The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

Background  

The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues.     

Biotransformation of plantain pseudostem fibres using local enzyme sources; analysis of their potential as commercial poultry feed

Plantain pseudo-stem fibres (PPS) were valorized in this study by subjecting to simultaneous saccharification and fermentation (SSF) and afterwards, their complex carbohydrates and monosaccharides, mycotoxins, protein qualities, and free radical scavenging potentials were compared to those of commercial poultry feeds (CPF). The SSF of PPS was achieved using digestive juice of the snail; Archachatina marginata, and yeast, while standard methods like HPLC-UV, HPLC-DAD, monosaccharides and mycotoxin kits, and UV-VIS spectrophotometry were used for analysis. The cellulose, hemicellulose, pectin, lignin, extractives, and acetyl contents of PPS were significantly (p?<?.05) reduced when subjected to SSF. Glucose (41.1%), galactose (11.2%), mannose (1.7%), and fucose (1.8%) contents of the SSF-PPS were higher than those of the PPS and CPF while CPF showed higher contents of arabinose (8.2%), fructose (18.3%), and rhamnose (1.7%). No mycotoxin was detected in the PPS, while all aflatoxins (B₁, B₂, G₁, and G₂), citrinin, fumonisin B₁, and B₂, ochratoxin A and B contents of SSF-PPS were equivalent to those for CPF. Patulin (5.52×10^?4?µg/kg) and zearalenone (7.76×10^?6?µg/kg) contents of the SSF-PPS were lower than those for CPF (1.50×10^?3?µg/kg and 1.13×10^?5?µg/kg respectively). The total amino acids (TAA), total non-essential and essential amino acids (TNEAA and TEAA), total basic and branched chain amino acids (TBAA and TBCAA) of the SSF-PPS were higher than those of the PPS and CPF while the free radical scavenging potentials of the SSF-PPS were mostly concentration dependent, and showed significantly higher ABTS, DPPH, Ferric, OH, lipid peroxide, and superoxide radical scavenging potentials than the standards used. This study has shown that the valorization of the agricultural residue using SSF, improves carbohydrate, protein, mycotoxins, and in-vitro antioxidant properties suitable enough for poultry feeding.     

A motion-decomposition approach to address gimbal lock in the 3-cylinder open chain mechanism description of a joint coordinate system at the glenohumeral joint

In this study, the standard-sequence properties of a joint coordinate system were implemented for the glenohumeral joint by the use of a set of instantaneous geometrical planes. These are: a plane that is bound by the humeral long axis and an orthogonal axis that is the cross product of the scapular anterior axis and this long axis, and a plane that is bounded by the long axis of the humerus and the cross product of the scapular lateral axis and this long axis. The relevant axes are updated after every decomposition of a motion component of a humeral position. Flexion, abduction and rotation are then implemented upon three of these axes and are applied in a step-wise uncoupling of an acquired humeral motion to extract the joint coordinate system angles. This technique was numerically applied to physiological kinematics data from the literature to convert them to the joint coordinate system and to visually reconstruct the motion on a set of glenohumeral bones for validation.     

Specificity of clinical examinations for testing glenohumeral ligament integrity: a computational study

An accurate diagnosis of glenohumeral joint (GHJ) instability is essential for an effective surgical intervention. There is presently no known comprehensive algorithm of clinical tests for the confirmation of the functional integrity of glenohumeral ligaments (GHLs). A validated computational GHL strain analyser was applied to a set of GHJ kinematics data from the literature to simulate 57 different physiological clinical examination manoeuvres. An algorithm that integrates the GHL pre-straining activities at the toe region of the stress–strain curve was developed for the quantification of ligament loading from prevailing strains. This was used to upgrade the strain analyser and applied to produce a matrix of the various GHL loadings and sensitivities during the manoeuvres. The investigation magnified the likely impact of anatomical variations of GHL attachments as possible causes of misdiagnoses during clinical examinations of GHJ dysfunction. This can serve as an assistive guide to ascertain the functional condition of a specific GHL during symptomatic clinical examinations.     

Keratinocyte cadherin desmoglein 1 controls melanocyte behavior through paracrine signaling

The epidermis is the first line of defense against ultraviolet (UV) light from the sun. Keratinocytes and melanocytes respond to UV exposure by eliciting a tanning response dependent in part on paracrine signaling, but how keratinocyte:melanocyte communication is regulated during this response remains understudied. Here, we uncover a surprising new function for the keratinocyte‐specific cell–cell adhesion molecule desmoglein 1 (Dsg1) in regulating keratinocyte:melanocyte paracrine signaling to promote the tanning response in the absence of UV exposure. Melanocytes within Dsg1‐silenced human skin equivalents exhibited increased pigmentation and altered dendrite morphology, phenotypes which were confirmed in 2D culture using conditioned media from Dsg1‐silenced keratinocytes. Dsg1‐silenced keratinocytes increased melanocyte‐stimulating hormone precursor (Pomc) and cytokine mRNA. Melanocytes cultured in media conditioned by Dsg1‐silenced keratinocytes increased Mitf and Tyrp1 mRNA, TYRP1 protein, and melanin production and secretion. Melanocytes in Dsg1‐silenced skin equivalents mislocalized suprabasally, reminiscent of early melanoma pagetoid behavior. Together with our previous report that UV reduces Dsg1 expression, these data support a role for Dsg1 in controlling keratinocyte:melanocyte paracrine communication and raise the possibility that a Dsg1‐deficient niche contributes to pagetoid behavior, such as occurs in early melanoma development.     

