Estimating differential latent variable graphical models with applications to brain connectivity

Differential graphical models are designed to represent the difference between the conditional dependence structures of two groups, and thus are of particular interest for scientific investigations. Motivated by modern applications, this manuscript considers an extended setting where each group is generated by a latent variable Gaussian graphical model. Due to the existence of latent factors, the differential network is decomposed into sparse and low-rank components, both of which are symmetric indefinite matrices. We estimate these two components simultaneously using a two-stage procedure: (i) an initialization stage, which computes a simple, consistent estimator, and (ii) a convergence stage, implemented using a projected alternating gradient descent algorithm applied to a nonconvex objective, initialized using the output of the first stage. We prove that given the initialization, the estimator converges linearly with a nontrivial, minimax optimal statistical error. Experiments on synthetic and real data illustrate that the proposed nonconvex procedure outperforms existing methods.

AI detection of M. Tuberculosis pathogens using Generative Adversarial Network (GAN) analyses

Background

Rapid identification of pathogens is critical to outbreak detection and sentinel surveillance; however most diagnoses are made in laboratory settings. Advancements in artificial intelligence (AI) and computer vision offer unprecedented opportunities to facilitate detection and reduce response time in field settings. An initial step is the creation of analysis algorithms for offline mobile computing applications.

Methods

AI models to identify objects using computer vision are typically “trained” on previously labeled images. The scarcity of labeled image-libraries creates a bottleneck, requiring thousands of labor hours to annotate images by hand to create “training data.” We describe the applicability of Generative Adversarial Network (GAN) methods to amass sufficient training data with minimal manual input.

Results

Our AI models are built with a performance score of 0.84-0.93 for M. Tuberculosis, a measure of the AI model's accuracy using precision and recall. Our results demonstrate that our GAN pipeline boosts model robustness and learnability of sparse open source data.

Conclusions

The use of labeled training data to identify M. Tuberculosis developed using our GAN pipeline techniques demonstrates the potential for rapid identification of known pathogens in field settings. Our work paves the way for the development of offline mobile computing applications to identify pathogens outside of a laboratory setting. Advancements in artificial intelligence (AI) and computer vision offer unprecedented opportunities to decrease detection time in field settings by combining these technologies. Further development of these capabilities can improve time-to-detection and outbreak response significantly.

Key messages

Rapidly deploy AI detectors to aid in disease outbreak and surveillance. Our concept aligns with deploying responsive alerting capabilities to address dynamic threats in low resource, offline computing environs.

Vaginal compared with intramuscular progestogen for preventing preterm birth in high-risk pregnant women (VICTORIA study): a multicentre, open-label randomised trial and meta-analysis

OBJECTIVE

To compare the efficacy of two types of progestogen therapy for preventing preterm birth (PTB) and to review the relevant literature.

DESIGN

A multicentre, randomised, open-label, equivalence trial and a meta-analysis.

SETTING

Tertiary referral hospitals in South Korea.

POPULATION

Pregnant women with a history of spontaneous PTB or short cervical length (<25 mm).

METHODS

Eligible women were screened and randomised at 16-22 weeks of gestation to receive either 200 mg of vaginal micronised progesterone daily (vaginal group) or an intramuscular injection of 250 mg 17α-hydroxyprogesterone caproate weekly (IM group). Stratified randomisation was carried out according to participating centres and indications for progestogen therapy. This trial was registered at ClinicalTrials.gov (NCT02304237).

MAIN OUTCOME MEASURE

Preterm birth (PTB) before 37 weeks of gestation.

RESULTS

A total of 266 women were randomly assigned and a total of 247 women (119 and 128 women in the vaginal and IM groups, respectively) were available for the intention-to-treat analysis. Risks of PTB before 37 weeks of gestation did not significantly differ between the two groups (22.7 versus 25.8%, P = 0.571). The difference in PTB risk between the two groups was 3.1% (95% CI -7.6 to 13.8%), which was within the equivalence margin of 15%. The meta-analysis results showed no significant differences in the risk of PTB between the vaginal and IM progestogen treatments.

