scholarly journals Loss-of-Function Mutations in the Dpp and Opp Permeases Render Erwinia amylovora Resistant to Kasugamycin and Blasticidin S

2018 ◽  
Vol 31 (8) ◽  
pp. 823-832 ◽  
Author(s):  
Yixin Ge ◽  
Jae Hoon Lee ◽  
Baishi Hu ◽  
Youfu Zhao
Keyword(s):  
Minimal Medium ◽  
Erwinia Amylovora ◽  
Quantitative Polymerase Chain Reaction ◽  
Bioinformatic Analysis ◽  
The United States ◽  
Bacterial Disease ◽  
Loss Of Function ◽  
Rich Medium ◽  
Enhanced Resistance ◽  
Blasticidin S

Extensive use of the antibiotic streptomycin to control fire blight disease of apples and pears, caused by the enterobacterial plant pathogen Erwinia amylovora, leads to the development of streptomycin-resistant strains in the United States and elsewhere. Kasugamycin (Ksg) has been permitted to be used as an alternative or replacement to control this serious bacterial disease. In this study, we investigated the role of two major peptide ATP-binding cassette transporter systems in E. amylovora, the dipeptide permease (Dpp) and oligopeptide permease (Opp), in conferring sensitivity to Ksg and blasticidin S (BcS). Minimum inhibitory concentration and spot dilution assays showed that the dpp deletion mutants exhibited slightly enhanced resistance to Ksg in rich medium, whereas the opp mutant exhibited slightly enhanced resistance to Ksg in minimal medium and BcS in rich medium. Deletion of both dpp and opp conferred a higher level of resistance to Ksg in both rich and minimal media, whereas deletion of opp alone was sufficient to confer high level of resistance to BcS in minimal medium. In addition, bioinformatic analysis combined with reverse transcription-quantitative polymerase chain reaction showed that the Rcs phosphorelay system negatively regulates opp expression and the rcsB mutant was more sensitive to both Ksg and BcS in minimal medium as compared with the wild type. An electrophoresis motility shift assay further confirmed the direct binding of the RcsA/RcsB proteins to the promoter region of the opp operon. However, neither the Dpp nor the Opp permeases contributed to disease progress on immature pears, hypersensitive response on tobacco leaves, or exopolysaccharide amylovoran production. These results suggested that Ksg and BcS employ the Dpp and Opp permeases to enter E. amylovora cells and the Dpp and Opp permeases act synergistically for illicit transport of antibiotics.

scholarly journals Complete Genome Sequence of the Fire Blight Pathogen Strain Erwinia amylovora Ea1189

2020 ◽  
Vol 33 (11) ◽  
pp. 1277-1279 ◽  
Author(s):  
Menghao Yu ◽  
Jugpreet Singh ◽  
Awais Khan ◽  
George W. Sundin ◽  
Youfu Zhao
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Fire Blight ◽  
Molecular Mechanisms ◽  
Erwinia Amylovora ◽  
De Novo ◽  
The United States ◽  
Bacterial Disease ◽  
Circular Chromosome

Erwinia amylovora causes fire blight, the most devastating bacterial disease of apples and pears in the United States and worldwide. The model strain E. amylovora Ea1189 has been extensively used to understand bacterial pathogenesis and molecular mechanisms of bacterial-plant interactions. In this work, we sequenced and assembled the de novo genome of Ea1189, using a combination of long Oxford Nanopore Technologies and short Illumina sequence reads. A complete gapless genome assembly of Ea1189 consists of a 3,797,741-bp circular chromosome and a 28,259-bp plasmid with 3,472 predicted genes, including 78 transfer RNAs, 22 ribosomal RNAs, and 20 noncoding RNAs. A comparison of the Ea1189 genome to previously sequenced E. amylovora complete genomes showed 99.94 to 99.97% sequence similarity with 314 to 946 single nucleotide polymorphisms. We believe that the availability of the complete genome sequence of strain Ea1189 will further support studies to understand evolution, diversity and structural variations of Erwinia strains, as well as the molecular basis of E. amylovora pathogenesis and its interactions with host plants, thus facilitating the development of effective management strategies for this important disease.

scholarly journals Occurrence of SARS-CoV-2 RNA in Six Municipal Wastewater Treatment Plants at the Early Stage of COVID-19 Pandemic in The United States

Pathogens ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 798
Author(s):  
Samendra P. Sherchan ◽  
Shalina Shahin ◽  
Jeenal Patel ◽  
Lauren M. Ward ◽  
Sarmila Tandukar ◽  
...  
Keyword(s):  
United States ◽  
Wastewater Treatment ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Quantitative Polymerase Chain Reaction ◽  
The United States ◽  
Secondary Effluent ◽  
Untreated Wastewater ◽  
Treatment Processes ◽  
Wastewater Samples

