Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are diverse immune systems found in many prokaryotic genomes that target invading foreign DNA such as bacteriophages and plasmids. There are multiple types of CRISPR with arguably the most enigmatic being Type IV. During an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a Type IV-A3 CRISPR-Cas system was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the UK (isolated in 2017). Sequence analysis of all other genomes available in GenBank revealed that this CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on a bacterial chromosome. This system is exclusively located on IncHI1B/ IncFIB plasmids and is associated with multiple putative transposable elements. Expression of the cas loci was confirmed in the available clinical isolates by RT-PCR. In all cases, the CRISPR-Cas system has a single CRISPR array (CRISPR1) upstream of the cas loci which has several, conserved, spacers which, amongst things, match regions within conjugal transfer genes of IncFIIK/ IncFIB(K) plasmids. Our results reveal a Type IV-A3 CRISPR-Cas system exclusively located on IncHI1B/ IncFIB plasmids in Enterobacteriaceae that is likely to be able to target IncFIIK/ IncFIB(K) plasmids presumably facilitating intracellular, inter-plasmid competition

The ARGOS Gene Family Functions in a Negative Feedback Loop to Desensitize Plants to Ethylene

Ethylene plays critical roles in plant growth and development, including the regulation of cell expansion, senescence, and the response to biotic and abiotic stresses. Elements of the initial signal transduction pathway have been determined, but we are still defining regulatory mechanisms by which the sensitivity of plants to ethylene is modulated. We report here that members of the ARGOS gene family of Arabidopsis, previously implicated in the regulation of plant growth and biomass, function as negative feedback regulators of ethylene signaling. Expression of all four members of the ARGOS family is induced by ethylene, but this induction is blocked in ethylene-insensitive mutants. The dose dependence for ethylene induction varies among the ARGOS family members, suggesting that they could modulate responses across a range of ethylene concentrations. GFP-fusions of ARGOS and ARL localize to the endoplasmic reticulum, the same subcellular location as the ethylene receptors and other initial components of the ethylene signaling pathway. Seedlings with increased expression of ARGOS family members exhibit reduced ethylene sensitivity based on physiological and molecular responses

A clinical epidemiology and molecular attribution evaluation of adenoviruses in pediatric acute gastroenteritis: A case-control study

The objective of this study was to characterize the etiological role of human adenovirus (HAdV) serotypes in pediatric gastroenteritis. Using a case-control design, we compared the frequencies of HAdV serotypes between children with ≥3 episodes of vomiting or diarrhea within 24 h and \u3c7 days of symptoms (i.e., cases) and those with no infectious symptoms (i.e., controls). Stool samples and/or rectal swabs underwent molecular serotyping with cycle threshold (Ct) values provided by multiplex real-time reverse transcription-PCR testing. Cases without respiratory symptoms were analyzed to calculate the proportion of disease attributed to individual HAdV serotypes (i.e., attributable fraction). Between December 2014 and August 2018, adenoviruses were detected in 18.8% (629/3,347) of cases and 7.2% (97/1,355) of controls, a difference of 11.6% (95% confidence interval [CI], 9.6%, 13.5%). In 96% (95% CI, 92 to 98%) of HAdV F40/41 detections, the symptoms could be attributed to the identified serotype; when serotypes C1, C2, C5, and C6 were detected, they were responsible for symptoms in 52% (95% CI, 12 to 73%). Ct values were lower among cases than among controls

Assessment of total phenolic and flavonoid contents of selected fruits and vegetables

This work was conceptualized with the goal to investigate different fruits and vegetables for their comparative investigation of total phenolic and total flavonoid contents. The total phenolic content of 9 fruits and 12 vegetables used in the current study was determined by Folin-Ciocalteau assay. In addition, total flavonoid content was identified through catechin and aluminum colorimetric analysis. The ratio among the phenolic and flavonoid contents of fruits and vegetables extracts were also analyzed. Our results showed that methanolic extract of Citrullus lanatus had higher contents of phenolics and flavonoids (215±1.24 mg GAE/100 g and 73±0.81 mg CE/100 g) than other fruits. Moreover, maturity process of fruits from unripened to fully ripened stage showed significant increase in the total phenolic and flavonoid contents. Fruits under study had shown flavonoids/phenolics ratio of 0.32, which indicates that these fruits contained about 32% of flavonoid contents. Among vegetables, the greatest value of phenolic contents was observed in Capsicum annuum (213±1.24 mg GAE/100 g), and total flavonoid content in Raphanus sativus (45±1.24 mg CE/100 g). Vegetables showed lower ratios of flavonoids/phenolics (0.11-0.2) indicating lesser total flavonoid content (11-20%) as compared with fruits. The obtained results indicate that fruits and vegetables could be attributed to a potential source of natural phenolics and flavonoids in the pharmaceutical and food industry. Moreover, the antioxidant activities of these selected fruits and vegetables should also be determined in order to explore their beneficial effects against the prevention and management of disorders caused by oxidative stress

Identifying Hubs in Protein Interaction Networks

In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust.In this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction.We find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks