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Bayesian Prediction of ATC Codes from Integration of Biochemical data with applications in Drug Discovery against Neglected Diseases

By: Thomas Olson and Rachel Beasley

Computer Science

Faculty Advisor: Dr. Rahul Singh and Dr. Anagha Kulkarni

The low success rates and rising cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. A key component of the drug discovery process is the identification of initial set of compounds or “leads”, which undergo a complex process of biochemical investigations and development to come up with drugs. Unfortunately, a predominant majority of lead compounds fail due to reasons of efficacy, pharmacokinetics, or toxicity. The effectiveness of the drug discovery process can be significantly increased by minimizing this attrition. / The Anatomical Therapeutic Chemical (ATC), is a World Health Organization (WHO) proposed classification that assigns codes to compounds based on their therapeutic, pharmacological and chemical characteristics as well as the in-vivo site of activity. Clearly, the ability to predict the ATC code of an arbitrary compound with high accuracy can go a long way minimizing failure amongst compounds selected as leads. We propose a computational solution to this problem. The proposed method utilizes a Bayesian Classifier - a technique from statistical machine learning and incorporates information about a compound’s structure, chemical interactions, and protein interactions to determine its ATC code. Using 2335 drugs from the CHEMBL database, we have validated our method and found that a prediction based on the chemical interaction between a query compound and reference compounds as well as structural similarity provided prediction accuracies as high as 81.2%. As part of our ongoing research, we are developing techniques that will allow us to incorporate phenotypic effects caused by drug action as another source of information about a compound. Such data can be especially important in finding cures against neglected parasitic diseases, where the action of drugs is measured in terms of holistic effects on parasites.

91 GP2

Extension to TypeScript compiler

By: Yanxing Wang and Jie Dong

Computer Science

Faculty Advisor: Dr. Arno Puder

JavaScript is the programming language that drives web applications. With the rise of the World-Wide Web, JavaScript has become one of the key technologies used by millions of web developers. One feature of JavaScript is that it is dynamically typed, which means that the programmer does not need to provide type information. While this allows for rapid prototyping, it also makes it difficult to check for programming errors at compile time. / / TypeScript is a superset of JavaScript that adds static typing. Invented by Microsoft, it enjoys increasing popularity. In this project we extend the TypeScript type system by primitive types as well as structural types that enhance type safety, while allowing the generation of more efficient code.

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Development of ZomBee Watch iPhone Mobile Client

By: Dainius Grimalauskas

Computer Science

Faculty Advisor: Dr. Dragutin Petkovic

ZomBee Watch is a citizen science project sponsored by the San Francisco State University Department of Biology, the San Francisco State University Center for Computing for Life Sciences and the Natural History Museum of LA County. ZomBee Watch was initiated as a follow-up to the discovery that the Zombie Fly Apocephalus borealis is parasitizing honeybees in California and possibly other areas of North America. Parasitized honeybees show "zombie-like" behavior leaving their hives at night. These bees are attracted to nearby lights where they become disoriented and die. / A website https://www.zombeewatch.org was developed by the SFSU Computer Science department together with the SFSU Biology department to track these bees. It allows the user to observe incidences of bee infestation on the map and to submit samples on-line in predefined three-step process. ZomBee Mobile is an extension to the ZomBee Watch project. The goal of this project was to design and develop an iPhone application and accompanied server side application, which would allow users to create and submit zombee samples even when there is no Internet connection and later when the connection is available to upload them to the ZomBee Watch web server database of samples. A challenge in developing this application was the 3-step sample submission process and to constantly be able to track Internet connection status so the user always knows what is happening with his samples. For the development of our mobile application, we used the most modern Software Engineering methods such as Agile processes, User Centered Design and focus groups. Application was developed using Objective-C (iOS development programming language), XCode (iOS development IDE), Django (Python-based framework) and RESTful API for integration and communication with existing zombeewatch.org website. Both the mobile client and server application prototypes are tested and operational.

