini. During the initial 15 min of gravistimulation, the amount of large polyribosomes transiently decreased. The transient decrease in polyribosome levels was accompanied by a transient decrease in polyribosome-associated mRNA. After 30 min of gravistimulation, the levels of polyribosomes and the amount of polyribosome-associated mRNA gradually increased over 24 h up to 3- to 4-fold of the initial value. Within 15 min of gravistimulation, total levels of transcripts coding for calreticulin and calmodulin were elevated 5-fold in maize pulvinus total RNA. Transcripts coding for calreticulin and calmodulin were recruited into polyribosomes within 15 min of gravistimulation. Over 4 h of gravistimulation, a gradual increase in the association of calreticulin and calmodulin transcripts with polyribosomes was seen predominantly in the lower one-half of the maize pulvinus; the association of transcripts for vacuolar invertase with polyribosomes did not change over this period. Our results suggest that within 15 min of gravistimulation, the translation of the majority of transcripts associated with polyribosomes decreased, resembling a general stress response. Recruitment of calreticulin and calmodulin transcripts into polyribosomes occurred predominantly in the lower pulvinus one-half during the first 4 h when the presentation time for gravistimulation in the maize pulvinus is not yet complete.

Molecular cloning and characterization of PELP1, a novel human coregulator of estrogen receptor alpha

Nuclear hormone receptors (NRs) are transcription factors whose activity is regulated by ligands and by coactivators or corepressors. We report the characterization of a new NR coregulator: proline-, glutamic acid-, leucine-rich protein 1 (PELP1), a novel human protein that comprises 1,282 amino acids and is localized on chromosome 17. The primary structure of PELP1 consists of several motifs present in most transcriptional regulators including nine NR-interacting boxes (LXXLL motifs), a zinc finger, and glutamic acid- and proline-rich regions. We demonstrate that PELP1 is a coactivator of estrogen receptor alpha (ERalpha). PELP1 enhances 17beta-estradiol-dependent transcriptional activation from the estrogen response element in a dose-dependent manner. PELP1 interacts with ERalpha and also with general transcriptional coactivators p300 and cAMP response element-binding protein-binding protein. PELP1 was differentially expressed in various human and murine tissues with the highest expression levels in the testes, mammary glands, and brain. We also provide evidence supporting the developmental regulation of PELP1 expression in murine mammary glands, the detectable expression of PELP1 in human mammary cancer cell lines, and the enhanced expression of PELP1 in human breast tumors. These findings suggest that PELP1 is a novel coregulator of ERalpha and may have a role in breast cancer tumorigenesis.

Immunobead RT-PCR versus regular RT-PCR amplification of CEA mRNA in peripheral blood

PURPOSE

The reverse transcription polymerase chain reaction (RT-PCR) amplification of tumor-specific mRNA has been used for the detection of cancer cells in peripheral blood. More recently, an immunomagnetic isolation and reverse transcription polymerase chain reaction (immunobead RT-PCR) was developed which has reportedly significant advantages over the previous RT-PCR analysis. In our study, we compared these two methods using a model set of peripheral blood containing tumor cells under standardized conditions.

MATERIAL AND METHODS

In order to compare the false positive rate, normal peripheral blood samples from five volunteers were analyzed by both methods. A model set of peripheral blood containing tumor cells was established by adding SNUC4 human colon cancer cells to peripheral blood collected from normal volunteers not showing any nonspecific bands upon electrophoresis of the PCR products. RT-PCR amplification of carcinoembryonic antigen (CEA) mRNA was done with total RNA and mRNA prepared from this model sample. In immunobead RT-PCR analysis, mRNA was prepared from the cells isolated with anti-CEA antibody-coated magnetic beads or anti-Ber-EP4 antibody-coated magnetic beads before the RT-PCR analysis.

RESULT

The immunobead RT-PCR yielded no non-specific band, while the regular RT-PCR using total RNA did show non-specific band formation in all five samples. When mRNA rather than total RNA was used, nonspecific bands were formed in three of the five samples. Immunobead RT-PCR allowed the detection of 10(1) tumor cells in 1 ml of peripheral blood. The regular RT-PCR analysis had a detection limit of 10(2) tumor cells in 1 ml of peripheral blood.

CONCLUSION

The immunobead RT-PCR proved to be more sensitive and specific than the regular RT-PCR at least in our model system.

Solution structure of the dimeric cytoplasmic domain of syndecan-4

The syndecans, transmembrane proteoglycans which are involved in the organization of cytoskeleton and/or actin microfilaments, have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions. Since previous studies indicate that the function of the syndecan-4 cytoplasmic domain is dependent on its oligomeric status, the conformation of the syndecan-4 cytoplasmic domain itself is important in the understanding of its biological roles. Gel filtration results show that the syndecan-4 cytoplasmic domain (4L) itself forms a dimer stabilized by ionic interactions between peptides at physiological pH. Commensurately, the NMR structures demonstrate that syndecan-4L is a compact intertwined dimer with a symmetric clamp shape in the central variable V region with a root-mean-square deviation between backbone atom coordinates of 0.95 A for residues Leu(186)-Ala(195). The molecular surface of the 4L dimer is highly positively charged. In addition, no intersubunit NOEs in membrane proximal amino acid resides (C1 region) have been observed, demonstrating that the C1 region is mostly unstructured in the syndecan-4L dimer. Interestingly, two parallel strands of 4L form a cavity in the center of the dimeric twist similar to our previously reported 4V structure. The overall topology of the central variable region within the 4L structure is very similar to that of 4V complexed with the phosphatidylinositol 4,5-bisphosphate; however, the intersubunit interaction mode is affected by the presence of C1 and C2 regions. Therefore, we propose that although the 4V region in the full cytoplasmic domain has a tendency for strong peptide--peptide interaction, it may not be enough to overcome the repulsion of the C1 regions of syndecan-4L.

