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Plasmid acquired antimicrobial resistance in staphylococcus epidermidis in a peritonitis case
No full textAim: To sequence the genomes of three longitudinal S. epidermidis isolates (C099, C100 and C101) obtained from a patient with peritonitis.
Background: Coagulase-negative staphylococci such as S. epidermidis are common colonizers on human skin, however as opportunistic pathogens they can cause serious infections. S. epidermidis is resistant to a range of antibiotics such as methicillin and tetracycline and most antimicrobial resistance (AMR) genes are plasmid encoded. Plasmids can facilitate the rapid spread of AMR between bacteria and we have observed this in S. epidermidis isolates obtained from a treatment resistant peritonitis case.
Method: C099 was isolated from the patient on day 1 of infection, C100 was obtained on day 6 and C101 was obtained on day 15. DNA was extracted using lysostaphin lysis of cells followed by the use of the Monarch® Genomic DNA purification kit. Extracted DNA was checked for quality and sequenced using the Illumina NextSeq and Oxford Nanopore MinION. Replicons were confirmed using gel electrophoresis. Genomes were assembled using long nanopore sequence reads using Flye. Final assemblies were polished with both long reads using Racon and with short reads (Illumina) using Pilon. The broth micro-dilution (BMD) method was performed using Sensititre™ Custom plates according to manufacturer's instructions (Thermo Scientific™).
Results: A total of five plasmids were identified in C099 and six in C100 and C101. Sequencing confirmed the additional plasmid in C100 and C101 contained the ermC gene. Both C100 and C101 were resistant to erythromycin using the BMD method.
Conclusions: The rapid acquisition of erythromycin resistance highlights the issue of increasing AMR in bacteria. Sequencing can be used for surveillance and to further study the emergence of AMR in peritonitis cases
Evaluating dimensionality reduction for genomic prediction
Get PDFThe development of genomic selection (GS) methods has allowed plant breeding programs to select favorable lines using genomic data before performing field trials. Improvements in genotyping technology have yielded high-dimensional genomic marker data which can be difficult to incorporate into statistical models. In this paper, we investigated the utility of applying dimensionality reduction (DR) methods as a pre-processing step for GS methods. We compared five DR methods and studied the trend in the prediction accuracies of each method as a function of the number of features retained. The effect of DR methods was studied using three models that involved the main effects of line, environment, marker, and the genotype by environment interactions. The methods were applied on a real data set containing 315 lines phenotyped in nine environments with 26,817 markers each. Regardless of the DR method and prediction model used, only a fraction of features was sufficient to achieve maximum correlation. Our results underline the usefulness of DR methods as a key pre-processing step in GS models to improve computational efficiency in the face of ever-increasing size of genomic data
Gene editing of the representative WRKY family members in an elite malting barley cultivar RGT Planet by CRISPR/Cas9
Get PDFBarley is one of the world’s most economically important cereal crops and a superb model plant for genetic studies and elucidation of plant responses to environmental changes and stress-associated events due to its exceptional adaptations to broad climatic and environmental conditions. CRISPR/Cas system has a great potential for crop genetic improvement and has revolutionised genetics research and crop breeding. CRISPR-based gene targeting can accelerate the improvement of market-oriented traits and elite varieties through precision crop breeding. WRKY transcription factors (TFs), as a superfamily of TFs, constitute one of the largest transcription factor families in plants. WRKY TFs with diverse biological functions play a pivotal role in activating several developmental and physiological processes and fine-tuning signalling pathways and defence responses. However, little is known about the exact growth and developmental functions of WRKY family members in barley. In this study, 14 representative WRKY transcription factors were selected from different WRKY groups based on phylogenetic analysis. Pooled gRNAs were synthesised for multiplex CRISPR/Cas9 mutagenesis. gRNA constructs carrying one, two or three gRNA cassettes