Coxsackievirus infection induces direct pancreatic β cell killing but poor antiviral CD8+ T cell responses

Coxsackievirus B (CVB) infection of pancreatic β cells is associated with β cell autoimmunity and type 1 diabetes. We investigated how CVB affects human β cells and anti-CVB T cell responses. β cells were efficiently infected by CVB in vitro, down-regulated human leukocyte antigen (HLA) class I, and presented few, selected HLA-bound viral peptides. Circulating CD8+ T cells from CVB-seropositive individuals recognized a fraction of these peptides; only another subfraction was targeted by effector/memory T cells that expressed exhaustion marker PD-1. T cells recognizing a CVB epitope cross-reacted with β cell antigen GAD. Infected β cells, which formed filopodia to propagate infection, were more efficiently killed by CVB than by CVB-reactive T cells. Our in vitro and ex vivo data highlight limited CD8+ T cell responses to CVB, supporting the rationale for CVB vaccination trials for type 1 diabetes prevention. CD8+ T cells recognizing structural and nonstructural CVB epitopes provide biomarkers to differentially follow response to infection and vaccination.

Coxsackievirus infection induces direct pancreatic β-cell killing but poor anti-viral CD8+ T-cell responses

Coxsackievirus B (CVB) infection of pancreatic β cells is associated with β-cell autoimmunity. We investigated how CVB impacts human β cells and anti-CVB T-cell responses. β cells were efficiently infected by CVB in vitro, downregulated HLA Class I and presented few, selected HLA-bound viral peptides. Circulating CD8+ T cells from CVB-seropositive individuals recognized only a fraction of these peptides, and only another sub-fraction was targeted by effector/memory T cells that expressed the exhaustion marker PD-1. T cells recognizing a CVB epitope cross-reacted with the β-cell antigen GAD. Infected β cells, which formed filopodia to propagate infection, were more efficiently killed by CVB than by CVB-reactive T cells. Thus, our in-vitro and ex-vivo data highlight limited T-cell responses to CVB, supporting the rationale for CVB vaccination trials for type 1 diabetes prevention. CD8+ T cells recognizing structural and non-structural CVB epitopes provide biomarkers to differentially follow response to infection and vaccination.

EARLY ONSET OF MODY5 DUE TO HAPLOINSUFFICIENCY OF HNF1B

Objective

To report 2 patients with haploinsufficiency of hepatic nuclear factor 1 homeobox B (HNF1B) that results in the onset of maturity onset diabetes of the young type 5 (MODY5) before 3 years of age.

Methods

We present 2 unusual patients with MODY5 that was diagnosed at 33 and 22 months of age, respectively. We describe the presentations, clinical course, and genetic tests of both patients, and lastly, we review the literature on the prevalence and the age of presentation of MODY5 both in children and in adult patients.

Results

The first patient had severe congenital renal dysplasia, and deoxyribonucleic acid microarray indicated the deletion of 17q12. Hemoglobin A1c (HbA1c) was obtained due to the concern of MODY5, and the initial level (6.6%, 49 mmol/mol) was abnormally elevated. The second patient had mild renal dysplasia and 17q12 deletion encompassing the HNF1B gene. Hyperglycemia was identified during an episode of respiratory illness. HbA1c (6.2%, 44 mmol/mol) level was abnormally elevated. Pancreatic autoantibodies were absent in both patients. Diet modification resulted in an improvement of HbA1c in both patients.

Conclusion

Our report highlights the importance of considering MODY5 in patients with congenital anomalies of kidney. Identification of children with MODY5 permits early management of hyperglycemia.

Dimension and morphology of the mandibular condyle in class i patients in cone beam computed tomography

To evaluate the anterior-posterior (A-P)/medial-lateral (M-L) dimension, and morphology of the mandibular condyle in patients aged 18 to 65 years with Class I skeletal pattern on Cone Beam CT scans. Materials and Methods: Seventy one scans were evaluated using RealScan 2.0 software. The dimension was determined by points A (most anterior in the sagittal plane), P (most posterior in the sagittal plane), M (most interior in the coronal plane), L (most exterior in the coronal plane). The morphology of the condyle was evaluated in two coronal and sagittal planes, being classified as: round, flat, convex or mixed. The size of the condyle was analyzed by descriptive statistics and the morphology by frequency distribution. For the bivariate analysis, the Student's t-test was applied. Results: Measurements were obtained for the A-P diameter of the right condyle (RC) (8.72mm ± 1.25mm) and the left condylar (LC) (8.50mm ± 1.50mm), the M-L diameter of the RC (19.24mm ± 2.03mm) and the LC (18.97mm ± 1.87mm). There were significant differences in the male M-L dimension of the LC compared to the female (p=0.002). The most prevalent morphology of RC (35.21) and IQ (23.94) in the coronal plane was round. Conclusion: The A-P dimension of the right and left condyle is similar in both genders; however, there are differences in the M-L dimension of the left male condyle. The most prevalent morphology of the right and left condyle was round in the sagittal plane with the exception of the coronal plane.

