Commissural axon guidance in the developing spinal cord: from Cajal to the present day.

During neuronal development, the formation of neural circuits requires developing axons to traverse a diverse cellular and molecular environment to establish synaptic contacts with the appropriate postsynaptic partners. Essential to this process is the ability of developing axons to navigate guidance molecules presented by specialized populations of cells. These cells partition the distance traveled by growing axons into shorter intervals by serving as intermediate targets, orchestrating the arrival and departure of axons by providing attractive and repulsive guidance cues. The floor plate in the central nervous system (CNS) is a critical intermediate target during neuronal development, required for the extension of commissural axons across the ventral midline. In this review, we begin by giving a historical overview of the ventral commissure and the evolutionary purpose of decussation. We then review the axon guidance studies that have revealed a diverse assortment of midline guidance cues, as well as genetic and molecular regulatory mechanisms required for coordinating the commissural axon response to these cues. Finally, we examine the contribution of dysfunctional axon guidance to neurological diseases.

Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and Polyamidoamine Dendrimers.

Dendrimers provide a means to control the synthesis of gold nanoparticles and stabilize their suspensions. However, design of improved dendrimers for this application is hindered by a lack of understanding how the dendrimers and synthesis conditions determine nanoparticle morphology and suspension stability. In the present work, we evaluate the effect of polyamidoamine (PAMAM) dendrimers terminated with different functional groups (-OH or -NH3+) and different synthesis conditions on the morphology of the resulting gold nanoparticles and their stability in solution. We leverage molecular dynamics (MD) simulations to identify the atomic interactions that underlie adsorption of PAMAM dendrimers to gold surface and how the thermodynamics of this adsorption depends on the terminal functional groups of the dendrimers. We find that gold nanoparticles formed with hydroxyl-terminated PAMAM (PAMAM-OH) rapidly aggregate, whereas those formed with PAMAM-NH3+ are stable in solution for months of storage. Synthesis under ultrasound sonication is shown to be more rapid than that under agitation, with sonication producing smaller nanoparticles. Free-energy calculations in MD simulations show that all dendrimers have a high affinity for the gold surface, although PAMAM-OH and its oxidized aldehyde form (PAMAM-CHO) have a greater affinity for the nanoparticle surface than PAMAM-NH3+. Although adsorption of PAMAM-OH and PAMAM-CHO has both favorable entropy and enthalpy, adsorption of PAMAM-NH3+ is driven by a strong enthalpic component subject to an unfavorable entropic component.

Novel specific peptides as superior surface stabilizers for silver nano structures: role of peptide chain length.

Three new collagen mimetic peptides containing the CLK motif as anchoring arms were tested for silver nanoparticle surface stabilization. Our experimental and molecular dynamics data indicate that peptide length has an important effect not only in the resulting nanosilver's colloidal stability, but also in the biological performance of the composite.

Close encounters with DNA.

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Nipah virus outbreak with person-to-person transmission in a district of Bangladesh, 2007.

In February 2007 an outbreak of Nipah virus (NiV) encephalitis in Thakurgaon District of northwest Bangladesh affected seven people, three of whom died. All subsequent cases developed illness 7-14 days after close physical contact with the index case while he was ill. Cases were more likely than controls to have been in the same room (100% vs. 9.5%, OR undefined, P<0.001) and to have touched him (83% vs. 0%, OR undefined, P<0.001). Although the source of infection for the index case was not identified, 50% of Pteropus bats sampled from near the outbreak area 1 month after the outbreak had antibodies to NiV confirming the presence of the virus in the area. The outbreak was spread by person-to-person transmission. Risk of NiV infection in family caregivers highlights the need for infection control practices to limit transmission of potentially infectious body secretions.

Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore.

Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence--GAATTC--in the absence of a Mg(2+) ion cofactor. We have previously shown that there is a voltage threshold for permeation of DNA bound to restriction enzymes through a nanopore that is associated with a nanonewton force required to rupture the complex. By introducing mutations in the DNA, we now show that this threshold depends on the recognition sequence and scales linearly with the dissociation energy, independent of the pore geometry. To predict the effect of mutation in a base pair on the free energy of dissociation, MD is used to qualitatively rank the stability of bonds in the EcoRI-DNA complex. We find that the second base in the target sequence exhibits the strongest binding to the protein, followed by the third and first bases, with even the flanking sequence affecting the binding, corroborating our experiments.

