Parameter estimation of a susceptible–infected–recovered–dead computer worm model

Computer worms are serious threats to Internet security and have caused billions of dollars of economic losses during the past decades. In this study, we implemented a susceptible–infected–recovered–dead (SIRD) model of computer worms and analyzed the characteristics and mechanisms of worm transmission. We applied the ordinary differential equation model to simulate the transmission process of computer worms and estimated the unknown parameters of the SIRD model through the methods of least squares, Markov chain Monte Carlo, and ensemble Kalman filtering (ENKF). The results reveal that the proposed SIRD model is more accurate than the susceptible–exposed–infected–recovered–susceptible model with respect to parameter estimation.

Synergistic Killing and Re-Sensitization of Pseudomonas aeruginosa to Antibiotics by Phage-Antibiotic Combination Treatment

Multidrug-resistant (MDR) Pseudomonas aeruginosa infections pose a serious health threat. Bacteriophage–antibiotic combination therapy is a promising candidate for combating these infections. A 5-phage P. aeruginosa cocktail, PAM2H, was tested in combination with antibiotics (ceftazidime, ciprofloxacin, gentamicin, meropenem) to determine if PAM2H enhances antibiotic activity. Combination treatment in vitro resulted in a significant increase in susceptibility of MDR strains to antibiotics. Treatment with ceftazidime (CAZ), meropenem, gentamicin, or ciprofloxacin in the presence of the phage increased the number of P. aeruginosa strains susceptible to these antibiotics by 63%, 56%, 31%, and 81%, respectively. Additionally, in a mouse dorsal wound model, seven of eight mice treated with a combination of CAZ and PAM2H for three days had no detectable bacteria remaining in their wounds on day 4, while all mice treated with CAZ or PAM2H alone had ~107 colony forming units (CFU) remaining in their wounds. P. aeruginosa recovered from mouse wounds post-treatment showed decreased virulence in a wax worm model, and DNA sequencing indicated that the combination treatment prevented mutations in genes encoding known phage receptors. Treatment with PAM2H in combination with antibiotics resulted in the re-sensitization of P. aeruginosa to antibiotics in vitro and a synergistic reduction in bacterial burden in vivo.

A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer’s disease

Bicyclic peptides have great therapeutic potential since they can bridge the gap between small molecules and antibodies by combining a low molecular weight of about 2 kDa with an antibody-like binding specificity. Here we apply a recently developed in silico rational design strategy to produce a bicyclic peptide to target the C-terminal region (residues 31–42) of the 42-residue form of the amyloid β peptide (Aβ42), a protein fragment whose aggregation into amyloid plaques is linked with Alzheimer’s disease. We show that this bicyclic peptide is able to remodel the aggregation process of Aβ42 in vitro and to reduce its associated toxicity in vivo in a C. elegans worm model expressing Aβ42. These results provide an initial example of a computational approach to design bicyclic peptides to target specific epitopes on disordered proteins.

Parallel-Channel Electrotaxis and Neuron Screening of Caenorhabditis elegans

In this paper, we report a novel microfluidic method to conduct a Caenorhabditis elegans electrotaxis movement assay and neuronal imaging on up to 16 worms in parallel. C. elegans is a model organism for neurodegenerative disease and movement disorders such as Parkinson’s disease (PD), and for screening chemicals that alleviate protein aggregation, neuronal death, and movement impairment in PD. Electrotaxis of C. elegans in microfluidic channels has led to the development of neurobehavioral screening platforms, but enhancing the throughput of the electrotactic behavioral assay has remained a challenge. Our device consisted of a hierarchy of tree-like channels for worm loading into 16 parallel electrotaxis screening channels with equivalent electric fields. Tapered channels at the ends of electrotaxis channels were used for worm immobilization and fluorescent imaging of neurons. Parallel electrotaxis of worms was first validated against established single-worm electrotaxis phenotypes. Then, mutant screening was demonstrated using the NL5901 strain, carrying human α-synuclein in the muscle cells, by showing the associated electrotaxis defects in the average speed, body bend frequency (BBF), and electrotaxis time index (ETI). Moreover, chemical screening of a PD worm model was shown by exposing the BZ555 strain, expressing green fluorescence protein (GFP) in the dopaminergic neurons (DNs), to 6-hydroxydopamine neurotoxin. The neurotoxin-treated worms exhibited a reduction in electrotaxis swimming speed, BBF, ETI, and DNs fluorescence intensity. We envision our technique to be used widely in C. elegans-based movement disorder assays to accelerate behavioral and cellular phenotypic investigations.

