Systematic approaches to mine, predict and visualize biological functions

With advances in high-throughput technologies and next-generation sequencing, the amount of genomic and proteomic data is dramatically increasing in the post-genomic era. One of the biggest challenges that has arisen is the connection of sequences to their activities and the understanding of their cellular functions and interactions. In this dissertation, I present three different strategies for mining, predicting and visualizing biological functions. In the first part, I present the COMputational Bridges to Experiments (COMBREX) project, which facilitates the functional annotation of microbial proteins by leveraging the power of scientific community. The goal is to bring computational biologists and biochemists together to expand our knowledge. A database-driven web portal has been built to serve as a hub for the community. Predicted annotations will be deposited into the database and the recommendation system will guide biologists to the predictions whose experimental validation will be more beneficial to our knowledge of microbial proteins. In addition, by taking advantage of the rich content, we develop a web service to help community members enrich their genome annotations. In the second part, I focus on identifying the genes for enzyme activities that lack genetic details in the major biological databases. Protein sequences are unknown for about one-third of the characterized enzyme activities listed in the EC system, the so-called orphan enzymes. Our approach considers the similarities between enzyme activities, enabling us to deal with broad types of orphan enzymes in eukaryotes. I apply our framework to human orphan enzymes and show that we can successfully fill the knowledge gaps in the human metabolic network. In the last part, I construct a platform for visually analyzing the eco-system level metabolic network. Most microbes live in a multiple-species environment. The underlying nutrient exchange can be seen as a dynamic eco-system level metabolic network. The complexity of the network poses new visualization challenges. Using the data predicted by Computation Of Microbial Ecosystems in Time and Space (COMETS), I demonstrate that our platform is a powerful tool for investigating the interactions of the microbial community. We apply it to the exploration of a simulated microbial eco-system in the human gut. The result reflects both known knowledge and novel mutualistic interactions, such as the nutrients exchanges between E. coli, C. difficile and L. acidophilus

Reproductive biology of blue marlin (Makaira nigricans) in the western Pacific Ocean

The reproductive biology of blue marlin (Makaira nigricans) was assessed from 1001 fish (ranging from 121 to 275 cm in eye-to-fork length; EFL) caught by Taiwanese offshore longliners in the western Pacific Ocean from September 2000 to December 2001 and from 843 gonad samples from these fish, The overall sex ratio of the catch was approximately 1:1 dur ing the sampling period, but blue marlin are sexually dimorphic; females are larger than males. Reproductive activity (assessed by histology), a gonadosomatic index, and the distribution of oocyte diameters, indicated that spawning occurred predominantly from May to September. The estimated sizes-at-maturity (EFL50) were 179.76 ±1.01 cm (mean ±standard error) for females and 130 ±1 cm EFL for males. Blue marlin are multiple spawners and oocytes develop asynchronously. The proportion of mature females with ovaries containing postovulatory follicles (0.41) and hydrated oocytes (0.34) indicated that the blue marlin spawned once every 2–3 days on average. Batch fecundity (BF) for 26 females with the most advanced oocytes (≥1000 μm), but without postovulatory follicles, ranged from 2.11 to 13.50 million eggs (6.94 ± 0.54 million eggs). The relationships between batch fecundity (BF, in millions of eggs) and EFL and round weight (RW, kg) were BF = 3.29 × 10 –12 EFL5.31 (r2 = 0.70) and BF = 1.59 × 10–3 RW 1.73 (r2= 0.67), respectively. The parameters estimated in this study are key information for stock assessments of blue marlin in the western Pacific Ocean and will contribute to the conservation and sustainable yield o

Visualization of metabolic interaction networks in microbial communities using VisANT 5.0

The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues.This work was supported by the National Institutes of Health, R01GM103502-05 to CD, ZH and DS. Partial support was also provided by grants from the Office of Science (BER), U.S. Department of Energy (DE-SC0004962), the Joslin Diabetes Center (Pilot & Feasibility grant P30 DK036836), the Army Research Office under MURI award W911NF-12-1-0390, National Institutes of Health (1RC2GM092602-01, R01GM089978 and 5R01DE024468), NSF (1457695), and Defense Advanced Research Projects Agency Biological Technologies Office (BTO), Program: Biological Robustness In Complex Settings (BRICS), Purchase Request No. HR0011515303, Program Code: TRS-0 Issued by DARPA/CMO under Contract No. HR0011-15-C-0091. Funding for open access charge: National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (R01GM103502-05 - National Institutes of Health; 1RC2GM092602-01 - National Institutes of Health; R01GM089978 - National Institutes of Health; 5R01DE024468 - National Institutes of Health; DE-SC0004962 - Office of Science (BER), U.S. Department of Energy; P30 DK036836 - Joslin Diabetes Center; W911NF-12-1-0390 - Army Research Office under MURI; 1457695 - NSF; HR0011515303 - Defense Advanced Research Projects Agency Biological Technologies Office (BTO), Program: Biological Robustness In Complex Settings (BRICS); HR0011-15-C-0091 - DARPA/CMO; National Institutes of Health)Published versio

Whole-genome sequencing analysis of quorumsensing Aeromonas hydrophila strain M023 from freshwater

YesAeromonas hydrophila is a well-known waterborne pathogen that recently was found to infect humans. Here, we report the draft genome of a freshwater isolate from a Malaysian waterfall, A. hydrophila strain M023, which portrays N-acylhomoserine lactone-dependent quorum sensing.University of Malaya via High Impact Research Grants (UM C/625/1/HIR/MOHE/CHAN/01, A-000001-50001, and UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027

Understanding the quorum-sensing bacterium Pantoea stewartii strain M009 with whole-genome sequencing analysis

YesPantoea stewartii is known to be the causative agent of Stewart's wilt, which usually affects sweet corn (Zea mays) with the corn flea beetle as the transmission vector. In this work, we present the whole-genome sequence of Pantoea stewartii strain M009, isolated from a Malaysian tropical rainforest waterfall.University of Malaya via High Impact Research Grants (UM C/625/1/HIR/MOHE/CHAN/01 no. A-000001- 50001 and UM C/625/1/HIR/MOHE/CHAN/14/1 no. H-50001-A000027

Integrating expert-based objectivist and nonexpert-based subjectivist paradigms in landscape assessment

This thesis explores the integration of objective and subjective measures of landscape aesthetics, particularly focusing on crowdsourced geo-information. It addresses the increasing importance of considering public perceptions in national landscape governance, in line with the European Landscape Convention's emphasis on public involvement. Despite this, national landscape assessments often remain expert-centric and top-down, facing challenges in resource constraints and limited public engagement. The thesis leverages Web 2.0 technologies and crowdsourced geographic information, examining correlations between expert-based metrics of landscape quality and public perceptions. The Scenic-Or-Not initiative for Great Britain, GIS-based Wildness spatial layers, and LANDMAP dataset for Wales serve as key datasets for analysis. The research investigates the relationships between objective measures of landscape wildness quality and subjective measures of aesthetics. Multiscale geographically weighted regression (MGWR) reveals significant correlations, with different wildness components exhibiting varying degrees of association. The study suggests the feasibility of incorporating wildness and scenicness measures into formal landscape aesthetic assessments. Comparing expert and public perceptions, the research identifies preferences for water-related landforms and variations in upland and lowland typologies. The study emphasizes the agreement between experts and non-experts on extreme scenic perceptions but notes discrepancies in mid-spectrum landscapes. To overcome limitations in systematic landscape evaluations, an integrative approach is proposed. Utilizing XGBoost models, the research predicts spatial patterns of landscape aesthetics across Great Britain, based on the Scenic-Or-Not initiatives, Wildness spatial layers, and LANDMAP data. The models achieve comparable accuracy to traditional statistical models, offering insights for Landscape Character Assessment practices and policy decisions. While acknowledging data limitations and biases in crowdsourcing, the thesis discusses the necessity of an aggregation strategy to manage computational challenges. Methodological considerations include addressing the modifiable areal unit problem (MAUP) associated with aggregating point-based observations. The thesis comprises three studies published or submitted for publication, each contributing to the understanding of the relationship between objective and subjective measures of landscape aesthetics. The concluding chapter discusses the limitations of data and methods, providing a comprehensive overview of the research

What’s Cooking? – Cognitive Training of Executive Function in the Elderly

Executive function involves the efficient and adaptive engagement of the control processes of updating, shifting, and inhibition (Miyake, 2000) to guide behavior toward a goal. It is associated with decrements in many other cognitive functions due to aging (West, 1996; Raz, 2000) with itself particularly vulnerable to the effect of aging (Treitz et al., 2007). Cognitive training in the form of structural experience with executive coordination demands exhibited effective enhancement in the elderly (Hertzog et al., 2008). The current study was thus aimed at the development and evaluation of a training regime for executive function in the elderly. The breakfast cooking task of Craik and Bialystok (2006) was adapted into a multitasking training task in a session (pre-test vs. post-test) by group (control vs. training). In the training condition, participants constantly switched, updated, and planned in order to control the cooking of several foods and concurrently performed a table setting secondary task. Training gains were exhibited on task related measures. Transfer effect was selectively observed on the letter–number sequencing and digit symbol coding test. The cooking training produced short term increase in the efficiency of executive control processing. These effects were interpreted in terms of the process overlap between the training and the transfer tasks

A Novel Model Considered Mass and Energy Conservation for Both Liquid and Vapor in Adsorption Refrigeration System.

In this paper, we proposed a dynamic model for a two-bed adsorption refrigeration system. Different from most existing researches which assume saturation vaper pressure in each device, the proposed method models the pressure in each device by considering both the liquid and vaper content in the device. Therefore, it can be more accurate in describing the system response and more suitable for studying the system instrumentation. The components included in this system model are: adsorption bed, evaporator, condenser, expansion valve, and etc. Each device is modeled based on the energy and mass conservation. Furthermore, the adsorption phenomenon is modeled by the “Freundlich equation,†and “linear driving force model.†The phase change of the refrigerant in evaporator and condenser is modeled by Hertz-Knudsen theory. In a case study, the pressure of the adsorption bed during the adsorption process is estimated to be 0.7kPa by the proposed model, while it was 1.6kPa by conventional method which assuming saturated vapor pressure. The coefficient-of-performance of the adsorption system is estimated to be 0.246 by this model, 0.36 by conventional method, and 0.28 by experimental data. The proposed model can estimate system performance more accurate than the conventional method. Moreover, the proposed model also inspire a new instrumentation strategy for the adsorption system, in which the system efficiency is improved and the pressure surge is avoided

SWITCHING THE HORIZONTAL GRF TO THE PATH OF PROGRESSION IN THE TABLE TENNIS FOREHAND DRIVE

Knowing the kinetic strategies of the lower limbs is a crucial factor to investigate the forehand drive which comprises the changes of the foot placement. It is difficult to directly evaluate the movement of feet with the data of ground reaction force (GRF) and impulse (GRI).This study tried to analyze table tennis forehand drives via the GRF and GRI data based upon the anatomical perspective. The motion and the GRF data were collected from eight right-handed Taiwanese elite table tennis players. The horizontal GRF data were transformed to a reference frame and then integrated with time to get the GRI. During the forehand drive shot, the participants performed a greater lateral impulse to cause the trunk rotation and decelerated their body from initial to mid-phase and then accelerated the body to perform a forehand drive shot