were assembled and delivered into RGT Planet, a high yielding spring malting barley with superior agronomic traits. A collection of 105 mutant lines with remarkable phenotypic variations were obtained. An average mutation frequency in the T0 population created by the pooled CRISPR/Cas9 was 89.74% containing multiple mutations. This study, for the first time, provided strong evidence of the roles of HvWRKY39 in tiller development and HvWRKY32 in spike development, grain filling, and kernel weight. Evaluation of yield components revealed the contribution of HvWRKY32 and HvWRKY39 toward increasing barley yield potential by approximately 20%. Our findings also demonstrated the roles of HvWRKY TFs in root development and root architecture. These results indicated that TFs have tremendous potential to enhance crop improvement and boost crop yield. This study established a promising genomic editing platform with the modern barley variety RGT Planet. The mutant library generated from this study provides a valuable resource for further detailed functional genomics in barley
Load-velocity relationships and predicted maximal strength: A systematic review of the validity and reliability of current methods
Get PDFMaximal strength can be predicted from the load-velocity relationship (LVR), although it is important to understand methodological approaches which ensure the validity and reliability of these strength predictions. The aim of this systematic review was to determine factors which influence the validity of maximal strength predictions from the LVR, and secondarily to highlight the effects of these factors on the reliability of predictions. A search strategy was developed and implemented in PubMed, Scopus, Web of Science and CINAHL databases. Rayyan software was used to screen titles, abstracts, and full texts to determine their inclusion/eligibility. Eligible studies compared direct assessments of one-repetition maximum (1RM) with predictions performed using the LVR and reported prediction validity. Validity was extracted and represented graphically via effect size forest plots. Twenty-five eligible studies were included and comprised of a total of 842 participants, three different 1RM prediction methods, 16 different exercises, and 12 different velocity monitoring devices. Four primary factors appear relevant to the efficacy of predicting 1RM: the number of loads used, the exercise examined, the velocity metric used, and the velocity monitoring device. Additionally, the specific loads, provision of velocity feedback, use of lifting straps and regression model used may require further consideration
Evaluating distribution of foveal avascular zone parameters corrected by lateral magnification and their associations with retinal thickness
Get PDFPurpose
To examine the distribution of foveal avascular zone (FAZ) parameters, with and without correction for lateral magnification, in a large cohort of healthy young adults.
Design
Cross-sectional, observational cohort study.
Participants
A total of 504 healthy adults, 27 to 30 years of age.
Methods
Participants underwent a comprehensive ophthalmic examination including axial length measurement and OCT angiography (OCTA) imaging of the macula. OCT angiography images of combined superficial and deep retinal vessel plexuses were processed via a custom software to extract foveal avascular zone area (FAZA) and foveal density-300 (FD-300), the vessel density in a 300-μm wide annulus surrounding the FAZ, with and without correction for lateral magnification. Bland–Altman analyses were performed to examine the effect of lateral magnification on FAZA and FD-300, as well as to evaluate the interocular agreement in both parameters. Linear mixed-effects models were used to examine the relationship between retinal thicknesses and OCTA parameters.
Main Outcome Measures
The FAZA and FD-300, corrected for lateral magnification.
Results
The mean (standard deviation [SD]) of laterally corrected FAZA and FD-300 was 0.22 mm2 (0.10 mm2) and 51.9% (3.2%), respectively. Relative to uncorrected data, 55.6% of corrected FAZA showed a relative change > 5%, whereas all FD-300 changes were within 5%. There was good interocular symmetry (mean right eye–left eye difference, 95% limits of agreement [LoA]) in both FAZA (0.006 mm2, -0.05 mm2, to 0.07 mm2) and FD-300 (-0.05%, -5.39%, to 5.30%). There were significant negative associations between central retinal thickness and FAZA (β = -0.0029), as well as between central retinal thickness and FD-300 (β = -0.044), with the relationships driven by inner, not outer, retina.
