Founder effects in the assessment of HIV polymorphisms and HLA allele associations

Escape from T cell-mediated immune responses affects the ongoing evolution of rapidly evolving viruses such as HIV. By applying statistical approaches that account for phylogenetic relationships among viral sequences, we show that viral lineage effects rather than immune escape often explain apparent human leukocyte antigen (HLA)-mediated immune-escape mutations defined by older analysis methods. Phylogenetically informed methods identified immune-susceptible locations with greatly improved accuracy, and the associations we identified with these methods were experimentally validated. This approach has practical implications for understanding the impact of host immunity on pathogen evolution and for defining relevant variants for inclusion in vaccine antigens.     

Arsenic mobility and groundwater extraction in Bangladesh

High levels of arsenic in well water are causing widespread poisoning in Bangladesh. In a typical aquifer in southern Bangladesh, chemical data imply that arsenic mobilization is associated with recent inflow of carbon. High concentrations of radiocarbon-young methane indicate that young carbon has driven recent biogeochemical processes, and irrigation pumping is sufficient to have drawn water to the depth where dissolved arsenic is at a maximum. The results of field injection of molasses, nitrate, and low-arsenic water show that organic carbon or its degradation products may quickly mobilize arsenic, oxidants may lower arsenic concentrations, and sorption of arsenic is limited by saturation of aquifer materials.     

Antinociceptive effects of levomethadone in standing horses sedated with romifidine

ObjectiveTo evaluate the antinociceptive effect of a bolus of intravenous levomethadone administered to horses during romifidine constant rate infusion (CRI).Study designProspective, randomized, masked, crossover experimental study.AnimalsA group of eight adult Warmblood horses (seven geldings, one mare) aged 6.6 ± 4.4 years, weighing 548 ± 52 kg [mean ± standard deviation (SD)].MethodsLevomethadone 0.1 mg kg^–1 or an equivalent volume of saline (control) was administered intravenously to standing horses 60 minutes after starting a romifidine CRI. Blood samples to quantify romifidine and levomethadone plasma concentrations by capillary electrophoresis were collected up to 150 minutes after levomethadone administration. The nociceptive withdrawal reflex threshold (NWRT) was determined continuously using an automated threshold tracking device. Sedation and cardiopulmonary variables were assessed at regular intervals. A pharmacokinetic-pharmacodynamic (PK-PD) model was elaborated. Data are presented as mean ± SD or median (interquartile range, 25%–75%) where appropriate. Differences between groups were considered statistically significant for p < 0.05.ResultsHorses exhibited higher NWRTs after levomethadone administration than after saline (123 ± 9% versus 101 ± 9% relative to baseline, p < 0.05). The PK-PD model identified a contribution of levomethadone to the NWRT increase. Effect size was variable among individuals. No adverse reactions to levomethadone administration were observed. A slight effect of levomethadone on sedation scores was evident for the 60 minutes following its administration.Conclusions and Clinical RelevanceA single injection of levomethadone has the potential to increase the NWRT during romifidine CRI in horses and can be administered in combination with α₂-adrencoceptor agonists to enhance antinociception in horses. However, individual variation is marked.     

Biomass production of Lolio‐Cynosuretum grassland is not increased by plant‐species richness