93 UB

Comparing Runaway and Non-runaway Adolescents' Risk-Taking Behavior and Time Orientation

By: Erica B. Walker

Psychology

Faculty Advisor: Dr. Zena R. Mello

Time perspective is a multidimensional cognitive and motivational construct that comprises how individuals think and feel about the past, the present, and the future. One dimension is time orientation, defined as the emphasis placed on each time period (Mello, Finan, & Worrell, 2013). Past research has shown that variation in time orientation is related to academic achievement, hope, self-esteem, and risky behaviors, with an emphasis toward all time periods associated with better outcomes (Mello, Finan, & Worrell, 2013). To contribute toward research in this area, this study investigated how runaway and non-runaway adolescents varied in time orientation and risk behavior. Participants included 163 runaway adolescents and 581 non-runaway adolescents. Measures were the Time Orientation Scale (Mello & Worrell, 2007) and a risk-behavior composite. Results indicated that among runaways, time orientation predicted risky behavior (p <.05) with individuals oriented toward the future (M=2.92, SD=.65) or the present (M=2.45, SD=.88) reporting the highest risk behaviors, and past-future orientation the least (M=1.93, SD=.62). In contrast, non-runaways showed the lowest risk behavior for future oriented individuals (M=1.55, SD=.48). These results provide evidence that adolescents who runaway have a different relationship between perceiving time than those who do not runaway.

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How Color Affects Mood

By: Jessica Burgos, Faye Alvin, and Cindy Osaki

Psychology

Faculty Advisor: Dr. Margaret Lynch

The researchers in the study aimed to examine the effects of Schauss’ Baker-Miller Pink theory and the stimuli’s link to overall mood. We hypothesized that when being presented with the Brief Mood Introspection Scale (BMIS) printed on either Baker-Miller Pink, yellow, or white paper, Baker-Miller Pink would cause a positive affect in mood, while yellow would elicit a negative affect, and white cause no affective response.

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THE ASSOCIATION OF INTRAPERSONAL AND INTERPERSONAL EMOTION / / REGULATION PROCESSES WITH DEPRESSION

By: Kera Mallard and Sarah Wagner

Psychology

Faculty Advisor: Dr. Sarah Holley

There is a well-established link between depression and intrapersonal emotion regulation strategies. Emotional suppression is associated with depression, whereas reappraisal is protective (Gross & John, 2003). Recent research has focused on interpersonal regulatory processes such as partner support for managing stress (“dyadic coping”). Studies show that negative dyadic coping (NDC) negatively effects psychological well-being, whereas supportive dyadic coping (SDC) is beneficial (e.g., Bodenmann, 2008). This study evaluated whether interpersonal emotion regulation (NDC, SDC) was associated with depression above and beyond intrapersonal emotion regulation (suppression, reappraisal). / 249 couples completed a survey. Analyses were conducted separately for males and females using multiple regression models. In Step 1, covariates (age, relationship length) were entered. In Step 2, intrapersonal variables (suppression, reappraisal) were entered. In Step 3, interpersonal variables (NDC, SDC) were entered. Intrapersonal variables accounted for significant variance in depression for both males and females. Interpersonal variables accounted for additional variance in depression for males. There were no interaction effects between interpersonal and intrapersonal variables. This indicates that both interpersonal and intrapersonal regulation processes are uniquely associated with depression symptoms and would each be important therapeutic treatment targets

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Does Emotion Regulation Mediate the Link between Neuroticism and Demand-Withdraw?

By: Samuel Stark and Alina Belohlavek

Psychology

Faculty Advisor: Dr. Sarah Holley

A harmful pattern that is common during relationship conflict is termed “demand- / / withdraw.” Here, one partner blames or pressures while the other partner avoids or withdraws / / (Christensen, 1988). Research on factors underlying this deleterious pattern suggests that those / / higher in neuroticism (i.e., the tendency toward negative affectivity and emotional instability) / / engage in more demanding and withdrawing behaviors (Caughlin & Vangelisti, 2000). / / Neuroticism is also negatively associated with the ability to regulate emotions (Gross & John, / / 2003), which in turn is known to play a crucial role in facilitating adaptive relationship / / interactions (Levenson et al., 2013). This study examined whether emotion regulation mediated / / the association between neuroticism and demand-withdraw. Participants included 526 / / undergraduate students (264 men, 286 women). All measures were obtained via self-report. / / Mediation analyses were conducted using bootstrap confidence intervals to evaluate significance; / / analyses controlled for age, relationship length, gender, and sexual orientation. Results showed / / that emotion regulation mediated the association between neuroticism and the self- / / demand/partner-withdraw pattern (95 percent CI: 0.12, 0.29), as well as the partner-demand/self- / / withdraw pattern (95 percent CI: 0.13, 0.30). These results suggest that the link between / / neuroticism and demand-withdraw is accounted for by emotion regulation abilities. Thus, / / improving emotion regulation for people high in neuroticism may help decrease problematic / / demand-withdraw interactions during relationship conflicts.

97 UB

Cognitive flexibility and time perspective in college students

By: Victoria C. Paoloni

Psychology

Faculty Advisor: Dr. Zena R. Mello

This study is an examination of time perspective and cognitive flexibility. Time perspective refers to one's understanding of temporal periods, and cognitive flexibility refers to someone's adaptability in thinking in problem solving. Participants were surveyed online and filled out a demographics questionnaire, the Adolescent Time Inventory, and the Cognitive Flexibility Inventory. This study focuses specifically on the relationship between results from two subscales, Time Orientation and Time Relation from the ATI, and results from the CFI. It is hypothesized that higher cognitive flexibility will correlate with more balanced time orientations and higher levels of relatedness.

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DS1; Thaumarchaeota or not Thaumarchaeota? That is the Question

By: Ruth Keoviphone

Microbiology

Faculty Advisor: Dr. José R. de la Torre

Archaea is the newest domain of life, but much is still unknown about this archaic domain. Despite housing some of the oldest organisms ever to exist on Earth, not much is known about Archaea or the members of its domain. There are four phyla of Archaea that I will be investigating within this research: Crenarchaeota, Euryarchaeota, Korarchaeota, and the newest proposed phylum Thaumarchaeota. I will be analyzing the genome of Thaumarchaeota archaeon strain DS1 and show its relationship between Crenarchaeota, Euryarchaeota, Thaumarchaeota, and Korarchaeota. DS1 is currently placed in the Thaumarchaeota phylum due to the presence of the Thaumarchaeota-specific topoisomerase IB gene despite the lack of a nitrification gene. In order to determine the best classification for DS1, I will identify model organisms for each phylum and will compare key enzymes as well as the 16s rRNA. Then using this data, I will generate a phylogenetic tree in order to determine which phyla it belongs to. I hypothesise that DS1 will have the strongest relationship to the Thaumarchaeota phylum due to the presence of the topoisomerase IB gene.

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Gene and Function Analysis of Fe-S Assembly Protein SufB Within Thaumarchaeota Archaeon DS1

By: Alejandro Guerra

Microbiology

Faculty Advisor: Dr. José R. de la Torre

Yellowstone National Park consists of numerous phylogenetically deeply rooted and poorly understood Achaea, bacteria, and viruses. Diversity in thermal features consists of pH varying from 2 to 10, and temperatures from 40-92 degrees Celsius. Eco physiological studies of ammonia-oxidizing Thaumarchaeota suggest adaption to low ammonia concentrations and an autotrophic or possibly mixotrophic lifestyle. Within these Thaumarchaeota there is a certain organisms that we will be focusing on, Thaumarchaeota archaeon DS1 also known as Dragon Thaumarchaeota. Unable to grow culture of Dragon Thaumarchaeon leaves a lot of room for research and discovery. The gene FeS assembly protein SufB is required for critical biochemical pathways including respiration, Photosynthesis, and nitrogen fixation amongst different organisms. Thus we propose to identify this protein and compare it to other organisms to help us be able to better understand how DS1 gets its energy and possibly figure out how to culture it in the lab. We will do this by running different bioinformatics and genome analysis tools. These results will give us answers on potential lineage of DS1 within the Thaumarchaeota phylum, its origin, and the pathways that it utilizes. Potentially yielding the ability to culture DS1 and further study its importance to its environment, and other organisms.

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Fermentation of Alcohol dehydrogenase in DS1

By: Alireza Khadem Hosseini

Microbiology

Faculty Advisor: Dr. José R. de la Torre

Zn-dependent alcohol dehydrogenase catalyzes the oxidation of alcohol, which is part of oxidoreductase family that using NAD+ as electron acceptor, and regenerate the NAD+. Organisms use the process of fermentation yeast to produce alcoholic beverages. The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH (6). In yeast, and many bacteria alcohol dehydrogenase ferment glucose to CO2 and ethanol, which is hoping to play the same for Thaumarchaeota DS1. Trying to find the way of alcohol dehydrogenase regions fermentation same in Thaumarchaeota DS1 that the sample collected from the dragon spring in Yellowstone. Therefore hypothesize that finding proteins or amino acids from ADH and fermentation of alcohol exists in DS1. To do this, the helpful genomic analysis program is the use of BLAST, T coffee and IMG or JGI website. So could observe genome sequence that can help to find the details about existence of ADH in DS1.

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Phylogenetic Analysis of Carbon Monoxide Dehydrogenase in Thaumarchaeota DS1

By: Andrew Eramela

Microbiology

Faculty Advisor: Dr. José R. de la Torre

Carbon monoxide (CO) is a potentially deadly gas that can have devastating effects upon organisms. However, only a few groups of Archaea’s are capable of CO oxidation as an energy source; Euryarchaeota and Crenarchaeota. Presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within the archaea. Here I will focus on Thaumarchaeota DS1, an archaeon found in Dragon Springs at Yellowstone National Park that contains a carbon monoxide dehydrogenases (CODH) gene. Although DS1 contains CODH, little is known about the pathway processes and whether it may use CO as a source of energy. A phylogenetic analysis will be done to determine the gene transfer of CODH in Thaumarchaeota DS1. Organisms that code for CODH among the two known phylum’s will be compared to DS1 using online databases such as IMG and phylogeny.fr. I will use the IMG database to identify which species among the two phylum have the CODH gene. Then I will create and analyze a phylogenetic relationship using a phylogenetic comparative database. Phylogenetic analysis will show evidence of horizontal gene transfer of CODH in Thaumarchaeota DS1.

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Flagellar Motility and Structure of Thaumarchaeota DS1

By: Andrew Wong

Microbiology

Faculty Advisor: Dr. José R. de la Torre

Thaumarchaeota DS1, an uncultivated thermoacidophile, was sequenced from hot springs in Yellowstone National Park. Archaeal flagella are similar to bacteria flagella, in which both are used for motility. Having a flagellum can allow an organism to obtain food in different locations, which increases its rate of survival. Other archaeal flagella resemble the bacterial type IV pili. The flagella in archaea and bacteria contain regions with conserved N terminal-like domains. In another archaeon, Sulfolobus solfataricus, it also has a class III (type IV pili-like) pilin-like signal peptide, as well as other proteins that are used for the assembly of the flagellum. Proteins that have the class III signal sequence is cleaved by peptidases, an essential step for the assembly of the flagella. The structure of the flagella in DS1 has not been documented very well. I predict that DS1 will have a putative class III signal sequence and a N-terminal-like domain similar to Sulfolobus solfataricus.

 

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Punitive conservation of Thiamine in Thaumarchaeota archaeon DS1

By: Austin Lim

Microbiology

Faculty Advisor: Dr. José R. de la Torre

The three domain all evolved from L.E.C.A, the last evolutionary common ancestor that was around during Earth's early developments. As evolution progressed the three domains diverged, as this occurred essential genes were conserved among the all three domains. One such gene was a gene that encodes for thiamine converting enzymes; which help utilize and create thiamine diphosphate that is require for other metabolic pathways. Due to this I believe that the Thaumarchaeota archaeon DS1 is going to have enzymes that are conserved with other organism in it function to make the thiamine and will provide insight to better understand evolutionary phylogenetics of the gene. To solidify our understanding about phylogenetics and the organism I will be studying and trying to discover the missing genes that can convert thiamine to thiamine diphosphate and also understand how conserved regions compare to other thiamine enzymes. To discover this I am going to look for it by utilizing blast, img, Kegg and other databases for phylogeny to find the missing gene and compare it to other organisms thiamine pathway.

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Assessing the motility of Thaumarchaeota archaeon DS1

By: Benjamin Ta

Microbiology

Faculty Advisor: Dr. José R. de la Torre

Archaea have the ability to be motile and move to more favorable locations in an environment. There are two molecular systems driving the process of chemotaxis and they are the motility apparatus and the chemotaxis signal transduction system. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins involved with the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown. The organism of interest, Thaumarchaeota archaeon DS1, was discovered in the thermal springs of Yellowstone National Park and was genomically sequenced. Proteins involved in archaeal flagella assembly were found in DS1 by looking through the IMG database.I hypothesized that since Thaumarchaeota archaeon DS1 contains proteins involved in archaeal flagella assembly, then Thaumarchaeota archaeon DS1 must have gotten those genes through vertical gene transfer. The purpose of this study is gain insight into understanding archaeal motility and flagella by analyzing gene and protein homology associated with chemotaxis and archaeal flagella in the organism of interest and comparing them with other similar organisms in order to analyze the evolutionary development of flagellar genes in DS1 and to determine whether DS1 acquired flagellar genes through vertical gene transfer or horizontal gene transfer. / /

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Determining Carbon Fixation through the enzyme RuBisCO in DS1

By: Bianca Sapien

Microbiology

Faculty Advisor: Dr. José R. de la Torre

Thaumarchaeota archaeon Dragon Spring 1 or DS1 is a fairly new strain of archaea that was recently discovered and sequenced from the hot springs of Yellowstone National Park. Little is known about this organism other than the conditions it thrives in which leads to the question of the types of nutrients it is able to obtain for energy from its environment. The hot springs are abundant with CO2 which raises the theory that it could indeed obtain energy from carbon fixation. There are different methods of carbon fixation that can be used but the type that may be prevalent in DS1 is through an enzyme known as Ribulose-bisphosphate carboxylase or RuBisCO. This protein can fix inorganic carbon into 3- phosophoglycertate that will be used further to produce energy (Jacob P Beam et al., 2013). In this case the inorganic carbon source would be CO2. If DS1 has type III RuBisCO this would suggest that DS1 could use an alternative novel RuBisCO pathway in the same manner that has been observed in some strains of euryarchaeota that also have type III RuBisCO (Sato et al., 2007). Because RuBisCO is normally found in carbon fixation through the Calvin-Benson-Bassham cycle this novel pathway is considered an alternative to the Calvin Cycle. Comparison of the genes in DS1 to other euryarchaeota with the same type of enzyme will be carried out to determine if RuBisCO has the same function as the other organisms. During this novel pathway AMP is generated from an AMP salvage pathway. AMP is then converted to ribose 1,5 bisphosphate and then to ribulose 1,5 bisphosphate. RuBisCO would then convert ribulose 1,5 bisphosphate to 3-phosphoglycerate and this would be used as a source of energy (Sato, et all 2007). RuBisCO type III was identified is DS1. A comparison of the euryarchaeota Thermococcales kodakarenis that uses the novel RuBisCO pathway will be conducted in IMG. The KEGG pathways containing RuBisCO will be observed and compared as well as the genes surrounding RuBisCO. A phylogenetic tree will also be constructed using Blast by comparing the 16S rRNA of other archea that have RuBisCO type III to determine the function of RuBisCO type III compared to other archea. If DS1 is found to have the same pathway as some of the euryarchaeota then this would further suggest an evolutionary link between thaumarchaeota and other archaea that also have the RuBisCO genes. All of the archaea that have also been found to have RuBisCO type III have been determined to be anaerobic suggesting that DS1 may also in fact be anaerobic as well (Sato et al., 2007).