DREAM2 challenge.

In the Dialogue for Reverse Engineering Assessments and Methods Conference (DREAM2) BCL6 target identification challenge, we were given a list of 200 genes and tasked to identify which ones are the true targets of BCL6 using an independent panel of gene-expression data. Initial efforts using conventional motif-scanning approaches to find BCL6 binding sites in the promoters of the 200 genes as a means of identifying BCL6 true targets proved unsuccessful. Instead, we performed a large-scale comparative study of multiple expression data under different conditions. Specifically, we employed a supervised learning approach that learns and models the expression patterns under different conditions and controls from a training collection of known BCL6 targets and randomly chosen decoys. Genes in the given list whose expression matches well with that of the training set of known BCL6 targets are more likely to be BCL6 targets. Using this approach, we are able to identify BCL6 targets with high accuracy, making us joint best performers of the challenge.

Synthesis of "cactus" top-decorated aligned carbon nanotubes and their third-order nonlinear optical properties.

We report a new morphology of "cactus" top-decorated aligned carbon nanotubes grown by the PECVD method using pure C2H2 gas. Unlike most previous reports, no additional carrier gas is used for pretreatment. Carbon nanotubes can still grow and maintain the tubular structure underneath the "cactus" tops. It is proposed that the H atoms produced by the dissociation of C2H2 activate the catalyst nanoparticles. Scanning electron microscopy (SEM) shows that the top "cactus" morphology is composed of a large quantity of small nanosheets. Transmission electron microscopy (TEM) reveals the amorphous carbon nature of these "cactus" structures. The formation of these "cactus" structures is possibly due to covalent absorption and reconstruction of carbon atoms on the broken graphite layers of nanotubes produced by the strong ion bombardment under plasma. The third-order optical nonlinearities and nonlinear dynamics are also investigated. The third-order nonlinear susceptibility magnitude /chi(3)/ is found to be 2.2 x 10(-11) esu, and the relaxation process takes place in about 1.8 ps.

Fabrication of size-tunable gold nanoparticles array with nanosphere lithography, reactive ion etching, and thermal annealing.

Two-dimensional ordered arrays of gold (Au) nanoparticles were fabricated using two different variants of the nanosphere lithography technique. First, ordered arrays of polystyrene nanospheres on Si substrate were used as deposition masks through which gold films were deposited by electron beam evaporation. After the removal of the nanospheres, an array of triangular Au nanodisks was left on the Si substrate. After thermal annealing at increasing temperature, systematic shape transition of the nanostructures from original triangular Au nanodisks to rounded nanoparticles was observed. This approach allows us to systematically vary the size and morphology of the particles. In the second and novel technique, we made use of reactive ion etching to simultaneously reduce the dimension of the masking nanospheres and create arrays of nanopores on the substrate prior to the deposition of the Au films. These samples were subsequently annealed, which resulted in size-tunable and ordered Au nanoparticle arrays with the nanoparticles nested in the nanopores of the templated substrate. With the nanoparticles anchored in the nanopores, the substrate could be useful as a template for growth of other nanomaterials.

Viperin (cig5), an IFN-inducible antiviral protein directly induced by human cytomegalovirus.

Little is known about the mechanism by which IFNs inhibit human cytomegalovirus (HCMV) replication. Indeed, infection of fibroblasts with HCMV initiates the expression of a subset of type I IFN-inducible genes whose role in the infectious process is unclear. We describe here the identification of a cytoplasmic antiviral protein that is induced by IFNs, by HCMV infection, and by the HCMV envelope protein, glycoprotein B (gB). Stable expression of the protein in fibroblasts inhibits productive HCMV infection, down-regulating several HCMV structural proteins (gB, pp28, and pp65) known to be indispensable for viral assembly and maturation. We have named the protein viperin (for virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible). HCMV infection causes the redistribution of the induced viperin from its normal endoplasmic reticulum association, first to the Golgi apparatus and then to cytoplasmic vacuoles containing gB and pp28. Expression before HCMV infection reduces viperin redistribution from the endoplasmic reticulum to the Golgi apparatus and prevents vacuolar localization, perhaps reflecting the mechanism used by HCMV to evade the antiviral function.

Concentrated autologous plasma protein: a biochemically neutral solder for tissue welding.

BACKGROUND AND OBJECTIVE: Xenographic or allographic serum protein solders used for laser welding may have immunologic and/or pathogenic complications. The objective of these studies was to develop a safe, autologous solder. STUDY DESIGN/MATERIALS AND METHODS: Five methods of preparing concentrated autologous plasma protein solder (CAPPS) were evaluated. Next, the CAPPS was evaluated via (1) thermal denaturation studies using differential scanning calorimetry, (2) tissue welding studies to characterize both acute and healing properties. RESULTS: The optimal concentration method to produce CAPPS rapidly was a dialysis method using chemical (osmotic) forces. The CAPPS showed similar denaturation profiles to serum albumin (SA) solders. Acutely, CAPPS provided comparable breaking strengths to SA solders. At 7 days, there was no significant difference in breaking strength or histology between 50% human SA solder and CAPPS (using a porcine skin model). CONCLUSIONS: These studies demonstrate that the CAPPS system provides acceptable acute and chronic properties for laser welding.

Transcriptional scaffold: CIITA interacts with NF-Y, RFX, and CREB to cause stereospecific regulation of the class II major histocompatibility complex promoter.

Scaffold molecules interact with multiple effectors to elicit specific signal transduction pathways. CIITA, a non-DNA-binding regulator of class II major histocompatibility complex (MHC) gene transcription, may serve as a transcriptional scaffold. Regulation of the class II MHC promoter by CIITA requires strict spatial-helical arrangements of the X and Y promoter elements. The X element binds RFX (RFX5/RFXANK-RFXB/RFXAP) and CREB, while Y binds NF-Y/CBF (NF-YA, NF-YB, and NF-YC). CIITA interacts with all three. In vivo analysis using both N-terminal and C-terminal deletion constructs identified critical domains of CIITA that are required for interaction with NF-YB, NF-YC, RFX5, RFXANK/RFXB, and CREB. We propose that binding of NF-Y/CBF, RFX, and CREB by CIITA results in a macromolecular complex which allows transcription factors to interact with the class II MHC promoter in a spatially and helically constrained fashion.

GTP binding by class II transactivator: role in nuclear import.

Class II transactivator (CIITA) is a global transcriptional coactivator of human leukocyte antigen-D (HLA-D) genes. CIITA contains motifs similar to guanosine triphosphate (GTP)-binding proteins. This report shows that CIITA binds GTP, and mutations in these motifs decrease its GTP-binding and transactivation activity. Substitution of these motifs with analogous sequences from Ras restores CIITA function. CIITA exhibits little GTPase activity, yet mutations in CIITA that confer GTPase activity reduce transcriptional activity. GTP binding by CIITA correlates with nuclear import. Thus, unlike other GTP-binding proteins, CIITA is involved in transcriptional activation that uses GTP binding to facilitate its own nuclear import.

A defect in the nuclear translocation of CIITA causes a form of type II bare lymphocyte syndrome.

The severe immunodeficiency type II bare lymphocyte syndrome (BLS) lacks class II MHC gene transcription. One defect from a complementation group A type II BLS patient is a 24 aa deletion in the MHC class II transactivator (CIITA). We show here that the molecular defect present in this protein is a failure of CIITA to undergo nuclear translocation. This defect was mapped to a position-dependent, novel nuclear localization sequence that cannot be functionally replaced by a classical NLS. Fusion of this 5 aa motif to an unrelated protein leads to nuclear translocation. Furthermore, this motif is not critical for transactivation function. This is a description of a genetic disease resulting from a novel defect in the subcellular localization of a transcriptional coactivator.

Primary T-cell-rich B-cell lymphoma in the kidney presenting with acute renal failure and a second malignancy.

Infiltration of the kidney is commonly found in lymphoma, but acute renal failure arising from bilateral renal infiltration is uncommon. Primary renal lymphoma may occur and is usually of B-cell lineage. It is rare for patients with lymphoma to develop acute renal failure as their initial clinical presentation. Recently, an association between primary renal lymphoma and a second primary malignancy has been reported. We describe the first case of a renal T-cell-rich B-cell lymphoma presenting as acute renal failure, which was associated with a second primary pulmonary malignancy.

