Analysis of the complete mitochondrial genomes of two forensically important blowfly species: Lucilia caeasar and Lucilia illustris

Blowfly species of the family Calliphoridae can be used in forensic investigations to estimate the minimum post-mortem interval (PMI¬min). Lucilia caesar and Lucilia illustris (Diptera: Calliphoridae) are closely related and phenotypically similar, making reliable identification difficult, especially if specimens are in poor condition. To identify potential markers to genetically distinguish these species five complete mitochondrial genomes were sequenced: three for L. caesar (KM657111- KM657113) and two mitochondrial genomes for L. illustris (KM657109, KM 657110). The ND6 gene contained the most species-specific SNPs (1.71%), followed by the ND5 gene (1.68%) and then the COI gene (1.56%), identifying ND6 and ND5 as valuable loci for differentiating L. Caesar and L. illustris specimens

Categories of First-Order Quantifiers

One well known problem regarding quantifiers, in particular the 1storder quantifiers, is connected with their syntactic categories and denotations. The unsatisfactory efforts to establish the syntactic and ontological categories of quantifiers in formalized first-order languages can be solved by means of the so called principle of categorial compatibility formulated by Roman Suszko, referring to some innovative ideas of Gottlob Frege and visible in syntactic and semantic compatibility of language expressions. In the paper the principle is introduced for categorial languages generated by the Ajdukiewicz’s classical categorial grammar. The 1st-order quantifiers are typically ambiguous. Every 1st-order quantifier of the type k \u3e 0 is treated as a two-argument functorfunction defined on the variable standing at this quantifier and its scope (the sentential function with exactly k free variables, including the variable bound by this quantifier); a binary function defined on denotations of its two arguments is its denotation. Denotations of sentential functions, and hence also quantifiers, are defined separately in Fregean and in situational semantics. They belong to the ontological categories that correspond to the syntactic categories of these sentential functions and the considered quantifiers. The main result of the paper is a solution of the problem of categories of the 1st-order quantifiers based on the principle of categorial compatibility

A GPU-based finite-size pencil beam algorithm with 3D-density correction for radiotherapy dose calculation

Targeting at the development of an accurate and efficient dose calculation engine for online adaptive radiotherapy, we have implemented a finite size pencil beam (FSPB) algorithm with a 3D-density correction method on GPU. This new GPU-based dose engine is built on our previously published ultrafast FSPB computational framework [Gu et al. Phys. Med. Biol. 54 6287-97, 2009]. Dosimetric evaluations against Monte Carlo dose calculations are conducted on 10 IMRT treatment plans (5 head-and-neck cases and 5 lung cases). For all cases, there is improvement with the 3D-density correction over the conventional FSPB algorithm and for most cases the improvement is significant. Regarding the efficiency, because of the appropriate arrangement of memory access and the usage of GPU intrinsic functions, the dose calculation for an IMRT plan can be accomplished well within 1 second (except for one case) with this new GPU-based FSPB algorithm. Compared to the previous GPU-based FSPB algorithm without 3D-density correction, this new algorithm, though slightly sacrificing the computational efficiency (~5-15% lower), has significantly improved the dose calculation accuracy, making it more suitable for online IMRT replanning

On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF

<p>Abstract</p> <p>Background</p> <p>The Dbl-family of guanine nucleotide exchange factors (GEFs) activate the cytosolic GTPases of the Rho family by enhancing the rate of exchange of GTP for GDP on the cognate GTPase. This catalytic activity resides in the DH (Dbl-homology) domain, but typically GEFs are multidomain proteins containing other modules. It is believed that GEFs are autoinhibited in the cytosol due to supramodular architecture, and become activated in diverse signaling pathways through conformational change and exposure of the DH domain, as the protein is translocated to the membrane. A small family of RhoA-specific GEFs, containing the RGSL (regulators of G-protein signaling-like) domain, act as effectors of select GPCRs <it>via </it>Gα_12/13, although the molecular mechanism by which this pathway operates is not known. These GEFs include p115, LARG and PDZRhoGEF (PRG).</p> <p>Results</p> <p>Here we show that the autoinhibition of PRG is caused largely by an interaction of a short negatively charged sequence motif, immediately upstream of the DH-domain and including residues Asp706, Glu708, Glu710 and Asp712, with a patch on the catalytic surface of the DH-domain including Arg867 and Arg868. In the absence of both PDZ and RGSL domains, the DH-PH tandem with additional 21 residues upstream, is 50% autoinhibited. However, within the full-length protein, the PDZ and/or RGSL domains significantly restore autoinhibition.</p> <p>Conclusion</p> <p>Our results suggest a mechanism for autoinhibition of RGSL family of GEFs, in which the RGSL domain and a unique sequence motif upstream of the DH domain, act cooperatively to reduce the ability of the DH domain to bind the nucleotide free RhoA. The activation mechanism is likely to involve two independent steps, i.e. displacement of the RGSL domain and conformational change involving the autoinhibitory sequence motif containing several negatively charged residues.</p

Flexible Piezoresistive Polystyrene Composite Sensors Filled with Hollow 3D Graphitic Shells

The objective of this research was to develop highly effective conductive polymer composite (CPC) materials for flexible piezoresistive sensors, utilizing hollow three-dimensional graphitic shells as a highly conductive particulate component. Polystyrene (PS), a cost-effective and robust polymer widely used in various applications such as household appliances, electronics, automotive parts, packaging, and thermal insulation materials, was chosen as the polymer matrix. The hollow spherical three-dimensional graphitic shells (GS) were synthesized through chemical vapor deposition (CVD) with magnesium oxide (MgO) nanoparticles serving as a support, which was removed post-synthesis and employed as the conductive filler. Commercial multi-walled carbon nanotubes (CNTs) were used as a reference one-dimensional graphene material. The main focus of this study was to investigate the impact of the GS on the piezoresistive response of carbon/polymer composite thin films. The distribution and arrangement of GS and CNTs in the polymer matrix were analyzed using techniques such as X-ray diffraction and scanning electron microscopy, while the electrical, thermal, and mechanical properties of the composites were also evaluated. The results revealed that the PS composite films filled with GS exhibited a more pronounced piezoresistive response as compared to the CNT-based composites, despite their lower mechanical and thermal performance

Reduced Na+ and higher K+ channel expression and function contribute to right ventricular origin of arrhythmias in Scn5a+/− mice

Brugada syndrome (BrS) is associated with ventricular tachycardia originating particularly in the right ventricle (RV). We explore electrophysiological features predisposing to such arrhythmic tendency and their possible RV localization in a heterozygotic Scn5a+/− murine model. Nav1.5 mRNA and protein expression were lower in Scn5a+/− than wild-type (WT), with a further reduction in the RV compared with the left ventricle (LV). RVs showed higher expression levels of Kv4.2, Kv4.3 and KChIP2 in both Scn5a+/− and WT. Action potential upstroke velocity and maximum Na+ current (INa) density were correspondingly decreased in Scn5a+/−, with a further reduction in the RV. The voltage dependence of inactivation was shifted to more negative values in Scn5a+/−. These findings are predictive of a localized depolarization abnormality leading to slowed conduction. Persistent Na+ current (IpNa) density was decreased in a similar pattern to INa. RV transient outward current (Ito) density was greater than LV in both WT and Scn5a+/−, and had larger time constants of inactivation. These findings were also consistent with the observation that AP durations were smallest in the RV of Scn5a+/−, fulfilling predictions of an increased heterogeneity of repolarization as an additional possible electrophysiological mechanism for arrhythmogenesis in BrS

Differences in Ear Rot Resistance and Fusarium verticillioides-Produced Fumonisin Contamination Between Polish Currently and Historically Used Maize Inbred Lines

Poland is the fifth largest European country, in terms of maize production. Ear rots caused by Fusarium spp. are significant diseases affecting yield and causing grain mycotoxin contamination. Inbred lines, which are commonly used in Polish breeding programs, belong, mostly, to two distinct genetic categories: flint and dent. However, historically used lines belonging to the heterotic Lancaster, IDT and SSS groups were also present in previous Polish breeding programs. In the current study, 98 inbred lines were evaluated across a 2-year-long experiment, after inoculation with F. verticillioides and under natural infection conditions. Lancaster, IDT, SSS and SSS/IDT groups were characterized as the most susceptible ones and flint as the more resistant. Based on the results obtained, the moderately resistant and most susceptible genotypes were defined to determine the content of fumonisins (FBs) in kernel and cob fractions using the HPLC method. Fumonisin's content was higher in the grain samples collected from inoculated plants than in cobs. The association of visible Fusarium symptoms with fumonisin concentration in grain samples was significant. Conversely, the cobs contained more FB1 under natural infection, which may be related to a pathogen's type of growth, infection time or presence of competitive species. Using ddRADseq genome sampling method it was possible to distinguish a basal relationship between moderately resistant and susceptible genotypes. Genetic distance between maize genotypes was high. Moderately resistant inbreed lines, which belong to IDT and IDT/SSS belong to one haplotype. Genotypes which belong to the flint, dent or Lancaster group, and were characterized as moderately resistant were classified separately as the same susceptible one. This research has demonstrated that currently grown Polish inbred lines, as well the ones used in the past are a valid source of resistance to Fusarium ear rot. A strong association was observed between visible Fusarium symptoms with fumonisin concentration in grain samples, suggesting that selection in maize for reduced visible molds should reduce the risk of mycotoxin contamination. NGS techniques provide new tools for overcoming the long selection process and increase the breeding efficiency

A de novo substitution in BCL11B leads to loss of interaction with transcriptional complexes and craniosynostosis

Craniosynostosis, the premature ossification of cranial sutures, is a developmental disorder of the skull vault, occurring in approximately 1 in 2250 births. The causes are heterogeneous, with a monogenic basis identified in ~25% of patients. Using whole-genome sequencing, we identified a novel, de novo variant in BCL11B, c.7C>A, encoding an R3S substitution (p.R3S), in a male patient with coronal suture synostosis. BCL11B is a transcription factor that interacts directly with the nucleosome remodelling and deacetylation complex (NuRD) and polycomb-related complex 2 (PRC2) through the invariant proteins RBBP4 and RBBP7. The p.R3S substitution occurs within a conserved amino-terminal motif (RRKQxxP) of BCL11B and reduces interaction with both transcriptional complexes. Equilibrium binding studies and molecular dynamics simulations show that the p.R3S substitution disrupts ionic coordination between BCL11B and the RBBP4-MTA1 complex, a subassembly of the NuRD complex, and increases the conformational flexibility of Arg-4, Lys-5 and Gln-6 of BCL11B. These alterations collectively reduce the affinity of BCL11B p.R3S for the RBBP4-MTA1 complex by nearly an order of magnitude. We generated a mouse model of the BCL11B p.R3S substitution using a CRISPR-Cas9-based approach, and we report herein that these mice exhibit craniosynostosis of the coronal suture, as well as other cranial sutures. This finding provides strong evidence that the BCL11B p.R3S substitution is causally associated with craniosynostosis and confirms an important role for BCL11B in the maintenance of cranial suture patency

A comparative study of biodegradation of vinyl acetate by environmental strains

Four Gram-negative strains, E3_2001, EC1_2004, EC3_3502 and EC2_3502, previously isolated from soil samples, were subjected to comparative studies in order to select the best vinyl acetate degrader for waste gas treatment. Comparison of biochemical and physiological tests as well as the results of fatty acids analyses were comparable with the results of 16S rRNA gene sequence analyses. The isolated strains were identified as Pseudomonas putida EC3_2001, Pseudomonas putida EC1_2004, Achromobacter xylosoxidans EC3_3502 and Agrobacterium sp. EC2_3502 strains. Two additional strains, Pseudomonas fluorescens PCM 2123 and Stenotrophomonas malthophilia KB2, were used as controls. All described strains were able to use vinyl acetate as the only source of carbon and energy under aerobic as well as oxygen deficiency conditions. Esterase, alcohol dehydrogenase and aldehyde dehydrogenase were involved in vinyl acetate decomposition under aerobic conditions. Shorter degradation times of vinyl acetate were associated with accumulation of acetic acid, acetaldehyde and ethanol as intermediates in the culture fluids of EC3_2001 and KB2 strains. Complete aerobic degradation of vinyl acetate combined with a low increase in biomass was observed for EC3_2001 and EC1_2004 strains. In conclusion, P. putida EC1_2004 is proposed as the best vinyl acetate degrader for future waste gas treatment in trickle-bed bioreactors

Phosphate Binding with Sevelamer Preserves Mechanical Competence of Bone Despite Acidosis in Advanced Experimental Renal Insufficiency

Introduction Phosphate binding with sevelamer can ameliorate detrimental histomorphometric changes of bone in chronic renal insufficiency (CRI). Here we explored the effects of sevelamer-HCl treatment on bone strength and structure in experimental CRI. Methods Forty-eight 8-week-old rats were assigned to surgical 5/6 nephrectomy (CRI) or renal decapsulation (Sham). After 14 weeks of disease progression, the rats were allocated to untreated and sevelamer-treated (3% in chow) groups for 9 weeks. Then the animals were sacrificed, plasma samples collected, and femora excised for structural analysis (biomechanical testing, quantitative computed tomography). Results Sevelamer-HCl significantly reduced blood pH, and final creatinine clearance in the CRI groups ranged 30%-50% of that in the Sham group. Final plasma phosphate increased 2.4- to 2.9-fold, and parathyroid hormone 13- to 21-fold in CRI rats, with no difference between sevelamer-treated and untreated animals. In the femoral midshaft, CRI reduced cortical bone mineral density (-3%) and breaking load (-15%) (p Conclusions In this model of stage 3-4 CRI, sevelamer-HCl treatment ameliorated the decreases in femoral midshaft and neck mineral density, and restored bone strength despite prevailing acidosis. Therefore, treatment with sevelamer can efficiently preserve mechanical competence of bone in CRI.Peer reviewe