Effect of Breadmaking Process on In Vitro Gut Microbiota Parameters in Irritable Bowel Syndrome

A variety of foods have been implicated in symptoms of patients with Irritable Bowel Syndrome (IBS) but wheat products are most frequently cited by patients as a trigger. Our aim was to investigate the effects of breads, which were fermented for different lengths of time, on the colonic microbiota using in vitro batch culture experiments. A set of in vitro anaerobic culture systems were run over a period of 24 h using faeces from 3 different IBS donors (Rome Criteria–mainly constipated) and 3 healthy donors. Changes in gut microbiota during a time course were identified by fluorescence in situ hybridisation (FISH), whilst the small -molecular weight metabolomic profile was determined by NMR analysis. Gas production was separately investigated in non pH-controlled, 36 h batch culture experiments. Numbers of bifidobacteria were higher in healthy subjects compared to IBS donors. In addition, the healthy donors showed a significant increase in bifidobacteria (P<0.005) after 8 h of fermentation of a bread produced using a sourdough process (type C) compared to breads produced with commercial yeasted dough (type B) and no time fermentation (Chorleywood Breadmaking process) (type A). A significant decrease of δ-Proteobacteria and most Gemmatimonadetes species was observed after 24 h fermentation of type C bread in both IBS and healthy donors. In general, IBS donors showed higher rates of gas production compared to healthy donors. Rates of gas production for type A and conventional long fermentation (type B) breads were almost identical in IBS and healthy donors. Sourdough bread produced significantly lower cumulative gas after 15 h fermentation as compared to type A and B breads in IBS donors but not in the healthy controls. In conclusion, breads fermented by the traditional long fermentation and sourdough are less likely to lead to IBS symptoms compared to bread made using the Chorleywood Breadmaking Process.     

Dietary constraints of phytosaurian reptiles revealed by dental microwear textural analysis

Phytosaurs are a group of large, semi‐aquatic archosaurian reptiles from the Middle–Late Triassic. They have often been interpreted as carnivorous or piscivorous due to their large size, morphological similarity to extant crocodilians and preservation in fluvial, lacustrine and coastal deposits. However, these dietary hypotheses are difficult to test, meaning that phytosaur ecologies and their roles in Triassic food webs remain incompletely constrained. Here, we apply dental microwear textural analysis to the three‐dimensional sub‐micrometre scale tooth surface textures that form during food consumption to provide the first quantitative dietary constraints for five species of phytosaur. We furthermore explore the impacts of tooth position and cranial robustness on phytosaur microwear textures. We find subtle systematic texture differences between teeth from different positions along phytosaur tooth rows, which we interpret to be the result of different loading pressures experienced during food consumption, rather than functional partitioning of food processing along tooth rows. We find rougher microwear textures in morphologically robust taxa. This may be the result of seizing and processing larger prey items compared to those captured by gracile taxa, rather than dietary differences per se. We reveal relatively low dietary diversity between our study phytosaurs and that individual species show a lack of dietary specialization. Species are predominantly carnivorous and/or piscivorous, with two taxa exhibiting slight preferences for ‘harder’ invertebrates. Our results provide strong evidence for higher degrees of ecological convergence between phytosaurs and extant crocodilians than previously appreciated, furthering our understanding of the functioning and evolution of Triassic ecosystems.     

Exploring the role of structure and dynamics in the function of chymotrypsin inhibitor 2

Increasing awareness of the possible role of internal dynamics in protein function has led to the development of new methods for experimentally characterizing protein dynamics across multiple time scales, especially using NMR spectroscopy. A few analyses of the conformational dynamics of proteins ranging from nonallosteric single domains to multidomain allosteric enzymes are now available; however, demonstrating a connection between dynamics and function remains difficult on account of the comparative lack of studies examining both changes in dynamics and changes in function in response to the same perturbations. In previous work, we characterized changes in structure and dynamics on the ps–ns time scale resulting from hydrophobic core mutations in chymotrypsin inhibitor 2 and found that there are moderate, persistent global changes in dynamics in the absence of gross structural changes (Whitley et al., Biochemistry 2008;47:8566–8576). Here, we assay those and additional mutants for inhibitory ability toward the serine proteases elastase and chymotrypsin to determine the effects of mutation on function. Results indicate that core mutation has only a subtle effect on CI2 function. Using chemical shifts, we also studied the effect of complex formation on CI2 structure and found that perturbations are greatest at the complex interface but also propagate toward CI2's hydrophobic core. The structure–dynamics–function data set completed here suggests that dynamics plays a limited role in the function of this small model system, although we do observe a correlation between nanosecond-scale reactive loop motions and inhibitory ability for mutations at one key position in the hydrophobic core.     

PLTP activity decreases with weight loss: changes in PLTP are associated with changes in subcutaneous fat and FFA but not IAF or insulin sensitivity

Phospholipid transfer protein (PLTP) activity is elevated in obese and diabetic subjects. No prospective studies have examined the effect of weight loss on PLTP activity and assessed whether the resultant changes in activity are related to changes in body weight, insulin resistance, or both. PLTP activity was measured at baseline in 46 subjects (body mass index = 19-64 kg/m2) and after diet-induced weight loss in 19 of the obese subjects. Total body fat mass (FM) by dual-energy X-ray absorptiometry, intraabdominal fat (IAF), and abdominal subcutaneous fat (SQF) by CT scan, insulin sensitivity (SI) by frequently sampled intravenous glucose tolerance test, leptin, and lipids were determined. At baseline, PLTP activity correlated with FM (r = 0.36, P = 0.02) and SQF (r = 0.31, P = 0.045), but not with IAF (r = 0.16, P = 0.32) or SI (r = 0.10, P = 0.52). With diet-induced weight loss (16 +/- 7.3 kg), PLTP activity significantly decreased 9.1% (P = 0.002). The change in PLTP activity correlated with the change in SQF (r = 0.55, P = 0.014) (33.6% decrease), but not with IAF (r = 0.09, P = 0.73) or SI (r = 0.18, P = 0.44), and was highly correlated with the change in nonesterified fatty acid (NEFA) (r = 0.71, P < 0.001). In conclusion, elevated PLTP activity in obese subjects is likely a result of increased body fat, reflected by SQF, and is influenced by NEFAs but is not directly related to insulin resistance.     

The Relative Impact of Harvest and Fire upon Landscape-Level Dynamics of Older Forests: Lessons from the Northwest Forest Plan

Interest in preserving older forests at the landscape level has increased in many regions, including the Pacific Northwest of the United States. The Northwest Forest Plan (NWFP) of 1994 initiated a significant reduction in the harvesting of older forests on federal land. We used historical satellite imagery to assess the effect of this reduction in relation to: past harvest rates, management of non-federal forests, and the growing role of fire. Harvest rates in non-federal large-diameter forests (LDF) either decreased or remained stable at relatively high rates following the NWFP, meaning that harvest reductions on federal forests, which cover half of the region, resulted in a significant regional drop in the loss of LDF to harvest. However, increased losses of LDF to fire outweighed reductions in LDF harvest across large areas of the region. Elevated fire levels in the western United States have been correlated to changing climatic conditions, and if recent fire patterns persist, preservation of older forests in dry ecosystems will depend upon practical and coordinated fire management across the landscape. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Author Contributions: The study was conceived and designed by S.P.H., W.B.C., T.A.S, and M. M. The paper was written primarily by S.P.H, with editorial help by T.A.S. and W.B.C. The research itself, including mapping and analysis, was performed by S.P.H., D.P., M.G.W., and M.L. M.M. contributed additional methodologies related to the creation and validations of maps of historical older forests.     

Canine heparan sulfate sulfamidase and the molecular pathology underlying Sanfilippo syndrome type A in Dachshunds

Heparan sulfate sulfamidase (HSS) is a lysosomal exohydrolase that, when deficient, results in intralysosomal accumulation of heparan sulfate and the clinical phenotype of Sanfilippo syndrome type A. The first animal disease homolog of human Sanfilippo syndrome type A has been recently indentified in Dachshund littermates. To identify the molecular defect, the nucleotide sequences of the normal canine HSS gene and cDNA were determined using PCR-based approaches. The coding region showed 87% nucleotide homology, and 89% amino acid sequence homology, with human HSS. All exon-intron borders were conserved. Sequence analysis of the entire coding region with exon-intron boundaries was performed in the propositus, a healthy littermate, and six unrelated normal dogs. Comparison revealed a 3-bp deletion, 737-739delCCA, resulting in the loss of threonine at position 246 in both alleles of the propositus and in one allele of a healthy littermate. Prediction of the three-dimensional structure of canine HSS, based on homology with human arylsulfatases A and B, suggested the pathogenic effect of this deletion. Six other sequence variations in exons, and 10 in introns, appear to be benign polymorphisms. This study supports the potential development of a canine model of Sanfilippo syndrome type A to evaluate gene therapy for this disorder.     

Apparatus Composition, Growth, And Survivorship Of The Lower Ordovician Conodont paracordylodus Gracilis Lindström, 1955

Analysis of numerous conodont element clusters from the Lower Ordovician cherts of the Burubaital Formation in central Kazakhstan reveals that the apparatus of Paracordylodus gracilis Lindstro¨m, 1955 consisted of 15 elements: two M elements, nine S elements (including 1 S₀), and four P elements (2 P₁, 2 P₂). The clusters probably originated as faecal pellets, but the best preserved indicate that the architecture of the apparatus of P. gracilis was comparable to that of ozarkodinid conodonts, providing strong support for the hypothesis that the 15-element 2M-9S-4P apparatus plan was plesiomorphic for conodonts with morphologically complex elements. All the elements within the P. gracilis clusters appear to be at a similar stage of ontogeny, and there is no evidence for late addition or replacement of elements. Analysis of element growth suggests that the relative dimensions of some elements changed during ontogeny, but the available data support the hypothesis that the growth of the apparatus as a whole was isometric. The size distribution of P. gracilis in the Burubaital Formation suggests that individuals in a particular size range were preferentially selected for consumption by predators. The identity of these predators is unknown, but they may have included other P. gracilis .