Response to Frederic Bretzner et al. “Target Populations for First-In-Human Embryonic Stem Cell Research in Spinal Cord Injury”

We address concerns raised in this issue by Bretzner et al. (2011) by explaining the rationale for including subjects with subacute, neurologically complete spinal cord injuries in the Phase 1 trial of GRNOPC1. We also present elements of the informed consent process that minimize the likelihood of therapeutic misconception

Ecological condition of coastal ocean waters along the U.S. Mid-Atlantic Bight: 2006

In May 2006, the NOAA National Ocean Service (NOS), in conjunction with the EPA National Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters throughout the mid-Atlantic Bight (MAB) portion of the eastern U.S. continental shelf. The study area encompassed the region from Cape Cod, MA and Nantucket Shoals in the northeast to Cape Hatteras in the south, and was defined using a one nautical mile buffer of the shoreline extended seaward to the shelf break (~100-m depth contour). A total of 50 stations were targeted for sampling using standard methods and indicators applied in prior NOAA coastal studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna). Through coordination with the NOAA Fisheries Service/Northeast Fisheries Science Center (NFS/NEFSC), samples of summer flounder (Paralichthys dentatus) also were obtained from 30 winter 2007 bottom-trawl survey stations in overlapping portions of the study area and used for analysis of chemical-contaminant body burdens

Traumatic thoracic ASIA A examinations and potential for clinical trials

Study Design: Retrospective review of prospective database Objectives: To define the variability of neurologic examination and recovery after non-penetrating complete thoracic spinal cord injuries (ASIA A). Background Data: Neurologic examinations after SCI can be difficult and inconsistent. Unlike cervical SCI patients, alterations in thoracic (below T1) complete SCI (ASIA A – based on the ASIA Impairment Scale [AIS]) patients’ exams are based only on sensory testing, thus changes in the neurological level (NL) are determined only by sensory changes. Methods: A retrospective review of the placebo control patients in a multicenter prospective database utilized for the pharmacologic trial of Sygen. Patients were included if they had a complete thoracic SCI on initial evaluation, with completed ASIA examinations at follow-up weeks 4, 8, 16, 26 and 52. Specifically, pin prick (PP) and light touch (LT) were assessed and the absolute change was calculated as the number of spinal levels at a given observation time. Results 3165 patients were initially screened for the Sygen clinical trial, of which 57 were the control placebo patients used in this analysis. Alterations from the baseline exam (PP and LT) were fairly consistent and the median change/recovery in neurologic examination was one spinal level. Across all observations post-baseline, the average change for PP was 1.48 +/- 0.13 (mean +/- SE), and for LT, 1.40 +/-0.13. There were equal proportions of directional changes (none, improved, lost). Conclusions: Changes in a thoracic complete (ASIA A) SCI patient ASIA examination as measured through sensory modalities (PP/LT) are fairly uncommon. The overall examination had only 1-2 level variability across patients, indicating minimal change in the sensory exam over the follow-up period. Stability in the ASIA examination as measured through sensory modalities has thus been demonstrated over time, making it an excellent tool to monitor changes in neurologic function

Malaria Life Cycle Intensifies Both Natural Selection and Random Genetic Drift

Analysis of genome sequences of 159 isolates of Plasmodium falciparum from Senegal yields an extraordinarily high proportion (26.85%) of protein-coding genes with the ratio of nonsynonymous to synonymous polymorphism greater than one. This proportion is much greater than observed in other organisms. Also unusual is that the site-frequency spectra of synonymous and nonsynonymous polymorphisms are virtually indistinguishable. We hypothesized that the complicated life cycle of malaria parasites might lead to qualitatively different population genetics from that predicted from the classical Wright-Fisher (WF) model, which assumes a single random-mating population with a finite and constant population size in an organism with nonoverlapping generations. This paper summarizes simulation studies of random genetic drift and selection in malaria parasites that take into account their unusual life history. Our results show that random genetic drift in the malaria life cycle is more pronounced than under the WF model. Paradoxically, the efficiency of purifying selection in the malaria life cycle is also greater than under WF, and the relative efficiency of positive selection varies according to conditions. Additionally, the site-frequency spectrum under neutrality is also more skewed toward low-frequency alleles than expected with WF. These results highlight the importance of considering the malaria life cycle when applying existing population genetic tools based on the WF model. The same caveat applies to other species with similarly complex life cycles.Organismic and Evolutionary Biolog

Identification and Characterization of Small Molecule Inhibitors of a Class I Histone Deacetylase from Plasmodium falciparum