In utero virilization secondary to a maternal Krukenberg tumor: case report and review of literature

BACKGROUND

Krukenberg tumors are ovarian metastatic adenocarcinomas with a primary origin usually located in the stomach, colon, gallbladder, pancreas, or breast. Occasionally, these tumors produce virilization in the affected individual due to androgen production by luteinization of the tumoral stroma. It is believed that during pregnancy these tumors are more likely to increase androgen production due to the elevated levels of human chorionic gonadotropin (hCG). High maternal androgens can cross the placenta producing virilization of the female fetus.

CASE PRESENTATION

A 46,XX newborn female, whose mother was diagnosed with a metastatic ovarian tumor during her second trimester of gestation associated with worsening hirsutism and acne, was found to have ambiguous genitalia at birth. Testosterone levels in both the mother and infant were elevated. Follow-up laboratory tests showed progressive normalization of circulating androgens after delivery.

CONCLUSIONS

Krukenberg tumors are rare and may produce virilization of the mother and the female fetus when present during pregnancy.

Can estimates of genetic effective population size contribute to fisheries stock assessments?

Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For example, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries-independent method of indexing population size; inferring adult abundance from estimates of the genetic effective size of a population (N_e ). Recent studies of elasmobranch species have shown correspondence between N_e and ecologically determined estimates of the population size (N). Simulation studies have flagged the possibility that the range of N_e /N ratios across species may be more restricted than previously thought, and also show that declines in N_e track declines in the abundance of model fisheries species. These key developments bring this new technology closer to implementation in fisheries science, particularly for data-poor fisheries or species of conservation interest.

Reproductive biology and feeding habits of the prickly dogfish Oxynotus bruniensis

The reproductive biology and diet of prickly dogfish Oxynotus bruniensis, a deep-sea elasmobranch, endemic to the outer continental and insular shelves of southern Australia and New Zealand, and caught as by-catch in demersal fisheries, are described from specimens caught in New Zealand waters. A total of 53 specimens were obtained from research surveys and commercial fisheries, including juveniles and adults ranging in size from 33·5 to 75·6 cm total length (L_T ). Estimated size-at-maturity was 54·7 cm L_T in males and 64·0 cm L_T in females. Three gravid females (65·0, 67·5 and 71·2 cm L_T ) were observed, all with eight embryos. Size-at-birth was estimated to be 25-27 cm L_T . Vitellogenesis was not concurrent with embryo development. Analysis of diet from stomach contents, including DNA identification of prey using the mitochondrial genes cox1 and nadh2, revealed that O. bruniensis preys exclusively on the egg capsules of holocephalans, potentially making it the only known elasmobranch with a diet reliant solely upon other chondrichthyans. Based on spatial overlap with deep-sea fisheries, a highly specialized diet, and reproductive characteristics representative of a low productivity fish, the commercial fisheries by-catch of O. bruniensis may put this species at relatively high risk of overfishing.

Effect of antenatal betamethasone administration on rat cerebellar expression of type la metabotropic glutamate receptors (mGluRla) and anxiety-like behavior in the elevated plus maze

Preclinical studies indicate that endogenous or exogenous glucocorticoids acting during the pre- or postnatal periods produce a significant Purkinje cell dendritic atrophy, especially during late postnatal ages. The present authors hypothesized that the underlying sub- strate that may contribute in part to this morphological change is the under-expression of the metabotropic glutamate la receptor (mGluRl a) because its expression is correlated with Purkinje cell dendritic outgrowth. Therefore, in the current study, they analyzed the impact of antenatal betamethasone on the immunoreactive expression of the mGluR 1 a and on anxiety-like behavior in the elevated plus maze (EPM). Pregnant rats were randomly divided into two experimental groups: control (CONT) and betamethasone-treated (BET). At gestational day 20 (G20), BET rats were subcutaneously injected with a solution of 170 μg.kg(-1) of betamethasone, and CONT animals received a similar volume of saline. At postnatal days 22 (P22) and P52, BET and CONT offspring were evaluated behaviorally in the EPM, and their cerebella were immunohistochemically processed. Contrary to the uthors' expected results, animals that were prenatally treated with a single course of betamethasone did not exhibit under-expression of mGluRl a or behavioral changes consistent with anxiety-like behaviors.

A practical introduction to the hemodynamic analysis of the cardiovascular system with 4D Flow MRI

The 4D Flow MRI technique provides a three-dimensional representation of blood flow over time, making it possible to evaluate the hemodynamics of the cardiovascular system both qualitatively and quantitatively. In this article, we describe the application of the 4D Flow technique in a 3T scanner; in addition to the technical parameters, we discuss the advantages and limitations of the technique and its possible clinical applications. We used 4D Flow MRI to study different body areas (chest, abdomen, neck, and head) in 10 volunteers. We obtained 3D representations of the patterns of flow and quantitative hemodynamic measurements. The technique makes it possible to evaluate the pattern of blood flow in large and midsize vessels without the need for exogenous contrast agents.

