The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, ...have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.
Structured illumination microscopy is a method that can increase the spatial resolution of wide-field fluorescence microscopy beyond its classical limit by using spatially structured illumination ...light. Here we describe how this method can be applied in three dimensions to double the axial as well as the lateral resolution, with true optical sectioning. A grating is used to generate three mutually coherent light beams, which interfere in the specimen to form an illumination pattern that varies both laterally and axially. The spatially structured excitation intensity causes normally unreachable high-resolution information to become encoded into the observed images through spatial frequency mixing. This new information is computationally extracted and used to generate a three-dimensional reconstruction with twice as high resolution, in all three dimensions, as is possible in a conventional wide-field microscope. The method has been demonstrated on both test objects and biological specimens, and has produced the first light microscopy images of the synaptonemal complex in which the lateral elements are clearly resolved.
Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here ...we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4
T cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification, and exome sequencing is an effective platform to uncover tumour neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.
Cellular adaptations that occur during skeletal muscle hypertrophy in response to high-volume resistance training are not well-characterized. Therefore, we sought to explore how actin, myosin, ...sarcoplasmic protein, mitochondrial, and glycogen concentrations were altered in individuals that exhibited mean skeletal muscle fiber cross-sectional area (fCSA) hypertrophy following 6 weeks of high-volume resistance training. Thirty previously resistance-trained, college-aged males (mean ± standard deviation: 21±2 years, 5±3 training years) had vastus lateralis (VL) muscle biopsies obtained prior to training (PRE), at week 3 (W3), and at week 6 (W6). Muscle tissue from 15 subjects exhibiting PRE to W6 VL mean fCSA increases ranging from 320-1600 μm2 was further interrogated using various biochemical and histological assays as well as proteomic analysis. Seven of these individuals donated a VL biopsy after refraining from training 8 days following the last training session (W7) to determine how deloading affected biomarkers. The 15 fCSA hypertrophic responders experienced a +23% increase in mean fCSA from PRE to W6 (p<0.001) and, while muscle glycogen concentrations remained unaltered, citrate synthase activity levels decreased by 24% (p<0.001) suggesting mitochondrial volume decreased. Interestingly, repeated measures ANOVAs indicated that p-values approached statistical significance for both myosin and actin (p = 0.052 and p = 0.055, respectively), and forced post hoc tests indicated concentrations for both proteins decreased ~30% from PRE to W6 (p<0.05 for each target). Phalloidin-actin staining similarly revealed actin concentrations per fiber decreased from PRE to W6. Proteomic analysis of the sarcoplasmic fraction from PRE to W6 indicated 40 proteins were up-regulated (p<0.05), KEGG analysis indicated that the glycolysis/gluconeogenesis pathway was upregulated (FDR sig. <0.001), and DAVID indicated that the following functionally-annotated pathways were upregulated (FDR value <0.05): a) glycolysis (8 proteins), b) acetylation (23 proteins), c) gluconeogenesis (5 proteins) and d) cytoplasm (20 proteins). At W7, sarcoplasmic protein concentrations remained higher than PRE (+66%, p<0.05), and both actin and myosin concentrations remained lower than PRE (~-50%, p<0.05). These data suggest that short-term high-volume resistance training may: a) reduce muscle fiber actin and myosin protein concentrations in spite of increasing fCSA, and b) promote sarcoplasmic expansion coincident with a coordinated up-regulation of sarcoplasmic proteins involved in glycolysis and other metabolic processes related to ATP generation. Interestingly, these effects seem to persist up to 8 days following training.
We examined if resistance training affected muscle NAD
and NADH concentrations as well as nicotinamide phosphoribosyltransferase (NAMPT) protein levels and sirtuin (SIRT) activity markers in ...middle-aged, untrained (MA) individuals. MA participants (59±4 years old; n=16) completed 10 weeks of full-body resistance training (2 d/wk). Body composition, knee extensor strength, and vastus lateralis muscle biopsies were obtained prior to training (Pre) and 72 hours following the last training bout (Post). Data from trained college-aged men (22±3 years old, training age: 6±2 years old; n=15) were also obtained for comparative purposes. Muscle NAD
(+127%, p<0.001), NADH (+99%, p=0.002), global SIRT activity (+13%, p=0.036), and NAMPT protein (+15%, p=0.014) increased from Pre to Post in MA participants. Additionally, Pre muscle NAD
and NADH in MA participants were lower than college-aged participants (p<0.05), whereas Post values were similar between cohorts (p>0.10). Interestingly, muscle citrate synthase activity levels (i.e., mitochondrial density) increased in MA participants from Pre to Post (+183%, p<0.001), and this increase was significantly associated with increases in muscle NAD
(r
=0.592, p=0.001). In summary, muscle NAD
, NADH, and global SIRT activity are positively affected by resistance training in middle-aged, untrained individuals. Whether these adaptations facilitated mitochondrial biogenesis remains to be determined.
Laboratory studies of atmospheric chemistry characterize the nature of atmospherically relevant processes down to the molecular level, providing fundamental information used to assess how human ...activities drive environmental phenomena such as climate change, urban air pollution, ecosystem health, indoor air quality, and stratospheric ozone depletion. Laboratory studies have a central role in addressing the incomplete fundamental knowledge of atmospheric chemistry. This article highlights the evolving science needs for this community and emphasizes how our knowledge is far from complete, hindering our ability to predict the future state of our atmosphere and to respond to emerging global environmental change issues. Laboratory studies provide rich opportunities to expand our understanding of the atmosphere via collaborative research with the modeling and field measurement communities, and with neighboring disciplines.
Despite signs of infection-including taste loss, dry mouth and mucosal lesions such as ulcerations, enanthema and macules-the involvement of the oral cavity in coronavirus disease 2019 (COVID-19) is ...poorly understood. To address this, we generated and analyzed two single-cell RNA sequencing datasets of the human minor salivary glands and gingiva (9 samples, 13,824 cells), identifying 50 cell clusters. Using integrated cell normalization and annotation, we classified 34 unique cell subpopulations between glands and gingiva. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral entry factors such as ACE2 and TMPRSS members were broadly enriched in epithelial cells of the glands and oral mucosae. Using orthogonal RNA and protein expression assessments, we confirmed SARS-CoV-2 infection in the glands and mucosae. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibiting ACE2 and TMPRSS expression and sustained SARS-CoV-2 infection. Acellular and cellular salivary fractions from asymptomatic individuals were found to transmit SARS-CoV-2 ex vivo. Matched nasopharyngeal and saliva samples displayed distinct viral shedding dynamics, and salivary viral burden correlated with COVID-19 symptoms, including taste loss. Upon recovery, this asymptomatic cohort exhibited sustained salivary IgG antibodies against SARS-CoV-2. Collectively, these data show that the oral cavity is an important site for SARS-CoV-2 infection and implicate saliva as a potential route of SARS-CoV-2 transmission.
Limited evidence exists regarding differentially expressed biomarkers between previously-trained low versus high hypertrophic responders in response to resistance training. Herein, 30 college-aged ...males (training age 5 ± 3 years; mean ± SD) partook in 6 weeks of high-volume resistance training. Body composition, right leg vastus lateralis (VL) biopsies, and blood were obtained prior to training (PRE) and at the 3-week (W3) and 6-week time points (W6). The 10 lowest (LOW) and 10 highest (HIGH) hypertrophic responders were clustered based upon a composite hypertrophy score of PRE-to-W6 changes in right leg VL mean muscle fiber cross-sectional area (fCSA), VL thickness assessed via ultrasound, upper right leg lean soft tissue mass assessed via dual x-ray absorptiometry (DXA), and mid-thigh circumference. Two-way ANOVAs were used to compare biomarker differences between the LOW and HIGH clusters over time, and stepwise linear regression was performed to elucidate biomarkers that explained significant variation in the composite hypertrophy score from PRE to W3, W3 to W6, and PRE to W6 in all 30 participants. PRE-to-W6 HIGH and LOW responders exhibited a composite hypertrophy change of +10.7 ± 3.2 and -2.1 ± 1.6%, respectively (
< 0.001). Compared to HIGH responders, LOW responders exhibited greater PRE type II fCSA (+18%,
= 0.022). Time effects (
< 0.05) existed for total RNA/mg muscle (W6 > W3 > PRE), phospho (p)-4EBP1 (PRE > W3&W6), pan-mTOR (PRE > W3 < W6), p-mTOR (PRE > W3 < W6), pan-AMPKα (PRE > W3 < W6), pan-p70s6k (PRE > W3), muscle ubiquitin-labeled proteins (PRE > W6), mechano growth factor mRNA (W6 > W3&PRE), 45S rRNA (PRE > W6), and muscle citrate synthase activity (PRE > W3&W6). No interactions existed for the aforementioned biomarkers and/or other assayed targets (muscle 20S proteasome activity, serum total testosterone, muscle androgen receptor protein levels, muscle glycogen, or serum creatine kinase). Regression analysis indicated PRE type II fiber percentage (
= 0.152, β = 0.390,
= 0.033) and PRE type II fCSA (
= 0.207, β = -0.455,
= 0.019) best predicted the PRE-to-W6 change in the composite hypertrophy score. While our sample size is limited, these data suggest: (a) HIGH responders may exhibit more growth potential given that they possessed lower PRE type II fCSA values and (b) possessing a greater type II fiber percentage as a trained individual may be advantageous for hypertrophy in response to resistance training.
In recent decades, the world has witnessed an array of harmful invasions by exotic marine organisms. To provide the public and policymakers with better information on the status of exotic species in ...southern California waters, and to assess differences between port and non-port areas, a Rapid Assessment Survey of selected habitat types in sheltered waters between San Diego and Oxnard was conducted in the summer of 2000. The objectives included comparing the prevalence of exotic species among habitats and regions and between recent and past surveys; obtaining reference data for future assessments of changes in invasion status and the effectiveness of prevention or control efforts; detecting new invasions; and documenting significant range extensions. Twenty-two sites were sampled to include the three major commercial port areas in southern California, non-port-area marinas and lagoon sites. Sampling included dock fouling and adjacent soft-bottom benthos, nearby intertidal sites, and selected subtidal lagoon habitats. Samples were collected by a variety of manual techniques. Sixty-nine of the species collected are exotic, including representatives from two algal divisions and six invertebrate phyla. Ascidians are especially well-represented (14 exotic species) and widely occurring, and some bivalves and bryozoans also occur very widely. The numbers and proportions of exotic taxa were not significantly greater in port areas than in non-port areas.PUBLICATION ABSTRACT
Plasmodium berghei and Plasmodium chabaudi are widely used model malaria species. Comparison of their genomes, integrated with proteomic and microarray data, with the genomes of Plasmodium falciparum ...and Plasmodium yoelii revealed a conserved core of 4500 Plasmodium genes in the central regions of the 14 chromosomes and highlighted genes evolving rapidly because of stage-specific selective pressures. Four strategies for gene expression are apparent during the parasites' life cycle: (i) housekeeping; (ii) host-related; (iii) strategy-specific related to invasion, asexual replication, and sexual development; and (iv) stage-specific. We observed posttranscriptional gene silencing through translational repression of messenger RNA during sexual development, and a 47-base 3' untranslated region motif is implicated in this process.
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