Nanoscale hydrophobic interaction and nanobubble nucleation

We report large-scale atomistic simulation of midrange nanoscale hydrophobic interaction, manifested by the nucleation of nanobubble between nanometer-sized hydrophobes at constrained equilibrium. When the length scale of the hydrophobes is greater than 2 nm, the nanobubble formation shows hysteresis behavior resembling the first-order transition. Calculation of the potential of mean force versus interhydrophobe distance provides a quantitative measure of the strength of the nanoscale hydrophobic interaction.

Characteristics of sensitometric curves of radiographic films

A new type of radiographic film, EDR (extended dose range) film, has been recently become available for film dosimetry. It is particularly attractive for composite isodose verification of intensity modulated radiation therapy because of its low sensitivity relative to the more common Kodak XV film. For XV film, the relationship between optical density and dose, commonly known as the sensitometric curve, depends linearly on the dose at low densities. Unlike XV film, the sensitometric curve of EDR film irradiated by megavoltage x rays is not linearly dependent on the dose at low densities. In this work, to understand the mechanisms governing the shape of the sensitometric curves, EDR film was studied with kilovoltage x rays, 60Co gamma rays, megavoltage x rays, and electron beams. As a comparison, XV film was also studied with the same beams mentioned above. The model originally developed by Silberstein [J. Opt. Soc. Am. 35, 93-107, 1945)] is used to fit experimental data. It is found that the single hit model can be used to predict the sensitometric curve for XV films irradiated by all beams used in this work and for EDR films exposed to kilovoltage x rays. For EDR film irradiated by 60Co gamma rays, megavoltage x rays, and electron beams, the double hit model is used to fit the sensitometric curves. For doses less than 100 cGy, a systematic difference between measured densities and that predicted by the double hit model is observed. Possible causes of the observed differences are discussed. The results of this work provide a theoretical explanation of the sensitometric behavior of EDR film.

Exogenous peptide and protein expression levels using retroviral vectors in human cells

Pseudotyped retroviral vectors combine the advantages of broad host range, high expression, stable chromosomal integration, and ease of preparation. These vectors greatly facilitate delivery into mammalian cells of sequences encoding individual peptide inhibitors-including those with therapeutic utility-and inhibitor libraries. However, retroviral vectors vary in behavior, particularly with respect to expression levels in different cell lines. Expression level is especially important in transdominant experiments because the concentration of an inhibitor (for example, an expressed peptide) is one of the key determinants in the degree of complex formation between the inhibitor and its target. Thus, inhibitor concentration should have an impact on the expressivity and/or penetrance of an induced phenotype. Here, we compare several retroviral vectors and human cell lines for relative expression levels using a green fluorescent protein reporter. We show for a subset of these lines that cellular protein concentrations produced by single-copy vectors range up to about 2 microM. We also examine other variables that contribute to expression level, such as the nature of the expressed protein's carboxy terminus. Finally, we test the effect of increased concentration on phenotype with a nine-amino-acid peptide derived from the human papilloma virus protein E7 which overcomes E7-mediated cell growth.

Assessment of cervical ligamentous injury in trauma patients using MRI

During a 7-year period, a consecutive retrospective series of 89 trauma patients at a Level One trauma center who had negative standard radiographs with suspected occult cervical injury were administered a cervical magnetic resonance imaging (MRI) scan. The MRI studies were fully able to assess the ligamentous status of the cervical spine in all patients and were the final step in determining the treatment of the spine. Of the total 89 patients, 82 had no ligamentous injury, and 7 had ligamentous injury. Two patients underwent surgery because of the findings on the MRI study. MRI studies of patients with negative standard radiographs but with suspected occult cervical injury are excellent and safe studies for the evaluation of cervical spinal stability because of their ability to detect ligamentous injuries that are not evident on plain radiographs.

Diffuse lamellar keratitis: incidence, associations, outcomes, and a new classification system

PURPOSE

To evaluate the incidence, associations, and visual outcomes in patients with diffuse lamellar keratitis (DLK) after laser in situ keratomileusis (LASIK).

SETTING

University-based refractive surgery center, Boston, Massachusetts, USA.

METHODS

This retrospective review comprised 2711 eyes that had LASIK between September 1996 and September 1999. All eyes that developed DLK after LASIK were included. They were divided into type I DLK (center sparing) or type II DLK (center involved) and then subdivided into A (sporadic-DLK not diagnosed in other patients treated on the same day) or B (cluster-other patients identified with DLK). Type IA corresponded to center sparing, sporadic; type IB, center sparing, cluster; type IIA, center involved, sporadic; and type IIB, center involved, cluster. The main outcome measures were incidence of DLK after LASIK, time to diagnosis, time to resolution, and changes in best spectacle-corrected visual acuity (BSCVA). Unpaired t tests were used for statistical analyses.

RESULTS

Thirty-six eyes (1.3%) developed DLK. Type I occurred in 58.3% of cases (type IA, n = 18; type IB, n = 3) and type II, in 41.7% (type IIA, n = 10; type IIB, n = 5). The mean time to diagnosis was not statistically significantly different between type I (1.8 days) and type II (1.1 days). Fourteen eyes (38.9%) developed DLK after an epithelial defect, representing an odds ratio of 13 times. The association with an epithelial defect was statistically significantly greater with type I (11/21 eyes, 52.4%) than with type II (3/15 eyes, 20.0%; P =.05). The mean time to resolution was 3.5 days in type I (type IA = 3.6 days; type IB = 2.7 days). This was significantly shorter than in type II, which had a mean time to resolution of 12.1 days (type IIA = 9.3 days; type IIB = 10.2 days) (P =.001). Loss of 2 or more lines of BSCVA occurred in 2 of 5 patients with type IIB and in no patients with types IA, IB, or IIA.

CONCLUSIONS

Epithelial defects after LASIK increased the risk of DLK occurrence, especially type I. Type II DLK was associated with a prolonged time to resolution and carried a significantly higher risk of BSCVA loss than type I.

Time-frequency analysis of temporomandibular joint (TMJ) clicking sounds using radially Gaussian Kernels

Temporomandibular joint (TMJ) sounds and motion were recorded during two clinically-derived movements--simple jaw opening and jaw protrusion followed by opening--from ten patients. A new time-frequency method--radially Gaussian kernel distribution--was applied to classify the TMJ clicking sounds into six groups, type I to type VI, based on the time-frequency patterns of energy distribution. The number of clicks and percentage of each type were examined. Relations between the two movements were examined by the prevalence of each type. A detailed classification of TMJ clicking sounds is provided by time-frequency patterns and may provide a better understanding of temporomandibular disorders.

Effectiveness of surveillance of central catheter-related bloodstream infection in an ICU in Korea

OBJECTIVE

To determine whether surveillance and infection control interventions decrease the incidence of catheter-related (CR) bloodstream infections (BSIs) in Korea.

SETTING

A medical-surgical intensive care unit (ICU) of a university hospital in Korea.

DESIGN

The CR infection rate of the intervention period was compared to that of historical controls for a 4-month period.

PATIENTS

All patients with a central venous catheter in the intensive care unit (ICU) from October 1998 to January 1999.

METHODS

Active infection control programs were initiated during the intervention period. Data collected included patient characteristics, risk factors of CR infection, and the microbiology laboratory results. Laboratory-proven CR infection rates were compared between the intervention group and control group.

RESULTS

304 catheters were inserted into 248 patients. The intervention group and the control group showed similar characteristics, but more patients in the intervention group received steroid therapy, and subclavian insertion was more common in the intervention group. CR BSI occurred in 1.3 per 1,000 catheter-days in the intervention group and 4.2 in the control group (binomial test, P=.14). CR infections were associated with the duration of ICU admission by multivariate logistic regression.

CONCLUSIONS

The data suggested that an active infection surveillance and control program could reduce the rate of CR

Antiangiogenic effect of KR31372 in rat sponge implant model

A rat sponge implant model was used to examine the antiangiogenic effect of KR31372. Topical administration of angiotensin II (AII, 100 ng, daily) into the sponges enhanced the basal sponge-induced neovascularization, leading to higher clearance of (99m)Tc, increased retention of dye in the vessels, and increased numbers of blood vessels. These AII-induced changes were significantly suppressed by oral administration of KR31372 (1 mg/kg for 7 days). Angiogenic effect of recombinant human VEGF(165) (200 ng) was modestly higher than that of AII, which was also significantly inhibited by KR31372. KR31372-mediated suppression of (99m)Tc clearance was reversed by glibenclamide. Levcromakalim showed a modestly suppressive effect on the AII-induced angiogenesis. In conclusion, KR31372 exerted a strong inhibitory effect on the sponge-induced neovascularization, in part, through mediation of glibenclamide-sensitive K(+) channel activation. It is suggested that it may have therapeutic potential in the treatment of angiogenic disorders.

Plasmalemmal repair of severed neurites of PC12 cells requires Ca(2+) and synaptotagmin

Ca(2+) and synaptotagmin (a Ca(2+)-binding protein that regulates axolemmal fusion of synaptic vesicles) play essential roles in the repair of axolemmal damage in invertebrate giant axons. We now report that neurites of a rat pheochromocytoma (PC12) cell line transected and maintained in a serum medium form a dye barrier (exclude an external hydrophilic fluorescent dye) and survive for 24-hr posttransection (based on morphology and retention of another hydrophilic dye internally loaded at 6-hr posttransection). Some (25%) transected neurites that form a dye barrier regrow. Most (83%) neurites transected in a saline solution containing divalent cations (PBS(++)) also exclude entry of an externally placed hydrophilic fluorescent dye at 15-min posttransection. In contrast, only 14 or 17% of neurites maintained in a divalent cation-free solution (PBS(=)) or in PBS(=) + Mg(2+), respectively, form a dye barrier. Neurites that do not form a dye barrier do not survive for 24 hr. When PC12 neurites are loaded with an antibody to squid synaptotagmin, most (81%) antibody-loaded neurites do not form a dye barrier, whereas most (>/=81%) neurites loaded with heat-inactivated antibody or preimmune IgG do form a barrier. These data show that: 1) transected neurites of PC12 cells have mechanism(s) for plasmalemmal repair (dye barrier formation and survival); 2) Ca(2+) is necessary for dye barrier formation, which occurs minutes after transection and is necessary for survival and regrowth; and 3) synaptotagmin is an essential mediator of barrier formation. The similarity in the requirements for plasmalemmal repair in this mammalian cell preparation with those reported previously for invertebrate axons suggests that mechanisms necessary for plasmalemmal repair have been conserved phylogenetically.

Axolemmal repair requires proteins that mediate synaptic vesicle fusion

A damaged cell membrane is repaired by a seal that restricts entry or exit of molecules and ions to that of the level passing through an undamaged membrane. Seal formation requires elevation of intracellular Ca(2+) and, very likely, protein-mediated fusion of membranes. Ca(2+) also regulates the interaction between synaptotagmin (Syt) and syntaxin (Syx), which is thought to mediate fusion of synaptic vesicles with the axolemma, allowing transmitter release at synapses. To determine whether synaptic proteins have a role in sealing axolemmal damage, we injected squid and crayfish giant axons with an antibody that inhibits squid Syt from binding Ca(2+), or with another antibody that inhibits the Ca(2+)-dependent interaction of squid Syx with the Ca(2+)-binding domain of Syt. Axons injected with antibody to Syt did not seal, as assessed at axonal cut ends by the exclusion of extracellular hydrophilic fluorescent dye using confocal microscopy, and by the decay of extracellular injury current compared to levels measured in uninjured axons using a vibrating probe technique. In contrast, axons injected with either denatured antibody to Syt or preimmune IgG did seal. Similarly, axons injected with antibody to Syx did not seal, but did seal when injected with either denatured antibody to Syx or preimmune IgG. These results indicate an essential involvement of Syt and Syx in the repair (sealing) of severed axons. We suggest that vesicles, which accumulate and interact at the injury site, re-establish axolemmal continuity by Ca(2+)-induced fusions mediated by proteins such as those involved in neurotransmitter release.

Geometry of a complex formed by double strand break repair proteins at a single DNA end: recruitment of DNA-PKcs induces inward translocation of Ku protein

Ku protein and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are essential components of the double-strand break repair machinery in higher eukaryotic cells. Ku protein binds to broken DNA ends and recruits DNA-PKcs to form an enzymatically active complex. To characterize the arrangement of proteins in this complex, we developed a set of photocross-linking probes, each with a single free end. We have previously used this approach to characterize the contacts in an initial Ku-DNA complex, and we have now applied the same technology to define the events that occur when Ku recruits DNA-PKcs. The new probes allow the binding of one molecule of Ku protein and one molecule of DNA-PKcs in a defined position and orientation. Photocross-linking reveals that DNA-PKcs makes direct contact with the DNA termini, occupying an approximately 10 bp region proximal to the free end. Characterization of the Ku protein cross-linking pattern in the presence and absence of DNA-PKcs suggests that Ku binds to form an initial complex at the DNA ends, and that recruitment of DNA-PKcs induces an inward translocation of this Ku molecule by about one helical turn. The presence of ATP had no effect on protein-DNA contacts, suggesting that neither DNA-PK-mediated phosphorylation nor a putative Ku helicase activity plays a role in modulating protein conformation under the conditions tested.

Photocross-linking of an oriented DNA repair complex. Ku bound at a single DNA end

Ku protein binds broken DNA ends, triggering a double-strand DNA break repair pathway. The spatial arrangement of the two Ku subunits in the initial Ku-DNA complex, when the Ku protein first approaches the broken DNA end, is not well defined. We have investigated the geometry of the complex using a novel set of photocross-linking probes that force Ku protein to be constrained in position and orientation, relative to a single free DNA end. Results suggest that this complex is roughly symmetric and that both Ku subunits make contact with an approximately equal area of the DNA. The complex has a strongly preferred orientation, with Ku70-DNA backbone contacts located proximal and Ku80-DNA backbone contacts located distal to the free end. Ku70 also contacts functional groups in the major groove proximal to the free end. Ku80 apparently does not make major groove contacts. Results are consistent with a model where the Ku70 and Ku80 subunits contact the major and minor grooves of DNA, respectively.

The publication rates of presentations at major Spine Specialty Society meetings (NASS, SRS, ISSLS)

STUDY DESIGN

A review of all the presentations at three major spine specialty meetings held over a 3-year period.

OBJECTIVES

To determine the rate of publication in peer-reviewed journals after presentations at major spine meetings conducted annually by the following three organizations: North American Spine Society (NASS), Scoliosis Research Society (SRS), and International Society for the Study of the Lumbar Spine (ISSLS).