CONCLUSION

Compared with vaginal progesterone, treatment with intramuscular progestin might increase the risk of PTB before 37 weeks of gestation by as much as 13.8%, or reduce the risk by as much as 7.6%, in women with a history of spontaneous PTB or with short cervical length.

TWEETABLE ABSTRACT

Vaginal and intramuscular progestogen showed equivalent efficacy for preventing preterm birth before 37 weeks of gestation.

Lateral Posterior Choroidal Collateral Anastomosis Predicts Recurrent Ipsilateral Hemorrhage in Adult Patients with Moyamoya Disease

BACKGROUND AND PURPOSE

Choroidal collateral anastomosis is associated with hemorrhage recurrence in patients with Moyamoya disease. However, the relationship between recurrent ipsilateral hemorrhage and choroidal collateral anastomosis subtypes (anterior choroidal artery anastomosis, lateral posterior choroidal artery anastomosis, and medial posterior choroidal artery anastomosis) is unclear. This study aimed to assess this potential association in adult patients with Moyamoya disease.

MATERIALS AND METHODS

Patients angiographically diagnosed with Moyamoya disease who underwent conservative treatment between January 2008 and December 2018 were included in this retrospective study. Two readers assessed the angiographic images to identify choroidal collateral anastomosis subtypes, and Cox proportional hazard regression models were used to estimate the risk of recurrent hemorrhage associated with each subtype.

RESULTS

Thirty-nine patients (mean age = 45.2 years) were included in this study. During 52.4 ± 37.0 months of follow-up, recurrent ipsilateral hemorrhage occurred in 48.7% (19/39) of patients. Patients with recurrent hemorrhage had a higher prevalence of choroidal collateral (94.8% versus 60.0%; P = .02) and lateral posterior choroidal artery (78.9% versus 25.0%; P < .01) anastomoses than those without recurrent hemorrhage. Lateral posterior choroidal artery anastomosis was associated with recurrent hemorrhage before (hazard ratio = 6.66; 95% CI, 2.18-20.39; P < .01) and after (hazard ratio = 5.78; 95% CI, 1.58-21.13; P < .01) adjustments were made for age, sex, and other confounding factors.

CONCLUSIONS

Choroidal collateral anastomosis is responsible for most cases of recurrent hemorrhage in adult patients with Moyamoya disease; lateral posterior choroidal artery anastomosis is a significant risk factor for these recurrent events.

Comparison of Kaposi Sarcoma Risk in Human Immunodeficiency Virus-Positive Adults Across 5 Continents: A Multiregional Multicohort Study

BACKGROUND

We compared Kaposi sarcoma (KS) risk in adults who started antiretroviral therapy (ART) across the Asia-Pacific, South Africa, Europe, Latin, and North America.

METHODS

We included cohort data of human immunodeficiency virus (HIV)-positive adults who started ART after 1995 within the framework of 2 large collaborations of observational HIV cohorts. We present incidence rates and adjusted hazard ratios (aHRs).

RESULTS

We included 208140 patients from 57 countries. Over a period of 1066572 person-years, 2046 KS cases were diagnosed. KS incidence rates per 100000 person-years were 52 in the Asia-Pacific and ranged between 180 and 280 in the other regions. KS risk was 5 times higher in South African women (aHR, 4.56; 95% confidence intervals [CI], 2.73-7.62) than in their European counterparts, and 2 times higher in South African men (2.21; 1.34-3.63). In Europe, Latin, and North America KS risk was 6 times higher in men who have sex with men (aHR, 5.95; 95% CI, 5.09-6.96) than in women. Comparing patients with current CD4 cell counts ≥700 cells/µL with those whose counts were <50 cells/µL, the KS risk was halved in South Africa (aHR, 0.53; 95% CI, .17-1.63) but reduced by ≥95% in other regions.

CONCLUSIONS

Despite important ART-related declines in KS incidence, men and women in South Africa and men who have sex with men remain at increased KS risk, likely due to high human herpesvirus 8 coinfection rates. Early ART initiation and maintenance of high CD4 cell counts are essential to further reducing KS incidence worldwide, but additional measures might be needed, especially in Southern Africa.