A library of approximately 2000 small molecules biased toward inhibition of histone deacetylases was assayed for antimalarial activity in a high-throughput P. falciparum viability assay. Active compounds were cross-analyzed for induction of histone hyperacetylation in a human myeloma cell line to identify HDAC inhibitors with selectivity for P. falciparum over the human host. To verify on-target selectivity, pfHDAC-1 was expressed and purified and a biochemical assay for pfHDAC-1 activity was established.Chemistry and Chemical Biolog

Ecological Condition of Coastal Ocean Waters within Stellwagen Bank National Marine Sanctuary: 2008

In June 2008, the NOAA National Ocean Service (NOS), in conjunction with the EPA National Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters within the boundaries of Stellwagen Bank National Marine Sanctuary (SBNMS). The sanctuary lies approximately 20 nautical miles east of Boston, MA in the southwest Gulf of Maine between Cape Ann and Cape Cod and encompassing 638 square nautical miles (2,181 km2). A total of 30 stations were targeted for sampling using standard methods and indicators applied in prior NOAA coastal studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna, fish tissue contaminant levels). Depths ranged from 31 – 137 m throughout the study area. About 76 % of the area had sediments composed of sands ( 80 % siltclay). About 70 % of the area (represented by 21 sites) had sediment total organic carbon (TOC) concentrations 50 mg/g). Surface salinities ranged from 30.6 – 31.5 psu, with the majority of the study region (approximately 80 % of the area) having surface salinities between 30.8 and 31.4 psu. Bottom salinities varied between 32.1 and 32.5 psu, with bottom salinities at all sites having values above the range of surface salinities. Surface-water temperatures varied between 12.1 and 16.8 ºC, while near-bottom waters ranged in temperature from 4.4 – 6.2 ºC. An index of density stratification (Δσt) indicated that the waters of SBNMS were stratified at the time of sampling. Values of Δσt at 29 of the 30 sites sampled in this study (96.7 % of the study area) varied from 2.1 – 3.2, which is within the range considered to be indicative of strong vertical stratification (Δσt > 2) and typical of the western Gulf of Maine in summer. Levels of dissolved oxygen (DO) were confined to a fairly narrow range in surface (8.8 – 10.4 mg/L) and bottom (8.5 – 9.6 mg/L) waters throughout the survey area. These levels are within the range considered indicative of good water quality (> 5 mg/L) with respect to DO. None of these waters had DO at low levels (< 2 mg/L) potentially harmful to benthic fauna and fish

Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal

Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs), use of rapid diagnostic tests (RDTs) for malaria detection, and deployment of artemisinin combination therapy (ACT). Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.Human Evolutionary BiologyOrganismic and Evolutionary Biolog

Ten-year safety of pluripotent stem cell transplantation in acute thoracic spinal cord injury.

OBJECTIVE: The purpose of this study was to evaluate the safety of oligodendrocyte progenitor cells (LCTOPC1) derived from human pluripotent stem cells administered between 7 and 14 days postinjury to patients with T3 to T11 neurologically complete spinal cord injury (SCI). The rationale for this first-in-human trial was based on evidence that administration of LCTOPC1 supports survival and potential repair of key cellular components and architecture at the SCI site. METHODS: This study was a multisite, open-label, single-arm interventional clinical trial. Participants (n = 5) received a single intraparenchymal injection of 2 × 106 LCTOPC1 caudal to the epicenter of injury using a syringe positioning device. Immunosuppression with tacrolimus was administered for a total of 60 days. Participants were followed with annual in-person examinations and MRI for 5 years at the time of this report and will be followed with annual telephone questionnaires for 6 to 15 years postinjection. The primary endpoint was safety, as measured by the frequency and severity of adverse events related to the LCTOPC1 injection, the injection procedure, and/or the concomitant immunosuppression administered. The secondary endpoint was neurological function as measured by sensory scores and lower-extremity motor scores as measured by the International Standards for Neurological Classification of Spinal Cord Injury examinations. RESULTS: No unanticipated serious adverse events related to LCTOPC1 have been reported with 98% follow-up of participants (49 of 50 annual visits) through the first 10 years of the clinical trial. There was no evidence of neurological decline, enlarging masses, further spinal cord damage, or syrinx formation. MRI results during the long-term follow-up period in patients administered LCTOPC1 cells showed that 80% of patients demonstrated T2 signal changes consistent with the formation of a tissue matrix at the injury site. CONCLUSIONS: This study provides crucial first-in-human safety data supporting the pursuit of future human embryonic stem cell-derived therapies. While we cannot exclude the possibility of future adverse events, the experience in this trial provides evidence that this cell type can be well tolerated by patients, with an event-free period of up to 10 years. Based on the safety profile of LCTOPC1 obtained in this study, a cervical dose escalation trial was initiated (NCT02302157)

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms