Using molecular mechanics to predict bulk material properties of fibronectin fibers

The structural proteins of the extracellular matrix (ECM) form fibers with finely tuned mechanical properties matched to the time scales of cell traction forces. Several proteins such as fibronectin (Fn) and fibrin undergo molecular conformational changes that extend the proteins and are believed to be a major contributor to the extensibility of bulk fibers. The dynamics of these conformational changes have been thoroughly explored since the advent of single molecule force spectroscopy and molecular dynamics simulations but remarkably, these data have not been rigorously applied to the understanding of the time dependent mechanics of bulk ECM fibers. Using measurements of protein density within fibers, we have examined the influence of dynamic molecular conformational changes and the intermolecular arrangement of Fn within fibers on the bulk mechanical properties of Fn fibers. Fibers were simulated as molecular strands with architectures that promote either equal or disparate molecular loading under conditions of constant extension rate. Measurements of protein concentration within micron scale fibers using deep ultraviolet transmission microscopy allowed the simulations to be scaled appropriately for comparison to in vitro measurements of fiber mechanics as well as providing estimates of fiber porosity and water content, suggesting Fn fibers are approximately 75% solute. Comparing the properties predicted by single molecule measurements to in vitro measurements of Fn fibers showed that domain unfolding is sufficient to predict the high extensibility and nonlinear stiffness of Fn fibers with surprising accuracy, with disparately loaded fibers providing the best fit to experiment. This work shows the promise of this microstructural modeling approach for understanding Fn fiber properties, which is generally applicable to other ECM fibers, and could be further expanded to tissue scale by incorporating these simulated fibers into three dimensional network models

Analysis of repetitive element DNA methylation by MethyLight

Repetitive elements represent a large portion of the human genome and contain much of the CpG methylation found in normal human postnatal somatic tissues. Loss of DNA methylation in these sequences might account for most of the global hypomethylation that characterizes a large percentage of human cancers that have been studied. There is widespread interest in correlating the genomic 5-methylcytosine content with clinical outcome, dietary history, lifestyle, etc. However, a high-throughput, accurate and easily accessible technique that can be applied even to paraffin-embedded tissue DNA is not yet available. Here, we report the development of quantitative MethyLight assays to determine the levels of methylated and unmethylated repeats, namely, Alu and LINE-1 sequences and the centromeric satellite alpha (Satα) and juxtacentromeric satellite 2 (Sat2) DNA sequences. Methylation levels of Alu, Sat2 and LINE-1 repeats were significantly associated with global DNA methylation, as measured by high performance liquid chromatography, and the combined measurements of Alu and Sat2 methylation were highly correlative with global DNA methylation measurements. These MethyLight assays rely only on real-time PCR and provide surrogate markers for global DNA methylation analysis. We also describe a novel design strategy for the development of methylation-independent MethyLight control reactions based on Alu sequences depleted of CpG dinucleotides by evolutionary deamination on one strand. We show that one such Alu-based reaction provides a greatly improved detection of DNA for normalization in MethyLight applications and is less susceptible to normalization errors caused by cancer-associated aneuploidy and copy number changes

Current-Induced Step Bending Instability on Vicinal Surfaces

We model an apparent instability seen in recent experiments on current induced step bunching on Si(111) surfaces using a generalized 2D BCF model, where adatoms have a diffusion bias parallel to the step edges and there is an attachment barrier at the step edge. We find a new linear instability with novel step patterns. Monte Carlo simulations on a solid-on-solid model are used to study the instability beyond the linear regime.Comment: 4 pages, 4 figure

Is adrenalectomy necessary during unilateral nephrectomy for Wilms Tumor? A report from the Children\u27s Oncology Group.

