Mitochondrial fusion requires the coordinated fusion of the outer and inner membranes. Three large GTPases--OPA1 and the mitofusins Mfn1 and Mfn2--are essential for the fusion of mammalian ...mitochondria. OPA1 is mutated in dominant optic atrophy, a neurodegenerative disease of the optic nerve. In yeast, the OPA1 ortholog Mgm1 is required for inner membrane fusion in vitro; nevertheless, yeast lacking Mgm1 show neither outer nor inner membrane fusion in vivo, because of the tight coupling between these two processes. We find that outer membrane fusion can be readily visualized in OPA1-null mouse cells in vivo, but these events do not progress to inner membrane fusion. Similar defects are found in cells lacking prohibitins, which are required for proper OPA1 processing. In contrast, double Mfn-null cells show neither outer nor inner membrane fusion. Mitochondria in OPA1-null cells often contain multiple matrix compartments bounded together by a single outer membrane, consistent with uncoupling of outer versus inner membrane fusion. In addition, unlike mitofusins and yeast Mgm1, OPA1 is not required on adjacent mitochondria to mediate membrane fusion. These results indicate that mammalian mitofusins and OPA1 mediate distinct sequential fusion steps that are readily uncoupled, in contrast to the situation in yeast.
The negative impact of obesity on physical fitness and motor abilities has been documented in youth of various ages; however, this issue has not been explored in youth with mild intellectual ...disabilities (ID). Youth with ID are considered more overweight, less physically fit, and less motor proficient than peers without ID, so it is important to determine if these variables are associated in this population. The purpose of this study was to examine the relationship between body mass index (BMI), physical fitness, and motor skills in a large sample of youth with mild ID.
A systematic, stratified sampling method was used to select 444 youth with mild ID, aged 6-18 years, from eight special education schools in Hong Kong. Physical fitness was assessed using items from the national Hong Kong assessment: 6- (ages 6-8 years) or 9- (ages 9-18 years) minute run, sit-up, isometric push-up, sit and reach, and sum of skinfold. Functional motor skills were assessed in 244 youth from the fitness sample using the Test of Gross Motor Development-II. Subjects were categorized into normal or overweight/obese BMI groups based on international cutoff points.
Approximately 20% of the sample was classified as overweight/obese (average BMI normal = 17.47+/-2.69; overweight/obese = 24.78+/-4.05). ANCOVA controlling for age and gender revealed group differences in the run (P = 0.001) and push-ups (P = 0.05), but not in the motor or other fitness variables. After controlling for age and gender, BMI was correlated with the run (r = -0.27, P < 0.001) and push ups (r = -0.18, P = 0.008). Age and gender were entered as the first block in hierarchical regression and accounted for most of the variance in all dependent variables, except sit and reach. The inclusion of BMI in the second block added to the model for run and push-ups only (deltaR2 run = 0.04, push-ups = 0.03, P<0.001).
Overweight/obesity is minimally associated with aerobic fitness and muscular strength in youth with mild ID. BMI did not impact other fitness measures (sit-up, sit and reach) or motor skills in the sample. The undesirable level of overweight/obesity in this sample requires increased attention and immediate intervention.
Purpose
Wiswesser Line Notation (WLN) is a old line notation for encoding chemical compounds for storage and processing by computers. Whilst the notation itself has long since been surpassed by ...SMILES and InChI, distribution of WLN during its active years was extensive. In the context of modernising chemical data, we present a comprehensive WLN parser developed using the OpenBabel toolkit, capable of translating WLN strings into various formats supported by the library. Furthermore, we have devised a specialised Finite State Machine l, constructed from the rules of WLN, enabling the recognition and extraction of chemical strings out of large bodies of text. Available open-access WLN data with corresponding SMILES or InChI notation is rare, however ChEMBL, ChemSpider and PubChem all contain WLN records which were used for conversion scoring. Our investigation revealed a notable proportion of inaccuracies within the database entries, and we have taken steps to rectify these errors whenever feasible.
Scientific contribution
Tools for both the extraction and conversion of WLN from chemical documents have been successfully developed. Both the Deterministic Finite Automaton (DFA) and parser handle the majority of WLN rules officially endorsed in the three major WLN manuals, with the parser showing a clear jump in accuracy and chemical coverage over previous submissions. The GitHub repository can be found here:
https://github.com/Mblakey/wiswesser
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Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating bacterial infections with bacteriophages alone or in combination with traditional antibiotics, has been ...demonstrated in emergency cases in the United States and in other countries, however remains to be approved for wide-spread use in the US. One limiting factor is a lack of guidelines for assessing the genomic safety of phage candidates. We present the phage characterization workflow used by our team to generate data for submitting phages to the Federal Drug Administration (FDA) for authorized use. Essential analysis checkpoints and warnings are detailed for obtaining high-quality genomes, excluding undesirable candidates, rigorously assessing a phage genome for safety and evaluating sequencing contamination. This workflow has been developed in accordance with community standards for high-throughput sequencing of viral genomes as well as principles for ideal phages used for therapy. The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria. We propose these guidelines as a minimum standard for phages being submitted to the FDA for review as investigational new drug candidates.
The introduction of benchtop sequencers has made adoption of whole genome sequencing possible for a broader community of researchers than ever before. Concurrently, metagenomic sequencing (MGS) is ...rapidly emerging as a tool for interrogating complex samples that defy conventional analyses. In addition, next-generation sequencers are increasingly being used in clinical or related settings, for instance to track outbreaks. However, information regarding the analytical sensitivity or limit of detection (LoD) of benchtop sequencers is currently lacking. Furthermore, the specificity of sequence information at or near the LoD is unknown.
In the present study, we assess the ability of three next-generation sequencing platforms to identify a pathogen (viral or bacterial) present in low titers in a clinically relevant sample (blood). Our results indicate that the Roche-454 Titanium platform is capable of detecting Dengue virus at titers as low as 1X102.5 pfu/mL, corresponding to an estimated 5.4X104 genome copies/ml maximum. The increased throughput of the benchtop sequencers, the Ion Torrent PGM and Illumina MiSeq platforms, enabled detection of viral genomes at concentrations as low as 1X104 genome copies/mL. Platform-specific biases were evident in sequence read distributions as well as viral genome coverage. For bacterial samples, only the MiSeq platform was able to provide sequencing reads that could be unambiguously classified as originating from Bacillus anthracis.
The analytical sensitivity of all three platforms approaches that of standard qPCR assays. Although all platforms were able to detect pathogens at the levels tested, there were several noteworthy differences. The Roche-454 Titanium platform produced consistently longer reads, even when compared with the latest chemistry updates for the PGM platform. The MiSeq platform produced consistently greater depth and breadth of coverage, while the Ion Torrent was unequaled for speed of sequencing. None of the platforms were able to verify a single nucleotide polymorphism responsible for antiviral resistance in an Influenza A strain isolated from the 2009 H1N1 pandemic. Overall, the benchtop platforms perform well for identification of pathogens from a representative clinical sample. However, unlike identification, characterization of pathogens is likely to require higher titers, multiple libraries and/or multiple sequencing runs.
Although cells express hundreds of metalloenzymes, the mechanisms by which apoenzymes receive their metal cofactors are largely unknown. Poly(rC)-binding proteins PCBP1 and PCBP2 are multifunctional ...adaptor proteins that bind iron and deliver it to ferritin for storage or to prolyl and asparagyl hydroxylases to metallate the mononuclear iron center. Here, we show that PCBP1 and PCBP2 also deliver iron to deoxyhypusine hydroxylase (DOHH), the dinuclear iron enzyme required for hypusine modification of the translation factor eukaryotic initiation factor 5A. Cells depleted of PCBP1 or PCBP2 exhibited loss of DOHH activity and loss of the holo form of the enzyme in cells, particularly when cells were made mildly iron-deficient. Lysates containing PCBP1 and PCBP2 converted apo-DOHH to holo-DOHH in vitro with greater efficiency than lysates lacking PCBP1 or PCBP2. PCBP1 bound to DOHH in iron-treated cells but not in control or iron-deficient cells. Depletion of PCBP1 or PCBP2 had no effect on the cytosolic Fe-S cluster enzyme xanthine oxidase but led to loss of cytosolic aconitase activity. Loss of aconitase activity was not accompanied by gain of RNA-binding activity, a pattern suggesting the incomplete disassembly of the 4Fe-4S cluster. PCBP depletions had minimal effects on total cellular iron, mitochondrial iron levels, and heme synthesis. Thus, PCBP1 and PCBP2 may serve as iron chaperones to multiple classes of cytosolic nonheme iron enzymes and may have a particular role in restoring metal cofactors that are spontaneously lost in iron deficient cells.
This Minimodule discusses radiation cataracts and makes some basic suggestions for practicing radiologists.
For many years radiation-induced cataracts were considered unlikely by most radiologists. ...Recent data suggest that the likelihood is much higher than previously thought, and the International Commission on Radiological Protection has suggested lower exposure limits.
Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome ...size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing.
This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage.
Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.
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