Biology subjects

Gutierrez, R. A.

Publications and source records attributed to Gutierrez, R. A..

18 recordsLinked to original sources

bioRxiv2026

Paleometabolomics reveals impacts of abiotic factors on rodent midden metabolism over the last 50,000 years.

Metabolomics and paleoecology combined can reveal how past ecosystems worked, helping us predict future changes more accurately. Pioneering studies are needed to shed light on the potential of the so-called paleometabolomics and to standardise its application. Here, we deployed an untargeted metabolomic workflow on a timeline (200 to 49,600 cal yr BP) of rodent middens that efficiently and reproducibly captured rodent midden metabolic diversity, recovering 79% of the richness detected in 15 contemporary plant species. We found that midden chemical diversity and metabolites were influenced by the midden composition, age, and environment. Variation at the metabolite level in middens could fit age, past temperature and precipitation levels with an R{superscript 2} > 88% and their plant composition. Compounds and families responding to climate variation included lipids (e.g. glycerophospholipids) and other metabolites linked to redox status such as phenolics (e.g. flavonoids, lignans). The responses of significant midden chemical indices and compounds to abiotic pressures were supported by their response in plants collected near the midden sites to temperature and soil water content across an elevation gradient. Overall, our results not only showcase paleometabolomics as a powerful tool to reconstruct past ecosystem dynamics and metabolic evolutionary trajectories, but also to uncover relevant chemical families that could serve as trackers of past -and potentially future- climate fluctuations.

ecology↗

bioRxiv2024

Photosynthetic and Genetic Adaptations Underpinning the Resilience of Cistanthe longiscapa in the Atacama Desert

O_LIThe Atacama Desert is one of the most hostile environments for life. However, the plant species Cistanthe longiscapa (C. longiscapa) completes its life cycle in the Atacama Desert after sporadic rainfall. C_LIO_LIPhysiological analyses under controlled environmental conditions revealed superior photosynthetic performance, better light acclimation mechanisms, and larger accumulation of photosystem II in C. longiscapa compared to its mesophilic sister species. C_LIO_LIC. longiscapa shows evolutionary expansions in gene families related to DNA repair, photosynthesis, and protein homeostasis. In addition, we observed substantial gene duplication and polymorphic variations between coastal and inland populations in the Atacama Desert. Finally, our assembled mitochondrial genome provides genetic information for all DNA-containing compartments of C. longiscapa. C_LIO_LIDiurnal oscillations of malic acid and time-resolved transcriptome analyses of plants harvested in the Atacama Desert indicate that C. longiscapa engages in CAM metabolism. We observed significant differences in transcripts encoding plastid-localized proteins, including those involved in carbon metabolism, light harvesting, and photoprotection, highlighting the critical role of chloroplasts in the adaptation of C. longiscapa to the Atacama Desert. C_LIO_LIOur study provides physiological and genetic evidence for the adaptations of C. longiscapa and advances our understanding of how plants can cope with extreme environmental conditions. C_LI

plant biology↗

bioRxiv2024

Effect of temperature on circadian clock functioning of trees in the context of global warming

Plant survival in a warmer world requires the timely adjustment of biological processes to cyclical changes in the new environment. Circadian oscillators have been proposed to contribute to thermal adaptation and plasticity in plants, due to their ability to maintain periodicity in biological rhythms over a wide temperature range, promoting fitness. However, the influence of temperature and circadian clock performance on plant behaviour in natural ecosystems is not well understood. Here we used two co-occurring Nothofagus tree species from the Patagonian forests that are adapted to contrasting thermal environments derived from their different altitudinal profiles. We revealed that the upper thermal limits for accurate clock function are linked to the species thermal niches and contribute to seedling plasticity in natural environments. We computationally identified 24 circadian clock-related genes, which showed a high degree of structural conservation with clock genes from both annual and perennial species, and very similar patterns of gene expression to those of Arabidopsis thaliana. Warm temperatures produced a strong transcriptomic rearrangement, which affected the expression of clock-related genes and direct clock targets, evidencing the extent of clock functioning disruption by temperature. N. pumilio, the species from colder environments, showed reduced ability to keep rhythmicity at high temperatures compared to N. obliqua, which inhabits warmer zones. Accordingly, N. pumilio, but not N. obliqua, showed a limited oscillator function in warmer zones of the forest, reduced survival, and growth. Together, our results highlight the potential role of a resonating oscillator in ecological adaptation to a warming environment.

plant biology↗

bioRxiv2023

Convergent and divergent responses of the rhizosphere chemistry and bacterial communities to a stress gradient in the Atacama Desert.

Plants can modulate their rhizosphere chemistry, thereby influencing microbe communities. Although our understanding of rhizosphere chemistry is growing, knowledge of its responses to abiotic constraints is limited, especially in realistic ecological contexts. Here, we combined predictive metabolomics with bacterial sequencing data to investigate whether rhizosphere chemistry responded to environmental constraints and shaped bacterial communities across an elevation gradient in the Atacama Desert. We found that metabolic adjustments of rhizosphere chemistry predicted the environment of four plant species independently of year, identifying important rhizosphere metabolic biomarkers. Inter-species predictions unveiled significant biochemical convergences. Subsequently, we linked metabolic predictors to variation in the abundance of operational taxonomic units (OTUs). Chemical response influenced distinct and common bacterial families between species and vegetation belts. The annotation of chemical markers and correlated bacterial families highlighted critical biological processes such as nitrogen starvation, metal pollution and plant development and defence. Overall, this study demonstrates a unique metabolic set likely involved in improving plant resilience to harsh edaphic conditions. Besides, the results emphasise the need to integrate ecology with plant metabolome and microbiome approaches to explore plant-soil interactions and better predict their responses to climate change and consequences for ecosystem dynamics.

ecology↗

bioRxiv2023

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity in many parts of the world. Understanding the conserved molecular mechanisms that evolve in wild plant species adapted to harsh environments is crucial in developing new strategies for sustainable agriculture. Yet our knowledge of such mechanisms in wild species is scant, particularly in extreme environments. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama plant species and phylogenetically related plant species that do not live in Atacama (Sister species). We analyzed pathway and reaction enrichment to understand the biochemical commonalities and differences of wild Atacama plant species. To gain insights into the mechanisms that ensure plant survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and Sister species. We found significant biochemical convergences in primary and secondary metabolism characterized by reactions enriched in at least 50% of the Atacama species across major plant phylogenetic lineages. Analysis of the annotation indicated potential advantages against drought, salinity, high solar irradiance, and nitrogen starvation. These findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh environmental conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses in these Atacama species. Hence, genes underlying these adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

plant biology↗

bioRxiv2022

Signaling pathways involved in the repression of root nitrate uptake by nitrate in Arabidopsis thaliana

In Arabidopsis thaliana, root high-affinity nitrate (NO3-) uptake depends mainly on NRT2.1, 2.4 and 2.5, which are repressed by high NO3- supply at the transcript level. For NRT2.1, this regulation is due to the action of (i) feedback downregulation by N metabolites and (ii) repression by NO3- itself mediated by the transceptor NRT1.1(NPF6.3). However, for NRT2.4 and NRT2.5 the signaling pathway(s) remain unknown along with the molecular elements involved. Here we show that unlike NRT2.1, NRT2.4 and NRT2.5 are not induced in a NO3- reductase mutant but are strongly upregulated following replacement of NO3- by ammonium (NH4+) as the N source. Moreover, increasing NO3- concentration in a mixed nutrient solution with constant NH4+ concentration results in a gradual repression of NRT2.4 and NRT2.5, which is suppressed in a nrt1.1 mutant. This indicates that NRT2.4 and NRT2.5 are subjected to repression by NRT1.1-mediated NO3- sensing, and not to feedback repression by reduced N metabolites. We further show that key regulators of NRT2s transporters, such as HHO1, HRS1, PP2C, LBD39, BT1 and BT2, are also regulated by NRT1.1-mediated NO3- sensing, and that several are involved in NO3- repression of NRT2.1, 2.4 and 2.5. Finally, we provide evidence that it is the phosphorylated form of NRT1.1 at the T101 residue, which is most active in triggering the NRT1.1-mediated NO3- regulation of all these genes. Altogether, these data led to propose a regulatory model for high-affinity NO3- uptake in Arabidopsis, highlighting several NO3- transduction cascades downstream the phosphorylated form of the NRT1.1 transceptor. One sentence summaryCharacterisation and identification of molecular elements involved in the signaling pathways repressing NRT2s transporters and root nitrate uptake in response to nitrate.

plant biology↗

bioRxiv2022

Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots

Nitrate (NO3-) is a signaling molecule that regulates gene expression in plants. The nitrate response has been extensively characterized at the transcriptome level. However, we know little about RNA nucleocytoplasmic dynamics during nitrate response. To understand the role of mRNA localization during the nitrate response, we isolated mRNA from the nucleus, cytoplasm, and whole-cells from nitrate-treated Arabidopsis roots and performed RNA-seq. We identified 402 differentially localized transcripts (DLTs) in response to nitrate. DLTs were enriched in GO-terms related to metabolism, response to stimulus, and transport. DLTs showed five localization patterns: nuclear reduction, cytoplasmic reduction, nuclear accumulation, cytoplasmic accumulation, or delayed-cytoplasmic accumulation in response to nitrate. DLTs exhibited large changes in RNA polymerase II occupancy of cognate genes and high mRNA turnover rates, indicating these are rapidly replaced mRNAs. The NITRATE REDUCTASE 1 (NIA1) transcript exhibited the largest changes in synthesis and decay. Using single-molecule RNA FISH, we showed that NIA1 nuclear accumulation occurs mainly at transcription sites. The decay profiles for NIA1 showed a higher half-life when the transcript accumulated in the nucleus than in the cytoplasm. We propose that regulating nucleocytoplasmic mRNA distribution allows tuning transcript availability of fastly replaced mRNAs, controlling plants adaptive response to nitrogen nutrient signals.

molecular biology↗

bioRxiv2020

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data.

MicroRNAs (miRNAs) are small non-coding RNAs that are key players in the regulation of gene expression. In the last decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on pre-existing reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from sRNA-seq data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animals species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Finally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2ref) that performs an a posteriori exhaustive search to identify the precursor sequences. The code of BrumiR is freely available at https://github.com/camoragaq/BrumiR.

bioinformatics↗

bioRxiv2020

Arabidopsis thaliana interaction with Ensifer meliloti can support plant growth under N-deficiency

Nitrogen (N) is an essential macronutrient for plants. Some plant species obtain this nutrient by interacting with N-fixing bacteria. These beneficial interactions are well described in legumes but have also been observed in non-legume plant species that are unable to form root nodules. We studied the expanding role of beneficial plant-bacteria interactions for N-nutrition in the widely used model plant Arabidopsis thaliana. We found that the bacteria Ensifer meliloti enhanced A. thaliana growth under severe N-deficiency conditions, allowing plants to complete their life cycle. Our results showed that bacteria colonize the rhizosphere associated with the epidermis of the plant root. We also demonstrated that A. thaliana possesses genes that are critical for this beneficial interaction and are required for plant-growth promotion by E. meliloti under N-deficiency. This work shows association between A. thaliana and E. meliloti for plant nutrition under severe N-deficiency, and suggests that plants have conserved-molecular mechanisms to interact with N-fixing bacteria to procure N and escape adverse conditions. Under these circumstances, the supply of N via N-fixation is critical for survival, allowing the plant to complete its life cycle. Our findings provide a new framework and an experimental model system that expand our understanding of plant-rhizobia interactions for plant N-nutrition.

plant biology↗

bioRxiv2020

Phosphoproteomics after nitrate treatments reveal an important role for PIN2 phosphorylation in control of root system architecture.

Nitrate is an important signaling molecule that commands genome-wide gene expression changes that impact metabolism, physiology, plant growth and development. Although gene expression responses to nitrate at the mRNA level have been characterized in great detail, the impact of nitrate signaling at the proteome level has been much less explored. Most signaling pathways involve post-translational modifications of key protein factors and chiefly among these modifications is protein phosphorylation. In an effort to identify new components involved in nitrate responses in plants, we performed analyses of the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. We identified 268 phosphoproteins that show significant changes at 5 min or 20 min after nitrate treatments. The large majority of these proteins (96%) are coded by genes that are not modulated at the expression level in response to nitrate treatments in publicly available transcriptome data. Proteins identified by 5 min include potential signaling-components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with protein binding, transporter activity or hormone metabolism functions. Interestingly, the phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants in response to nitrate at 5 min was significantly different (95%) as compared to wild-type plants. This result is consistent with the role of NRT1.1 as a key component of a nitrate signaling pathway that involves phosphoproteomic changes. Our integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We experimentally validated the role of PIN2 phosphorylation in both primary and lateral root growth responses to nitrate. Our data provide new insights into the phosphoproteome and identifies novel protein components that are regulated post-translationally, such as PIN2, in nitrate responses in Arabidopsis thaliana roots.

plant biology↗

bioRxiv2020

Modulation of root growth by nutrient-defined fine-tuning of polar auxin transport

Nitrogen is an essential macronutrient and its availability in soil plays a critical role in plant growth, development and impacts agricultural productivity. Plants have evolved different strategies to sense and respond to heterogeneous nitrogen distribution. Modulating root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to varying nitrogen sources are poorly understood. Here, using a combination of physiological, live in vivo high- and super resolution imaging, we describe a novel adaptation strategy of root growth on available nitrogen source. We show that growth, i.e. tissue-specific cell division and elongation rates are fine-tuned by modulating auxin flux within and between tissues. Changes in auxin redistribution are achieved by nitrogen source dependent post-translational modification of PIN2, a major auxin efflux carrier, at an uncharacterized, evolutionary conserved phosphosite. Further, we generate a computer model based on our results which successfully recapitulate our experimental observations and creates new predictions that could broaden our understanding of root growth mechanisms in the dynamic environment.

