Biology subjects

Nicholson, C.

Publications and source records attributed to Nicholson, C..

3 recordsLinked to original sources

bioRxiv2025

Climate-Driven Ecosystem Productivity Changes Restructure Food Systems

Climate change affects food systems through multiple pathways, yet the isolated effects of climate-driven ecosystem productivity changes remain poorly understood. While field studies translate productivity changes to crop yields, at larger scales yield conflates productivity with management and technology, and critically, productivity changes occur across all vegetation types, not just agricultural lands. We isolate ecosystem productivity changes to trace their propagation through food systems across three socioeconomic scenarios (SSP1-2.6, SSP3-7.0, SSP5-8.5) by coupling the CLASSIC land surface model with GCAM integrated assessment model. Productivity changes lead to crops systematically shifting from human consumption to animal feed and bioenergy (up to 15% reallocation), while there is a significant transition of managed agricultural lands to unmanaged lands by up to 6 million km2 as productivity gains enable less intensive land use. These changes drive extreme regional divergence, with food production volume changing from +35% to -28% and substantial portfolio reorganization. Disruptions peak under regional rivalry (SSP3-7.0), revealing how fragmented governance amplifies biophysical feedbacks beyond climate forcing alone. While how much we eat may remain stable, ecosystem productivity fundamentally reshapes what we eat and where to source it.

ecology↗

bioRxiv2020

Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes

Long-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length, and are therefore particularly relevant for microbiome studies. However, due to the higher per-base error rates than typical short-read sequencing, the application of long-read sequencing on microbiomes remains largely unexplored. Here we deeply sequenced two human microbiota mock community samples (HM-276D and HM-277D) from the Human Microbiome Project. We showed that assembly programs consistently achieved high accuracy (~99%) and completeness (~99%) for bacterial strains with adequate coverage. We also found that long-read sequencing provides accurate estimates of species-level abundance (R=0.94 for 20 bacteria with abundance ranging from 0.005% to 64%). Our results demonstrate the feasibility to characterize complete microbial genomes and populations from error-prone Nanopore sequencing data, but also highlight necessary bioinformatics improvements for future metagenomics tool development.

genomics↗

bioRxiv2017

Bcl11b is a Newly Identified Regulator of Vascular Smooth Muscle Phenotype and Arterial Stiffness

B-cell leukemia 11b (Bcl11b) is a zinc-finger transcription factor known as master regulator of T lymphocytes and neuronal development during embryogenesis. Bcl11b-interacting protein COUP-TFII is required for atrial development and vasculogenesis, however a role of Bcl11b in the adult cardiovascular system is unknown. A genome-wide association study (GWAS) recently showed that a gene desert region downstream of BCL11B and known to function as BCL11B enhancer harbors single nucleotide polymorphisms (SNPs) associated with increased arterial stiffness. Based on these human findings, we sought to examine relations between Bcl11b and arterial function using mice with Bcl11b deletion. We report for the first time that Bcl11b is expressed in vascular smooth muscle (VSM) and transcriptionally regulates the expression of VSM contractile proteins smooth muscle myosin and smooth muscle -actin. Lack of Bcl11b in VSM-specific Bcl11b null mice (BSMKO) resulted in increased expression of Ca++-calmodulin-dependent serine/threonine phosphatase calcineurin in BSMKO VSM cells, cultured in serum-free condition, and in BSMKO aortas, which showed an inverse correlation with levels of phosphorylated VASPS239, a regulator of cytoskeletal actin rearrangements. Moreover, decreased pVASPS239 in BSMKO aortas was associated with increased actin polymerization (F/G actin ratio). Functionally, aortic force, stress and wall tension, measured ex vivo in organ baths, were increased in BSMKO aortas and BSMKO mice had increased pulse wave velocity, the in vivo index of arterial stiffness, compared to WT littermates. Despite having no effect on baseline blood pressure or angiotensin II-induced hypertension, Bcl11b deletion in VSM increased the incidence of aortic aneurysms in BSMKO mice. Aneurysmal aortas from angII-treated BSMKO mice had increased number of apoptotic VSM cells. In conclusion, we identified VSM Bcl11b as a novel and crucial regulator of VSM cell phenotype and vascular structural and functional integrity.

physiology↗