Course-based undergraduate research experiences (CUREs) are laboratory courses that integrate broadly relevant problems, discovery, use of the scientific process, collaboration, and iteration to ...provide more students with research experiences than is possible in individually mentored faculty laboratories. Members of the national Malate dehydrogenase CUREs Community (MCC) investigated the differences in student impacts between traditional laboratory courses (control), a short module CURE within traditional laboratory courses (mCURE), and CUREs lasting the entire course (cCURE). The sample included approximately 1,500 students taught by 22 faculty at 19 institutions. We investigated course structures for elements of a CURE and student outcomes including student knowledge, student learning, student attitudes, interest in future research, overall experience, future GPA, and retention in STEM. We also disaggregated the data to investigate whether underrepresented minority (URM) outcomes were different from White and Asian students. We found that the less time students spent in the CURE the less the course was reported to contain experiences indicative of a CURE. The cCURE imparted the largest impacts for experimental design, career interests, and plans to conduct future research, while the remaining outcomes were similar between the three conditions. The mCURE student outcomes were similar to control courses for most outcomes measured in this study. However, for experimental design, the mCURE was not significantly different than either the control or cCURE. Comparing URM and White/Asian student outcomes indicated no difference for condition, except for interest in future research. Notably, the URM students in the mCURE condition had significantly higher interest in conducting research in the future than White/Asian students.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The TRIM family of proteins is distinguished by its tripartite motif (TRIM). Typically, TRIM proteins contain a RING finger domain, one or two B-box domains, a coiled-coil domain and the more ...variable C-terminal domains. TRIM16 does not have a RING domain but does harbour two B-box domains. Here we showed that TRIM16 homodimerized through its coiled-coil domain and heterodimerized with other TRIM family members; TRIM24, Promyelocytic leukaemia (PML) protein and Midline-1 (MID1). Although, TRIM16 has no classic RING domain, three-dimensional modelling of TRIM16 suggested that its B-box domains adopts RING-like folds leading to the hypothesis that TRIM16 acts as an ubiquitin ligase. Consistent with this hypothesis, we demonstrated that TRIM16, devoid of a classical RING domain had auto-polyubiquitination activity and acted as an E3 ubiquitin ligase in vivo and in vitro assays. Thus via its unique structure, TRIM16 possesses both heterodimerization function with other TRIM proteins and also has E3 ubiquitin ligase activity.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Animal density is a fundamental parameter in ecology and conservation, and yet it has remained difficult to measure. For terrestrial mammals and birds, camera‐traps have dramatically improved our ...ability to collect systematic data across a large number of species, but density estimation (except for species with natural marks) is still faced with statistical and logistical hurdles, including the requirement for auxiliary data and large sample sizes, and an inability to incorporate covariates.
To fill this gap in the camera‐trapper's statistical toolbox, we extended the existing Random Encounter Model (REM) to the multi‐species case in a Bayesian framework. This multi‐species REM can incorporate covariates and provides parameter estimates for even the rarest species. As input to the model, we used information directly available in the camera‐trap data. The model outputs posterior distributions for the REM parameters—movement speed, activity level, the effective angle and radius of the camera‐trap detection zone, and density—for each species. We applied this model to an existing dataset for 35 species in Borneo, collected across old‐growth and logged forest. Here, we added animal position data derived from the image sequences in order to estimate the speed and detection zone parameters.
The model revealed a decrease in movement speeds, and therefore day‐range, across the species community in logged compared to old‐growth forest, whilst activity levels showed no consistent trend. Detection zones were shorter, but of similar width, in logged compared to old‐growth forest. Overall, animal density was lower in logged forest, even though most species individually occurred at higher density in logged forest. However, the biomass per unit area was substantially higher in logged compared to old‐growth forest, particularly among herbivores and omnivores, likely because of increased resource availability at ground level. We also included body mass as a variable in the model, revealing that larger‐bodied species were more active, had more variable speeds, and had larger detection zones.
Caution is warranted when estimating density for semi‐arboreal and fossorial species using camera‐traps, and more extensive testing of assumptions is recommended. Nonetheless, we anticipate that multi‐species density estimation could have very broad application.
Genetic risk scores (GRS) have been developed that differentiate individuals with type 1 diabetes from those with other forms of diabetes and are starting to be used for population screening; ...however, most studies were conducted in European-ancestry populations. This study identifies novel genetic variants associated with type 1 diabetes risk in African-ancestry participants and develops an African-specific GRS.
