Biology subjects

Diaz, M.

Publications and source records attributed to Diaz, M..

28 records · Page 2Linked to original sources

bioRxiv2022

The MIF SNP rs755622 is a germline determinant of tumor immune activation in Glioblastoma

While immunotherapies have shown durable responses for multiple tumors, their efficacy remains limited in some advanced cancers, including glioblastoma. This may be due to differences in the immune landscape, as the glioblastoma microenvironment strongly favors immunosuppressive myeloid cells, which are linked to an elevation in immune-suppressive cytokines, including macrophage migration inhibitory factor (MIF). We now find that a single-nucleotide polymorphism (SNP) rs755622 in the MIF promoter associates with increased leukocyte infiltration in glioblastoma. Furthermore, we identified lactotransferrin expression as being associated with the rs755622 SNP, which could also be used as a biomarker for immune infiltrated tumors. These findings provide the first example in glioblastoma of a germline SNP that underlies differences in the immune microenvironment and identifies high lactotransferrin as a potential factor promoting immune activation.

cancer biology↗

bioRxiv2021

Biological integrity enhances the qualitative effectiveness of conditional mice-oak mutualisms

Scatter-hoarding decisions by rodents are key for the long-term maintenance of scattered tree populations. Decisions are determined by seed value, competition and predation risk, so that they can be influenced by the integrity of the biological system composed by trees, rodents, ungulate competitors, and rodent predators. We manipulate and model the oak-mice interaction in a Spanish dehesa, an anthropogenic savanna system suffering chronic tree regeneration failure, and quantify the joint effect of intrinsic and extrinsic factors on acorn dispersal effectiveness. First, we conducted a large-scale cafeteria field experiment, where we modified ungulate presence and predation risk, and followed mouse scatter-hoarding decisions under contrasting levels of moonlight and acorn availability. Then, we estimated the net effects of competition and risk by means of transition probability models that simulated mouse scatter-hoarding decisions according to the environmental context. Our results show that suboptimal conditions for mice balance the interaction towards the mutualism as they force mice to forage less efficiently. Under stressful conditions (predation risks and presence of ungulates), lack of antipredatory cover around dehesa trees limited transportation of acorns, but also precluded mice activities outside tree canopies. As a result, post-dispersal predation rates were reduced and large acorns had a higher probability to survive. Our work shows that inter-specific interactions preventing efficient foraging by scatter-hoarders benefitted seed dispersal. Therefore, the maintenance of the full set of producers, consumers, dispersers and predators in ecosystems is key for promoting seed dispersal effectiveness in conditional mutualisms.

ecology↗

bioRxiv2021

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.

Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year has caused 2.29 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for effectively controlling the pandemic and informing vaccine platform development. Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates, but with occasional mutation loss. The last quartile of 2020 revealed a concerning accumulation of mostly novel low frequency replacement mutations in the Spike protein, and a hypermutable glutamine residue near the putative furin cleavage site. Finally, the end of the year data revealed the presence of known variants of concern including B.1.1.7, which has acquired additional Spike mutations. Overall, our results suggest that predominant viral sequences are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. This high level of existing variation, even at low frequencies and especially in the Spike-encoding region may be become problematic when superspreader events, akin to serial Founder Events in evolution, drive these rare mutations to prominence. AUTHOR SUMMARYThe pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused the death of more than 2.29 million people and continues to be a severe threat internationally. Although simple measures such as social distancing, periodic lockdowns and hygiene protocols were immediately put into force, the infection rates were only temporarily minimized. When infection rates exploded again new variants of the virus began to emerge. Our study focuses on a representative set of sequences from the United States throughout 2020 and early 2021. We show that the driving force behind the variants of public health concern, is widespread infection and superspreader events. In particular, we show accumulation of mutations over time with little loss from genetic drift, including in the Spike region, which could be problematic for vaccines and therapies. This lurking accumulated genetic variation may be a superspreader event from becoming more common and lead to variants that can escape the immune protection provided by the existing vaccines.

genetics↗

bioRxiv2020

CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing

The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a tiling PCR approach followed by Oxford Nanopore sequencing (ONT) of up to 96 samples at a time. There is a need, however, for a flexible, platform agnostic, method that can provide multiple throughput options depending on changing requirements as the pandemic peaks and troughs. Here we present CoronaHiT, a method capable of multiplexing up to 96 small genomes on a single MinION flowcell or >384 genomes on Illumina NextSeq, using transposase mediated addition of adapters and PCR based addition of barcodes to ARTIC PCR products. We demonstrate the method by sequencing 95 and 59 SARS-CoV-2 genomes for routine and rapid outbreak response runs, respectively, on Nanopore and Illumina platforms and compare to the standard ARTIC LoCost nanopore method. Of the 154 samples sequenced using the three approaches, genomes with [≥] 90% coverage (GISAID criteria) were generated for 64.3% of samples for ARTIC LoCost, 71.4% for CoronaHiT-ONT, and 76.6% for CoronaHiT-Illumina and have almost identical clustering on a maximum likelihood tree. In conclusion, we demonstrate that CoronaHiT can multiplex up to 96 SARS-CoV-2 genomes per MinION flowcell and that Illumina sequencing can be performed on the same libraries, which will allow significantly higher throughput. CoronaHiT provides increased coverage for higher Ct samples, thereby increasing the number of high quality genomes that pass the GISAID QC threshold. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally, to help control the pandemic.

genomics↗

bioRxiv2019

Idioblasts as pathways for distributing water absorbed by leaf surfaces to the mesophyll in Capparis odoratissima

Capparis odoratissima is a tree species native to semi-arid environments of the northern coast of South America where low soil water availability coexists with frequent nighttime fog. Previous work with this species demonstrated that C. odoratissima is able to use water absorbed through its leaves at night to enhance leaf hydration, photosynthesis, and growth. Here, we combine detailed anatomical evaluations of the leaves of C. odoratissima, with water and dye uptake experiments in the laboratory. We used immunolocalization of pectin and arabinogalactan protein epitopes to characterize the chemistry of foliar water uptake pathways. The abaxial surfaces of C. odoratissima leaves are covered with overlapping, multicellular peltate hairs, while the adaxial surfaces are glabrous but with star-shaped "structures" at regular intervals. Despite these differences in anatomy, both surfaces are able to absorb condensed water, but this ability is most significant on the upper surface. Rates of evaporative water loss from the upper surface, however, are coincident with cuticle conductance. Numerous idioblasts connect the adaxial leaf surface and the adaxial peltate hairs, which contain hygroscopic substances such as arabinogalactan proteins and pectins. The highly specialized anatomy of the leaves of C odoratissima fulfills the dual function of avoiding excessive water loss due to evaporation, while maintaining the ability to absorb liquid water. Cell-wall related hygroscopic compounds present in the peltate hairs and idioblasts create a network of microchannels that maintain leaf hydration and promote the uptake of aerial water.

plant biology↗

bioRxiv2019

Light-mediated circuit switching in the Drosophila neuronal clock network

The circadian clock is a timekeeper but also helps adapt physiology to the outside world. This is because an essential feature of clocks is their ability to adjust (entrain) to the environment, with light being the most important signal. Whereas Cryptochrome-mediated entrainment is well understood in Drosophila, integration of light information via the visual system lacks a neuronal or molecular mechanism. Here we show that a single photoreceptor sub-type is essential for long day adaptation. These cells activate key circadian neurons, namely the lLNvs, which release the neuropeptide PDF. Using a cell-specific CRISPR/Cas9 assay, we show that PDF directly interacts with neurons important for evening (E) activity timing. Interestingly, this pathway is specific for light entrainment and appears to be dispensable in constant darkness (DD). The results therefore indicate that external cues cause a rearrangement of neuronal hierarchy, which is a novel form of plasticity.

neuroscience↗

bioRxiv2018

Stress alters social behavior and sensitivity to pharmacological activation of kappa opioid receptors in an age-specific manner in Sprague Dawley rats

The dynorphin/kappa (DYN/KOR) system has been identified as a primary target of stress due to behavioral effects, such as dysphoria, aversion, and anxiety-like alterations that result from activation of this system. Numerous adaptations in the DYN/KOR system have also been identified in response to stress. However, whereas most studies examining the function of the DYN/KOR system have been conducted in adults, there is growing evidence suggesting that this system is ontogenetically regulated. Likewise, the outcome of exposure to stress also differs across ontogeny. Based on these developmental similarities, the objective of this study was to systematically test effects of a selective KOR agonist, U62066, on various aspects of social behavior across ontogeny in non-stressed male and female rats as well as in males and females with a prior history of repeated exposure to restraint (90 min/day, 5 exposures). We found that the social consequences of repeated restraint differed as a function of age: juvenile stress produced substantial increases in play fighting, whereas adolescent and adult stress resulted in decreases in social investigation and social preference. The KOR agonist U62066 dose-dependently reduced social behaviors in non-stressed adults, producing social avoidance at the highest dose tested, while younger animals displayed reduced sensitivity to this socially suppressing effect of U62066. Interestingly, in stressed animals, the socially suppressing effects of the KOR agonist were blunted at all ages, with juveniles and adolescents exhibiting increased social preference in response to certain doses of U62066. Taken together, these findings support the hypothesis that the DYN/KOR system changes with age and differentially responds and adapts to stress across development.

neuroscience↗

bioRxiv2018

RsmV a small non-coding regulatory RNA in Pseudomonas aeruginosa that sequesters RsmA and RsmF from target mRNAs