The mechanical response of hIAPP nanowires based on different bending direction simulations

Amyloid proteins, implicated in numerous aging-related diseases, possess remarkable mechanical properties. Polymorphism leads to different arrangements of β sheets in amyloid fibrils, which changes the characteristics of the hydrogen bond network that determines their mechanical properties and structural characteristics. We performed bending simulations using molecular dynamics methods under constant-velocity conditions in different bending directions. Two different fibril structures, parallel/homo and parallel/hetero, of hIAPP amyloids were considered. Though the bending configuration influences the toughness of the material, our results indicate that the basic material behavior is affected by the β-sheet arrangement that is determined by the type of polymorphism in amyloid fibrils.

Randomized controlled comparison of combined general and epidural anesthesia versus general anesthesia on diaphragmatic function after laparoscopic prostatectomy

BACKGROUND

Little is known about the effect of anesthetic technique on postoperative diaphragmatic function, which is associated with postoperative morbidity and recovery in patients undergoing laparoscopic pelvic surgery. The aim of this trial was to study the effect of combined general and epidural anesthesia versus general anesthesia on postoperative diaphragmatic function measured by ultrasonography in patients undergoing robot-assisted laparoscopic radical prostatectomy (RALRP).

METHODS

Fifty-four patients undergoing RALRP were enrolled prospectively. Study population was randomized to receive general (group G, N.=27) or combined general and epidural (group GE, N.=27) anesthesia. Diaphragmatic inspiratory amplitude (DIA), and inspiration and expiration time (Ti and Te, respectively) were measured by M-mode ultrasonography during quiet/deep breathing and sniffing before the surgery and on postoperative days (POD) 1 and 2. Diaphragmatic inspiratory and expiratory velocities (DIV and DEV) were also calculated (DIA/Ti and DIA/Te, respectively). Spirometry was performed in addition to ultrasonography.

RESULTS

DIA during deep breathing and sniffing was significantly decreased on POD 1 in group G, while it was preserved in group GE. These reductions in diaphragmatic function were restored to preoperative values on POD 2 in both groups. Vital capacity and peak expiratory flow were diminished in group G on POD 1 and 2. However, spirometry revealed no impairment in group GE except for vital capacity on POD 1. The correlation coefficients (R2) between diaphragmatic function and spirometry variables ranged from 0.231 to 0.286. Postoperaitve pain was comparable.

CONCLUSION

Combined general and epidural anesthesia may attenuate the severity of postoperative diaphragmatic dysfunction after RALRP compared to conventional general anesthesia.

Evaluation of acid-base status in brain dead donors and the impact of metabolic acidosis on organ retrieval

BACKGROUND

Pathophysiologic changes after brain death can lead to acid-base disturbances. The primary aim of this study was to clarify the acid-base state and its source in brain dead donors using Stewart's approach. Additionally, we investigated whether the presence of metabolic acidosis affected the number of organs retrieved from donors.

METHODS

A retrospective review of electronic medical records was performed for brain dead donors who had undergone organ harvesting during the past 5 years in a tertiary medical center. The parameters related to acid-base disturbance and the number of organs retrieved from the donors was assessed.

RESULTS

Sixty one brain dead donors were evaluated in this study. Twenty three (37.7%) of these patients had metabolic acidosis at the initial diagnosis of brain death. Metabolic acidosis resulted from hyperchloremia and a large strong ion gap. The severity of metabolic acidosis was masked by hypernatremia and hypoalbuminemia. In addition, donors without metabolic acidosis also showed mixed acid-base disturbances in which metabolic acidosis induced by significant hyperchloremia was combined with metabolic alkalosis caused by hypoalbuminemia and hypernatremia. Although more organs were retrieved from the donors without metabolic acidosis than those with metabolic acidosis (P=0.012), serum albumin level (P=0.010) and donor age (P<0.001), rather than metabolic acid-base disturbances, significantly correlated with the number of organs retrieved in multivariate regression analysis.

CONCLUSION

Most brain dead donors exhibited metabolic acid-base disturbances. However, rather than metabolic acidosis, serum albumin level and donor age were well correlated with the number of organs retrieved.