We generated single nucleotide polymorphism (SNP) data with the ImmunoChip on 1,021 African-ancestry participants with type 1 diabetes and 2,928 control participants. HLA class I and class II alleles were imputed using SNP2HLA. Logistic regression models were used to identify genome-wide significant (
< 5.0 × 10
) SNPs associated with type 1 diabetes in the African-ancestry samples and validate SNPs associated with risk in known European-ancestry loci (
< 2.79 × 10
).
African-specific (HLA-
*03:01-HLA-
*02:01) and known European-ancestry HLA haplotypes (HLA-
*03:01-HLA-
*05:01-HLA-
*02:01, HLA-
*04:01-HLA-
*03:01-HLA-
*03:02) were significantly associated with type 1 diabetes risk. Among European-ancestry defined non-HLA risk loci, six risk loci were significantly associated with type 1 diabetes in subjects of African ancestry. An African-specific GRS provided strong prediction of type 1 diabetes risk (area under the curve 0.871), performing significantly better than a European-based GRS and two polygenic risk scores in independent discovery and validation cohorts.
Genetic risk of type 1 diabetes includes ancestry-specific, disease-associated variants. The GRS developed here provides improved prediction of type 1 diabetes in African-ancestry subjects and a means to identify groups of individuals who would benefit from immune monitoring for early detection of islet autoimmunity.
Neuroblastoma is a common childhood cancer with almost a third of those affected still dying, thus new therapeutic strategies need to be explored. Current experimental therapies focus mostly on ...inhibiting oncogenic transcription factor signalling. Although LIN28B, DICER and other RNA-binding proteins (RBPs) have reported roles in neuroblastoma development and patient outcome, the role of RBPs in neuroblastoma is relatively unstudied. In order to elucidate novel RBPs involved in
-amplified and other high-risk neuroblastoma subtypes, we performed differential mRNA expression analysis of RBPs in a large primary tumour cohort (
= 498). Additionally, we found via Kaplan-Meier scanning analysis that 685 of the 1483 tested RBPs have prognostic value in neuroblastoma. For the top putative oncogenic candidates, we analysed their expression in neuroblastoma cell lines, as well as summarised their characteristics and existence of chemical inhibitors. Moreover, to help explain their association with neuroblastoma subtypes, we reviewed candidate RBPs' potential as biomarkers, and their mechanistic roles in neuronal and cancer contexts. We found several highly significant RBPs including RPL22L1, RNASEH2A, PTRH2, MRPL11 and AFF2, which remain uncharacterised in neuroblastoma. Although not all RBPs appear suitable for drug design, or carry prognostic significance, we show that several RBPs have strong rationale for inhibition and mechanistic studies, representing an alternative, but nonetheless promising therapeutic strategy in neuroblastoma treatment.
Toll-like receptors (TLRs) initiate immune responses by recognizing pathogen-associated molecules, but the molecular basis for recognition is poorly understood. In particular, it is unclear how ...receptor-ligand interactions lead to the initiation of downstream signaling. Here, we describe the mechanism by which TLR3 recognizes its ligand, double-stranded RNA (dsRNA), and forms an active signaling complex. We show that dsRNA binds saturably, specifically, and reversibly to a defined ligand-binding site (or sites) on the TLR3 ectodomain (TLR3ecd). Binding affinities increase with both buffer acidity and ligand size. Purified TLR3ecd protein is exclusively monomeric in solution, but through a highly cooperative process, it forms dimers when bound to dsRNA, and multiple TLR3ecd dimers bind to long dsRNA strands. The smallest dsRNA oligonucleotides that form stable complexes with TLR3ecd (40-50 bp) each bind one TLR3ecd dimer, and these are also the smallest oligonucleotides that efficiently activate TLR3 in cells. We conclude that TLR3 assembles on dsRNA as stable dimers and that the minimal signaling unit is one TLR3 dimer.
Toll-like receptors (TLRs) are the major cell-surface initiators of inflammatory responses to pathogens. They bind a wide variety of pathogenic substances through their ectodomains (ECDs). Here, we ...ask: what is the structural basis for this interaction? Toll-like receptor ECDs comprise 19–25 tandem copies of a motif known as the leucine-rich repeat (LRR). No X-ray structure of a TLR-ECD is currently available but there are several high-resolution LRR-containing proteins that can be used to model TLRs. We suggest that the basic framework of TLRs is a horseshoe-shaped solenoid that contains an extensive β-sheet on its concave surface, and numerous ligand-binding insertions. Together, these insertions and the β-sheet could provide a binding surface that is 10-fold greater in area than binding surfaces in antibodies and T-cell receptors.
Protein‐protein interactions (PPIs) are a crucial part of intracellular communication and function. The “rules” for specificity and/or selection of a protein‐protein interaction are not completely ...understood, but protein modifications, such as phosphorylation, have been implicated in this process. Suppressor of IKKepsilon (SIKE) is associated with multiple, distinct proteins including TANK‐binding kinase 1 (TBK1), STRIPAK (striatin‐interacting phosphatase and kinase), and cytoskeletal proteins tubulin and actinin. Although SIKE’s function is not fully defined in these complexes, protein modification has been observed in SIKE (phosphorylated at six serine residues: 133, 185, 187, 188, 190, and 198) that may direct PPI formation: Co‐immunoprecipitation revealed that the tubulin interaction was enhanced with the phosphomimetic SIKE (S133/185/187/188/190/198E). We hypothesize that the quaternary state of SIKE, regulated by phosphorylation, dictates SIKE PPI formation. Using the SIKE phosphomimetic mutant, size exclusion chromatography and chemical crosslinking studies showed a monomeric species, whereas native SIKE separated as a dimer. These studies support SIKE undergoing a phosphorylation‐induced change in quaternary state. Prior computational assessment of dimer interface stability with single phosphomimetic substitutions identified S187E, S190E, and S198E as significantly different from WT on a per residue basis. Phosphomimetic mutants for these sites were created and sequence confirmed. In SEC, the phosphomimetic point mutations shift the elution pattern from primarily dimer to containing more monomeric species. To assess SIKE interactions with tubulin, SIKE constructs were labeled using a maleimide‐thiol conjugation to BODIPY TMR. BODIPY‐labeled SIKE, phosphomimetic point mutations, and S6E SIKE interactions with tubulin were monitored using fluorescence polarization. These PPI assays assess the effect of phosphorylation in the selection of SIKE interaction partners. Together, this work advances our understanding of the role that phosphorylation‐induced changes in quaternary state play in regulating protein interactions.
Innate immunity is the first line of defense against invading pathogens. Toll-like receptors (TLRs) act as sentinels of the innate immune system, sensing a variety of ligands from lipopolysaccharide ...to flagellin to dsRNA through their ligand-binding domain that is composed of leucine-rich repeats (LRRs). Ligand binding initiates a signaling cascade that leads to the up-regulation of inflammation mediators. In this study, we have expressed and crystallized the ectodomain (ECD) of human TLR3, which recognizes dsRNA, a molecular signature of viruses, and have determined the molecular structure to 2.4-Å resolution. The overall horseshoe-shaped structure of the TLR3-ECD is formed by 23 repeating LRRs that are capped at each end by specialized non-LRR domains. The extensive β-sheet on the molecule's concave surface forms a platform for several modifications, including insertions in the LRRs and 11 N-linked glycans. The TLR3-ECD structure indicates how LRR loops can establish distinct pathogen recognition receptors.
The DsRNA Binding Site of Human Toll-Like Receptor 3 Bell, Jessica K.; Askins, Janine; Hall, Pamela R. ...
Proceedings of the National Academy of Sciences - PNAS,
06/2006, Letnik:
103, Številka:
23
Journal Article
Recenzirano
Odprti dostop
Pathogen recognition by Toll-like receptors (TLRs) initiates innate immune responses that are essential for inhibiting pathogen dissemination and for the development of acquired immunity. The TLRs ...recognize pathogens with their N-terminal ectodomains (ECD), but the molecular basis for this recognition is not known. Recently we reported the x-ray structure for unliganded TLR3-ECD; however, it has proven difficult to obtain a crystal structure of TLR3 with its ligand, dsRNA. We have now located the TLR3 ligand binding site by mutational analysis. More than 50 single-residue mutations have been generated throughout the TLR3-ECD, but only two, H539E and N541A, resulted in the loss of TLR3 activation and ligand binding functions. These mutations locate the dsRNA binding site on the glycan-free, lateral surface of TLR3 toward the C terminus and suggest a model for dsRNA binding and TLR3 activation.
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