Parkinson's disease and schizophrenia interactomes contain temporally distinct gene clusters underlying comorbid mechanisms and unique disease processes

Genome-wide association studies suggest significant overlaps in Parkinson's disease (PD) and schizophrenia (SZ) risks, but the underlying mechanisms remain elusive. The protein-protein interaction network ('interactome') plays a crucial role in PD and SZ and can incorporate their spatiotemporal specificities. Therefore, to study the linked biology of PD and SZ, we compiled PD- and SZ-associated genes from the DisGeNET database, and constructed their interactomes using BioGRID and HPRD. We examined the interactomes using clustering and enrichment analyses, in conjunction with the transcriptomic data of 26 brain regions spanning foetal stages to adulthood available in the BrainSpan Atlas. PD and SZ interactomes formed four gene clusters with distinct temporal identities (Disease Gene Networks or 'DGNs'1-4). DGN1 had unique SZ interactome genes highly expressed across developmental stages, corresponding to a neurodevelopmental SZ subtype. DGN2, containing unique SZ interactome genes expressed from early infancy to adulthood, correlated with an inflammation-driven SZ subtype and adult SZ risk. DGN3 contained unique PD interactome genes expressed in late infancy, early and late childhood, and adulthood, and involved in mitochondrial pathways. DGN4, containing prenatally-expressed genes common to both the interactomes, involved in stem cell pluripotency and overlapping with the interactome of 22q11 deletion syndrome (comorbid psychosis and Parkinsonism), potentially regulates neurodevelopmental mechanisms in PD-SZ comorbidity. Our findings suggest that disrupted neurodevelopment (regulated by DGN4) could expose risk windows in PD and SZ, later elevating disease risk through inflammation (DGN2). Alternatively, variant clustering in DGNs may produce disease subtypes, e.g., PD-SZ comorbidity with DGN4, and early/late-onset SZ with DGN1/DGN2.

Cold Collisions of Ro-Vibrationally Excited D2 Molecules

The H₂ + H₂ system has long been considered a benchmark system for ro-vibrational energy transfer in bimolecular collisions. However, most studies thus far have focused on collisions involving H₂ molecules in the ground vibrational level or in the first excited vibrational state. While H₂ + H₂/HD collisions have received wide attention due to the important role they play in astrophysics, D₂ + D₂ collisions have received much less attention. Recently, Zhou et al. [ Nat. Chem. 2022, 14, 658-663, DOI: 10.1038/s41557-022-00926-z] examined stereodynamic aspects of rotational energy transfer in collisions of two aligned D₂ molecules prepared in the v = 2 vibrational level and j = 2 rotational level. Here, we report quantum calculations of rotational and vibrational energy transfer in collisions of two D₂ molecules prepared in vibrational levels up to v = 2 and identify key resonance features that contribute to the angular distribution in the experimental results of Zhou et al. The quantum scattering calculations were performed in full dimensionality and using the rigid-rotor approximation using a recently developed highly accurate six-dimensional potential energy surface for the H₄ system that allows descriptions of collisions involving highly vibrationally excited H₂ and its isotopologues.

Efficacy of Gamma Irradiation in Improving the Microbial and Physical Quality Properties of Dried Chillies (Capsicum annuum L.): A Review

