PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction

Peptidoglycan recognition proteins (PGRPs) are ubiquitous among animals and play pivotal functions in insect immunity. Non-catalytic PGRPs are involved in the activation of immune pathways by binding to the peptidoglycan (PGN), whereas amidase PGRPs are capable of cleaving the PGN into non-immunogenic compounds. Drosophila PGRP-LB belongs to the amidase PGRPs and downregulates the immune deficiency (IMD) pathway by cleaving meso-2,6-diaminopimelic (meso-DAP or DAP)-type PGN. While the recognition process is well analyzed for the non-catalytic PGRPs, little is known about the enzymatic mechanism for the amidase PGRPs, despite their essential function in immune homeostasis. Here, we analyzed the specific activity of different isoforms of Drosophila PGRP-LB towards various PGN substrates to understand their specificity and role in Drosophila immunity. We show that these isoforms have similar activity towards the different compounds. To analyze the mechanism of the amidase activity, we performed site directed mutagenesis and solved the X-ray structures of wild-type Drosophila PGRP-LB and its mutants, with one of these structures presenting a protein complexed with the tracheal cytotoxin (TCT), a muropeptide derived from the PGN. Only the Y78F mutation abolished the PGN cleavage while other mutations reduced the activity solely. Together, our findings suggest the dynamic role of the residue Y78 in the amidase mechanism by nucleophilic attack through a water molecule to the carbonyl group of the amide function destabilized by Zn²⁺.     

Visceral Adipose Tissue Displays Unique Metabolomic Fingerprints in Obesity,Pre-Diabetes and Type 2 Diabetes

Visceral adipose tissue (VAT) metabolic profiling harbors the potential to disentangle molecular changes underlying obesity-related dysglycemia. In this study, the VAT exometabolome of subjects with obesity and different glycemic statuses are analyzed. The subjects (n = 19) are divided into groups according to body mass index and glycemic status: subjects with obesity and euglycemia (Ob+NGT, n = 5), subjects with obesity and pre-diabetes (Ob+Pre-T2D, n = 5), subjects with obesity and type 2 diabetes under metformin treatment (Ob+T2D, n = 5) and subjects without obesity and with euglycemia (Non-Ob, n = 4), used as controls. VATs are incubated in culture media and extracellular metabolite content is determined by proton nuclear magnetic resonance (¹H-NMR). Glucose consumption is not different between the groups. Pyruvate and pyroglutamate consumption are significantly lower in all groups of subjects with obesity compared to Non-Ob, and significantly lower in Ob+Pre-T2D as compared to Ob+NGT. In contrast, isoleucine consumption is significantly higher in all groups of subjects with obesity, particularly in Ob+Pre-T2D, compared to Non-Ob. Acetate production is also significantly lower in Ob+Pre-T2D compared to Non-Ob. In sum, the VAT metabolic fingerprint is associated with pre-diabetes and characterized by higher isoleucine consumption, accompanied by lower acetate production and pyruvate and pyroglutamate consumption. We propose that glucose metabolism follows different fates within the VAT, depending on the individuals’ health status.     

Genetic Susceptibility to Periodontal Disease in Down Syndrome: A Case-Control Study

Severe periodontitis is prevalent in Down syndrome (DS). This study aimed to identify genetic variations associated with periodontitis in individuals with DS. The study group was distributed into DS patients with periodontitis (n = 50) and DS patients with healthy periodontium (n = 36). All samples were genotyped with the “Axiom Spanish Biobank” array, which contains 757,836 markers. An association analysis at the individual marker level using logistic regression, as well as at the gene level applying the sequence kernel association test (SKAT) was performed. The most significant genes were included in a pathway analysis using the free DAVID software. C12orf74 (rs4315121, p = 9.85 × 10⁻⁵, OR = 8.84), LOC101930064 (rs4814890, p = 9.61 × 10⁻⁵, OR = 0.13), KBTBD12 (rs1549874, p = 8.27 × 10⁻⁵, OR = 0.08), PIWIL1 (rs11060842, p = 7.82 × 10⁻⁵, OR = 9.05) and C16orf82 (rs62030877, p = 8.92 × 10⁻⁵, OR = 0.14) showed a higher probability in the individual analysis. The analysis at the gene level highlighted PIWIL, MIR9-2, LHCGR, TPR and BCR. At the signaling pathway level, PI3K-Akt, long-term depression and FoxO achieved nominal significance (p = 1.3 × 10⁻², p = 5.1 × 10⁻³, p = 1.2 × 10⁻², respectively). In summary, various metabolic pathways are involved in the pathogenesis of periodontitis in DS, including PI3K-Akt, which regulates cell proliferation and inflammatory response.     

