Biology subjects

Koh, K.

Publications and source records attributed to Koh, K..

14 recordsLinked to original sources

bioRxiv2026

Lens species genome assemblies reveal evolutionarily fragile chromosomes associated with pericentric inversions

The genus Lens is comprised of seven diploid species, including the cultivated crop Lentil, and six wild relatives often used in breeding programs for beneficial allele introgression. Lens species are proposed to exhibit considerable levels of genome structural variation both within and between species, which has implications for plant breeding and evolutionary genomics. Plant centromeres are key regions involved in chromosomal stability, where structural changes can be linked to meiotic abnormalities, resulting in inversions, translocations, and deletions of chromosomal segments. Fabeae centromeres are known to be diverse and do not fit the centromere drive model. The origins of this centromere diversity and the evolutionary trends remain unclear, but recent studies suggest that centromere structural variation plays a role in creating new sequence combinations that contribute to the unique centromere evolution patterns observed in legumes. We sequenced, assembled, and performed gene synteny analysis in the genomes of all seven Lens species using long-read sequencing technologies. We also located and characterized the centromeres in these genomes through ChIP-seq experiments to better understand their role in Lens chromosomal stability. Synteny analysis reveals that Lens genomes have undergone extensive rearrangements during evolution, with multiple translocations and inversions identified between species. Specific Lens chromosomes appear more susceptible to rearrangements over time. These same chromosomes also exhibit higher rates of rearrangement throughout Lens speciation. Fragile chromosomes are associated with the occurrence of pericentric inversions, likely disrupting stability. The diversity in satellite sequences in Lens centromeres likely results from structural changes accumulated throughout Lens evolution. These findings suggest that genome and centromere structure play significant roles in generating centromere diversity within this legume genus.

genomics↗

bioRxiv2025

A new subgenome of the Camelina genus reveals genome dominance is controlled by chromosomal proximity

Camelina sativa is an oilseed of the Brassicaceae, whose close relatives vary in ploidy number, providing a novel platform for studying plant genome evolution. The availability of diploid, tetraploid and hexaploid species of Camelina allow the evolutionary trajectory and fate of duplicated genes in the neopolyploid Camelina species to be elucidated. Here we report an improved assembly of the widely used C. sativa reference DH55 and three new genome assemblies of Camelina microcarpa; one tetraploid CN119243 (2n = 26), and two hexaploids with divergent chromosome numbers, Type 1 - CN119205 (2n=40) and Type 2 - CN120025 (2n=38). The tetraploid represents the first step in the evolutionary path to form C. sativa, while the hexaploids suggest three divergent lineages in the formation of higher ploidy Camelina species. The previously uncharacterized fourth subgenome found in C. microcarpa Type 2, although showing some homology to the C. sativa diploid progenitor genome, C. neglecta, showed numerous unique chromosomal rearrangements differentiating it from other subgenomes present in known Camelina species. Although this species was recently formed, the second subgenome showed gene expression dominance, which was in contrast to both 2n=40 Camelina species where the third subgenome was dominant. The expression dominance in Type 2 C. microcarpa contradicted the accepted two-step evolutionary process which led to the generation of related Brassicaceae species. However, the observed genome dominance in all Camelina species was negatively correlated with inter-subgenome chromatin interaction frequencies, suggesting that chromosome confirmation and proximity in the nucleus contributes to this mechanism of genome evolution. Despite the differences in genome structure, successful inter-specific hybridization provided evidence of chromosomal exchange between the divergent third sub-genomes of C. sativa and C. microcarpa Type 2, opening up a novel avenue to new diversity in the established oilseed. Key pointsO_LIAn improved genomic understanding of Camelina species and identification of distinct subgenome structures and relationships, which will facilitate strategies to increase the genetic diversity in C. sativa. C_LIO_LISubgenome evolution and subgenome dominance in polyploids is associated with chromosomal architecture and proximity in the nucleus. C_LIO_LIGenome assemblies representing all ploidy levels in the Camelina genus provide a unique and valuable platform for polyploid research. C_LI

genomics↗

bioRxiv2025

Drosophila Pyruvate Kinase Links Metabolic State with Circadian Output via TARANIS and PDF

The circadian clock generates [~]24-hour rhythms that anticipate daily environmental changes. Circadian clock and glucose metabolism are tightly interconnected, and both are disrupted in aging and disease. To examine how glucose hypometabolism impacts circadian rhythm, we downregulated glycolytic enzymes - Hexokinase-C (Hex-C), Phosphofructokinase (Pfk), and Pyruvate kinase (Pyk) - in Drosophila clock cells. Only Hex-C and Pyk knock-down (KD) altered period, lengthening and shortening rhythms, respectively. Notably, Pyk KD induced period shortening persisted in adult-specific KD (AKD), indicating a role independent of developmental effects. Pyk AKD reduced both PERIOD and Pigment-dispersing factor (PDF) protein levels, with PDF loss driving the short-period phenotype. Mechanistically, the transcriptional co-regulator TARANIS (TARA) was required: Pyk AKD lowered tara expression, while tara overexpression rescued PDF and circadian period. Our findings identify a novel PYK-TARA-PDF regulatory axis linking glycolytic activity to circadian neuropeptide output, providing mechanistic insight into how metabolic dysfunction contributes to circadian disruption in aging and neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Increased neuronal activity restores circadian functionin Drosophila models of C9orf72-ALS/FTD

Circadian rhythm disruptions are common across neurodegenerative diseases, but their link to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) remains unclear. The C9orf72 hexanucleotide repeat expansion is the most prevalent genetic cause of ALS/FTD. Here, we used Drosophila models expressing toxic arginine-rich dipeptides (PR or GR) or GGGGCC hexanucleotide repeats to investigate circadian deficits in C9orf72-ALS/FTD. We found that circadian rhythmicity and period length were disrupted in a repeat number-, dosage-, and age-dependent manner. Additionally, we observed lower levels of the neuropeptide PDF, a key regulator of free-running circadian rhythms, as well as decreased projection complexity and reduced neuronal activity in PDF-expressing neurons. Importantly, increases in neuronal activity significantly restored circadian function under select conditions. These results implicate reduced neuronal activity in C9orf72-ALS/FTD circadian deficits, underscoring the importance of precisely tuned, circuit- and stage-specific interventions. HighlightsO_LIC9orf72 dipeptide and nucleotide repeats disrupt circadian rhythms in Drosophila C_LIO_LICircadian dysfunction with reduced PDF and neurites emerges before neuron loss C_LIO_LIIncreased neuronal activity rescues mild circadian dysfunction C_LIO_LIActivity-based rescue is effective across ages and models when precisely tuned C_LI

neuroscience↗

bioRxiv2024

Effects of sex, mating status, and genetic background on circadian behavior in Drosophila

Circadian rhythms play a crucial role in regulating behavior, physiology, and health. Sexual dimorphism, a widespread phenomenon across species, influences circadian behaviors. Additionally, post-mating physiological changes in females are known to modulate various behaviors, yet their effects on circadian rhythms remain underexplored. Here, using Drosophila melanogaster, a powerful model for studying circadian mechanisms, we systematically assessed the impact of sex and mating status on circadian behavior. We measured circadian period length and rhythm strength in virgin and mated males and females, including females mated to males lacking Sex Peptide (SP), a key mediator of post-mating changes. Across four wild-type and control strains, we found that males consistently exhibited shorter circadian periods than females, regardless of mating status, suggesting that circadian period length is a robust sexually dimorphic trait. In contrast, rhythm strength was influenced by the interaction between sex and mating status, with female mating generally reducing rhythm strength in the presence of SP signaling. Notably, genetic background significantly modulated these effects on rhythm strength. Our findings demonstrate that while circadian period length is a stable sex-specific trait, rhythm strength is shaped by a complex interplay between sex, mating status, and genetic background. This study advances our understanding of how sex and mating influence circadian rhythms in Drosophila and provides a foundation for future research into sexually dimorphic mechanisms underlying human diseases associated with circadian disruptions.

neuroscience↗

bioRxiv2024

Sleep induced by mechanosensory stimulation provides cognitive and health benefits in Drosophila

Study ObjectivesSleep is a complex phenomenon regulated by various factors, including sensory input. Anecdotal observations have suggested that gentle rocking helps babies fall asleep, and experimental studies have verified that rocking promotes sleep in both humans and mice. Recent studies have expanded this understanding, demonstrating that gentle vibration also induces sleep in Drosophila. Natural sleep serves multiple functions, including learning and memory, synaptic downscaling, and clearance of harmful substances associated with neurodegenerative diseases. Here, we investigated whether vibration-induced sleep provides similar cognitive and health benefits in Drosophila. MethodsWe administered gentle vibration to flies that slept very little due to a forced activation of wake-promoting neurons and investigated how the vibration influenced learning and memory in the courtship conditioning paradigm. Additionally, we examined the effects of VIS on synaptic downscaling by counting synapse numbers of select neurons. Finally, we determined whether vibration could induce sleep in Drosophila models of Alzheimers disease (AD) and promote the clearance of Amyloid {beta} (A{beta}) and Tubulin Associated Unit (TAU). ResultsVibration-induced sleep enhanced performance in a courtship conditioning paradigm and reduced the number of synapses in select neurons. Moreover, vibration improved sleep in Drosophila models of AD, promoting the clearance of A{beta} and TAU. ConclusionsMechanosensory stimulation offers a promising non-invasive avenue for enhancing sleep, potentially providing associated cognitive and health benefits. Significance StatementSleep is critical for a healthy mind and body, and sleep disturbances are commonly associated with neurodegenerative diseases such as Alzheimers disease. Sleep is influenced by sensory input, and mechanical stimulation, such as gentle rocking and vibration, has been shown to promote sleep in various species, including humans, mice, and fruit flies. This study demonstrates that gentle vibration not only helps flies sleep better but also improves their performance in a learning and memory task and makes their brains more efficient in clearing harmful substances. Notably, vibration can facilitate the clearance of Amyloid {beta} and the TAU proteins, which accumulate in Alzheimers disease. These results highlight the potential for gentle mechanosensory stimulation to promote sleep and cognitive health.

neuroscience↗

bioRxiv2023

TARANIS interacts with VRILLE and PDP1 to modulate the circadian transcriptional feedback mechanism in Drosophila

The molecular clock that generates daily rhythms of behavior and physiology consists of interlocked transcription-translation feedback loops. In Drosophila, the primary feedback loop involving the CLOCK-CYCLE transcriptional activators and the PERIOD-TIMELESS transcriptional repressors is interlocked with a secondary loop involving VRILLE (VRI) and PAR DOMAIN PROTEIN 1 (PDP1), a repressor and activator of Clock transcription, respectively. Whereas extensive studies have found numerous transcriptional, translational, and post-translational modulators of the primary loop, relatively little is known about the secondary loop. In this study, using male and female flies as well as cultured cells, we demonstrate that TARANIS (TARA), a Drosophila homolog of the TRIP-Br/SERTAD family of transcriptional coregulators, functions with VRI and PDP1 to modulate the circadian period and rhythm strength. Knocking down tara reduces rhythm amplitude and can shorten the period length, while overexpressing TARA lengthens the circadian period. Additionally, tara mutants exhibit reduced rhythmicity and lower expression of the PDF neuropeptide. We find that TARA can form a physical complex with VRI and PDP1, enhancing their repressor and activator functions, respectively. The conserved SERTA domain of TARA is required to regulate the transcriptional activity of VRI and PDP1, and its deletion leads to reduced locomotor rhythmicity. Consistent with TARAs role in enhancing VRI and PDP1 activity, overexpressing tara has a similar effect on the circadian period and rhythm strength as simultaneously overexpressing vri and Pdp1. Together, our results suggest that TARA modulates circadian behavior by enhancing the transcriptional activity of VRI and PDP1. Statement of SignificanceInternal molecular clocks generating circadian rhythms of around 24 hours broadly impact behavior and physiology, and circadian dysfunction is associated with various neurological and metabolic diseases. The Drosophila circadian clock is a valuable model for understanding the molecular mechanisms underlying daily rhythms as many components of the clock are highly conserved. In this study, we identify a conserved gene, taranis, as a novel regulator of the Drosophila molecular clock. We show that TARANIS modulates circadian behavior by physically interacting with and enhancing the transcriptional activity of clock proteins VRILLE and PDP1. Since mammalian homologs of VRILLE and PDP1 also function in the molecular clock, our results have implications for understanding the mammalian circadian clock.

neuroscience↗

bioRxiv2023

Modulation and Neural Correlates of Postmating Sleep Plasticity in Drosophila Females

Sleep is essential, but animals may forgo sleep to engage in other critical behaviors, such as feeding and reproduction. Previous studies have shown that female flies show decreased sleep after mating, but our understanding of the process is limited. Here, we report that postmating nighttime sleep loss is modulated by diet and sleep deprivation, demonstrating a complex interaction among sleep, reproduction, and diet. We also report that female-specific pC1 neurons and sleep-promoting dorsal fan-shaped body (dFB) neurons are required for postmating sleep plasticity. Activating pC1 neurons leads to sleep suppression on standard fly culture media but has little sleep effect on sucrose-only food. Published connectome data suggest indirect, inhibitory connections among pC1 subtypes. Using calcium imaging, we show that activating the pC1e subtype inhibits dFB neurons. We propose that pC1 and dFB neurons integrate the mating status, food context, and sleep drive to modulate postmating sleep plasticity. HighlightsO_LIDiet and sleep drive modulate female nighttime postmating sleep loss C_LIO_LIFemale-specific pC1 neurons are required for postmating sleep loss C_LIO_LISleep-promoting dFB-projecting neurons are required for postmating sleep loss C_LIO_LIActivating pC1 subtypes promotes wakefulness and inhibits dFB-projecting neurons C_LI eTOC blurbAnimals evaluate environmental conditions and internal states to make behavioral choices. Duhart et al. show that the decision to stay awake after mating in Drosophila females is modulated by food composition and sleep history and mediated by female-specific pC1 neurons acting upstream of the dFB sleep center.

neuroscience↗

bioRxiv2022

Lack of accelerated ovarian aging in a follicle-stimulating hormone receptor haploinsufficiency model

Follicle-stimulation hormone (FSH) and FSH receptor (FSHR) signaling is essential for lifelong ovarian and endocrine functions in females. Previous studies have reported that Fshr haploinsufficiency in female mice led to accelerated ovarian aging, including anticipated progressive fertility decline, irregular estrus cycles, increased follicular atresia and premature ovarian failure at 7 to 9 months of age. Interestingly, these phenotypes resemble key characteristics of human menopause and thus Fshr haploinsufficiency was proposed as a promising research mouse model of menopause. However, the Fshr haploinsufficiency model had not been fully explored, especially at the molecular level. In this study, we characterized the ovarian and endocrine functions of a Fshr heterozygous knockout allele that was generated on the C57BL/6 genetic background as part of the Knockout Mouse Project (KOMP). Based on our analyses of these mice using a breeding assay, ovarian tissue histology and serum hormone quantifications (i.e. FSH, AMH, INHA) analyses, the KOMP Fshr heterozygous knockout female mice do not show the anticipated phenotypes of ovarian aging in terms of fertility and endocrine function. We further confirmed that the expression of Fshr is unaltered in the ovaries of the KOMP Fshr heterozygous knockout animals compared to wild-type. Together, our data suggests that the KOMP Fshr heterozygous knockout strain does not recapitulate the previously reported ovarian aging phenotypes associated to another model of Fshr haploinsufficiency.

genetics↗

bioRxiv2020

Modulation of sleep-courtship balance by nutritional status in Drosophila

Sleep is essential but incompatible with other behaviors, and thus sleep drive competes with other motivations. We previously showed Drosophila males balance sleep and courtship via octopaminergic neurons that act upstream of courtship-regulating P1 neurons (Machado et al., 2017). Here we show nutrition modulates the sleep-courtship balance and identify sleep-regulatory neurons downstream of P1 neurons. Yeast-deprived males exhibited attenuated female-induced nighttime sleep loss yet normal daytime courtship, which suggests male flies consider nutritional status in deciding whether the potential benefit of pursuing female partners outweighs the cost of losing sleep. Trans-synaptic tracing and calcium imaging identified dopaminergic neurons projecting to the protocerebral bridge (DA-PB) as postsynaptic partners of P1 neurons. Activation of DA-PB neurons led to reduced sleep in normally fed but not yeast-deprived males. Additional PB-projecting neurons regulated male sleep, suggesting several groups of PB-projecting neurons act downstream of P1 neurons to mediate nutritional modulation of the sleep-courtship balance.

neuroscience↗

bioRxiv2020

Prediction of novel components of bacterial ribosomes by crowd-sourced analysis of RNA sequencing data

Bacterial resistance to antibiotics is a growing problem that is projected to cause more deaths than cancer in 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the available antibiotics target the bacterial ribosomes, proteins that are involved in protein synthesis are thus prime targets for the development of novel antibiotics. However, experimental identification of these potential antibiotic target proteins can be labor-intensive and challenging, as these proteins are likely to be poorly characterized and specific to few bacteria. In order to identify these novel proteins, we established a Large-Scale Transcriptomic Analysis Pipeline in Crowd (LSTrAP-Crowd), where 285 individuals processed 26 terabytes of RNA-sequencing data of the 17 most notorious bacterial pathogens. In total, the crowd processed 26,269 RNA-seq experiments and used the data to construct gene co-expression networks, which were used to identify more than a hundred uncharacterized genes that were transcriptionally associated with protein synthesis. We provide the identity of these genes together with the processed gene expression data. The data can be used to identify other vulnerabilities or bacteria, while our approach demonstrates how the processing of gene expression data can be easily crowdsourced.

bioinformatics↗

bioRxiv2020

Sleep Induction by Mechanosensory Stimulation in Drosophila

People tend to fall asleep when gently rocked or vibrated. Experimental studies have shown rocking promotes sleep in humans and mice. The prevailing "synchronization" model proposes synchronization of brain activity to mechanosensory stimuli mediates the phenomenon. The alternative "habituation" model proposes habituation, a form of non-associative learning, mediates sleep induction by monotonous stimulation. Here we show that gentle vibration promotes sleep in Drosophila in part through habituation. Vibration-induced sleep (VIS) leads to the accrual of homeostatic sleep credit, is associated with reduced arousability, and can be suppressed by heightened arousal. Sleep induction improves over successive blocks of vibration and exhibits stimulus specificity, supporting the habituation model. Multiple mechanosensory organs mediate VIS, and the magnitude of sleep gain depends on the vibration frequency and genetic background. Our findings suggest habituation is a major contributor to VIS, but synchronization of brain activity may play a role under certain stimulus conditions.

neuroscience↗

bioRxiv2019

Antagonistic Regulation of Circadian Output and Synaptic Development by the E3 Ubiquitin Ligase JETLAG and the DYSCHRONIC-SLOWPOKE Complex

Circadian output genes act downstream of the clock to promote rhythmic changes in behavior and physiology, yet their molecular and cellular functions are not well understood. Here we characterize an interaction between regulators of circadian entrainment, output and synaptic development in Drosophila that influences clock-driven anticipatory increases in morning and evening activity. We previously showed the JETLAG (JET) E3 Ubiquitin ligase resets the clock upon light exposure, while the PDZ protein DYSCHRONIC (DYSC) regulates circadian locomotor output and synaptic development. Surprisingly, we find that JET and DYSC antagonistically regulate synaptic development at the larval neuromuscular junction, and reduced JET activity rescues arrhythmicity of dysc mutants. Consistent with our prior finding that DYSC regulates SLOWPOKE (SLO) potassium channel expression, jet mutations also rescue circadian and synaptic phenotypes in slo mutants. Collectively, our data suggest that JET, DYSC and SLO promote circadian output in part by regulating synaptic morphology.\n\nHighlightsO_LILoss of DYSC differentially impacts morning and evening oscillators\nC_LIO_LIReduced JET activity rescues the dysc and slo arrhythmic phenotype\nC_LIO_LIReduced JET activity causes synaptic defects at the larval NMJ\nC_LIO_LIJET opposes DYSC and SLO function at the NMJ synapse\nC_LI

neuroscience↗

bioRxiv2016

Regulation of sleep plasticity by a thermo-sensitive circuit in Drosophila

Sleep is a highly conserved and essential behaviour in many species, including the fruit fly Drosophila melanogaster. In the wild, sensory signalling encoding environmental information must be integrated with sleep drive to ensure that sleep is not initiated during detrimental conditions. However, the molecular and circuit mechanisms by which sleep timing is modulated by the environment are unclear. Here we introduce a novel behavioural paradigm to study this issue. We show that in male fruit flies, onset of the daytime siesta is delayed by ambient temperatures above 29{degrees}C. We term this effect Prolonged Morning Wakefulness (PMW). We show that signalling through the TrpA1 thermo-sensor is required for PMW, and that TrpA1 specifically impacts siesta onset, but not night sleep onset, in response to elevated temperatures. We identify two critical TrpA1-expressing circuits and show that both contact DN1p clock neurons, the output of which is also required for PMW. Finally, we identify the circadian blue-light photoreceptor CRYPTOCHROME as a molecular regulator of PMW. We propose a model in which the Drosophila nervous system integrates information encoding temperature, light, and time to dynamically control when sleep is initiated. Our results provide a platform to investigate how environmental inputs co-ordinately regulate sleep plasticity.

neuroscience↗