Genetic variation in TIMP1 but not MMPs predict excess FEV1 decline in two general population-based cohorts

Background

An imbalance in Matrix MetalloProteases (MMPs) and Tissue Inhibitors of MMPs (TIMPs) contributes to Chronic Obstructive Pulmonary Disease (COPD) development. Longitudinal studies investigating Single Nucleotide Polymorphisms (SNPs) in MMPs and TIMPs with respect to COPD development and lung function decline in the general population are lacking.

Methods

We genotyped SNPs in MMP1 (G-1607GG), MMP2 (-1306 C/T), MMP9 (3 tagging SNPs), MMP12 (A-82G and Asn357Ser) and TIMP1 (Phe124Phe and Ile158Ile) in 1390 Caucasians with multiple FEV₁ measurements from a prospective cohort study in the general population. FEV₁ decline was analyzed using linear mixed effect models adjusted for confounders. Analyses of the X-chromosomal TIMP1 gene were stratified according to sex. All significant associations were repeated in an independent general population cohort (n = 1152).

Results

MMP2 -1306 TT genotype carriers had excess FEV₁ decline (-4.0 ml/yr, p = 0.03) compared to wild type carriers. TIMP1 Ile158Ile predicted significant excess FEV₁ decline in both males and females. TIMP1 Phe124Phe predicted significant excess FEV₁ decline in males only, which was replicated (p = 0.10) in the second cohort. The MMP2 and TIMP1 Ile158Ile associations were not replicated. Although power was limited, we did not find associations with COPD development.

Conclusions

We for the first time show that TIMP1 Phe124Phe contributes to excess FEV₁ decline in two independent prospective cohorts, albeit not quite reaching conventional statistical significance in the replication cohort. SNPs in MMPs evidently do not contribute to FEV₁ decline in the general population.     

A tetravalent dengue nanoparticle stimulates antibody production in mice

Background

Dengue is a major public health problem worldwide, especially in the tropical and subtropical regions of the world. Infection with a single Dengue virus (DENV) serotype causes a mild, self-limiting febrile illness called dengue fever. However, a subset of patients experiencing secondary infection with a different serotype progresses to the severe form of the disease, dengue hemorrhagic fever/dengue shock syndrome. Currently, there are no licensed vaccines or antiviral drugs to prevent or treat dengue infections. Biodegradable nanoparticles coated with proteins represent a promising method for in vivo delivery of vaccines.

Findings

Here, we used a murine model to evaluate the IgG production after administration of inactivated DENV corresponding to all four serotypes adsorbed to bovine serum albumin nanoparticles. This formulation induced a production of anti-DENV IgG antibodies (p < 0.001). However, plaque reduction neutralization assays with the four DENV serotypes revealed that these antibodies have no neutralizing activity in the dilutions tested.

Conclusions

Our results show that while the nanoparticle system induces humoral responses against DENV, further investigation with different DENV antigens will be required to improve immunogenicity, epitope specicity, and functional activity to make this platform a viable option for DENV vaccines.     

Distribution and natural infection status of synantrophic triatomines (Hemiptera: Reduviidae), vectors of Trypanosoma cruzi,reveals new epidemiological scenarios for chagas disease in the Highlands of Colombia

IntroductionUpdating the distribution and natural infection status of triatomine bugs is critical for planning, prioritizing, and implementing strategies to control Chagas disease (CD), especially after vector reduction programs. After carrying out a control program, the Department of Boyaca contains the highest number of Colombian municipalities certified by PAHO to be free of intradomiciliary transmission of Trypanosoma cruzi by Rhodnius prolixus. The present work describes the spatial distribution, natural infection (NI), and molecular characterization of T. cruzi in synanthropic triatomines from the Department of Boyaca in 2017 and 2018.Materials and methodsAn entomological survey was conducted in 52 municipalities in Boyaca known to have had previous infestations of triatomine bugs. Insects were collected through active searches carried out by technical personnel from the Secretary of Health and community members using Triatomine Collection Stations (PITs-acronym in Spanish). For evaluation of natural infection, triatomines were identified morphologically and grouped in pools of one to five individuals of the same species collected in the same household. DNA derived from the feces of each pool of insects was analyzed by PCR for the presence of T. cruzi using primers flanking the satellite DNA of the parasite. SL-IR primers were used to differentiate TCI from the other DTUs and to identify different genotypes. The distribution of the collected triatomines was analyzed to determine any vector hotspots using spatial recreation.ResultsA total of 670 triatomine bugs was collected, belonging to five species: Triatoma dimidiata (73.2%), Triatoma venosa (16.7%), Panstrongylus geniculatus (5.7%), Rhodnius prolixus (4.4%), and Panstrongylus rufotuberculatus (0.4%), from 29 of the 52 municipalities. In total, 71.6% of the bugs were collected within houses (intradomiciliary) and the rest around the houses (peridomiciliary). Triatoma dimidiata was the most widely distributed species and had the highest natural infection index (37.8%), followed by T. venosa and P. geniculatus. TcI was the only DTU found, with the TcI Dom genotype identified in 80% of positive samples and TcI sylvatic in the other insects. Spatial analysis showed clusters of T. dimidiata and T. venosa in the northeast and southwest regions of Boyaca.ConclusionsAfter some municipalities were certified free of natural transmission within houses (intradomiciliary transmission) of T. cruzi by R. prolixus, T. dimidiata has become the most prevalent vector present, and represents a significant risk of resurgent CD transmission. However, T. venosa, P. geniculatus, and P. rufotuberculatus also contribute to the increased risk of transmission. The presence of residual R. prolixus may undo the successes achieved through vector elimination programs. The molecular and spatial analysis used here allows us to identify areas with an ongoing threat of parasite transmission and improve entomological surveillance strategies.