Protein structural variation in computational models and crystallographic data

Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validation is typically limited to individual modes for a single protein. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational variance. Normal modes from four simple elastic network model potentials and from the CHARMM forcefield are calculated for a data set of 83 diverse, ultrahigh resolution crystal structures. While all five potentials provide good predictions of the magnitude of flexibility, the methods that consider all atoms have a clear edge at prediction of directionality, and the CHARMM potential produces the best agreement. The low-frequency modes from different potentials are similar, but those computed from the CHARMM potential show the greatest difference from the elastic network models. This was illustrated by computing the dynamic correlation matrices from different potentials for a PDZ domain structure. Comparison of normal mode results with anisotropic temperature factors opens the possibility of using ultrahigh resolution crystallographic data as a quantitative measure of molecular flexibility. The comprehensive evaluation demonstrates the costs and benefits of using normal mode potentials of varying complexity. Comparison of the dynamic correlation matrices suggests that a combination of topological and chemical potentials may help identify residues in which chemical forces make large contributions to intramolecular coupling.Comment: 17 pages, 4 figure

Improved methods for detection of β-galactosidase (lacZ) activity in hard tissue

The ß-galactosidase gene (lacZ) of Escherichia coli is widely used as a reporter gene. The expression of lacZ can be detected by enzyme-based histochemical staining using chromogenic substrates such as 5-bromo-4-chloro-3-indolyl-ß-D: -galactoside (X-gal). Because the enzymatic activity of lacZ is vulnerable to high temperatures and acid treatment for demineralization, detection of lacZ on paraffinized sections is difficult, especially for hard tissues, which require demineralization before sectioning in paraffin. To circumvent this problem, whole-mount X-gal staining before sectioning is performed. However, detection of lacZ activity in the center of larger portions of hard whole adult tissues is challenging. In this study, focusing on fixation procedures, we determined the conditions conducive to improved detection of lacZ activity in deeper areas of whole tissues. We used an annexin a5 (Anxa5)-lacZ reporter mouse model in which the Anxa5 expression in hard tissue is indicated by lacZ activity. We found that lacZ activity could be detected throughout the periodontal ligament of adult mice when fixed in 100% acetone, whereas it was not detected in the periodontal ligament around the root apex fixed in glutaraldehyde and paraformaldehyde. This staining could not be detected in wild-type mice. Acetone maintains the lacZ activity within 48 h of fixation at both 4°C and at room temperature. In conclusion, acetone is the optimal fixative to improve permeability for staining of lacZ activity in large volumes of adult hard tissues

Suicide ideation of individuals in online social networks

Suicide explains the largest number of death tolls among Japanese adolescents in their twenties and thirties. Suicide is also a major cause of death for adolescents in many other countries. Although social isolation has been implicated to influence the tendency to suicidal behavior, the impact of social isolation on suicide in the context of explicit social networks of individuals is scarcely explored. To address this question, we examined a large data set obtained from a social networking service dominant in Japan. The social network is composed of a set of friendship ties between pairs of users created by mutual endorsement. We carried out the logistic regression to identify users' characteristics, both related and unrelated to social networks, which contribute to suicide ideation. We defined suicide ideation of a user as the membership to at least one active user-defined community related to suicide. We found that the number of communities to which a user belongs to, the intransitivity (i.e., paucity of triangles including the user), and the fraction of suicidal neighbors in the social network, contributed the most to suicide ideation in this order. Other characteristics including the age and gender contributed little to suicide ideation. We also found qualitatively the same results for depressive symptoms.Comment: 4 figures, 9 table

Pharmacokinetics and safety of capmatinib with food in patients with MET-dysregulated advanced solid tumors

