Dynamics and diversity of the 'Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of 'Atopobium cluster' isolates

This study monitored the dynamics and diversity of the human faecal 'Atopobium cluster' over a 3-month period using a polyphasic approach. Fresh faecal samples were collected fortnightly from 13 healthy donors (6 males and 7 females) aged between 26 and 61 years. Fluorescence in situ hybridization was used to enumerate total (EUB338mix) and 'Atopobium cluster' (ATO291) bacteria, with counts ranging between 1.12 × 1011 and 9.95 × 1011, and 1.03 × 109 and 1.16 × 1011 cells (g dry weight faeces)-1, respectively. The 'Atopobium cluster' population represented 0.2-22 % of the total bacteria, with proportions donor-dependent. Denaturing gradient gel electrophoresis (DGGE) using 'Atopobium cluster'-specific primers demonstrated faecal populations of these bacteria were relatively stable, with bands identified as Collinsella aerofaciens, Collinsella intestinalis/Collinsella stercoris, Collinsella tanakaei, Coriobacteriaceae sp. PEAV3-3, Eggerthella lenta, Gordonibacter pamelaeae, Olsenella profusa, Olsenella uli and Paraeggerthella hongkongensis in the DGGE profiles of individuals. Colony PCR was used to identify 'Atopobium cluster' bacteria isolated from faeces (n = 224 isolates). 16S rRNA gene sequence analysis of isolates demonstrated Collinsella aerofaciens represented the predominant (88 % of isolates) member of the 'Atopobium cluster' found in human faeces, being found in nine individuals. Eggerthella lenta was identified in three individuals (3.6 % of isolates). Isolates of Collinsella tanakaei, an 'Enorma' sp. and representatives of novel species belonging to the 'Atopobium cluster' were also identified in the study. Phenotypic characterization of the isolates demonstrated their highly saccharolytic nature and heterogeneous phenotypic profiles, and 97 % of the isolates displayed lipase activity.

Time-dependent gel to gel transformation of a peptide based supramolecular gelator

A dipeptide with a long fatty acid chain at its N-terminus gives hydrogels in phosphate buffer in the pH range 7.0–8.5. The hydrogel with a gelator concentration of 0.45% (w/v) at pH 7.46 (physiological pH) provides a very good platform to study dynamic changes within a supramolecular framework as it exhibits remarkable change in its appearance with time. Interestingly, the first formed transparent hydrogel gradually transforms into a turbid gel within 2 days. These two forms of the hydrogel have been thoroughly investigated by using small angle X-ray scattering (SAXS), powder X-ray diffraction (PXRD), field emission scanning electron microscopic (FE-SEM) and high-resolution transmission electron microscopic (HR-TEM) imaging, FT-IR and rheometric analyses. The SAXS and low angle PXRD studies substantiate different packing arrangements for the gelator molecules for these two different gel states (the freshly prepared and the aged hydrogel). Moreover, rheological studies of these two gels reveal that the aged gel is stiffer than the freshly prepared gel.

Root elongation rate is correlated with the length of the bare root apex of maize and lupin roots despite contrasting responses of root growth to compact and dry soils

Background We investigated interacting effects of matric potential and soil strength on root elongation of maize and lupin, and relations between root elongation rates and the length of bare (hairless) root apex. Methods Root elongation rates and the length of bare root apexwere determined formaize and lupin seedlings in sandy loam soil of various matric potentials (−0.01 to −1.6 MPa) and bulk densities (0.9 to 1.5 Mg m−3). Results Root elongation rates slowed with both decreasing matric potential and increasing penetrometer resistance. Root elongation of maize slowed to 10 % of the unimpeded rate when penetrometer resistance increased to 2 MPa, whereas lupin elongated at about 40 % of the unimpeded rate. Maize root elongation rate was more sensitive to changes in matric potential in loosely packed soil (penetrometer resistances <1 MPa) than lupin. Despite these differing responses, root elongation rate of both species was linearly correlated with length of the bare root apex (r2 0.69 to 0.97). Conclusion Maize root elongation was more sensitive to changes in matric potential and mechanical impedance than lupin. Robust linear relationships between elongation rate and length of bare apex suggest good potential for estimating root elongation rates for excavated roots.

Stability of probiotic Lactobacillus plantarum in dry microcapsules under accelerated storage conditions

This study investigated the stability of freeze dried and fluid bed dried alginate microcapsules coated with chitosan containing model probiotic bacteria, Lactobacillus plantarum, during storage for up to 45 days at different water activities (0.11, 0.23, 0.40 and 0.70) and temperatures (4, 30 and 37 °C). The loss in cell viability was around 0.8 log in the case of fluid bed drying and around 1.3 in the case of freeze drying, with the former method resulting in dried capsules of smaller size (~ 1 mm vs 1.3 mm), more irregular shape, and with a rougher surface. In both cases, the water activity and water content were less than 0.25 and 10% w/w, respectively, which favours high storage stability. The storage stability studies demonstrated that as the water activity and temperature decreased the survival of the dried encapsulated cells increased. Considerably better survival was observed for fluid bed dried encapsulated cells compared to freeze dried encapsulated cells and freeze dried free cells with 10% sucrose (control), and in some cases, e.g. at 4 and 30 °C at water activities of 0.11, 0.23 and 0.40, there was more than 1 log difference after 45 days, with concentrations higher than 108 CFU/g after 45 days of storage. The results indicate that fluid bed drying is an effective and efficient manufacturing method to produce probiotic containing capsules with enhanced storage stability.

Evaluating nitrogen utilization efficiency of nonpregnant dry cows offered solely fresh cut grass at maintenance levels

The present study aimed to identify key parameters influencing N utilization and develop prediction equations for manure N output (MN), feces N output (FN), and urine N output (UN). Data were obtained under a series of digestibility trials with nonpregnant dry cows fed fresh grass at maintenance level. Grass was cut from 8 different ryegrass swards measured from early to late maturity in 2007 and 2008 (2 primary growth, 3 first regrowth, and 3 second regrowth) and from 2 primary growth early maturity swards in 2009. Each grass was offered to a group of 4 cows and 2 groups were used in each of the 8 swards in 2007 and 2008 for daily measurements over 6 wk; the first group (first 3 wk) and the second group (last 3 wk) assessed early and late maturity grass, respectively. Average values of continuous 3-d data of N intake (NI) and output for individual cows ( = 464) and grass nutrient contents ( = 116) were used in the statistical analysis. Grass N content was positively related to GE and ME contents but negatively related to grass water-soluble carbohydrates (WSC), NDF, and ADF contents ( < 0.01), indicating that accounting for nutrient interrelations is a crucial aspect of N mitigation. Significantly greater ratios of UN:FN, UN:MN, and UN:NI were found with increased grass WSC contents and ratios of N:WSC, N:digestible OM in total DM (DOMD), and N:ME ( < 0.01). Greater NI, animal BW, and grass N contents and lower grass WSC, NDF, ADF, DOMD, and ME concentrations were significantly associated with greater MN, FN, and UN ( < 0.05). The present study highlighted that using grass lower in N and greater in fermentable energy in animals fed solely fresh grass at maintenance level can improve N utilization, reduce N outputs, and shift part of N excretion toward feces rather than urine. These outcomes are highly desirable in mitigation strategies to reduce nitrous oxide emissions from livestock. Equations predicting N output from BW and grass N content explained a similar amount of variability as using NI and grass chemical composition (excluding DOMD and ME), implying that parameters easily measurable in practice could be used for estimating N outputs. In a research environment, where grass DOMD and ME are likely to be available, their use to predict N outputs is highly recommended because they strongly improved of the equations in the current study.

