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On page 3 showing 41 ~ 60 papers out of 1,409 papers

Adaptation of Drosophila larva foraging in response to changes in food resources.

  • Marina E Wosniack‎ et al.
  • eLife‎
  • 2022‎

All animals face the challenge of finding nutritious resources in a changing environment. To maximize lifetime fitness, the exploratory behavior has to be flexible, but which behavioral elements adapt and what triggers those changes remain elusive. Using experiments and modeling, we characterized extensively how Drosophila larvae foraging adapts to different food quality and distribution and how the foraging genetic background influences this adaptation. Our work shows that different food properties modulated specific motor programs. Food quality controls the traveled distance by modulating crawling speed and frequency of pauses and turns. Food distribution, and in particular the food-no food interface, controls turning behavior, stimulating turns toward the food when reaching the patch border and increasing the proportion of time spent within patches of food. Finally, the polymorphism in the foraging gene (rover-sitter) of the larvae adjusts the magnitude of the behavioral response to different food conditions. This study defines several levels of control of foraging and provides the basis for the systematic identification of the neuronal circuits and mechanisms controlling each behavioral response.


Toxocara cati larva migrans in domestic pigs--detected at slaughterhouse control in Norway.

  • Rebecca K Davidson‎ et al.
  • Acta veterinaria Scandinavica‎
  • 2012‎

Routine Trichinella meat inspection at the slaughterhouse detected one larva in a pooled batch of 100 pig samples. The larva was sent to the Norwegian Veterinary Institute (NVI) for species identification.Morphological examination revealed that the larva was not Trichinella spp. Molecular analysis was performed. PCR and sequencing of 5S/ITS identified the larva as Toxocara cati. A second round of digests was carried out at the meat inspection laboratory, in smaller batches to try to identify the infected animal. No further larvae were detected and it was not possible to identify which of the 100 animals the larva had come from. This is the first time that Toxocara cati has been reported in slaughterhouse pigs in Norway.Although the infected individual could not be identified, the meat originated from one of six potential farms. A small survey regarding rodent control and cats was sent to each of these farms. Cats had restricted access to food storage areas (two farms reported that cats had access) whilst none of the farms allowed cats into the production housing. Cats were, however, present on all the farms (mostly stray cats of unknown health status). Half of the farms also reported seeing rodents in the pig housing during the previous six months and half reported finding rodents in the feed and straw storage areas. We were unable to narrow down the source of infection - however contamination of food or bedding material, with cat faeces or infected rodents, in addition to the presence of infected rodents in pig housing remain potential routes of infection.


Bacterial fatty acids enhance recovery from the dauer larva in Caenorhabditis elegans.

  • Tiffany K Kaul‎ et al.
  • PloS one‎
  • 2014‎

The dauer larva is a specialized dispersal stage in the nematode Caenorhabditis elegans that allows the animal to survive starvation for an extended period of time. The dauer does not feed, but uses chemosensation to identify new food sources and to determine whether to resume reproductive growth. Bacteria produce food signals that promote recovery of the dauer larva, but the chemical identities of these signals remain poorly defined. We find that bacterial fatty acids in the environment augment recovery from the dauer stage under permissive conditions. The effect of increased fatty acids on different dauer constitutive mutants indicates a role for insulin peptide secretion in coordinating recovery from the dauer stage in response to fatty acids. These data suggest that worms can sense the presence of fatty acids in the environment and that elevated levels can promote recovery from dauer arrest. This may be important in the natural environment where the dauer larva needs to determine whether the environment is appropriate to support reproductive growth following dauer exit.


A molecular and neuronal basis for amino acid sensing in the Drosophila larva.

