Mapping and measuring proteomes

Comunicaciones a congreso

Getting to the bottom of it : geoarchaeological and paleobotanical investigations for early transitions in the Maya Lowlands

The cultural transition from the Archaic (8000 to 2000 BC) to the Preclassic Period (2000 BC – AD 250) in the Neotropics is critical for understanding the early development of Maya civilization in the Lowlands. This dissertation presents a model for some of the earliest inhabitants in northern Belize and explores the magnitude and timing of impacts concerning initial human-environmental interactions during the early stages of the Holocene. Specifically, geoarchaeological and paleobotanical evidence concerning the transition of subsistence strategies from semi-nomadic hunting and gathering into more intensive agricultural subsistence strategies in the Maya Lowlands. A multi-proxy approach addresses questions related to early anthropogenic change tied to the success of early sedentary villages in northern Belize. Insight concerning the long occupation of Colha and manipulation of the Blue Creek rejollada provide an opportunity to understand cultural transitions and trajectories of early Archaic people. This dissertation provides new radiocarbon dates, archaeological excavations, and environmental histories for Colha and the Blue Creek rejollada. The paleobotanical component of this research includes a dental calculus study expanding on food consumption, food processing, and evidence for the use of economic fibrous materials. An ethnobotanical component of this research contributes to understanding early Maya economic systems by providing overlap in horticultural and agricultural practices in the region despite cultural and temporal distances between ancient and modern people. Together, multiple lines of evidence expand and refine understanding of early human-environmental dynamics, which become integral to the success of subsequent Maya populationsAnthropolog

FDA Experience with Medical Countermeasures under the Animal Rule

The Food and Drug Administration issued a final rule in May 2002 to permit the Agency to approve drugs or license biological products on the basis of animal efficacy studies for use in ameliorating or preventing serious or life-threatening conditions caused by exposure to lethal or permanently disabling toxic biological, chemical, radiological, or nuclear substances. Only two drugs were approved in the first nine years of the “Animal Rule” despite massive investment by the federal government since 2001 to stimulate development of medical countermeasures to biological threats. This article therefore examines the Food and Drug Administration reviews made public after approval of those two drugs and the public discussion at the Agency's Anti-Infective Drugs Advisory Committee of one biological product under development under the Animal Rule. Despite the paucity of approved drugs or licensed biological products as medical countermeasures, several investigational drugs have been placed in the National Strategic Stockpile for use as medical countermeasures, if needed

Geoarchaeological and archaeobotanical approaches to human-environmental interactions during the Archaic to Preclassic Periods in Northwestern Belize

textThis report reviews human-environmental interactions in Northwestern Belize during the transition from Archaic (8000 to 4000 B.P.) to Preclassic periods (4000 B.P. to 2000 B.P.). Specifically, the transition of subsistence strategies from nomadic hunter-gatherer to more sedentary food production, which we still do not fully understand in the tropical lowlands of the Maya region. It is during this pivotal era that early to mid-Holocene humans domesticated a wide variety of plants and animals, establishing a new human niche strategy that dramatically changed environments around the world. This report considers how human niche construction, a theoretical framework that expressly attributes populations with deliberate ecosystem engineering strategies, plays an integral role in the Anthropocene. I present my plans for analyzing sediments and microbotanical remains to contribute to knowledge about paleoenvironment and human-landscape interactions to provide direct evidence for transformative behavior by humans.Anthropolog

Evaluating family satisfaction on an advanced certification palliative care unit.

Inpatient palliative care programs with The Joint Commission (TJC) Advanced Certification for Palliative Care are accountable for evaluating multiple health outcomes, including family satisfaction. A midwestern urban hospital’s palliative care unit received certification in January 2019. To comply with TJC standards, a clear data management and evaluation plan for family satisfaction data was needed. Investigation of the previous family satisfaction measure processes revealed areas in need of improvement in the satisfaction survey distribution, data collection, and evaluation processes. Satisfaction surveys were often unable to be distributed to families of deceased patients because the documented mailing address was a nursing facility. Survey data that were collected were entered in multiple spreadsheets, making data management and evaluation cumbersome. This project’s purpose was to implement an improved satisfaction survey distribution process and an evaluation plan for family satisfaction data for a Palliative Care Inpatient Unit with TJC Advanced Certification. The new distribution process identified and documented family addresses so the staff can mail surveys to the intended participant rather than the deceased patient’s nursing facility. A new data management plan utilizes pivot tables for data collection and evaluation. Over a three-month period, the survey distribution rate increased from 80.5% in 2019 to 88% in 2020. Survey data for 2019 were entered into the pivot tables. The process change strengthened the unit’s distribution and data management processes to improve family satisfaction data collection, evaluation ability, ease of dissemination, and use of data to improve palliative care. Future evaluation should assess the impact of the process change on survey response rates

Electroblotting onto activated glass. High efficiency preparation of proteins from analytical sodium dodecyl sulfate-polyacrylamide gels for direct sequence analysis

We have developed a new method for the isolation of proteins for microsequencing. It consists of electrophoretic transfer (electroblotting) of proteins or their cleavage fragments onto activated glass filter paper sheets immediately after separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The proteins are immobilized on the glass fiber sheets by ionic interactions or by covalent attachment. A wide range of proteins can be prepared in this fashion with no apparent restriction due to solubility, size, charge, or other intrinsic properties of the proteins. As little as 50 ng of the transferred proteins can be detected using Coomassie Blue or fluorescent dye staining procedures and even smaller amounts of radiolabeled proteins by autoradiography. After detection, the protein- containing bands or spots are cut out and inserted directly into a gas- phase sequenator. The piece of glass fiber sheet acts as a support for the protein during the sequencing. Amounts of protein in the 5- to 150- pmol range can be sequenced, and extended runs can be obtained from the blotted samples because of improved stepwise yields and lower backgrounds. The method has been successfully applied to the sequencing of a variety of proteins and peptides isolated from one-dimensional and two-dimensional polyacrylamide gels

Molecular architecture of human polycomb repressive complex 2.

Polycomb Repressive Complex 2 (PRC2) is essential for gene silencing, establishing transcriptional repression of specific genes by tri-methylating Lysine 27 of histone H3, a process mediated by cofactors such as AEBP2. In spite of its biological importance, little is known about PRC2 architecture and subunit organization. Here, we present the first three-dimensional electron microscopy structure of the human PRC2 complex bound to its cofactor AEBP2. Using a novel internal protein tagging-method, in combination with isotopic chemical cross-linking and mass spectrometry, we have localized all the PRC2 subunits and their functional domains and generated a detailed map of interactions. The position and stabilization effect of AEBP2 suggests an allosteric role of this cofactor in regulating gene silencing. Regions in PRC2 that interact with modified histone tails are localized near the methyltransferase site, suggesting a molecular mechanism for the chromatin-based regulation of PRC2 activity.DOI:http://dx.doi.org/10.7554/eLife.00005.001

Fostering Equity & Diversity in Faculty Recruitment

Participating in a search for a new faculty member, whether as a search committee member, search committee chairperson, department chairperson, or dean, poses unique challenges for those in academics. Though we may be an expert in conducting rigorous research, a prolific writer, or a gifted “sage on the stage” in the classroom, few of us are also experts in academic recruiting. All too frequently we bumble through the search process, hoping fervently that the person we ultimately hire – the person who will likely be our colleague for decades – is someone who will turn out to be a serious scholar, productive researcher, collegial colleague, and an engaging educator

Mol. Cell. Proteomics

Chemical cross-linking in combination with mass spectrometric analysis offers the potential to obtain low-resolution structural information from proteins and protein complexes. Identification of peptides connected by a cross-link provides direct evidence for the physical interaction of amino acid side chains, information that can be used for computational modeling purposes. Despite impressive advances that were made in recent years, the number of experimentally observed cross-links still falls below the number of possible contacts of cross-linkable side chains within the span of the cross-linker. Here, we propose two complementary experimental strategies to expand cross-linking data sets. First, enrichment of cross-linked peptides by size exclusion chromatography selects cross-linked peptides based on their higher molecular mass, thereby depleting the majority of unmodified peptides present in proteolytic digests of cross-linked samples. Second, we demonstrate that the use of proteases in addition to trypsin, such as Asp-N, can additionally boost the number of observable cross-linking sites. The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe