Biology subjects

Hernandez, L. M.

Publications and source records attributed to Hernandez, L. M..

10 recordsLinked to original sources

bioRxiv2025

Integrating image-based phenotyping and GWAS to map tolerance to Spittlebug nymphs in interspecific Urochloa grasses

Urochloa grasses are among the most widely used forage grasses across the tropics. Spittlebugs (Hemiptera: Cercopidae) are major pests of tropical Urochloa (syn. Brachiaria) pastures, severely reducing forage productivity and quality. Understanding the genetic basis of host-plant resistance is essential for developing durable resistant cultivars. Here, we combined high-throughput image-based phenotyping and genome-wide association studies (GWAS) to dissect the genetic architecture of tolerance to Aeneolamia varia nymphs in 339 interspecific F hybrids derived from crosses between resistant sexual and susceptible apomictic Urochloa parents. Digital image analysis using both unsupervised (DQU) and supervised (DTR) quantification pipelines enabled precise estimation of plant damage, yielding moderate to high broad-sense heritability estimates (H{superscript 2} = 0.49-0.66). In contrast, insect survival (NTS) exhibited low to moderate correlations with all damage traits and lower heritability estimates (H{superscript 2} = 0.42). Using 57,051 high-quality SNPs aligned to the genome of the hybrid cultivar Basilisk, GWAS models identified 18 quantitative trait loci (QTL) for plant damage traits, but none for insect survival (antibiosis). Six robust QTL on chromosomes 1, 6, 7, 27, 29, and 36 were consistently detected across models and phenotyping methods, explaining up to 21.5% of phenotypic variance. Candidate gene analysis revealed proteins involved in hormone signalling, oxidative stress response, and cell wall modification, suggesting multifaceted tolerance mechanisms. These results provide a foundational set of molecular markers associated with spittlebug tolerance in Urochloa, useful for marker-assisted and genomic selection in our forage breeding programme.

plant biology↗

bioRxiv2022

The molecular genetic landscape of human brain size variation

Human brain size increases dynamically through early development, peaks in adolescence, and varies up to two-fold among adults. Although previous studies have elucidated changes in brain size across evolution, development, traits, and diseases, the molecular underpinnings of interindividual variation in brain size remain unknown. Here, we leverage postmortem brain RNA sequencing and estimates of brain weight (BW) in 2,531 individuals across three independent datasets, to identify 928 genes that show genome-wide significant associations with either higher or lower BW (BW+, BW-, respectively). These BW gene sets showed distinct neurodevelopmental trajectories and spatial patterns that mapped onto developmental, functional and cellular axes of brain organization. Expression differences among evolutionarily conserved BW genes were predictive of interspecies differences in brain size, and functional annotation of BW genes revealed enrichment for neurogenesis and cell-cell communication. Genome-wide, transcriptome-wide, and phenome-wide association analyses of in vivo neuroimaging phenotypes confirmed that the genetic regulation of BW-transcripts influences cortical surface area and volume, as well as behavioral traits related to brain function and disease. Cumulatively, our study represents a major step towards the goal of delineating the causal mechanisms of human brain size variation in health and disease.

neuroscience↗

bioRxiv2022

TEMPRANILLO homologs in apple regulate flowering time in the woodland strawberry Fragaria vesca

Many economically valuable fruit trees belong to the Rosaceae family. The long juvenile period of fruit trees makes their breeding costly and time-consuming. Therefore, flowering time regulation and shortening the juvenile phase have been a breeding priority for genetic improvement of fruit tree crops. TEMPRANILLO genes act as floral inhibitors in Arabidopsis and so, two orthologs of this gene were isolated here from apple (Malus domestica) and functionally analysed in Arabidopsis and woodland strawberry by being overexpressed in both model plants, and partially silenced in strawberry. The overexpression of MdTEM genes down-regulated FvFT1, FvGA3OX1, and FvGA3OX2 genes in strawberry. The overexpression lines exhibited delayed flowering, both in terms of days to flowering and the number of leaves at flowering. RNAi-mediated silencing of TEM resulted in early flowering plants. These plants flowered approximately five days earlier than wild type plants with a lower number of leaves. However, the overexpression of MdTEM genes could not functionally rescue the Arabidopsis mutants. According to the results, it can be concluded that MdTEM1 and MdTEM2 are orthologs of FvTEM gene, which play an important role in regulating the juvenile phase and flowering time through controlling FT and GA biosynthetic gene expression.

plant biology↗

bioRxiv2021

White matter microstructure shows sex differences in late childhood: Evidence from 6,797 children

Sex differences in white matter microstructure have been robustly demonstrated in the adult brain using both conventional and advanced diffusion-weighted magnetic resonance imaging (dMRI) approaches. However, sex differences in white matter microstructure prior to adulthood remain poorly understood; previous developmental work focused on conventional microstructure metrics and yielded mixed results. Here we rigorously characterized sex differences in white matter microstructure among over 6,000 children from the Adolescent Brain Cognitive Development (ABCD) Study who were between 9 and 10 years old. Microstructure was quantified using both the conventional model - diffusion tensor imaging (DTI) - and an advanced model, restriction spectrum imaging (RSI). DTI metrics included fractional anisotropy (FA) and mean, axial, and radial diffusivity (MD, AD, RD). RSI metrics included normalized isotropic, directional, and total intracellular diffusion (N0, ND, NT). We found significant and replicable sex differences in DTI or RSI microstructure metrics in every white matter region examined across the brain. Sex differences in FA were regionally specific. Across white matter regions, boys exhibited greater MD, AD, and RD than girls, on average. Girls displayed increased N0, ND, and NT compared to boys, on average, suggesting greater cell and neurite density in girls. Together, these robust and replicable findings provide an important foundation for understanding sex differences in health and disease.

neuroscience↗

bioRxiv2021

Flow cytometry-based determination of ploidy from dried leaf specimens in genomically complex collections of the tropical forage grass Urochloa s. l.

We aimed to develop an optimized approach to determine ploidy for dried leaf material in a germplasm collection of a tropical forage grass group, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. The methods enable robust identification of ploidy levels (coefficient of variation, CV, typically <5%). Ploidy of some 353 forage grass accessions (ploidy range from 2 to 9), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes used in the current breeding programs at CIAT and EMBRAPA: the brizantha and humidicola agamic complexes are variable, with multiple ploidy levels and DNA content. U. brizantha has odd level of ploidy (x=5), and the relative differences in nuclear DNA content between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed some aneuploidy.

genomics↗

bioRxiv2020

JAK1 palmitoylation by ZDHHC3/7 is Essential for Neuropoietic Cytokine Signaling and DRG Neuron Survival

Janus Kinase-1 (JAK1) plays key roles in pro-survival signaling during neurodevelopment and in responses to neuronal injury. JAK1 was identified as a potential palmitoyl-protein in high-throughput studies, but the importance of palmitoylation for JAK1s roles in neurons has not been addressed. Here, we report that JAK1 is endogenously palmitoylated in cultured Dorsal Root Ganglion (DRG) neurons and, using an shRNA knockdown/rescue approach, reveal that JAK1 palmitoylation is important for neuropoietic cytokine-dependent signaling and neuronal survival. We further identify the related palmitoyl acyltransferases (PATs) ZDHHC3 and ZDHHC7 as dominant regulators of JAK1 palmitoylation in transfected non-neuronal cells and endogenously in neurons. At the molecular level, palmitoylation is critical for JAK1s kinase activity in transfected cells and even in vitro, likely because palmitoylation facilitates transphosphorylation of key sites in the JAK1 activation loop. These findings provide new insights into palmitoylation-dependent control of neuronal development and survival.

neuroscience↗

bioRxiv2020

The Palmitoyl Acyltransferase ZDHHC14 Controls Kv1-Family Potassium Channel Clustering at the Axon Initial Segment

The palmitoyl acyltransferase (PAT) ZDHHC14 is highly expressed in the hippocampus and is the only PAT predicted to bind Type I PDZ domain-containing proteins. However, ZDHHC14s neuronal roles are unknown. Here, we identify the PDZ domain-containing Membrane-associated Guanylate Kinase (MaGUK) PSD93 as a direct ZDHHC14 interactor and substrate. PSD93, but not other MaGUKs, localizes to the Axon Initial Segment (AIS). Using lentiviral-mediated shRNA knockdown in rat hippocampal neurons, we find that ZDHHC14 controls palmitoylation and AIS clustering of PSD93 and also of Kv1 potassium channels, which directly bind PSD93. Neurodevelopmental expression of ZDHHC14 mirrors that of PSD93 and Kv1 channels and, consistent with ZDHHC14s importance for Kv1 channel clustering, loss of ZDHHC14 decreases outward currents and increases action potential firing in hippocampal neurons. To our knowledge, these findings identify the first neuronal roles and substrates for ZDHHC14 and reveal a previously unappreciated role for palmitoylation in control of neuronal excitability. Impact StatementZDHHC14 controls palmitoylation and axon initial segment targeting of PSD93 and Kv1-family potassium channels, events that are essential for normal neuronal excitability.

neuroscience↗

bioRxiv2020

Digital imaging outperforms traditional scoring methods of spittlebug tolerance in Urochloa humidicola hybrids

American spittlebug complex (Hemiptera: Cercopidae) is a critical pest for existing Urochloa humidicola cultivars in the neotropical savannas. The U. humidicola breeding program of the International Center for Tropical Agriculture aims to increase tolerance to spittlebugs. To develop U. humidicola genotypes with superior tolerance to spittlebugs than existing cultivars, adequate screening methods ought to be deployed. Currently, visual scores of plant damage by spittlebugs is the standard method to screen for variation in plant tolerance. However, visual scoring is prone to human bias, is of medium throughput and relies of the expertise of well-trained personnel. In this study, we compared estimations of plant damage from two alternative methods (SPAD measurements and digital images) and visual scoring from an inexpert evaluator with the plant damage estimated from an expert. This information should instruct if different methods could be implemented in the U. humidicola breeding program. Time needed to evaluate damage was recorded for each method. Lins correlation coefficient, Pearsons correlation coefficient and broad sense heritability values were also calculated. Overall, damage estimated from digital images showed the highest throughput (twice as fast as visual scoring from an expert); high correlations with visual scoring (r > 0.80, p < 0.0001); and heritability values for plant damage as good or better (> 0.7) than those obtained by visual scoring from an expert. Our results indicate that digital imaging is a phenotyping method that might improve the efficiency of breeding for increased tolerance to spittlebugs in U. humidicola. HighlightDigital imaging outperformed standard scoring method of spittlebug tolerance in Urochloa humidicola, suggesting that this method might improve the efficiency of breeding for such stress.

plant biology↗

bioRxiv2020

Network signature of complement component 4 variation in the human brain identifies convergent molecular risk for schizophrenia

The most significant common variant association for schizophrenia (SCZ) reflects increased expression of the complement component 4A (C4A). Yet, it remains unclear how C4A interacts with other SCZ risk genes and whether the complement system is more broadly implicated in SCZ pathogenesis. Here, we integrate several existing, large-scale genetic and transcriptomic datasets to interrogate the functional role of the complement system and C4A in the human brain. Surprisingly, we find no significant genetic enrichment among known complement system genes for SCZ. Conversely, brain co-expression network analyses using C4A as a seed gene revealed that genes down-regulated when C4A expression increased exhibit strong and specific genetic enrichment for SCZ risk. This convergent genomic signal reflected neuronal, synaptic processes and was sexually dimorphic and most prominent in frontal cortical brain regions. Overall, these results indicate that synaptic pathways--rather than the complement system--are the driving force conferring SCZ risk.

genomics↗

bioRxiv2019

Affective reactivity during adolescence: Associations with age, puberty and testosterone

Adolescence is a period of heightened social engagement that is accompanied by normative changes in neural reactivity to affective stimuli. It is also a period of concurrent endocrine and physical changes associated with puberty. A growing body of research suggests that hormonal shifts during adolescence impact brain development, but minimal research in humans has examined the relationship between intra-individual changes in puberty and brain function. The current study examines linear and nonlinear changes in affective reactivity in a longitudinal sample of 82 adolescents who underwent three fMRI sessions between the ages of 9 and 18 years. Changes in response to affective facial stimuli were related to age, pubertal stage, and testosterone levels. Using multilevel modelling, we highlight extensive nonlinear development of socio-emotional responsivity across the brain. Results include mid-pubertal peaks in amygdala and hippocampus response to fearful expressions, as well as sex differences in regions subserving social and self-evaluative processes. However, testosterone levels exhibited inverse patterns of association with neural response compared to pubertal stage in females (e.g. U-shaped relationship with the amygdala and hippocampus). Findings highlight potentially unique roles of age, pubertal stage and testosterone on socio-emotional development during adolescence, as well as sex differences in these associations.

neuroscience↗