Not all fish are equal: functional biodiversity of cartilaginous fishes (Elasmobranchii and Holocephali) in Chile

A review of the primary literature on the cartilaginous fishes (sharks, skates, rays and chimaeras), together with new information suggests that 106 species occur in Chilean waters, comprising 58 sharks, 30 skates, 13 rays and five chimaeras. The presence of 93 species was confirmed, although 30 species were encountered rarely, through validated catch records and sightings made in artisanal and commercial fisheries and on specific research cruises. Overall, only 63 species appear to have a range distribution that normally includes Chilean waters. Actual reliable records of occurrence are lacking for 13 species. Chile has a cartilaginous fish fauna that is relatively impoverished compared with the global species inventory, but conservative compared with countries in South America with warm-temperate waters. The region of highest species richness occurs in the mid-Chilean latitudes of c. 30-40° S. This region represents a transition zone with a mix of species related to both the warm-temperate Peruvian province to the north and cold-temperate Magellan province to the south. This study provides clarification of species occurrence and the functional biodiversity of Chile's cartilaginous fish fauna.

Comparative morphology of the egg cases of Asymbolus analis, Asymbolus rubiginosus and Figaro boardmani (Carcharhiniformes: Scyliorhinidae) from southern Queensland, Australia

Descriptions of the egg cases of three catsharks, Asymbolus analis, Asymbolus rubiginosus and Figaro boardmani, are provided from 65 egg cases obtained from fishing surveys carried out on the continental shelf of southern Queensland, Australia. Egg cases of A. analis, A. rubiginosus and F. boardmani have the same basic morphology; they are typically vase-shaped, dorso-ventrally flattened and yellow and brown-tan in colour. The shape of the posterior border in terms of horn length and tendril thickness is the specific characteristic discriminating these three catsharks: enclosed horns in F. boardmani, short horns and tendrils in A. rubiginosus and long, coiled tendrils in A. analis. A non-parametric statistical approach was used as an exploratory tool for egg case identification in which six proportional measurements were sufficient to discriminate between species. Three egg cases of F. boardmani were recovered from the stomachs of three A. rubiginosus, which provided the first evidence of catshark-catshark predator-prey interaction.

Reproductive biology of Zearaja chilensis (Chondrichthyes: Rajidae) in the south-east Pacific Ocean

Between 2000 and 2002, three artisanal landing sites were sampled in southern Chile, with data on population structure and reproductive development collected from 5477 yellownose skates Zearaja chilensis. Total length (L(T) ) ranged from 33 to 158 cm for females and 34 to 155 cm for males. No sexual dimorphism was evident in disc size (length or width) or in L(T)-mass relationships. The smallest mature female was 95 cm L(T) and the size at which 50% were mature (L(T50) ) was 109 cm. Males matured between 80 and 90 cm L(T) with a L(T50) of 88 cm. Although the largest Z. chilensis captured by the artisanal fishery was 155 cm L(T) , 89% of landings comprised relatively small, immature fish. This situation may compromise the stock integrity if intrinsic vulnerability and probable long-life span of Z. chilensis are considered. Consequences for the survival of the species and possible signs of a fishery collapse must be reviewed by management authorities by consideration of both artisanal and industrial landings in Chile.

In vitro amodiaquine resistance and its association with mutations in pfcrt and pfmdr1 genes of Plasmodium falciparum isolates from Nigeria

Amodiaquine (AQ) is currently being used as a partner drug in combination with artesunate for treatment of uncomplicated malaria in most endemic countries of Africa. In the absence of molecular markers of artemisinin resistance, molecular markers of resistance to AQ may be useful for monitoring the development and spread of parasites resistance to Artesunate-Amodiaquine combination. This study was designed to assess the potential role of polymorphisms on pfcrt and pfmdr1 genes and parasite in vitro susceptibility for epidemiological surveillance of amodiaquine resistance in Plasmodium falciparum. The modified schizont inhibition assay was used to determine in vitro susceptibility profiles of 98 patients' isolates of P. falciparum to amodiaquine. Polymorphisms on parasites pfcrt and pfmdr1 genes were determined with nested PCR followed by sequencing. The geometric mean (GM) of AQ 50% inhibitory concentration (IC-50) in the 97 P. falciparum isolates was 20.48 nM (95% CI 16.53-25.36 nM). Based on the cut-off value for AQ in vitro susceptibility, 87% (84) of the P. falciparum isolates were sensitive to AQ (GM IC-50=16.32 nM; 95%CI 13.3-20.04 nM) while 13% were resistant to AQ in vitro (GM IC-50=88.73nM; 95%CI 69.67-113.0nM). Molecular analysis showed presence of mutant CVIET pfcrt haplotype, mutant pfmdr1Tyr86 allele and the double mutant CVIET pfcrt haplotype+pfmdr1Tyr86 in 72%, 49% and 35%, respectively. The GM IC-50 of isolates harboring the wild-type pfcrt CVMNK haplotype+pfmdr1Asn86 allele (3.93nM; 95%CI 1.82-8.46 nM) was significantly lower (p=0.001) than those isolates harboring the double mutant pfcrt CVIET haplotype+pfmdr1Tyr86 allele (50.40 nM; 95%CI 40.17-63.24 nM). Results from this study suggest that polymorphisms in pfcrt and pfmdr1 genes are important for AQ resistance and therefore may be useful for epidemiological surveillance of P. falciparum resistance to AQ.

