Directionality of sound perception in the external ear of the dog

Sound pressure level of tone was measured using a probe tube microphone at entrance to the dog's external meatus as a function of the azimuth of the sound source. It was demonstrated that directionality of the dog's external ear and corresponding values of interaural intensity differences (delta I) were gradually increased as the tone frequency raised from 0.5 to 40 kHz. Transfer in pinnae locations from lateral to frontal positions (one of the components of orientation reaction to an unexpected sound) resulted in some narrowing of directionality diagrams and in a displacement of their maxima towards the head midline. It was calculated that owing to this effects the extent of monotonic part of the function relating delta I and azimuth of a source were enlarged. The lateral pinnae position was suggested to be optimal for sound detection and the frontal one for localization of the moving sound source.     

Dynamics of local maxima chains in spectra of human electroencephalogram

The continuous wavelet transform was applied to the human EEG signals recorded in different states of brain activity. The dynamics of local maxima chains in the matrices of the continuous wavelet transform coefficients was studied. The typologization method was developed for local maxima chains to separate by their drift in the frequency space as well as by dynamics of their signal “energy.” The method proved to be highly informative. It was shown that it was highly sensitive to a selection of one of two responses to the test question. It is determined that local maxima chains in most cases are gradually increasing and decreasing in the frequency space and by changes in the values of their continuous wavelet transform coefficients. The functional asymmetry in local maxima chains types’ distribution is determined. The results obtained allow us to consider the types of the local maxima chains dynamics as a new phenomenon of EEG activity.     

The activity of methyl benzoquate and clopidol against Eimeria maxima: synergy and drug resistance.

Synergy between clopidol and methyl benzoquate against Eimeria maxima was shown to be supra-additive. Collateral sensitivity to these drugs could not be demonstrated in resistant lines of this parasite. Resistance to methyl benzoquate and clopidol was not transferred when lines of E. maxima, resistant to the respective drugs, were propagated together. The failure to demonstrate this phenomenon was judged not to be due to synergy between the drugs. Attempts to induce simultaneous was readily acquired by a line of E. maxima resistant to clopidol. Induced resistance to clopidol in a methyl benzoquate-resistant line required numerous passages.     

Chaos in a minimal model of the alternative pathway of the complement system

In previous work, we introduced a minimal model of the alternative pathway of the complement. We also limited our analysis to a reduced set of parameter values because, for some parameters, experimentally supported estimates were not found. On the other hand, changes in value of some parameters may be a result of a pathological condition. Therefore, here we extend our analysis and include a wider range of values of five of the physiologically relevant parameters. For all the parameters considered, we observe chaotic oscillations, and we construct bifurcation diagrams using Poincaré sections of local maxima.     

Optimal production of cellulolytic enzymes and their location in trichoderma pseudokonigii

The maximum production of cellulose enzymes (FPactivity, CMcellulase and β-glucosidase) in the culture filtrate was observed at 27°C and pH 5.0, except for β-glucosidase, being at 6.0. The levels of extracellular enzymes in shake and stationary culture conditions was almost equal although they reached their maxima earlier in the former. The distribution of the three enzymes in extracellular, cytosol and cell debris fractions revealed most of the FPactivity and CMcellulase occurring extracellulary. More than 50% of the β-glucosidase was present in the cell debris fraction.     

Enantioselective sulfation of β2-receptor agonists by the human intestine and the recombinant M-form phenolsulfotransferase

The β₂-receptor agonist class of drugs is metabolized in humans almost exclusively by sulfate conjugation. The objective of this investigation was to determine the influence of chemical structure on the stereoselectivity of the sulfoconjugation of these chiral drugs. The pure enantiomers of six β₂-agonists, including those clinically most widely used, were all effectively sulfated both by the cytosol of the human intestine and the recombinant human M-form phenolsulfotransferase (PST). Whereas the apparent K_m values (K_m,app) for the sulfation of the individual drug enantiomers by the intestinal cytosol varied widely, ranging from 4.8 μM for (S)-isoproterenol to 889 μM for (S)-albuterol, these K_m,app values were highly correlated with those obtained with M-PST (correlation coefficient 0.994). In contrast, the M-PST V_max,app values were similar for all drug enantiomers, ranging from 276 to 914 pmol min⁻¹ mg⁻¹ protein, implying that substrate binding to M-PST by far is the main determinant of the sulfation activity. For isoproterenol, the K_m,app for M-PST was 6.1 times higher for the active (R)- than for the inactive (S)-enantiomer. For other β₂-agonists, the stereoselectivity decreased towards unity as the K_m,app increased. However, for albuterol, containing a hydroxymethyl substituent at the aromatic ring, the stereoselectivity was dramatically reversed, with 10 times higher K_m,app for the inactive (S)- than for the active (R)-enantiomer. Chirality 10:800–803, 1998. © 1998 Wiley-Liss, Inc.     

羊草草原群落水平格局研究 Ⅱ.二维网函数插值法

本文用二维网函数插值法,对羊草草原群落14种主要植物种群的个体分布格局作了分析。 根据网格法获取的数据资料,应用插值公式计算网点值,全部计算过程由电子计算机实现。计算结果由计算机输出并打印出每个种群的个体分布格局图。 分布格局图提供了以下信息: 1.14种植物种群个体的空间分布类型; 2.聚块的大小; 3.聚块的合计面积。 种群的镶嵌格局图直观的反映了种群之间在空间上的配置关系,并可给出镶嵌体的类型。讨论了研究种群个体分布格局的取样面积以及应用插值法存在的问题。     

A disulfide bridge near the active site of carbapenem-hydrolyzing class A β-lactamases might explain their unusual substrate profile

Bacterial resistance to β-lactam antibiotics, a clinically worrying and recurrent problem, is often due to the production of β-lactamases, enzymes that efficiently hydrolyze the amide bond of the β-lactam nucleus. Imipenem and other carbapenems escape the activity of most active site serine β-lactamases and have therefore become very popular drugs for antibacterial chemotherapy in the hospital environment. Their usefulness is, however, threatened by the appearance of new β-lactamases that efficiently hydrolyze them. This study is focused on the structure and properties of two recently described class A carbapenemases, produced by Serratia marcescens and Enterobacter cloacae strains and leads to a better understanding of the specificity of β-lactamases. In turn, this will contribute to the design of better antibacterial drugs. Three-dimensional models of the two class A carbapenemases were constructed by homology modeling. They suggested the presence, near the active site of the enzymes, of a disulfide bridge (C69-C238) whose existence was experimentally confirmed. Kinetic parameters were measured with the purified Sme-1 carbapenemase, and an attempt was made to explain its specific substrate profile by analyzing the structures of minimized Henri-Michaelis complexes and comparing them to those obtained for the “classical” TEM-1 β-lactamase. The peculiar substrate profile of the carbapenemases appears to be strongly correlated with the presence of the disulfide bridge between C69 and C238. Proteins 27:47–58 © 1997 Wiley-Liss, Inc.     

Biphasic and dosage-dependent regulation of osteoclastogenesis by β-catenin

Wnt/β-catenin signaling is a critical regulator of skeletal physiology. However, previous studies have mainly focused on its roles in osteoblasts, while its specific function in osteoclasts is unknown. This is a clinically important question because neutralizing antibodies against Wnt antagonists are promising new drugs for bone diseases. Here, we show that in osteoclastogenesis, β-catenin is induced during the macrophage colony-stimulating factor (M-CSF)-mediated quiescence-to-proliferation switch but suppressed during the RANKL-mediated proliferation-to-differentiation switch. Genetically, β-catenin deletion blocks osteoclast precursor proliferation, while β-catenin constitutive activation sustains proliferation but prevents osteoclast differentiation, both causing osteopetrosis. In contrast, β-catenin heterozygosity enhances osteoclast differentiation, causing osteoporosis. Biochemically, Wnt activation attenuates whereas Wnt inhibition stimulates osteoclastogenesis. Mechanistically, β-catenin activation increases GATA2/Evi1 expression but abolishes RANKL-induced c-Jun phosphorylation. Therefore, β-catenin exerts a pivotal biphasic and dosage-dependent regulation of osteoclastogenesis. Importantly, these findings suggest that Wnt activation is a more effective treatment for skeletal fragility than previously recognized that confers dual anabolic and anti-catabolic benefits.     

178 Targeting “Beta lactamase-C” in development of novel anti-tuberculosis therapeutics

Tuberculosis is a common, and in many cases lethal, infectious disease caused by various strains of Mycobacterium, usually Mycobacterium tuberculosis. (Kumar et al., 2007) In addition, co-infection with Mycobacterium tuberculosis and HIV (TB/HIV), especially in Africa, and multidrug resistant and extensively drug-resistant tuberculosis in all regions, (WHO, 2010) makes it important to develop novel therapeutics against this bacterium. Penicillin like β-Lactam antibiotics are among the most clinically prescribed drugs for anti-bacterial therapeutics. The general mechanism of action involved the inhibition of enzyme d,d-transpeptidases, which takes part in the biosynthesis of the bacterial cell wall (Heesemann, 1993). A major strategy of bacterial resistance to β-lactams is the production of β-lactamases that catalyze the hydrolysis of β-lactams, leading to the inactivation of the antibiotics. β-Lactams have not been used in clinical practice to treat TB infections, because an active penicillinase was reported in M. tuberculosis (Lessel, 1996). BlaC is a class A β-lactamase that contains a nucleophilic serine residue (Ser70) and shares sequence homology with the penicillin-binding protein domain of the ancestral d,d-transpeptidases. Recent studies including our lab show that β-lactam drugs like Clavulanate, Carbapenem, and Meropenem are used primarily against this type of resistant bacteria (Hugonnet et al., 2009). β-lactamase induces the same acetylating reaction with all of these drugs but cannot induce deacetylation. As a result, those drugs remain attached with β-lactamase even after the distortion of their β-lactam ring. At this time, secondary treatment has been done by applying previously used potent penicillin like β-lactam drugs with this primarily treated β-lactamase. In current study, we conducted kinetic and mass spectrometric analysis of different BlaC inhibitors, like NXL104 (Xu et al., 2012) and showed that how they quantitatively inactivates BlaC by forming a carbamyl linkage with the enzyme. In addition, we determined the three-dimensional structures of the different reactive forms of these drugs for better understanding the undergoing mechanisms involved in this inhibition process. Based on our understanding, we are trying to develop novel small molecules with better inhibitory process.     

Phase behavior of an intact monoclonal antibody

Understanding protein phase behavior is important for purification, storage, and stable formulation of protein drugs in the biopharmaceutical industry. Glycoproteins, such as monoclonal antibodies (MAbs) are the most abundant biopharmaceuticals and probably the most difficult to crystallize among water-soluble proteins. This study explores the possibility of correlating osmotic second virial coefficient (B(22)) with the phase behavior of an intact MAb, which has so far proved impossible to crystallize. The phase diagram of the MAb is presented as a function of the concentration of different classes of precipitants, i.e., NaCl, (NH4)2SO4, and polyethylene glycol. All these precipitants show a similar behavior of decreasing solubility with increasing precipitant concentration. B(22) values were also measured as a function of the concentration of the different precipitants by self-interaction chromatography and correlated with the phase diagrams. Correlating phase diagrams with B(22) data provides useful information not only for a fundamental understanding of the phase behavior of MAbs, but also for understanding the reason why certain proteins are extremely difficult to crystallize. The scaling of the phase diagram in B(22) units also supports the existence of a universal phase diagram of a complex glycoprotein when it is recast in a protein interaction parameter.     

Analytical lessons learned from selected therapeutic protein drug comparability studies

The successful implementation of process and product changes for a therapeutic protein drug, both during clinical development and after commercialization, requires a detailed evaluation of their impact on the protein's structure and biological functionality. This analysis is called a comparability exercise and includes a data driven assessment of biochemical equivalence and biological characterization using a cadre of analytical methodologies. This review focuses on describing analytical results and lessons learned from selected published therapeutic protein comparability case studies both for bulk drug substance and final drug product. An overview of the currently available analytical methodologies typically used is presented as well as a discussion of new emerging analytical techniques. The potential utility of several novel analytical approaches to comparability studies is discussed including distribution and stability of protein drugs in vivo, and enhanced evaluation of higher-order protein structure in actual formulations using hydrogen/deuterium exchange mass spectrometry, two-dimensional nuclear magnetic resonance fingerprinting or empirical phase diagrams. In addition, new methods for detecting and characterizing protein aggregates and particles are presented as these degradants are of current industry-wide concern. The critical role that analytical methodologies play in elucidating the structure–function relationships for therapeutic protein products during the overall assessment of comparability is discussed.     

A simple, sensitive and specific radioreceptor assay for beta-adrenergic antagonist drugs.

