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.

Superconductivity in chromium nitrides Pr3Cr10-xN11 with strong electron correlations

Exploration of superconductivity in Cr-based compounds has attracted considerable interest because only a few Cr-based superconductors (CrAs, A2Cr3As3 and ACr3As3 (A = K, Rb, Cs, Na)) have been discovered so far and they show an unconventional pairing mechanism. We report the discovery of bulk superconductivity at 5.25 K in chromium nitride in Pr3Cr10-xN11 with a cubic lattice structure. A relatively large upper critical field of H c2(0) ∼ 12.6 T is determined, which is larger than the estimated Pauli-paramagnetic pair-breaking magnetic field. The material has a large electronic specific-heat coefficient of 170 mJ K-2 mol-1-about 10 times larger than that estimated by the electronic structure calculation, which suggests that correlations between 3d electrons are very strong in Pr3Cr10-xN11, and thus quantum fluctuations might be involved. Electronic structure calculations show that the density of states at the Fermi energy are contributed predominantly by Cr 3d electrons, implying that the superconductivity results mainly from the condensation of Cr 3d electrons. Pr3Cr10-xN11 represents a rare example of possible unconventional superconductivity emerging in a 3D system with strong electron correlations. Nevertheless, clarification of the specific pairing symmetry needs more investigation.

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.

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.

[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.

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.

Induction of osteopontin gene expression during mammary gland involution and effects of glucocorticoid on its expression in mammary epithelial cells

To understand the molecular mechanisms of mammary gland involution, an involution-induced clone was identified from a cDNA library of mouse mammary gland by differential screening. Characterization of a clone by sequencing and northern analysis showed that expression of the osteopontin gene was induced during involution of mouse mammary gland. But induction of the osteopontin gene was not observed in apoptotic HC11 mammary epithelial cells under serum starvation. In HC11 cells, dexamethasone treatment from the seeding stage showed five-fold induction of osteopontin gene expression, but the expression was not changed when dexamethasone was added to confluent cells.

Role of the guanosine triphosphatase Rac2 in T helper 1 cell differentiation

T helper 1 (TH1) cells mediate cellular immunity, whereas TH2 cells potentiate antiparasite and humoral immunity. We used a complementary DNA subtraction method, representational display analysis, to show that the small guanosine triphosphatase Rac2 is expressed selectively in murine TH1 cells. Rac induces the interferon-gamma (IFN-gamma) promoter through cooperative activation of the nuclear factor kappa B and p38 mitogen-activated protein kinase pathways. Tetracycline-regulated transgenic mice expressing constitutively active Rac2 in T cells exhibited enhanced IFN-gamma production. Dominant-negative Rac inhibited IFN-gamma production in murine T cells. Moreover, T cells from Rac2-/- mice showed decreased IFN-gamma production under TH1 conditions in vitro. Thus, Rac2 activates TH1-specific signaling and IFN-gamma gene expression.

Expression of activated CDC42 induces T cell apoptosis in thymus and peripheral lymph organs via different pathways

CDC42, a Ras-related small GTP binding protein, is involved in diverse cellular functions in lymphocytes. We generated transgenic mice expressing constitutively active murine CDC42 (Q61L) under the control of the human CD2 promoter. Transgenic mice showed smaller thymi with a dramatic reduction of CD4+CD8+, CD4+ and CD8+ thymocytes and with increase of CD4-CD8- thymocytes at CD25-CD44+ and CD25+ stage. A high percentage of the transgenic thymocytes were apoptotic, explaining the reduction of cellularity and size of the thymus. Mature T cells (TCR alphabeta+) in peripheral lymph organs, spleen and lymph node, were also dramatically reduced, and exhibited massive apoptosis. Expression of Fas and Fas ligand on both thymocytes and peripheral T cells was upregulated in transgenic mice, but the increased apoptosis in the thymus was independent of Fas (CD95), whereas peripheral spleen and lymph node T cell apoptosis was Fas dependent. Thus, activated CDC42 triggers distinct apoptotic pathways in thymocytes and peripheral T cells.