Purpose: In the Phase II GEOMETRY mono-1 study, the potent and selective mesenchymal-epithelial transition (MET) inhibitor capmatinib exhibited considerable efficacy in MET exon 14 skipping (METex14)–mutated metastatic non–small cell lung cancer at a dose of 400 mg BID. The current recommended dose is 400 mg BID in tablet formulation, with or without food. This article reports the pharmacokinetic (PK) profile, safety, and tolerability of capmatinib 300 and 400 mg BID given with food in MET-dysregulated advanced solid tumors. Methods: This multicenter, open-label, Phase I study enrolled adult patients with MET-dysregulated advanced solid tumors. In the dose escalation phase, capmatinib tablets were orally administered at a dose of 300 mg BID with food; if tolerated, the dose escalation cohort of 400 mg BID was to be opened to enrollment. In the expansion phase, patients were to be enrolled at the higher of the tolerated doses. Tablets were taken within 30 minutes of an unrestricted meal type, except on cycle 1 day 1 (C1D1) and cycle 1 day 7 (C1D7), when they were given with a high-fat meal. The primary objectives were to determine the higher of the tolerated study doses and assess PK variables, with a secondary objective of safety. Findings: Overall, 35 patients (300 mg BID, n = 8; 400 mg BID, n = 27) with MET-dysregulated advanced solid tumors were enrolled; all patients had received prior antineoplastic therapy, and the most common primary site was lung (45.7%). Among PK-evaluable patients, the median T for capmatinib after administration with a high-fat meal (on C1D1/C1D7) was 4.0 to 5.6 hours across doses. At steady state (C1D7), capmatinib accumulation was low across dose levels (geometric mean of accumulation ratios, 1.29–1.69), with an increase in exposure (AUC and C ) from 300 to 400 mg BID. There were no occurrences of dose-limiting toxicity. All patients experienced at least 1 adverse event, and treatment-related adverse events occurred in 28 patients (80%; 300 mg BID, n = 6; 400 mg BID, n = 22), the most frequent of which were fatigue (37.1%) and nausea (34.3%). Implications: Capmatinib tablet formulation at a dose of up to 400 mg BID with food is well tolerated in patients with MET-dysregulated advanced solid tumors, with safety observations consistent with the existing profile under fasted conditions. These findings support the capmatinib dosing recommendation of 400 mg BID with or without food. ClinicalTrials.gov identifier: NCT02925104

Combinations of β-lactam or aminoglycoside antibiotics with plectasin are synergistic against methicillin-sensitive and methicillin-resistant Staphylococcus aureus.

Bacterial infections remain the leading killer worldwide which is worsened by the continuous emergence of antibiotic resistance. In particular, methicillin-sensitive (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) are prevalent and the latter can be difficult to treat. The traditional strategy of novel therapeutic drug development inevitably leads to emergence of resistant strains, rendering the new drugs ineffective. Therefore, rejuvenating the therapeutic potentials of existing antibiotics offers an attractive novel strategy. Plectasin, a defensin antimicrobial peptide, potentiates the activities of other antibiotics such as β-lactams, aminoglycosides and glycopeptides against MSSA and MRSA. We performed in vitro and in vivo investigations to test against genetically diverse clinical isolates of MSSA (n = 101) and MRSA (n = 115). Minimum inhibitory concentrations (MIC) were determined by the broth microdilution method. The effects of combining plectasin with β-lactams, aminoglycosides and glycopeptides were examined using the chequerboard method and time kill curves. A murine neutropenic thigh model and a murine peritoneal infection model were used to test the effect of combination in vivo. Determined by factional inhibitory concentration index (FICI), plectasin in combination with aminoglycosides (gentamicin, neomycin or amikacin) displayed synergistic effects in 76-78% of MSSA and MRSA. A similar synergistic response was observed when plectasin was combined with β-lactams (penicillin, amoxicillin or flucloxacillin) in 87-89% of MSSA and MRSA. Interestingly, no such interaction was observed when plectasin was paired with vancomycin. Time kill analysis also demonstrated significant synergistic activities when plectasin was combined with amoxicillin, gentamicin or neomycin. In the murine models, plectasin at doses as low as 8 mg/kg augmented the activities of amoxicillin and gentamicin in successful treatment of MSSA and MRSA infections. We demonstrated that plectasin strongly rejuvenates the therapeutic potencies of existing antibiotics in vitro and in vivo. This is a novel strategy that can have major clinical implications in our fight against bacterial infections