SUMMARY OF BACKGROUND DATA

The rate of publication for presentations at national and international meetings has been determined for medical and surgical subspecialties. This rate has been used to judge the quality of the content of the meetings and to determine the validity of the research presentations.

METHODS

All presentations either in poster or oral presentation form were entered into a database covering a 3-year period for spine specialty meetings conducted annually by the following three organizations: NASS 1990 to 1992, SRS 1991 to 1993, and ISSLS 1991 to 1993. A computer search for each abstract was performed with the Melvyl Medline Plus database to determine if the abstract had been published in a peer-reviewed journal from 1990 to the end of 1997. Publication rates for presentations at these three meetings were determined over a 3-year period.

RESULTS

A total of 1186 abstracts were listed over a 3-year period in the final programs of these three meetings for the years 1991 to 1993 (SRS, ISSLS) and 1990 to 1992 (NASS). Of these 1186 abstracts, 516 were published in peer-reviewed journals, giving an overall publication rate of 43.5%. The publication rates for the three different meetings (NASS, SRS, ISSLS) were similar, with values of 40%, 47%, and 45% respectively. More than 90% of the publications resulting from these meetings were published within a period of 4 years from the data of the meeting.

CONCLUSIONS

The publication rates of presentations at three major spine specialty meetings are high and quite comparable with the publication rates of meetings in other medical subspecialties. This reflects the high quality of the meeting programs and validates their selection process.

Structures of the HIV-1 capsid protein dimerization domain at 2.6 A resolution

The human immunodeficiency virus type I (HIV-1) capsid protein is initially synthesized as the central domain of the Gag polyprotein, and is subsequently proteolytically processed into a discrete 231-amino-acid protein that forms the distinctive conical core of the mature virus. The crystal structures of two proteins that span the C-terminal domain of the capsid are reported here: one encompassing residues 146-231 (CA146-231) and the other extending to include the 14-residue p2 domain of Gag (CA146-p2). The isomorphous CA146-231 and CA146-p2 structures were determined by molecular replacement and have been refined at 2.6 A resolution to R factors of 22.3 and 20.7% (Rfree = 28.1 and 27.5%), respectively. The ordered domains comprise residues 148-219 for CA146-231 and 148-218 for CA146-p2, and their refined structures are essentially identical. The proteins are composed of a 310 helix followed by an extended strand and four alpha-helices. A crystallographic twofold generates a dimer that is stabilized by parallel packing of an alpha-helix 2 across the dimer interface and by packing of the 310 helix into a groove created by alpha-helices 2 and 3 of the partner molecule. CA146-231 and CA146-p2 dimerize with the full affinity of the intact capsid protein, and their structures therefore reveal the essential dimer interface of the HIV-1 capsid.

Dual effect of nitric oxide on the hyperpolarization-activated inward current (I(f)) in sino-atrial node cells of the rabbit

Using the whole-cell voltage-clamp technique, we have investigated the effect of nitric oxide (NO) donor (sodium nitroprusside, SNP) on hyperpolarization-activated inward current, I(f), in isolated rabbit sinoatrial node (SAN) cells. I(f) in the basal state increased when NO was applied but decreased when I(f) was pre-stimulated by isoproterenol (ISO) or by adding cAMP to the pipette solution. Both the stimulatory and the inhibitory effects of NO were abolished by guanylyl cyclase inhibitor, methylene blue (MB), suggesting that the effect of NO is mediated by cGMP. The inhibitory effect of NO was abolished when I(f) was pre-stimulated by 3-isobutyl-1-methylxanthine (IBMX), which is a phosphodiesterase (PDE) inhibitor, or by adding 8Br-cAMP (which is resistant to PDE) to the pipette solution. An analogue of cGMP, 8Br-cGMP, which is a potent stimulator of cGMP-dependent protein kinase (PKG) but has little effect on PDE, did not inhibit I(f) when I(f) was pre-stimulated by ISO. In its basal state, I(f) was still increased by 8Br-cGMP, and this effect was not prevented by the pretreatment with H-7, PKG inhibitor. The effect of acetylcholine (ACh) was not identical to that of NO: I(f) decreased when pre-stimulated not only by ISO, but also by IBMX. The above results suggest that via cGMP, NO exerts a dual effect on I(f): the inhibitory effect is mediated by cGMP-stimulated PDE, and the stimulatory effect may be attributable to direct binding of cGMP to I(f) channels.

Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids

The Ku protein-DNA-dependent protein kinase system is one of the major pathways by which cells of higher eukaryotes respond to double-strand DNA breaks. The components of the system are evolutionarily conserved and homologs are known from a number of organisms. The Ku protein component binds directly to DNA ends and may help align them for ligation. Binding of Ku protein to DNA also nucleates formation of an active enzyme complex containing the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). The interaction between Ku protein, DNA-PKcs and nucleic acids has been extensively investigated. This review summarizes the results of these biochemical investigations and relates them to recent molecular genetic studies that reveal highly characteristic repair and recombination defects in mutant cells lacking Ku protein or DNA-PKcs.

