Knot Theory: from Fox 3-colorings of links to Yang-Baxter homology and Khovanov homology

This paper is an extended account of my "Introductory Plenary talk at Knots in Hellas 2016" conference We start from the short introduction to Knot Theory from the historical perspective, starting from Heraclas text (the first century AD), mentioning R.Llull (1232-1315), A.Kircher (1602-1680), Leibniz idea of Geometria Situs (1679), and J.B.Listing (student of Gauss) work of 1847. We spend some space on Ralph H. Fox (1913-1973) elementary introduction to diagram colorings (1956). In the second section we describe how Fox work was generalized to distributive colorings (racks and quandles) and eventually in the work of Jones and Turaev to link invariants via Yang-Baxter operators, here the importance of statistical mechanics to topology will be mentioned. Finally we describe recent developments which started with Mikhail Khovanov work on categorification of the Jones polynomial. By analogy to Khovanov homology we build homology of distributive structures (including homology of Fox colorings) and generalize it to homology of Yang-Baxter operators. We speculate, with supporting evidence, on co-cycle invariants of knots coming from Yang-Baxter homology. Here the work of Fenn-Rourke-Sanderson (geometric realization of pre-cubic sets of link diagrams) and Carter-Kamada-Saito (co-cycle invariants of links) will be discussed and expanded. Dedicated to Lou Kauffman for his 70th birthday.Comment: 35 pages, 31 figures, for Knots in Hellas II Proceedings, Springer, part of the series Proceedings in Mathematics & Statistics (PROMS

Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair.

Repair of double strand DNA breaks (DSBs) can result in gene disruption or gene modification via homology directed repair (HDR) from donor DNA. Altering cellular responses to DSBs may rebalance editing outcomes towards HDR and away from other repair outcomes. Here, we utilize a pooled CRISPR screen to define host cell involvement in HDR between a Cas9 DSB and a plasmid double stranded donor DNA (dsDonor). We find that the Fanconi Anemia (FA) pathway is required for dsDonor HDR and that other genes act to repress HDR. Small molecule inhibition of one of these repressors, CDC7, by XL413 and other inhibitors increases the efficiency of HDR by up to 3.5 fold in many contexts, including primary T cells. XL413 stimulates HDR during a reversible slowing of S-phase that is unexplored for Cas9-induced HDR. We anticipate that XL413 and other such rationally developed inhibitors will be useful tools for gene modification

Heavy Meson Production in Proton-Nucleus Reactions with Empirical Spectral Functions

We study the production of $K^+, \rho, \omega$ and $\phi$ mesons in $p + ^{12}C$ reactions on the basis of empirical spectral functions. The high momentum, high removal energy part of the spectral function is found to be negligible in all cases close to the absolute threshold. Furthermore, the two-step process ($pN \rightarrow \pi N N; \pi N \rightarrow N + K^+, \rho, \omega, \phi$) dominates the cross section at threshold energies in line with earlier calculations based on the folding model.Comment: 18 pages, LaTeX, plus 14 postscript figures, submitted to Z. Phys.

Drosophila APC2 and APC1 Have Overlapping Roles in the Larval Brain Despite Their Distinct Intracellular Localizations

The tumor suppressor APC and its homologs, first identified for a role in colon cancer, negatively regulate Wnt signaling in both oncogenesis and normal development, and play Wnt-independent roles in cytoskeletal regulation. Both Drosophila and mammals have two APC family members. We further explored the functions of the Drosophila APCs using the larval brain as a model. We found that both proteins are expressed in the brain. APC2 has a highly dynamic, asymmetric localization through the larval neuroblast cell cycle relative to known mediators of embryonic neuroblast asymmetric divisions. Adherens junction proteins also are asymmetrically localized in neuroblasts. In addition they accumulate with APC2 and APC1 in nerves formed by axons of the progeny of each neuroblast-ganglion mother cell cluster. APC2 and APC1 localize to very different places when expressed in the larval brain: APC2 localizes to the cell cortex and APC1 to centrosomes and microtubules. Despite this, they play redundant roles in the brain; while each single mutant is normal, the zygotic double mutant has severely reduced numbers of larval neuroblasts. Our experiments suggest that this does not result from misregulation of Wg signaling, and thus may involve the cytoskeletal or adhesive roles of APC proteins

Organizational aspects and implementation of data systems in large-scale epidemiological studies in less developed countries

BACKGROUND: In the conduct of epidemiological studies in less developed countries, while great emphasis is placed on study design, data collection, and analysis, often little attention is paid to data management. As a consequence, investigators working in these countries frequently face challenges in cleaning, analyzing and interpreting data. In most research settings, the data management team is formed with temporary and unskilled persons. A proper working environment and training or guidance in constructing a reliable database is rarely available. There is little information available that describes data management problems and solutions to those problems. Usually a line or two can be obtained in the methods section of research papers stating that the data are doubly-entered and that outliers and inconsistencies were removed from the data. Such information provides little assurance that the data are reliable. There are several issues in data management that if not properly practiced may create an unreliable database, and outcomes of this database will be spurious. RESULTS: We have outlined the data management practices for epidemiological studies that we have modeled for our research sites in seven Asian countries and one African country. CONCLUSION: Information from this model data management structure may help others construct reliable databases for large-scale epidemiological studies in less developed countries

Community Health Environment Scan Survey (CHESS): a novel tool that captures the impact of the built environment on lifestyle factors