CIITA stimulation of transcription factor binding to major histocompatibility complex class II and associated promoters in vivo.

CIITA is a master transactivator of the major histocompatibility complex class II genes, which are involved in antigen presentation. Defects in CIITA result in fatal immunodeficiencies. CIITA activation is also the control point for the induction of major histocompatibility complex class II and associated genes by interferon-gamma, but CIITA does not bind directly to DNA. Expression of CIITA in G3A cells, which lack endogenous CIITA, followed by in vivo genomic footprinting, now reveals that CIITA is required for the assembly of transcription factor complexes on the promoters of this gene family, including DRA, Ii, and DMB. CIITA-dependent promoter assembly occurs in interferon-gamma-inducible cell types, but not in B lymphocytes. Dissection of the CIITA protein indicates that transactivation and promoter loading are inseparable and reveal a requirement for a GTP binding motif. These findings suggest that CIITA may be a new class of transactivator.

Activation and transdominant suppression of MHC class II and HLA-DMB promoters by a series of C-terminal class II transactivator deletion mutants.

The class II transactivator (CIITA) is a highly specific transcription factor that activates only genes known to be involved in the class II MHC processing pathway, including class II MHC, invariant chain, and HLA-DMA/B genes. In this work, we show the requirement of a new region in CIITA that is critical for its function. Deletion mutants lacking varying length of the C terminus show that the C-terminal 41 amino acids of CIITA are indispensable for the activation of both the conventional DRA and nonconventional DMB promoters. This region contains a highly charged stretch of amino acids that is homologous to a yeast transcription factor, repression activator protein-1 (RAP1)-interacting factor 1. Mutants lacking the C terminus were tested in a transdominant-negative assay to examine their capacity to block the wild-type CIITA function. Two of these deletion mutants suppressed the activity of endogenously expressed wild-type CIITA to activate both DRA and DMB promoters. It may be possible to utilize these mutants to modulate MHC class II and DM gene expression.

Induction of MHC class I expression by the MHC class II transactivator CIITA.

Major histocompatibility complex (MHC) class I-deficient cell lines were used to demonstrate that the MHC class II transactivator (CIITA) can induce surface expression of MHC class I molecules. CIITA induces the promoter of MHC class I heavy chain genes. The site alpha DNA element is the target for CIITA-induced transactivation of class I. In addition, interferon-gamma (IFNgamma)-induced MHC class I expression also requires an intact site alpha. The G3A cell line, which is defective in CIITA induction, does not induce MHC class I antigen and promoter in response to IFNgamma. Trans-dominant-negative forms of CIITA reduce class I MHC promoter function and surface antigen expression. Collectively, these data argue that CIITA has a role in class I MHC gene induction.

Importance of acidic, proline/serine/threonine-rich, and GTP-binding regions in the major histocompatibility complex class II transactivator: generation of transdominant-negative mutants.

The class II transactivator (CIITA) is a master transcription regulator of gene products involved in the exogenous antigen presentation pathway, including major histocompatibility complex (MHC) class II, invariant chain, and DM. An extensive analysis of the putative functional domains of CIITA is undertaken here to explore the action of CIITA. Antibodies to CIITA protein were produced to verify that these mutant proteins are expressed. Both acidic and proline/serine/threonine-rich domains are essential for class II MHC promoter activation. In addition, three guanine nucleotide-binding motifs are essential for CIITA activity. Of these mutants, two exhibited strong transdominant-negative functions. These two mutants provide a plausible approach to manipulate MHC class II expression and immune responses.

The DMB promoter: delineation, in vivo footprint, trans-activation, and trans-dominant suppression.

The HLA-DM loci encode the heterodimeric unconventional class II MHC molecules that are coexpressed with conventional class II MHC molecules. DM molecules are essential for the proper formation and function of conventional class II MHC molecules. This report characterizes the DMB promoter both by in vivo footprint and by in vitro functional analysis and reveals a promoter structure similar to that of conventional class II MHC genes. DR-negative mutant cell lines selectively defective in the transcription factor or class II trans-activator (CIITA) were used to reveal a requirement for both these factors in DMB promoter activation. Complementation of defective cell lines with the appropriate transcription factor reconstituted DMB promoter activation. Further analysis with CIITA identified several mutant forms of CIITA that are trans-dominant-negative mutants, i.e., they suppressed DMB promoter activation by transfected and endogenous CIITA. These mutants may be used in abiological setting to down-regulate the function of DM in Ag processing.