PURPOSE: To determine whether performing adrenalectomy at the time of nephrectomy for unilateral Wilms tumor impacts clinical outcome. METHODS: We reviewed information on all patients enrolled on National Wilms Tumor Study-4 and -5. Data were abstracted on patient demographics, tumor characteristics, surgical and pathologic status of the adrenal gland, and patient outcomes. The primary endpoints were intraoperative spill and five-year event-free survival (EFS) in patients who did or did not undergo adrenalectomy. RESULTS: Of 3825 patients with complete evaluable data, the adrenal was left in situ in 2264 (57.9%) patients, and was removed completely in 1367 patients (36.7%) or partially in 194 patients (5.2%). Of the adrenal glands removed, 68 (4.4%) contained tumor. Adrenal involvement was more common in patients with stage 3 (9.8%) than stage 2 disease (1.9%; p \u3c 0.0001). After controlling for stage and histopathology, five-year EFS was similar whether or not the adrenal gland was removed (p = 0.48), or involved with tumor (p = 0.81); however, intraoperative spill rates were higher in patients undergoing adrenalectomy (26.1% vs 15.5%, p \u3c 0.0001), likely due to larger tumor size or technical factors. No patient had clinical evidence of adrenal insufficiency or tumor recurrence in the adrenal gland during follow-up (median 9.9 years). CONCLUSIONS: Sparing the adrenal gland during nephrectomy for unilateral Wilms tumor was not associated with a higher incidence of intraoperative spill and was associated with a similar oncologic outcome, on a per-stage basis, with cases where the adrenal was removed. Thus, adrenalectomy should not be considered mandatory during radical nephrectomy for Wilms tumor

Genosenor Technology Development

Contains table of contents for Part IV, table of contents for Section 1, and reports on two research projects.Genometrix, Inc. Contract GMX-GH00776-04Defense Advanced Research Projects AgencyU.S. Air Force - Office of Scientific Researc

Serum Concentrations of Polychlorinated Biphenyls in Relation to in Vitro Fertilization Outcomes

Background: Human exposure to polychlorinated biphenyls (PCBs) remains widespread. PCBs have been associated with adverse reproductive health outcomes including reduced fecundability and increased risk of pregnancy loss, although the human data remain largely inconclusive

Reclutamiento de la merluza argentina, Merluccius hubbsi, del stock patagónico: una revisión de las principales características que afectan el potencial reproductivo y la supervivencia durante las primeras etapas de la vida

Understanding the causes that generate variability of recruitment in marine populations constitutes one of the greatest challenges in fishery science. Our predictive capacity to explain these variations is relatively low, due to the interaction of exogenous and endogenous factors, which vary across time and space within populations. In order to gain information on recruitment fluctuations of the Argentine hake (Merluccius hubbsi) from Patagonian stock, we reviewed the results obtained analyzing the reproductive ecology, trophic and energetic dynamics during different stages of development of this species, and its relationship with environmental variables. We observed that the reproductive potential is strongly influenced by characteristics of the parental stock, particularly females, in terms of their size, age and condition. This feature, called ‘maternal effect’, suggests that the spawning stock biomass, commonly used as an index of productivity in fishery assessment, is a poor predictor of recruitment. We also observed that survival during hake early life is affected by the spatial coincidence with the North Patagonian Frontal System, characterized by a high concentration of nutrients, high productivity, and food availability. Physical conditions and larval density in the nursery area affected the nutritional state and mortality of hake, mainly by competition for food or predation. It was observed that the transition of juveniles from pelagic to demersal habitat occurs over a longer period than previously recognized for this species, stressing the importance of using acoustic information to complement data from bottom trawls. This is one of the main topics to be further developed in order to estimate new recruitment indices for Argentine hake, along with other research items proposed to improve stock assessment.Comprender las causas que generan la variabilidad del reclutamiento en las poblaciones marinas constituye uno de los mayores desafíos de la ciencia pesquera. Nuestra capacidad predictiva para explicar estas variaciones es relativamente baja, debido a la interacción de factores exógenos y endógenos, que varían en el tiempo y el espacio dentro de las poblaciones. Con el fin de obtener información sobre las fluctuaciones en el reclutamiento de la merluza argentina (Merluccius hubbsi) del stock patagónico, revisamos los resultados obtenidos analizando la ecología reproductiva, la dinámica trófica y energética durante las diferentes etapas de desarrollo de esta especie y su relación con variables ambientales. Observamos que el potencial reproductivo está fuertemente influenciado por las características parentales, particularmente de las hembras, en cuanto a su tamaño, edad y condición. Esta característica, denominada “efecto materno”, sugiere que la biomasa de la población reproductora, comúnmente utilizada como índice de productividad en la evaluación de pesquerías, es un predictor deficiente del reclutamiento. También observamos que la supervivencia durante los primeros años de vida de la merluza se ve afectada por la coincidencia espacial con el Sistema Frontal Norpatagónico, caracterizado por una alta concentración de nutrientes, alta productividad y disponibilidad de alimento. Las condiciones físicas y la densidad larvaria en la zona de crianza afectaron el estado nutricional y la mortalidad de la merluza, principalmente por competencia por alimento o depredación. Se observó que la transición del hábitat pelágico al demersal en los juveniles se produce durante un período más extenso que el reconocido anteriormente para esta especie, lo que destaca la importancia de utilizar los registros acústicos para complementar la información de las redes de arrastre de fondo. Este es uno de los principales temas a desarrollar para estimar nuevos índices de reclutamiento de merluza argentina, junto con otras líneas de investigación propuestas para mejorar la evaluación del stock