Use of a recombinant parvovirus to facilitate screening for human melanoma cell clones expressing tetracycline-responsive transactivators

The tetracycline regulatory (TET) system provides a useful means of controlling foreign gene expression in mammalian cells. Exploiting this system in cultured cells requires the prior isolation, from the cells of interest, of transfectant clones expressing the necessary TET transactivator, tTA, or reverse transactivator, rtTA. We describe a simple screening procedure for identifying transfectant clones expressing a properly regulated transactivator, and the application of this method to isolating clones of human melanoma cells expressing either tTA or rtTA. Clones in multi-well plates are transduced by exposure to a recombinant parvovirus containing a luciferase reporter, under control of a promoter responsive to the TET system transactivators. Transactivation of reporter expression in the presence or absence of doxycycline (DOXY) is determined after one to two days, using a rapid luciferase assay. Screening is easier and more reproducible with this transduction method than with conventional transient transfection of analogous reporter plasmids. Clones of two human melanoma cell lines showing >100-200-fold transactivation after transfection with either tTA or rtTA were readily identified using this method.

[Cloning and expression of the E. coli serine hydroxymethyltransferase gene (glyA)]

The E. coli K12 glyA gene(13 kb), encoding serine hydroxymethyltransferase (SHMT), has been cloned in the plasmid vector pBR329 using insertion inactivation and complementation test. Subcloning of segments of the original insert (13 kb) into plasmids pBR322, pBR329 and pSMY901 established that a 2.6 kb PstI-EcoR fragment carries the glyA gene. The 12 strains of transforments containing recombined plasmid. were obtained. SHMT and glyA gene product level in strains carrying glyA plasmids were different. No SHMT activity was observed in host strains. The glyA gene products for JM109(pSM13), K12(pSM13), K12(pSM14) and K12(pSM15) account for 15.7%, 15.4%, 11.8%, and 9.48% of the total dissoluble cell protein, respectively.

Decreased apoptosis in the brain and premature lethality in CPP32-deficient mice

Programmed cell death (apoptosis) is a prominent feature of the development of the immune and nervous systems. The identification of the Caenorhabditis elegans cell death gene, ced-3, as a prototype of the interleukin-1beta converting enzyme (ICE) protease family has led to extensive evidence implicating these enzymes in apoptosis. Among the ten or more members of the ICE protease family, CPP32/yama/apopain exhibits the highest similarity to CED-3 in both sequence homology and substrate specificity. To analyse its function in vivo, we generated CPP32-deficient mice by homologous recombination. These mice, born at a frequency lower than expected by mendelian genetics, were smaller than their littermates and died at 1-3 weeks of age. Although their thymocytes retained normal susceptibility to various apoptotic stimuli, brain development in CPP32-deficient mice was profoundly affected, and discernible by embryonic day 12, resulting in a variety of hyperplasias and disorganized cell deployment. These supernumerary cells were postmitotic and terminally differentiated by the postnatal stage. Pyknotic clusters at sites of major morphogenetic change during normal brain development were not observed in the mutant embryos, indicating decreased apoptosis in the absence of CPP32. Thus CPP32 is shown to play a critical role during morphogenetic cell death in the mammalian brain.

Essential region for self-replication of Coryneform bacteria plasmid pXZ10145

A pTSK series of recombinant plasmids were constructed by cloning DNA fragments of pXZ10145 or its deleted deriviate pATN65 into plasmid vector pACYC177 of E. coli. Experiment results of Coryneform bacteria transformation with these pTSK plasmids allowed us to localize the essential region for self-replication on plasmid pXZ10145. The minimal replication region of the pXZ10145 was located on a 1.2kb Nael-Nrul DNA fragment in which only one open reading frame was found. This ORF was believed to be encoded a trans-acting replication factor. The replication origin (oriV) was locate on a 0.3kb NaeI-SalI fragment which was within the ORF region.