The Effect of Recorded Maternal Voice on Perioperative Anxiety and Emergence in Children

This study was performed to test if hearing a recorded maternal voice reduces anxiety, emergence agitation and anaesthetic requirements in children. With written informed consent, children scheduled for cardiac catheterisation under intravenous ketamine anaesthesia and their mothers (n=46) were randomly assigned to either the mother-voice (MV) or control group. While the MV group (n=23) listened via headphones to a recording of their mothers’ voices during the perioperative period, the control group (n=23) wore headphones with no auditory stimulation. Ketamine requirements and haemodynamics were recorded. Anxiety of the patients and the parents were measured before and after the procedure with the modified Yale preoperative anxiety scale and Spielberger's State-Trait Anxiety Inventory, respectively. Emergence agitation was graded. The demographic and haemodynamic data were comparable, except for a longer procedure time in the MV group. Mothers’ State-Trait Anxiety Inventory was not different preoperatively between the groups. Mothers’ state and trait anxiety was lower after the procedure in the MV group compared with the preoperative values. In the control group only maternal state anxiety was diminished after the procedure. There was no significant group difference with respect to ketamine requirement (5.1±1.9 mg vs 4.9±1.6 mg, P=0.645). The anxiety score of children was lower in the MV group before the procedure (modified Yale preoperative anxiety scale score 35±12 vs 28±9, P=0.038), but there was no significant difference postoperatively. Emergence agitation was attenuated in the MV group (P=0.005).

Effect of ultrasonic treatment on swine wastewater solubilization

In order to accelerate hydrolysis known to be the rate-limiting step of the overall digestion process for swine wastewater, an ultrasonic treatment process was tested for the solubilization of the swine wastewater. The effectiveness of ultrasonic solubilization of the swine wastewater under various operational conditions was compared by means of an increment of soluble organics in the treated swine wastewater and the hydrolysis rate constant. Ultrasonic treatment resulted in the high degree of solubilization of particulate organics in the swine wastewater and the degree of solubilization increased with increasing supplied energy. The highest extent of an increment of SCOD concentration and SCOD/TCOD ratio at the end of the operation time of 60 min was 109.7 and 117.5%, respectively, under 120 W power output and 20(o)C operating temperature conditions. The observed highest hydrolysis rate constant described by pseudo-first order rate constant was 2.94 h(-1) under the same conditions. Based on the estimated activation energy from modeling using the Arrhenius equation, ultrasonic solubilization of the swine wastewater under higher supplied energy conditions was more dependent on the operating temperature, which was consistent with the experimentally obtained results. Based on the investigation into the effect of gas type and gas delivery methods for ultrasonic solubilization of the swine wastewater, oxygen gas bubbling through the liquid showed the highest degree of an increment of soluble organics possibly attributed to the influent of oxygen in an increase of radicals during the sonolysis.

A theoretical model for F-actin remodeling in vascular smooth muscle cells subjected to cyclic stretch

A constrained mixture theory model was developed and used to estimate remodeling of F-actin in vascular smooth muscle cells that were subjected to 10% equibiaxial stretching for up to 30min. The model was based on a synthesis of data on time-dependent changes in atomic force microscopy measured cell stiffness and immunofluorescence measured focal adhesion associated vinculin as well as data on stress fiber stiffness and pre-stretch. Results suggest that an observed acute (after 2min of stretching) increase in cell stiffness is consistent with an increased stretch of the originally present F-actin plus an assembly of new F-actin having nearly homeostatic values of stretch. Moreover, the subsequent (after 30min of stretching) decrease in cell stiffness back towards the baseline value is consistent with a replacement of the overstretched original filaments with the new (reassembled), less stretched filaments. That is, overall cell response is consistent with a recently proposed concept of "tensional homeostasis" whereby cells seek to maintain constant certain mechanical factors via a remodeling of intracellular and transmembrane proteins. Although there is a need to refine the model based on more comprehensive data sets, using multiple experimental approaches, the present results suggest that a constrained mixture theory can capture salient features of the dynamics of F-actin remodeling and that it offers some advantages over many past methods of modeling, particularly those based on classical linearized viscoelasticity.