Egg capsules of the dusky catshark Bythaelurus canescens (Carcharhiniformes, Scyliorhinidae) from the south-eastern Pacific Ocean

The external morphology of the egg capsule of Bythaelurus canescens and its fixation to the substratum are described. Bythaelurus canescens egg capsules are typically vase-shaped, dorso-ventrally flattened, pale yellow in colour when fresh and covered by 12-15 longitudinal ridges. The anterior border of the capsule is straight, whereas the posterior border is semicircular. Two horns bearing long, coiled tendrils arise from the anterior and posterior ends of the capsule. The presence of longitudinal ridges and long coiled tendrils at both anterior and posterior ends of the capsule readily distinguish these egg capsules from those of other chondrichthyans occurring in the south-east Pacific Ocean.

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments

By exerting mechanical force, it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup. The model includes different elements of the experimental setup (beads, handles, and RNA sequence) and limitations of the instrument (time lag of the force-feedback mechanism and finite bandwidth of data acquisition). We investigated the influence of the instrument on the measured hopping rates. Results from the model are in good agreement with the experiments reported in the companion article. The comparison between theory and experiments allowed us to infer the values of the intrinsic molecular rates of the RNA hairpin alone and to search for the optimal experimental conditions to do the measurements. We conclude that the longest handles and softest traps that allow detection of the folding/unfolding signal (handles approximately 5-10 Kbp and traps approximately 0.03 pN/nm) represent the best conditions to obtain the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules.

Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers

When mixed together, DNA and polyaminoamide dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension curves (FECs). A characteristic force plateau (around 10 pN) and hysteresis between the pulling and relaxation cycles are observed for different dendrimer sizes, indicating the existence of a first-order transition between two phases (condensed and extended) of the fiber. Upon salt variation FECs change noticeably confirming that electrostatic forces drive the condensation transition. We propose a simple model for the decondensing transition that qualitatively reproduces the FECs and which is confirmed by atomic force microscopy images.

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

Atomic force microscopes and optical tweezers are widely used to probe the mechanical properties of individual molecules and molecular interactions, by exerting mechanical forces that induce transitions such as unfolding or dissociation. These transitions often occur under nonequilibrium conditions and are associated with hysteresis effects-features usually taken to preclude the extraction of equilibrium information from the experimental data. But fluctuation theorems allow us to relate the work along nonequilibrium trajectories to thermodynamic free-energy differences. They have been shown to be applicable to single-molecule force measurements and have already provided information on the folding free energy of a RNA hairpin. Here we show that the Crooks fluctuation theorem can be used to determine folding free energies for folding and unfolding processes occurring in weak as well as strong nonequilibrium regimes, thereby providing a test of its validity under such conditions. We use optical tweezers to measure repeatedly the mechanical work associated with the unfolding and refolding of a small RNA hairpin and an RNA three-helix junction. The resultant work distributions are then analysed according to the theorem and allow us to determine the difference in folding free energy between an RNA molecule and a mutant differing only by one base pair, and the thermodynamic stabilizing effect of magnesium ions on the RNA structure.

A two-state kinetic model for the unfolding of single molecules by mechanical force

We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states) separated by an intermediate barrier. We compute the probability distribution for the dissipated work and give analytical expressions for the average and variance of the distribution. To first order, the amount of dissipated work is directly proportional to the rate of application of force (the loading rate) and to the relaxation time of the molecule. The model yields estimates for parameters that characterize the unfolding kinetics under force in agreement with those obtained in recent experimental results. We obtain a general equation for the minimum number of repeated experiments needed to obtain an equilibrium free energy, to within k(B)T, from nonequilibrium experiments by using the Jarzynski formula. The number of irreversible experiments grows exponentially with the ratio of the average dissipated work, W(dis) to k(B)T.

[Neurohagiography. Lamberto Caesaraugustanus, the cephalophoric: holy patron of Spanish neurology?]

Until now Neurology has lacked a patron saint who, taking the most advantage of the rich cultural tradition inherited from our past and independently of the religious ideology of each one, can be helpful approach in the neurologist figure to different people. An Ad Hoc Committee from the Neurology History Study Group of the SEN has researched the medical hagiography with any kind of neurological relationship (neurohagiography), in order to make a hagiography study of every saint related to our speciality, with the added luck of proposing a patron for Neurology with hispanic origin. In this pioneer study of historiographic research different documents related with the medical hagiography have been studied, especially the Index ac Status Causarum, and information coming from different national ecclesiastic archives. A total of 342 saints share the patronage of 137 diseases, of which a 27,7% are related in some way to Neurology. Headache constitutes the prime cause of the invocations, with 20 saints. Another 11 saints plead for epilepsy; to these we also must add another six for so called possessed patients. Therefore, two of the three main causes of invocation (headache, fever and epilepsy) come up to chronic processes. Of all the saints with a hispanic origin candidates to the patronage of the neurologists San Lamberto Caesaraugustanus stands out, who died in the year 303 during Diocletian persecution. Belonging to the selected standing of "cephalophoric martyrs" (those beheahed who carry their own head in their hands), he was able to walk an important distance (about six kilometres) with his head split from the body, a fact only understood as a suprahuman phenomenon thanks to which he has becomes the brain transplant pioneer.