  • Vincent Croset‎ et al.
  • Scientific reports‎
  • 2016‎

Amino acids are important nutrients for animals, reflected in conserved internal pathways in vertebrates and invertebrates for monitoring cellular levels of these compounds. In mammals, sensory cells and metabotropic glutamate receptor-related taste receptors that detect environmental sources of amino acids in food are also well-characterised. By contrast, it is unclear how insects perceive this class of molecules through peripheral chemosensory mechanisms. Here we investigate amino acid sensing in Drosophila melanogaster larvae, which feed ravenously to support their rapid growth. We show that larvae display diverse behaviours (attraction, aversion, neutral) towards different amino acids, which depend upon stimulus concentration. Some of these behaviours require IR76b, a member of the variant ionotropic glutamate receptor repertoire of invertebrate chemoreceptors. IR76b is broadly expressed in larval taste neurons, suggesting a role as a co-receptor. We identify a subpopulation of these neurons that displays physiological activation by some, but not all, amino acids, and which mediate suppression of feeding by high concentrations of at least a subset of these compounds. Our data reveal the first elements of a sophisticated neuronal and molecular substrate by which these animals detect and behave towards external sources of amino acids.


Pigmented and nonpigmented ocelli in the brain vesicle of the ascidian larva.

  • Takeo Horie‎ et al.
  • The Journal of comparative neurology‎
  • 2008‎

The vertebrate-type opsin, Ci-opsin1, is localized in the outer segments of the photoreceptor cells of larvae of the ascidian Ciona intestinalis. The absorption spectrum of the photopigment reconstituted from Ci-opsin1 and 11-cis-retinal suggested that the photopigment is responsible for photic behavior of the larvae. The structure and function of Ci-opsin1-positive photoreceptor cells were examined by immunohistochemistry, confocal microscopy, electron microscopy, laser ablation, and behavioral analysis. Ciona larvae have three morphologically distinct groups of photoreceptor cells in the brain vesicle. Group I and group II photoreceptor cells are associated with the ocellus pigment cell on the right side of the brain vesicle. The outer segments of the group I photoreceptor cells are regularly arranged inside the small cavity encircled by the cup-shaped pigment cell. The outer segments of the group II photoreceptor cells are located outside the pigment cavity and exposed to the lumen of the brain vesicle. The outer segments of the group III photoreceptor cells are located near the otolith on the left ventral side of the brain vesicle. Thus, the brain vesicle of the ascidian larva has two ocelli: a 'conventional' pigmented ocellus containing the group I and group II photoreceptor cells and a novel nonpigmented ocellus solely consisting of the group III photoreceptor cells. Laser ablation experiments suggest that the pigmented ocellus is responsible for the photic swimming behavior. The nonpigmented ocellus might relate to later developmental or physiological events, such as metamorphosis, because Ci-opsin1 immunoreactivity appears in the late larval stage and becomes intense just before the onset of metamorphosis.


Sensorimotor pathway controlling stopping behavior during chemotaxis in the Drosophila melanogaster larva.

  • Ibrahim Tastekin‎ et al.
  • eLife‎
  • 2018‎

Sensory navigation results from coordinated transitions between distinct behavioral programs. During chemotaxis in the Drosophila melanogaster larva, the detection of positive odor gradients extends runs while negative gradients promote stops and turns. This algorithm represents a foundation for the control of sensory navigation across phyla. In the present work, we identified an olfactory descending neuron, PDM-DN, which plays a pivotal role in the organization of stops and turns in response to the detection of graded changes in odor concentrations. Artificial activation of this descending neuron induces deterministic stops followed by the initiation of turning maneuvers through head casts. Using electron microscopy, we reconstructed the main pathway that connects the PDM-DN neuron to the peripheral olfactory system and to the pre-motor circuit responsible for the actuation of forward peristalsis. Our results set the stage for a detailed mechanistic analysis of the sensorimotor conversion of graded olfactory inputs into action selection to perform goal-oriented navigation.


Development of a lecithotrophic pilidium larva illustrates convergent evolution of trochophore-like morphology.

  • Marie K Hunt‎ et al.
  • Frontiers in zoology‎
  • 2017‎

The pilidium larva is an idiosyncrasy defining one clade of marine invertebrates, the Pilidiophora (Nemertea, Spiralia). Uniquely, in pilidial development, the juvenile worm forms from a series of isolated rudiments called imaginal discs, then erupts through and devours the larval body during catastrophic metamorphosis. A typical pilidium is planktotrophic and looks like a hat with earflaps, but pilidial diversity is much broader and includes several types of non-feeding pilidia. One of the most intriguing recently discovered types is the lecithotrophic pilidium nielseni of an undescribed species, Micrura sp. "dark" (Lineidae, Heteronemertea, Pilidiophora). The egg-shaped pilidium nielseni bears two transverse circumferential ciliary bands evoking the prototroch and telotroch of the trochophore larva found in some other spiralian phyla (e.g. annelids), but undergoes catastrophic metamorphosis similar to that of other pilidia. While it is clear that the resemblance to the trochophore is convergent, it is not clear how pilidium nielseni acquired this striking morphological similarity.


