Wh-indefinites in Chinese have received great attention and discussion in the literature. This thesis investigates the status of Chinese wh-indefinites and their behaviors in the so-called donkey sentence. A typical example of wh-indefinite will be like the following: (4) Ta bu xiang zai shuo shenme le he not want again say what LE ¡¥He does not want to say anything again.¡¦ ¥L¤£·Q¦A»¡¤°»ò¤F¡C In this thesis, accounts of wh-indefinites as variables, polarity items and quantifiers from Huang (1982), Li (1992), Cheng (1991, 1994) and Lin (1996, 1998) are provided and this thesis discusses the problems each account presents. Countering Li¡¦s (1992) work, this work argue that wh-indefinite like zenmeyang ¡¦how¡¦ and weishenme ¡¥why¡¦ cannot be directly treated as variables since they feature variables only if they appear after an auxiliary (under which situation they will express purpose or method) in a donkey sentence according to Tsai (1999, 2000), see the following examples: (5) a. Akiu hui wei (le) shenme cizhi wo jiu hui wei (le) shenme cizhi¡@ Akiu will for LE what resign I then will for LE what resign ¡¥If Akiu will resign for the purpose x, I will then also resign for the purpose x.¡¦ ªüQ·|¬°¡]¤F¡^¤°»òÃ㾡A§Ú´N·|¬°¡]¤F¡^¤°»òÃ㾡C b. *Akiu wei (le) shenme hui cizhi wo jiu wei (le) shenme hui cizhi Akiu for LE what will resign I then will LE what will resign Intended ¡¥If Akiu will resign because of the reason x, I will then also resign because of the reason x. *ªüQ¬°¤F¤°»ò·|Ã㾡A§Ú´N¬°¤F¤°»ò·|Ã㾡C (Tsai¡¦s 2000, 15 glossed and translated by the author) Avoiding treating wh-indefinites as variables, we may treat them as quantifiers according to Huang¡¦s observation. But Huang¡¦s (1982) quantifier account of wh-indefinites is also rejected because I observe that wh-indefinites do not exhibit island sensitivity. Then we are led to another treatment: treating wh-indefinites as polarity items because they are sensitive to polarity environment. Aside from the sensitivity to polarity environment, Lin¡¦s (1996) work argues that wh-indefinites are licensed as polarity items if the sentence is subject to NEEC- non-entailment of existence condition. NEEC tells us that if (part of) a sentence does not have the existential import of object; wh-words can be licensed as wh-indefinites. This faces challenge because there are cases presupposing existential import yet the wh-indefinite is licensed. In chapter 3, two types of donkey sentences are identified in Cheng and Huang¡¦s (1996) work and are accounted with different approaches-Unselective Binding and E-type analysis. Though accepting their viewpoint generally, Lin (1996) makes a distinction between one-case and multi-case reading and opens the possibility of universal interpretation in ruguo-conditionals. Later I introduce Indirect binding approach to account both types of donkey sentences. Indirect Binding argues that some quantified expression plays the role as associating the indefinite with the anaphoric element in donkey sentences: (6) [Everyone who ti keeps a dogj]i like itj. The example here captures the very basic idea of Indirect Binding: the chunk of expression, which has the indefinite a dog in its scope, c-commands the pronoun it and hence relates it to the indefinite. I extend it to the analysis of Chinese donkey sentences and discover that although Indirect Binding does not target at a particular status, the condition that the indirect binder must c-command the indefinite seems to suggest that c-commanding is the way of licensing a wh-indefinite, which echoes Li¡¦s and Cheng¡¦s analyses. In Chapter 4, I introduce wh-indefinites in Japanese and Korean respectively and conclude that quantificational force comes from the environment but not from wh-indefinites themselves, countering Huang (1982). Finally, I suggest that licensing a wh-word as a wh-indefinite is through being c-commanded by the relevant operators. It is so because of Li¡¦s and Cheng¡¦s observation of wh-indefinites licensing and also of a condition in Indirect Binding that indirect binders must c-command the indefinite in order to have it as in its scope, as I have mentioned. This thesis then provides a viewpoint that perhaps, wh-indefinites can be treated uniformly as polarity items considering that Indirect Binding approach explains their behavior in donkey sentences. This thesis also opens the door for analyzing wh-indefinites in donkey sentences under Indirect Binding in other languages. Keywords¡G Wh-indefinite, polarity item, variable, quantifier, donkey phenomenon, Indirect Binding

<p>The initiation of two major processes in the eukaryotic cell, gene transcription and DNA replication, is regulated largely through interactions between proteins or protein complexes and DNA. Although a lot is known about the interacting proteins and their role in regulating transcription and replication, the specific DNA binding motifs of many regulatory proteins and complexes are still to be determined. For this purpose, many computational tools for DNA motif discovery have been developed in the last two decades. These tools employ a variety of strategies, from exhaustive search to sampling techniques, with the hope of finding over-represented motifs in sets of co-regulated or co-bound sequences. Despite the variety of computational tools aimed at solving the problem of motif discovery, their ability to correctly detect known DNA motifs is still limited. The motifs are usually short and many times degenerate, which makes them difficult to distinguish from genomic background. We believe the most efficient strategy for improving the performance of motif discovery is not to use increasingly complex computational and statistical methods and models, but to incorporate more of the biology into the computational techniques, in a principled manner. To this end, we propose a novel motif discovery algorithm: PRIORITY. Based on a general Gibbs sampling framework, PRIORITY has a major advantage over other motif discovery tools: it can incorporate different types of biological information (e.g., nucleosome positioning information) to guide the search for DNA binding sites toward regions where these sites are more likely to occur (e.g., nucleosome-free regions). </p><p>We use transcription factor (TF) binding data from yeast chromatin immunoprecipitation (ChIP-chip) experiments to test the performance of our motif discovery algorithm when incorporating three types of biological information: information about nucleosome positioning, information about DNA double-helical stability, and evolutionary conservation information. In each case, incorporating additional biological information has proven very useful in increasing the accuracy of motif finding, with the number of correctly identified motifs increasing with up to 52%. PRIORITY is not restricted to TF binding data. In this work, we also analyze origin recognition complex (ORC) binding data and show that PRIORITY can utilize DNA structural information to predict the binding specificity of the yeast ORC. </p><p>Despite the improvement obtained using additional biological information, the success of motif discovery algorithms in identifying known motifs is still limited, especially when applied to sequences bound in vivo (such as those of ChIP-chip) because the observed protein-DNA interactions are not necessarily direct. Some TFs associate with DNA only indirectly via protein partners, while others exhibit both direct and indirect binding. We propose a novel method to distinguish between direct and indirect TF-DNA interactions, integrating in vivo TF binding data, in vivo nucleosome occupancy data, and in vitro motifs from protein binding microarrays. When applied to yeast ChIP-chip data, our method reveals that only 48% of the ChIP-chip data sets can be readily explained by direct binding of the profiled TF, while 16% can be explained by indirect DNA binding. In the remaining 36%, we found that none of the motifs used in our analysis was able to explain the ChIP-chip data, either because the data was too noisy or because the set of motifs was incomplete. As more in vitro motifs become available, our method can be used to build a complete catalog of direct and indirect TF-DNA interactions.</p> / Dissertation