Using measured pKa, LogP and solubility to investigate supersaturation and predict BCS class.

Ionization, lipophilicity and solubility have a profound influence on the transport properties of drug molecules. We will present an overview of why physicochemical properties are important, before discussing how the properties are related to each other. Findings are based on research in our own laboratories using our commercial instruments and software to measure the pKa, lipophilicity (LogP) and intrinsic solubility (LogS0) of 84 marketed ionizable drugs. In general, the most lipophilic molecules were the least soluble in water. Plots of LogP vs. LogS0 show results for these drugs clustered according to other properties, including melting point, number of H-bond donors and acceptors, ability to supersaturate, and BCS class. Molecules with high melting point tended to have a larger number of H-bond donors and acceptors, and to be less soluble than predicted from their LogP. Molecules with low melting point tended to have little H-bond donor capacity, and tended to be more soluble than predicted from their LogP. Molecules that could form supersaturated solutions tended to have higher melting points, and to be less soluble than predicted from their LogP. Molecules in BCS Classes I-III tended to cluster in different parts of the plot. It is proposed that comparing measured LogP and LogS0 of new molecules with these plots will facilitate a quick assessment of their likely BCS Class.

Risk factors for Nipah virus encephalitis in Bangladesh.

Nipah virus (NiV) is a paramyxovirus that causes severe encephalitis in humans. During January 2004, twelve patients with NiV encephalitis (NiVE) were identified in west-central Bangladesh. A case-control study was conducted to identify factors associated with NiV infection. NiVE patients from the outbreak were enrolled in a matched case-control study. Exact odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by using a matched analysis. Climbing trees (83% of cases vs. 51% of controls, OR 8.2, 95% CI 1.25-infinity) and contact with another NiVE patient (67% of cases vs. 9% of controls, OR 21.4, 95% CI 2.78-966.1) were associated with infection. We did not identify an increased risk for NiV infection among persons who had contact with a potential intermediate host. Although we cannot rule out person-to-person transmission, case-patients were likely infected from contact with fruit bats or their secretions.

Stretching and unzipping nucleic acid hairpins using a synthetic nanopore.

We have explored the electromechanical properties of DNA by using an electric field to force single hairpin molecules to translocate through a synthetic pore in a silicon nitride membrane. We observe a threshold voltage for translocation of the hairpin through the pore that depends sensitively on the diameter and the secondary structure of the DNA. The threshold for a diameter 1.5 < d < 2.3 nm is V > 1.5 V, which corresponds to the force required to stretch the stem of the hairpin, according to molecular dynamics simulations. On the other hand, for 1.0 < d < 1.5 nm, the threshold voltage collapses to V < 0.5 V because the stem unzips with a lower force than required for stretching. The data indicate that a synthetic nanopore can be used like a molecular gate to discriminate between the secondary structures in DNA.

SARS transmission in Vietnam outside of the health-care setting.

To evaluate the risk of transmission of SARS coronavirus outside of the health-care setting, close household and community contacts of laboratory-confirmed SARS cases were identified and followed up for clinical and laboratory evidence of SARS infection. Individual- and household-level risk factors for transmission were investigated. Nine persons with serological evidence of SARS infection were identified amongst 212 close contacts of 45 laboratory-confirmed SARS cases (secondary attack rate 4.2%, 95% CI 1.5-7). In this cohort, the average number of secondary infections caused by a single infectious case was 0.2. Two community contacts with laboratory evidence of SARS coronavirus infection had mild or sub-clinical infection, representing 3% (2/65) of Vietnamese SARS cases. There was no evidence of transmission of infection before symptom onset. Physically caring for a symptomatic laboratory-confirmed SARS case was the only independent risk factor for SARS transmission (OR 5.78, 95% CI 1.23-24.24).