On atomic force microscopy and the constitutive behavior of living cells

Atomic force microscopy (AFM) is one of many new technologies available to study the mechanical properties and mechanobiological responses of living cells. Despite the widespread usage of this technology, there has been little attempt to develop new theoretical frameworks to interpret the associated data. Rather, most analyses rely on the classical Hertz solution for the indentation of an elastic half-space within the context of linearized elasticity. In contrast, we propose a fully nonlinear, constrained mixture model for adherent cells that allows one to account separately for the contributions of the three primary structural constituents of the cytoskeleton. Moreover, we extend a prior solution for a small indentation superimposed on a finite equibiaxial extension by incorporating in this mixture model for the special case of an initially random distribution of constituents (actin, intermediate filaments, and microtubules). We submit that this theoretical framework will allow an improved interpretation of indentation force-depth data from a sub-class of atomic force microscopy tests and will serve as an important analytical check for future finite element models. The latter will be necessary to exploit further the capabilities of both atomic force microscopy and nonlinear mixture theories for cell behavior.

Environmental assessment of water, sediment and plants in the Mankyeong River, ROK

This study was carried out to evaluate water quality, sediment and plant vegetation in eight tributaries of the Mankyeong River for enhancement of natural purification. Among the tributaries, the Iksancheon water had the highest concentration of BOD, T-N and NH4-N due to inflow of swine wastes from the livestock district. The Yucheon water had the highest level of electrical conductivity and SO4(2-) due to inflow of mis-treated wastewater from industrial districts. The Tabcheon had generally similar concentrations of nitrogen and phosphate to that of the upstream of the Mankyeong River: agricultural activity along the Tabcheon appeared to have little negative influence to the water quality. Among various sediments, concentration of organic matter, nitrogen and phosphate were high in the Iksancheon and the Yucheon due to the livestock wastes and industrial wastes. There were 282 species of plants during summer with 43 aquatic plants, 57 hydrophytes, 178 waterside plants and 4 terrestrial plants. Some plant resources were recommended due to much absorption of nitrogen and phosphate for enhancement of natural purification. C. demersum and H. verticillata were recommended in the submerged aquatic plants, H. dubia, N. indica and N. subinteperrimum in the floating leaf aquatic plants, P. communis, Z. latifolia and T. orientalis in the emerged aquatic plants, C. scutata and P. distichum in the waterside plants.

Comparison of scan-angle method and convective cloud differential method in retrieving tropospheric ozone from TOMS

Tropospheric ozone, derived from the Scan-Angle Method (SAM) and the Convective Cloud Differential (CCD) method, exhibits a noticeable abundance over the South Atlantic, where it is associated with biomass-burning in the austral spring. This feature is also seen in the distribution of carbon monoxide observed from Measurements Of Pollution In The Troposphere (MOPITT). In the boreal burning season, however, the distribution of the results from SAM and MOPITT-CO present an enhancement related to the biomass-burning over North Africa that does not appear in the CCD results. The relationship of the results from SAM and MOPITT-CO is better than those of the results from the CCD and MOPITT-CO for the December-February period. Conversely, the latter relationship is better than the former for the October-November period. The two methods, SAM and CCD, show higher correlation in the southern burning season, but lower correlation in the northern burning season. The influence of biomass burning on ozone amounts is clearly seen in the SAM results of the elevated ozone over northern equatorial Africa during the northern burning season, but is not present in the CCD results.

Elastodynamics and arterial wall stress

Recent advances in molecular and cell biology have emphasized the fundamental importance of mechanical factors in regulating the structure and function of cells and extracellular matrix in the vasculature. Consequently, there is an ever-greater motivation to calculate accurately the stress and strain fields in the arterial wall and how they change with disease, injury, and clinical treatment. Although there is an extensive literature on arterial mechanics, our understanding is still far from complete. In this paper, we review some of the salient findings with regard to wall properties, suggest some possible improvements in the calculation of wall stress, and identify some unresolved problems for further research.

