Identification of potent,selective and orally bioavailable phenyl ((R)-3-phenylpyrrolidin-3-yl)sulfone analogues as RORγt inverse agonists

An X-ray crystal structure of one of our previously discovered RORγt inverse agonists bound to the RORγt ligand binding domain revealed that the cyclohexane carboxylic acid group of compound 2 plays a significant role in RORγt binding, forming four hydrogen bonding and ionic interactions with RORγt. SAR studies centered around the cyclohexane carboxylic acid group led to identification of several structurally diverse and more potent compounds, including new carboxylic acid analogues 7 and 20, and cyclic sulfone analogues 34 and 37. Notably, compounds 7 and 20 were found to maintain the desirable pharmacokinetic profile of 2.     

Environmental analysis of producing biochar and energy recovery from pulp and paper mill biosludge

Sweden is one of the largest exporters of pulp and paper products in the world. It follows that huge quantities of sludge rich in carbonaceous organic material and containing heavy metals are generated. This paper carried out a comparative environmental analysis of three different technologies, which can be adopted to produce biochar and recover energy from the biosludge, using landfilling as the reference case. These three thermochemical biosludge management systems—using incineration, pyrolysis, and hydrothermal carbonization (HTC)—were modeled using life cycle assessment (LCA). Heat generated in the incineration process (System A) was considered to be for captive consumption within the kraft pulp mills. It was assumed that the biochars—pyrochar and hydrochar—produced from pyrolysis (System B) and HTC (System C), respectively, were added to the forest soils. The LCA results show that all the alternative systems considerably improve the environmental performance of biosludge management, relative to landfilling. For all systems, there are net reductions in greenhouse gas emissions (–0.89, –1.43, and –1.13 tonnes CO₂‐equivalent per tonne dry matter biosludge in Systems A, B, and C, respectively). System B resulted in the lowest potential eutrophication and terrestrial ecotoxicity impacts, whereas System C had the least acidification potential. The results of this analysis show that, from an environmental point of view, biochar soil amendment as an alternative method for handling pulp and paper mill biosludge is preferable to energy recovery. However, an optimal biochar system needs to factor in the social and economic contexts as well.     

Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome

Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.     

Using hardware models to quantify sensory data acquisition across the rat vibrissal array

Our laboratory investigates how animals acquire sensory data to understand the neural computations that permit complex sensorimotor behaviors. We use the rat whisker system as a model to study active tactile sensing; our aim is to quantitatively describe the spatiotemporal structure of incoming sensory information to place constraints on subsequent neural encoding and processing. In the first part of this paper we describe the steps in the development of a hardware model (a 'sensobot') of the rat whisker array that can perform object feature extraction. We show how this model provides insights into the neurophysiology and behavior of the real animal. In the second part of this paper, we suggest that sensory data acquisition across the whisker array can be quantified using the complete derivative. We use the example of wall-following behavior to illustrate that computing the appropriate spatial gradients across a sensor array would enable an animal or mobile robot to predict the sensory data that will be acquired at the next time step.     

Elementary mode analysis to study the preculturing effect on the metabolic state of Lactobacillus rhamnosus during growth on mixed substrates

Quantification of metabolism through elementary modes offers insights into the working of a metabolic network. We have determined the fluxes of elementary modes through linear optimization using the stoichiometry of the elementary modes as a constraint. We apply this methodology to obtain insights into the effect of preculturing on growth of Lactobacillus rhamnosus on medium containing mixed substrates. L. rhamnosus, a microaerophilic organism, produces flavor compounds such as diacetyl and acetoin during growth on glucose and citrate. The uptake of citrate has been shown to be sensitive to preculturing states of the cells. Elementary modes demonstrated that citrate was utilized by the organism as a sole carbon source. Further, both glucose and citrate was catabolized by this organism through aerobic and anaerobic routes. The flux analysis indicated that only 21 elementary modes were operational during growth of L. rhamnosus on glucose and citrate. Glucose specifically accounted for 6 elementary modes, while the remaining 15 involved citrate as substrate. The modes associated with glucose were mainly operational when cells were precultured on glucose. It was observed that all the 21 modes contributed to the fluxes when the cells were precultured on citrate. The NADH recycling through lactate formation and oxygen uptake were dependent on the preculturing state. The analysis also demonstrated that preculturing on citrate yielded better productivity of diacetyl and acetoin.     

Novel interactions between NFATc1 (Nuclear Factor of Activated T cells c1) and STAT-3 (Signal Transducer and Activator of Transcription-3) mediate G protein-coupled receptor agonist, thrombin-induced biphasic expression of cyclin D1, with first phase influencing cell migration and second phase directing cell proliferation

Thrombin, a G protein-coupled receptor agonist, induced a biphasic expression of cyclin D1 in primary vascular smooth muscle cells. Although both phases of cyclin D1 expression require binding of the newly identified cooperative complex, NFATc1·STAT-3, to its promoter, the second phase, which is more robust, depends on NFATc1-mediated recruitment of p300 onto the complex and the subsequent acetylation of STAT-3. In addition, STAT-3 is tyrosine-phosphorylated in a biphasic manner, and the late phase requires NFATc1-mediated p300-dependent acetylation. Furthermore, interference with acetylation of STAT-3 by overexpression of acetylation null STAT-3 mutant led to the loss of the late phase of cyclin D1 expression. EMSA analysis and reporter gene assays revealed that NFATc1·STAT-3 complex binding to the cyclin D1 promoter led to an enhanceosome formation and facilitated cyclin D1 expression. In the early phase of its expression, cyclin D1 is localized mostly in the cytoplasm and influenced cell migration. However, during the late and robust phase of its expression, cyclin D1 is translocated to the nucleus and directed cell proliferation. Together, these results demonstrate for the first time that the dual function of cyclin D1 in cell migration and proliferation is temperospatially separated by its biphasic expression, which is mediated by cooperative interactions between NFATc1 and STAT-3.     

Change in rigidity in the activated form of the glucose/galactose receptor from Escherichia coli: a phenomenon that will be key to the development of biosensors

Recently a periplasmic glucose/galactose binding protein, GGRQ26C, immobilized on a gold surface has been used as an active part of a glucose biosensor based on quartz microbalance technique. However the nature of the glucose detection was not clear. Here we have found that the receptor protein film immobilized on the gold surface increases its rigidity when glucose is added, which explains the unexpected detection signal. To study the rigidity change, we developed a new fast and simple method based on using atomic force microscopy (AFM) in tapping mode. The method was verified by explicit measurements of the Young's modulus of the protein film by conventional AFM methods. Since there are a host of receptors that undergo structural change when activated by ligand, AFM can play a key role in the development and/or optimization of biosensors based on rigidity changes in biomolecules.     

Endometrial and endocervical secretion: the search for histochemical differentiation

OBJECTIVE: To determine the ideal histochemical stain to differentiate between non-neoplastic and neoplastic endocervix and endometrium. STUDY DESIGN: A total of 90 cases representing nonneoplastic cervix, non-neoplastic endometrium, endocervical adenocarcinoma and endometrial adenocarcinoma were stained with toluidine blue (TB); methylene blue (MB); mucicarmine (MUC); periodic acid-Schiff before and after diastase digestion (PAS, PAS-D); Alcian blue, pH 2.5 (AB); and periodic acid-Schiff after Alcian blue, pH 2.5 (PAB). Cases were blinded and randomly divided between two pathologists for evaluation of the staining and the staining distribution of the glandular epithelium by means of a 36-color scheme. RESULTS: The majority of non-neoplastic endocervix samples stained blue with MB (57%), fuchsia with MUC (70%), magenta with PAS (77%) and PAS-D (73%) and dark turquoise with AB (70%). The majority of non-neoplastic endometrium samples stained slate blue with TB (60%) and pink with PAS-D (53.3%). There is statistical difference (p < 0.05) in the color of the epithelium and secretions between the non-neoplastic cervix and endometrium. The malignant glands of endocervical origin could be differentiated significantly (p = 0.043) from non-neoplastic endocervical epithelium by MUC. The epithelium of the non-neoplastic endometrium is significantly differentiated from malignant endometrium using TB (p = 0.015) and MB (p = 0.038). Endocervical carcinoma could be significantly differentiated from endometrial carcinoma by MB. The staining in endocervical adenocarcinoma and endometrial carcinoma was predominantly present in both apical and cytoplasmic locations compared to their non-neoplastic counterparts (endocervix, p = 0.003; endometrium, p = 0.049). CONCLUSION: This study showed that a panel of histochemical stains could differentiate glandular cells of endocervical epithelium from endometrium.     

Optimization of enzymatic hydrolysis and ethanol fermentation from AFEX-treated rice straw

An abundant agricultural residue, rice straw (RS) was pretreated using ammonia fiber expansion (AFEX) process with less than 3% sugar loss. Along with commercial cellulase (Spezyme® CP) at 15 filter paper unit/g of glucan, the addition of Multifect® Xylanase at 2.67 mg protein/g glucan and Multifect® Pectinase at 3.65 mg protein/g glucan was optimized to greatly increase sugar conversion of AFEX-treated RS. During enzymatic hydrolysis even at 6% glucan loading (equivalent to 17.8% solid loading), about 80.6% of glucan and 89.6% of xylan conversions (including monomeric and oligomeric sugars) were achieved. However, oligomeric glucose and xylose accounted for 12.3% of the total glucose and 37.0% of the total xylose, respectively. Comparison among the three ethanologenic strains revealed Saccharomyces cerevisiae 424A(LNH-ST) to be a promising candidate for RS hydrolysate with maximum ethanol metabolic yield of 95.3% and ethanol volumetric productivity of 0.26 g/L/h. The final concentration of ethanol at 37.0 g/L was obtained by S. cerevisiae 424A(LNH-ST) even with low cell density inoculum. A biorefinery combining AFEX pretreatment with S. cerevisiae 424A(LNH-ST) in separate hydrolysis and fermentation could achieve 175.6 g EtOH/kg untreated rice straw at low initial cell density (0.28 g dw/L) without washing pretreated biomass, detoxification, or nutrient supplementation.