Dried chilli is one of the highly traded spices globally and is well-known for its natural flavour, colour, and unique pungent taste. It is rich in nutrients and has medicinal benefits. During the dehydration and storage process, the proliferation of unwanted microorganisms in dried chilli is unavoidable. Recently, the occurrence of toxigenic fungi and faecal coliforms has been widespread that can cause severe illness and even death. Therefore, sanitation treatment is highly required to decontaminate undesirable microorganisms. Among the common sanitation treatments applied, food irradiation is gaining attention worldwide because of concern for post-harvest loss, foodborne disease, and more stringent regulation in dried chilli trading. Irradiation can successfully preserve dried chilli from pathogenic bacteria with minimal disturbance to critical physical properties, such as pungency and colour. It can also save dried chilli from secondary pollution by storing it into final packing before radiation which helps in distribution to market promptly after treatment. Furthermore, radiation does not leave any chemical residues after the treatment, ensuring the quality and safety of the dried chilli. The efficiency of radiation depends mainly on the initial level of contamination and the persistence of the harmful microorganism. A low irradiation dose is sufficient for dried chili to reduce microbial load to an acceptable level and eliminate pathogens even though a minimum radiation dose of 10 kGy is required for complete sterilization. However, high dosage may affect the colour properties. Gamma radiation, X-ray, and electron beam radiation are the three approved radiation sources for dried chilli in most countries and proven effective for dried chilli preservation. Thus, this review paper highlights the microbial and physical quality properties in gamma radiated dried chillies.

Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes

Mechanisms underlying anxiety disorders remain elusive despite the discovery of several associated genes. We constructed the protein-protein interaction networks (interactomes) of six anxiety disorders and noted enrichment for striatal expression among common genes in the interactomes. Five of these interactomes shared distinctive overlaps with the interactomes of genes that were differentially expressed in two striatal compartments (striosomes and matrix). Generalized anxiety disorder and social anxiety disorder interactomes showed exclusive and statistically significant overlaps with the striosome and matrix interactomes, respectively. Systematic gene expression analysis with the anxiety disorder interactomes constrained to contain only those genes that were shared with striatal compartment interactomes revealed a bifurcation among the disorders, which was influenced by the anterior cingulate cortex, nucleus accumbens, amygdala and hippocampus, and the dopaminergic signaling pathway. Our results indicate that the functionally distinct striatal pathways constituted by the striosome and the matrix may influence the etiological differentiation of various anxiety disorders.

Optimisation of Flight and Maintenance Planning for Defence Aviation with Modified Artificial Bee Colony Algorithm

The planning of flight operations and maintenance is a crucial activity for both commercial and military aircraft. Military aircraft have to be always mission-ready. The task of ensuring this can become quite challenging when several operational requirements and maintenance constraints are to be fulfilled simultaneously. This paper, therefore, addresses the optimisation of flight and maintenance planning (FMP) when several diverse factors such as aircraft flying hours (AFH), flight cycles (FC), calendar life, annual flying requirement (AFR), etc. are to be factored in. Such a problem has not been considered previously. Because the problem can become unwieldy to solve by other methods, two schemes, that is, the genetic algorithm (GA) and modified artificial bee colony (ABC) algorithm for constrained optimisation have been utilised. The objective is to maximise the utilisation rate (UR) of aircraft, while also satisfying other operational and maintenance constraints. The algorithm is tested on a fleet of eight aircraft. In addition to a one-year planning period, a planning horizon of ten years has also been simulated. The results show that both the GA and modified ABC algorithm can be effectively used to solve the FMP problem.

Assessing the clinical significance of echocardiograms in determining treatment of patent ductus arteriosus in neonates

BACKGROUND

To evaluate the utility of echocardiogram (ECHO) in detection and treatment of patent ductus arteriosus (PDA) and hemodynamically significant PDA (hsPDA) in preterm neonates.

METHODS

This was a retrospective case-control study of all preterm infants born or admitted to the level III Neonatal Intensive Care Unit in McMaster Children's Hospital from January 2009 to January 2013. These cases were further classified into the following sub-groups: group A) hsPDA confirmed on ECHO; and the control, group B) PDA (but not hemodynamically significant) confirmed on ECHO. Patients without an ECHO were excluded from all analyses. The primary outcome was incidence of treatment for PDA.

RESULTS

PDA treatment was administered in 83.3% and 11.2% of patients in groups A and B respectively (P < 0.05). Among patients with a hsPDA within group A, 17% did not receive treatment, while 11% of patients with non-hemodynamically significant PDA received treatment for the PDA. Within the cohort of patients who received treatment for a hsPDA, gestational age below 35 weeks as well as murmurs heard on auscultation were both found to be predictors of treatment.