HLA-DR expression in B-lymphocytes in vitro is not suppressed by the absence of exogenous antigens

The proper loading of exogenous peptide antigens affects the transport and cell surface expression of MHC class II molecules. In the present study, the goal was to determine to what extent this step determines the cell surface expression level of MHC class II molecules, such as the HLA-DR. EBV-transformed B-cells, were cultured either in a serum- and protein-free medium, or in a medium that contained different concentrations of exogenous antigens. Using HLA-DR-specific antibodies, the induction of the MHC class II expression was observed in cells that were cultured under serum-and protein-free conditions, when compared to those cultured with exogenous protein antigens. This upregulation was completely suppressed to the normal level by the addition of a high concentration of hen egg lysozyme to the serum- and protein-free medium. This indicates that exogenous proteins regulate the HLA-DR expression. To further examine whether this modulation is controlled at the transcription level, the expression of the HLA-DR beta-chain mRNA was analyzed by reverse transcription-PCR and Northern blots. The same levels of HLA-DRB mRNA were detectable in both culture conditions, indicating that the present observation is dependent on some regulatory mechanisms at the post-transcriptional level. This might include a different pathway for trafficking of HLA-DR molecules to the cell surface, since peptide-binding assays revealed that a high proportion of cell surface HLA-DR molecules under the serum- and protein-free condition were transported to the cell surface without associated peptide antigens.

Determination of rat leptin activity in vitro using a novel luciferase reporter assay

Leptin is small cytokine-like protein that is involved in appetite and body weight regulation. Due to increased interest in using leptin as an anti-obesity reagent, recombinant forms of leptin have been produced for several species, including humans, mice, rats, pigs, dogs, sheep etc. The biological activities of such recombinant proteins were determined using various in vitro or in vivo systems; however so far, no specific assay system for rat leptin is available. Since rats are representative animal models in obesity research, the establishment of a biological assay system for determining rat leptin activity has been eagerly awaited. This study describes the generation of such a system using chinese hamster ovary (CHO)-cells that were transfected with the long form of the rat leptin receptor isoform, OB-Rb, whereby a signal transduces and activators of transcription-sensitive luciferase reporter system is further employed to quantify the leptin-mediated signals. This system is the first rat-specific leptin bioassay system that has been reported. It is expected that this assay will be used to further quantify and determine leptin activity from various biological fluids and sources.

[Isolation and identification of the broad spectrum antimicrobial peptide AP311 produced by Lactobacillus acidophilus]

The heat stable antimicrobial peptide (AP311) produced by Lactobacillus acidophilus was isolated and identified. The AP311 has broad spectrum of inhibition including many Gram-positive and Gram-negative bacteria. The inhibition activity of AP311 was lost upon treatment with trypsin, subtilisin, proteanase K, chymotrypsin and pepsin. Inhibition activity of AP311 was decreased with pH increasing. The AP311 is very stable at acidic condition (pH2-4) even if heating at 100 degrees C for 30 min. But it was inactivated at basic pH (pH12) and the activity was restored completely upon reversion to acidic. The AP311 was not precipitated and inactivated by various organic solvents, except n-butanol. When the precipitate was redissolved in 0.02 mol/L HC1, its activity was restored. Based on its proteinaceous nature, broad spectrum of inhibition, we propose that AP311 should be considered the broad spectrum antimicrobial peptide.

Enhanced CD4+ T cell proliferation and Th2 cytokine production in DR6-deficient mice

We have found that DR6, a member of the TNF receptor family, is highly expressed in resting T cells and downregulated in activated T cells. DR6-targeted mutant mice were generated and showed normal development. However, DR6(-/-) CD4(+) T cells hyperproliferated in response to TCR-mediated stimulation and protein antigen challenge. Activated DR6(-/-) CD4(+) T cells exhibited upregulated CD25 expression and enhanced proliferation in response to exogenous IL-2 stimulation. In addition, increased CD28 and reduced CTLA-4 expression were observed in these cells. Enhanced Th2 cytokine production by activated DR6(-/-) CD4(+) T cells was associated with the increased transcription factor NF-ATc in nuclei. DR6, therefore, functions as a regulatory receptor for mediating CD4(+) T cell activation and maintaining proper immune responses.