In experimental grasslands, a positive relationship between biomass production and plant diversity has often been found. Here, we compared a moderately species‐rich old sward with its grass‐dominated counterpart (12 vs. 8 species per 2.5 m², or 8.3 vs. 0.7% yield proportion of dicots at the start of the experiment) established by herbicide application. We hypothesized an increased N, P and K uptake in the diverse sward related to a higher colonization rate with arbuscular mycorrhizal fungi (AMF), the presence of legumes, and complementary nutrient use of plant species. Phosphorus or N fertilizer application (according to contributions of AMF or legumes) were expected to balance the assumed smaller biomass production of the grass compared to the diverse sward. In two experimental years, N, P and K uptake, biomass production, N₂ fixation, and intra‐ and extraradical AMF colonization were investigated in an untreated control and plots that were fertilized with P and N in a low (P1: 20 kg P ha^?1; N1: 50 kg N ha^?1) or a high dose (P2: 100 kg P ha^?1; N2: 500 kg N ha^?1) in both swards. Biomass production was larger in the grass compared to the diverse sward. The N, P and K uptake, accumulated over three harvests (or 1.5 years), was also larger in the grass sward. The biomass production ranged from 5.3 to 10.0 t ha^?1 and accumulated nutrient uptake from 82 to191 kg N ha^?1, 19 to 31 kg P ha^?1 and 112 to 221 kg K ha^?1. Small legume proportions resulted in an accumulated N₂ fixation between 0 and 3 kg ha^?1. In the second year, the root length colonized with AMF structures was larger in the diverse compared to the grass sward, and the root length colonized with arbuscules and coils was larger in the N2 treatment compared to the control in the diverse sward. There were hints to higher AMF abundance under conditions of limited P availability (low soil P content, high N:P ratio in plant biomass). We conclude that in semi‐natural grassland of moderate species richness several factors may affect the relationship between plant diversity and productivity, i.e., management, plant species identity, and the number of the plant species of the low‐diversity level.     

An acetylenic alkaloid from the calcareous sponge Leucetta sp

A new acetylenic alkaloid was isolated from the sponge Leucetta sp. The structure was established by analyzing spectroscopic data. The alkaloid showed cytotoxicity IC₅₀ 2.5 μg/mL against NBT-T2 cells.     

Color and surface chemistry changes of extracted wood flour after heating at 120 °C

To investigate the effect of heat on color and surface chemistry of wood flour (WF), unextracted, extracted and delignified samples of commercial WF were heated at 120 °C for 24 h and analyzed by colorimetry, diffuse reflectance visible (DRV), attenuated total reflectance Fourier transform infrared (ATR-FTIR) and Fourier transform Raman (FT-Raman) spectroscopies. Unextracted samples showed a slight increase in CIEL^*a^*b^* color coordinates, a ^* and b ^*. Compared with unextracted samples, color changes of the extracted samples varied with composition of the extraction solvents with generally smaller increases in a ^* and larger decreases in b ^* values. Delignified samples were marked by even larger increases in both a ^* and b ^* values. The color changes could be explained by analysis of the respective DRV, FTIR and FT-Raman spectra of the samples before and after heating. Heating of the extracted WF at 120 °C resulted in a red shift of the absorption at 430 nm and increase in absorption in the violet-blue spectral region of visible light. Delignified samples showed even more pronounced absorption in this spectral region after heating.     

Biofilm development within a larval rearing tank of the tropical rock lobster, Panulirus ornatus

The role of bacterial biofilms in disease processes is becoming increasingly recognised in both clinical and environmental settings. Biofilm development within a rearing tank of the tropical rock lobster Panulirus ornatus was studied to evaluate if the biofilm is a reservoir for potentially pathogenic bacteria that cause mass larval mortalities. Within a 5000 L larval rearing tank, fiberglass microscope slides were systematically distributed during a standard rearing attempt to assess biofilm development. Culture-based counts for two media types, TCBS and Marine Agar (MA), demonstrated increased bacterial densities until days 11 and 13 respectively. For both media types, a drop in the plate counts was followed by a subsequent increase towards the end of the experiment. Scanning electron microscopy (SEM) confirmed that cell densities decreased between days 13 and 17, most likely due to sloughing of the biofilm into the water column. SEM images revealed distinct changes in dominant morphologies reflecting a succession of bacterial populations. A dynamic succession of microbial species during biofilm development was also demonstrated using denaturing gradient gel electrophoresis (DGGE) profiling of bacterial 16S rRNA genes in combination with statistical ordination analysis. Prominent changes in the DGGE profiles coincided with the decrease in bacterial numbers observed by SEM and plating on MA between days 13 and 17. Fluorescence in situ hybridization (FISH) identified -Proteobacteria as being numerically abundant in the biofilm. This was supported by results from DGGE analysis, which retrieved only sequences affiliated with - and γ-Proteobacteria. DGGE bands affiliated with Vibrio became dominant towards the end of the larval run (days 21 to 24). A Vibrio harveyi strain isolated from the biofilm late in the larval rearing trial (day 24) demonstrated increased larval mortality in small scale phyllosoma survival studies. The detection of Vibrionaceae at the end of the larval trial coincided with mass phyllosoma mortality and show that the biofilm is a reservoir for potentially pathogenic bacteria.     