APP-Induced Patterned Neurodegeneration Is Exacerbated by APOE4 in Caenorhabditis elegans

Genetic and epidemiological studies have found that variations in the amyloid precursor protein (APP) and the apoliopoprotein E (APOE) genes represent major modifiers of the progressive neurodegeneration in Alzheimer’s disease (AD). An extra copy of or gain-of-function mutations in APP correlate with early onset AD. Compared to the other variants (APOE2 and APOE3), the ε4 allele of APOE (APOE4) hastens and exacerbates early and late onset forms of AD. Convenient in vivo models to study how APP and APOE4 interact at the cellular and molecular level to influence neurodegeneration are lacking. Here, we show that the nematode C. elegans can model important aspects of AD including age-related, patterned neurodegeneration that is exacerbated by APOE4. Specifically, we found that APOE4, but not APOE3, acts with APP to hasten and expand the pattern of cholinergic neurodegeneration caused by APP. Molecular mechanisms underlying how APP and APOE4 synergize to kill some neurons while leaving others unaffected may be uncovered using this convenient worm model of neurodegeneration.

INCREASED HSP25 DRIVES THE TRANSITION FROM PROTEASOME TO AUTOPHAGY-MEDIATED DEGRADATION UNDER PROTEOTOXIC STRESS

Accumulation of protein aggregates are a common pathology in many neurodegenerative disorders. This accumulation may be due to a function decline in the protein homeostasis network known to occur during the aging process. Small heat shock proteins are a class of molecular chaperones that assist in protein folding and ameliorates the degradation activity of the proteasome and autolysosome thereby decreasing disease-associated aggregates. Prior work in rodents and C. elegans has shown expression levels of the small heat shock protein 25 (HSP25) correlates with maximum lifespan potential. Increased levels of HSP25 extends lifespan in a transgenic C. elegans model. This lifespan extension is dependent on skn-1 with evidence suggesting an enrichment in several skn-1-related pathways, such as lysosomal genes. Concomitantly, proteasome activity declines while autolysosome activity increases. This observation might suggest a switch from proteasome degradation to autophagy as the main driver of protein degradation in C. elegans in this transgenic model. To investigate if a reduction of proteasome function and elevated lysosomal gene activation during aging and under proteotoxic stress are modulated by HSP25 we have crossed our HSP25-transgenic worm with an aggregating and non-aggregating tau worm model. This work will elucidate a possible mechanism that explains the change in the protein degradation response pathways potentially modulated by HSP25 during increased protein misfolding.

Hopf bifurcation of a delayed worm model with two latent periods

We investigate a delayed epidemic model for the propagation of worm in wireless sensor network with two latent periods. We derive sufficient conditions for local stability of the worm-induced equilibrium of the system and the existence of Hopf bifurcation by regarding different combination of two latent time delays as the bifurcation parameter and analyzing the distribution of roots of the associated characteristic equation. In particular, we investigate the direction and stability of the Hopf bifurcation by means of the normal form theory and center manifold theorem. To verify analytical results, we present numerical simulations. Also, the effect of some influential parameters of sensor network is properly executed so that the oscillations can be reduced and removed from the network.

Repurposing the Streptococcus mutans CRISPR-Cas9 System to Understand Essential Gene Function

A recent genome-wide screen identified ∼300 essential or growth-supporting genes in the dental caries pathogen Streptococcus mutans. To be able to study these genes, we built a CRISPR interference tool around the Cas9 nuclease (Cas9Smu) encoded in the S. mutans UA159 genome. Using a xylose-inducible dead Cas9Smu with a constitutively active single-guide RNA (sgRNA), we observed titratable repression of GFP fluorescence that compared favorably to that of Streptococcus pyogenes dCas9 (Cas9Spy). We then investigated sgRNA specificity and proto-spacer adjacent motif (PAM) requirements. Interference by sgRNAs did not occur with double or triple base-pair mutations, or if single base-pair mutations were in the 3’ end of the sgRNA. Bioinformatic analysis of >450 S. mutans genomes allied with in vivo assays revealed a similar PAM recognition sequence as the Cas9Spy. Next, we created a comprehensive library of sgRNA plasmids that were directed at essential and growth-supporting genes. We discovered growth defects for 77% of the CRISPRi strains expressing sgRNAs. Phenotypes of CRISPRi strains, across several biological pathways, were assessed using fluorescence microscopy. A variety of cell structure anomalies were observed, including segregational instability of the chromosome, enlarged cells, and ovococci-to-rod shape transitions. CRISPRi was also employed to observe how silencing of cell wall glycopolysaccharide biosynthesis (rhamnose-glucose polysaccharide, RGP) affected both cell division and pathogenesis in a wax worm model. The CRISPRi tool and sgRNA library are valuable resources for characterizing essential genes in S. mutans, some of which could prove to be promising therapeutic targets.