The flexible and heterogeneous nature of carbohydrate chains often renders glycoproteins refractory to traditional structure determination methods. Small-angle X-ray scattering (SAXS) can be a useful tool for obtaining structural information of these systems. All-atom modeling of glycoproteins with flexible glycan chains was applied to interpret the solution SAXS data for a set of glycoproteins. For simpler systems (single glycan, with a well-defined protein structure), all-atom modeling generates models in excellent agreement with the scattering pattern and reveals the approximate spatial occupancy of the glycan chain in solution. For more complex systems (several glycan chains, or unknown protein substructure), the approach can still provide insightful models, though the orientations of glycans become poorly determined. Ab initio shape reconstructions appear to capture the global morphology of glycoproteins but in most cases offer little information about glycan spatial occupancy. The all-atom modeling methodology is available as a web server at http://salilab.org/allosmod-foxs.

Cyclin E, a regulatory subunit of cyclin-dependent kinase 2 (CDK2), is central to the initiation of DNA replication at the G₁/S checkpoint. Tight temporal control of cyclin E is essential to the coordination of cell-cycle processes and the maintenance of genome integrity. Overexpression of cyclin E in human tumors was first observed in the 1990s and led to the identification of oncogenic roles for deregulated cyclin E in experimental models. A decade later, low-molecular-weight cyclin E (LMW-E) isoforms were observed in aggressive tumor subtypes. Compared with full-length cyclin E, LMW-E hyperactivates CDK2 through increased complex stability and resistance to the endogenous inhibitors p21^CIP1 and p27^KIP1 LMW-E is predominantly generated by neutrophil elastase-mediated proteolytic cleavage, which eliminates the N-terminal cyclin E nuclear localization signal and promotes cyclin E's accumulation in the cytoplasm. Compared with full-length cyclin E, the aberrant localization and unique stereochemistry of LMW-E dramatically alters the substrate specificity and selectivity of CDK2, increasing tumorigenicity in experimental models. Cytoplasmic LMW-E, which can be assessed by IHC, is prognostic of poor survival and predicts resistance to standard therapies in patients with cancer. These patients may benefit from therapeutic modalities targeting the altered biochemistry of LMW-E or its associated vulnerabilities. Cancer Res; 78(19); 5481-91. ©2018 AACR.

Broad-based prostate-specific antigen (PSA) screening has saved lives but at a substantial human and financial cost. One way of mitigating this harm, while maintaining and possibly improving the benefit, is by focusing screening efforts on men at higher risk. With age, race, and family history as the only risk factors, many men lack any reliable data to inform their prostate cancer (PCa) screening decisions. Complexities including history of previous negative biopsies, interpretation of negative and/or equivocal mpMRI findings, and patient comorbidities further compound the already complicated decisions surrounding PCa screening and early detection. The authors present cases that provide real-world examples of how a single nucleotide polymorphism-based test can provide patients and providers with personalized PCa risk assessments and allow for development of improved risk-stratified screening regimens.

Globally, gastrointestinal (GI) infections by enteric pathogens are the second-leading cause of morbidity and mortality in children under five years of age (≤5 years). While GI pathogen exposure in households has been rigorously examined, there is little data about young children's exposure in public domains. Moreover, public areas in low-income settings are often used for other waste disposal practices in addition to human feces, such as trash dumping in areas near households. If young children play in public domains, they might be exposed to interrelated and highly concentrated microbial, chemical, and physical hazards. This study performed structured observations at 36 public areas in an internally displaced persons community that has transitioned into a formal settlement in Haiti. We documented how often young children played in public areas and quantified behaviors that might lead to illness and injury. Children ≤5 years played at all public sites, which included infants who played at 47% of sites. Children touched and mouthed plastic, metal and glass trash, food and other objects from the ground, ate soil (geophagia) and drank surface water. They also touched latrines, animals, animal feces and open drainage canals. Hand-to-mouth contact was one of the most common behaviors observed and the rate of contact significantly differed among developmental stages (infants: 18/h, toddlers: 11/h and young children: 9/h), providing evidence that children could ingest trace amounts of animal/human feces on hands that may contain GI pathogens. These findings demonstrate that water, sanitation and hygiene interventions could be more effective if they consider exposure risks to feces in public domains. Furthermore, this research highlights the need for waste-related interventions to address the broader set of civil conditions that create unsafe, toxic and contaminated public environments where young children play.

