Biology subjects

Li Xie

Publications and source records attributed to Li Xie.

4 recordsLinked to original sources

bioRxiv2016

The validity of pairwise models in predicting community dynamics

Pairwise models are commonly used to describe many-species communities. In these models, a focal species receives additive fitness effects from pairwise interactions with other species in the community (\"pairwise additivity assumption\"), and all pairwise interactions are represented by a single canonical equation form (\"universality assumption\"). Here, we analyze the validity of pairwise modeling. We build mechanistic reference models for chemical-mediated interactions in microbial communities, and attempt to derive corresponding pairwise models. Even when one species affects another via a single chemical mediator, different forms of pairwise models are appropriate for consumable versus reusable mediators, with the wrong model producing qualitatively wrong predictions. For multi-mediator interactions, a canonical model becomes even less tenable. These results, combined with potential violation of the pairwise additivity assumption in communities of more than two species, suggest that although pairwise modeling can be useful, we should examine its validity before employing it.

Ecology↗

bioRxiv2016

Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia

Over 100 genetic loci harbor schizophrenia associated variants, yet how these common variants confer risk is uncertain. The CommonMind Consortium has sequenced dorsolateral prefrontal cortex RNA from schizophrenia cases (n=258) and control subjects (n=279), creating the largest publicly available resource to date of gene expression and its genetic regulation; [~]5 times larger than the latest release of GTEx. Using this resource, we find that [~]20% of the schizophrenia risk loci have common variants that could explain regulation of brain gene expression. In five loci, these variants modulate expression of a single gene: FURIN, TSNARE1, CNTN4, CLCN3 or SNAP91. Experimentally altered expression of three of them, FURIN, TSNARE1, and CNTN4, perturbs the proliferation and apoptotic index of neural progenitors and leads to neuroanatomical deficits in zebrafish. Furthermore, shRNA mediated knock-down of FURIN1 in neural progenitor cells derived from human induced pluripotent stem cells produces abnormal neural migration. Although 4.2% of genes (N = 693) display significant differential expression between cases and controls, 44% show some evidence for differential expression. All fold changes are [≤] 1.33, and an independent cohort yields similar differential expression for these 693 genes (r = 0.58). These findings are consistent with schizophrenia being highly polygenic, as has been reported in investigations of common and rare genetic variation. Co-expression analyses identify a gene module that shows enrichment for genetic associations and is thus relevant for schizophrenia. Taken together, these results pave the way for mechanistic interpretations of genetic liability for schizophrenia and other brain diseases.

Genomics↗

bioRxiv2016

The Plasmodium falciparum drugome and its polypharmacological implications

Malaria is a disease contracted by over 200 million people each year, mostly in developing countries. The primary causative agent, Plasmodium falciparum (P. falciparum) has shown increased resistance to existing drugs, hence new treatments are needed quickly. To this end we performed a high-throughput systems-level analysis, mapping existing FDA drugs with the potential for repurposing against targets from the P. falciparum structural proteome. The resulting P. falciparum drugome (P.falciparum-drugome) was used to prioritize potential new anti-malaria candidate targets and highlight some novel FDA approved drugs that have apparent anti-malaria effects for possible use as multi-target therapeutics.

Systems Biology↗

bioRxiv2016

Combating Chagas Disease Through Inhibition of Tiam1, a Rho GTPase Guanine Nucleotide Exchange Factor

Chagas disease is a major cardiovascular affliction primarily endemic to Latin American countries, affecting some ten to twelve million people worldwide. The currently available drugs, Benznidazole and Nifurtimox, are ineffective in the chronic stages and induce severe side effects. In an attempt to improve this situation we use an in silico drug repurposing strategy to correlate drug-protein interactions with positive clinical outcomes. The strategy involves a protein functional site similarity search, along with computational docking studies and, given the findings, a phosphatidylinositol (PIP) strip test to determine the activity of Posaconazole, a recently developed antifungal triazole, in conjunction with Tiam1, a Rho GTPase Guanine Nucleotide Exchange Factor. The results from both computational and in vitro studies indicate possible inhibition of phosphoinositides via Posaconazole, preventing Rho GTPase-induced proliferation of T. cruzi, the etiological agent of Chagas Disease.

Bioinformatics↗