The bacteriophage straight phi29 portal motor can package DNA against a large internal force

As part of the viral infection cycle, viruses must package their newly replicated genomes for delivery to other host cells. Bacteriophage straight phi29 packages its 6.6-microm long, double-stranded DNA into a 42 x 54 nm capsid by means of a portal complex that hydrolyses ATP. This process is remarkable because entropic, electrostatic and bending energies of the DNA must be overcome to package the DNA to near-crystalline density. Here we use optical tweezers to pull on single DNA molecules as they are packaged, thus demonstrating that the portal complex is a force-generating motor. This motor can work against loads of up to 57 pN on average, making it one of the strongest molecular motors reported to date. Movements of over 5 microm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force-velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Notably, the packaging rate decreases as the prohead is filled, indicating that an internal force builds up to approximately 50 pN owing to DNA confinement. Our data suggest that this force may be available for initiating the ejection of the DNA from the capsid during infection.

Effect of poly(ADP-ribosyl)ation and Mg2+ ions on chromatin structure revealed by scanning force microscopy

Poly(ADP-ribosyl)ation of nuclear proteins is responsible for major changes in the high-order chromatin structure. The effects of this post-translation modification on nuclear architecture were examined at different Mg2+ concentrations using scanning force microscopy. A quantitative analysis of the internucleosomal distance, the width, and the volume of chromatin fibers imaged in tapping mode reveals that poly(ADP-ribosyl)ation induces a complete relaxation and decondensation of the chromatin structure. Our data, on the center-to-center distance between adjacent nucleosomes and on the fiber width, indicate that the poly(ADP-ribosyl)ated fibers remain significantly decondensed even in the presence of Mg2+. Our results also show that the Mg2+ assumes an important role in the folding of chromatin structure, but Mg2+ is not able to restore the native feature of chromatin, when the fibers are depleted of H1/H5 histones. The combined effect of post-translation modification and cation ions on the chromatin structure shows that poly(ADP-ribosyl)ation could promote accessibility to DNA even in those nuclear processes that require Mg2+.

[Prospective follow-up of a HIV infected population with and without access to antiretroviral therapy: impact of survival and complications]

BACKGROUND

Three-drug antiretroviral therapy (ART-3) has reduced complications and improved survival in HIV+ patients. The Chilean Public Health System began dual therapy (ART-2) in 1997, covering approximately 40% of patients in need.

AIM

To report the results of a follow-up of patients with and without access to ART in a Chilean public hospital.

PATIENT AND METHODS

Prospective follow-up of patients with ART-2 and 3 (cases) and patients with no access to ART (controls). All patients needed ART but it was available to a minority of them. Selection for ART was at random. Follow-up was between 6-24 months (11/96 to 3/99). Basal and periodic clinical and laboratory parameters were determined. Mortality and occurrence of new AIDS-defining events (ADE) were compared statistically using chi square.

RESULTS

One hundred and fifty cases (106 ART2, 28 ART3 and 16 ART2 expanded to ART3) and 166 controls were studied. Basal parameters were similar except prior ART (32.7 and 18.7% in cases and controls respectively). Close to 1/3 patients had AIDS. Cases had a mean follow up of 527 days; controls, 478. Six cases (4%) (5 in ART-2) and 17 controls (10%) died. Mortality x 100/pts/yr was 2.7 in cases and 7.7 in controls, p < 0.05. ADE per 100/pts/yr was 21 in cases (24.4 in ART2, 15.1 in TAR3) and 54.5 in controls, p < 0.05. Cases had a reduction of: esophageal candidiasis (84%), tuberculosis (75%), cryptococcosis and toxoplasmosis (66%), P carinii pneumonia (55%) and bacterial pneumonia (46%) and they had fewer hospitalizations (73%). Late assessment: 70 of 101 ART-2 patients had changed to ART-3 (1 death); 22 of 101 kept original ART-2 (12 dead, 10 alive), 39 of 43 ART-3 patients were alive and 1 died.

CONCLUSIONS

Short-term ART-2 and 3 significantly reduced mortality (60% and 73%) ADE (65% and 76% respectively) and hospitalizations. Benefits of ART-2 were short lived. Resource-constrained countries cannot depend on weaker than standard ART for proper care of people with HIV disease.

The physics of molecular motors

Molecular motors convert chemical energy into mechanical force and movement. Operating at energies just above those of the thermal bath, these motors experience large fluctuations, and their physical description must be necessarily stochastic. Here, motor operation is described as a biased diffusion on a potential energy surface defined by the interactions of the motor with its track and its fuel. These ideas are illustrated with a model of the rotary movement of the F(o) motor.

Reversible unfolding of single RNA molecules by mechanical force

Here we use mechanical force to induce the unfolding and refolding of single RNA molecules: a simple RNA hairpin, a molecule containing a three-helix junction, and the P5abc domain of the Tetrahymena thermophila ribozyme. All three molecules (P5abc only in the absence of Mg2+) can be mechanically unfolded at equilibrium, and when kept at constant force within a critical force range, are bi-stable and hop between folded and unfolded states. We determine the force-dependent equilibrium constants for folding/unfolding these single RNA molecules and the positions of their transition states along the reaction coordinate.

