Biology subjects

Garcia, A.

Publications and source records attributed to Garcia, A..

82 records · Page 5Linked to original sources

bioRxiv2019

FACT mediates cohesin function on chromatin

Cohesin is a key regulator of genome architecture with roles in sister chromatid cohesion 1,2 and the organisation of higher-order structures during interphase 3 and mitosis 4,5. The recruitment and mobility of cohesin complexes on DNA is restricted by nucleosomes 6-8. Here we show that cohesin role in chromosome organisation requires the histone chaperone FACT. Depletion of FACT in metaphase cells affects cohesin stability on chromatin reducing its accumulation at pericentric regions and binding on chromosome arms. Using Hi-C, we show that cohesin-dependent TAD (Topological Associated Domains)-like structures in G1 and metaphase chromosomes are disrupted in the absence of FACT. Surprisingly, sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our results uncover a role for FACT in genome organisation by facilitating cohesin-dependent compartmentalization of chromosomes into loop domains.

molecular biology↗

bioRxiv2019

Genotyping complex structural variation at the malaria-associated human glycophorin locus using a PCR-based strategy

Structural variation in the human genome can affect risk of disease. An example is a complex structural variant of the human glycophorin gene cluster, called DUP4, which is associated with a clinically-significant level of protection against severe malaria. The human glycophorin gene cluster harbours at least 23 distinct structural variants and accurate genotyping of this complex structural variation remains a challenge. Here, we use a PCR-based strategy to genotype structural variation at the human glycophorin gene cluster. We validate our approach, based on a triplex paralogue ratio test (PRT) combined with junction-fragment specific PCR, on publically-available samples from the 1000 Genomes project. We then genotype a longitudinal birth cohort using small amounts of DNA at low cost. Our approach readily identifies known deletions and duplications, and can potentially identify novel variants for further analysis. It will allow exploration of genetic variation at the glycophorin locus, and investigation of its relationship with malaria, in large sample sets at minimal cost, using standard molecular biology equipment.

genetics↗

bioRxiv2019

Why Montane Anolis Lizards Are Moving Downhill While Puerto Rico Warms

1Because Puerto Rico has warmed in recent decades, ectotherms there should have shifted their elevational ranges uphill. However, by comparing historical versus recent distributional records of Anolis lizards, we found that three \"montane-forest\" species have instead moved downhill in recent decades, almost to sea level. This downward shift appears related to the massive regeneration of Puerto Rican forests - especially in lowland areas - which started in the mid-20th century when the islands economy began shifting from agriculture to manufacturing. The magnitude of local cooling caused by regenerated forests swamps recent climate warming, seemingly enabling cool-adapted \"montane\" lizards to track forests as they spread downhill from mountain refugia into abandoned plantations. Thus, contemporary distributional patterns are likely converging to those prior to the arrival of European settlers, who cleared most lowland forests for agriculture, thereby restricting forests and associated fauna to high-elevation remnants. In contrast with the montane species, three lowland species expanded their ranges to higher elevations in recent decades; but whether this movement reflects warming, land-use shifts, or hurricane-induced destruction of upland forests is unclear.

ecology↗

bioRxiv2019

A Nanoemulsion as an Effective Treatment Against Human Pathogenic Fungi

The emergence of immunocompromising diseases such as HIV/AIDS or other immunosuppressive medical conditions have opened an opportunity for fungal infections to afflict patients globally. An increase antifungal drug resistant fungi have posed a serious threat to patients. Combining these circumstances with a limited variety of antifungal drugs available to treat patients has left us in a situation where we need to develop new therapeutic approaches that are less prone to development of resistance by pathogenic fungi. In this study we present the utilization of the nanoemulsion NB-201 to control human pathogenic fungi. We found that the NB-201 exhibited in vitro activity against C. albicans, including both planktonic growth and biofilms. Furthermore, treatments with NB-201 significantly reduced the fungal burden at the infection site and presented enhanced healing process after subcutaneous infections by multidrug resistant C. albicans in a murine host system. NB-201 also exhibited in vitro growth inhibition activity against other fungal pathogens, including Cryptococcus spp, Aspergillus fumigatus, and Mucorales. Due to the nature of the activity of this nanoemulsion, there is a minimized chance of drug resistance to develop, thus presents a novel treatment to control fungal wound or skin infections.

microbiology↗

bioRxiv2019

Synthetic Genetic Codes Designed to Hinder Evolution

One challenge in engineering organisms is guaranteeing system behavior over many generations. Spontaneous mutations that arise before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such that all point mutations in protein-coding sequences are selected against. Synthetic genetic systems so-encoded should \"fail safely\" in response to many individual spontaneous mutations. We designed a family of such fail-safe codes and analyzed their expected effect on the evolution of engineered organisms via simulation. We predict that fail-safe codes supporting expression of 20 or 15 amino acids could slow the evolution of proteins in so-encoded organisms to 30% or 0% the rate of standard-code organisms, respectively. We also designed quadruplet-codon codes that should be capable of encoding at least 20 amino acids while ensuring all single point mutations in protein-coding sequences are selected against. We show by in vitro experiments that a reduced set of 21 tRNA is capable of expressing a protein whose coding sequence is recoded to use a fail-safe code, whereas a standard-code encoding is not expressed. Our work suggests that a rationally depleted but otherwise natural translation system should yield biological systems with intrinsically reduced evolutionary capacity, and that so-encoded hypoevolvable organisms might be less likely to invade new niches or outcompete native populations.

synthetic biology↗

bioRxiv2019

Muscle MACF1 maintains myonuclei and mitochondria localization through microtubules to control muscle functionalities

Skeletal muscle is made from multinuclear myofiber, where myonuclei are positioned at the periphery or clustered below neuromuscular junctions (NMJs). While mispositioned myonuclei are the hallmark of numerous muscular diseases, the molecular machinery maintaining myonuclei positioning in mature muscle is still unknown. Here, we identified microtubule-associated protein MACF1 as an evolutionary conserved regulator of myonuclei positioning, in vitro and in vivo, controlling the \"microtubule code\" and stabilizing the microtubule dynamics during myofibers maturation, preferentially at NMJs. Specifically, MACF1 governs myonuclei motion, mitochondria positioning and structure and acetylcholine receptors (AChRs) clustering. Macf1-KO in young and adult mice decreases muscle excitability and causes evolutionary myonuclei positioning alterations in adult mice, paralleled with high mitochondria content and improved resistance to fatigue. We present MACF1 as a primary actor of the maintenance of synaptic myonuclei and AChRs clustering, peripheral myonuclei positioning and mitochondria organization through the control of microtubule network dynamics in muscle fibers.

cell biology↗

bioRxiv2019

H7N6 Low Pathogenic Avian Influenza outbreak in commercial turkey farms in Chile caused by a native South American Lineage

In December of 2016, low pathogenic avian influenza (LPAI) caused by an H7N6 subtype was confirmed in a grow-out turkey farm located in Valparaiso Region, Chile. Depopulation of exposed animals, zoning, animal movement control and active surveillance were implemented to contain the outbreak. Two weeks later, a second turkey grow-out farm located 70 km north of the first site was also infected by H7N6 LPAI, which subsequently spilled over to one backyard poultry flock. The virus involved in the outbreak shared a close genetic relationship with viruses collected from Chilean aquatic birds viruses. The A/turkey/Chile/2017(H7N6) LPAI virus belonged to a native South American lineage. Based on the H7 and most of the internal genes phylogenies, these viruses were also closely related to the viruses that caused a highly pathogenic avian influenza outbreak in Chile in 2002. Results from this study help understand the regional dynamics of influenza outbreaks, highlighting the importance of local native viruses circulating in the natural reservoir hosts.

epidemiology↗

bioRxiv2018

Image-based Phenotyping and Disease Screening of Multiple Populations for resistance to Verticillium dahliae in cultivated strawberry Fragaria x ananassa

1.0Verticillium dahliae is a highly detrimental pathogen of soil cultivated strawberry (Fragaria x ananassa). Breeding of Verticillium wilt resistance into commercially viable strawberry cultivars can help mitigate the impact of the disease. In this study we describe novel sources of resistance identified in biparental strawberry populations, creating a wealth of data for breeders to exploit. Pathogen-informed experiments have allowed the differentiation of subclade-specific resistance responses, through studying V. dahliae subclade II-1 specific resistance in the cultivar Redgauntlet and subclade II-2 specific resistance in Fenella and Chandler.\n\nA large-scale low-cost phenotyping platform was developed utilising automated unmanned vehicles and near infrared imaging cameras to assess field-based disease trials. The images were used to calculate disease susceptibility for infected plants through the normalized difference vegetation index score. The automated disease scores showed a strong correlation with the manual scores.\n\nA co-dominant resistant QTL; FaRVd3D, present in both Redgauntlet and Hapil cultivars exhibited a major effect of 18.3 % when the two resistance alleles were combined. Another allele, FaRVd5D, identified in the Emily cultivar was associated with an increase in Verticillium wilt susceptibility of 17.2%, though whether this allele truly represents a susceptibility factor requires further research, due to the nature of the bi-parental cross.\n\nMarkers identified in bi-parental populations were validated across a set of 92 accessions to determine whether they remained closely linked to resistance genes in the wider germplasm. The resistant markers FaRVd2B from Redgauntlet and FaRVd6D from Chandler were associated with resistance across the wider germplasm. Furthermore, comparison of imaging versus manual phenotyping revealed the automated platform could identify three out of four disease resistance markers. As such, this automated wilt disease phenotyping platform is considered to be a good, time saving, substitute for manual assessment.

genetics↗

bioRxiv2018

First genome-wide association study of non-severe malaria in two birth cohorts in Benin: hints towards the involvement of the STAT3 pathway.

Recent research efforts to identify genes involved in the susceptibility to P. falciparum malaria have focused on severe forms of malaria, with several genome-wide association studies (GWAS) and multi-center analyses published this past decade. Here we present the first GWAS performed on mild malaria susceptibility in young children, designed to identify genetic variants involved in innate immunity or innate resistance mechanisms. Two cohorts of infants from southern Benin (525 and 250 individuals respectively), used as discovery and replication cohorts, were closely followed from birth to 18-24 months of age, with an assessment of a space-and time-dependent risk of exposure to vector bites. GWAS was performed on 15.5 million genotyped and imputed variants, with the susceptibility of infants to mild malaria attacks and to malaria infections as a whole (both symptomatic and asymptomatic). Infant susceptibility to malaria was assessed by considering all malaria events occurring during the follow-up using a Cox-model for recurrent events. We found strong statistical support for a role of PTPRT, a tyrosine phosphatase receptors involved in STAT3 pathway, with the protection against both mild malaria attacks and malaria infections (p=9.70x10-8 and p=1.78x10-7 respectively in the discovery cohort, and both p < 0.05 in the replication cohort). Furthermore, our study highlights several other genes, among them, UROC1, ACER3 and the PLAG2 cluster, whose biological functions are relevant in malaria infection. Results show that despite the difficulty of setting up such longitudinal field studies, GWAS on non-severe malaria can successfully identify new candidate genes and inform physiological mechanisms underlying natural protection against malaria.\n\nAUTHOR SUMMARYMalaria remains a major worldwide public health problem with circa 219 million cases and 435,000 deaths per year. As for many infectious diseases, the genetics of the host plays a role in the disease course. So far, most studies on such genetic factors focused on severe malaria forms. Our study aimed to find factors associated with simple forms (asymptomatic forms and uncomplicated clinical forms). We used dense genome-wide data of two cohorts of infants closely followed during two years in Benin, and we incorporated an environmental risk of exposure estimated at individual level from entomological, climatic, and environmental data. This allowed us to unravel several genes that appear to play a role in the susceptibility to malaria infection, thus demonstrating the feasibility of a genome-wide approach on non-severe forms. Functional studies are needed to confirm the role of the genetic factors highlighted here. Some of these genes represent interesting targets for future prevention strategies and drug development.

genetics↗

bioRxiv2018

Standardized Informatics Computing Platform for Advancing Biomedical Discovery Through Data Sharing

ObjectiveThe goal is to develop a standardized informatics computing system that can support end-to-end research data lifecycle management for biomedical research applications.\n\nMaterials and MethodsDesign and implementation of biomedical research informatics computing system (BRICS) is demonstrated. The system architecture is modular in design with several integrated tools: global unique identifier, validation, upload, download and query tools that support user friendly informatics system capability.\n\nResultsBRICS instances were deployed to support research for improvements in diagnosis of traumatic brain injury, biomarker discovery for Parkinsons Disease, the National Ophthalmic Disease Genotyping and Phenotyping network, the informatics core for the Center for Neuroscience and Regenerative Medicine, the Common Data Repository for Nursing Science, Global Rare Diseases Patient Registry, and National Institute of Neurological Disorders and Stroke Clinical Informatics system for trials and research.\n\nDiscussionData deidentification is conducted by using global unique identifier methodology. No personally identifiable information exists on the BRICS supported repositories. The Data Dictionary provides defined Common Data Elements and Unique Data Elements, specific to each of the BRICS instance that enables Query Tool to search through research data. All instances are supported by the Medical Imaging Processing, statistical analysis R, and Visualization software program.\n\nConclusionThe BRICS core modules can be easily adapted for various biomedical research needs thereby reducing cost in developing new instances for additional biomedical research needs. It provides user friendly tools for researchers to query and aggregate genetic, phenotypic, clinical and medical imaging data. Data sets are findable, accessible and reusable for researchers to foster new research on various diseases.

bioinformatics↗