Adaptation in spiking neurons based on the noise shaping neural coding hypothesis

Shin, Koch and Douglas [Shin, J., Koch, C., & Douglas, R. (1999). Adaptive neural coding dependent on the time-varying statistics of the somatic input current. Neural Computation, 11, 1983-2003] proposed an adaptive neural coding model that makes spiking neurons adapt its input/output relation to the stimulus statistics. In a surprisingly precise manner, the adaptive neural coding model has been supported by recent experiments. However, the previous report has two problems: (a) although the adaptive neural coding model was developed based on the noise shaping neural coding hypothesis, their connection was not explained clearly in the previous report; and (b) the previous model did not suggest a biologically plausible method to estimate the stimulus mean and variance from spike-evoked intracellular calcium concentration. In this paper, I present how the noise shaping neural coding hypothesis produced such a precise model without any available experimental data at that time. Moreover, I propose a computational model for a biologically plausible signal statistics extraction from spike-evoked intracellular calcium concentration. An asymmetry in contrast adaptation time between increasing and decreasing variance, observed in biological experiments, is explained using the signal statistics extraction method. In addition, a new perspective on the relationship between the spike train of spiking neurons and EEG (or local field potential (LFP)) is suggested based on the noise shaping neural coding hypothesis.

Adaptor protein Lad relays PDGF signal to Grb2 in lung cells: a tissue-specific PDGF signal transduction

Lad was previously identified as an adaptor protein binding to the SH2 domain of Lck (1). Specific detection of Lad mRNA in lung cells, as well as, in T cells led us to investigate the signaling pathways regulating Lad in lung cells. We found that (i) upon PDGF stimulation, Lad expression is induced in lung cells, especially in the bronchial epithelial cells; (ii) Lad is tyrosine phosphorylated upon PDGF stimulation and is associated with PDGF receptor; (iii) upon PDGF stimulation, Grb2 is recruited to Lad in human embryonic lung cells; (iv) overexpression of Lad elevated AP-1 promoter activity by two- to threefold, whereas dominant negative Lad abrogated PDGF-dependent activation of AP-1 promoter. These results provide a novel mechanism of PDGF-dependent signaling, in which Lad acts as an adaptor in a tissue-specific manner, linking PDGF signal to Grb2 and subsequent activation of AP-1.

New triterpenoid saponins from the sponge Erylus nobilis

Erylosides G--J (1--4), four new triterpenoid saponins, were isolated from the sponge Erylus nobilis collected from Jaeju Island, Korea. On the basis of the results of combined chemical and spectral analyses, the structures of the aglycones were determined to be lanostane-based, modified penasterols. The oligosaccharide portions were composed of one unit each of L-arabinose, D-galactose, and 2-N-acetyl-D-glucosamine (1 and 3) or two units of L-arabinose and one unit of 2-N-acetyl-D-glucosamine (2 and 4). These compounds exhibited moderate cytotoxicty against a human leukemia cell line.

Treatment of vitamin K deficiency in cystic fibrosis: Effectiveness of a daily fat-soluble vitamin combination

OBJECTIVE

Patients with cystic fibrosis (CF) and pancreatic insufficiency (PI) commonly have vitamin K deficiency, and those with CF-associated liver disease (CFLD) have universal vitamin K deficiency. We evaluated the effectiveness of an oral fat-soluble vitamin combination (ADEKs) to treat patients with vitamin K deficiency.

STUDY DESIGN

Patients with PI and CF (mean age, 15 years; range, 0.6 to 46 years) including 6 with advanced CFLD were prospectively enrolled in a study of a fat-soluble vitamin combination taken on a daily basis. None had received vitamin K supplementation for at least 4 months before the study. Fat-soluble vitamin combination supplementation was given for a minimum of 4 months; the mean vitamin K intake was 0.18 mg/d (SD = 0.1, range, 0 to 0.3). The primary outcome was change in plasma PIVKA-II (prothrombin in vitamin K absence).

RESULTS

Before supplementation 58 (81%) of 72 patients had abnormal PIVKA-II levels (>2.9 ng/mL). After supplementation 29 (40%) had abnormal PIVKA-II levels (P =.001). All 6 patients with advanced CFLD had abnormal PIVKA-II levels (median, range of 20.8, 5.5 to 55 ng/mL) before treatment, which corrected to normal in 50% (4.1, 2.1 to 65 ng/mL). Four patients, 2 with CFLD, had a prolonged prothrombin time (>13.5 seconds) at both time periods.

CONCLUSIONS

An oral fat-soluble vitamin combination with a modest amount of vitamin K can, as a daily supplement, improve the PIVKA-II levels in patients with PI and CF.