plant biology↗

bioRxiv2020

Transcription factor TGA2 is essential for UV-B stress tolerance controlling oxidative stress in Arabidopsis

Plants possess a diversity of Reactive Oxygen Species (ROS)-processing enzymes involved in sensing and controlling ROS levels under basal and stressful conditions. There is little information on the transcriptional regulators that control the expression of these ROS-processing enzymes, particularly at the onset of the defense response to abiotic stress. Filling this gap, this paper reports a critical role for Arabidopsis TGA class II factors (TGA2, TGA5, and TGA6) in the tolerance response to UV-B light and photooxidative stress, by activating the expression of genes with antioxidative roles. We identified two clusters of genes responsive to UV-B and activated by TGA2/5/6 were identified using RNAseq and clustering analysis. The GSTU gene family, which encodes glutathione transferase enzymes from the Tau subclass, was overrepresented in these clusters. We corroborated the TGA2-mediated activation in response to UV-B for three model genes (GSTU7, GSTU8, and GSTU25) using RT-qPCR and ChIP analyses. Interestingly, using tga256 mutant and TGA2- and GSTU7-complemented mutant plants, we demonstrated that TGA2-mediated induction of GSTU genes is essential to control ROS levels and oxidative damage after UV-B and MeV treatments. This evidence positions TGA class II factors, particularly TGA2, as a key players in the redox signaling network of Arabidopsis plants. HighlightArabidopsis TGA2 transcription factor is part of the redox-signaling network controlling ROS levels and oxidative damage in tolerance response to UV-B and photooxidative stress, via activation of antioxidant GSTU genes.

plant biology↗

bioRxiv2020

A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR

The technique RT-qPCR for viral RNA detection is the current worldwide strategy used for early detection of the novel coronavirus SARS-CoV-2. RNA extraction is a key pre-analytical step in RT-qPCR, often achieved using commercial kits. However, the magnitude of the COVID-19 pandemic is causing disruptions to the global supply chains used by many diagnostic laboratories to procure the commercial kits required for RNA extraction. Shortage in these essential reagents is even more acute in developing countries with no means to produce kits locally. We sought to find an alternative procedure to replace commercial kits using common reagents found in molecular biology laboratories. Here we report a method for RNA extraction that takes about 40 min to complete ten samples, and is not more laborious than current commercial RNA extraction kits. We demonstrate that this method can be used to process nasopharyngeal swab samples and yields RT-qPCR results comparable to those obtained with commercial kits. Most importantly, this procedure can be easily implemented in any molecular diagnostic laboratory. Frequent testing is crucial for individual patient management as well as for public health decision making in this pandemic. Implementation of this method could maintain crucial testing going despite commercial kit shortages.

molecular biology↗

bioRxiv2019

Differences in berry primary and secondary metabolisms identified by transcriptomic and metabolic profiling of two table grape color somatic variants

Anthocyanins are flavonoids responsible for the color of berries in skin-pigmented grapevine (Vitis vinifera L.). Due to the widely adopted vegetative propagation of this species, somatic mutations occurring in meristematic cell layers can be fixed and passed into the rest of the plant when cloned. In this study we focused on the transcriptomic and metabolic differences between two color somatic variants. Using microscopic, metabolic and mRNA profiling analyses we compared the table grape cultivar (cv.) Red Globe (RG, with purplish berry skin) and cv. Chimenti Globe (CG, with a contrasting reddish berry skin color). As expected, significant differences were found in the composition of flavonoids and other phenylpropanoids, but also in their upstream precursors shikimate and phenylalanine. Among primary metabolites, sugar phosphates related with sucrose biosynthesis were less accumulated in cv. CG. The red-skinned cv. CG only contained di-hydroxylated anthocyanins (i.e. peonidin and cyanidin) while the tri-hydroxylated derivatives malvidin, delphinidin and petunidin were absent, in correlation to the reddish cv. CG skin coloration. Transcriptomic analysis showed alteration in flavonoid metabolism and terpenoid pathways and in primary metabolism such as sugar content. Eleven flavonoid 35-hydroxylase gene copies were down-regulated in cv. CG. This family of cytochrome P450 oxidoreductases are key in the biosynthesis of tri-hydroxylated anthocyanins. Many transcription factors appeared down-regulated in cv. CG in correlation to the metabolic and transcriptomic changes observed. The use of molecular markers and its confirmation with our RNA-seq data showed the exclusive presence of the null MYBA2 white allele (i.e. homozygous in both L1 and L2 layers) in the two somatic variants. Therefore, the differences in MYBA1 expression seem sufficient for the skin pigmentation differences and the changes in MYBA target gene expression in cv. Chimenti Globe.

plant biology↗

bioRxiv2019

Genome-wide Analysis In Response to N and C Identifies New Regulators for root AtNRT2 Transporters

In Arabidopsis thaliana, the High-Affinity Transport System (HATS) for root NO3- uptake depends mainly on four NRT2 transporters, namely NRT2.1, NRT2.2, NRT2.4 and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways have been shown to control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 genes expression to the interaction of these signals has never been specifically investigated and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4 and NRT2.5 in response to N/C signals. Our systems analysis of the data highlighted the potential role of three putative transcription factors, TGA3, MYC1 and bHLH093. Functional analysis of mutants combined with yeast one hybrid experiments confirmed that all 3 transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals.\n\nOne sentence summaryIdentification of three transcription factors involved in the regulation of NRT2s transporters using a systems biology approach and NRT2.1 as target gene in response to combinations of N/C treatments

plant biology↗

bioRxiv2018

Common variants in ABCG8 and TRAF3 genes confer risk for gallstone disease and gallbladder cancer in admixed Latinos with Mapuche Native American ancestry

BackgroundLatin Americans and Chilean Amerindians have the highest prevalence of cholesterol gallstone disease (GSD) and gallbladder cancer (GBC) in the world. A handful of loci have been associated with GSD in populations of predominantly European ancestry, however they only explain a small portion of the population-attributable risk of the disease.\n\nMethodsWe performed a genome-wide association study (GWAS) for GSD in 1,095 admixed Latinos with Mapuche Native American Ancestry, followed by a replication analysis of 10 candidate single nucleotide polymorphisms (SNPs) with suggestive genome-wide significance (P<1x10-5) in 1,643 individuals. Disease status was assessed by cholecystectomy or abdominal ultrasonography. Logistic regression analyses were adjusted for age, sex, BMI, Type 2 Diabetes and Amerindian ancestry. Associated variants were further examined in two large GSD European populations and in a Chilean gallbladder cancer (GBC) cohort. We determined the expression levels of a novel GSD-candidate gene in normal and GSD-tissue samples.\n\nResultsWe consistently replicated the ABCG8 gene (rs11887534; P=3.24x10-8, OR=1.74) associated with GSD in admixed Latinos and identified a novel candidate signal within the TRAF3 gene on chromosome 14 (rs12882491; P=1.11x10-7, OR=1.40). ABCG8 and TRAF3 variants also conferred risk to GBC. Gene expression analyses indicated that TRAF3 levels were significantly decreased in the gallbladder (P=0.015) and the duodenal mucosa (P=0.001) of affected GSD individuals compared to healthy controls.\n\nConclusionsWe confirmed ABCG8 and identified TRAF3 both associated with GSD and GBC in admixed Latinos. Decreased TRAF3 expression levels could enhance gallbladder inflammation as is observed in GSD and GSD-associated GBC.

genetics↗

bioRxiv2018

Whole genome sequence of Mapuche-Huilliche Native Americans

BackgroundWhole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant.\n\nResultsHere we present a high-quality complete genome sequence of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile (85% genomic and 98% exonic coverage at > 30X), with 96-97% high confidence calls. We found approximately 3.1x106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs that are not included in current sequencing databases. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a marginally admixed population from the Southern Cone, whose genetic component is derived from early Native American ancestors. In addition, we found that HUI genomes display highly divergent and novel variants with potential functional impact that converge in ontological categories essential in cell metabolic processes.\n\nConclusionsMapuche-Huilliche genomes contain a unique set of small- and large-scale genomic variants in functionally linked genes, which may contribute to susceptibility for the development of common complex diseases or traits in admixed Latinos and Native American populations. Our data represents an ancestral reference panel for population-based studies in Native and admixed Latin American populations.

genomics↗

bioRxiv2018

Loop Assembly: a simple and open system for recursive fabrication of DNA circuits

High efficiency methods for DNA assembly are based on sequence overlap between fragments or Type IIS restriction endonuclease cleavage and ligation. These have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets and serial manipulations for the different stages of assembly. We present Loop assembly, based on a recursive approach to DNA fabrication. Alternate use of two Type IIS restriction endonucleases and corresponding vector sets allows efficient and parallel assembly of large DNA circuits. Plasmids containing standard Level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.

synthetic biology↗