Identification of genetic risk factors for cerebellar mutism in pediatric brain tumor patients

Following posterior fossa surgery for resection of childhood medulloblastoma and primitive neuroectodermal tumor (M/PNET), cerebellar mutism (CM) may develop. This is a condition of absent or diminished speech in a conscious patient with no evidence of oral apraxia, which can be accompanied by other symptoms of the posterior fossa syndrome complex, which includes ataxia and hypotonia. Little is known about the etiology. Therefore, we conducted a SNP, gene, and pathway-level analysis to assess the role of host genetic variation on the risk of CM in M/PNET subjects following treatment. Cases (n= 20) and controls (n= 53) were recruited from the Childhood Cancer Epidemiology and Prevention Center, in Houston, TX. DNA samples were genotyped using the Illumina Human 1M Quad SNP chip. Ten pathways were identified from logistic regression used to identify the marginal effect of each SNP on CM risk. The minP test was conducted to identify associations between SNPs categorized to genes and CM risk. Pathways were assessed to determine if there was a significant enrichment of genes in the pathway compared to all other pathways. There were 78 genes that reached the threshold of min P ≤0.05 in 948 genes. The Neurotoxicity pathway was the most significant pathway after adjusting for multiple comparisons (q=0.040 and q=0.005, using Fisher's exact test and a test of proportions, respectively). Most genes within the Neurotoxicity pathway that reached a threshold of minP ≤0.05 were known to have an apoptosis function, possibly inducing neuronal apoptosis in the dentatothalamocortical pathway, and may be important in CM etiology in this population. This is the first study to assess the potential role of genetic risk factors on CM. As an exploratory study, these results should be replicated in a larger sample. ^

The role of suppressor factors in the regulation of immune responses by ultraviolet radiation -induced suppressor T lymphocytes

The purpose of these studies was to determine the role of suppressor factors (TsF) in the regulation of immune responses by ultraviolet radiation-induced suppressor T lymphocytes (Ts). The Ts were induced following epicutaneous sensitization with contact allergens to an unirradiated site on mice irradiated five days earlier with 40 kJ/m$\sp2$ UVB (280-320 nm) radiation. The spleens of such mice contain afferent, hapten-specific, Thy-1$\sp+$, Lyt-1$\sp+$,2$\sp-$ Ts that suppress in vivo contact hypersensitivity (CHS) and antibody responses and the in vitro generation of cytotoxic T lymphocytes (CTL). Four approaches were used to determine the role of TsF. First, lysates produced from sonically-disrupted Ts were injected i.v. into normal animals; they inhibited CHS in vivo in a nonspecific manner. The lysates suppressed the induction and elicitation of CHS, and they inhibited the in vitro generation of CTL. Lysates prepared from splenocytes obtained from unirradiated mice or UV-irradiated, unsensitized mice failed to inhibit either response. Second, supernatants from cultures containing Ts, normal syngeneic responder lymphocytes, and hapten-modified stimulator cells were injected i.v. into normal recipients. They inhibited the induction of CHS and did so in a hapten-specific manner. Cellular and kinetic requirements were observed for the generation of suppressive activity. Splenocytes from mice treated with Ts supernatants suppressed CHS when transferred into normal animals. The supernatants also suppressed the in vitro generation of specific CTL. Third, the TsF-specific B16G monoclonal antibody was tested for its ability to modulate the effects of UV radiation in vivo. The i.v. injection of B16G into UV-irradiated mice reduced the suppression of CHS. Splenocytes of B16G-treated mice transferred into normal recipients, and they suppressed CHS, indicating that the Ts were not depleted. Fourth, B16G was used to isolate a putative TsF by antibody immunoadsorbance. When the B16G-bound fraction was eluted and injected i.v. into normal animals, it suppressed CHS and represented a 900-fold enrichment of activity over the starting material, based on specific activity. By SDS-PAGE, the B16G-bound material contained nondisulfide-linked 45- and 50-kDa components. These results suggest that TsF may play an immunoregulatory role in CHS. The isolation of a UV radiation-induced TsF lends credence to the involvement of such molecules. ^

Benthic foraminifers, isotopes and varimax factors at DSDP Holes 72-517 and 72-518

