The microbial ecology of bacterial lignocellulosic degradation in the ocean

The overarching theme of my dissertation is to study the role of bacteria in lignocellulose degradation. In recent years, more research has investigated the biodegradability of lignocellulose for biofuel production. The components of the lignocellulosic plant cell wall are considered intrinsically recalcitrant due to their structure. However, we hypothesize that these components are not intrinsically recalcitrant but their biodegradation is contingent on the environmental conditions, particularly the bacterial diversity. We believe bacteria will become especially important in lignocellulose degradation in conditions that are unfavorable for white-rot fungi. Therefore, we investigated the potential for lignin degradation by bacteria in the ocean where fungi would likely be rare. This knowledge would gather insight into allochthonous terrestrial organic carbon cycling in the ocean, a basic science knowledge gap in the complex ocean carbon cycle. Also, our investigation into the microbial ecology of marine lignocellulolytic bacteria may find new hosts of stress-tolerant commercial enzymes for biofuels and lignin valorization

Immune DNA signature of T-cell infiltration in breast tumor exomes.

Tumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deep TCRB sequencing. In 1,078 TCGA breast cancer exomes, the fraction of CDR3 reads was associated with TILs fraction, tumor purity, adaptive immunity gene expression signatures and improved survival in Her2+ patients. Only 2/839 TCRB clonotypes were shared between patients and none associated with a specific HLA allele or somatic driver mutations. The iDNA biomarker enriches the comprehensive dataset collected through TCGA, revealing associations with other molecular features and clinical outcomes

Sleepless in Seoul: `The Ant and the Metrohopper'

One of Aesop's (La Fontain's) famous fables `The Ant and the Grasshopper' is widely known to give a moral lesson through comparison between the hard working ant and the party-loving grasshopper. Here we show a slightly different version of this fable, namely, "The Ant and the Metrohopper," which describes human mobility patterns in modern urban life. Numerous real transportation networks and the trajectory data have been studied in order to understand mobility patterns. We study trajectories of commuters on the public transportation of Metropolitan Seoul, Korea. Smart cards (Integrated Circuit Cards; ICCs) are used in the public transportation system, which allow collection of transit transaction data, including departure and arrival stations and time. This empirical analysis provides human mobility patterns, which impact traffic forecasting and transportation optimization, as well as urban planning.Comment: to be appeared in Journal of the Korean Physical Societ

Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil

Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30

Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus

The aqueous extract of yerba mate, a South American tea beverage made from Ilex paraguariensis leaves, has demonstrated bactericidal and inhibitory activity against bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). The gas chromatography-mass spectrometry (GC-MS) analysis of two unique fractions of yerba mate aqueous extract revealed 8 identifiable small molecules in those fractions with antimicrobial activity. For a more comprehensive analysis, a data analysis pipeline was assembled to prioritize compounds for antimicrobial testing against both MRSA and methicillin-sensitive S.aureus using forty-two unique fractions of the tea extract that were generated in duplicate, assayed for activity, and analyzed with GC-MS. As validation of our automated analysis, we checked our predicted active compounds for activity in literature references and used authentic standards to test for antimicrobial activity. 3,4-dihydroxybenzaldehyde showed the most antibacterial activity against MRSA at low concentrations in our bioassays. In addition, quinic acid and quercetin were identified using random forests analysis and 5-hydroxy pipecolic acid was identified using linear discriminant analysis. We also generated a ranked list of unidentified compounds that may contribute to the antimicrobial activity of yerba mate against MRSA. Here we utilized GC-MS data to implement an automated analysis that resulted in a ranked list of compounds that likely contribute to the antimicrobial activity of aqueous yerba mate extract against MRSA

Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils

Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal–Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts

MYC and BCL2 overexpression is associated with a higher class of Memorial Sloan-Kettering Cancer Center prognostic model and poor clinical outcome in primary diffuse large B-cell lymphoma of the central nervous system

Table S1. Correlation of BCL6 expression and clinicopathological variables; Table S2. MYC translocation and copy number change in MYC positive cases. (DOCX 24 kb

Changes in the incidence of cardiopulmonary resuscitation before and after implementation of the Life-Sustaining Treatment Decisions Act