Proteomic analyses of murine macrophages treated with Bacillus anthracis lethal toxin.

Bacillus anthracis is the etiological agent of anthrax and the bacterium produces a tripartite anthrax toxin composed of protective antigen (PA), lethal factor (LF) and edema factor (EF). PA represents the binding domain of the toxin and acts in concert with either LF, a metalloprotease, or EF, an adenylate cyclase, to form lethal toxin (LeTx) or edema toxin (EdTx), respectively. We analyzed the proteomics response of two murine macrophage cell lines (J774.1A and RAW264.7) following B. anthracis LeTx treatment to detect unique host proteins involved in anthrax infection using difference in-gel electrophoresis (DIGE) followed by nanoLC-MS for identification of the proteins. The comparative proteomics approach identified a set of proteins in each cell line that was consistently upregulated when the two macrophage cell lines were treated with LeTx. The upregulated proteins include those involved in energy metabolism, cytoskeleton structure and stress response. A subset of five proteins (ATP synthase beta subunit, beta-actin, Hsp70, vimentin, and Hsp60 homolog) was identified that were commonly upregulated in both cell lines. The proteomic data suggest the involvement of reactive oxygen species (ROS) in cell lysis as seen by the upregulation of proteins that lead to the production of ROS in both the cell lines used in our study. However, proteins that afford protection against ROS may play an important role in the survival of the macrophage to LeTx infection as shown by the differences in proteomic responses of the two cell lines to the action of LeTx. These identified proteins may have the potential to be used as biomarkers for diagnostics and therapeutics.

Evaluation of the protective effects of quinacrine against Bacillus anthracis Ames.

Bacillus anthracis has gained notoriety as a dangerous biological weapon because of its virulence and ability to produce highly resistant spores. In addition, the ability of this organism to produce plasmid-encoded edema toxin (EdTx) and lethal toxin (LeTx) plays a pivotal role in the pathogenesis of anthrax. In this study, the efficacy of quinacrine was evaluated against the effects of anthrax toxins in vitro and its ability to provide protection against challenge with B. anthracis Ames strain spores in an intranasal mouse and guinea pig model. Quinacrine protected murine macrophages in vitro against cytotoxicity and cAMP production induced by LeTx and EdTx, respectively, at concentrations of 40-80 microM, most likely by preventing acidification of the endosomes. However, animals dosed with human equivalent doses of quinacrine were not protected against respiratory spore challenge. The failure of quinacrine to provide protection against inhalation anthrax was attributed to our inability to attain inhibitory concentrations of the drug in the serum or tissues. After daily administration of 43.3 mg quinacrine to guinea pigs (300 g), serum levels after 96 h were only 9.9 microM, a concentration not sufficient to protect macrophages in vitro. Administration of high doses of quinacrine (86.6 mg/kg) was toxic to the animals. These results illustrate some of the difficulties in developing protective therapeutic strategies against inhalation anthrax even when antitoxic drugs appear effective in vitro.

High-voltage SPM oxidation of ZrN: materials for multiscale applications.

Scanning probe microscope (SPM) oxidation was used to form zirconium oxide features on 200 nm thick ZrN films. The features exhibit rapid yet controlled growth kinetics, even in contact mode with 70 V dc applied between the probe tip and substrate. The features grown for times longer than 10 s are higher than 200 nm, and reach more than 1000 nm in height after 300 s. Long-time oxidation experiments and selective etching of the oxides and nitrides lead us to propose that as the oxidation reaches the silicon substrate, delamination occurs with the simultaneous formation of a thin layer of new material at the ZrN/Si interface. High-voltage oxide growth on ZrN is fast and sustainable, and the robust oxide features are promising candidates for multiscale (nanometre-to-micrometre) applications.

Disseminated infection with Bartonella henselae as a cause of spontaneous splenic rupture.

A 65-year-old man developed massive hemoperitoneum secondary to spontaneous splenic rupture. Histopathological analysis of the spleen demonstrated necrotizing granulomas. Results of serological tests indicated infection with a species of Bartonella, and immunohistochemical staining established Bartonella henselae as the cause of splenitis. To our knowledge, this represents the first reported case of spontaneous splenic rupture caused by infection with a species of Bartonella.

Serologic evidence of Rickettsia akari infection among dogs in a metropolitan city.

OBJECTIVE: To determine whether dogs in New York, NY are naturally infected with Rickettsia akari, the causative agent of rickettsialpox in humans. DESIGN: Serologic survey. ANIMALS: 311 dogs. PROCEDURE: Serum samples were obtained from dogs as a part of a study on Rocky Mountain spotted fever and borreliosis or when dogs were examined at area veterinary clinics for routine care. Dog owners were asked to complete a questionnaire inquiring about possible risk factors at the time serum samples were obtained. Samples were tested for reactivity to spotted fever group rickettsiae by use of an enzyme immunoassay (EIA). Twenty-two samples for which results were positive were tested by use of an indirect immunofluorescence antibody (IFA) assay followed by confirmatory cross-absorption testing. RESULTS: Results of the EIA were positive for 24 (7.7%) dogs. A history of tick infestation and increasing age were significantly associated with whether dogs were seropositive. Distribution of seropositive dogs was focal. Seventeen of the 22 samples submitted for IFA testing had titers to R rickettsii and R akari; for 11 of these, titers to R akari were higher than titers to R rickettsii. Cross-absorption testing indicated that in 6 of 7 samples, infection was caused by R akari. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that dogs can be naturally infected with R akari. Further studies are needed to determine the incidence of R akari infection in dogs, whether infection is associated with clinical illness, and whether dogs can serve as sentinels for human disease.

Urban zoonoses caused by Bartonella, Coxiella, Ehrlichia, and Rickettsia species.

The last half of the 20th Century witnessed an increase in the occurrence and recognition of urban zoonoses caused by members of the genera Bartonella, Coxiella, Ehrlichia, and Rickettsia, all traditionally considered to be members of the family Rickettsiaceae. In recent years, new human pathogens (Bartonella elizabethae, Bartonella henselae, and Rickettsia felis) have been recognized in urban environments. Other newly recognized pathogens (Ehrlichia chaffeensis and Ehrlichia phagocytophila in the United States) have sylvan zoonotic cycles but are present in urban areas because their vertebrate hosts and associated ectoparasitic arthropod vectors are able to survive in cities. Still other agents, which were primarily of historical importance (Bartonella quintana) or have not traditionally been associated with urban environments (Rickettsia rickettsii), have been recognized as causes of human disease in urban areas. Some diseases that have traditionally been associated with urban environments, such as rickettsialpox (caused by Rickettsia akari) and murine typhus (caused by Rickettsia typhi), still occur in large cities at low or undetermined frequencies and often go undetected, despite the availability of effective measures to diagnose and control them. In addition, alternate transmission cycles have been discovered for Coxiella burnetii, Rickettsia prowazekii, and R. typhi that differ substantially from their established, classic cycles, indicating that the epidemiology of these agents is more complex than originally thought and may be changing. Factors leading to an increase in the incidence of illnesses caused by these bacteria in urban areas include societal changes as well as intrinsic components of the natural history of these organisms that favor their survival in cities. Transovarial and transstadial transmission of many of the agents in their arthropod hosts contributes to the highly focal nature of many of the diseases they cause by allowing the pathogens to persist in areas during adverse times when vertebrate amplifying hosts may be scarce or absent. Domesticated animals (primarily cats, dogs, and livestock) or commensal rodents [primarily Norway rats (Rattus norvegicus) and house mice (Mus musculus)] can serve as vertebrate amplifying hosts and bring these agents and their ectoparasitic arthropod vectors into direct association with humans and help maintain transmission cycles in densely populated urban areas. The reasons for the increase in these urban zoonoses are complex. Increasing population density worldwide, shifts in populations from rural areas to cities, increased domestic and international mobility, an increase in homelessness, the decline of inner-city neighborhoods, and an increase in the population of immunosuppressed individuals all contribute to the emergence and recognition of human diseases caused by these groups of agents. Due to the focal nature of infections in urban areas, control or prevention of these diseases is possible. Increased physician awareness and public health surveillance support will be required to detect and treat existing urban infections caused by these agents, to determine the disease burden caused by them, to design and implement control programs to combat and prevent their spread, and to recognize emerging or resurging infections caused by members of these genera as they occur.

Fort Chaffee revisited: the epidemiology of tick-borne rickettsial and ehrlichial diseases at a natural focus.

A retrospective cohort study was conducted among troops training at Fort Chaffee, Arkansas, from May through June 1997, to identify infections caused by tick-borne pathogens. Serum samples were tested by IFAs for antibodies to selected Rickettsia and Ehrlichia species and by an investigational EIA for spotted fever group Rickettsia lipopolysaccharide antigens. Of 1,067 guardsmen tested, 162 (15.2%) had antibodies to one or more pathogens. Of 93 guardsmen with paired serum samples, 33 seroconverted to Rickettsia rickettsii or spotted fever group rickettsiae (SFGR) and five to Ehrlichia species. Most (84.8%) of the personnel who seroconverted to SFGR were detected only by EIA, and seropositivity was significantly associated with an illness compatible with a tick-borne disease. In addition, 34 (27%) of 126 subjects with detectable antibody titers reported a compatible illness. The primary risk factor for confirmed or probable disease was finding > 10 ticks on the body. Doxycycline use and rolling up of long sleeves were protective against seropositivity. The risk of transmission of tick-borne pathogens at Fort Chaffee remains high, and use of the broadly reactive EIA suggests that previous investigations may have underestimated the risk for infection by SFGR. Measures to prevent tick bite and associated disease may require reevaluation.

Evidence of rodent-associated Bartonella and Rickettsia infections among intravenous drug users from Central and East Harlem, New York City.

We tested serum samples collected in 1997 and 1998 from a cohort of 204 injection drug users (IDUs) recruited from Central and East Harlem, New York City, New York, for antibodies reactive with seven rickettsial or Bartonella spp. antigens. Rodent-associated Bartonella elizabethae and Rickettsia akari were the primary etiologic agents of interest. The testing panel also included Bartonella henselae, Bartonella quintana, Rickettsia prowazekii, Rickettsia rickettsii, and Rickettsia typhi. The highest prevalence of seroreactive serum samples (46%) was found with B. elizabethae antigens; 10% of the samples reacted with B. henselae antigens, while 2% reacted with B. quintana antigens. Reactivity to the latter two antigens was likely due to cross-reactivity with B. elizabethae antigens in most instances. Among the spotted fever group rickettsiae, 18 (9%) samples reacted with R. akari, including 10 samples (5%) that also reacted with R. rickettsii. Cross-adsorption studies demonstrated that most of the spotted fever group rickettsiae antibodies were due to R. akari infections. Among the typhus group rickettsiae, 5 samples reacted weakly to R. prowazekii antigens, and no samples reacted with R. typhi antigens. These findings suggest that Harlem IDUs are commonly exposed to two rodent-associated zoonotic agents. Further study of IDU populations may help elucidate transmission cycles of these agents in inner cities where higher levels of transmission occur.

Detection of antibodies reactive with Ehrlichia chaffeensis in the raccoon.

Antibodies reactive with Ehrlichia chaffeensis were detected in raccoon (Procyon lotor) serum samples by using an indirect immunofluorescence assay. Samples from 411 raccoons trapped in the southeastern United States from 1977 to 1999 were tested. Serologically reactive samples with reciprocal titers of > or =16 were detected from 83 raccoons (20%) from 13 of 16 counties in eight states, indicating that raccoons are commonly exposed to E. chaffeensis. Samples collected as early as 1977 were positive. A polymerase chain reaction assay specific for E. chaffeensis failed to detect the presence of ehrlichial DNA in serum samples from 20 representative seroreactive raccoons. Because of serologic cross-reactivity among antigens derived from different Ehrlichia spp., additional immunologic, molecular, or culture-based studies will be required to confirm E. chaffeensis infections of raccoons in the southeastern United States.