Biology subjects

Miller, J. B.

Publications and source records attributed to Miller, J. B..

12 recordsLinked to original sources

bioRxiv2026

UP-REGULATION OF SYNAPTOBREVIN-2 TO DELAY AGE-RELATED COGNITIVE IMPAIRMENT

The slowing of executive function and memory impairment are the leading hallmarks of cognitive decline with age. The exact cause of this change is unknown and is the focus of aging research. Expression levels of Vesicle Associated Membrane Protein 2 (VAMP2)/Synaptobrevin-2 (syb2) are decreased with age. Here we report results from a novel transgenic mouse model (TgV2) that overexpresses syb2. We hypothesized that overexpression of syb2 improves synaptic function during aging, thus it delays dementia. Aged TgV2 mice, which maintained syb2 levels, performed better in spatial memory tests than 2-year-old WT control mice, which had lost half of syb2 due aging. In hippocampal CA1 synapses of aged TgV2 mice, long-term potentiation was increased. These effects of maintained syb2 levels were beneficial for both males and females providing improved synaptic plasticity. These results indicate that overexpression of syb2 supports cognitive function throughout the aging process and better resist age-related synaptic dysfunction.

neuroscience↗

bioRxiv2025

Self-assembling protein materials with genetically programmable morphology and size

Materials are challenging to synthetically program down to the atom level. Nature, however, excels at creating hierarchical materials from nanoscale building blocks, a feat that remains a major challenge in synthetic systems. A deeper understanding of the molecular rules governing self-assembly would unlock the potential for designing genetically programmable materials with atomic precision. Hexameric bacterial microcompartment (BMC-H) proteins offer a powerful model system for exploring this question. These sequence-defined proteins naturally assemble into complex architectures and can be expressed biologically, making them ideal candidates for studying how minor sequence variations influence supramolecular structure. In this work, we leverage cell-free protein synthesis (CFPS) alongside immunostaining and super-resolution microscopy to investigate the self-assembly behavior of two BMC-H proteins, PduA and PduJ. We find that both proteins form micro-to millimeter scale structures when expressed in vitro. Further, we demonstrate how single point mutation changes lead PduA and PduJ to form significantly different supramolecular structures when produced using CFPS. These studies support the future exploration of self-assembling proteins as programmable scaffolds in broad materials applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/666636v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@3376faorg.highwire.dtl.DTLVardef@c81730org.highwire.dtl.DTLVardef@6a6a5borg.highwire.dtl.DTLVardef@6cb4ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Sequencing the gaps: dark genomic regions persist in CHM13 despite long-read advances

Comprehensive genomic analysis is essential for advancing our understanding of human genetics and disease. However, short-read sequencing technologies are inherently limited in their ability to resolve highly repetitive, structurally complex, and low-mappability genomic regions, previously coined as "dark" regions. Long-read sequencing technologies, such as PacBio and Oxford Nanopore Technologies (ONT), offer improved resolution of these regions, yet they are not perfect. With the advent of the new Telomere-to-Telomere (T2T) CHM13 reference genome, exploring its effect on dark regions is prudent. In this study, we systematically analyze dark regions across four human genome references--HG19, HG38 (with and without alternate contigs), and CHM13--using both short- and long-read sequencing data. We found that dark regions increase as the reference becomes more complete, especially dark-by-MAPQ regions, but that long-read sequencing significantly reduces the number of dark regions in the genome, particularly within gene bodies. However, we identify potential alignment challenges in long-read data, such as centromeric regions. These findings highlight the importance of both reference genome selection and sequencing technology choice in achieving a truly comprehensive genomic analysis.

bioinformatics↗

bioRxiv2025

Systematic contextual biases in SegmentNT relevant to all nucleotide transformer models

Recent advances in large language models (LLMs) have extended to genomic applications, yet model robustness relative to context is unclear. Here, we demonstrate two intrinsic biases (input sequence length and nucleotide position) affecting SegmentNT results, a model included with the Nucleotide Transformer that provides nucleotide-level predictions of biological features. We demonstrate that nucleotide position within the input sequence (beginning, middle, or end) alters the nature of SegmentNTs raw prediction probabilities, which can be standardized to improve prediction consistency. While longer input sequence length improves model performance, diminishing returns suggest a surprisingly small input length of [~]3,072 nucleotides might be sufficient for many applications. We further identify a 24-nucleotide periodic oscillation in SegmentNTs prediction probabilities, revealing an intrinsic bias potentially linked to the models training tokenization (6-mers) and architecture. We identify potential approaches to account for these biases and provide generalizable insights for utilizing nucleotide-resolution functional prediction models.

bioinformatics↗

bioRxiv2025

Ramp sequence may explain synonymous variant association with Alzheimer's disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA)

BACKGROUNDSynonymous variant NC_000007.14:g.100373690T>C (rs2405442:T>C) in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA) gene was previously associated with decreased risk for Alzheimers disease (AD) in genome-wide association studies, but its biological impact is largely unknown. OBJECTIVEWe hypothesized that rs2405442:T>C decreases mRNA and protein levels by destroying a ramp of slowly translated codons at the 5 end of PILRA. METHODSWe assessed rs2405442:T>C predicted effects on PILRA through quantitative polymerase chain reactions (qPCR) and enzyme-linked immunosorbent assays (ELISA) using Chinese hamster ovary (CHO) cells. RESULTSBoth mRNA (P=1.9184 x 10-13) and protein (P=0.01296) levels significantly decreased in the mutant versus the wildtype in the direction that we predicted based on destroying a ramp sequence. CONCLUSIONSWe show that rs2405442:T>C alone directly impacts PILRA mRNA and protein expression, and ramp sequences may play a role in regulating AD-associated genes without modifying the protein product. Research in ContextO_LISystematic review: Genetic variants identified through genome-wide association studies often lack biological support for their association with Alzheimers disease. Although synonymous variant rs2405442:T>C in PILRA was previously reported as protective against Alzheimers disease, its effects have generally been attributed to linkage with missense variant, rs1859788:A>G. C_LIO_LIInterpretation: We show that rs2405442:T>C alone decreases mRNA and protein levels by destroying a ramp of slowly translated codons at the beginning of PILRA. We also show that a ramp sequence is present in PILRA and likely regulates mRNA and protein levels, thus offering a plausible biological mechanism explaining rs2405442:T>C association with Alzheimers disease independent of rs1859788:A>G. C_LIO_LIFuture directions: We provide the first protocol to evaluate how disease-associated variants impact ramp sequences, which could explain why some genetic variants are reported by genome-wide association studies. Future studies might examine if the ramp sequence could be therapeutically targeted to regulate PILRA expression without changing the protein product. C_LI

genetics↗

bioRxiv2023

Using deep long-read RNAseq in Alzheimer's disease brain to assess clinical relevance of RNA isoform diversity

Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimers disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples include WDR4 (61%; microcephaly), MYL3 (44%; hypertrophic cardiomyopathy), and MTHFS (25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms include CPLX2 (10%; schizophrenia, epilepsy) and MAOB (9%; targeted for Parkinsons disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimers disease genes such as APP (A{beta} precursor protein; five), MAPT (tau protein; four), and BIN1 (eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimers cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a "single" gene.

genomics↗

bioRxiv2022

CIPK-B is essential for salt stress signalling in Marchantia polymorpha

O_LICalcium signalling is central to many plant processes, with families of calcium decoder proteins having expanded across the green lineage and redundancy existing between decoders. The liverwort Marchantia polymorpha has fast become a new model plant, but it is unclear what calcium decoders exist in this species. C_LIO_LIWe have performed phylogenetic analyses to identify the Calcineurin B-Like (CBL) and CBL-Interacting Protein Kinase (CIPK) network of M. polymorpha. We analysed CBL-CIPK expression during salt stress, and determined protein-protein interactions using yeast two-hybrid and bimolecular fluorescence complementation. We also created genetic knockouts using CRISPR/Cas9. C_LIO_LIWe confirm that M. polymorpha has two CIPKs and three CBLs. Both CIPKs and only one CBL show salt-responsive transcriptional changes. All M. polymorpha CBL-CIPKs interact with each other in planta. Knocking out CIPK-B causes increased sensitivity to salt suggesting that this CIPK is involved in salt signalling. C_LIO_LIWe have identified CBL-CIPKs that form part of a salt tolerance pathway in M. polymorpha. Phylogeny and interaction studies imply that these CBL-CIPKs form an evolutionarily conserved Salt Overly Sensitive (SOS) pathway. Hence, salt responses may be some of the early functions of CBL-CIPK networks and increased abiotic stress tolerance required for land plant emergence. C_LI

plant biology↗

bioRxiv2022

RNA G-quadruplex structure contributes to cold adaptation in plants

Nucleotide composition is suggested to infer gene functionality and ecological adaptation of species to distinct environments. However, the underlying biological function of nucleotide composition dictating environmental adaptations is largely unknown. Here, we systematically analyzed the nucleotide compositions of transcriptomes across 1000 plants (1KP) and their corresponding habitats. Intriguingly, we found that plants growing in cold climates have guanine (G)-enriched transcriptomes, which are prone to forming RNA G-quadruplex structures. Both immunofluorescence detection and in vivo structure profiling revealed that RNA G-quadruplex formation in plants was globally enhanced in response to cold. Cold-responsive RNA G-quadruplexes strongly enhanced mRNA stability, rather than affecting translation. Disruption of individual RNA G-quadruplex promoted mRNA decay in the cold, leading to impaired plant cold response. Therefore, we propose that plants adopted RNA G-quadruplex structure as a molecular marker to facilitate their adaptation to the cold during evolution.

molecular biology↗

bioRxiv2020

A Comprehensive Analysis of the Phylogenetic Signal in Ramp Sequences in 211 Vertebrates

BackgroundRamp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. MethodsRamp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene. ResultsParsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a p-value of approximately zero as compared to random chance. DiscussionRamp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.

evolutionary biology↗

bioRxiv2019

Codon Pairs are Phylogenetically Conserved: Codon pairing as a new class of phylogenetic characters

Identical codon pairing and co-tRNA codon pairing increase translational efficiency within genes when two codons that encode the same amino acid are located within a ribosomal window. By examining both identical and co-tRNA codon pairing across 23 423 species, we determined that both pairing techniques are phylogenetically informative across all domains of life using either an alignment-free or parsimony framework. We also determined that conserved codon pairing typically has a smaller window size than the length of a ribosome. We also analyzed frequencies of codon pairing for each codon to determine which codons are most likely to pair. The alignment-free method does not require orthologous gene annotations and recovers species relationships that are comparable to other alignment-free techniques. Parsimony generally recovers phylogenies that are more congruent with the established phylogenies than the alignment-free method. However, four of the ten taxonomic groups do not have sufficient ortholog annotations and are therefore recoverable using only the alignment-free methods. Since the recovered phylogenies using only codon pairing largely match established phylogenies and are comparable to other algorithms, we propose that codon pairing biases are phylogenetically conserved and should be considered in conjunction with current techniques in future phylogenomic studies. Furthermore, the phylogenetic conservation of codon pairing indicates that codon pairing plays a greater role in the speciation process than previously acknowledged.\n\nAvailabilityAll scripts used to recover and compare phylogenies, including documentation and test files, are freely available on GitHub at https://github.com/ridgelab/codon_pairing.

evolutionary biology↗

bioRxiv2019

Codon Use and Aversion is Largely Phylogenetically Conserved Across the Tree of Life

Using parsimony, we analyzed codon usages across 12 337 species and 25 727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890 814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codons congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25 771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1 109x more likely to be congruent with species relationships in the OTL than would be expected by random chance. Using the OTL as a reference, we show that codon usage is phylogenetically conserved within orthologous genes in archaea, bacteria, plants, mammals, and other vertebrates. We also show how to use our provided framework to test different tree hypotheses by confirming the placement of turtles as sister taxa to archosaurs.\n\nAvailabilityAll scripts, a README, and necessary test files are freely available on GitHub at https://github.com/ridgelab/codon_congruence\n\nContactperry.ridge@byu.edu

evolutionary biology↗

bioRxiv2019

Failure to detect synergy between variants in transferrin and hemochromatosis and Alzheimer’s disease in large cohort

Alzheimers disease (AD) is the most common cause of dementia and, despite decades of effort, there is no effective treatment. In the last decade, many association studies have identified genetic markers that are associated with AD status. Two of these studies suggest that an epistatic interaction between variants rs1049296 in the Transferrin (TF) gene and rs1800562 in the Homeostatic Iron Regulator (HFE) gene, commonly known as \"the hemochromatosis gene\", is in genetic association with AD. TF and HFE are involved in the transport and regulation of iron in the brain, and disrupting these processes exacerbates AD pathology through increased neurodegeneration and oxidative stress. However, by using a significantly larger dataset from the Alzheimers Disease Genetics Consortium (ADGC), we fail to detect an association between TF rs1049296 or HFE rs1800562 with AD risk (TF rs1049296 p=0.38 and HFE rs1800562 p=0.40). In addition, logistic regression with an interaction term and a Synergy Factor Analysis (SFA) both failed to detect epistasis between TF rs1049296 and HFE rs1800562 (SF=0.94; p=0.48) in AD cases. Each of these analyses had sufficient statistical power (Power>0.99), suggesting that previously-reported associations may be the result of more complex epistatic interactions, genetic heterogeneity, or were false-positive associations due to limited sample sizes.

genetics↗