Extraction algorithms for cortical control of arm prosthetics

Now that recordings of multiple, individual action potentials are being made with chronic electrodes, it seems that previous work showing simple encoding of movement parameters in these spike trains can be used as a real-time control signal for prosthetic arms. Efficient extraction algorithms can compensate for the limited ensemble sample acquired with this emerging technology.     

Adaptation to phosphate deprivation in osteoblast-like cells

The rat osteosarcoma cell line UMR-106–01 has an osteoblast-like phenotype. When grown in monolyer culture these cells transport inroganic phosphate and L-alanine via Na⁺-dependent transport systems. Exposure of these cells to a low phosphate medium for 4 h produced a 60–70 per cent increase in Na⁺-dependent phosphate uptake compared to control cells maintained in medium with a normal phosphate concentration. In contrast, Na⁺-dependent alanine uptake and Na⁺-independent phosphate uptake were not changed during phosphate deprivation. The increased phosphate uptake was due, in part, to an increased V_max and was blocked completely by pretreatment with cycloheximide (70 μM). In these cells recovery of intracellular pH after acidification with NH₄Cl is due primarily to the Na⁺/H⁺ exchange system. The rate of this recovery process, monitored with a pH sensitive indicator (BCECF), was decreased by more than 50 per cent in phosphate-deprived cells compared to controls indicating that Na⁺/H⁺ exchange was inhibited during phosphate deprivation.     

Broad-scale geographic patterns in the distribution of vertically-transmitted, asexual endophytes in four naturally-occurring grasses in Sweden

The presence and distribution of vertically-transmitted, asexual Neotyphodium/Epichloë endophytes in four species of widely distributed grasses, all members of the sub-family Pooideae, were determined at 57 spatially-distinct sites across Sweden in naturally-occurring grass populations. While these endophytes are well-studied in agricultural systems, much less is known about their abundance and distribution in non-agricultural systems at larger scales across landscapes. We used two screening methods to detect endophytes: 1) visual inspection of fixed, stained grass shoots, and 2) immunoblot cards with monoclonal antibodies specific for Neotyphodium / Epichloë endophytes. Infection frequency (i.e. the proportion of individuals) varied widely among species and among sites, a finding common to most studies performed in non-agricultural ecosystems. Festuca rubra had the highest overall infection frequency (23% visual screening, 27% immunoblot screening), while Deschampsia flexuosa (4%) and Poa trivialis (4%) had low frequencies of infection. None of the sampled Agrostis capillaris populations were infected. In F. rubra , the within-site infection frequency varied from 0 to 100%. A significant altitudinal gradient was found for F. rubra , with the infection frequency of the vertically-transmitted endophyte Epichloë festucae decreasing with increasing altitude above sea level. The high variation across and within grass species at different geographical locations that ours and others' studies reveal, agree with suggestions that agronomic model systems cannot be readily extrapolated to understand the ecological role of endophytes in native grasses in the wild. Further investigation into the underlying cause of the observed altitudinal gradient is required to understand broader-scale patterns in the distribution of endophyte-infected grasses.     

Neuropeptide modulation of microcircuits

Neuropeptides provide functional flexibility to microcircuits, their inputs and effectors by modulating presynaptic and postsynaptic properties and intrinsic currents. Recent studies have relied less on applied neuropeptide and more on their neural release. In rhythmically active microcircuits (central pattern generators, CPGs), recent studies show that neuropeptide modulation can enable particular activity patterns by organizing specific circuit motifs. Neuropeptides can also modify microcircuit output indirectly, by modulating circuit inputs. Recently elucidated consequences of neuropeptide modulation include changes in motor patterns and behavior, stabilization of rhythmic motor patterns and changes in CPG sensitivity to sensory input. One aspect of neuropeptide modulation that remains enigmatic is the presence of multiple peptide family members in the same nervous system and even the same neurons.     

The chemical interactions underlying tomato flavor preferences

Although human perception of food flavors involves integration of multiple sensory inputs, the most salient sensations are taste and olfaction. Ortho- and retronasal olfaction are particularly crucial to flavor because they provide the qualitative diversity so important to identify safe versus dangerous foods. Historically, flavor research has prioritized aroma volatiles present at levels exceeding the orthonasally measured odor threshold, ignoring the variation in the rate at which odor intensities grow above threshold. Furthermore, the chemical composition of a food in itself tells us very little about whether or not that food will be liked. Clearly, alternative approaches are needed to elucidate flavor chemistry. Here we use targeted metabolomics and natural variation in flavor-associated sugars, acids, and aroma volatiles to evaluate the chemistry of tomato fruits, creating a predictive and testable model of liking. This nontraditional approach provides novel insights into flavor chemistry, the interactions between taste and retronasal olfaction, and a paradigm for enhancing liking of natural products. Some of the most abundant volatiles do not contribute to consumer liking, whereas other less abundant ones do. Aroma volatiles make contributions to perceived sweetness independent of sugar concentration, suggesting a novel way to increase perception of sweetness without adding sugar.     

Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease

The relative abundance of different groups of sulphate-reducing bacteria (SRB) in faecal DNA collected before and after therapy from patients suffering from Crohn's disease (CD), irritable bowel syndrome (IBS) or ulcerative colitis (UC) has been compared with that from healthy controls. Growth tests revealed that SRB were not more abundant in samples from patients with CD before treatment than in the healthy control group. For most of the 128 samples available, these preliminary results were confirmed using degenerate PCR primers that amplify the dsrAB gene. However, some samples from patients with CD before treatment contained a growth inhibitor that was absent from IBS or UC samples. In-depth sequencing of PCR-generated dsrB fragments revealed that the diversity detected was surprisingly low, with only eight strains of SRB and the sulphite-reducing bacterium, Bilophila wadsworthia, detected above the 0.1% threshold. The proportion of the two major species detected, B. wadsworthia and Desulfovibrio piger, was as high as 93.5% of the total SRB population in the healthy control group and lower in all patient groups. Four previously undescribed species were found: it is impossible to predict whether they are sulphate or sulphite-reducing bacteria.     

Antibody-Dependent Cellular Cytotoxicity-Mediating Antibodies from an HIV-1 Vaccine Efficacy Trial Target Multiple Epitopes and Preferentially Use the VH1 Gene Family

The ALVAC-HIV/AIDSVAX-B/E RV144 vaccine trial showed an estimated efficacy of 31%. RV144 secondary immune correlate analysis demonstrated that the combination of low plasma anti-HIV-1 Env IgA antibodies and high levels of antibody-dependent cellular cytotoxicity (ADCC) inversely correlate with infection risk. One hypothesis is that the observed protection in RV144 is partially due to ADCC-mediating antibodies. We found that the majority (73 to 90%) of a representative group of vaccinees displayed plasma ADCC activity, usually (96.2%) blocked by competition with the C1 region-specific A32 Fab fragment. Using memory B-cell cultures and antigen-specific B-cell sorting, we isolated 23 ADCC-mediating nonclonally related antibodies from 6 vaccine recipients. These antibodies targeted A32-blockable conformational epitopes (n = 19), a non-A32-blockable conformational epitope (n = 1), and the gp120 Env variable loops (n = 3). Fourteen antibodies mediated cross-clade target cell killing. ADCC-mediating antibodies displayed modest levels of V-heavy (VH) chain somatic mutation (0.5 to 1.5%) and also displayed a disproportionate usage of VH1 family genes (74%), a phenomenon recently described for CD4-binding site broadly neutralizing antibodies (bNAbs). Maximal ADCC activity of VH1 antibodies correlated with mutation frequency. The polyclonality and low mutation frequency of these VH1 antibodies reveal fundamental differences in the regulation and maturation of these ADCC-mediating responses compared to VH1 bNAbs.     

Microbial and Geochemical Assessment of Bauxitic Un-mined and Post-mined Chronosequence Soils from Mocho Mountains, Jamaica

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20?years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.     

A novel pollination mode,saprocantharophily, in Duguetia cadaverica (Annonaceae): A stinkhorn (Phallales) flower mimic

Duguetia cadaverica (Annonaceae), a small understory tree of humid primary forest from the Guianas to Pará state, Brazil, unites several unusual blossom and floral characters such as flagelliflory and putrid-smelling flowers, respectively. The few pollination studies conducted in the large genus Duguetia have shown that species are usually cantharophilous, pollinated by either small (mostly Nitidulidae) or large specialized dynastid (Scarabaeidae) beetles. Foul-smelling flowers are a novelty within the genus, and to better understand their significance, we undertook a study of the reproductive biology and flower scent chemistry of D. cadaverica. In a primary forest of French Guiana, we observed and measured morphology and phenology of trees and flowers; additionally, flower pollination chamber temperature was measured and insect visitors to flowers observed. Flower scent was collected in situ and later analyzed in the laboratory by GC–MS. Flowers are visited by small beetles of a single Pycnocnemus species (Nitidulidae), which are the only insects observed to enter the pollination chamber. Moreover, flowers evince a rhythm in sexual stage, scent emission and temperature, which finds correspondence in behavioral characters of the putative nitidulid pollinator, such as timing of entry and exit from the pollination chamber. Floral scent analysis revealed an unusual, previously undescribed combination of chemical odor classes. The earthy, rank flower scent contained 18 compounds, among them fatty acid derivatives, terpenoids and N- and S-bearing compounds. The most abundant volatiles were 1-octen-3-ol, 3-octanone, and (E)-2-octenol, which are characteristic earthy odors of fungi; additionally, there were sulfides and 4-methylpentanoic acid, which are molecules associated with carcass and cheese odors, respectively.