Background The Life-Sustaining Treatment (LST) Decisions Act allows withholding and withdrawal of LST, including cardiopulmonary resuscitation (CPR). In the present study, the incidence of CPR before and after implementation of the Act was compared. Methods This was a retrospective review involving hospitalized patients who underwent CPR at a single center between February 2016 and January 2020 (pre-implementation period, February 2016 to January 2018; post-implementation period, February 2018 to January 2020). The primary outcome was monthly incidence of CPR per 1,000 admissions. The secondary outcomes were duration of CPR, return of spontaneous circulation (ROSC) rate, 24-hour survival rate, and survival-to-discharge rate. The study outcomes were compared before and after implementation of the Act. Results A total of 867 patients who underwent CPR was included in the analysis. The incidence of CPR per 1,000 admissions showed no significant difference before and after implementation of the Act (3.02±0.68 vs. 2.81±0.75, P=0.255). The ROSC rate (67.20±0.11 vs. 70.99±0.12, P=0.008) and survival to discharge rate (20.24±0.09 vs. 22.40±0.12, P=0.029) were higher after implementation of the Act than before implementation. Conclusions The incidence of CPR did not significantly change for 2 years after implementation of the Act. Further studies are needed to assess the changes in trends in the decisions of CPR and other LSTs in real-world practice

Stormwater Harvesting and Reuse in Montgomery County Parks

Final project for ENSP400 (Fall 2017). University of Maryland, College Park.Stormwater management is a vital practice that allows urban areas to mitigate negative water quality impacts associated with urban development. The Montgomery County Department of Parks seeks to increase their reuse of stormwater as part of its commitment to furthering sustainability practices within the parks system and to minimize their impact on the environment. The project seeks to assist the Department of Parks by researching possible stormwater harvesting and filtration systems to implement in Cabin John Regional Park. This paper examines stormwater reuse for irrigation on Shirley Povich Field, a baseball field located northwest of the ice rink. The four objectives for this research project were as follows: (1) assess current stormwater flow and collection potential off of hardscape around Cabin John Regional Park, (2) analyze similar projects elsewhere to build the groundwork for developing a plan to harvest stormwater, (3) develop a generalized set of procedures that provide options for stormwater harvesting at different locations within Montgomery County Parks using the data gathered in in Objective 1, and (4) develop the most efficient and cost effective system to harvest and filter stormwater. This paper will provide suggestions on possible placement of a system, ways to store the collected stormwater, and other recommendations for components of a stormwater reuse system. The processes used to generate these plans for Cabin John are summarized in Appendix A so that they can be applied to other Montgomery County Parks locations. This project comprises a number of fields related to environmental science and policy, scientific analysis of water quality, biological and ecological studies, topography analysis of the terrain of the park, the mechanics of stormwater management structures, economic analysis, and research of applicable policies and permitting processes associated with implementing such projects. Based on the research findings, a rainwater collection and reuse system for irrigating Shirley Povich Field would not be a financially reasonable decision for Cabin John Regional Park due to the high upfront implementation costs, which include retrofitting required and a low return on investment. However, this type of system may be more cost effective at new parks where retrofitting would not be required. A more cost-effective way Cabin John Regional Park could reduce its water demand would be investing in a smart irrigation system with a soil moisture sensor that would reduce water use without the prohibitive retrofitting costs.Montgomery Count

Infant feeding and the energy transition: A comparison between decarbonising breastmilk substitutes with renewable gas and achieving the global nutrition target for breastfeeding

Highlights: • Breastfeeding and breastfeeding support can contribute to mitigating climate change. • Achieving global nutrition targets will save more emissions than fuel-switching. • Breastfeeding support programmes support a just transition. • This work can support the expansion of mitigation options in energy system models. Abstract: Renewable gas has been proposed as a solution to decarbonise industrial processes, specifically heat demand. As part of this effort, the breast-milk substitutes industry is proposing to use renewable gas as a substitute for fossil natural gas. However, decarbonising the industrial processing of breast-milk substitutes can increase social license for these products, potentially undermining breastfeeding. World Health Organisation nutrition targets aim to increase exclusive breastfeeding to at least 50% globally by 2025 to improve maternal, infant, and young child health and nutrition. This target will have implications for the energy transition. A weakness of existing energy models is that demands for end-use products such as breast-milk substitutes are typically not considered explicitly. This paper develops an analytical framework for explicitly representing infant feeding methods in energy systems models. We compare the emissions saved in Ireland from decarbonising the industrial processing of breast-milk substitutes with renewable gas with the emissions saved by an increase in exclusive breastfeeding to 50% in both Ireland and a key export market, China. We demonstrate that the emissions saved from achieving the minimum global breastfeeding target are greater than when renewable gas is used to displace natural gas in the production of breast-milk substitutes in Ireland. We discuss the decarbonisation of breast-milk substitutes in relation to the principle of justice as non-maleficence, a principle based on the commitment to avoid harm, a novel application of a principle of justice. We conclude that breastfeeding support can be considered a demand-side measure for mitigating climate change by reducing the demand for energy services to produce breast-milk substitutes. A key recommendation is to position breastfeeding support as both a public health and a climate justice issue that is relevant for a just transition. The framework developed for this paper could be applied to support the inclusion of a wider range of mitigation options with social justice outcomes in energy system models. [Open access