Context-dependent neocentromere activity in synthetic yeast chromosome VIII

Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synthetic eukaryotic organism by assembling the genome of Saccharomyces cerevisiae. With the completion of synthetic chromosome VIII (synVIII) described here, this goal is within reach. In addition to writing the yeast genome, we sought to manipulate an essential functional element: the point centromere. By relocating the native centromere sequence to various positions along chromosome VIII, we discovered that the minimal 118-bp CEN8 sequence is insufficient for conferring chromosomal stability at ectopic locations. Expanding the transplanted sequence to include a small segment (~500 bp) of the CDEIII-proximal pericentromere improved chromosome stability, demonstrating that minimal centromeres display context-dependent functionality </p

Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains

We describe the complete synthesis, assembly, debugging, and characterization of a synthetic 404,963 bp chromosome, synIX (synthetic chromosome IX). Combined chromosome construction methods were used to synthesize and integrate its left arm (synIXL) into a strain containing previously described synIXR. We identified and resolved a bug affecting expression of EST3, a crucial gene for telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains, we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. Both steps of this chromosome substitution method were efficient. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these chromosomes. </p

Tropical root responses to global changes:A synthesis

Tropical ecosystems face escalating global change. These shifts can disrupt tropical forests' carbon (C) balance and impact root dynamics. Since roots perform essential functions such as resource acquisition and tissue protection, root responses can inform about the strategies and vulnerabilities of ecosystems facing present and future global changes. However, root trait dynamics are poorly understood, especially in tropical ecosystems. We analyzed existing research on tropical root responses to key global change drivers: warming, drought, flooding, cyclones, nitrogen (N) deposition, elevated (e) CO2, and fires. Based on tree species‐ and community‐level literature, we obtained 266 root trait observations from 93 studies across 24 tropical countries. We found differences in the proportion of root responsiveness to global change among different global change drivers but not among root categories. In particular, we observed that tropical root systems responded to warming and eCO2 by increasing root biomass in species‐scale studies. Drought increased the root: shoot ratio with no change in root biomass, indicating a decline in aboveground biomass. Despite N deposition being the most studied global change driver, it had some of the most variable effects on root characteristics, with few predictable responses. Episodic disturbances such as cyclones, fires, and flooding consistently resulted in a change in root trait expressions, with cyclones and fires increasing root production, potentially due to shifts in plant community and nutrient inputs, while flooding changed plant regulatory metabolisms due to low oxygen conditions. The data available to date clearly show that tropical forest root characteristics and dynamics are responding to global change, although in ways that are not always predictable. This synthesis indicates the need for replicated studies across root characteristics at species and community scales under different global change factors

Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function

We designed and synthesized synI, which is ~21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems  </p

Environmental and biological controls on Mg and Li in deep-sea scleractinian corals

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Earth and Planetary Science Letters 300 (2010): 215-225, doi:10.1016/j.epsl.2010.09.029.Deep-sea scleractinian corals precipitate aragonite skeletons that provide valuable archives of past ocean conditions. During calcification biological mediation causes variability in trace metal incorporation and isotopic ratios of the aragonite such that signals caused by environmental controls can be overwhelmed. This complicates the interpretation of geochemical proxies used for paleo-reconstructions. In this study we examine the environmental controls on the Mg/Li ratio of 34 individuals from seven genera of deep-sea scleractinian corals: Desmophyllum, Balanophyllia, Caryophyllia, Enallopsammia, Flabellum, Trochocyanthus, and Lophelia. In addition we examine the distributions of Mg and Li in Desmophyllum and Balanophyllia using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Both Mg/Ca and Li/Ca ratios increased by more than a factor of 2 in the center of calcification regions compared to the outer, fibrous regions of the coral skeleton. As a result, replicate ~10 mg subsamples of coral show less variability in the Mg/Li ratio than Mg/Ca. Microscale Mg and Li results are consistent with Rayleigh-type incorporation of trace metals with additional processes dominating composition within centers of calcification. Comparison of Mg/Li to seawater properties near the site of collection shows that the ratio is not controlled by either carbonate ion or salinity. It appears that temperature is the major control on the Mg/Li ratio. For all 34 samples the temperature correlation (R2=0.62) is significantly better than for Mg/Ca (R2=0.06). For corals of the family Caryophyllidae the R2 value increases to 0.82 with the exclusion of one sample that was observed to have an altered, chalky texture. Despite this excellent correlation the scatter in the data suggests that the Mg/Li ratio of deep-sea corals cannot be used to reconstruct temperature to better than approximately ±1.6°C without better temperature control and additional calibration points on modern coral samples.Financial Support was provided by the USGS WHOI Co-operative agreement, NSF-ANT grant numbers 0636787 and 80295700 and the WHOI Ocean Life Institute. David Case was supported by the WHOI Summer Student Fellowship

Toward a Coordinated Understanding of Hydro-Biogeochemical Root Functions in Tropical Forests for Application in Vegetation Models

Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest–climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine-root strategies for soil resource exploration, (2) coupling and trade-offs in fine-root water vs nutrient acquisition, and (3) aboveground–belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground–belowground hydro-nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Manipulating the 3D organization of the largest synthetic yeast chromosome

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes. </p

The neighbourhood environment and use of neighbourhood resources in older adults with and without lower limb osteoarthritis:results from the Hertfordshire Cohort Study

This study aimed to examine the associations of perceptions of neighbourhood cohesion and neighbourhood problems and objectively measured neighbourhood deprivation with the use of neighbourhood resources by older adults with and without lower limb osteoarthritis (LLOA), and to assess whether these relationships are stronger in older persons with LLOA than in those without the condition. Data from the Hertfordshire Cohort Study were used. American College of Rheumatology classification criteria were used to diagnose clinical LLOA (knee and/or hip osteoarthritis). Use of neighbourhood resources was assessed using the Home and Community Environment instrument. Participants were asked about their perceptions of neighbourhood cohesion and neighbourhood problems. Objective neighbourhood deprivation was assessed using the Index of Multiple Deprivation score based on 2010 census data. Of the 401 participants (71–80 years), 74 (18.5 %) had LLOA. The neighbourhood measures were not significantly associated with use of resources in the full sample. A trend for a negative association between use of public transport and perceived neighbourhood problems was observed in participants with LLOA (OR = 0.77, 99 % CI = 0.53–1.12), whereas a trend for a positive association between perceived neighbourhood problems and use of public transport was found in participants without LLOA (OR = 1.18, 99 % CI = 1.00–1.39). The perception of more neighbourhood problems seems only to hinder older adults with LLOA to make use of public transport. Older adults with LLOA may be less able to deal with neighbourhood problems and more challenging environments than those without the condition