D4-GDI, a substrate of CPP32, is proteolyzed during Fas-induced apoptosis

Apoptosis (programmed cell death) is a fundamental process for normal development of multicellular organisms, and is involved in the regulation of the immune system, normal morphogenesis, and maintenance of homeostasis, ICE/CED-3 family cysteine proteases have been implicated directly in apoptosis, but relatively few of the substrates through which their action is mediated have been identified. Here we report that D4-GDI, an abundant hematopoietic cell GDP dissociation inhibitor for the Ras-related Rho family GTPases, is a substrate of the apoptosis protease CPP32/Yama/Apopain. D4-GDI was rapidly truncated to a 23-kDa fragment in Jurkat cells with kinetics that parallel the onset of apoptosis following Fas cross-linking with agonistic antibody or treatment with staurosporine. Fas- and staurosporine-induced apoptosis as well as cleavage of D4-GDI were inhibited by the ICE inhibitor, YVAD-cmk. D4-GDI was cleaved in vitro by recombinant CPP32 expressed in Escherichia coli to form a 23-kDa fragment. The CPP32-mediated cleavage of D4-GDI was completely inhibited by 1 microM DEVD-CHO, a reported selective inhibitor of CPP32. In contrast, the ICE-selective inhibitors, YVAD-CHO or YVAD-cmk, did not inhibit CPP32-mediated D4-GDI cleavage at concentrations up to 50 microM. N-terminal sequencing of the 23-kDa D4-GDI fragment demonstrated that D4-GDI was cleaved between Asp19 and Ser20 of the poly(ADP-ribose) polymerase-like cleavage sequence DELD19S. These data suggest that regulation by D4-GDI of Rho family GTPases may be disrupted during apoptosis by CPP32-mediated cleavage of the GDI protein.

Genetic probing of the first and second transmembrane helices of the plasma membrane H(+)-ATPase from Saccharomyces cerevisiae

Structural features of the putative helical hairpin region comprising transmembrane segments 1 (TM1) and 2 (TM2) of the yeast plasma membrane H(+)-ATPase were probed by site-directed mutagenesis. The importance of phenylalanine residues Phe-116, Phe-119, Phe-120, Phe-126, Phe-144, Phe-159, and Phe-163 was explored by alanine replacement mutagenesis. It was found that substitutions at all positions, except Phe-120 and Phe-144, produced viable enzymes, although a range of cellular growth phenotypes were observed like hygromycin B resistance and low pH sensitivity, which are linked to in vivo action of the H(+)-ATPase. Lethal positions Phe-120 and Phe-144, could be replaced with tryptophan to produce viable enzyme, although the F144W mutant was highly perturbed. ATP hydrolysis measurements showed that Km was not significantly altered for most mutant enzymes, whereas Vmax was moderately reduced with two mutants, F144W and F163A, showing less than 50% of the normal activity. Double Phe-->Ala mutations in TM1 and TM2 were constructed to examine whether such substitutions would result in a higher degree of enzyme destabilization. Mutant F116A/F119A was viable and gave a normal phenotype, while F159A/F163A was not viable. Other double mutants, F116A/F159A and F119AF/159A, which are predicted to lie juxtaposed on TM1 and TM2, produced non-functional enzymes. However, a viable F119V/F159A mutant was isolated and showed hygromycin B resistance. These results suggest that double mutations eliminating 2 phenylalanine residues strongly destabilize the enzyme. A putative proline kink at Gly-122/Pro-123 in TM1 is not essential for enzyme action since these residues could be variously substituted (G122A or G122N; P123A, P123G, or P123F) producing viable enzymes with moderate effects on in vitro ATP hydrolysis or proton transport. However, several substitutions produced prominent growth phenotypes, suggesting that local perturbations were occurring. The location of Pro-123 is important because Gly-122 and Pro-123 could not be exchanged. In addition, a double Pro-Pro created by a G122P mutation was lethal, suggesting that maintenance of an alpha-helical structure is important. Other mutations in the hairpin, including modification of a buried charged residue, E129A, were not critical for enzyme action. These data are consistent with the view that the helical hairpin comprising TM1 and TM2 has important structural determinants that contribute to its overall stability and flexibility.