Pliocene changes in the vertical water mass structure of the western South Atlantic are inferred from changes in benthic foraminiferal assemblages and stable isotopes from DSDP Holes 516A, 517, and 518. Factor analysis of 34 samples from Site 518 reveals three distinct benthic foraminiferal assemblages that have been associated with specific subsurface water masses in the modern ocean. These include a Nuttalides umbonifera assemblage (Factor 1) associated with Antarctic Bottom Water (AABW), a Globocassidulina subglobosa-Uvigerina peregrina assemblage (Factor 2) associated with Circumpolar Deep Water (CPDW), and an Oridorsalis umbonatus-Epistominella exigua assemblage associated with North Atlantic Deep Water (NADW). Bathymetric gradients in d13C between Holes 516A (1313 m), 517 (2963 m), and 518 (3944 m) are calculated whenever possible to monitor the degree of similarity and/or difference in the apparent oxygen utilization (AOU) of water masses located at these depths during the Pliocene. Changes in bathymetric d13C gradients coupled with benthic foraminiferal assemblages record fundamental changes in the vertical water mass structure of the Vema Channel during the Pliocene from 4.1 to 2.7 Ma. At Site 518, the interval from 4.1 to 3.6 Ma is dominated by the N. umbonifera (Factor 1) and O. umbonatus-E. exigua (Factor 3) assemblages. The d13C gradient between Holes 518 (3944 m) and 516A (1313 m) undergoes rapid oscillations during this interval though no permanent increase in the gradient is observed. However, d13C values at Site 518 are clearly lighter during this interval. These conditions may be related to increased bottom water activity associated with the re-establishment of the West Antarctic Ice Sheet in the late Gilbert Chron (-4.2 to 3.6 Ma) (Osborn et al., 1982). The interval from 3.6 to 3.2 Ma is marked by a dominance of the G. subglobosa-U. peregrina (Factor 2) assemblage and lack of a strong d13C gradient between Holes 518 (3944 m) and 516A (1313 m). We suggest that shallow circumpolar waters expanded to depths of a least 3944 m (Site 518) during this time. The most profound faunal and isotopic change occurs at 3.2 Ma, and is marked by dominance of the N. umbonifera (Factor 1) and O. umbonatus-E. exigua (Factor 3) assemblages, a 1.1 per mil enrichment in d18O, and a large negative increase in the d13C gradient between Holes 518 and 516A. These changes at Site 518 record the vertical displacement of circumpolar waters by AABW and NADW. This change in vertical water mass structure at 3.2 Ma was probably related to a global cooling event and/or final closure of the Central American seaway. A comparison of the present-day d13C structure of the Vema Channel with a reconstruction between 3.2 and 2.7 Ma indicates that circulation patterns during this late Pliocene interval were similar to those of the modern western South Atlantic.

The influence of environmental factors on the growth of lichens in the field

The majority of studies of the effects of environmental factors on lichen growth have been carried out in the field. Growth of lichens in the field has been measured as absolute growth rate (e.g., length growth, radial growth, diameter growth, area growth, or dry weight gain per unit of time) or as a relative growth rate, expressed per unit of thallus area or weight, e.g., thallus specific weight. Seasonal fluctuations in growth in the field often correlate best with changes in average or total rainfall or frequency of rain events through the year. In some regions of the world, temperature is also an important climatic factor influencing growth. Interactions between microclimatic factors such as light intensity, temperature, and moisture are particularly important in determining local differences in growth especially in relation to aspect and slope of rock surface, or height on a tree. Factors associated with the substratum including type, chemistry, texture, and porosity can all influence growth. In addition, growth can be influenced by the degree of nutrient enrichment of the substratum associated with bird droppings, nitrogen, phosphate, salinity, or pollution. Effects of environmental factors on growth can act directly to restrict species distribution or indirectly by altering the competitive balance among different species in a community.

Novel methodology for in situ carbon dioxide enrichment of benthic ecosystems

Future climate change will likely represent a major stress to shallow aquatic and coastal marine communities around the world. Most climate change research, particularly in regards to increased pCO2 and ocean acidification, relies on ex situ mesocosm experimentation, isolating target organisms from their environment. Such mesocosms allow for greater experimental control of some variables, but can often cause unrealistic changes in a variety of environmental factors, leading to “bottle effects.” Here we present an in situ technique of altering dissolved pCO2within nearshore benthic communities (e.g., macrophytes, algae, and/or corals) using submerged clear, open-top chambers. Our technique utilizes a flow-through design that replicates natural water flow conditions and minimizes caging effects. The clear, open-top design additionally ensures that adequate light reaches the benthic community. Our results show that CO2 concentrations and pH can be successfully manipulated for long durations within the open-top chambers, continuously replicating forecasts for the year 2100. Enriched chambers displayed an average 0.46 unit reduction in pH as compared with ambient chambers over a 6-month period. Additionally, CO2 and HCO3 – concentrations were all significantly higher within the enriched chambers. We discuss the advantages and disadvantages of this technique in comparison to other ex situ mesocosm designs used for climate change research.

