Modeling growth of specific spoilage organisms in tilapia: Comparison Baranyi with chi-square automatic interaction detection (CHAID) model

Tilapia is an important aquatic fish, but severe spoilage of tilapia is most likely related to the global aquaculture. The spoilage is mostly caused by specific spoilage organisms (SSO). Therefore, it is very important to use microbial models to predict the growth of SSO in tilapia. This study firstly verified Pseudomonas and Vibrio as the SSO of tilapia, then established microbial growth models based on Baranyi and chi-square automatic interaction detection (CHAID) models and compared their effectiveness. The results showed that both Baranyi model and CHAID model are appropriate for predicting the growth of microorganism. Baranyi model fits the microorganism growth better than CHAID model overall though CHAID model fits well at stationary phase. CHAID model predicts the microorganism growth accurately when the rate of change of the experiment data is big.Key words: Specific spoilage organisms (SSO), tilapia, chi-square automatic interaction detection (CHAID), Baranyi, shelf-life

Numerical Modeling Studies of Wake Vortex Transport and Evolution Within the Planetary Boundary Layer

In support of the wake vortex effect of the Terminal Area Productivity program, we have put forward four tasks to be accomplished in our proposal. The first task is validation of two-dimensional wake vortex-turbulence interaction. The second task is investigation of three-dimensional interaction between wake vortices and atmospheric boundary layer (ABL) turbulence. The third task is ABL studies. The, fourth task is addition of a Klemp-Durran condition at the top boundary for TASS model. The accomplishment of these tasks will increase our understanding of the dynamics of wake vortex and improve forecasting systems responsible for air safety and efficiency. The first two tasks include following three parts: (a) Determine significant length scale for vortex decay and transport, especially the length scales associated with the onset of Crow instability (Crow, 1970); (b) Study the effects of atmospheric turbulence on the decay of the wake vortices; and (c) Determine the relationships between decay rate, transport properties and atmospheric parameters based on large eddy simulation (LES) results and the observational data. These parameters may include turbulence kinetic energy, dissipation rate, wind shear and atmospheric stratification. The ABL studies cover LES modeling of turbulence structure within planetary boundary layer under transition and stable stratification conditions. Evidences have shown that the turbulence in the stable boundary layer can be highly intermittent and the length scales of eddies are very small compared to those in convective case. We proposed to develop a nesting grid mesh scheme and a modified Klemp-Durran conditions (Klemp and Wilhelmson, 1978) at the top boundary for TASS model to simulate planetary boundary layer under stable stratification conditions. During the past year, our group has made great efforts to carry out the above mentioned four tasks simultaneously. The work accomplished in the last year will be described in the next section

Identification of a Novel Plasmid-Borne Gentamicin Resistance Gene in Nontyphoidal Salmonella Isolated from Retail Turkey

The spread of antibiotic-resistant bacteria presents a global health challenge. Efficient surveillance of bacteria harboring antibiotic resistance genes (ARGs) is a critical aspect to controlling the spread. Increased access to microbial genomic data from many diverse populations informs this surveillance but only when functional ARGs are identifiable within the data set. Current, homology-based approaches are effective at identifying the majority of ARGs within given clinical and nonclinical data sets for several pathogens, yet there are still some whose identities remain elusive. By coupling phenotypic profiling with genotypic data, these unknown ARGs can be identified to strengthen homology-based searches. To prove the efficacy and feasibility of this approach, a published data set from the U.S. National Antimicrobial Resistance Monitoring System (NARMS), for which the phenotypic and genotypic data of 640 Salmonella isolates are available, was subjected to this analysis. Six isolates recovered from the NARMS retail meat program between 2011 and 2013 were identified previously as phenotypically resistant to gentamicin but contained no known gentamicin resistance gene. Using the phenotypic and genotypic data, a comparative genomics approach was employed to identify the gene responsible for the observed resistance in all six of the isolates. This gene, grdA, is harbored on a 9,016-bp plasmid that is transferrable to Escherichia coli, confers gentamicin resistance to E. coli, and has never before been reported to confer gentamicin resistance. Bioinformatic analysis of the encoded protein suggests an ATP binding motif. This work demonstrates the advantages associated with coupling genomics technologies with phenotypic data for novel ARG identification

Development and Application of a High-Resolution Thin-Film Probe

This paper documents the development, characterization, and application of a high-resolution thin-film magnetic-field probe. Probe diameter ranged from 5-μm to 100-μm. The 100-μm probe exhibits a 250-7μm improvement in spatial resolution compared to a conventional loop probe, measured at a height of 250 μm over differential traces with a 118-μm spacing. Electric field rejection was improved using shielding and using a 180-degree hybrid junction to separate common-mode (electric field) and differential-mode (primarily magnetic field) coupling. A network analyzer with narrow band filtering was used to detect the relatively weak signal from the probe and to allow detection of phase information. An application of the probe is demonstrated where the probe is used to identify the magnitude and phase of magnetic fields produced by currents in very closely-spaced IC package pins

A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages

As antimicrobial signalling molecules, type III or lambda interferons (IFNλs) are critical for defence against infection by diverse pathogens, including bacteria, fungi and viruses. Counter-intuitively, expression of one member of the family, IFNλ4, is associated with decreased clearance of hepatitis C virus (HCV) in the human population; by contrast, a natural frameshift mutation that abrogates IFNλ4 production improves HCV clearance. To further understand how genetic variation between and within species affects IFNλ4 function, we screened a panel of all known extant coding variants of human IFNλ4 for their antiviral potential and identify three that substantially affect activity: P70S, L79F and K154E. The most notable variant was K154E, which was found in African Congo rainforest ‘Pygmy’ hunter-gatherers. K154E greatly enhanced in vitro activity in a range of antiviral (HCV, Zika virus, influenza virus and encephalomyocarditis virus) and gene expression assays. Remarkably, E154 is the ancestral residue in mammalian IFNλ4s and is extremely well conserved, yet K154 has been fixed throughout evolution of the hominid genus Homo, including Neanderthals. Compared to chimpanzee IFNλ4, the human orthologue had reduced activity due to amino acid K154. Comparison of published gene expression data from humans and chimpanzees showed that this difference in activity between K154 and E154 in IFNλ4 correlates with differences in antiviral gene expression in vivo during HCV infection. Mechanistically, our data show that the human-specific K154 negatively affects IFNλ4 activity through a novel means by reducing its secretion and potency. We thus demonstrate that attenuated activity of IFNλ4 is conserved among humans and postulate that differences in IFNλ4 activity between species contribute to distinct host-specific responses to—and outcomes of—infection, such as HCV infection. The driver of reduced IFNλ4 antiviral activity in humans remains unknown but likely arose between 6 million and 360,000 years ago in Africa

A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages

As antimicrobial signalling molecules, type III or lambda interferons (IFNλs) are critical for defence against infection by diverse pathogens, including bacteria, fungi and viruses. Counter-intuitively, expression of one member of the family, IFNλ4, is associated with decreased clearance of hepatitis C virus (HCV) in the human population; by contrast, a natural frameshift mutation that abrogates IFNλ4 production improves HCV clearance. To further understand how genetic variation between and within species affects IFNλ4 function, we screened a panel of all known extant coding variants of human IFNλ4 for their antiviral potential and identify three that substantially affect activity: P70S, L79F and K154E. The most notable variant was K154E, which was found in African Congo rainforest ‘Pygmy’ hunter-gatherers. K154E greatly enhanced in vitro activity in a range of antiviral (HCV, Zika virus, influenza virus and encephalomyocarditis virus) and gene expression assays. Remarkably, E154 is the ancestral residue in mammalian IFNλ4s and is extremely well conserved, yet K154 has been fixed throughout evolution of the hominid genus Homo, including Neanderthals. Compared to chimpanzee IFNλ4, the human orthologue had reduced activity due to amino acid K154. Comparison of published gene expression data from humans and chimpanzees showed that this difference in activity between K154 and E154 in IFNλ4 correlates with differences in antiviral gene expression in vivo during HCV infection. Mechanistically, our data show that the human-specific K154 negatively affects IFNλ4 activity through a novel means by reducing its secretion and potency. We thus demonstrate that attenuated activity of IFNλ4 is conserved among humans and postulate that differences in IFNλ4 activity between species contribute to distinct host-specific responses to—and outcomes of—infection, such as HCV infection. The driver of reduced IFNλ4 antiviral activity in humans remains unknown but likely arose between 6 million and 360,000 years ago in Africa

Intravascular cell delivery device for therapeutic VEGF-induced angiogenesis in chronic vascular occlusion

AbstractSite specific targeting remains elusive for gene and stem cell therapies in the cardiovascular field. One promising option involves use of devices that deliver larger and more sustained cell/gene payloads to specific disease sites using the versatility of percutaneous vascular access technology. Smooth muscle cells (SMCs) engineered to deliver high local concentrations of an angiogenic molecule (VEGF) were placed in an intravascular cell delivery device (ICDD) in a porcine model of chronic total occlusion (CTO) involving ameroid placement on the proximal left circumflex (LCx) artery. Implanted SMC were retained within the ICDD and were competent for VEGF production in vitro and in vivo. Following implantation, micro-CT analyses revealed that ICDD-VEGF significantly enhanced vasa vasora microvessel density with a concomitant increase in tissue VEGF protein levels and formation of endothelial cell colonies suggesting increased angiogenic potential. ICDD-VEGF markedly enhanced regional blood flow determined by microsphere and contrast CT analysis translating to a functional improvement in regional wall motion and global left ventricular (LV) systolic and diastolic function. Our data indicate robust, clinically relevant angiogenesis can be achieved in a human scale porcine chronic vascular occlusion model following ICDD-VEGF-based delivery of angiogenic cells. This may have implications for percutaneous delivery of numerous therapeutic factors promoting creation of microvascular bypass networks in chronic vaso-occlusive diseases