Characterization of the RNA binding properties of Ku protein

Ku protein, a heterodimer of 70 and 83 kDa polypeptides, is the regulatory component of the DNA-dependent protein kinase (DNA-PK). Ku protein binds to DNA ends and is essential for DNA double-strand break repair and V(D)J recombination. Although there is some evidence that Ku protein also binds RNA, its RNA binding properties have not been systematically explored. In the present study, Ku-binding RNAs were identified using systematic evolution of ligands by exponential enrichment (SELEX) technology. These RNAs were assigned to three classes based on common sequence motifs. Most of the selected RNAs bound to Ku protein with a Kd < or = 2 nM, comparable to the affinity of DNA fragments for Ku protein under similar conditions. Many of the RNAs inhibited DNA-PK activity by competing with DNA for a common binding site in Ku protein. None of several RNAs that were tested activated DNA-PK in the absence of DNA. The identification of diverse RNAs that bind avidly to Ku protein is consistent with the idea that natural RNAs may serve as modulators of DNA-PK activity. Moreover, the RNAs identified in this study may have utility as tools for experimental manipulation of DNA double-strand break repair activity in cells and cell extracts.

cGMP facilitates calcium current via cGMP-dependent protein kinase in isolated rabbit ventricular myocytes

The effect of guanosine 3',5'-cyclic monophosphate (cGMP) on L-type Ca current (ICa) was investigated in a study of rabbit ventricular myocytes using the whole-cell patch-clamp technique. Intracellular application of cGMP (100 MUm) increased ICa in the absence of isoprenaline or forskolin. 8-Bromo-cGMP (100 muM) and 8-(4-chlorophenylthio)-cGMP (8-pCPT-cGMP, 400 muM), relatively specific stimulators of cGMP-dependent protein kinase (cGMP-PK), also increased ICa. The stimulatory effect of 8-pCPT-cGMP was suppressed by Rp-8-chlorophenylthio-cGMP (400 muM), a phosphodiesterase-resistant cGMP-PK inhibitor. When ICa was increased by bath application of the non-specific phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine (IBMX, 100 muM), 8-pCPT-cGMP (400 muM) resulted in additional stimulation of ICa. In the presence of 8-pCPT-cGMP, additional applications of isoprenaline (1 muM) or forskolin (1 muM) induced a further increase in ICa. From these results, it could be concluded that the activation of cGMP-dependent protein kinase is involved in the facilitation of ICa by cGMP in rabbit ventricular myocytes.

Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein

The cellular protein, cyclophilin A (CypA), is incorporated into the virion of the type 1 human immunodeficiency virus (HIV-1) via a direct interaction with the capsid domain of the viral Gag polyprotein. We demonstrate that the capsid sequence 87His-Ala-Gly-Pro-Ile-Ala92 (87HAGPIA92) encompasses the primary cyclophilin A binding site and present an X-ray crystal structure of the CypA/HAGPIA complex. In contrast to the cis prolines observed in all previously reported structures of CypA complexed with model peptides, the proline in this peptide, Pro 90, binds the cyclophilin A active site in a trans conformation. We also report the crystal structure of a complex between CypA and the hexapeptide HVGPIA, which also maintains the trans conformation. Comparison with the recently determined structures of CypA in complexes with larger fragments of the HIV-1 capsid protein demonstrates that CypA recognition of these hexapeptides involves contacts with peptide residues Ala(Val) 88, Gly 89, and Pro 90, and is independent of the context of longer sequences.

Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein

The carboxyl-terminal domain, residues 146 to 231, of the human immunodeficiency virus-1 (HIV-1) capsid protein [CA(146-231)] is required for capsid dimerization and viral assembly. This domain contains a stretch of 20 residues, called the major homology region (MHR), which is conserved across retroviruses and is essential for viral assembly, maturation, and infectivity. The crystal structures of CA(146-231) and CA(151-231) reveal that the globular domain is composed of four helices and an extended amino-terminal strand. CA(146-231) dimerizes through parallel packing of helix 2 across a dyad. The MHR is distinct from the dimer interface and instead forms an intricate hydrogen-bonding network that interconnects strand 1 and helices 1 and 2. Alignment of the CA(146-231) dimer with the crystal structure of the capsid amino-terminal domain provides a model for the intact protein and extends models for assembly of the central conical core of HIV-1.

Heat shock transcription factor 1 binds selectively in vitro to Ku protein and the catalytic subunit of the DNA-dependent protein kinase

Heat shock transcription factor 1 (HSF1) functions as the master regulator of the heat shock response in eukaryotes. We have previously shown that, in addition to its role as a transcription factor, HSF1 stimulates the activity of the DNA-dependent protein kinase (DNA-PK). DNA-PK is composed of two components: a 460-kDa catalytic subunit and a 70- and 86-kDa heterodimeric regulatory component, also known as the Ku protein. We report here that HSF1 binds specifically to each of the two components of DNA-PK. Binding occurs in the absence of DNA. The complex with the Ku protein is stable and forms at a stoichiometry close to unity between the Ku protein heterodimer and the active HSF1 trimer. The binding is blocked by antibodies against HSF1. Our results show that HSF1 also binds directly, but more weakly, to the catalytic subunit of DNA-PK. Both interactions are dependent on a specific region within the HSF1 regulatory domain. This sequence is necessary but not sufficient for HSF1 stimulation of DNA-PK activity. The ability of HSF1 to interact with both components of DNA-PK provides a potential mechanism for the activation of DNA-PK in response to heat and other forms of stress.

