Model Construction and Transformation: A Study Exploring Students' Causal Explanations of Everday Phenomena

Master'sMASTER OF SCIENC

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Metagenomic sequence classification is a procedure to assign sequences to their source genomes. It is one of the important steps for metagenomic sequence data analysis. Although many methods exist, classification of high-throughput metagenomic sequence data in a limited time is still a challenge. We present here an ultra-fast metagenomic sequence classification system (MetaBinG) using graphic processing units (GPUs). The accuracy of MetaBinG is comparable to the best existing systems and it can classify a million of 454 reads within five minutes, which is more than 2 orders of magnitude faster than existing systems. MetaBinG is publicly available at http://cbb.sjtu.edu.cn/~ccwei/pub/software/MetaBinG/MetaBinG.php

Towards biological characters of interactions between transcription factors and their DNA targets in mammals

Abstract Background In post-genomic era, the study of transcriptional regulation is pivotal to decode genetic information. Transcription factors (TFs) are central proteins for transcriptional regulation, and interactions between TFs and their DNA targets (TFBSs) are important for downstream genes’ expression. However, the lack of knowledge about interactions between TFs and TFBSs is still baffling people to investigate the mechanism of transcription. Results To expand the knowledge about interactions between TFs and TFBSs, three biological features (sequence feature, structure feature, and evolution feature) were utilized to build TFBS identification models for studying binding preference between TFs and their DNA targets in mammals. Results show that each feature does have fairly well performance to capture TFBSs, and the hybrid model combined all three features is more robust for TFBS identification. Subsequently, correspondence between TFs and their TFBSs was investigated to explore interactions among them in mammals. Results indicate that TFs and TFBSs are reciprocal in sequence, structure, and evolution level. Conclusions Our work demonstrates that, to some extent, TFs and TFBSs have developed a coevolutionary relationship in order to keep their physical binding and maintain their regulatory functions. In summary, our work will help understand transcriptional regulation and interpret binding mechanism between proteins and DNAs.</p

The Production of Oxalate by <i>Aspergillus niger</i> under Different Lead Concentrations

In this study, using a typical acid-producing fungi, Aspergillus niger (A. niger, CGMCC 23272), we investigated the capacity of organic acid production under different lead (Pb) concentrations. A. niger has a high Pb tolerance, which can maintain the growth of hypha at 1500 mg/L Pb concentration. Oxalic acid is the primary organic acid produced by A. niger. A. niger was shown to maintain the ability to produce oxalic acid under different Pb concentrations, which ranged from 522.8 to 1130.5 mg/L. The formed lead oxalate also confirmed the production of oxalic acid by A. niger. Meanwhile, the formation of lead oxalate minerals dominated the resistance of Pb toxicity by A. niger. More than 95% of Pb cations were removed by A. niger under different Pb concentrations. The high Pb toxicity (1500 mg/L) could stimulate pyruvate dehydrogenase enzyme activities, which increased from 0.05 to 0.13 nmol/min/g after three days of incubation. The low Pb toxicity (500 and 1000 mg/L) could improve the production of oxalic acid by A. niger. This indicates that the metabolism of organic acid by A. niger can be improved by a high Pb concentration via the tricarboxylic acid cycle

Plant growth patterns in a tripartite strip relay intercrop are shaped by asymmetric aboveground competition

Intercropping is a promising model for ecological intensification of modern agriculture. Little information is available on how species growth patterns are affected by size-asymmetric above- and belowground competitive interactions, especially in intercrops with more than two species. We studied plant growth and competitive interactions in a novel intercropping system with three species: wheat, watermelon and maize. Wheat and maize are grown sequentially (as a double cropping system) in narrow strips while watermelon is grown between the cereal strips, with partial overlap in growing period with the two cereals. Growth patterns were monitored over two years and described with logistic growth curves. Root barriers were used to study the effect of belowground interactions. Wheat produced 31% greater yield per plant in the intercrop than in the sole crop but 24% lower yield per unit total (inter)crop area. Wheat yield increase per plant was associated with faster growth and substantial overyielding in the outer rows of wheat strips. Watermelon did not competitively affect wheat. Watermelon biomass was substantially reduced at the time of wheat harvest. However, compensatory growth after wheat harvest and greater allocation to fruits resulted in a good yield of intercropped watermelon, 92% of monoculture yields, at final harvest. Intercropped maize produced 32% lower grain yield per plant and per unit area than sole maize, as a consequence of later sowing and a changed plant configuration in the intercrop as compared to the sole crop, and competitive effects of watermelon, as shown by comparison with a skip-row maize system without watermelon. Root barriers did not affect yield of any of the species, indicating that aboveground competitive interactions in this case played a more important role in shaping the observed growth responses than belowground interactions. Plant interactions in this tripartite intercrop system are consistent with the hypothesis of size-asymmetric competition for light