An operator-induced conformational change in the C-terminal domain of the λ repressor

4,4'-bis(1-anilino-8-naphthalenesulfonic acid (Bis-ANS), an environment-sensitive fluorescent probe for hydrophobic region of proteins, binds specifically to the C-terminal domain of λ repressor. The binding is characterized by positive cooperativity, the magnitude of which is dependent on protein concentration in the concentration range where dimeric repressor aggregates to a tetramer. In this range, positive cooperativity becomes more pronounced at higher protein concentrations. This suggests a preferential binding of Bis-ANS to the dimeric form of the repressor. Binding of single operator OR1 to the N-terminal domain of the repressor causes enhancement of fluorescence of the C-terminal domain bound Bis-ANS. The binding of single operator OR1 also leads to quenching of fluorescence of tryptophan residues, all of which are located in the hinge or the C-terminal domain. Thus two different fluorescent probes indicate an operator-induced conformational change which affects the C-terminal domain. The significance of this conformational change with respect to the function of λ repressor has been discussed

Pathological relevance of post-translationally modified alpha-synuclein (pSer87, pSer129, nTyr39) in idiopathic Parkinson’s disease and Multiple System Atrophy

Aggregated alpha-synuclein (a-synuclein) is the main component of Lewy bodies (LBs), Lewy neurites (LNs), and glial cytoplasmic inclusions (GCIs), which are pathological hallmarks of idiopathic Parkinson’s disease (IPD) and multiple system atrophy (MSA), respectively. Initiating factors that culminate in forming LBs/LNs/GCIs remain elusive. Several species of a-synuclein exist, including phosphorylated and nitrated forms. It is unclear which a-synuclein post-translational modifications (PTMs) appear within aggregates throughout disease pathology. Herein we aimed to establish the predominant a-synuclein PTMs in post-mortem IPD and MSA pathology using immunohistochemistry. We examined the patterns of three a-synuclein PTMs (pS87, pS129, nY39) simultaneously in pathology- affected regions of 15 PD, 5 MSA, 6 neurologically normal controls. All antibodies recognized LBs, LNs, and GCIs, albeit to a variable extent. pS129 a-synuclein antibody was particularly immunopositive for LNs and synaptic dot-like structures followed by nY39 a- synuclein antibody. GCIs, neuronal inclusions, and small threads were positive for nY39 a- synuclein in MSA. Quantification of the LB scores revealed that pS129 a-synuclein was the dominant and earliest a-synuclein PTM followed by nY39 a-synuclein, while lower amounts of pSer87 a-synuclein appeared later in disease progression in PD. These results may have implications for novel biomarker and therapeutic developments

Energy absorption by "sparse" systems: beyond linear response theory

The analysis of the response to driving in the case of weakly chaotic or weakly interacting systems should go beyond linear response theory. Due to the "sparsity" of the perturbation matrix, a resistor network picture of transitions between energy levels is essential. The Kubo formula is modified, replacing the "algebraic" average over the squared matrix elements by a "resistor network" average. Consequently the response becomes semi-linear rather than linear. Some novel results have been obtained in the context of two prototype problems: the heating rate of particles in Billiards with vibrating walls; and the Ohmic Joule conductance of mesoscopic rings driven by electromotive force. Respectively, the obtained results are contrasted with the "Wall formula" and the "Drude formula".Comment: 8 pages, 7 figures, short pedagogical review. Proceedings of FQMT conference (Prague, 2011). Ref correcte

Organic and inorganic nitrogen amendments reduce biodegradation of biodegradable plastic mulch films