The interaction of moist convection and mid-level dry air in the advance of the onset of the Indian monsoon

The advance of the onset of the Indian monsoon is here explained in terms of a balance between the low-level monsoon flow and an over-running intrusion of mid-tropospheric dry air. The monsoon advances, over a period of about 6 weeks, from the south of the country to the northwest. Given that the low-level monsoon winds are westerly or southwesterly, and the midlevel winds northwesterly, the monsoon onset propagates upwind relative to midlevel flow, and perpendicular to the low-level flow, and is not directly caused by moisture flux toward the northwest. Lacking a conceptual model for the advance means that it has been hard to understand and correct known biases in weather and climate prediction models. The mid-level northwesterlies form a wedge of dry air that is deep in the far northwest of India and over-runs the monsoon flow. The dry layer is moistened from below by shallow cumulus and congestus clouds, so that the profile becomes much closer to moist adiabatic, and the dry layer is much shallower in the vertical, toward the southeast of India. The profiles associated with this dry air show how the most favourable environment for deep convection occurs in the south, and onset occurs here first. As the onset advances across India, the advection of moisture from the Arabian Sea becomes stronger, and the mid-level dry air is increasingly moistened from below. This increased moistening makes the wedge of dry air shallower throughout its horizontal extent, and forces the northern limit of moist convection to move toward the northwest. Wetting of the land surface by rainfall will further reinforce the north-westward progression, by sustaining the supply of boundary layer moisture and shallow cumulus. The local advance of the monsoon onset is coincident with weakening of the mid-level northwesterlies, and therefore weakened mid-level dry advection.

The 2014 hot, dry summer in Northeast Asia

Northeast Asia experienced a severe drought in summer 2014. Sea surface temperature forcing may have increased the risk of low precipitation, but model biases preclude reliable attribution to anthropogenic forcing.

Fire, climate and vegetation linkages in the Bolivian Chiquitano Seasonally Dry Tropical Forest

South American seasonally-dry tropical forests (SDTF) are critically endangered, with only a small proportion of their original distribution remaining. This paper presents a 12,000 year reconstruction of climate change, fire and vegetation dynamics in the Bolivian Chiquitano SDTF, based upon pollen and charcoal analysis, to examine the resilience of this ecosystem to drought and fire. Our analysis demonstrates a complex relationship between climate, fire and floristic composition over multi-millennial time scales, and reveals that moisture variability is the dominant control upon community turnover in this ecosystem. Maximum drought during the early Holocene, consistent with regional drought reconstructions, correlates with a period of significant fire activity between 8,000 and 7,000 cal yr BP which resulted in a decrease in SDTF diversity. As fire activity declined, but severe regional droughts persisted through the mid-Holocene, SDTF, including Anadenanthera and Astronium, became firmly established in the Bolivian lowlands. The trend of decreasing fire activity during the last two millennia promotes the idea among forest ecologists that SDTF are threatened by fire. Our analysis shows that the Chiquitano seasonally dry biome has been more resilient to Holocene changes in climate and fire regime than previously assumed, but raises questions over whether this resilience will continue in the future under increased temperatures and drought coupled with a higher frequency anthropogenic fire regime.

The effect of simulated flooding post-anthesis on pre-harvest sprouting and subsequent seed longevity in contrasting rice cultivars

Unpredictable flooding is a major constraint to rice production. It can occur at any growth stage. The effect of simulated flooding post-anthesis on yield and subsequent seed quality of pot-grown rice (Oryza sativa L.) plants was investigated in glasshouses and controlled-environment growth cabinets. Submergence post-anthesis (9-40 DAA) for 3 or 5 days reduced seed weight of japonica rice cv. Gleva, with considerable pre-harvest sprouting (up to 53%). The latter was greater the later in seed development and maturation that flooding occurred. Sprouted seed had poor ability to survive desiccation or germinate normally upon rehydration, whereas the effects of flooding on the subsequent air-dry seed storage longevity (p50) of the non-sprouted seed fraction was negligible. The indica rice cvs IR64 and IR64Sub1 (introgression of submergence tolerance gene Submergence1A-1) were both far more tolerant to flooding post-anthesis than cv. Gleva: four days’ submergence of these two near-isogenic cultivars at 10-40 DAA resulted less than 1% sprouted seeds. The presence of the Sub1A-1 allele in cv. IR64Sub1 was verified by gel electrophoresis and DNA sequencing. It had no harmful effect on loss in seed viability during storage compared with IR64 in both control and flooded environments. Moreover, the germinability and changes in dormancy during seed development and maturation were very similar to IR64. The efficiency of using chemical spray to increase seed dormancy was investigated in the pre-harvest sprouting susceptible rice cv. Gleva. Foliar application of molybdenum at 100 mg L-1 reduced sprouted seeds by 15-21% following 4 days’ submergence at 20-30 DAA. Analyses confirmed that the treatment did result in molybdenum uptake by the plants, and also tended to increase seed abscisic acid concentration. The latter was reduced by submergence and declined exponentially during grain ripening. The selection of submergence-tolerant varieties was more successful than application of molybdenum in reducing pre-harvest sprouting.