Background: Novel1 1This study was performed on behalf of the Community Interventions for Health (CIH) collaboration. efforts and accompanying tools are needed to tackle the global burden of chronic disease. This paper presents an approach to describe the environments in which people live, work, and play. Community Health Environment Scan Survey (CHESS) is an empirical assessment tool that measures the availability and accessibility, of healthy lifestyle options lifestyle options. CHESS reveals existing community assets as well as opportunities for change, shaping community intervention planning efforts by focusing on community-relevant opportunities to address the three key risk factors for chronic disease (i.e. unhealthy diet, physical inactivity, and tobacco use). Methods: The CHESS tool was developed following a review of existing auditing tools and in consultation with experts. It is based on the social-ecological model and is adaptable to diverse settings in developed and developing countries throughout the world. Results: For illustrative purposes, baseline results from the Community Interventions for Health (CIH) Mexico site are used, where the CHESS tool assessed 583 food stores and 168 restaurants. Comparisons between individual-level survey data from schools and community-level CHESS data are made to demonstrate the utility of the tool in strategically guiding intervention activities. Conclusion: The environments where people live, work, and play are key factors in determining their diet, levels of physical activity, and tobacco use. CHESS is the first tool of its kind that systematically and simultaneously examines how built environments encourage/discourage healthy eating, physical activity, and tobacco use. CHESS can help to design community interventions to prevent chronic disease and guide healthy urban planning

Practical three color live cell imaging by widefield microscopy

Live cell fluorescence microscopy using fluorescent protein tags derived from jellyfish and coral species has been a successful tool to image proteins and dynamics in many species. Multi-colored aequorea fluorescent protein (AFP) derivatives allow investigators to observe multiple proteins simultaneously, but overlapping spectral properties sometimes require the use of sophisticated and expensive microscopes. Here, we show that the aequorea coerulescens fluorescent protein derivative, PS-CFP2 has excellent practical properties as a blue fluorophore that are distinct from green or red fluorescent proteins and can be imaged with standard filter sets on a widefield microscope. We also find that by widefield illumination in live cells, that PS-CFP2 is very photostable. When fused to proteins that form concentrated puncta in either the cytoplasm or nucleus, PSCFP2 fusions do not artifactually interact with other AFP fusion proteins, even at very high levels of over-expression. PSCFP2 is therefore a good blue fluorophore for distinct three color imaging along with eGFP and mRFP using a relatively simple and inexpensive microscope

Immunodominant HIV-1 Cd4+ T Cell Epitopes in Chronic Untreated Clade C HIV-1 Infection

Background: A dominance of Gag-specific CD8+ T cell responses is significantly associated with a lower viral load in individuals with chronic, untreated clade C human immunodeficiency virus type 1 (HIV-1) infection. This association has not been investigated in terms of Gag-specific CD4+ T cell responses, nor have clade C HIV-1–specific CD4+ T cell epitopes, likely a vital component of an effective global HIV-1 vaccine, been identified. Methodology/Principal Findings: Intracellular cytokine staining was conducted on 373 subjects with chronic, untreated clade C infection to assess interferon-gamma (IFN-γ) responses by CD4+ T cells to pooled Gag peptides and to determine their association with viral load and CD4 count. Gag-specific IFN-γ–producing CD4+ T cell responses were detected in 261/373 (70%) subjects, with the Gag responders having a significantly lower viral load and higher CD4 count than those with no detectable Gag response (p<0.0001 for both parameters). To identify individual peptides targeted by HIV-1–specific CD4+ T cells, separate ELISPOT screening was conducted on CD8-depleted PBMCs from 32 chronically infected untreated subjects, using pools of overlapping peptides that spanned the entire HIV-1 clade C consensus sequence, and reconfirmed by flow cytometry to be CD4+ mediated. The ELISPOT screening identified 33 CD4+ peptides targeted by 18/32 patients (56%), with 27 of the 33 peptides located in the Gag region. Although the breadth of the CD4+ responses correlated inversely with viral load (p = 0.015), the magnitude of the response was not significantly associated with viral load. Conclusions/Significance: These data indicate that in chronic untreated clade C HIV-1 infection, IFN-γ–secreting Gag-specific CD4+ T cell responses are immunodominant, directed at multiple distinct epitopes, and associated with viral control

Fabrication and verification of conjugated AuNP-antibody nanoprobe for sensitivity improvement in electrochemical biosensors

Abstract This study was designed to obtain covalently coupled conjugates as means for achieving higher stability and better coverage of the AuNPs by antibodies on the particle surface suitable for sensor performance enhancement. Starting by using a modified protocol, colloid gold solution, with mean AuNP core size of ~6 nm was synthesized. The protocol used for conjugation of AuNPs to osteocalcin antibody in this study relies on covalent and electrostatic attractions between constituents. Varieties of conjugates with varying combinations of crosslinkers and different concentrations were successfully synthesized. The obtained products were characterized and their properties were studied to determine the best candidate in sense of antibody - antigen reactivity. Using AuNP-GSH-NHS-Ab combination (1:1:1), the tertiary structure of the protein was maintained and thus the antibody remained functional in the future steps. This one-pot method provided a simple method for covalently coupling antibodies on the particle surface while keeping their functionality intact. The AuNP content of the solution also accelerated electron transfer rate and thus amplifies the detection signal. With the developed and discussed technique herein, a simple solution is modeled to be used for measuring serum levels of biomarkers in single and/or multiplexed sensor systems