Biodegradable mulch films (BDMs) are a sustainable and promising alternative to non-biodegradable polyethylene mulches used in crop production systems. Nitrogen amendments in the form of fertilizers are used by growers to enhance soil and plant-available nutrients; however, there is limited research on how these additions impact the biodegradation of BDMs tilled into soils. A 4-month laboratory incubation study using soil microcosms was used to investigate the effects of inorganic (ammonium nitrate) and organic (urea and amino acids) nitrogen application on biodegradation of BDMs. We investigated the response of soil bacterial, fungal, and ammonia-oxidizing microbial abundance along with soil nitrogen pools and enzyme activities. Microcosms were comprised of soils from two diverse climates (Knoxville, TN, USA, and Mount Vernon, WA, USA) and BioAgri, a biodegradable mulch film made of Mater-Bi®, a bioplastic raw material containing starch and poly(butylene adipate-co-terephthalate) (PBAT). Both organic and inorganic nitrogen amendments inhibited mulch biodegradation, soil bacterial abundances, and enzyme activities. The greatest inhibition of mulch biodegradation in TN soils was observed with urea amendment where biodegradation was reduced by about 6 % compared to the no-nitrogen control. In WA soils, all nitrogen amendments suppressed biodegradation by about 1 % compared to the no-nitrogen control. Ammonia monooxygenase amoA gene abundances were increased in TN soils in all treatments but reduced for all treatments in WA soils. However, a significantly higher nitrate concentration and a lower ammonium concentration were seen for all nitrogen treatments compared to no-nitrogen controls in both TN and WA. This study suggests that the addition of nitrogen, particularly inorganic amendments, could slow down mulch biodegradation but that mulch biodegradation does not negatively affect soil nitrification activity.</p

A general analysis with trilinear and bilinear R-parity violating couplings in the light of recent SNO data

We analyse an extension of the minimal supersymmetric standard model including the dominant trilinear and bilinear R-parity violating contributions. We take the trilinear terms from the superpotential and the bilinear terms from the superpotential as well as the scalar potential. We compute the neutrino masses induced by those couplings and determine the allowed ranges of the R-parity violating parameters that are consistent with the latest SNO results, atmospheric data and the Chooz constraint. We also estimate the effective mass for neutrinoless double beta decay in such scenarios.Comment: 7 pages, Revtex, 1 PS figur

Minimal SUSY SO(10) model and predictions for neutrino mixings and leptonic CP violation

We discuss a minimal Supersymmetric SO(10) model where B-L symmetry is broken by a {\bf 126} dimensional Higgs multiplet which also contributes to fermion masses in conjunction with a {\bf 10} dimensional superfield. This minimal Higgs choice provides a partial unification of neutrino flavor structure with that of quarks and has been shown to predict all three neutrino mixing angles and the solar mass splitting in agreement with observations, provided one uses the type II seesaw formula for neutrino masses. In this paper we generalize this analysis to include arbitrary CP phases in couplings and vevs. We find that (i) the predictions for neutrino mixings are similar with $U_{e3}\simeq 0.18$ as before and other parameters in a somewhat bigger range and (ii) that to first order in the quark mixing parameter $\lambda$ (the Cabibbo angle), the leptonic mixing matrix is CP conserving. We also find that in the absence of any higher dimensional contributions to fermion masses, the CKM phase is different from that of the standard model implying that there must be new contributions to quark CP violation from the supersymmetry breaking sector. Inclusion of higher dimensional terms however allows the standard model CKM phase to be maintained.Comment: 22 pages, 6 figure

Intervention effects of Ganoderma lucidum spores on epileptiform discharge hippocampal neurons and expression of Neurotrophin-4 and N-Cadherin

Epilepsy can cause cerebral transient dysfunctions. Ganoderma lucidum spores (GLS), a traditional Chinese medicinal herb, has shown some antiepileptic effects in our previous studies. This was the first study of the effects of GLS on cultured primary hippocampal neurons, treated with Mg2+ free medium. This in vitro model of epileptiform discharge hippocampal neurons allowed us to investigate the anti-epileptic effects and mechanism of GLS activity. Primary hippocampal neurons from <1 day old rats were cultured and their morphologies observed under fluorescence microscope. Neurons were confirmed by immunofluorescent staining of neuron specific enolase (NSE). Sterile method for GLS generation was investigated and serial dilutions of GLS were used to test the maximum non-toxic concentration of GLS on hippocampal neurons. The optimized concentration of GLS of 0.122 mg/ml was identified and used for subsequent analysis. Using the in vitro model, hippocampal neurons were divided into 4 groups for subsequent treatment i) control, ii) model (incubated with Mg2+ free medium for 3 hours), iii) GLS group I (incubated with Mg2+ free medium containing GLS for 3 hours and replaced with normal medium and incubated for 6 hours) and iv) GLS group II (neurons incubated with Mg2+ free medium for 3 hours then replaced with a normal medium containing GLS for 6 hours). Neurotrophin-4 and N-Cadherin protein expression were detected using Western blot. The results showed that the number of normal hippocampal neurons increased and the morphologies of hippocampal neurons were well preserved after GLS treatment. Furthermore, the expression of neurotrophin-4 was significantly increased while the expression of N-Cadherin was decreased in the GLS treated group compared with the model group. This data indicates that GLS may protect hippocampal neurons by promoting neurotrophin-4 expression and inhibiting N-Cadherin expression

Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data

The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well as processing pipelines and analysis tools. Gene Ontology (GO, geneontology.org) is a major resource for gene enrichment analysis. The aim of this project, funded by the Alzheimer's Research United Kingdom (ARUK) foundation and led by the University College London (UCL) biocuration team, was to enhance the GO resource by developing new neurological GO terms, and use GO terms to annotate gene products associated with dementia. Specifically, proteins and protein complexes relevant to processes involving amyloid-beta and tau have been annotated and the resulting annotations are denoted in GO databases as 'ARUK-UCL'. Biological knowledge presented in the scientific literature was captured through the association of GO terms with dementia-relevant protein records; GO itself was revised, and new GO terms were added. This literature biocuration increased the number of Alzheimer's-relevant gene products that were being associated with neurological GO terms, such as 'amyloid-beta clearance' or 'learning or memory', as well as neuronal structures and their compartments. Of the total 2055 annotations that we contributed for the prioritised gene products, 526 have associated proteins and complexes with neurological GO terms. To ensure that these descriptive annotations could be provided for Alzheimer's-relevant gene products, over 70 new GO terms were created. Here, we describe how the improvements in ontology development and biocuration resulting from this initiative can benefit the scientific community and enhance the interpretation of dementia data

Lepton Flavor Violation and the Origin of the Seesaw Mechanism

The right--handed neutrino mass matrix that is central to the understanding of small neutrino masses via the seesaw mechanism can arise either (i) from renormalizable operators or (ii) from nonrenormalizable or super-renormalizable operators, depending on the symmetries and the Higgs content of the theory beyond the Standard Model. In this paper, we study lepton flavor violating (LFV) effects in the first class of seesaw models wherein the \nu_R Majorana masses arise from renormalizable Yukawa couplings involving a B-L = 2 Higgs field. We present detailed predictions for \tau -> \mu + \gamma and \mu -> e + \gamma branching ratios in these models taking the current neutrino oscillation data into account. Focusing on minimal supergravity models, we find that for a large range of MSSM parameters suggested by the relic abundance of neutralino dark matter and that is consistent with Higgs boson mass and other constraints, these radiative decays are in the range accessible to planned experiments. We compare these predictions with lepton flavor violation in the second class of models arising entirely from the Dirac Yukawa couplings. We study the dependence of the ratio r \equiv B(\mu -> e+\gamma)/B(\tau ->\mu +\gamma) on the MSSM parameters and show that measurement of r can provide crucial insight into the origin of the seesaw mechanism.Comment: 20 pages, Revtex, 7 figure

Parkinson's disease-linked mutations in VPS35 induce dopaminergic neurodegeneration

Mutations in the vacuolar protein sorting 35 homolog (VPS35) gene at the PARK17 locus, encoding a key component of the retromer complex, were recently identified as a new cause of late-onset, autosomal dominant Parkinson's disease (PD). Here we explore the pathogenic consequences of PD-associated mutations in VPS35 using a number of model systems. VPS35 exhibits a broad neuronal distribution throughout the rodent brain, including within the nigrostriatal dopaminergic pathway. In the human brain, VPS35 protein levels and distribution are similar in tissues from control and PD subjects, and VPS35 is not associated with Lewy body pathology. The common D620N missense mutation in VPS35 does not compromise its protein stability or localization to endosomal and lysosomal vesicles, or the vesicular sorting of the retromer cargo, sortilin, SorLA and cation-independent mannose 6-phosphate receptor, in rodent primary neurons or patient-derived human fibroblasts. In yeast we show that PD-linked VPS35 mutations are functional and can normally complement VPS35 null phenotypes suggesting that they do not result in a loss-of-function. In rat primary cortical cultures the overexpression of human VPS35 induces neuronal cell death and increases neuronal vulnerability to PD-relevant cellular stress. In a novel viral-mediated gene transfer rat model, the expression of D620N VPS35 induces the marked degeneration of substantia nigra dopaminergic neurons and axonal pathology, a cardinal pathological hallmark of PD. Collectively, these studies establish that dominant VPS35 mutations lead to neurodegeneration in PD consistent with a gain-of-function mechanism, and support a key role for VPS35 in the development of PD