Biology subjects

Gomez, G.

Publications and source records attributed to Gomez, G..

6 recordsLinked to original sources

bioRxiv2019

Viral fitness determines the magnitude of transcriptomic and epigenomic reprogramming of defense responses in plants

Although epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus (TuMV) with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses were larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Several transposable elements (TEs) located in different chromatin contexts and epigenetic-related genes were also affected. Correspondingly, mutant plants having loss or gain of repressive marks were, respectively, more tolerant and susceptible to TuMV, with a more efficient response against the ancestral isolate. In wild-type plants both isolates induced similar levels of cytosine methylation changes, including in and around TEs and stress-related genes. Results collectively suggested that apart from RNA silencing and basal immunity systems, DNA methylation and histone modification pathways may also be required for mounting proper antiviral defenses in plants and that the effectiveness of this type of regulation strongly depends on the degree of viral adaptation to the host.

evolutionary biology↗

bioRxiv2019

Lokiarchaeon exhibits homoacetogenesis

The proposed Asgard superphylum of Archaea comprises the closest archaeal relatives of eukaryotes, whose genomes hold clues pertaining to the nature host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Genomes of the Asgard candidate Phylum Candidatus Lokiarchaeota [Lokiarchaeon] suggest an acetogenic H2 -dependent lifestyle5 and mixotrophic capabilities6. However, data on the activity of Lokiarchaeon are currently lacking, and the ecology of the host cell that acquired the mitochondrion is debated4,7. Here, we show that in anoxic marine sediments underlying highly productive waters on the Namibian continental shelf Lokiarchaeon gene expression increases with depth below the seafloor, and was significantly different across a redox gradient spanning hypoxic to sulfidic conditions. Notably, Lokiarchaeon increased expression of genes involved in growth, carbohydrate metabolism, and the H2-dependent Wood-Ljungdahl (WLP) carbon fixation pathway under the most reducing (sulfidic) conditions. Quantitative stable isotope probing experiments revealed multiple populations of Lokiarchaeota utilizing both CO2 and diatomaceous extracellular polymeric substances (dEPS) as carbon sources over a 10-day incubation under anoxic conditions. This apparent anaerobic mixotrophic metabolism was consistent with the expression of Lokiarchaeon genes involved in transport and fermentation of sugars and amino acids. Remarkably, several Asgard populations were more enriched with 13C-dEPS compared to the community average, indicating a preference for dEPS as a growth substrate. The qSIP and gene expression data indicate a metabolism of \"Candidatus Lokiarchaeota\" similar to that of sugar fermenting homoacetogenic bacteria8, namely that Lokiarchaeon can couple fermentative H2 production from organic substrates with electron bifurcation and the autotrophic and H2-dependent WLP. Homoacetogenesis allows to access a wide range of substrates and relatively high ATP gain during acetogenic sugar fermentation8 thereby providing an ecological advantage for Lokiarchaeon in anoxic, energy limited settings.

microbiology↗

bioRxiv2019

Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon

miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyze the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analyzed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analyzed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.

plant biology↗

bioRxiv2019

Zygomorphic flowers have fewer visitors

Botanists have long identified bilaterally symmetrical (zygomorphic) flowers with more specialized pollination interactions than radially symmetrical (actinomorphic) flowers. Zygomorphic flowers facilitate more precise contact with pollinators, guide pollinator behaviour, and exclude less effective pollinators. However, whether zygomorphic flowers are actually visited by a smaller subset of available pollinator species has not been broadly evaluated. We compiled 53,609 floral visitation records in 159 communities and classified the plants floral symmetry. Globally and within individual communities, plants with zygomorphic flowers are indeed visited by fewer species. At the same time, zygomorphic flowers share a somewhat larger proportion of their visitor species with other co-occurring plants, and have particularly high sharing with co-occurring plants that also have zygomorphic flowers. Visitation sub-networks for zygomorphic species also show differences that may arise from reduced visitor diversity, including greater connectance, greater web asymmetry, and lower coextinction robustness of both plants and visitor species -- but these changes do not necessarily translate to whole plant-visitor communities. These results provide context for widely documented associations between zygomorphy and diversification and imply that species with zygomorphic flowers may face greater risk of extinction due to pollinator loss.

ecology↗

bioRxiv2019

Are tropical reptiles really declining? A six-year survey of snakes in Drake Bay, Costa Rica, and the role of temperature, rain and light

Introductionstudies in the last two decades have found declining snake populations in both temperate and tropical sites, including informal reports from Drake Bay, Costa Rica.\n\nObjectiveto investigate if reports of decreasing snake populations in Drake Bay had a real basis, and if environmental factors, particularly temperature, rain and light, have played a role in that decrease.\n\nMethodswe worked at Drake Bay from 2012 through 2017 and made over 4000 h of transect counts. Using head flashlights we surveyed a transect covered by lowland tropical rainforest at an altitude of 12-38 m above sea level, near the Agujas River, mostly at 1930-2200 hours. We counted all the snakes that we could see along the transect.\n\nResultssnake counts increase from August to September and then decline rapidly. The May snakes/rainfall peaks coincide, but the second snake peak occurs one month before the rain peak; we counted more snakes in dry nights, with the exception of Imantodes cenchoa which was equally common despite rain conditions. We saw less Leptodeira septentrionalis on bright nights, but all other species were unaffected. Along the six years, the number of species with each diet type remained relatively constant, but the number of individuals declined sharply for those that feed on amphibians and reptiles. We report Rhadinella godmani, a highland species, at 12-38 m of altitude.\n\nConclusionnight field counts of snakes in Drake Bay, Costa Rica, show a strong decline from 2012 through 2017.

ecology↗

bioRxiv2019

Tau pathology in cognitively normal older adults: Associations with brain atrophy and cognitive decline

INTRODUCTIONTau pathology, a hallmark of Alzheimers disease, is observed in the brains of virtually all individuals over 70.\n\nMETHODSUsing 18F-AV-1451 (18F-flortaucipir) PET, we evaluated tau pathology in 54 cognitively normal participants (mean age 77.5, SD 8.9) from the Baltimore Longitudinal Study of Aging. We assessed associations between PET signal and age, sex, race, and amyloid positivity. We investigated relationships between regional signal and retrospective rates of change in regional volumes and cognitive function adjusting for age, sex, and amyloid status.\n\nRESULTSGreater age, male sex, black race, and amyloid positivity were associated with higher 18F-AV-1451 retention in distinct brain regions. Retention in the entorhinal cortex was associated with lower entorhinal volume ({beta} = -1.124, SE = 0.485, p = 0.025) and a steeper decline in memory performance ({beta} = -0.086, SE = 0.039, p = 0.029).\n\nDISCUSSIONAssessment of medial temporal tau pathology will provide insights into early structural brain changes associated with later cognitive impairment and Alzheimers disease.

neuroscience↗