Applying readily accessible graphical techniques to assess curvilinear relationships and detect outliers. The case of protective family processes

The purpose of this article is to use data from a study of protective family processes to illustrate how readily accessible graphical techniques can supplement correlation and regression analyses. Graphical techniques can help to (a) better understand family process data from a descriptive standpoint, (b) minimize erroneous statistical conclusions, and (c) clarify theoretically important relationships among variables. Following a brief description of the substantive area selected for illustration of the graphical techniques, data from a study employing multimethod measurement procedures (N = 146) are employed to illustrate two graphical technique applications in the analysis of a predictor (marital quality) of a study outcome variable (parent-child affective quality). Instructions for the application of relevant procedures in SAS and SPSS statistical packages are provided.

Molecular recognition in the HIV-1 capsid/cyclophilin A complex

The HIV-1 capsid protein (CA) makes an essential interaction with the human peptidyl prolyl isomerase, cyclophilin A (CypA), that results in packaging of CypA into the virion at a CA to CypA stoichiometry of approximately 10:1. The 231 amino acid residue capsid protein is composed of an amino-terminal CypA binding domain (1 to approximately 151; CA151) and a carboxyl-terminal dimerization domain (approximately 151 to 231). We find that CypA binds dimeric CA and monomeric CA151 with identical intrinsic affinities (K[d] = 16(+/-4) microM). This result demonstrates that capsid dimerization and cyclophilin A binding are not thermodynamically coupled and suggests that the substoichiometric ratio of CypA in the HIV-1 virion results from the intrinsic stability of the CA/CypA complex. In the known co-crystal structure of the CA151/CypA complex, CypA binding is mediated exclusively by an exposed capsid loop that spans residues Pro85 to Pro93. The energetic contributions to CypA binding were quantified for each residue in this loop, and the results demonstrate that the Gly89-Pro90 dipeptide is the primary cyclophilin A recognition motif, with Pro85, Val86, His87, Ala88, and Pro93 also making energetically favorable contacts. These studies reveal that the active site of CypA, which can catalyze the isomerization of proline residues in vitro, also functions as a sequence-specific, protein-binding motif in HIV-1 replication.

Ku proteins join DNA fragments as shown by atomic force microscopy

The binding of the Ku protein to DNA was investigated using the atomic force microscope. Ku was found to bind predominantly to the ends of double-stranded DNA. Experiments with plasmid DNA revealed that Ku does not bind to circular plasmids but does bind to plasmids that have been linearized by treatment with ionizing radiation. The binding of Ku to poly(dG-dC) x poly(dG-dC) polynucleotides and to a 400-bp DNA EcoRI fragment resulted in a shift in the fragment size distribution to include longer fragments, with internally binding Ku. Furthermore, we observed images consistent with fragments joined together by Ku, showing an interaction with two ends of DNA. These observations suggest that Ku may play a role in physically orienting DNA for ligation by binding the ends of adjacent DNA molecules.

Subretinal aspiration biopsy of ocular lymphoma

PURPOSE

Large-cell lymphoma can be difficult to diagnose because vitreous biopsies may fail to disclose neoplastic cells.

METHODS

We report one such case in which diagnosis was confirmed by subretinal aspiration of yellow-white infiltrates using a pars plana approach.

RESULTS

A 67-year-old woman with recurrent bilateral uveitis was diagnosed with large-cell lymphoma by subretinal aspiration of yellow-white infiltrates after two vitreous biopsies and a concurrent retinal biopsy failed to confirm the diagnosis.

CONCLUSIONS

When the suspicion of intraocular lymphoma remains high despite previous negative vitreous biopsies, retinal biopsy and aspiration biopsy of subretinal lesions may enhance the diagnostic yield.

Actual half-life of alpha-fetoprotein as a prognostic tool in pediatric malignant tumors

In a retrospective study, the prognostic value of monitoring the decay of alpha-fetoprotein (AFP) was assessed. Serum AFP was determined serially in 18 children with malignant germ-cell or hepatic tumors: 7 endodermal sinus tumor, 3 embryonal carcinoma, 5 malignant teratoma, 2 hepatoblastomas, and 1 hepatocellular carcinoma. The actual half-life (AHL) of AFP was computed after surgical resection of the tumor. In group 1, which had complete resection and no recurrence during follow-up (n = 13), the AHL of AFP was 4.0 +/- 0.9 days. In group 2, which had incomplete resection or recurrence during follow-up (n = 5), the AHL of AFP was 24.8 +/- 20 days, significantly longer than that of group 1 (P = 0.0026). The increased AHL of AFP indicated residual active tumor after surgical resection. The AHL of AFP may be more sensitive than serial monitoring of AFP in detecting preclinical recurrence after surgical resection of AFP-secreting tumors. Treatment strategies can be based on AFP clearance, and prospective clinical trials are warranted.

Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid

The HIV-1 capsid protein forms the conical core structure at the center of the mature virion. Capsid also binds the human peptidyl prolyl isomerase, cyclophilin A, thereby packaging the enzyme into the virion. Cyclophilin A subsequently performs an essential function in HIV-1 replication, possibly helping to disassemble the capsid core upon infection. We report the 2.36 A crystal structure of the N-terminal domain of HIV-1 capsid (residues 1-151) in complex with human cyclophilin A. A single exposed capsid loop (residues 85-93) binds in the enzyme's active site, and Pro-90 adopts an unprecedented trans conformation. The structure suggests how cyclophilin A can act as a sequence-specific binding protein and a nonspecific prolyl isomerase. In the crystal lattice, capsid molecules assemble into continuous planar strips. Side by side association of these strips may allow capsid to form the surface of the viral core. Cyclophilin A could then function by weakening the association between capsid strips, thereby promoting disassembly of the viral core.

Protective factors and young adolescent tendency to abstain from alcohol use: a model using two waves of intervention study data

Two waves of data from a family-focused preventive intervention project were used to test a model of the influence of protective factors on young adolescents' tendency toward alcohol abstinence. Prior theoretical and empirical work guided the specification of hypothesized effects of the protective factors affectional relationship with parents, affiliation with prosocial peers, and mastery-esteem on tendency toward alcohol abstinence. The tested model controlled for preintervention measures and included specified interrelations of protective factors across time. Structural equation analysis indicated that the model fit the data. Two of the hypothesized cross-time effects, however, were not supported.

Structure of the amino-terminal core domain of the HIV-1 capsid protein

The three-dimensional structure of the amino-terminal core domain (residues 1 through 151) of the human immunodeficiency virus-type 1 (HIV-1) capsid protein has been solved by multidimensional heteronuclear magnetic resonance spectroscopy. The structure is unlike those of previously characterized viral coat proteins and is composed of seven alpha helices, two beta hairpins, and an exposed partially ordered loop. The domain is shaped like an arrowhead, with the beta hairpins and loop exposed at the trailing edge and the carboxyl-terminal helix projecting from the tip. The proline residue Pro1 forms a salt bridge with a conserved, buried aspartate residue (Asp51), which suggests that the amino terminus of the protein rearranges upon proteolytic maturation. The binding site for cyclophilin A, a cellular rotamase that is packaged into the HIV-1 virion, is located on the exposed loop and encompasses the essential proline residue Pro90. In the free monomeric domain, Pro90 adopts kinetically trapped cis and trans conformations, raising the possibility that cyclophilin A catalyzes interconversion of the cis- and trans-Pro90 loop structures.

Differential transcription of baculovirus late and very late promoters: fractionation of nuclear extracts by phosphocellulose chromatography

An in vitro transcription system based on cytidine-free cassette was developed for the late 39k gene and the very late polyhedrin gene of Autographa californica nuclear polyhedrosis virus (AcNPV). Optimization of transcription conditions revealed that a preincubation step was not required for transcription of late and very late promoters, although preincubation was essential for efficient transcription from an early promoter. The 39k and polyhedrin constructs were actively transcribed by nuclear extracts prepared from AcNPV-infected Spodoptera frugiperda cells at 12 or 36 h postinfection but not by nuclear extracts prepared from uninfected or infected cells harvested during the early phase of infection. Transcription from the very late polyhedrin promoter was fivefold higher than that from the 39k late promoter with the nuclear extract prepared at 36 h postinfection. The 36-h extract was fractionated by phosphocellulose chromatography. Transcription activity eluted in two fractions, at 0.3 and 0.5 M KCl. Both the 39k and polyhedrin constructs were transcribed by these fractions; however, the patterns of late and very late transcription were distinctly different. With the 0.3 M fraction, incorporation into the 39k transcript was approximately 10-fold higher than incorporation into the polyhedrin transcript. Alternatively, with the 0.5 M fraction, transcription of the polyhedrin construct was twofold higher than transcription of the 39k construct. These results indicate that this in vitro system will be useful for purification and identification of factors that discriminate between late and very late promoters.