In this study, we investigated the occurrence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) RNA in primary influent (n = 42), secondary effluent (n = 24) and tertiary treated effluent (n = 34) collected from six wastewater treatment plants (WWTPs A–F) in Virginia (WWTP A), Florida (WWTPs B, C, and D), and Georgia (WWTPs E and F) in the United States during April–July 2020. Of the 100 wastewater samples analyzed, eight (19%) untreated wastewater samples collected from the primary influents contained SARS-CoV-2 RNA as measured by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assays. SARS-CoV-2 RNA were detected in influent wastewater samples collected from WWTP A (Virginia), WWTPs E and F (Georgia) and WWTP D (Florida). Secondary and tertiary effluent samples were not positive for SARS-CoV-2 RNA indicating the treatment processes in these WWTPs potentially removed SARS-CoV-2 RNA during the secondary and tertiary treatment processes. However, further studies are needed to understand the log removal values (LRVs) and transmission risks of SARS-CoV-2 RNA through analyzing wastewater samples from a wider range of WWTPs.

scholarly journals The Metabolic Bone Disease X-linked Hypophosphatemia: Case Presentation, Pathophysiology and Pharmacology

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 563
Author(s):  
Jon Vincze ◽  
Brian W. Skinner ◽  
Katherine A. Tucker ◽  
Kory A. Conaway ◽  
Jonathan W. Lowery ◽  
...  
Keyword(s):  
Vitamin D ◽  
Biological Effects ◽  
Fibroblast Growth Factor 23 ◽  
Elevated Serum ◽  
Fractional Excretion ◽  
The United States ◽  
Vitamin D Supplementation ◽  
Loss Of Function ◽  
Case Presentation ◽  
Serum Inorganic Phosphate

The authors present a stereotypical case presentation of X-linked hypophosphatemia (XLH) and provide a review of the pathophysiology and related pharmacology of this condition, primarily focusing on the FDA-approved medication burosumab. XLH is a renal phosphate wasting disorder caused by loss of function mutations in the PHEX gene (phosphate-regulating gene with homologies to endopeptidases on the X chromosome). Typical biochemical findings include elevated serum levels of bioactive/intact fibroblast growth factor 23 (FGF23) which lead to (i) low serum phosphate levels, (ii) increased fractional excretion of phosphate, and (iii) inappropriately low or normal 1,25-dihydroxyvitamin D (1,25-vitD). XLH is the most common form of heritable rickets and short stature in patients with XLH is due to chronic hypophosphatemia. Additionally, patients with XLH experience joint pain and osteoarthritis from skeletal deformities, fractures, enthesopathy, spinal stenosis, and hearing loss. Historically, treatment for XLH was limited to oral phosphate supplementation, active vitamin D supplementation, and surgical intervention for cases of severe bowed legs. In 2018, the United States Food and Drug Administration (FDA) approved burosumab for the treatment of XLH and this medication has demonstrated substantial benefit compared with conventional therapy. Burosumab binds circulating intact FGF23 and blocks its biological effects in target tissues, resulting in increased serum inorganic phosphate (Pi) concentrations and increased conversion of inactive vitamin D to active 1,25-vitD.

scholarly journals Sources of SARS-CoV-2 and Other Microorganisms in Dental Aerosols

2021 ◽  
pp. 002203452110159
Author(s):  
A.P. Meethil ◽  
S. Saraswat ◽  
P.P. Chaudhary ◽  
S.M. Dabdoub ◽  
P.S. Kumar
Keyword(s):  
Infection Control ◽  
Dental Treatment ◽  
Quantitative Polymerase Chain Reaction ◽  
The United States ◽  
Control Measures ◽  
Personal Protection ◽  
Personal Protection Equipment ◽  
Linear Discriminant ◽  
16S Sequencing ◽  
Asymptomatic Patients

On March 16, 2020, 198,000 dentists in the United States closed their doors to patients, fueled by concerns that aerosols generated during dental procedures are potential vehicles for transmission of respiratory pathogens through saliva. Our knowledge of these aerosol constituents is sparse and gleaned from case reports and poorly controlled studies. Therefore, we tracked the origins of microbiota in aerosols generated during ultrasonic scaling, implant osteotomy, and restorative procedures by combining reverse transcriptase quantitative polymerase chain reaction (to identify and quantify SARS-CoV-2) and 16S sequencing (to characterize the entire microbiome) with fine-scale enumeration and source tracking. Linear discriminant analysis of Bray-Curtis dissimilarity distances revealed significant class separation between the salivary microbiome and aerosol microbiota deposited on the operator, patient, assistant, or the environment ( P < 0.01, analysis of similarities). We also discovered that 78% of the microbiota in condensate could be traced to the dental irrigant, while saliva contributed to a median of 0% of aerosol microbiota. We also identified low copy numbers of SARS-CoV-2 virus in the saliva of several asymptomatic patients but none in aerosols generated from these patients. Together, the bacterial and viral data encourage us to conclude that when infection control measures are used, such as preoperative mouth rinses and intraoral high-volume evacuation, dental treatment is not a factor in increasing the risk for transmission of SARS-CoV-2 in asymptomatic patients and that standard infection control practices are sufficiently capable of protecting personnel and patients from exposure to potential pathogens. This information is of immediate urgency, not only for safe resumption of dental treatment during the ongoing COVID-19 pandemic, but also to inform evidence-based selection of personal protection equipment and infection control practices at a time when resources are stretched and personal protection equipment needs to be prioritized.

scholarly journals Clinical, Genetics, and Bioinformatic Characterization of Mutations Affecting an Essential Region of PLS3 in Patients with BMND18

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Ting Chen ◽  
Haiying Wu ◽  
Chenxi Zhang ◽  
Jiarong Feng ◽  
Linqi Chen ◽  
...  
Keyword(s):  
Novel Mutation ◽  
Homology Modelling ◽  
Gene Sequencing ◽  
Bioinformatic Analysis ◽  
Actin Binding ◽  
Clinical Genetics ◽  
Loss Of Function ◽  
Mineral Density ◽  
Trait Locus ◽  
The Impact

Background. Bone mineral density quantitative trait locus 18 (BMND18, OMIM #300910) is a type of early-onset osteogenesis imperfecta (OI) caused by loss-of-function mutations in the PLS3 gene, which encodes plastin-3, a key protein in the formation of actin bundles throughout the cytoskeleton. Here, we report a patient with PLS3 mutation caused BMND18 and evaluated all the reported disease-causing mutations by bioinformatic analysis. Methods. Targeted gene sequencing was performed to find the disease-causing mutation in our patient. Bioinformatic analyses mainly including homology modelling and molecular dynamics stimulation were conducted to explore the impact of the previously reported mutations on plastin-3. Results. Gene sequencing showed a novel nonsense mutation (c.745G > T, p.E249X), which locates at a highly conserved region containing residues p.240–266 (LOOP-1) in the PLS3 gene. Further bioinformatic analyses of the previously reported mutations revealed that LOOP-1 is predicted to physically connect the calponin-homology 1 (CH1) and CH2 domains of the ABD1 fragment and spatially locates within the interface of ABD1 and ABD2. It is crucial to the conformation transition and actin-binding function of plastin-3. Conclusions. This report identified a novel mutation that truncates the PLS3 gene. Moreover, bioinformatic analyses of the previous reported mutations in PLS3 gene lead us to find a critical LOOP-1 region of plastin-3 mutations at which may be detrimental to the integral conformation of plastin-3 and thus affect its binding to actin filament.

Development of a Tibial Slider to Evaluate and Validate a Finite Element Model for Friction in Total Knee Implants

2000 ◽  
Author(s):  
Michael D. Nowak ◽  
Kenneth Shaw ◽  
Courtland Lewis
Keyword(s):  
United States ◽  
Finite Element ◽  
Knee Replacement ◽  
Severe Pain ◽  
Element Model ◽  
The United States ◽  
Loss Of Function ◽  
Articular Surfaces ◽  
Joint Disorder ◽  
Total Knee

Abstract More than 200,000 people in the United States annually undergo knee replacement as a means of diminishing pain and stiffness and restoring mobility, and the number is expected to increase with further advancements in joint replacement procedures [Duke, 1999]. Total knee replacement is performed on people with severe degenerative joint disorder such as osteoarthritis in which the articular surfaces of the knee deteriorate, leading to severe pain, limitation or loss of function and/or deformity of the joint.

scholarly journals IRLnc: A novel functional noncoding RNA contributes to intramuscular fat deposition

2020 ◽  
Author(s):  
Ligang Wang ◽  
Zhong-Yin Zhou ◽  
Tian Zhang ◽  
Longchao Zhang ◽  
Xinhua Hou ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Meat Quality ◽  
Noncoding Rna ◽  
Quantitative Polymerase Chain Reaction ◽  
Intramuscular Fat ◽  
Human Beings ◽  
Loss Of Function ◽  
Similar Expression Pattern ◽  
Positive Meaning ◽  
Independent Effects