Swimming against the tide: A study of a youth enrichment program seeking to empower inner-city Black youth

Serious inequities in our K-12 public education system, particularly in regard to the quality of education in predominately Black inner-city schools, are well-documented in the literature (Freeman, 1998; Ross, 1998). Moreover, there is general agreement that the most effective means of ameliorating that situation is through well-thought-out after-school programs and partnership initiatives (Beck, 1993; Gardner et al., 2001). ^ The purpose of this qualitative study was to examine the programmatic interventions of a youth enrichment program for inner-city Black youth currently in place at the Overtown Youth Center (OYC) in Miami, Florida, in order to: (a) discern those factors that support its claim that it is making a difference in students’ lives, (b) explore how any such factors are implemented, and (c) determine whether its interventions have served to equalize the playing field for these youth. ^ Two primary methods of data collection were used for this study. The first was participant observation conducted over the course of two years through a partnership initiative established and led by this author. The second was through in-depth interviews of the Center’s founder, staff, and students. Secondary methods used were the recording of informal conversations and the analysis of written documents. ^ Analysis of the data yielded four features of the Center that are indispensible to the students’ growth. The center provides the youth with (a) physical and psychological safety, (b) supportive relationships, (c) exposure to cultural and educational opportunities, and (d) assistance in building self-esteem. ^ The most significant finding of the study was that OYC has been successful at making a difference in students’ lives and at increasing their aspirations to attend college. By addressing the full spectrum of their needs, the Center has given them many of the necessary tools with which to compete and thereby helped equalize their opportunities to succeed in school and in life. ^ The study also noted a number of challenges for the Center to examine. The main issues that need to be addressed more seriously are staff turnover, staff indifference, nepotism, inconsistent student attendance, and insufficient focus on racial issues and African-American-centered education. Meeting those challenges would engender even greater positive outcomes.^

Indirect and direct controls of macroinvertebrates and small fish by abiotic factors and trophic interactions in the Florida Everglades

1. The roles of nutrients, disturbance and predation in regulating consumer densities have long been of interest, but their indirect effects have rarely been quantified in wetland ecosystems. The Florida Everglades contains gradients of hydrological disturbance (marsh drying) and nutrient enrichment (phosphorus), often correlated with densities of macroinvertebrate infauna (macroinvertebrates inhabiting periphyton), small fish and larger invertebrates, such as snails, grass shrimp, insects and crayfish. However, most causal relationships have yet to be quantified. 2.  We sampled periphyton (content and community structure) and consumer (small omnivores, carnivores and herbivores, and infaunal macroinvertebrates inhabiting periphyton) density at 28 sites spanning a range of hydrological and nutrient conditions and compared our data to seven a priori structural equation models. 3.  The best model included bottom-up and top-down effects among trophic groups and supported top-down control of infauna by omnivores and predators that cascaded to periphyton biomass. The next best model included bottom-up paths only and allowed direct effects of periphyton on omnivore density. Both models suggested a positive relationship between small herbivores and small omnivores, indicating that predation was unable to limit herbivore numbers. Total effects of time following flooding were negative for all three consumer groups even when both preferred models suggested positive direct effects for some groups. Total effects of nutrient levels (phosphorus) were positive for consumers and generally larger than those of hydrological disturbance and were mediated by changes in periphyton content. 4.  Our findings provide quantitative support for indirect effects of nutrient enrichment on consumers, and the importance of both algal community structure and periphyton biomass to Everglades food webs. Evidence for top-down control of infauna by omnivores was noted, though without substantially greater support than a competing bottom-up-only model.

