Biology subjects

Miller, Z.

Publications and source records attributed to Miller, Z..

10 recordsLinked to original sources

bioRxiv2026

A CURE for synthetic regulation of gene expression: Rapid screening of guide RNA efficacy as a framework for enabling undergraduate research in plant synthetic biology

Course-based Undergraduate Research Experiences (CUREs) have emerged as a transformative approach to science education, expanding access to authentic research opportunities beyond the traditional undergraduate research assistant (URA) training. By embedding research into a curriculum, CUREs engage a broad and diverse population of students in a classroom environment that emphasizes experimental design, data analysis, and scientific communication. However, this has been difficult to develop for fields such as plant synthetic biology due to the long timescales of plant transformation. One avenue around this problem is to utilize a recent innovation that enables high throughput and rapid screening of gRNA efficacy by leveraging viral-based delivery of guide RNAs (gRNAs). In this work, we develop and validate a CURE with undergraduate students at Colorado State University (CSU). Students worked in teams to design and test efficacy of gRNAs targeting a Cas9-based transcriptional repressor to different regions of the promoters of the three GIBBERELLIN INSENSITIVE 1 genes (GID1a, GID1b, and GID1c) in Arabidopsis thaliana. Over the semester, students generated and analyzed gene expression data to understand the efficiency of twelve new gRNAs. We further validated CURE student-identified gRNAs with an undergraduate research assistant (URA) that assessed target gene expression and phenotypic outcomes in stable transgenic lines expressing SynTF constructs with the strongest gRNAs from the class. We further describe the curriculum structure to facilitate adoption at other institutions and present student-generated datasets demonstrating the utility of ViN-based screening for identifying effective SynTF gRNAs for plant functional genomics and engineering.

synthetic biology↗

bioRxiv2025

Data-driven Cognitive Clusters in Persistent Developmental Dyslexia

Developmental dyslexia is a neurodevelopmental condition characterized by persistent reading difficulties despite adequate intelligence and educational opportunities. The cognitive underpinnings of dyslexia remain incompletely understood. Although multiple causal pathways have been proposed, there is a gap in studies that can reliably identify dyslexia subtypes based on comprehensive evaluations that go beyond measures of reading and phonology. We employed one of the largest detailed samples of children with developmental dyslexia resistant to intervention, consisting of 147 extensively phenotyped school-age children aged 7-14 years who were recruited from specialized schools for students with learning differences. We implemented data-driven analyses leveraging a comprehensive neuropsychological assessment to delineate cognitive subdomains and characterize the heterogeneity in the sample. Hierarchical clustering of 24 cognitive measures aided in constructing a framework to subsequently interpret emerging clusters. Four clusters emerged, predominantly associated with: Processing Speed & Executive Function, Visuospatial & Mathematical Reasoning, Phonological Manipulation, and Verbal Short-term Memory & Word Retrieval. Subsequent latent profile analysis identified two distinct dyslexia profiles: one characterized by marked difficulties in executive functioning and processing speed, and another displaying impairments primarily in verbal short-term memory and word retrieval relative to the other profile. Importantly, both profiles exhibited comparable severity of persistent reading difficulties despite their divergent cognitive profiles. These findings show that phenotypically similar reading impairments can arise from distinct underlying cognitive factors, emphasizing the role of comprehensive neuropsychological evaluation in developing tailored interventions for affected children.

neuroscience↗

bioRxiv2022

Cortical dynamics of speech feedback control in non-fluent Primary Progressive Aphasia

Primary Progressive Aphasia (PPA) is a clinical syndrome in which patients progressively lose speech and language abilities. The non-fluent variant of PPA (nfvPPA) is characterised by impaired motor speech and agrammatism. To date, no study in nfvPPA patients has either examined speech motor control behaviour or imaged the speech motor control network during vocal production. Here, we did this using a novel structure-function imaging approach integrating magnetoencephalographic imaging of neural oscillations with voxel-based morphometry (VBM). We examined task-induced non-phase-locked neural oscillatory activity during a vocal motor control task, where participants were prompted to phonate the vowel /{square}/ for [~]2.4s while the pitch of their auditory feedback was shifted either up or down by 100 cents for a period of 400ms mid-utterance. Participants were 18 nfvPPA patients (14 female, mean age = 67.79 {+/-} 8.02 years) and 17 controls (13 female, mean age = 64.81 {+/-} 5.76 years). Patients showed a smaller compensation response to pitch perturbation than controls (p < 0.05). Task-induced neural oscillations across five frequency bands were reconstructed in source space for each subject during pitch feedback perturbation. Patients exhibited reduced task-induced alpha-band (8-12Hz) neural activity unrelated to their atrophy patterns, in the right temporal lobe and the right temporoparietal junction (p < 0.01) from 250ms to 750ms after pitch perturbation onset. Patients also showed increased task-induced beta-band (12-30Hz) activity also unrelated to cortical atrophy in the left dorsal sensorimotor cortex, left premotor cortex and the left supplementary motor area (p < 0.01) from 50ms to 150ms after pitch perturbation onset. Reduced average alpha-band power at the peak voxel in the temporoparietal cluster in the right hemisphere could predict speech motor impairment in patients ({beta} = 3.41, F = 8.31, p = 0.0128) whereas increased average beta-band power at the peak voxel in the left dorsal sensorimotor cluster could not ({beta} = -1.75, F = 1.72, p = 0.2123). Collectively, these results suggest significant disruption in sensorimotor integration during vocal production in nfvPPA patients which occurs unrelated to patterns of atrophy. These findings highlight how multimodal structure-function imaging in PPA enhances our understanding of its pathophysiological sequelae.

neuroscience↗

bioRxiv2020

Neural dynamics of semantic categorization in semantic variant of Primary Progressive Aphasia.

Semantic representations are processed along a posterior-to-anterior gradient reflecting a shift from perceptual (e.g., it has eight legs) to conceptual (e.g., venomous spiders are rare) information. One critical region is the anterior temporal lobe (ATL): patients with semantic variant primary progressive aphasia (svPPA), a clinical syndrome associated with ATL neurodegeneration, manifest a deep loss of semantic knowledge. We test the hypothesis that svPPA patients perform semantic tasks by over-recruiting areas implicated in perceptual processing. We compared MEG recordings of svPPA patients and healthy controls during a categorization task. While behavioral performance did not differ, svPPA patients showed indications of greater activation over bilateral occipital cortices and superior temporal gyrus, and inconsistent engagement of frontal regions. These findings suggest a pervasive reorganization of brain networks in response to ATL neurodegeneration: the loss of this critical hub leads to a dysregulated (semantic) control system, and defective semantic representations are seemingly compensated via enhanced perceptual processing. Impact StatementFollowing anterior temporal lobe neurodegeneration, defective semantic representations are compensated via enhanced perceptual processing and associated with a dysregulation of the semantic control system.

neuroscience↗

bioRxiv2019

Taking the sub-lexical route: brain dynamics of reading in the semantic variant of Primary Progressive Aphasia.

Reading aloud requires mapping an orthographic form to a phonological one. The mapping process relies on sub-lexical statistical regularities (e.g., "oo" to |u{square}|) or on learned lexical associations between a specific visual form and a series of sounds (e.g., yacht to /j{square}t/). Computational, neuroimaging, and neuropsychological evidence suggest that sub-lexical, phonological and lexico-semantic processes rely on partially distinct neural substrates: a dorsal (occipito-parietal) and a ventral (occipito-temporal) route, respectively. Here, we investigated the spatiotemporal features of orthography-to-phonology mapping, capitalizing on the time resolution of magnetoencephalography and the unique clinical model offered by patients with semantic variant of Primary Progressive Aphasia (svPPA). Behaviorally, svPPA patients manifest marked lexico-semantic impairments including difficulties in reading words with exceptional orthographic to phonological correspondence (irregular words). Moreover, they present with focal neurodegeneration in the anterior temporal lobe (ATL), affecting primarily the ventral, occipito-temporal, lexical route. Therefore, this clinical population allows for testing of specific hypotheses on the neural implementation of the dualroute model for reading, such as whether damage to one route can be compensated by over-reliance on the other. To this end, we reconstructed and analyzed time-resolved whole-brain activity in 12 svPPA patients and 12 healthy age-matched controls while reading irregular words (e.g., yacht) and pseudowords (e.g., pook). Consistent with previous findings that the dorsal route is involved in sub-lexical, phonological processes, in control participants we observed enhanced neural activity over dorsal occipito-parietal cortices for pseudowords, when compared to irregular words. This activation was manifested in the beta-band (12-30 Hz), ramping up slowly over 500 ms after stimulus onset and peaking at [~]800 ms, around response selection and production. Consistent with our prediction, svPPA patients did not exhibit this temporal pattern of neural activity observed in controls this contrast. Furthermore, a direct comparison of neural activity between patients and controls revealed a dorsal spatiotemporal cluster during irregular word reading. These findings suggest that the sub-lexical/phonological route is involved in processing both irregular and pseudowords in svPPA. Together these results provide further evidence supporting a dual-route model for reading aloud mediated by the interplay between lexico-semantic and sub-lexical/phonological neuro-cognitive systems. When the ventral route is damaged, as in the case of neurodegeneration affecting the ATL, partial compensation appears to be possible by over-recruitment of the slower, serial attention-dependent, dorsal one. Abbreviated SummaryBorghesani et al. investigate brain dynamics during irregular word reading using magnetoencephalographic imaging in patients with semantic variant of primary progressive aphasia. Due to ventral anterior temporal lobe neurodegeneration, patients show greater reliance of dorsal, occipito-parietal brain regions - providing novel evidence for the interplay between ventral and dorsal routes for reading.

neuroscience↗

bioRxiv2019

Regional and hemispheric susceptibility of the temporal lobe to FTLD-TDP-43-C pathology

Post-mortem studies show that focal anterior temporal lobe (ATL) neurodegeneration is most often caused by frontotemporal lobar degeneration TDP-43 type C pathology. Clinically, these patients are described with different terms, such as semantic variant primary progressive aphasia (svPPA), semantic dementia (SD), or right temporal variant frontotemporal dementia (FTD) depending on whether the predominant symptoms affect language, semantic knowledge for object or people, or socio-emotional behaviors. ATL atrophy presents with various degrees of lateralization, with right-sided cases considered rarer even though estimation of their prevalence is hampered by the paucity of studies on well-characterized, pathology-proven cohorts. Moreover, it is not clear whether left and right variants show a similar distribution of atrophy within the ATL cross-sectionally and longitudinally. Here we study the largest cohort to-date of pathology-proven TDP-43-C cases diagnosed during life as svPPA, SD or right temporal variant FTD. We analyzed clinical, cognitive, and neuroimaging data from 30 cases, a subset of which was followed longitudinally. Guided by recent structural and functional parcellation studies, we constructed four bilateral ATL regions of interest (ROIs). The computation of an atrophy lateralization index allowed the comparison of atrophy patterns between the two hemispheres. This led to an automatic, imaging-based classification of the cases as left-predominant or right-predominant. We then compared the two groups in terms of regional atrophy patterns within the ATL ROIs (cross-sectionally) and atrophy progression (longitudinally). Results showed that 40% of pathology proven cases of TDP-43-C diagnosed with a temporal variant presented with right-lateralized atrophy. Moreover, the findings of our ATL ROI analysis indicated that, irrespective of atrophy lateralization, atrophy distribution within both ATLs follows a medial-to-lateral gradient. Finally, in both left and right cases, atrophy appeared to progress to the contralateral ATL, and from the anterior temporal pole to posterior temporal and orbitofrontal regions. Taken together, our findings indicate that incipient right predominant ATL atrophy is common in TDP-43-C pathology, and that distribution of damage within the ATLs appears to be the same in left- and right- sided variants. Thus, regardless of differences in clinical phenotype and atrophy lateralization, both temporal variants of FTD should be viewed as a spectrum presentation of the same disease. Highlights Anterior temporal lobe (ATL) degeneration is most often caused by FTLD-TDP type C pathology Cases can present with predominantly left (60%) or right (40%) ATL atrophy Within ATLs, medial regions are more vulnerable than lateral ones The observed spectrum of clinical phenotypes is driven by atrophy lateralization Left and right temporal variants of FTD should be considered the same disease

neuroscience↗

bioRxiv2019

A sorghum Practical Haplotype Graph facilitates genome-wide imputation and cost-effective genomic prediction

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, we developed a sorghum Practical Haplotype Graph (PHG) pangenome database that stores all identified haplotypes and variant information for a given set of individuals. We developed two PHGs in sorghum, one with 24 individuals and another with 398 individuals, that reflect the diversity across genic regions of the sorghum genome. 24 founders of the Chibas sorghum breeding program were sequenced at low coverage (0.01x) and processed through the PHG to identify genome-wide variants. The PHG called SNPs with only 5.9% error at 0.01x coverage - only 3% lower than its accuracy when calling SNPs from 8x coverage sequence. Additionally, 207 progeny from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes in the progeny were imputed from the parental haplotypes available in the PHG and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from 0.57-0.73 for different traits, and are similar to prediction accuracies obtained with genotyping-by-sequencing (GBS) or markers from sequencing targeted amplicons (rhAmpSeq). This study provides a proof of concept for using a sorghum PHG to call and impute SNPs from low-coverage sequence data and also shows that the PHG can unify genotype calls from different sequencing platforms. By reducing the amount of input sequence needed, the PHG has the potential to decrease the cost of genotyping for genomic selection, making GS more feasible and facilitating larger breeding populations that can capture maximum recombination. Our results demonstrate that the PHG is a useful research and breeding tool that can maintain variant information from a diverse group of taxa, store sequence data in a condensed but readily accessible format, unify genotypes from different genotyping methods, and provide a cost-effective option for genomic selection for any species.

genomics↗

bioRxiv2019

Alzheimer's disease clinical variants show distinct regional patterns of neurofibrillary tangle accumulation

BackgroundNeurofibrillary tangle (NFT) pathology in Alzheimers disease (AD) follows a stereotypic progression well-characterized by Braak staging. However, some AD cases show deviations from the Braak staging scheme. In this study, we tested the hypothesis that these variations in the regional distribution of tau pathology are linked to heterogeneity in the clinical phenotypes of AD. MethodsWe included a clinicopathological cohort of ninety-four AD cases enriched for atypical clinical presentations. Subjects underwent apolipoprotein E (APOE) genotyping and neuropsychological testing. Main cognitive domains (executive, visuospatial, language, and memory function) were assessed using an established composite z-score. We assessed NFT density and distribution from thioflavin S fluorescent microscopy throughout four neocortical and two hippocampal regions. A mathematical algorithm classifying AD cases into typical, hippocampal sparing (HpSp), and limbic predominant (LP) subtypes based on regional NFT burden was compared to unbiased hierarchical clustering for cases with Braak stage > IV. ResultsPatients diagnosed with logopenic primary progressive aphasia showed significantly higher NFT density in the superior temporal gyrus relative to patients diagnosed with Alzheimer-type dementia (p = 0.0091), while patients with corticobasal syndrome showed significantly higher NFT density in the primary motor cortex (p = 0.0205). Hierarchical clustering identified three discrete clusters of patients characterized respectively by low overall NFT burden (n = 18), high overall burden (n = 30), and cortical-predominant burden (n = 24). A regionally specific effect was observed for visuospatial ability; higher NFT density in the angular gyrus ({beta} = - 0.0921, p = 0.0099) and in the CA1 sector of the hippocampus ({beta} = -0.0735, p = 0.0380) was significantly associated with more severe visuospatial dysfunction, modulated by age of death. ConclusionsOur results suggest domain-specific functional consequences of regional NFT accumulation. In particular, we observed focal aggregation of NFT density in clinically relevant regions among different clinical AD variants. Continued work to map the regionally specific clinical consequences of tau accumulation presents an opportunity to increase understanding of disease mechanisms underlying atypical clinical manifestations.

pathology↗

bioRxiv2017

Comparison of one-stage and two-stage genome-wide association studies

Linear mixed models are widely used in humans, animals, and plants to conduct genome-wide association studies (GWAS). A characteristic of experimental designs for plants is that experimental units are typically multiple-plant plots of families or lines that are replicated across environments. This structure can present computational challenges to conducting a genome scan on raw (plot-level) data. Two-stage methods have been proposed to reduce the complexity and increase the computational speed of whole-genome scans. The first stage of the analysis fits raw data to a model including environment and line effects, but no individual marker effects. The second stage involves the whole genome scan of marker tests using summary values for each line as the dependent variable. Missing data and unbalanced experimental designs can result in biased estimates of marker association effects from two-stage analyses. In this study, we developed a weighted two-stage analysis to reduce bias and improve power of GWAS while maintaining the computational efficiency of two-stage analyses. Simulation based on real marker data of a diverse panel of maize inbred lines was used to compare power and false discovery rate of the new weighted two-stage method to single-stage and other two-stage analyses and to compare different two-stage models. In the case of severely unbalanced data, only the weighted two-stage GWAS has power and false discovery rate similar to the one-stage analysis. The weighted GWAS method has been implemented in the open-source software TASSEL.

genetics↗

bioRxiv2016

A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

Modulating days to flowering is a key mechanism in plants for adapting to new environments, and variation in days to flowering drives population structure by limiting mating. To elucidate the genetic architecture of flowering across maize, a quantitative trait, we mapped flowering in five global populations, a diversity panel (Ames) and four half-sib mapping designs, Chinese (CNNAM), US (USNAM), and European Dent (EUNAM-Dent) and Flint (EUNAM-Flint). Using whole-genome projected SNPs, we tested for joint association using GWAS, resampling GWAS and two regional approaches; Regional Heritability Mapping (RHM) (1, 2) and a novel method, Boosted Regional Heritability Mapping (BRHM). Direct overlap in significant regions detected between populations and flowering candidate genes was limited, but whole-genome cross-population predictive abilities were [≤]0.78. Poor predictive ability correlated with increased population differentiation (r = 0.41), unless the parents were broadly sampled from across the North American temperate-tropical germplasm gradient; uncorrected GWAS results from populations with broadly sampled parents were well predicted by temperate-tropical FSTs in machine learning. Machine learning between GWAS results also suggested shared architecture between the American panels and, more distantly, the European panels, but not the Chinese panel. Machine learning approaches can reconcile non-linear relationships, but the combined predictive ability of all of the populations did not significantly enhance prediction of physiological candidates. While the North American-European temperate adaption is well studied, this study suggest independent temperate adaptation evolved in the Chinese panel, most likely in China after 1500, a finding supported by differential gene ontology term enrichment between populations.

genetics↗