Solution structure, backbone dynamics, and stability of a double mutant single-chain monellin. structural origin of sweetness

Single-chain monellin (SCM), which is an engineered 94-residue polypeptide, has been characterized as being as sweet as native two-chain monellin. Data from gel-filtration high performance liquid chromatography and NMR has proven that SCM exists as a monomer in aqueous solution. In order to determine the structural origin of the taste of sweetness, we engineered several mutant SCM proteins by mutating Glu(2), Asp(7), and Arg(39) residues, which are responsible for sweetness. In this study, we present the solution structure, backbone dynamics, and stability of mutant SCM proteins using circular dichroism, fluorescence, and NMR spectroscopy. Based on the NMR data, a stable alpha-helix and five-stranded antiparallel beta-sheet were identified for double mutant SCM. Strands beta1 and beta2 are connected by a small bulge, and the disruption of the first beta-strand were observed with SCM(DR) comprising residues of Ile(38)-Cys(41). The dynamical and folding characteristics from circular dichroism, fluorescence, and backbone dynamics studies revealed that both wild type and mutant proteins showed distinct dynamical as well as stability differences, suggesting the important role of mutated residues in the sweet taste of SCM. Our results will provide an insight into the structural origin of sweet taste as well as the mutational effect in the stability of the engineered sweet protein SCM.

New lactone-containing metabolites from a marine-derived bacterium of the genus Streptomyces

Six novel metabolites containing a lactone moiety as a common structural feature, along with the previously described (-)-blastmycinolactol, have been isolated from the cultivation broth of a bacterium of the genus Streptomyces isolated from marine sediment. On the basis of the results of combined spectroscopic analysis, the structures of the new compounds have been determined as butenolides and 3-hydroxy-gamma-butyrolactones.

A single trial analysis of hippocampal theta frequency during nonsteady wheel running in rats

It has been suggested that hippocampal theta rhythm codes some aspects of motor behavior, but previous studies of the correlation between theta frequency and steady whole body locomotion speed using both linear tracks and wheels have provided inconsistent if not contradictory results. Because the relationship between temporal dynamics of theta frequency and non-steady (or dynamic) whole body locomotion speed can help clarify this issue, single trials of hippocampal EEG were analyzed together with nonsteady wheel running speed recorded during rats perform spontaneous normal locomotion in a wheel. Changes in theta frequency within single trials show positive or negative correlation with nonsteady wheel running speed. As the mean running speed increases and the standard deviation of running speed decreases in a single trial, the correlation between temporal dynamics of theta frequency and nonsteady wheel running speed within the single trial tends to be positive. In addition, we found that the amount of deceleration is also related to the polarity of the correlation coefficients.

New xenicane diterpenoids from the gorgonian Acalycigorgia inermis

Eight diterpenes and norditerpenes including five new xenicane metabolites (4--8) have been isolated from the gorgonian Acalycigorgia inermis. The structures of these compounds have been determined by combined spectroscopic analysis. The new compounds exhibited significant cytotoxicity against a human leukemia cell-line.

Design considerations for association studies of candidate genes in families

In genetic epidemiologic studies, investigators often use generalized linear models to evaluate the relationships between a disease trait and covariates, such as one or more candidate genes or an environmental exposure. Recently, attention has turned to study designs that mandate the inclusion of family members in addition to a proband. Standard models for analysis assume independent observations, which is unlikely to be true for family data, and the usual standard errors for the regression parameter estimates may be too large or too small, depending on the distribution of the covariates within and between families. The consequences of familial correlation on the study efficiency can be measured by a design effect that is equivalent to the relative information in a sample of unrelated individuals compared to a sample of families with the same number of individuals. We examine design effects for studies in association, and illustrate how the design effect is influenced by the intra-familial distribution of covariate values such as would be expected for a candidate gene. Typical design effects for a candidate gene range between 1.1 and 2.4, depending on the size of the family and the amount of unexplained familial correlation. These values correspond to a modest 10% increase in the required sample size up to more than doubling the requirements. Design effect values are useful in study design to compare the efficiency of studies that sample families versus independent individuals and to determine sample size requirements that account for familial correlation.

Analysis of upstream elements in the HuC promoter leads to the establishment of transgenic zebrafish with fluorescent neurons

HuC encodes an RNA binding protein homologous to Drosophila elav that serves as an excellent early marker for differentiating neurons. We have characterized the promoter of the zebrafish HuC gene by examining the ability of 5'-upstream fragments to drive expression of green fluorescent protein (GFP) in live embryos. We determined that 2.8 kb of the 5'-flanking sequence is sufficient to restrict GFP gene expression to neurons. The core promoter spans 251 base pairs and contains a CCAAT box and one SP1 sequence but no TATA box is present near the transcription start site. A putative MyT1 binding site and at least 17 E-box sequences are necessary to maintain the neuronal specificity of HuC expression. Interestingly, sequential removal of the putative MyT1 binding site and 14 distal E boxes does not appear to abolish neuronal expression; rather, it leads to a progressive expansion of GFP expression into muscle cells. Further removal of the three proximal E boxes eliminates neuronal and muscle specificity of GFP expression and leads to ubiquitous expression of GFP in the whole body. Identification of key components of the HuC promoter has led to the establishment of a stable zebrafish transgenic line (HuC-GFP) in which GFP is expressed specifically in neurons. We crossed mind bomb (mib) fish with this line to visualize their neurogenic phenotype in live mib(-/-) mutant embryos. This cross illustrates how HuC-GFP fish could be used in the future to identify and analyze zebrafish mutants with an aberrant pattern of early neurons.

A novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases

Endothelial monocyte-activating polypeptide II (EMAP II) is a novel pro-apoptotic cytokine that shares sequence homology with the C-terminal regions of several tRNA synthetases. Pro-EMAP II, the precursor of EMAP II, is associated with the multi-tRNA synthetase complex and facilitates aminoacylation activity. The structure of human EMAP II, solved at 1.8 A resolution, revealed the oligomer-binding fold for binding different tRNAs and a domain that is structurally homologous to other chemokines. The similar structures to the RNA binding motif of EMAP II was previously observed in the anticodon binding domain of yeast Asp-tRNA synthetase (AspRSSC) and the B2 domain of Thermus thermophilus Phe-tRNA synthetase. The RNA binding pattern of EMAP II is likely to be nonspecific, in contrast to the AspRSSC. The peptide sequence that is responsible for cytokine activity is located, for the most part, in the beta1 strand. It is divided into two regions by a neighboring loop.

NMR studies on novel antitumor drug candidates, deoxoartemisinin and carboxypropyldeoxoartemisinin

Artemisinin and its derivatives, which have been known as antimalarial drugs, have also demonstrated their cytotoxicity against tumor cells. It has been proposed that antitumor activity depends on the lipophilicity of functional group on artemisinin derivatives. Solution structures of two artemisinin derivatives as antitumor drug candidates, deoxoartemisinin and carboxypropyldeoxoartemisinin, were determined by NMR spectroscopy to elucidate structure-activity relationship. According to biological assay, antitumor efficiencies are not dependent upon lipophilicity. Instead, these compounds demonstrated their distinctive structural features of boat/chair conformation and capability to interact with receptors, as they have different efficiencies on antitumor activity. Especially, carboxypropyl moiety or carbonyl moiety in artemisinin derivatives influences the conformation and stability of ring structure. Although the detailed mechanism of antitumor activity by artemisinin derivatives has not been addressed, we suggest that antitumor activity is not determined only with lipophilicity and that artemisinin derivatives have specific target proteins in each type of cancer.

Complete congenital bony syngnathia in a case of oromandibular limb hypogenesis syndrome

Congenital fusion of the maxilla and mandible (syngnathia) is rare and can present in a wide range of severity from single mucosal bands (synechiae) to complete bony fusion (synostosis). Congenital synostosis of the mandible and maxilla is even less common than synechiae, with only 19 cases reported in the literature. Most of them have presented as an incomplete, unilateral fusion. Only three of the reported cases showed more extensive but still incomplete, intermaxillary bony fusion. We present a case of complete bony fusion of the maxilla and mandible associated with a cleft palate, hypoglossia, micrognathia, unilateral choanal atresia, and limb abnormalities as a feature of oromandibular limb hypogenesis syndrome. Details of operative management are presented.

New triterpenoid saponins from the sponge Melophlus isis

Four new triterpenoid saponins were isolated, along with two known 30-norlanostane-type saponins- sarasinosides A(1) (1) and A(3) (2)-from the sponge Melophlus isis collected from Guam. The structures of these new compounds (3-6) proved to be 30-norlanosta-8(14),24-dien-23-ones bearing two hydroxyl groups or the corresponding methoxy groups at the 9alpha,15alpha- and 9alpha, 15beta-positions and the pentasaccharide portion identical with those of 1 and 2 at the 3beta position, by spectral, chemical, and GC analyses.

Pregnancy in cystic fibrosis. Fetal and maternal outcome

OBJECTIVE

To assess the effect of pregnancy on pulmonary function and survival in women with cystic fibrosis (CF) and to assess the fetal outcome.

DESIGN

Cohort study. The data analyzed were collected from the Toronto CF database, chart review, and patient questionnaire.

SETTING

Tertiary-care center.

PATIENTS

All women with CF who, at the time of diagnosis or pregnancy, attended the Toronto Cystic Fibrosis Clinics between 1961 and 1998.

RESULTS

From 1963 to 1998, there were 92 pregnancies in 54 women. There were 11 miscarriages and 7 therapeutic abortions. Forty-nine women gave birth to 74 children. The mean follow-up time was 11 +/- 8 years. One patient was lost to follow-up shortly after delivery, and one was lost after 12 years. The overall mortality rate was 19% (9 of 48 patients). Absence of Burkholderia cepacia (p < 0.001), pancreatic sufficiency (p = 0.01), and prepregnancy FEV(1) > 50% predicted (p = 0.03) were associated with better survival rates. When adjusted for the same parameters, pregnancy did not affect survival compared to the entire adult female CF population. The decline in FEV(1) was comparable to that in the total CF population. Three women had diabetes mellitus, and seven developed gestational diabetes. There were six preterm infants and one neonatal death. CF was diagnosed in two children.

CONCLUSIONS

The maternal and fetal outcome is good for most women with CF. Risk factors for mortality are similar to those for the nonpregnant CF population. Pregnancies should be planned so that there is opportunity for counseling and optimization of the medical condition. Good communication between the CF team and the obstetrician is important.

Adhesion to target cells is disrupted by the killer cell inhibitory receptor

Killer cell immunoglobulin-like receptors (KIR) inhibit the cytotoxic activity of natural killer (NK) cells by recruitment of the tyrosine phosphatase SHP-1 to immunoreceptor tyrosine-based inhibition motif (ITIM) sequences in the KIR cytoplasmic tail [1]. The precise steps in the NK activation pathway that are inhibited by KIR are yet to be defined. Here, we have studied whether the initial step of adhesion molecule LFA-1-dependent adhesion to target cells was altered by the inhibitory signal. Using stable expression of an HLA-C-specific KIR in the NK cell line YTS [2] and a two-color flow cytometry assay for conjugate formation, we show that adhesion to a target cell expressing cognate HLA-C was disrupted by KIR engagement. Conjugate formation was abruptly interrupted by KIR within less than 5 minutes. Inhibition of adhesion to target cells was mediated by a chimeric KIR molecule carrying catalytically active SHP-1 in place of its cytoplasmic tail. These results suggest that other ITIM-bearing receptors, many of which have no known function, may regulate adhesion in a wide variety of cell types.

Comparison of evidence for linkage from different analytic methods

In a randomly chosen replicate of extended pedigrees from GAW10, we conducted robust multipoint genome scans for linkage using a dense marker map. For analysis of the quantitative traits, we selected sibships from the pedigrees, and for analysis of disease status, small families of affected relatives were selected. Lod-score likelihood analyses were conducted in the full pedigrees and in the affected relative families for selected regions. We located a flanking marker for MG1 on chromosome 5, and identified marker regions including MG2, MG4, and MG5 on chromosomes 8 and 9. The analytic methods were consistent for the major gene with a strong effect; false positive errors on chromosomes 1 and 10 could have been eliminated by requiring evidence from more than one method.

Segregation analysis in Shwachman-Diamond syndrome: evidence for recessive inheritance

Shwachman-Diamond syndrome is a rare disorder of unknown cause. Reports have indicated the occurrence of affected siblings, but formal segregation analysis has not been performed. In families collected for genetic studies, the mean paternal age and mean difference in parental ages were found to be consistent with the general population. We determined estimates of segregation proportion in a cohort of 84 patients with complete sibship data under the assumption of complete ascertainment, using the Li and Mantel estimator, and of single ascertainment with the Davie modification. A third estimate was also computed with the expectation-maximization (EM) algorithm. All three estimates supported an autosomal recessive mode of inheritance, but complete ascertainment was found to be unlikely. Although there are no overt signs of disease in adult carriers (parents), the use of serum trypsinogen levels to indicate exocrine pancreatic dysfunction was evaluated as a potential measure for heterozygote expression. No consistent differences were found in levels between parents and a normal control population. Although genetic heterogeneity cannot be excluded, our results indicate that simulation and genetic analyses of Shwachman-Diamond syndrome should consider a recessive model of inheritance.

Substrate recognition through a PDZ domain in tail-specific protease

Tail-specific protease (Tsp) is a periplasmic enzyme that selectively degrades proteins bearing a nonpolar C-terminus. Its substrate specificity suggests that Tsp may contain a substrate recognition domain, which selectively binds to the nonpolar C-termini of substrate proteins, separate from its catalytic site. In this work, we show that substrate recognition of Tsp is mediated by a PDZ domain, a small protein module that promotes protein-protein interactions by binding to internal or C-terminal sequences of their partner proteins. Partial proteolysis by V8 protease at a single peptide bond immediately N-terminal to the PDZ domain resulted in two distinct and relatively stable fragments and complete loss of catalytic activity. Photoaffinity labeling with a fluorescent nonpolar peptide caused the covalent attachment of the peptide to a single site on the Tsp protein. Systematic deletion mutagenesis of Tsp localized the binding site to amino acids 206-307, a region that completely encompasses the putative PDZ domain (217-301). The isolated PDZ domain (amino acids 206-334) is capable of folding into a well-behaved structure and binds to a nonpolar peptide with a dissociation constant (K(D)) of 1.9 microM, similar to that of the intact Tsp protein. Site-directed mutagenesis of a surface residue at the peptide binding site of the PDZ domain, valine 229, to Glu or Gln resulted in an increase in the K(M) value but had no effect on the k(cat) value. The use of a separate substrate recognition domain such as a PDZ domain may be a general mechanism for achieving selective protein degradation.

New xenicane diterpenoids from the gorgonian Acalycigorgia inermis

Acalycixeniolides D-G [corrected] (1-4), four new diterpenoids of the xenicane class, have been isolated from the gorgonian Acalycigorgia inermis. The structures of these compounds have been determined by combined spectroscopic methods. These compounds exhibited cytotoxicity against a human leukemia cell-line.

Neuroendocrine function and response to stress in mice with complete disruption of glucagon-like peptide-1 receptor signaling

Glucagon-like peptide-1 (GLP-1), a potent regulator of glucose homeostasis, is also produced in the central nervous system, where GLP-1 has been implicated in the neuroendocrine control of hypothalamic-pituitary function, food intake, and the response to stress. The finding that intracerebroventricular GLP-1 stimulates LH, TSH, corticosterone, and vasopressin secretion in rats prompted us to assess the neuroendocrine consequences of disrupting GLP-1 signaling in mice in vivo. Male GLP-1 receptor knockout (GLP-1R-/-) mice exhibit reduced gonadal weights, and females exhibit a slight delay in the onset of puberty; however, male and female GLP-1R-/- animals reproduce successfully and respond appropriately to fluid restriction. Although adrenal weights are reduced in GLP-1R-/- mice, hypothalamic CRH gene expression and circulating levels of corticosterone, thyroid hormone, testosterone, estradiol, and progesterone are normal in the absence of GLP-1R-/- signaling. Intriguingly, GLP-1R-/- mice exhibit paradoxically increased corticosterone responses to stress as well as abnormal responses to acoustic startle that are corrected by glucocorticoid treatment. These findings suggest that although GLP-1R signaling is not essential for development and basal function of the murine hypothalamic-pituitary-adrenal axis, abrogation of GLP-1 signaling is associated with impairment of the behavioral and neuroendocrine responses to stress.

Direct interaction of the CD38 cytoplasmic tail and the Lck SH2 domain. Cd38 transduces T cell activation signals through associated Lck

CD38 ligation has been shown to induce activation of intracellular signaling cascade in T lymphocytes through a Lck-dependent pathway. However, it is not clear how Lck initiates the CD38-mediated signaling process. In the present study, we showed that CD38 and Lck were physically associated through the cytoplasmic tail and the Src homology 2 domain, respectively. This was evidenced by coimmunoprecipitation of Lck with CD38 and Lck with isolated CD38 cytoplasmic domain from T cell lysate, cell lysate of COS-7 cells cotransfected with cDNAs of Lck and CD38, or a mixture of in vitro translated CD38 and Lck. Because the CD38 cytoplasmic domain does not contain any tyrosine residue, the interaction should be independent of phosphotyrosine. The interaction was further confirmed by in vitro interaction between a purified Lck Src homology 2 domain and a nonphosphosynthetic peptide corresponding to the membrane proximal region of the CD38 cytoplasmic domain. In addition, CD38 ligation resulted in an elevated tyrosine kinase activity of the CD38-associated Lck and ultimate activation of interleukin-2 gene transcription. Furthermore, expression of a kinase-deficient Lck mutant suppressed interleukin-2 gene activation in a dose-dependent manner. These results strongly suggested that CD38 ligation indeed tranduced signals for T cell activation using its associated Lck.

Relationship between the tertiary structures of mastoparan B and its analogs and their lytic activities studied by NMR spectroscopy

Mastoparan B (MP-B), an antimicrobial cationic tetradecapeptide amide isolated from the venom of the hornet Vespa basalis, is an amphiphilic alpha-helical peptide. MP-B possesses a variety of biological activities, such as mast cells degradation histamine release, erythrocyte lysis and inhibition of the growth of gram-positive and gram-negative bacteria. In order to study the relationship between the structure and the biological activity of MP-B, we used four analogs by replacing amino acids with alanine. Tertiary structures of MP-B and its analogs in 2,2,2-trifluoroethanol (TFE)-containing aqueous solution have been determined by NMR spectroscopy and molecular modeling. The results indicate that [Ala4]MP-B and [Ala12]MP-B with higher hydrophobicity adopt a higher content of amphiphilic helical structures, and have better antimicrobial and hemolytic activities than MP-B. However, [Ala3]MP-B and [Ala9]MP-B with lower hydrophobicity have disordered structures. [Ala3]MP-B and [Ala9]MP-B have low antimicrobial activity and much less hemolytic activity relative to MP-B. It is likely that tryptophan residue in MP-B and appropriate hydrophobicity of MP-B to induce alpha-helical structure is essential for the antibacterial and hemolytic activity of MP-B. This study can aid understanding of the structure-activity relationship of MP-B and to design peptides to possess lytic activity.

Evaluation of the contribution of environmental factors

For the simulated data of GAW11, the roles of two environmental factors, E1 and E2, were investigated. Logistic regression analyses measuring the association between outcome (either mild or severe disease versus no disease) and E1 and E2 exposure indicated that E1 was a risk factor for disease (either mild or severe) but that E2 was not associated with outcome. Linkage analyses were performed for strata defined by E1 and E2 exposure. A specific disease locus was identified in these stratified analyses where this locus would not have been identified with an unstratified linkage analysis. Finally, stratified generalized transmission disequilibrium test analyses yielded several false positive results.

Detecting interactions between gene, site, and environmental variables using GAP

Regressive models that incorporate measured variables and assumed genetic parameters were used to detect interactions between gene, research site, and environmental variables in GAW11 Problem 2. Replicates 1 to 5 were used in the analyses. Significant three-way gene x environment x site interactions were seen for all models, regardless of what assumptions were made about genetic transmission. Therefore, regressive models within each of the four sites were examined for significant gene x environment interactions. At one site, there was a pattern of gene x environment interaction that was consistent in most of the genetic models assumed. Joint and separate segregation and linkage analyses were compared in this site. No patterns of gene x environment interaction were seen in the other sites. Results from this analysis show that regressive modeling can identify complex interactions in data from heterogeneous populations even when ascertainment assumptions are violated.