Effect of Termination of Long-term Free Air CO2 Enrichment on Physiology and Carbon Allocation in a Loblolly Pine Dominated Forest

This dissertation examined the response to termination of CO2 enrichment of a forest ecosystem exposed to long-term elevated atmospheric CO2 condition, and aimed at investigating responses and their underlying mechanisms of two important factors of carbon cycle in the ecosystem, stomatal conductance and soil respiration. Because the contribution of understory vegetation to the entire ecosystem grew with time, we first investigated the effect of elevated CO2 on understory vegetation. Potential growth enhancing effect of elevated CO2 were not observed, and light seemed to be a limiting factor. Secondly, we examined the importance of aerodynamic conductance to determine canopy conductance, and found that its effect can be negligible. Responses of stomatal conductance and soil respiration were assessed using Bayesian state space model. In two years after the termination of CO2 enrichment, stomatal conductance in formerly elevated CO2 returned to ambient level, while soil respiration became smaller than ambient level and did not recovered to ambient in two years.

The response of surf-zone phytoplankton to nutrient enrichment (Cassino Beach, Brazil)

To understand the mechanisms that trigger changes in chlorophyll a and species composition in the phytoplankton of the surf-zone at Cassino Beach (RS), we performed two short nutrient-enrichment experiments (4–5 days each) during the summer and winter of 2010. Seawater was incubated under controlled conditions of temperature (summer 25± 3 °C, winter 18±1 °C), salinity (summer 28, winter 26) and irradiance (100 μmol m−2 s−1 ). Dissolved inorganic nutrients were added in various concentrations in the summer (silicate, Si; nitrate, N; phosphate, P) and winter (N, P) experiments. Samples were taken daily for cell counts and chlorophyll a analysis. In both experiments, chlorophyll a values and cell density showed a significant increase (mainly diatoms) in the treatments with nitrate addition, regardless of the proportion added. In the summer experiment, the largest chlorophyll a increase, approximately threefold (31.5 to 89.5 μg L−1 ), was observed in the NP treatment due to the growth of Asterionellopsis glacialis (Castracane) Round, Skeletonema tropicum Cleve, Thalassiosira sp. Cleve and Pseudo-nitzschia spp. Peragallo. The maximum growth was obtained in the SiNP treatment for S. tropicum (μ=0.7), Thalassiosira (μ= 1.9) and Pseudo-nitzschia (μ= 1.3) and in the SiN treatment for A. glacialis (μ= 1.0). In the winter experiment, the chlorophyll a content increased 4.2 and 5.5 times, respectively, in the N and NP treatments (maxima 38.8 μg L−1 and 31.5 μg L−1 ), where A. glacialis (μ= 1.7–1.9) and Cylindrotheca closterium (Ehrenberg) Reimann & J.C. Lewin (μ= 1.0–1.96) showed the highest amount of growth. These results indicate that nitrate is the most important nutrient controlling phytoplankton chlorophyll a at sandy Cassino Beach. However, the responses of different species to enrichment during the summer and winter indicated that other factors also played a role. A. glacialis, present during both seasons, presented the highest growth rate during the winter, whereas during the summer it was independent of nutrient enrichment but coincided with the lowest growth of S. tropicum. This finding suggested the occurrence of allelopathic interactions between these species. During the summer, multi-enrichment (SiNP) favoured the best growth of S. tropicum, Pseudo-nitzschia spp. and Thalassiosira sp. These results indicated that the phytoplankton composition and diversity in the surf zone of Cassino Beach are shaped by the availability of silicate and phosphorus as well as by the availability of nitrate.

Dispersive liquid–liquid microextraction for metals enrichment: A useful strategy for improving sensitivity of laser-induced breakdown spectroscopy in liquid samples analysis

A rapid and efficient Dispersive Liquid–Liquid Microextraction (DLLME) followed by Laser-Induced Breakdown Spectroscopy detection (LIBS) was evaluated for simultaneous determination of Cr, Cu, Mn, Ni and Zn in water samples. Metals in the samples were extracted with tetrachloromethane as pyrrolidinedithiocarbamate (APDC) complexes, using vortex agitation to achieve dispersion of the extractant solvent. Several DLLME experimental factors affecting extraction efficiency were optimized with a multivariate approach. Under optimum DLLME conditions, DLLME-LIBS method was found to be of about 4.0–5.5 times more sensitive than LIBS, achieving limits of detection of about 3.7–5.6 times lower. To assess accuracy of the proposed DLLME-LIBS procedure, a certified reference material of estuarine water was analyzed.