Regional maps of vegetation structure are necessary for delineating species habitats and for supporting conservation and ecological analyses. A systematic approach that can discriminate a wide range of meaningful and detailed vegetation classes is still lacking for neotropical savannas. Detailed vegetation mapping of savannas is challenged by seasonal vegetation dynamics and substantial heterogeneity in vegetation structure and composition, but fine spatial resolution imagery (<10 m) can improve map accuracy in these heterogeneous landscapes. Traditional pixel-based classification methods have proven problematic for fine spatial resolution data due to increased within-class spectral variability. Geographic Object-Based Image Analysis (GEOBIA) is a robust alternative method to overcome these issues. We developed a systematic GEOBIA framework accounting for both spectral and spatial features to map Cerrado structural types at 5-m resolution. This two-step framework begins with image segmentation and a Random Forest land cover classification based on spectral information, followed by spatial contextual and topological rules developed in a systematic manner in a GEOBIA knowledge-based approach. Spatial rules were defined a priori based on descriptions of environmental characteristics of 11 different physiognomic types and their relationships to edaphic conditions represented by stream networks (hydrography), topography, and substrate. The Random Forest land cover classification resulted in 10 land cover classes with 84.4% overall map accuracy and was able to map 7 of the 11 vegetation classes. The second step resulted in mapping 13 classes with 87.6% overall accuracy, of which all 11 vegetation classes were identified. Our results demonstrate that 5-m spatial resolution imagery is adequate for mapping land cover types of savanna structural elements. The GEOBIA framework, however, is essential for refining land cover categories to ecological classes (physiognomic types), leading to a higher number of vegetation classes while improving overall accuracy.

This study tests the hypothesis that silicon and calcium ions combinatorially target gene expression during osteoblast differentiation. MC3T3-E1 subclone 4 osteoblast progenitors (transformed mouse calvarial osteoblasts) were exposed to Si(4+) (from Na(2)SiO(3)) and Ca(2+) (from CaCl(2):H(2)O) ion treatments both individually (0.4 mM each + control treatment) and combinatorially (0.4 mM Si(4+) + 0.4 mM Ca(2+) + control treatment) and compared to control treated (α-minimum essential medium, 10% fetal bovine serum, and 1% penicillin-streptomycin) cells. Cell proliferation studies showed no significant increase in cell density between treatments over 5 days of culture. Cellular differentiation studies involved addition of ascorbic acid (50 mg/L) for all treatments. Relative gene expression was determined for collagen type 1 (Col(I)α1/Col(I)α2), core-binding factor a (cbfa1/Runx2), and osteocalcin (OCN), which indicated osteoblast progenitor differentiation into a mineralizing phenotype. Increased Si(4+) or Ca(2+) ion treatments enhanced Col(I)α1, Col(I)α2, Runx2, and OCN expression, while increased Si(4+) + Ca(2+) ion treatments enhanced OCN expression. Moreover, it was found that a Si(4+)/Ca(2+) ratio of unity was optimal for maximal expression of OCN. Collagen fiber bundles were dense, elongated, and thick within extracellular matrices (ECM) exposed to Si(4+) and Si(4+) + Ca(2+) treatments, while collagen fiber bundles were sparse, short, and thin within Ca(2+) and control treated ECM. These results indicated that individual ions enhance multiple osteogenic gene expression, while combined ion treatments enhance individual gene expression. In addition, these results indicated that Si(4+) enhanced osteoblast gene expression and ECM formation at higher levels than Ca(2+). These results support the larger concept that ions (possibly released from bioactive glasses) could control bone formation by targeting osteoblast marker expression.