CONCLUSION

While the ECHO remains the gold standard for detecting pathological PDA, there is evidence that other traditional clinical measures continue to guide clinical practice and treatment decisions. Further research is required to gain an understanding of how clinical measures and ECHO may be used in conjunction to optimize resource utilization.

Prediction of a Feshbach Resonance in the Below-the-Barrier Reactive Scattering of Vibrationally Excited HD with H

Quantum reactive scattering calculations on the vibrational quenching of HD due to collisions with H were carried out employing an accurate potential energy surface. The state-to-state cross sections for the chemical reaction HD(v = 1, j = 0) + H → D + H₂(v' = 0, j') at collision energies between 1 and 10 000 cm^-1 are presented, and a Feshbach resonance in the low-energy regime, below the reaction barrier, is observed for the first time. The resonance is attributed to coupling with the vibrationally adiabatic potential correlating to the v = 1, j = 1 level of the HD molecule, and it is dominated by the contribution from a single partial wave. The properties of the resonance, such as its dynamic behavior, phase behavior, and lifetime, are discussed.

Potentially repurposable drugs for COVID-19 identified from SARS-CoV-2 Host Protein Interactome

We previously presented the protein-protein interaction network - the 'HoP' or the host protein interactome - of 332 host proteins that were identified to interact with 27 nCoV19 viral proteins by Gordon et al. Here, we studied drugs targeting the proteins in this interactome to identify whether any of them may potentially be repurposable against SARS-CoV-2. We studied each of the drugs using the BaseSpace Correlation Engine and identified those that induce gene expression profiles negatively correlated with SARS-associated expression profile. This analysis resulted in 20 drugs whose differential gene expression (drug versus normal) had an anti-correlation with differential expression for SARS (viral infection versus normal). These included drugs that were already being tested for their clinical activity against SARS-CoV-2, those with proven activity against SARS-CoV/MERS-CoV, broad-spectrum antiviral drugs, and those identified/prioritized by other computational re-purposing studies. In summary, our integrated computational analysis of the HoP interactome in conjunction with drug-induced transcriptomic data resulted in drugs that may be repurposable for COVID-19.

Interactome of SARS-CoV-2 / nCoV19 modulated host proteins with computationally predicted PPIs

World over, people are looking for solutions to tackle the pandemic coronavirus disease (COVID-19) caused by the virus SARS-CoV-2/nCoV-19. Notable contributions in biomedical field have been characterizing viral genomes, host transcriptomes and proteomes, repurposable drugs and vaccines. In one such study, 332 human proteins targeted by nCoV19 were identified. We expanded this set of host proteins by constructing their protein interactome, including in it not only the known protein-protein interactions (PPIs) but also novel, hitherto unknown PPIs predicted with our High-precision Protein-Protein Interaction Prediction (HiPPIP) model that was shown to be highly accurate. In fact, one of the earliest discoveries made possible by HiPPIP is related to activation of immunity upon viral infection. We found that several interactors of the host proteins are differentially expressed upon viral infection, are related to highly relevant pathways, and that the novel interaction of NUP98 with CHMP5 may activate an antiviral mechanism leading to disruption of viral budding. We are making the interactions available as downloadable files to facilitate future systems biology studies and also on a web-server at http://hagrid.dbmi.pitt.edu/corona that allows not only keyword search but also queries such as "PPIs where one protein is associated with 'virus' and the interactors with 'pulmonary'".

Controlling rotational quenching rates in cold molecular collisions

The relative orientation and alignment of colliding molecules plays a key role in determining the rates of chemical processes. Here, we examine in detail a prototypical example: rotational quenching of HD in cold collisions with H₂. We show that the rotational quenching rate from j = 2 → 0, in the v = 1 vibrational level, can be maximized by aligning the HD along the collision axis and can be minimized by aligning the HD at the so called magic angle. This follows from quite general helicity considerations and suggests that quenching rates for other similar systems can also be controlled in this manner.