LHC Searches for Non-Chiral Weakly Charged Multiplets

Because the TeV-scale to be probed at the Large Hadron Collider should shed light on the naturalness, hierarchy, and dark matter problems, most searches to date have focused on new physics signatures motivated by possible solutions to these puzzles. In this paper, we consider some candidates for new states that although not well-motivated from this standpoint are obvious possibilities that current search strategies would miss. In particular we consider vector representations of fermions in multiplets of $SU(2)_L$ with a lightest neutral state. Standard search strategies would fail to find such particles because of the expected small one-loop-level splitting between charged and neutral states.Comment: 16 pages, 9 figure

Super Weyl invariance: BPS equations from heterotic worldsheets

It is well-known that the beta functions on a string worldsheet correspond to the target space equations of motion, e.g. the Einstein equations. We show that the BPS equations, i.e. the conditions of vanishing supersymmetry variations of the space-time fermions, can be directly derived from the worldsheet. To this end we consider the RNS-formulation of the heterotic string with (2,0) supersymmetry, which describes a complex torsion target space that supports a holomorphic vector bundle. After a detailed account of its quantization and renormalization, we establish that the cancellation of the Weyl anomaly combined with (2,0) finiteness implies the heterotic BPS conditions: At the one loop level the geometry is required to be conformally balanced and the gauge background has to satisfy the Hermitean Yang-Mills equations.Comment: 1+31 pages LaTeX, 5 figures; final version, discussion relation Weyl invariance and (2,0) finiteness extended, typos correcte

Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria

The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli

The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with less changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: 1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation, and 2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.Comment: 14 pages, 8 figures, to be published in PLoS Computational Biolog

ARC OF RECREATION 2.0 Connecting the McKnight Rail Trail From Mason Square to Union Station, Springfield MA

ARC OF RECREATION 2.0 Connecting the McKnight Rail Trail From Mason Square to Union Station, Springfield MA ARC OF RECREATION 2.0 is a Senior Urban Design Studio that created design concepts to envision the McKnight Rail Trail on an abandoned railroad corridor as a place to walk, bike, recreate, and congregate and to connect Mason Square to Union Station. Arc of Recreation was a name that was coined over 10 years ago through a different project at UMass. Finally realization is within reach. The City published a feasibility study in 2014 and has freed a construction budget of $430,000 for the first phases.The McKnight neighborhood hosts a diverse demographic that would benefit to an implemented rail trail in their community. With health complications including obesity and diabetes, the trail can provide a free means of transportation to the metro center that encourages an active lifestyle and increased employment in the neighborhood. Children will be able to utilize a safe passage to school, such as the nearby Rebecca M. Johnson Middle School, as well as young adults working part time jobs in the neighborhood and surrounding areas. The trail will connect from Union Station in downtown to Mason Square in the east. Access along the trail route will enable more community members to enter the trail and use it. Therefore it creates a more equitable transportation network that can be shared by all residents. The Studio created design concepts including first phase tactical interventions that make the street and public space experience enticing to visitors and engaging for the local residents, workers, and their families. The designs reflect the feedback of local community members through community meetings and a design charrette. In conclusion, the envisioned trail will foster community engagement and interaction to steer the future development of the neighborhood. The following measures are crucial for a successful rail trail: • Improvement of major street crossings to enable safe use of the trail during all day and nighttime hours. • Integration of on street bike lanes and the trail to create a bicycle loop around the neighborhood. Expand the downtown bike-share stations for entry points to the trail. • Create accessibility to public parks in the City through a network of safe streets with extensive tree plantings. Envision a trail that allows for access to the Connecticut River Walk and Bikeway. • Embrace the industrial and underused architecture through public art. • Protect existing wetlands on the trail through bypasses and boardwalks. • Raise awareness for the rich ecology on the trail through signage and education. • Create diverse opportunities to play for all ages and demographics. • Create areas for urban gardening to connect trail and community. • Creation of spaces on the trail where the community comes together and hold events and meetings. • Design for activities throughout the year including the winter season. • Rezone the trail to Open Space to guide its future development as a functioning rail trail