Association of Hexachlorobenzene (HCB), Dichlorodiphenyltrichloroethane (DDT), and Dichlorodiphenyldichloroethylene (DDE) with in Vitro Fertilization (IVF) Outcomes

Background: Hexachlorobenzene (HCB), dichlorodiphenyltrichloroethane (DDT), and dichlorodiphenyldichloroethylene (DDE) are persistent chlorinated pesticides with endocrine activity that may adversely affect the early stages of human reproduction

Pseudomonas aeruginosa Adaptation to Lungs of Cystic Fibrosis Patients Leads to Lowered Resistance to Phage and Protist Enemies

Pathogenic life styles can lead to highly specialized interactions with host species, potentially resulting in fitness trade-offs in other ecological contexts. Here we studied how adaptation of the environmentally transmitted bacterial pathogen, Pseudomonas aeruginosa, to cystic fibrosis (CF) patients affects its survival in the presence of natural phage (14/1, ΦKZ, PNM and PT7) and protist (Tetrahymena thermophila and Acanthamoebae polyphaga) enemies. We found that most of the bacteria isolated from relatively recently intermittently colonised patients (1-25 months), were innately phage-resistant and highly toxic for protists. In contrast, bacteria isolated from long time chronically infected patients (2-23 years), were less efficient in both resisting phages and killing protists. Moreover, chronic isolates showed reduced killing of wax moth larvae (Galleria mellonella) probably due to weaker in vitro growth and protease expression. These results suggest that P. aeruginosa long-term adaptation to CF-lungs could trade off with its survival in aquatic environmental reservoirs in the presence of microbial enemies, while lowered virulence could reduce pathogen opportunities to infect insect vectors; factors that are both likely to result in poorer environmental transmission. From an applied perspective, phage therapy could be useful against chronic P. aeruginosa lung infections that are often characterized by multidrug resistance: chronic isolates were least resistant to phages and their poor growth will likely slow down the emergence of beneficial resistance mutations

H5N1 Whole-Virus Vaccine Induces Neutralizing Antibodies in Humans Which Are Protective in a Mouse Passive Transfer Model

BACKGROUND: Vero cell culture-derived whole-virus H5N1 vaccines have been extensively tested in clinical trials and consistently demonstrated to be safe and immunogenic; however, clinical efficacy is difficult to evaluate in the absence of wide-spread human disease. A lethal mouse model has been utilized which allows investigation of the protective efficacy of active vaccination or passive transfer of vaccine induced sera following lethal H5N1 challenge. METHODS: We used passive transfer of immune sera to investigate antibody-mediated protection elicited by a Vero cell-derived, non-adjuvanted inactivated whole-virus H5N1 vaccine. Mice were injected intravenously with H5N1 vaccine-induced rodent or human immune sera and subsequently challenged with a lethal dose of wild-type H5N1 virus. RESULTS: Passive transfer of H5N1 vaccine-induced mouse, guinea pig and human immune sera provided dose-dependent protection of recipient mice against lethal challenge with wild-type H5N1 virus. Protective dose fifty values for serum H5N1 neutralizing antibody titers were calculated to be ≤1∶11 for all immune sera, independently of source species. CONCLUSIONS: These data underpin the confidence that the Vero cell culture-derived, whole-virus H5N1 vaccine will be effective in a pandemic situation and support the use of neutralizing serum antibody titers as a correlate of protection for H5N1 vaccines