Recombinant expression of biologically active rat leptin in Escherichia coli

Leptin is a 16-kDa nonglycosylated hormone that is produced in mature adipocytes and which acts primarily in the hypothalamus to reduce food intake and body weight. While the rat is a representative laboratory animal model in obesity research, so far recombinant rat leptin was not available. In the present study, rat leptin was recombinantly expressed in Escherichia coli and purified in a bioactive form to provide a further tool for the analysis of leptin functions in rats. Leptin cDNA was cloned by RT-PCR from total RNA of SD rat adipocytes, and overexpression was achieved by subcloning the leptin cDNA into the pET-29a vector, which enabled the recombinant expression of rat leptin as an S-peptide-tagged fusion protein. Since the fusion proteins were expressed in inclusion bodies, after purification of the insoluble fraction, leptin proteins were refolded by sequential dialysis into physiological buffers. The biological activity of this recombinant protein was confirmed in proliferation assays using leptin-sensitive rat insulinoma cells as well as a newly developed leptin-sensitive luciferase assay system. The specific binding of the S-tagged leptin to leptin-receptor-expressing cells was further shown by flow cytometry using fluorescence-conjugated S-proteins.

The pro domain of beta-secretase does not confer strict zymogen-like properties but does assist proper folding of the protease domain

beta-Secretase (BACE) is a membrane-bound aspartyl protease that cleaves the amyloid precursor protein to generate the N terminus of the amyloid beta peptide. BACE is expressed as a precursor protein containing Pre, Pro, protease, transmembrane, and cytosolic domains. A soluble BACE derivative (PreProBACE460) that is truncated between the protease and transmembrane domains was produced by baculovirus-mediated expression. ProBACE460 was purified from conditioned media of infected insect cells using immobilized concanavalin A and immobilized BACE inhibitor, P10-P4' Stat(Val). Furin cleaves ProBACE460 between the Pro and protease regions to generate mature BACE460. The k(cat)/K(m) of ProBACE460 when assayed with a polypeptide substrate is only 2.3-fold less than that of BACE460. This finding and the similar inhibitory potency of P10-P4' Stat(Val) for ProBACE460 and BACE460 suggest that the Pro domain has little effect on the BACE active site. Exposure of ProBACE460 to guanidine denaturation/renaturation results in a 7-fold higher recovery of BACE activity than when BACE460 is similarly treated. The presence of free BACE Pro peptide during renaturation of BACE460 but not ProBACE460 increases recovery of activity. These findings show that the Pro domain in ProBACE460 does not suppress activity as in a strict zymogen but does appear to facilitate proper folding of an active protease domain.

Transcriptional coregulators of the nuclear receptor superfamily: coactivators and corepressors

Nuclear receptors, many of which undergo a major conformational change upon binding specific ligand, belong to a superfamily of proteins that bind to specific DNA sequences and control gene transcription. They regulate the assembly of a transcriptional preinitiation complex at the promoter of target genes and modulate their expression in response to ligand. In particular, nuclear receptors repress or stimulate transcription by recruiting corepressor or coactivator proteins, in addition to directly contacting the basal transcription machinery. In this review, we discuss recent progress in studies of these transcriptional coregulators of nuclear receptors.

Two distinct nuclear receptor-interaction domains and CREB-binding protein-dependent transactivation function of activating signal cointegrator-2

ASC-2 is a recently isolated transcriptional cointegrator molecule, which is amplified in human cancers and stimulates transactivation by nuclear receptors, AP-1, nuclear factor kappaB (NFkappaB), serum response factor (SRF), and numerous other transcription factors. ASC-2 contained two nuclear receptor-interaction domains, both of which are dependent on the integrity of their core LXXLL sequences. Surprisingly, the C-terminal LXXLL motif specifically interacted with oxysterol receptor LXRss, whereas the N-terminal motif bound a broad range of nuclear receptors. These interactions appeared to be essential because a specific subregion of ASC-2 including the N- or C-terminal LXXLL motif acted as a potent dominant negative mutant with transactivation by appropriate nuclear receptors. In addition, the autonomous transactivation domain (AD) of ASC-2 was found to consist of three separable subregions; i.e. AD1, AD2, and AD3. In particular, AD2 and AD3 were binding sites for CREB binding protein (CBP), and CBP-neutralizing E1A repressed the autonomous transactivation function of ASC-2. Furthermore, the receptor transactivation was not enhanced by ASC-2 in the presence of E1A and significantly impaired by overexpressed AD2. From these results, we concluded that ASC-2 directly binds to nuclear receptors and recruits CBP to mediate the nuclear receptor transactivation in vivo.