Mechanical manipulation of single titin molecules with laser tweezers

Titin (also known as connectin) is a giant filamentous polypeptide of multi-domain construction spanning between the Z- and M-lines of the vertebrate muscle sarcomere. The molecule is significant in maintaining sarcomeric structural integrity and generating passive muscle force via its elastic properties. Here we summarize our efforts to characterize titin's elastic properties by manipulating single molecules with force-measuring laser tweezers. The titin molecules can be described as an entropic spring in which domain unfolding occurs at high forces during stretch and refolding at low forces during release. Statistical analysis of a large number (> 500) of stretch-release experiments and comparison of experimental data with the predictions of the wormlike chain theory permit the estimation of unfolded titin's mean persistence length as 16.86 A (+/- 0.11 SD). The slow rates of unfolding and refolding compared with the rates of stretch and release, respectively, result in a state of non-equilibrium and the display of force hysteresis. Folding kinetics as the source of non-equilibrium is directly demonstrated here by the abolishment of force hysteresis in the presence of chemical denaturant. Experimental observations were well simulated by superimposing a simple domain folding kinetics model on the wormlike chain behavior of titin and considering the characteristics of the compliant laser trap. The original video presentation of this paper may be viewed on the web at http:¿www.pote.hu/mm/prezentacio/mkpres/++ +mkpres.htm.

Mechanical fatigue in repetitively stretched single molecules of titin

Relaxed striated muscle cells exhibit mechanical fatigue when exposed to repeated stretch and release cycles. To understand the molecular basis of such mechanical fatigue, single molecules of the giant filamentous protein titin, which is the main determinant of sarcomeric elasticity, were repetitively stretched and released while their force response was characterized with optical tweezers. During repeated stretch-release cycles titin becomes mechanically worn out in a process we call molecular fatigue. The process is characterized by a progressive shift of the stretch-force curve toward increasing end-to-end lengths, indicating that repeated mechanical cycles increase titin's effective contour length. Molecular fatigue occurs only in a restricted force range (0-25 pN) during the initial part of the stretch half-cycle, whereas the rest of the force response is repeated from one mechanical cycle to the other. Protein-folding models fail to explain molecular fatigue on the basis of an incomplete refolding of titin's globular domains. Rather, the process apparently derives from the formation of labile nonspecific bonds cross-linking various sites along a pre-unfolded titin segment. Because titin's molecular fatigue occurs in a physiologically relevant force range, the process may play an important role in dynamically adjusting muscle's response to the recent history of mechanical perturbations.

Positive torsional strain causes the formation of a four-way junction at replication forks

The advance of a DNA replication fork requires an unwinding of the parental double helix. This in turn creates a positive superhelical stress, a (+)-DeltaLk, that must be relaxed by topoisomerases for replication to proceed. Surprisingly, partially replicated plasmids with a (+)-DeltaLk were not supercoiled nor were the replicated arms interwound in precatenanes. The electrophoretic mobility of these molecules indicated that they have no net writhe. Instead, the (+)-DeltaLk is absorbed by a regression of the replication fork. As the parental DNA strands re-anneal, the resultant displaced daughter strands base pair to each other to form a four-way junction at the replication fork, which is locally identical to a Holliday junction in recombination. We showed by restriction endonuclease digestion that the junction can form at either the terminus or the origin of replication and we visualized the structure with scanning force microscopy. We discuss possible physiological implications of the junction for stalled replication in vivo.

Grabbing the cat by the tail: manipulating molecules one by one

Methods for manipulating single molecules are yielding new information about both the forces that hold biomolecules together and the mechanics of molecular motors. We describe here the physical principles behind these methods, and discuss their capabilities and current limitations.

[Impact of antiretroviral therapy in mortality of Chilean HIV (+) patients: a case control study]

BACKGROUND

Combined antiretroviral therapy (AVR) has shown a protective effect (PE) on morbidity and survival in HIV (+) patients of industrialised countries where triple-drug therapy (ARV-3) is standard. In Chile the public health system began providing double-drug therapy in 1997 (ARV-2) with 2 reverse transcriptase inhibitors.

AIM

To assess the impact of ARV in morbimortality of HIV (+) patients in Chile after a year of follow up.

PATIENTS AND METHODS

Retrospective case-control (1:1) study. Cases were 97 patients followed during 1997 for 6 or more months and dying during that period. Each case had a control of the same gender and CDC stage, similar age and CD4 count, but surviving a same period of follow up. A comparison of ARV before and during follow up (rate and type) was done. P carinii prophylaxis, pneumococcal immunization at baseline or follow up, frequency of hospital admissions and occurrence of opportunistic infections in both groups were assessed. Odds ratio (OR) for mortality, hospitalization and opportunistic infections in ARV user, as well as treatment PE were calculated.

RESULTS

Twenty four (24.7%) cases and sixty six (68%) controls received ARV during follow up (p < 0.001), OR was 0.15 (CI 95% 0.08-0.3), p < 0.001, the PE was 6.6 for ARV users versus non users, among cases 19 patients received ARV-2 and five received ARV-3. Among controls, 41 patients received ARV-2 and 25 received ARV-3. These differences established an OR of 0.20 (CI 95% 0.09-0.04) and a PE of 5 for ARV-2 versus no ARV. For ARV-3 compared with no ARV the OR was 0.08 (CI 95% 0.003-0.26), and the PE 12.5. Fifty three (54.6%) cases and 13 (13.4%) controls required hospital admission, OR 0.49 (CI 95% 0.25-0.94), p = 0.03, and PE of 2.04 of ARV versus no ARV; 82 (85.3%) cases and 50 (51%) controls had opportunistic infections, OR 0.5 (CI 95% 0.26-0.96), p = 0.03 and PE of 2 for ARV versus no ARV. There were no significant differences in prior ARV, prophylaxis and immunisation between cases and controls.

CONCLUSIONS

This study showed the high impact of ARV in short term morbimortality of HIV(+) patients and the need to implement antiretroviral therapy to all patients as an official health policy. This study did not answer the question of the role, if any, of weaker-than standard antiretroviral therapy.

An integrated laser trap/flow control video microscope for the study of single biomolecules

We have developed an integrated laser trap/flow control video microscope for mechanical manipulation of single biopolymers. The instrument is automated to maximize experimental throughput. A single-beam optical trap capable of trapping micron-scale polystyrene beads in the middle of a 200-microm-deep microchamber is used, making it possible to insert a micropipette inside this chamber to hold a second bead by suction. Together, these beads function as easily exchangeable surfaces between which macromolecules of interest can be attached. A computer-controlled flow system is used to exchange the liquid in the chamber and to establish a flow rate with high precision. The flow and the optical trap can be used to exert forces on the beads, the displacements of which can be measured either by video microscopy or by laser deflection. To test the performance of this instrument, individual biotinylated DNA molecules were assembled between two streptavidin beads, and the DNA elasticity was characterized using both laser trap and flow forces. DNA extension under varying forces was measured by video microscopy. The combination of the flow system and video microscopy is a versatile design that is particularly useful for the study of systems susceptible to laser-induced damage. This capability was demonstrated by following the translocation of transcribing RNA polymerase up to 650 s.

Single-molecule studies of DNA mechanics

During the past decade, physical techniques such as optical tweezers and atomic force microscopy were used to study the mechanical properties of DNA at the single-molecule level. Knowledge of DNA's stretching and twisting properties now permits these single-molecule techniques to be used in the study of biological processes such as DNA replication and transcription.

Stretching of single collapsed DNA molecules

The elastic response of single plasmid and lambda phage DNA molecules was probed using optical tweezers at concentrations of trivalent cations that provoked DNA condensation in bulk. For uncondensed plasmids, the persistence length, P, decreased with increasing spermidine concentration before reaching a limiting value 40 nm. When condensed plasmids were stretched, two types of behavior were observed: a stick-release pattern and a plateau at approximately 20 pN. These behaviors are attributed to unpacking from a condensed structure, such as coiled DNA. Similarly, condensing concentrations of hexaammine cobalt(III) (CoHex) and spermidine induced extensive changes in the low and high force elasticity of lambda DNA. The high force (5-15 pN) entropic elasticity showed worm-like chain (WLC) behavior, with P two- to fivefold lower than in low monovalent salt. At lower forces, a 14-pN plateau abruptly appeared. This corresponds to an intramolecular attraction of 0.083-0.33 kT/bp, consistent with osmotic stress measurements in bulk condensed DNA. The intramolecular attractive force with CoHex is larger than with spermidine, consistent with the greater efficiency with which CoHex condenses DNA in bulk. The transition from WLC behavior to condensation occurs at an extension about 85% of the contour length, permitting looping and nucleation of condensation. Approximately half as many base pairs are required to nucleate collapse in a stretched chain when CoHex is the condensing agent.

Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase

Using an optical-trap/flow-control video microscopy technique, we followed transcription by single molecules of Escherichia coli RNA polymerase in real time over long template distances. These studies reveal that RNA polymerase molecules possess different intrinsic transcription rates and different propensities to pause and stop. The data also show that reversible pausing is a kinetic intermediate between normal elongation and the arrested state. The conformational metastability of RNA polymerase revealed by this single-molecule study of transcription has direct implications for the mechanisms of gene regulation in both bacteria and eukaryotes.

Single-molecule studies of the effect of template tension on T7 DNA polymerase activity

T7 DNA polymerase catalyses DNA replication in vitro at rates of more than 100 bases per second and has a 3'-->5' exonuclease (nucleotide removing) activity at a separate active site. This enzyme possesses a 'right hand' shape which is common to most polymerases with fingers, palm and thumb domains. The rate-limiting step for replication is thought to involve a conformational change between an 'open fingers' state in which the active site samples nucleotides, and a 'closed' state in which nucleotide incorporation occurs. DNA polymerase must function as a molecular motor converting chemical energy into mechanical force as it moves over the template. Here we show, using a single-molecule assay based on the differential elasticity of single-stranded and double-stranded DNA, that mechanical force is generated during the rate-limiting step and that the motor can work against a maximum template tension of approximately 34 pN. Estimates of the mechanical and entropic work done by the enzyme show that T7 DNA polymerase organizes two template bases in the polymerization site during each catalytic cycle. We also find a force-induced 100-fold increase in exonucleolysis above 40 pN.

