A breadboard for synthetic gene networks

Thesis (Ph.D.)--Boston UniversityInterest in the development of increasingly complex synthetic gene networks for the study of natural networks and engineering novel functions has necessitated new approaches to the design and construction of the plasmids upon which they are encoded. Current methods that focus on additive DNA assembly hinder post-construction substitutions. Such modifications are important in facilitating iterative design strategies, which are prevalent due to imperfectly characterized biological components and contexts. We present an approach for the design, construction, and modification of synthetic gene networks termed the Gene Circuit Breadboard. It focuses on the ability to modify constructs to allow for tuning, troubleshooting, or repurposing of networks. We use a specified set of restriction enzymes in conjunction with a library of components that lack those restriction sites to maintain the uniqueness of the sites used for construction. Using this approach, we constructed a genetic toggle switch, added modified ssrA degradation tags to the genes in the toggle, and transformed the toggle into three- and four-node coherent feed-forward loops. The construction and tuning of these networks demonstrated both the need for and performance of our approach, as each circuit required modifications to achieve its intended behavior

Bi-Directional Evidence Linking Sentence Production and Comprehension: A Cross-Modality Structural Priming Study

Natural language involves both speaking and listening. Recent models claim that production and comprehension share aspects of processing and are linked within individuals (Pickering and Garrod, 2004, 2013; MacDonald, 2013; Dell and Chang, 2014). Evidence for this claim has come from studies of cross-modality structural priming, mainly examining processing in the direction of comprehension to production. The current study replicated these comprehension to production findings and developed a novel cross-modal structural priming paradigm from production to comprehension using a temporally sensitive online measure of comprehension, Event-Related Potentials. For Comprehension-to-Production priming, participants first listened to active or passive sentences and then described target pictures using either structure. In Production-to-Comprehension priming, participants first described a picture using either structure and then listened to target passive sentences while EEG was recorded. Comprehension-to-Production priming showed the expected passive sentence priming for syntactic choice, but not response time (RT) or average syllable duration. In Production-to-Comprehension priming, primed, versus unprimed, passive sentences elicited a reduced N400. These effects support the notion that production and comprehension share aspects of processing and are linked within the individual. Moreover, this paradigm can be used for the exploration priming at different linguistic levels as well as the influence of extra-linguistic factors on natural language use

Rapid, modular and reliable construction of complex mammalian gene circuits

We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction of synthetic gene circuits of up to 64 kb in size comprising 11 transcription units and 33 basic parts. We show robust gene expression control of multiple transcription units by small molecule inducers in human cells with transient transfection and stable chromosomal integration of these circuits. This framework enables development of complex gene circuits for engineering mammalian cells with unprecedented speed, reliability and scalability and should have broad applicability in a variety of areas including mammalian cell fermentation, cell fate reprogramming and cell-based assays.Synthetic Biology Engineering Research Center (SA5284-11210)United States. Defense Advanced Research Projects Agency (HR0011-12-C-0067)United States. Defense Advanced Research Projects Agency (DARPA-BAA-11-23)National Science Foundation (U.S.) (CBET-0939511)National Institutes of Health (U.S.). (5-R01-CA155320-02

Electrophysiological dynamics of Chinese phonology during visual word recognition in Chinese-English bilinguals

Silent word reading leads to the activation of orthographic (spelling), meaning, as well as phonological (sound) information. For bilinguals, native language information can also be activated automatically when they read words in their second language. For example, when Chinese-English bilinguals read words in their second language (English), the phonology of the Chinese translations is automatically activated. Chinese phonology, however, consists of consonants and vowels (segmental) and tonal information. To what extent these two aspects of Chinese phonology are activated is yet unclear. Here, we used behavioural measures, event-related potentials and oscillatory EEG to investigate Chinese segmental and tonal activation during word recognition. Evidence of Chinese segmental activation was found when bilinguals read English words (faster responses, reduced N400, gamma-band power reduction) and when they read Chinese words (increased LPC, gamma-band power reduction). In contrast, evidence for Chinese tonal activation was only found when bilinguals read Chinese words (gamma-band power increase). Together, our converging behavioural and electrophysiological evidence indicates that Chinese segmental information is activated during English word reading, whereas both segmental and tonal information are activated during Chinese word reading. Importantly, gamma-band oscillations are modulated differently by tonal and segmental activation, suggesting independent processing of Chinese tones and segments

Intra-sentential code-switching: cognitive and neural approaches

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Effects of language experience, use, and cognitive functioning on bilingual word production and comprehension

Contains fulltext : 184235.pdf (publisher's version ) (Closed access)Aims and objectives/purpose/research questions: Considerable research has investigated how bilinguals produce and comprehend words, focusing mainly on how bilinguals are able to select words from the appropriate language. Less research, however, has investigated whether production and comprehension involve the same underlying mechanisms. The present study explores this issue by examining whether production and comprehension, in the first language (L1) and second language (L2), are similarly influenced by factors relating to language experience, language use, and cognitive functioning. Design/methodology/approach: Spanish-English bilinguals living in an English-speaking environment completed a picture naming task and a lexical decision task in their L1 and L2. In addition, participants completed the Operation Span task testing working memory and the Flanker task testing inhibitory control, and completed a language history questionnaire probing their language experience, relative proficiency, and codeswitching behavior. Data and analysis: Performance on all tasks was submitted to correlation analyses and the impact of individual difference measures on word production and comprehension was assessed via regression analyses. Findings/conclusions: Results showed that (1) production and comprehension were more closely linked in L1 than in L2; (2) production in L1 and L2 was predicted by language proficiency; and (3) comprehension in L1 and L2 was predicted by working memory. Originality: This is the first study to compare lexical processing in production and comprehension in both L1 and L2 and how these processes are influenced by language experience, use, and cognitive factors. Significance/implications: Word production and comprehension appear to be more tightly linked in L1 than L2, but seem to rely on different processing mechanisms.18 p