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Biology subjects

Gomez, M. A.

Publications and source records attributed to Gomez, M. A..

5 recordsLinked to original sources

Naturalistic Object Representations Depend on Distance and Size Cues

Egocentric distance and real-world size are important cues for object perception and action. Nevertheless, most studies of human vision rely on two-dimensional pictorial stimuli that convey ambiguous distance and size information. Here, we use fMRI to test whether pictures are represented differently in the human brain from real, tangible objects that convey unambiguous distance and size cues. Participants directly viewed stimuli in two display formats (real objects and matched printed pictures of those objects) presented at different egocentric distances (near and far). We measured the effects of format and distance on fMRI response amplitudes and response patterns. We found that fMRI response amplitudes in the lateral occipital and posterior parietal cortices were stronger overall for real objects than for pictures. In these areas and many others, including regions involved in action guidance, responses to real objects were stronger for near vs. far stimuli, whereas distance had little effect on responses to pictures--suggesting that distance determines relevance to action for real objects, but not for pictures. Although stimulus distance especially influenced response patterns in dorsal areas that operate in the service of visually guided action, distance also modulated representations in ventral cortex, where object responses are thought to remain invariant across contextual changes. We observed object size representations for both stimulus formats in ventral cortex but predominantly only for real objects in dorsal cortex. Together, these results demonstrate that whether brain responses reflect physical object characteristics depends on whether the experimental stimuli convey unambiguous information about those characteristics. Significance StatementClassic frameworks of vision attribute perception of inherent object characteristics, such as size, to the ventral visual pathway, and processing of spatial characteristics relevant to action, such as distance, to the dorsal visual pathway. However, these frameworks are based on studies that used projected images of objects whose actual size and distance from the observer were ambiguous. Here, we find that when object size and distance information in the stimulus is less ambiguous, these characteristics are widely represented in both visual pathways. Our results provide valuable new insights into the brain representations of objects and their various physical attributes in the context of naturalistic vision.

neuroscience↗

CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production

Cassava (Manihot esculenta Crantz) is a starchy root crop that supports over a billion people in tropical and subtropical regions of the world. This staple, however, produces toxic cyanogenic compounds and requires processing for safe consumption. Excessive consumption of insufficiently processed cassava, in combination with protein-poor diets, can have neurodegenerative impacts. Reducing the cyanogen content by conventional breeding is problematic due to the heterozygous nature of the crop; recombination will generally disrupt a clonally propagated cultivars suite of desirable traits. To reduce cyanide levels in cassava, we used CRISPR-mediated mutagenesis to disrupt the cytochrome P450 genes CYP79D1 and CYP79D2 whose protein products catalyze the first step in cyanogenic glucoside biosynthesis. Knockout of both genes eliminated cyanide in leaves and storage roots of cassava accession 60444 and the West African, farmer-preferred cultivar TME 419. Although knockout of CYP79D2 alone resulted in significant reduction of cyanide, mutagenesis of CYP79D1 did not, indicating these paralogs have diverged in their function. Our work demonstrates cassava genome editing for food safety, reduced processing requirements, and environmental benefits that could be readily extended to other farmer-preferred cultivars.

plant biology↗

Exploring Leishmania-Host Interaction with Reactome, a Database of Biological Pathways and Processes

Leishmaniasis is a parasitic disease with a wide range of clinical manifestations. Multiple aspects of the Leishmania-host interaction, such as genetic factors and modulation of microbicidal functions in host cells, influence pathogenesis, disease severity and treatment outcome. How do scientists contend with this complexity? Here, we work towards representing detailed, contextual knowledge on Leishmania-host interactions in the Reactome pathway database to facilitate the extraction of novel mechanistic insights from existing datasets. The Reactome database uses a hierarchy of abstractions that allows for the incorporation of detailed contextual knowledge on biological processes matched to differentially expressed genes. It also includes tools for enhanced over-representation analysis that exploits this extra information. We conducted a systematic curation of published studies documenting different aspects of the Leishmania-host interaction. The "Leishmania infection pathway" included four sub-pathways: phagocytosis, killing mechanisms, cell recruitment, and Leishmania parasite growth and survival. As proof-of-principle of the usefulness of the released pathway, we used it to analyze two previously released transcriptomic datasets of human and murine macrophages infected with Leishmania. Our results provide insights on the participation of ADORA2B signaling pathway in the modulation of IL10 and IL6 in infected macrophages. This work opens the way for other researchers to contribute to, and make use of, the Reactome database. ImportanceLeishmaniasis is a neglected disease infectious disease which affects more than 1.5 million people annually. Many researchers in the field apply -omic technologies to dissect the basis of clinical and therapeutic outcomes and access drug targetable features in the host-parasite interaction, among others. However, getting mechanistic insights from -omics data to such end is not an easy task. The most common approach is to use the -omics data to inquire pathways databases. The retrieved list of pathways often contains vague names that lack the biological context. In this study, we worked to create the Leishmania infection pathway in the Reactome database. With two practical examples from transcriptomics and microarray data, we demonstrated how this pathway facilitates the analysis of such data. In both datasets, we found a common mechanism of IL10 and IL6 production that the authors did not advert in their previous analysis, providing proof-of-principle of the tools enhanced potential for knowledge extraction. Leishmania infection pathway is in its first version, and must be expanded to cover the current knowledge base of the Leishmania-host interaction. We strongly encourage contributions from domain experts for the completion of Leishmania infection pathways.

systems biology↗

Macrophage metallothioneins participate in the antileishmanial activity of antimonials

SYNOPSISO_ST_ABSBackgroundC_ST_ABSHost cell functions that participate in the pharmacokinetics and pharmacodynamics (PK/PD) of pentavalent antimonials for treatment of American cutaneous leishmaniasis (CL) are critical for drug efficacy. ObjectivesIn this study, we investigated whether macrophage mechanisms of xenobiotic detoxification contribute to drug-dependent elimination of intracellular Leishmania. MethodsTranscriptomes of primary macrophages from CL patients (n=6), exposed ex vivo to Leishmania infection and SbV were generated. Candidate genes were selected and validated using short harping RNA interference (shRNA) in THP-1 cells. ResultsStrong induction of metallothionein (MT) genes was observed upon Leishmania infection and exposure to SbV, with 7 MT genes (MT1 and MT2 family members) appearing within the top 20 up-regulated genes. Tandem knockdown (KD) of MT2-A and MT1-E, 1F, and 1X in THP-1 cells was achieved using a pan-MT shRNA., Intracellular parasite survival after SbV exposure was unaffected in tandem-KD cells, and this was a consequence of strong transcriptional upregulation of MTs by infection and SbV, overcoming the KD effect. Gene silencing of the metal transcription factor-1 (MTF-1) abrogated expression of MT1 and MT2-A genes. Upon exposure to SbV, intracellular survival of Leishmania in MTF-1KD cells was significantly enhanced (p [≤] 0.05). ConclusionsMTs are potent scavengers of heavy metals, and central elements of the mammalian cell machinery for xenobiotic detoxification. Results from this study highlight the participation of macrophage MTs in Sb-dependent parasite killing, revealing novel strategies for host-targeted optimization of antileishmanial drugs.

molecular biology↗

Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 confers elevated resistance to cassava brown streak disease

Cassava brown streak disease (CBSD) is a major constraint on cassava yields in East and Central Africa and threatens production in West Africa. CBSD is caused by two species of positive sense RNA viruses belonging to the family Potyviridae, genus Ipomovirus: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Diseases caused by the family Potyviridae require the interaction of viral genome-linked protein (VPg) and host eukaryotic translation initiation factor 4E (eIF4E) isoforms. Cassava encodes five eIF4E proteins: eIF4E, eIF(iso)4E-1, eIF(iso)4E-2, novel cap-binding protein-1 (nCBP-1), and nCBP-2. Protein-protein interaction experiments consistently found that VPg proteins associate with cassava nCBPs. CRISPR/Cas9-mediated genome editing was employed to generate ncbp-1, ncbp-2, and ncbp-1/ncbp-2 mutants in cassava cultivar 60444. Challenge with CBSV showed that ncbp-1/ncbp-2 mutants displayed delayed and attenuated CBSD aerial symptoms, as well as reduced severity and incidence of storage root necrosis. Suppressed disease symptoms were correlated with reduced virus titer in storage roots relative to wild-type controls. Our results demonstrate the ability to modify multiple genes simultaneously in cassava to achieve tolerance to CBSD. Future studies will investigate the contribution of remaining eIF4E isoforms on CBSD and translate this knowledge into an optimized strategy for protecting cassava from disease.

plant biology↗