Mössbauer study of the thermal decomposition of FeS2 in coal

The Mössbauer effect has been used to study the transformations of FeS₂ in four different coals: IL No. 6, Ky $\text{9}\text{14}$, Blacksville No. 2, and Powhatan No. 5. The transformations of FeS₂ in the coals were studied in an inert atmosphere. It was observed that the pyrrhotites formed from FeS₂ have a considerable reduction in the isomer shift at 440 °C as compared to the values obtained in the absence of coal. This effect is associated with the interaction of the pyrrhotites with the coal constituents at high temperatures. There is also a significant line-broadening at 440 °C. This broadening is due either to vacancy motion in the iron sulphides and/or to motional broadening due to particle motion in the coal-derived liquids. The percentage conversion of pyrite to pyrrhotite depends markedly on time as well as type of coal. The weathering of the coal has a detrimental effect on the rate of conversion of pyrite to pyrrhotite. The ferrous sulphate layers covering the pyrite particles hinder the removal of sulphur from that surface. The major factor affecting the $\text{Fe}\text{S}$ ratio is the total amount of sulphur available for H₂S formation. Partial H₂S pressure is the crucial quantity controlling the stoichiometry of the pyrrhotites. Hence, a high percentage of H₂S in the reactor at high temperature will assure the formation of pyrrhotites with a high number of metal vacancies.     

Isobaric vapor—liquid equilibria for binary systems composed of methyl butanoate with ethanol and with propan-1-ol at 114.66 and 127.99 kpa

Vapor-liquid equilibrium data for the binary systems methyl butanoate/ethanol and methyl butanoate/propan-l-ol at pressures of 114.66 and 127.99 kPa are presented. Both mixtures yield an azeotrope, the compositions (ester) of which decrease quasi-linearly as the pressure increases. The experimental data for all the binary mixtures were fitted to a suitable equation and then used for comparison with predictions by ASOG and UNIFAC methods. These group contribution models give a good estimation of activity coefficients with an overall mean error less than 5% for all cases.     

Fast finite difference Poisson solvers on heterogeneous architectures

In this paper we propose and evaluate a set of new strategies for the solution of three dimensional separable elliptic problems on CPU–GPU platforms. The numerical solution of the system of linear equations arising when discretizing those operators often represents the most time consuming part of larger simulation codes tackling a variety of physical situations. Incompressible fluid flows, electromagnetic problems, heat transfer and solid mechanic simulations are just a few examples of application areas that require efficient solution strategies for this class of problems. GPU computing has emerged as an attractive alternative to conventional CPUs for many scientific applications. High speedups over CPU implementations have been reported and this trend is expected to continue in the future with improved programming support and tighter CPU–GPU integration. These speedups by no means imply that CPU performance is no longer critical. The conventional CPU-control–GPU-compute pattern used in many applications wastes much of CPU’s computational power. Our proposed parallel implementation of a classical cyclic reduction algorithm to tackle the large linear systems arising from the discretized form of the elliptic problem at hand, schedules computing on both the GPU and the CPUs in a cooperative way. The experimental result demonstrates the effectiveness of this approach.     

Improving the performance of Invertible Bloom Lookup Tables

Invertible Bloom Lookup Tables (IBLTs) have been recently introduced as an extension of traditional Bloom filters. IBLTs store key-value pairs. Unlike traditional Bloom filters, IBLTs support both a lookup operation (given a key, return a value) and an operation that lists out all the key-value pairs stored. One issue with IBLTs is that there is a probability that a lookup operation will return “not found” for a key. In this paper, a technique to reduce this probability without affecting the storage requirement and only moderately increasing the search time is presented and evaluated. The results show that it can significantly reduce the probability of not returning a value that is actually stored in the IBLT. The overhead of the modified search procedure, compared to the standard IBLT search procedure, is small and has little impact on the average search time.     

A genetic tango attack against the David–Prasad RFID ultra‐lightweight authentication protocol

Radio frequency identification (RFID) is a powerful technology that enables wireless information storage and control in an economical way. These properties have generated a wide range of applications in different areas. Due to economic and technological constrains, RFID devices are seriously limited, having small or even tiny computational capabilities. This issue is particularly challenging from the security point of view. Security protocols in RFID environments have to deal with strong computational limitations, and classical protocols cannot be used in this context. There have been several attempts to overcome these limitations in the form of new lightweight security protocols designed to be used in very constrained (sometimes called ultra‐lightweight) RFID environments. One of these proposals is the David–Prasad ultra‐lightweight authentication protocol. This protocol was successfully attacked using a cryptanalysis technique named Tango attack. The capacity of the attack depends on a set of boolean approximations. In this paper, we present an enhanced version of the Tango attack, named Genetic Tango attack, that uses Genetic Programming to design those approximations, easing the generation of automatic cryptanalysis and improving its power compared to a manually designed attack. Experimental results are given to illustrate the effectiveness of this new attack.