Conclusions
We reported lateral magnification adjusted normative values for FAZA and FD-300 in a large cohort of young, healthy eyes. Clinicians should strongly consider accounting for lateral magnification when evaluating FAZA. Good interocular agreement in FAZA and FD-300 suggests the contralateral eye can be used as control data
Inactivating a herbicide-resistance transgene in Nicotiana tabacum plants using CRISPR/Cas9
No full textHerbicide and antibiotic tolerance genes serve as useful selectable markers for the development of transgenic plants expressing other transgenes. It may be desirable for regulatory or safety reasons to silence the herbicide tolerance trait after transformants have been selected. However, because the genes of interest and the marker gene are usually tightly linked, traditional segregation-based strategies for elimination of undesirable transgenes are usually unsuccessful. Here, we created Nicotiana tabacum plants that carry a single copy of a Cas9 gene, a nuclease in the clustered regularly interspaced short palindromic repeats (CRISPR) system, physically linked to the selectable marker gene bar for tolerance to the herbicide glufosinate (Basta, Liberty). Here, bar was targeted within the genome by introducing bar-specific single guide RNAs (sgRNAs) to the N. tabacum line in vitro, resulting in abolishment of the glufosinate-tolerance trait in mature plants. Sequence analysis of the bar gene revealed a frame-shift mutation at a sgRNA target site, confirming efficacy of the strategy
Gas to protein: Microbial single cell protein is an alternative to fishmeal in aquaculture
No full textMethanotrophic bacteria represent an appealing opportunity to convert methane, a potent greenhouse gas, into a highly nutritious animal feed ingredient, single-cell protein (SCP). SCP has a comparable or superior nutritional profile that to most conventional protein sources and can be produced within a lower environmental footprint. The present study investigated the effect of replacing fishmeal (FM) with methanotrophic SCP in diets for barramundi (Lates calcarifer), a carnivorous fish with a high demand for dietary protein and energy. Dietary inclusion levels of 0 %, 10 %, 20 % and 30 % SCP (representing 0, 25, 50 and 75 % FM replacement) were tested, with and without additives. Triplicate groups of juvenile barramundi were fed the diets over 31 days. The inclusion of SCP significantly improved weight gain and feed conversion efficiency (FCE). Dietary SCP inclusion supported good gut health, with decreasing trends of hepatosomatic index, improved plasma biochemistry, and no adverse histopathological changes. Barramundi fed the SCP diets showed an intact intestinal barrier and a significant improvement in villi and lamina propria area when fed the additive supplemented SCP diets. This study demonstrates that this SCP is highly palatable to barramundi (even without dietary additives) and can replace up to 75 % FM with significant improvements in growth and FCE
Sequential removal of selenate, nitrate and sulfate and recovery of elemental selenium in a multi-stage bioreactor process with redox potential feedback control
Get PDFBioreduction can facilitate oxyanions removal from wastewater. However, simultaneously removing selenate, nitrate and sulfate and recovering high-purity elemental selenium (Se0) from wastewater by a single system is difficult and may lead to carcinogenic selenium monosulfide (SeS) formation. To solve this issue, a two-stage biological fluidized bed (FBR) process with ethanol dosing based on oxidation-reduction potential (ORP) feedback control was developed in this study. FBR1 performance was first evaluated at various ORP setpoints (between −520 and −360 mV vs. Ag/AgCl) and elevated sulfate concentration. Subsequently, ethanol-fed FBR2 was used to reduce sulfate from FBR1 effluent, followed by an aerated sulfide oxidation reactor (SOR). At − 520 mV ≤ ORPs ≤ − 480 mV, FBR1 removed 100 ± 0.1% nitrate and 99.7 ± 0.3% selenate without sulfate reduction. At ORPs ≥ − 440 mV, selenate reduction was incomplete, whereas nitrate removal remained stable. Se0 recovery efficiency from FBR1 effluent was 37.5% with 71% Se purity. FBR2 converted 86% of the remaining sulfate in FBR1 effluent to hydrogen sulfide, but the over-oxidation of dissolved sulfide in SOR decreased the overall sulfate removal efficiency to ~46.3%. Overall, the two-stage FBR process with ORP feedback dosing of ethanol was effective for sequentially removing selenate, nitrate and sulfate and recovering Se0 from wastewater
A large study evaluation of evidence types containing offender fingerprints from recorded crimes in North Macedonia from 2005 to 2015
No full textThe Forensic Institute of the Republic of North Macedonia data set of 1,982 offender fingerprint identifications contributing to a conviction for crimes against property, was evaluated and analysed using contingency table statistical analysis techniques, chi-square test, fisher’s exact test and post hoc analysis. The data set was based on the forensic and court information available from 2005 to 2015 and pertained to the location, property type and evidence type. Interpretation of the data identified glass components, doors, windows, points of entry, cardboard and other packaging to be the most likely areas for locating offender fingerprints in non-residential and residential properties. In vehicle-based crimes, the front area (both left- and right-hand side) was the most likely to yield offender fingerprints.
This study reinforced the types of evidential items at property based crime scenes yielding offender fingerprints. In addition, the study seeks to provide recommendations for future data collection to enhance the data analysis and interpretation