Fillet shelf-life of Atlantic halibut Hippoglossus hippoglossus L. fed elevated levels of α-tocopheryl acetate

Fish fillet quality may be influenced by the antioxidant level in preslaughter diet. Thus, the effects of dietary α‐tocopheryl acetate supplementation and feeding time on the flesh quality of farmed Atlantic halibut Hippoglossus hippoglossus L. were investigated. Halibut of mean initial weight of 312 ± 12.3 g were divided into two groups and fed commercial diets, supplemented with different levels of α‐tocopheryl acetate at the dietary inclusion levels of 189 and 613 mg kg^?1 diet. Fish were sampled after 6,9,12 and 24 weeks. Over the experimental period, they reached a final mean weight of 1320 ± 108.4 g. Tissue α‐tocopherol of fillet and liver was significantly affected by the levels of α‐tocopheryl acetate given with the diets (P < 0.001). In storage on ice, fillets of fish fed the diets high in α‐tocopheryl acetate exhibited significantly lower (P < 0.001) levels of lipid oxidation. The colour of fillets in all groups deteriorated slightly, but diet did not affect this process. Halibut fed the supplemented diets for longer periods were better protected against lipid oxidation (P < 0.001) and colour deterioration (P < 0.01) than those fed for shorter periods. However, after 9 days of storage, lipid oxidation levels were still extremely low [< 0.6 µg malondialdehyde (MDA) g^?1 fillet], even in fillets of fish fed the low α‐tocopheryl acetate diet for a short period preslaughter. Different slaughtering methods tested at the end of the trial showed that percussive stunning can delay the onset of rigor mortis by 8–12 h compared with bleeding of the fish. These results suggest that halibut fillets have enhanced shelf‐life stability even at low doses of dietary α‐tocopheryl acetate, and that other factors in the antioxidant defence mechanisms of the species might play a major role in the prevention of lipid oxidation.     

Use of Best Management Practices and Pasture and Soil Quality on Maryland Horse Farms

Agricultural operations, including horse farms, can contribute nonpoint source (NPS) pollution to surface water. The use of best management practices (BMPs) is the most effective way to prevent the movement of pollutants to surface water from nonpoint source pollution. Previous mailed survey studies have assessed the use of BMPs at the county and state level, but a visual assessment of horse farms is necessary to validate survey results. An observational field study was conducted to assess BMP use and soil and pasture quality and to create a model to predict soil erosion on Maryland horse farms. Fifty-one farms were selected based on stocking density (acres per horse [ac horse^-1]), farm use, and presence of water on property. All farms were visited from September through November 2009. In each pasture with grazing horses, the correct use of BMPs was assessed, grass height and vegetative cover were measured, and composite soil samples were collected. Less than half of the 18 assessed BMPs were being used by participants. Although most participants maintained the recommended vegetative cover and grass height, soil erosion was a major problem in pastures. Most farms had optimum soil nutrient concentrations (Ca, K, and P), excessive Mg values, and basic soil pH. Vegetative cover and grass height measurements were positively correlated with stocking density (r = 0.345, P < .0001; and r = 0.291, P < .0001, respectively). Farm use was the only variable that predicted soil erosion on farms (P = .006). Farms used for pleasure were least likely to have soil erosion, whereas farms used for breeding were more likely to have soil erosion (P = .0058). Despite the low-to-moderate adoption of BMPs, the maintenance of recommended vegetative cover and grass height as well as optimum values of soil nutrients indicated participating Maryland horse farms have a low potential for nutrient movement and NPS pollution.