The Gram-negative opportunistic pathogen Pseudomonas aeruginosa has distinct genetic programs that favor either acute or chronic virulence gene expression. Acute virulence is associated with twitching and swimming motility, expression of a type III secretion system (T3SS), and the absence of alginate, Psl, or Pel polysaccharide production. Traits associated with chronic infection include growth as a biofilm, reduced motility, and expression of a type VI secretion system (T6SS). The Rsm post-transcriptional regulatory system plays an important role in the inverse control of phenotypes associated with acute and chronic virulence. RsmA and RsmF are RNA-binding proteins that interact with target mRNAs to control gene expression at the post-transcriptional level. Previous work found that RsmA activity is controlled by at least three small, non-coding regulatory RNAs (RsmW, RsmY, and RsmZ). In this study, we took an in-silico approach to identify additional sRNAs that might function in the sequestration of RsmA and/or RsmF and identified RsmV, a 192 nt transcript with four predicted RsmA/RsmF consensus binding sites. RsmV is capable of sequestering RsmA and RsmF in vivo to activate translation of tssA1, a component of the T6SS, and to inhibit T3SS gene expression. Each of the predicted RsmA/RsmF consensus binding sites contribute to RsmV activity. Electrophoretic mobility shifts assays show that RsmF binds RsmV with >10-fold higher affinity than RsmY and RsmZ. Gene expression studies revealed that the temporal expression pattern of RsmV differs from RsmW, RsmY, and RsmZ. These findings suggest that each sRNA may play distinct roles in controlling RsmA and RsmF activity.\n\nIMPORTANCEThe role of RsmF in post-transcriptional control of gene expression remains enigmatic. While numerous rsmA-dependent phenotypes are more pronounced in an rsmAF double mutant, deletion of rsmF alone has only modest effects. Understanding mechanisms that control RsmF activity will provide insight into additional roles for RsmF. In the current study we identify RsmV as an sRNA that controls RsmA and RsmF activity, and show that RsmV, RsmW, RsmY, and RsmZ are differentially expressed during growth.

microbiology↗

bioRxiv2017

Interactive Biology Cloud Lab Enables Authentic Inquiry-Based Science Learning At MOOC Scale

The Next Generation Science Standards (NGSS) and other national frameworks are calling for much more sophisticated approaches to STEM education, centered around the integration of complex experimentation (including real labs, not just simulations), data collection and analysis, modeling, and data-driven argumentation, i.e., students can behave like real scientists. How to implement such complex approaches in scalable ways is an unsolved challenge - both for presential and distance education. Here we report on the iterative design and large-scale deployment of an open online course with a \"biology cloud experimentation lab\" (using living cells) that engaged remote learners (> 300 students) in the scientific practices of experimentation, modeling and data analysis to investigate the phototaxis of a microorganism. We demonstrate (1) the robustness and scalability of the cloud lab technology (> 2, 300 experiments run), (2) the design principles and synergistic integration of multiple UI and learning activities and suitable data formats to facilitate NGSS-aligned science activities, and (3) design features that leverages the natural variability of real biology experiments to instigate authentic inquiry. This platform and course content are now suited for large-scale adaptation in formal K-16 education; and we provide recommendations for inquiry-based science learning in general.

scientific communication and education↗

bioRxiv2017

Age-Related Differences In The Influence Of Task-Irrelevant Information On The Neural Bases Of Phonological And Semantic Processes

Although aging is often associated with cognitive decline, there is considerable variability among individuals and across domains of cognition. Within language, several indicators of semantic processing show stability throughout the lifespan. However, older adults have increased difficulty with phonological aspects of language, especially in language production. While these behavioral patterns are established, the neurobiology associated with these behaviors are less clear. Previously we have shown that, older adults were slower and less accurate in phonological compared to semantic decisions, and that older adults didnt exhibit brain-behavior relationships. In the present study, we examined phonological and semantic processes in the presence of task-irrelevant information. Older and younger adults made phonological and semantic decisions about pictures in the presence of either phonologically-related or semantically-related words, which were unrelated to the task. Behavioral results indicated that overall older adults had slower reaction times and lower accuracy compared to younger adults, and that all adults were less efficient when making phonological compared to semantic decisions. Patterns of brain activation for the semantic condition showed that all adults engaged typical left-hemisphere language regions, and that this activation was positively correlated with efficiency. In contrast, the phonological condition elicited activation in bilateral precuneus and cingulate, but only younger adults showed a significant relationship between activation and efficiency. Our results suggest that the relationship between behavior and neural activation when processing phonological information declines with age, but that the core semantic system continues to be engaged throughout the lifespan, even in the presence of task-irrelevant information.

neuroscience↗