A scanning electron microscopy study of diseased root surfaces conditioned with EDTA gel plus Cetavlon after scaling and root planing

In the present investigation, a scanning electron microscopy analysis was performed to evaluate the effects of the topical application of ethylenediaminetetraacetic acid (EDTA) gel associated with Cetavlon (EDTAC) in removing the smear layer and exposing collagen fibers following root surface instrumentation. Twenty-eight teeth from adult humans, single rooted and scheduled for extraction due to periodontal reasons, were selected. Each tooth was submitted to manual (scaling and root planing) instrumentation alone or combined with ultrasonic instruments, with or without etching using a 24% EDTAC gel. Following extraction, specimens were processed and examined under a scanning electron microscope. A comparative morphological semi-quantitative analysis was performed; the intensity of the smear layer and the decalcification of cementum and dentinal surfaces were graded in 12 sets using an arbitrary scale ranging from 1 (area covered by a smear layer) to 4 (no smear layer). Root debridement with hand instruments alone or combined with ultrasonic instruments resulted in a similar smear layer covering the root surfaces. The smear layer was successfully removed from the surfaces treated with EDTAC, which exhibited numerous exposed dentinal tubules and collagen fibers. This study supports the hypothesis that manual instrumentation alone or instrumentation combined with ultrasonic instrumentation is unable to remove the smear layer, whereas the subsequent topical application of EDTAC gel effectively removes the smear layer, uncovers dentinal openings and exposes collagen fibers.

Clinical comparison between the bleaching efficacy of 37% peroxide carbamide gel mixed with sodium perborate with established intracoronal bleaching agent

Objective. The aim was to evaluate the bleaching efficacy of sodium perborate/37% carbamide peroxide paste and traditional sodium perborate/distilled water for intracoronal bleaching. Study design. Thirty patients with dark anterior teeth were divided into 2 groups (n = 15): group A: sodium perborate/ distilled water; and group B: sodium perborate/37% carbamide peroxide paste. The bleaching treatment limited each patient to the maximum of 4 changes of the bleaching agent. Initial and final color shades were measured using the Vita Lumin shade guide. Results. Data was analyzed with Wilcoxon test for initial and final comparison according to the bleaching agent, demonstrating efficacy of the bleaching treatment with both agents. Mann-Whitney test was used for comparison of the efficacy of the bleaching agents, showing that there was no significant difference between them. Conclusion. The sodium perborate/37% carbamide peroxide association for intracoronal bleaching has proven to be as effective as sodium perborate/distilled water. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2009; 107: e43-e47)

Fatty acid composition of intramuscular fat from Nellore steers fed dry or high moisture corn and calcium salts of fatty acids

The purpose of this work was to evaluate the fatty acid composition of the Longissimus muscle from carcasses of Nellore steers fed diets with calcium salts of fatty acids (CSFA) and high moisture corn. Forty eight steers were fed during 70 days four diets containing dry corn (DC), high moisture corn (HM). dry corn plus CSFA (DC-CSFA) or high moisture corn plus CSFA (HM-CSFA). Fatty acid composition of the Longissimus muscle was determined by gas chromatography. Corn type had no effect on the ether extract percentage and in the content of the majority of the fatty acids, although steers fed HMC showed higher levels of polyunsaturated fatty acids and polyunsaturated/saturated ratio. Feeding CSFA increased ether extract percentage but had no effect on total of saturated, unsaturated and saturated: unsaturated ratio. Both high moisture corn and calcium salts of fatty acids increased CIA (cis9, trans11) and total CIA concentrations in intramuscular fat (C) 2008 Elsevier B.V. All rights reserved.