Concomitant fracture of the coracoid and acromion after direct shoulder trauma.

Fractures of the acromial process or coracoid process of the scapula are rare. We present a combined fracture of the coracoid and acromion after direct trauma to the shoulder. An anteroposterior radiography with the central x-ray beam angled 25 degrees cephalad or an axillary lateral radiograph may be needed to detect these fractures.

Molecular analysis of G1B and G3A IFN gamma mutants reveals that defects in CIITA or RFX result in defective class II MHC and Ii gene induction.

Class II major histocompatibility complex (MHC) genes and the invariant (Ii) gene are inducible by interferon-gamma (IFN gamma) but not by interferon-alpha and interferon-beta. The promoter regions of these genes contain three regulatory elements that mediate constitutive and IFN gamma-induced expressions; however, none of the DNA-binding proteins that interact with these elements are regulated by IFN gamma. Recently, a gene coding for a transactivator (CIITA) of class II MHC genes that complements a HLA-DR-negative immunodeficiency has been isolated. Using one IFN gamma mutant cell line (G3A) that is selectively defective in HLA-DR and Ii induction, four lines of evidence are presented to show that CIITA mediates the IFN gamma induction of HLA-DR and Ii genes. Analysis of another mutant line, G1B, indicates that the lack of DRA and Ii gene induction by IFN gamma is correlated with the lack of RFX DNA binding activity, thus providing the link between RFX and an IFN gamma response.

Caffeine or theophylline for neonatal apnoea?

Caffeine, in the dose usually recommended (12.5 mg/kg loading dose and 3 mg/kg daily maintenance), and a higher dose regimen (25 mg/kg loading and 6 mg/kg daily maintenance), was compared with theophylline (7.5 mg/kg loading and 3 mg/kg thrice daily maintenance). The study was a randomised controlled trial in the treatment of a group of 44 infants of less than 31 weeks' gestation (mean gestational age 28.3 weeks) who were suffering from frequent apnoeic attacks. All three regimens produced a significant reduction in apnoeic attacks within 24 hours, but only the higher dose caffeine and theophylline groups showed a significant improvement in apnoea within eight hours. The use of caffeine for the treatment of neonatal apnoea is recommended, because a once daily dose is more easily administered, and because it was found that plasma concentrations were more predictable than those of theophylline. If used in very preterm infants, however, its is suggested that a higher dose regimen than that previously recommended be used to achieve a faster response.

Hepatitis B vaccine in the prevention of perinatally transmitted hepatitis B virus infection: final report on a West Midlands pilot study.

A four-dose vaccination schedule was used to interrupt perinatal transmission of hepatitis B virus from carrier mothers to their babies. Of 49 babies immunised and successfully followed up, 43 (88%) became immune: 15 out of 21 (71%) of babies born to HBeAg + mothers became immune, the other 6 becoming the only carrier babies in the study. Without immunisation a carrier rate in excess of 70% would have been expected in this high-risk group. Vaccine alone, given in a rapid immunisation schedule, protected the majority of babies at risk. In those babies in whom the carrier state occurred in spite of immunisation, infection may have taken place in utero, or the infant may have failed to produce adequate antibody in response to the vaccine.

Light transmission of phototherapy eyeshields.

Twelve types of phototherapy eyeshields showed peak light transmission of less than 0.1%, and none transmitted greater than 0.04% light in the 460 nm spectral region. Commercial eyeshields offered no advantage over locally made ones. The choice of shield may be less important than how it is secured over the infant's eyes.

Neonatal typhoid fever.

Three infants of Pakistani immigrant mothers developed typhoid fever in the neonatal period. All three survived, but two became chronic excretors of Salmonella typhi. The risk of an outbreak of typhoid fever in a maternity unit or special care baby unit is emphasized.