Adaptive neural coding dependent on the time-varying statistics of the somatic input current

It is generally assumed that nerve cells optimize their performance to reflect the statistics of their input. Electronic circuit analogs of neurons require similar methods of self-optimization for stable and autonomous operation. We here describe and demonstrate a biologically plausible adaptive algorithm that enables a neuron to adapt the current threshold and the slope (or gain) of its current-frequency relationship to match the man (or dc offset) and variance (or dynamic range or contrast) of the time-varying somatic input current. The adaptation algorithm estimates the somatic current signal from the spike train by way of the intracellular somatic calcium concentration, thereby continuously adjusting the neurons' firing dynamics. This principle is shown to work in an analog VLSI-designed silicon neuron.

Molecular responses of macrophages to porcine reproductive and respiratory syndrome virus infection

The detailed mechanism(s) by which porcine reproductive and respiratory syndrome virus (PRRSV) impairs alveolar Mo homeostasis and function remains to be elucidated. We used differential display reverse-transcription PCR (DDRT-PCR) to identify molecular genetic changes within PRRSV-infected Mo over a 24 h post infection period. From over 4000 DDRT-PCR amplicons examined, 19 porcine-derived DDRT-PCR products induced by PRRSV were identified and cloned. Northern blot analysis confirmed that four gene transcripts were induced during PRRSV infection. PRRSV attachment and penetration alone did not induce these gene transcripts. DNA sequence revealed that one PRRSV-induced expressed sequence tag (EST) encoded porcine Mx1, while the remaining 3 clones represented novel ESTs. A full-length cDNA clone for EST G3V16 was obtained from a porcine blood cDNA library. Sequence data suggests that it encodes an ubiquitin-specific protease (UBP) that regulates protein trafficking and degradation. In pigs infected in vivo, upregulated transcript levels were observed for Mx1 and Ubp in lung and tonsils, and for Mx1 in tracheobronchial lymph node (TBLN). These tissues correspond to sites for PRRSV persistence, suggesting that the Mx1 and Ubp genes may play important roles in clinical disease during PRRSV infection.

Prevalence of vitamin K deficiency in cystic fibrosis

BACKGROUND

Patients with cystic fibrosis (CF) are at risk of developing vitamin K deficiency because of pancreatic insufficiency, hepatobiliary disease, or both.

OBJECTIVE

Our objective was to determine the prevalence of vitamin K deficiency in unsupplemented patients with CF and to identify risk factors that might be associated with the deficiency.

DESIGN

Ninety-eight patients with CF-83 who were pancreatic insufficient (age: 15.2 +/- 10.7 y; range: 0.6-45.8 y), 15 who were pancreatic sufficient (age: 26.2 +/- 11.6 y; range: 6.5-45.3 y), and 62 healthy individuals (age: 16.2 +/- 12. 8 y; range: 1-45 y)-were studied prospectively. None had taken vitamin K supplements. Eight pancreatic-insufficient patients had advanced CF-associated liver disease. Plasma prothrombin in vitamin K absence (PIVKA-II) was measured by immunoassay. All control subjects had PIVKA-II concentrations <3 microg/L.

RESULTS

Seventy-eight percent of pancreatic-insufficient patients had PIVKA-II concentrations >/=3 microg/L (22.8 +/- 35.7 microg/L). All patients with CF-associated liver disease had abnormal PIVKA-II concentrations. The mean PIVKA-II concentration of pancreatic-insufficient patients with liver disease was greater than that of those without liver disease (46.6 +/- 65.3 compared with 15. 3 +/- 26.1 microg/L; P < 0.05). Five pancreatic-sufficient patients had mildly elevated PIVKA-II concentrations. Six (7%) pancreatic insufficient patients (3 with CF-associated liver disease) had mildly prolonged prothrombin time but no clinical bleeding. There was no correlation between PIVKA-II concentrations and severity of fat malabsorption or antibiotic use.

CONCLUSIONS

Vitamin K deficiency is common in unsupplemented patients with CF and pancreatic insufficiency and routine supplementation should be considered in all of these patients.

Shwachman syndrome: phenotypic manifestations of sibling sets and isolated cases in a large patient cohort are similar

OBJECTIVES

With the use of clinical data from a large international cohort, we evaluated and compared affected siblings and isolated cases.

STUDY DESIGN

Data from 116 families were collected, and patients conforming to our predetermined diagnostic criteria were analyzed. Phenotypic manifestations of affected siblings and singletons were compared with the use of t tests, Wilcoxon scores, and chi2 analysis.

RESULTS

Eighty-eight patients (33 female, 55 male; median age 5.20 years) fulfilled our predetermined diagnostic criteria for Shwachman syndrome; 63 patients were isolated cases, and 25 affected siblings were from 12 multiplex families. Steatorrhea was present in 86% (57 of 66), and 91% (78 of 86) displayed a low serum trypsinogen concentration. Patients older than 4 years more often had pancreatic sufficiency. Neutropenia occurred in 98%, anemia in 42%, and thrombocytopenia in 34%. Myelodysplasia or cytogenetic abnormalities were reported in 7 patients. Short stature with normal nutritional status was a prominent feature.

CONCLUSIONS

Clinical features among patients with Shwachman syndrome varied between patients and with age. Similarities in phenotype between isolated cases and affected sibling sets support the hypothesis that Shwachman syndrome is a single disease entity.

New Bis(Indole) alkaloids of the topsentin class from the sponge spongosorites genitrix

Four bis(indole) alkaloids of the topsentin class, including two new brominated compounds (1 and 2), have been isolated from the sponge Spongosorites genitrix collected from Jaeju Island, Korea. The structures of the novel compounds were determined by spectroscopic methods. These compounds exhibited moderate cytotoxicity against a human leukemia cell-line (K-562).

New acetylenic enol ethers of glycerol from the sponge Petrosia sp

Ten acetylenic enol ethers of glycerols, including six new compounds (1-6) and a linear acetylenic alcohol (7), have been isolated from a sponge of the genus Petrosia. The structures of the novel compounds were elucidated by spectroscopic methods. The absolute stereochemistry of 1-7 was determined by chemical transformations and the Mosher method. Some of these compounds exhibited weak cytotoxicity against a human leukemia cell-line (K-562).

P62 and the sequestosome, a novel mechanism for protein metabolism

In addition to selecting proteins for degradation by the 26S proteasome, ubiqitination appears to serve other regulatory functions, including for endosomal/lysosomal targeting, protein translocation, and enzyme modification. Currently, little is known how multiubiquitin chains are recognized by these cellular mechanisms. Within the 26S proteasome, one subunit (Mcb1/S5a) has been identified that has affinity for multiubiquitin chains and may function as a ubiquitin receptor. We recently found that a non-proteasomal protein p62 also preferentially binds multiubiquitin chains and forms a novel cytoplasmic structure "sequestosome" which serves as a storage place for ubiquitinated proteins. In the present manuscript, the role and regulation of p62 in relation to the sequestosomal function will be reviewed.

Immediate early response of the p62 gene encoding a non-proteasomal multiubiquitin chain binding protein

p62 is a cytoplasmic ubiquitin chain binding protein. Upon a variety of extracellular signals, both transcript and protein levels of p62 were rapidly increased. These signals include phorbol 12-myristate 13-acetate (PMA) and calcium ionomycin for peripheral blood mononuclear cells, serum or PDGF for serum-starved NIH3T3 cells, IL-3 for the G1 arrested pre-B cell line Ba/F3, and PMA for a human promyelocyte line U937. The elevation of p62 transcript level is due to temporal stabilization of mRNA and rapid activation of the p62 gene. Cycloheximide-induced enhanced transcription suggests the immediate early response of the p62 gene. The rapid induction of p62 indicates the presence of a novel ubiquitination-mediated regulatory mechanism during cell proliferation and differentiation.

New secosteroids from a gorgonian of the genus Muricella

Calicoferols F-I (2-5), four new 9,10-secosteroids, have been isolated from a gorgonian of the genus Muricella collected from Jaeju Island, Korea. The structures of these compounds have been determined by combined spectroscopic methods. Calicoferols exhibited significant cytotoxicity and inhibitory activity against PLA2.

JC virus infection in cells from lymphoid tissue

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease characterized by infection of oligodendrocytes by JC virus. The exact nature of the pathogenesis of PML is not known. The nature of the primary infection, the site of viral latency, and the route by which JCV enters the brain remain to be elucidated. Different laboratories have shown the presence of JCV in peripheral lymphocytes from immunosuppressed individuals, suggesting these cells as possible carriers of JCV to the brain. To examine this observation, we tested the susceptibility to JCV infection of cells from lymphoid organs, focusing our attention on CD34+ haematopoietic precursor cells and B lymphocytes. The results demonstrate that both these cell types are susceptible to JCV infection and, moreover, that JCV can infect only those cells that differentiate into lymphocytic lineage.

Five new polyacetylenes from a sponge of the genus petrosia

Petrocortynes D-H, novel C46 polyacetylenes, were isolated from a sponge of the genus Petrosia collected from Keomun Island, Korea. Petrocortyne D (2) is a 4,5-dihydro derivative of a diastereomer of petrocortyne A (1), and petrocortynes E-H (3-6) possess an additional allylic-hydroxyl group. The structures of these compounds were determined by combined chemical and spectral methods, and absolute configurations of most of the asymmetric carbon centers were determined by the modified Mosher's method. Limitations on the application of Mosher's method to allylic alcohols is discussed. Petrocortynes D-H exhibited moderate cytotoxicity and inhibitory activity against PLA2.

Genomic structure and promoter analysis of the p62 gene encoding a non-proteasomal multiubiquitin chain binding protein

p62 is a novel immediate early response gene encoding a ubiquitin chain binding protein. To investigate the mechanism of p62 gene expression, we isolated and characterized the 20 kb long human p62 gene. The p62 gene contains seven introns and eight exons. The splice sites conformed to the GT/AG rule, except introns 6 and 7 which used the unusual GC dinucleotides. The p62 promoter is TATA-less, and 357 nucleotides of the 5'-flanking region contain basic machineries for transcription. A reporter gene linked to 1800 nucleotides of the 5'-flanking region was rapidly activated by various extracellular signals. The presence of a CpG island as well as multiple binding sites for SP-1, AP-1, NF-kappaB, and Ets-1 family in the promoter region supports the regulated activation of the p62 gene.