Detection of pET-vector encoded, recombinant S-tagged proteins using the monoclonal antibody ATOM-2

The 15-meric S-tag is a truncated form of the S-peptide, which builds together with the 103 amino acid large S-protein the whole ribonuclease S-protein. Its small size and excessive solubility have made the S-tag an excellent fusion partner in the production of recombinant proteins, and a large variety of applications have been reported using the S-tag as a carrier. While S-tagged proteins were mostly detected and analyzed so far by use of their affinity to S-proteins, monoclonal antibodies (MAbs) for this tag have been not available. The generation of antibodies specific for S-tagged proteins is expected to broaden the range of applications of such S-tag fused recombinant proteins, and in this context, a novel MAb termed ATOM-2 was generated that specifically binds S-tagged proteins, which have been expressed using pET-vectors. Antigen specificity of ATOM-2 was confirmed in Western blot and enzyme-linked immunoadsorbent assay analysis, and using a series of amino acid deletion mutants, the binding epitope of ATOM-2 was precisely mapped. This showed that ATOM-2 recognizes the C-terminal part of the 15-meric S-tag in context with a few residues of vector encoded sequences. The core sequence for ATOM-2 binding epitope is "His-Met-Asp-Ser-Pro-Asp-Leu-Gly-Thr," which is present in all pET-expression vectors encoding S-tag fusion proteins. Because the ATOM-2 binding region does not overlap with the S-protein binding sequence, a convenient tool is provided for the simultaneous or alternative detection, purification, and analysis of recombinant S-tagged proteins to conventional S-proteins.

Downregulation of MHC class II expression by oxidant-induced apoptosis in EBV-transformed B-cells

The expression of MHC class II molecules is actively regulated upon various cellular stimuli. Since apoptosis is an inducible cellular process, it was asked whether cells undergoing apoptosis would also modulate their expression of class II molecules. Using an EBV-transformed B-cell line, the cell surface expression of HLA-DR molecules was analyzed by fluorescence-activated flow cytometry on normal and oxidant-treated apoptotic cells. A rapid and continuous decrease in HLA-DR expression was observed in apoptotic cells. RNA analysis and semiquantitative RT-PCR of cytoplasmic beta-actin mRNA showed that apoptotic cells contain partially degraded RNA and much lower amounts of beta-actin mRNA. Nevertheless, when compared after normalization of intact mRNA amounts, the HLA-DRB mRNA signals were of similar strength in normal and apoptotic cells as determined by semiquantitative RT-PCR. Thus, the decrease in the number of class II molecules during apoptosis underlies no specific program for downregulation of HLA-DRB mRNA transcription but is due to a nonspecific degradation of RNA molecules accompanied by cell death.

Inactivation of p16INK4a in primary tumors and cell lines of head and neck squamous cell carcinoma

Inactivation of the p16INK4a gene by mutation and deletion is common in head and neck squamous cell carcinoma (HNSCC). The present study demonstrates that hypermethylation of the 5' CpG islands can serve as an alternative mechanism for the inactivation of the p16INK4a gene in this tumor. We studied 11 HNSCC cell lines and 17 oral squamous cell carcinoma (OSCC) primary tumors for p16INK4a gene status by protein/mRNA and DNA genetic/epigenetic analyses to determine the incidence of its inactivation. Our study indicates that: (1) inactivation of p16 protein is frequent in HNSCC cell lines (6/11, 54.5%) and OSCC primary tumors (15/17, 88.2%), (2) inactivation of p16INK4a protein is commonly associated with the presence of gene alteration such as mutation, homozygous deletion and especially aberrant methylation, and (3) genomic sequencing of bisulfite-modified DNA shows that the carcinoma develops a heterogeneous pattern of hypermethylation.