The mechanochemistry of molecular motors

A theory of molecular motors is presented that explains how the energy released in single chemical reactions can generate mechanical motion and force. In the simplest case the fluctuating movements of a motor enzyme are well described by a diffusion process on a two-dimensional potential energy surface, where one dimension is a chemical reaction coordinate and the other is the spatial displacement of the motor. The coupling between chemistry and motion results from the shape of the surface, and motor velocities and forces result from diffusion currents on this surface. This microscopic description is shown to possess an equivalent kinetic mechanism in which the rate constants depend on externally applied forces. By using this equivalence we explore the characteristic properties of several broad classes of motor mechanisms and give general expressions for motor velocity versus load force for any member of each class. We show that in some cases simple plots of 1/velocity vs. 1/concentration can distinguish between classes of motor mechanisms and may be used to determine the step at which movement occurs.

Pulling chromatin fibers: computer simulations of direct physical micromanipulations

A low-resolution molecular model, which combines the known mechanical properties of protein-free DNA with the accumulating picture of chromatosome structure, has been developed to account for the stretching of single chromatin fibers by an imposed external force. Force-extension characteristics of sets of chains accumulated by Monte Carlo sampling are consistent with recently observed findings in the non-destructive regime (<20 pN imposed force), where the structure of the chromatosome remains intact. The correspondence between simulation and the relaxation phase of the experiment limits the equilibrium entry-exit angle of linker DNA on the chromatosome to W=50(+/-10) degrees and the effective DNA linker length to L(eff)=40(+/-5) bp. The computed force-extension characteristics are relatively insensitive to other parameters of the model, precluding their accurate estimation. The introduction of an attractive potential between closely spaced nucleosomes reproduces the added initial resistance of single fibers to extension at high salt conditions. The consideration of elastic linkers also improves the fitting of assorted classical measurements of unstressed chromatin structure in solution. The overall picture of chromatin that emerges is an irregular, fluctuating, three-dimensional, zig-zag structure with intact, mechanically stable chromatosome units and deformable linkers. The modeled fiber undergoes large-scale configurational rearrangements without significant perturbation of the constituent chromatosome beads, collapsing into a highly condensed form in response to small (<2kT) inter-nucleosomal attractions.

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure

Single chicken erythrocyte chromatin fibers were stretched and released at room temperature with force-measuring laser tweezers. In low ionic strength, the stretch-release curves reveal a process of continuous deformation with little or no internucleosomal attraction. A persistence length of 30 nm and a stretch modulus of approximately 5 pN is determined for the fibers. At forces of 20 pN and higher, the fibers are modified irreversibly, probably through the mechanical removal of the histone cores from native chromatin. In 40-150 mM NaCl, a distinctive condensation-decondensation transition appears between 5 and 6 pN, corresponding to an internucleosomal attraction energy of approximately 2.0 kcal/mol per nucleosome. Thus, in physiological ionic strength the fibers possess a dynamic structure in which the fiber locally interconverting between "open" and "closed" states because of thermal fluctuations.

Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme

Recent advances in single molecule manipulation methods offer a novel approach to investigating the protein folding problem. These studies usually are done on molecules that are naturally organized as linear arrays of globular domains. To extend these techniques to study proteins that normally exist as monomers, we have developed a method of synthesizing polymers of protein molecules in the solid state. By introducing cysteines at locations where bacteriophage T4 lysozyme molecules contact each other in a crystal and taking advantage of the alignment provided by the lattice, we have obtained polymers of defined polarity up to 25 molecules long that retain enzymatic activity. These polymers then were manipulated mechanically by using a modified scanning force microscope to characterize the force-induced reversible unfolding of the individual lysozyme molecules. This approach should be general and adaptable to many other proteins with known crystal structures. For T4 lysozyme, the force required to unfold the monomers was 64 +/- 16 pN at the pulling speed used. Refolding occurred within 1 sec of relaxation with an efficiency close to 100%. Analysis of the force versus extension curves suggests that the mechanical unfolding transition follows a two-state model. The unfolding forces determined in 1 M guanidine hydrochloride indicate that in these conditions the activation barrier for unfolding is reduced by 2 kcal/mol.

How RNA folds

We describe the RNA folding problem and contrast it with the much more difficult protein folding problem. RNA has four similar monomer units, whereas proteins have 20 very different residues. The folding of RNA is hierarchical in that secondary structure is much more stable than tertiary folding. In RNA the two levels of folding (secondary and tertiary) can be experimentally separated by the presence or absence of Mg2+. Secondary structure can be predicted successfully from experimental thermodynamic data on secondary structure elements: helices, loops, and bulges. Tertiary interactions can then be added without much distortion of the secondary structure. These observations suggest a folding algorithm to predict the structure of an RNA from its sequence. However, to solve the RNA folding problem one needs thermodynamic data on tertiary structure interactions, and identification and characterization of metal-ion binding sites. These data, together with force versus extension measurements on single RNA molecules, should provide the information necessary to test and refine the proposed algorithm.