The Autographa californica nuclear polyhedrosis virus ie2 gene encodes a transcriptional regulator

The baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV) expresses several immediate early genes in infected cells. One of these, ie2 (formerly called IEN), was mapped and identified by its ability to augment IE1-mediated transactivation of the delayed early 39k gene. IE2 also stimulated the expression of reporter genes linked to the ie1 promoter. To test whether the increase in expression was due to increased mRNA, primer extension analyses were performed. Spodoptera frugiperda cells were transfected with a plasmid encoding IE1 in the presence or the absence of a plasmid encoding IE2, and total cellular RNA was purified. Quantitative primer extension assays revealed that cells cotransfected with pIE1 and pIE2 contained higher levels of IE1 mRNA than cells transfected with pIE1 alone. To demonstrate directly that IE2 is a transcriptional regulator, in vitro transcription assays were performed. Nuclear extracts were prepared from S. frugiperda cells transfected with either pIE2 or pUC18. The extracts containing IE2 were more active than the control extracts in transcription of a C-free cassette linked to the IE1 promoter. Immunodepletion of IE2 from the transfected extracts reduced the transcription activity to that of the control extracts. Nuclear extracts prepared from IE2-transfected cells were also more active in transcription from the adenovirus major late promoter. Taken together, these results demonstrate that IE2 is a transcriptional regulator.

Functional dissection of the ie2 gene product of the baculovirus Autographa californica nuclear polyhedrosis virus

The PstI-N genomic fragment of Autographa californica nuclear polyhedrosis virus (AcNPV) encodes an immediate-early protein, IE2, that functions as a promiscuous transactivator of other early viral promoters and heterologous promoters both in vivo and in vitro. IE2 contains several sequence motifs that are common to transcriptional activators. We have employed site-directed mutagenesis coupled with transient-expression assays to identify the amino acid sequences of IE2 that are essential for transactivation. Sequential deletion of amino-terminal sequences of IE2 gradually decreased the activity of the protein. Carboxy-terminal truncations of IE2 resulted in a dramatic loss of transactivation activities. Analysis of IE2 internal-deletion mutants demonstrated that the acidic amino acid-rich region between amino acids 198 and 206 possessed significant transactivation potential for all target promoters tested. In addition, squelching phenomena exhibited by wild-type IE2 and IE2 deletions containing the acidic amino acid-rich region indirectly demonstrated that this region may be involved in interactions with factors of the basic transcription machinery.

An alternative method for sample size determination in substance misuse prevention research

There is considerable evidence that social science researchers often fail to adequately address statistical power and related sample size issues. This tendency has been particularly salient in substance misuse prevention research. Although failure to carefully address statistical power and sample size issues most frequently results in studies lacking statistical power, other problems can also occur. For example, sample size determination in controlled studies which focus on rates of substance initiation and similar measures require close consideration of baseline rates indicated by these measures. Otherwise, when conventional procedures for sample size determination are utilized, samples in these studies can exceed the size necessary for predesignated levels of power. This article presents a simple alternative to conventional procedures for sample size determination which can be applied to controlled study of substance initiation and similar outcomes.

Effect of amino acids on isolated colonic smooth muscle from the rabbit

The purpose of these studies was to evaluate the direct effect of amino acids on rabbit colonic smooth muscle. Isometric tension was measured in circular smooth muscle from the distal colon after the administration of 19 individual L-amino acids. L-Alanine, L-cysteine, L-serine and L-methionine stimulated a dose-dependent increase in isometric tension. The lowest concentration which increased tension of the tissue for each of these amino acids was between 1 X 10(-4) to 5 X 10(-4) M. At a concentration of 10(-3) M, each of these four amino acids stimulated smooth muscle to 40 to 60% of the maximum response to bethanechol (2050 +/- 105 mN/m2). The 15 other amino acids tested had less effect on the colonic smooth muscle. The smooth muscle response to the D-amino acids, D-alanine, D-cysteine or D-serine, was shifted 10-fold to the right. Neural blockade by tetrodotoxin, the alpha adrenergic receptor antagonist, phentolamine, or the alpha-2 antagonist, yohimbine, increased smooth muscle tension, but did not inhibit L-amino acid stimulation of the tissue. Atropine, naloxone or prazosin (alpha-1 adrenergic antagonist) had no effect on amino acid stimulation of the muscle. These data suggest that L-amino acids, alanine, serine, cysteine and methionine stimulate contraction of colonic circular smooth muscle, this response is stereospecific and amino acids appear to stimulate the smooth muscle directly and not through an effect on the myenteric neurons.

On the theory of speciation induced by transposable elements

A simple methematical model describes the invasion of panmictic, sexually reproducing populations by a newly introduced transposon. The model places important constraints on the properties that transposons must have to successfully invade a population and describes the kinetics with which such an invasion will occur. Invasibility conditions serve as a basis for new, detailed scenarios whereby transposon-mediated depression in fitness produces reproductive isolation of populations. These scenarios, in turn, lead to several speculations concerning the role of transposons in evolution.

Inhibition of Mycoplasma pneumoniae by actinomycin D

Growth of Mycoplasma pneumoniae was completely prevented by 0.06 mug of actinomycin D/ml, and 0.00375 mug/ml caused 90% inhibition. It thus appears that M. pneumoniae is more susceptible to actinomycin D than previously reported. Low concentrations (0.019 mug/ml) of the antibiotic primarily inhibited ribonucleic acid synthesis and high concentrations (20 mug/ml) inhibited both ribonucleic and deoxyribonucleic acid synthesis.