An unusual 100-million-year old holometabolan larva with a piercing mouth cone.

  • Joachim T Haug‎ et al.
  • PeerJ‎
  • 2020‎

Holometabola is a hyperdiverse group characterised by a strong morphological differentiation between early post-embryonic stages (= larvae) and adults. Adult forms of Holometabola, such as wasps, bees, beetles, butterflies, mosquitoes or flies, are strongly differentiated concerning their mouth parts. The larvae most often seem to retain rather plesiomorphic-appearing cutting-grinding mouth parts. Here we report a new unusual larva preserved in Burmese amber. Its mouth parts appear beak-like, forming a distinct piercing mouth cone. Such a morphology is extremely rare among larval forms, restricted to those of some beetles and lacewings. The mouth parts of the new fossil are forward oriented (prognathous). Additionally, the larva has distinct subdivisions of tergites and sternites into several sclerites. Also, the abdomen segments bear prominent protrusions. We discuss this unusual combination of characters in comparison to the many different types of holometabolan larvae. The here reported larva is a new addition to the 'unusual zoo' of the Cretaceous fauna including numerous, very unusual appearing forms that have gone extinct at the Cretaceous-Palaeogene boundary.


Ciliomotor circuitry underlying whole-body coordination of ciliary activity in the Platynereis larva.

  • Csaba Verasztó‎ et al.
  • eLife‎
  • 2017‎

Ciliated surfaces harbouring synchronously beating cilia can generate fluid flow or drive locomotion. In ciliary swimmers, ciliary beating, arrests, and changes in beat frequency are often coordinated across extended or discontinuous surfaces. To understand how such coordination is achieved, we studied the ciliated larvae of Platynereis dumerilii, a marine annelid. Platynereis larvae have segmental multiciliated cells that regularly display spontaneous coordinated ciliary arrests. We used whole-body connectomics, activity imaging, transgenesis, and neuron ablation to characterize the ciliomotor circuitry. We identified cholinergic, serotonergic, and catecholaminergic ciliomotor neurons. The synchronous rhythmic activation of cholinergic cells drives the coordinated arrests of all cilia. The serotonergic cells are active when cilia are beating. Serotonin inhibits the cholinergic rhythm, and increases ciliary beat frequency. Based on their connectivity and alternating activity, the catecholaminergic cells may generate the rhythm. The ciliomotor circuitry thus constitutes a stop-and-go pacemaker system for the whole-body coordination of ciliary locomotion.


An ancient FMRFamide-related peptide-receptor pair induces defence behaviour in a brachiopod larva.

  • Daniel Thiel‎ et al.
  • Open biology‎
  • 2017‎

Animal behaviour often comprises spatially separated sub-reactions and even ciliated larvae are able to coordinate sub-reactions of complex behaviours (metamorphosis, feeding). How these sub-reactions are coordinated is currently not well understood. Neuropeptides are potential candidates for triggering larval behaviour. However, although their immunoreactivity has been widely analysed, their function in trochozoan larvae has only been studied for a few cases. Here, we investigate the role of neuropeptides in the defence behaviour of brachiopod larvae. When mechanically disturbed, the planktonic larvae of Terebratalia transversa protrude their stiff chaetae and sink down slowly. We identified endogenous FLRFamide-type neuropeptides (AFLRFamide and DFLRFamide) in T. transversa larvae and show that the protrusion of the chaetae as well as the sinking reaction can both be induced by each of these peptides. This also correlates with the presence of FLRFamidergic neurons in the apical lobe and adjacent to the trunk musculature. We deorphanized the AFLRFamide/DFLRFamide receptor and detected its expression in the same tissues. Furthermore, the ability of native and modified FLRFamide-type peptides to activate this receptor was found to correspond with their ability to trigger behavioural responses. Our results show how FLRFamide-type neuropeptides can induce two coherent sub-reactions in a larva with a simple nervous system.