A radioreceptor assay for β-adrenergic blocking drugs described here is based on the ability of the blood content of drugs to compete with the binding of ³H-dihydroalprenolol (³H-DHA) to β-adrenergic receptors in calf cerebellar membranes. Plasma protein greatly inhibits the binding of ³H-DHA to β-receptors by binding the ³H-DHA so it is unavailable to the β-receptors. As little as 0.01 ml of human plasma in a final volume of 1 ml reduces binding 25–45%. Assays conducted on plasma dialysates can be performed without such inhibition. The radioreceptor assay is simple to perform as 100 samples can be processed in a morning. It is sensitive, detecting low nanomolar concentrations of plasma propranolol, and it is specific. No drugs clinically employed other than β-blocking agents compete for β-receptor binding. The assay detects all pharmacologically active metabolites of β-blocking drugs as well as the parent drug.     

The βI-galactosidase of Cicer arietinum is located in thickened cell walls such as those of collenchyma, sclerenchyma and vascular tissue

We report localisation of the chickpea βI-Gal, a member of the chickpea β-galactosidase family, which contains at least four members. After generation of specific antibodies, the distribution and cellular immunolocalisation of the protein in different organs and developmental stages of the plant was studied. βI-Gal protein is much longer than the other chickpea β-galactosidases because of the presence of a lectin-like domain in the carboxyl terminus of the protein. Western blot experiments indicated that the active βI-Gal retains this lectin-like domain for its function in the plant. The βI-Gal protein was mainly detected in cell walls of elongating organs, such as seedling epicotyls and stem internodes. An immunolocation study indicated a very good correlation between the presence of this βΙ-galactosidase and cells whose walls are thickening, not only in aged epicotyls and mature internodes in the final phase of elongation, but mostly in cells with a support function, such as collenchyma cells, xylem and phloem fibres and a layer of sclerenchyma cells surrounding the vascular cylinder (perivascular fibres). These results could suggest a function for the βI-Gal in modification of cell wall polymers, leading to thicker walls than the primary cell walls.     

Crystal structures of the apo form of β-fructofuranosidase from Bifidobacterium longum and its complex with fructose

We solved the 1.8 ? crystal structure of β-fructofuranosidase from Bifidobacterium longum KN29.1 - a unique enzyme that allows these probiotic bacteria to function in the human digestive system. The sequence of β-fructofuranosidase classifies it as belonging to the glycoside hydrolase family 32 (GH32). GH32 enzymes show a wide range of substrate specificity and different functions in various organisms. All enzymes from this family share a similar fold, containing two domains: an N-terminal five-bladed β-propeller and a C-terminal β-sandwich module. The active site is located in the centre of the β-propeller domain, in the bottom of a 'funnel'. The binding site, -1, responsible for tight fructose binding, is highly conserved among the GH32 enzymes. Bifidobacterium longum KN29.1 β-fructofuranosidase has a 35-residue elongation of the N-terminus containing a five-turn α-helix, which distinguishes it from the other known members of the GH32 family. This new structural element could be one of the functional modifications of the enzyme that allows the bacteria to act in a human digestive system. We also solved the 1.8 ? crystal structure of the β-fructofuranosidase complex with β-D-fructose, a hydrolysis product obtained by soaking apo crystal in raffinose.     

Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships

Disordered domains are long regions of intrinsic disorder that ideally have conserved sequences, conserved disorder, and conserved functions. These domains were first noticed in protein–protein interactions that are distinct from the interactions between two structured domains and the interactions between structured domains and linear motifs or molecular recognition features (MoRFs). So far, disordered domains have not been systematically characterized. Here, we present a bioinformatics investigation of the sequence–disorder–function relationships for a set of probable disordered domains (PDDs) identified from the Pfam database. All the Pfam seed proteins from those domains with at least one PDD sequence were collected. Most often, if a set contains one PDD sequence, then all members of the set are PDDs or nearly so. However, many seed sets have sequence collections that exhibit diverse proportions of predicted disorder and structure, thus giving the completely unexpected result that conserved sequences can vary substantially in predicted disorder and structure. In addition to the induction of structure by binding to protein partners, disordered domains are also induced to form structure by disulfide bond formation, by ion binding, and by complex formation with RNA or DNA. The two new findings, (a) that conserved sequences can vary substantially in their predicted disorder content and (b) that homologues from a single domain can evolve from structure to disorder (or vice versa), enrich our understanding of the sequence ? disorder ensemble ? function paradigm.     

Monte Carlo commissioning of radiotherapy LINAC—Introducing an improved methodology

PurposeMonte Carlo (MC) commissioning of medical linear accelerator (LINAC) is a time-consuming process involving a comparison between measured and simulated cross beam/lateral profiles and percentage depth doses (PDDs) for various field sizes. An agreement between these two data sets is sought by trial and error method while varying the incident electron beam parameters, such as electron beam energy or width, etc. This study aims to improve the efficiency of MC commissioning of a LINAC by assessing the feasibility of using a limited number of simulated PDDs.Materials and methodsUsing EGSnrc codes, a Varian Clinac 2100 unit has been commissioned for 6 MV photon beam, and a methodology has been proposed to identify the incident electron beam parameters in a speedier fashion. Impact of voxel size in 3-dimensions and cost functions used for comparison of the measured and simulated data have been investigated along with the role of interpolation.ResultsA voxel size of 1 × 1×0.5 cm³ has been identified as suitable for accurate and fast commissioning of the LIANC. The optimum number of simulated PDDs (required for further interpolation) has been found to be five.ConclusionThe present study suggests that PDDs alone at times can be insufficient for an unambiguous commissioning process and should be supported by including the lateral beam profiles in the process.     

Potential repurposing of known drugs as potent bacterial β-glucuronidase inhibitors

The active metabolite of the chemotherapeutic irinotecan, SN-38, is detoxified through glucuronidation and then excreted into the gastrointestinal tract. Intestinal bacteria convert the glucuronidated metabolite back to the toxic SN-38 using β-glucuronidase (GUS), resulting in debilitating diarrhea. Inhibiting GUS activity may relieve this side effect of irinotecan. In this study, we sought to determine whether any known drugs have GUS inhibitory activity. We screened a library of Food and Drug Administration-approved drugs with a cell-free biochemical enzyme assay using purified bacterial GUS. After triage, five drugs were confirmed to inhibit purified bacterial GUS. Three of these were the monoamine oxidase inhibitors nialamide, isocarboxazid, and phenelzine with average IC(50) values for inhibiting GUS of 71, 128, and 2300 nM, respectively. The tricyclic antidepressant amoxapine (IC(50) = 388 nM) and the antimalarial mefloquine (IC(50) = 1.2 μM) also had activity. Nialamide, isocarboxazid, and amoxapine had no significant activity against purified mammalian GUS but showed potent activity for inhibiting endogenous GUS activity in a cell-based assay using living intact Escherichia coli with average IC(50) values of 17, 336, and 119 nM, respectively. Thus, nialamide, isocarboxazid, and amoxapine have potential to be repurposed as therapeutics to reduce diarrhea associated with irinotecan chemotherapy and warrant further investigation for this use.     

Organization of nucleosomes and spacer DNA in chromatin fibres

In this paper we analyse in detail the orientation of X-ray diffraction diagrams obtained from the following materials: nucleosome cores, whole nuclei and the sodium and thallium salts of H1-depleted nucleohistone and of briefly digested chromatin. Our analysis indicates that spacer DNA is organized in bundles of parallel segments which contribute to the equatorial maxima in the diagrams. Several models are compatible with this organization, in particular a modified solenoid model in which the central part is filled with such a bundle of spacer DNA segments parallel to the axis of the fibre. It is also shown that spacer DNA is covered by histones, probably the N-terminal regions. This observation indicates that the differential activity of nucleases on chromatin is strongly influenced by conformational features of DNA. An analysis of the orientation of the low angle rings found in the X-ray diffraction patterns of H1-depleted nucleohistone shows that the 11 nm peak has maxima which are ～ 0.007 nm^?1 off the meridian. The 5.5 and 8 nm peaks have a meridional maximum plus two side maxima which occur at spacings between 0.02 and 0.055 nm^?1 from the meridian, depending on the conditions. A comparison of these results with those reported by Finch et al.¹ for crystals indicates that in fibres the nucleosome cores are arranged with their short axis perpendicular to the axis of the fibre. Some evidence on the path of DNA in the nucleosome cores is also obtained.     

Determination of drug levels in human serum by circular dichroism

A study of the applicability of circular dichroism (CD) for the determination of drug levels in human serum is described and a new method for the quantitative determination of optically active absorbing drugs having Cotton effects at wavelengths above 250 nm in human serum and/or plasma is proposed. The principal advantages of this method are speed, economy, and simplicity, no derivatization or chromatographic separation steps being needed. The validity of the CD determination was confirmed by analysis of variance, β-lactam antibiotics being chosen as model drugs. In addition, the validation studies performed confirm the accuracy and precision of the proposed method. For β-lactam antibiotics lacking Cotton effects above 250 nm, an alternative method based on the extraction of the drug from serum is considered. Chirality 10:507–512, 1998. © 1998 Wiley-Liss, Inc.