Abstract Background Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity and type 2 diabetes treatment. In this study, an IMF trait segregation population was used to perform RNA sequencing and to analyze the joint or independent effects of genes and long intergenic non-coding RNAs (lincRNAs) on IMF. Results A total of 26 genes including 6 LincRNA genes show significantly different expression between high- and low-IMF pigs. Interesting, one lincRNA gene, named IMF related LincRNA (IRLnc) not only has a 292-nt conserved region in 100 vertebrates but also has conserved up and down stream genes (<10 kb) in pig and humans. Real-time quantitative polymerase chain reaction (RT-qPCR) validation study indicated that nuclear receptor subfamily 4 group A member 3 (NR4A3) which located at the downstream of IRLnc has similar expression pattern with IRLnc. RNAi-mediated loss of function screens identified that IRLnc silencing could inhibit both of the RNA and protein expression of NR4A3. And the in-situ hybridization co-expression experiment indicates that IRLnc may directly binding to NR4A3. As the NR4A3 could regulate the catecholamine catabolism, which could affect insulin sensitivity, we inferred that IRLnc influence IMF decomposition by regulating the expression of NR4A3.Conclusions In conclusion, a novel functional noncoding variation named IRLnc have been found contribute to IMF by regulating the expression of NR4A3. These finding suggest novel mechanistic approach for treatment of insulin resistance in human beings and meat quality improvement in animal.

scholarly journals Ribosome Evolution and Structural Capacitance

2019 ◽  
Author(s):  
Ashley M Buckle ◽  
Malcolm Buckle
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Protein Evolution ◽  
Bioinformatic Analysis ◽  
Amino Acid Usage ◽  
Loss Of Function ◽  
Gain Of Function ◽  
Acceptor Stem ◽  
Ribosome Evolution ◽  
Disordered Regions

In addition to the canonical loss-of-function mutations, mutations in proteins may additionally result in gain-of-function through the binary activation of cryptic &lsquo;structural capacitance elements&rsquo;. Our previous bioinformatic analysis allowed us to propose a new mechanism of protein evolution - structural capacitance &ndash; that arises via the generation of new elements of microstructure upon mutations that cause a disorder-to-order (DO) transition in previously disordered regions of proteins. Here we propose that the DO transition is a necessary follow-on from expected early codon-anticodon and tRNA acceptor stem-amino acid usage, via the accumulation of structural capacitance elements - reservoirs of disorder in proteins. We develop this argument further to posit that structural capacitance is an inherent consequence of the evolution of the genetic code.

scholarly journals Crosstalk between microglia and patient-derived glioblastoma cells inhibit invasion in a three-dimensional gelatin hydrogel model

2020 ◽  
Author(s):  
Jee-Wei Emily Chen ◽  
Jan Lumibao ◽  
Sarah Leary ◽  
Jann N. Sarkaria ◽  
Andrew J. Steelman ◽  
...  
Keyword(s):  
Immune Cells ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Bioinformatic Analysis ◽  
The United States ◽  
Study Patient ◽  
Valuable Insight ◽  
Glioblastoma Cells ◽  
Contact Patterns ◽  
The Central Nervous System

ABSTRACTBackgroundGlioblastoma is the most common and deadly form of primary brain cancer, accounting for more than thirteen thousand new diagnoses annually in the United States alone. Microglia are the innate immune cells within the central nervous system, acting as a front-line defense against injuries and inflammation via a process that involves transformation from a quiescent to an activated phenotype. Crosstalk between GBM cells and microglia represents an important axis to consider in the development of tissue engineering platforms to examine pathophysiological processes underlying GBM progression and therapy.MethodsThis work used a brain-mimetic hydrogel system to study patient-derived glioblastoma specimens and their interactions with microglia. Here, glioblastoma cells were either cultured alone in 3D hydrogels or in co-culture with microglia in a manner that allowed secretome-based signaling but prevented direct GBM-microglia contact. Patterns of GBM cell invasion were quantified using a three-dimensional spheroid assay. Secretome and transcriptome (via RNAseq) were used to profile the consequences of GBM-microglia interactions.ResultsMicroglia displayed an activated phenotype as a result of GBM crosstalk. Three-dimensional migration patterns of patient derived glioblastoma cells showed invasion was significantly decreased in response to microglia paracrine signaling. Potential molecular mechanisms underlying with this phenotype were identified from bioinformatic analysis of secretome and RNAseq data.ConclusionThe data demonstrate a tissue engineered hydrogel platform can be used to investigate crosstalk between immune cells of the tumor microenvironment related to GBM progression. Such multidimensional models may provide valuable insight to inform therapeutic innovations to improve GBM treatment.

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