Biology subjects

Ning Li

Publications and source records attributed to Ning Li.

4 recordsLinked to original sources

bioRxiv2016

Gene mapping of nine agronomic traits and genome assembly by resequencing a foxtail millet RIL population

Foxtail millet (Setaria italica) provides food and fodder in semi-arid regions and infertile land. Resequencing of 184 foxtail millet recombinant inbred lines (RILs) was carried out to aid essential research on foxtail millet improvement. Bin map were constructed based on the RILs recombination data. By anchoring some unseated scaffolds and filling gaps, we update two original millet reference genomes Zhanggu and Yugu to produce second editions. Gene mapping of nine agronomic traits were done based on this RIL population. The genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding. Resequencing of the RILs could also provide an effective way for high quantity genome assembly and gene identification.

Genomics↗

bioRxiv2016

PIPI: PTM-Invariant Peptide Identification Using Coding Method

In computational proteomics, identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost increases exponentially with respect to the number of modifiable amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible modification patterns. Existing tools (e.g., MS-Alignment, ProteinProspector, and MODa) avoid enumerating modification patterns in database search by using an alignment-based approach to localize and characterize modified amino acids. This approach avoids enumerating all possible modification patterns in a database search. However, due to the large search space and PTM localization issue, the sensitivity of these tools is low. This paper proposes a novel method named PIPI to achieve PTM-invariant peptide identification. PIPI first codes peptide sequences into Boolean vectors and converts experimental spectra into real-valued vectors. Then, it finds the top 10 peptide-coded vectors for each spectrum-coded vector. After that, PIPI uses a dynamic programming algorithm to localize and characterize modified amino acids. Simulations and real data experiments have shown that PIPI outperforms existing tools by identifying more peptide-spectrum matches (PSMs) and reporting fewer false positives. It also runs much faster than existing tools when the database is large.

Bioinformatics↗

bioRxiv2015

Accelerated DNA evolution in rats is driven by differential methylation in sperm

Lamarckian inheritance has been largely discredited until the recent discovery of transgenerational epigenetic inheritance. However, transgenerational epigenetic inheritance is still under debate for unable to rule out DNA sequence changes as the underlying cause for heritability. Here, through profiling of the sperm methylomes and genomes of two recently diverged rat subspecies, we analyzed the relationship between epigenetic variation and DNA variation, and their relative contribution to evolution of species. We found that only epigenetic markers located in differentially methylated regions (DMRs) between subspecies, but not within subspecies, can be stably and effectively passed through generations. DMRs in response to both random and stable environmental difference show increased nucleotide diversity, and we demonstrated that it is variance of methylation level but not deamination caused by methylation driving increasing of nucleotide diversity in DMRs, indicating strong relationship between environment-associated changes of chromatin accessibility and increased nucleotide diversity. Further, we detected that accelerated fixation of DNA variants occur only in inter-subspecies DMRs in response to stable environmental difference but not intra-subspecies DMRs in response to random environmental difference or non-DMRs, indicating that this process is possibly driven by environment-associated fixation of divergent methylation status. Our results thus establish a bridge between Lamarckian inheritance and Darwinian selection.

Evolutionary Biology↗

bioRxiv2014

Online Self-Report Data for Duchenne Muscular Dystrophy confirms natural history and can be used to assess for therapeutic benefits

To assess the utility of online patient self-report outcomes in a rare disease, we attempted to observe the effects of corticosteroids in delaying age at fulltime wheelchair use in Duchenne muscular dystrophy (DMD) using data from 1,057 males from DuchenneConnect, an online registry. Data collected were compared to prior natural history data in regard to age at diagnosis, mutation spectrum, and age at loss of ambulation. Because registrants reported differences in steroid and other medication usage, as well as age and ambulation status, we could explore these data for correlations with age at loss of ambulation. Using multivariate analysis, current steroid usage was the most significant and largest independent predictor of improved wheelchair-free survival. Thus, these online self-report data were sufficient to retrospectively observe that current steroid use by patients with DMD is associated with a delay in loss of ambulation. Comparing commonly used steroid drugs, deflazacort prolonged ambulation longer than prednisone (median 14 years and 13 years, respectively). Further, use of Vitamin D and Coenzyme Q10, insurance status, and age at diagnosis after 4 years were also significant, but smaller, independent predictors of longer wheelchair-free survival. Nine other common supplements were also individually tested but had lower study power. This study demonstrates the utility of DuchenneConnect data to observe therapeutic differences, and highlights needs for improvement in quality and quantity of patient-report data, which may allow exploration of drug/therapeutic practice combinations impractical to study in clinical trial settings. Further, with the low barrier to participation, we anticipate substantial growth in the dataset in the coming years.

Physiology↗