Characterization of Vacuolating cytotoxin A binding to sphingomyelin in Helicobacter pylori pathogenesis

The main objective of my research project is to characterize vacuolating cytotoxin A (VacA) from Helicobacter pylori binding to an important host cell membrane lipid, sphingomyelin (SM). Previously, our laboratory showed that plasma membrane SM is important for the toxin biological activity, cell surface binding, and toxin-receptor direct interactions suggesting that SM is a receptor for VacA. Moreover, recent findings from our laboratory showed that R552, W603, and R647 of VacA are important that when changed to alanine, resulting in decreased SM-dependent VacA activity in gastric epithelial cells. However, the molecular basis of SM-VacA interactions remains unknown. My research focuses molecular on the detailed molecular mechanism by which these three residues of VacA interact with SM in SM-dependent toxin cellular activities. I will evaluate the hypothesis that R552, W603, and R647 on VacA facilitate its SM binding by interacting with the phosphorylcholine head group of SM. To test this hypothesis, I will conduct site-directed mutagenesis analysis to evaluate the specific properties of the three residues (R552/W603/R647) that are important for SM-dependent toxin cellular activities. I will evaluate the prediction that VacA interacts with SM through pi-cation interactions between the aromatic ring of tryptophan and choline moiety of head group of SM and ionic interactions between positively charged arginine residues and negatively charged phosphate moiety of SM. Testing this prediction, I am evaluating the toxin cellular activity of charge conservative and non-conservative single substitution mutations in the three residues. The results of this study will provide the framework for the molecular interactions behind VacA-SM interactions.Ope

High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform

Multiplexed single nucleotide polymorphism (SNP) markers have the potential to increase the speed and cost-effectiveness of genotyping, provided that an optimal SNP density is used for each application. To test the efficiency of multiplexed SNP genotyping for diversity, mapping and breeding applications in rice (Oryza sativa L.), we designed seven GoldenGate VeraCode oligo pool assay (OPA) sets for the Illumina BeadXpress Reader. Validated markers from existing 1536 Illumina SNPs and 44 K Affymetrix SNP chips developed at Cornell University were used to select subsets of informative SNPs for different germplasm groups with even distribution across the genome. A 96-plex OPA was developed for quality control purposes and for assigning a sample into one of the five O. sativa population subgroups. Six 384-plex OPAs were designed for genetic diversity analysis, DNA fingerprinting, and to have evenlyspaced polymorphic markers for quantitative trait locus (QTL) mapping and background selection for crosses between different germplasm pools in rice: Indica/Indica, Indica/Japonica, Japonica/Japonica, Indica/O. rufipogon, and Japonica/O. rufipogon. After testing on a diverse set of rice varieties, two of the SNP sets were re-designed by replacing poor-performing SNPs. Pilot studies were successfully performed for diversity analysis, QTL mapping, marker-assisted backcrossing, and developing specialized genetic stocks, demonstrating that 384-plex SNP genotyping on the BeadXpress platform is a robust and efficient method for marker genotyping in rice

The 2022 applied physics by pioneering women: a roadmap

International audienceAbstract Women have made significant contributions to applied physics research and development, and their participation is vital to continued progress. Recognizing these contributions is important for encouraging increased involvement and creating an equitable environment in which women can thrive. This Roadmap on Women in Applied Physics, written by women scientists and engineers, is intended to celebrate women’s accomplishments, highlight established and early career researchers enlarging the boundaries in their respective fields, and promote increased visibility for the impact women have on applied physics research. Perspectives cover the topics of plasma materials processing and propulsion, super-resolution microscopy, bioelectronics, spintronics, superconducting quantum interference device technology, quantum materials, 2D materials, catalysis and surface science, fuel cells, batteries, photovoltaics, neuromorphic computing and devices, nanophotonics and nanophononics, and nanomagnetism. Our intent is to inspire more women to enter these fields and encourage an atmosphere of inclusion within the scientific community

The 2022 applied physics by pioneering women: a roadmap

Women have made significant contributions to applied physics research and development, and their participation is vital to continued progress. Recognizing these contributions is important for encouraging increased involvement and creating an equitable environment in which women can thrive. This Roadmap on Women in Applied Physics, written by women scientists and engineers, is intended to celebrate women's accomplishments, highlight established and early career researchers enlarging the boundaries in their respective fields, and promote increased visibility for the impact women have on applied physics research. Perspectives cover the topics of plasma materials processing and propulsion, super-resolution microscopy, bioelectronics, spintronics, superconducting quantum interference device technology, quantum materials, 2D materials, catalysis and surface science, fuel cells, batteries, photovoltaics, neuromorphic computing and devices, nanophotonics and nanophononics, and nanomagnetism. Our intent is to inspire more women to enter these fields and encourage an atmosphere of inclusion within the scientific community

The 2022 applied physics by pioneering women: a roadmap

Women have made significant contributions to applied physics research and development, and their participation is vital to continued progress. Recognizing these contributions is important for encouraging increased involvement and creating an equitable environment in which women can thrive. This Roadmap on Women in Applied Physics, written by women scientists and engineers, is intended to celebrate women’s accomplishments, highlight established and early career researchers enlarging the boundaries in their respective fields, and promote increased visibility for the impact women have on applied physics research. Perspectives cover the topics of plasma materials processing and propulsion, super-resolution microscopy, bioelectronics, spintronics, superconducting quantum interference device technology, quantum materials, 2D materials, catalysis and surface science, fuel cells, batteries, photovoltaics, neuromorphic computing and devices, nanophotonics and nanophononics, and nanomagnetism. Our intent is to inspire more women to enter these fields and encourage an atmosphere of inclusion within the scientific community

Integrative analysis of drug response and clinical outcome in acute myeloid leukemia

Acute myeloid leukemia (AML) is a cancer of myeloid-lineage cells with limited therapeutic options. We previously combined ex vivo drug sensitivity with genomic, transcriptomic, and clinical annotations for a large cohort of AML patients, which facilitated discovery of functional genomic correlates. Here, we present a dataset that has been harmonized with our initial report to yield a cumulative cohort of 805 patients (942 specimens). We show strong cross-cohort concordance and identify features of drug response. Further, deconvoluting transcriptomic data shows that drug sensitivity is governed broadly by AML cell differentiation state, sometimes conditionally affecting other correlates of response. Finally, modeling of clinical outcome reveals a single gene, PEAR1, to be among the strongest predictors of patient survival, especially for young patients. Collectively, this report expands a large functional genomic resource, offers avenues for mechanistic exploration and drug development, and reveals tools for predicting outcome in AML. [Display omitted] •Acute myeloid leukemia patient cohort with clinical, molecular, drug response data•Validation and discovery of diverse biological features of drug response•Broad mapping of tumor cell differentiation state affecting response to drugs•Modeling reveals a strong and targetable determinant of clinical outcome Bottomly et al. present a functional genomic resource composed of molecular, clinical, and drug response data on acute myeloid leukemia patient specimens. Through integration of all of these data, they identify genetic and cell differentiation state features that predict drug response, and they utilize modeling to identify targetable determinants of clinical outcome

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field