Partially Defatted Hermetia illucens Larva Meal in Diet of Eurasian Perch (Perca fluviatilis) Juveniles.

  • Vlastimil Stejskal‎ et al.
  • Animals : an open access journal from MDPI‎
  • 2020‎

Insect meal is gaining increased attention in aquafeed formulations due to high protein content and an essential amino acid profile similar to that of fishmeal. To investigate insect meal in feed for European perch Perca fluviatilis, a promising candidate for European intensive culture, we replaced standard fishmeal with partially defatted black soldier fly Hermetia illucens larva meal at rates of 0%, 20%, 40% and 60% (groups CON, H20, H40 and H60, respectively) and compared growth performance, somatic indices, hematological parameters, whole-body proximate composition and occurrence of spleen lipidosis. In addition, we assessed the economic and environmental sustainability of the tested feeds by calculating economic conversion ratio (ECR) and economic profit index (EPI). The tested groups did not differ in survival rate. Significant differences were documented in final body weight and specific growth rate, with the highest values in CON, H20 and H40. The proximate composition of fish whole-body at the end of the experiment did not differ in dry matter, crude protein or ether extract, while organic matter, ash and gross energy composition showed significant differences. The fatty acid content and n-3/n-6 ratio showed a decreasing trend with increasing H. illucens larva meal inclusion. No differences were found in hematological parameters among tested groups. The H. illucens larva meal inclusion significantly affected ECR and EPI, even at 20% inclusion level the cost of diets did not differ from the control fish meal based diet. Results suggested that 40% inclusion of H. illucens larva meal can be used successfully in standard diets for perch.


Role of the subesophageal zone in sensorimotor control of orientation in Drosophila larva.

  • Ibrahim Tastekin‎ et al.
  • Current biology : CB‎
  • 2015‎

Chemotaxis is a powerful paradigm to investigate how nervous systems represent and integrate changes in sensory signals to direct navigational decisions. In the Drosophila melanogaster larva, chemotaxis mainly consists of an alternation of distinct behavioral modes: runs and directed turns. During locomotion, turns are triggered by the integration of temporal changes in the intensity of the stimulus. Upon completion of a turning maneuver, the direction of motion is typically realigned toward the odor gradient. While the anatomy of the peripheral olfactory circuits and the locomotor system of the larva are reasonably well documented, the neural circuits connecting the sensory neurons to the motor neurons remain unknown. We combined a loss-of-function behavioral screen with optogenetics-based clonal gain-of-function manipulations to identify neurons that are necessary and sufficient for the initiation of reorientation maneuvers in odor gradients. Our results indicate that a small subset of neurons residing in the subesophageal zone controls the rate of transition from runs to turns-a premotor function compatible with previous observations made in other invertebrates. After having shown that this function pertains to the processing of inputs from different sensory modalities (olfaction, vision, thermosensation), we conclude that the subesophageal zone operates as a general premotor center that regulates the selection of different behavioral programs based on the integration of sensory stimuli. The present analysis paves the way for a systematic investigation of the neural computations underlying action selection in a miniature brain amenable to genetic manipulations.


Metabolomic Effects of the Dietary Inclusion of Hermetia illucens Larva Meal in Tilapia.

  • Bo Ye‎ et al.
  • Metabolites‎
  • 2022‎

Black soldier fly (Hermetia illucens) larvae meal have been used as feed protein supplements in fish feed, but few researches have investigated the metabolomic effects of Hermetia illucens larvae meal supplements. Therefore, the metabolic effects on Nile tilapia were investigated by replacing 5%, 10%, and 20% of the dietary soybean meal in the basal diet with Hermetia illucens larvae meal, respectively. This study shows that 20% H. illucens larvae meal feed could promote tilapia average daily gain of upto 5.03 ± 0.18 g (mean ± SEM). It was found that the tricarboxylic acid cycle efficiency was improved by activating the enzymes of mitochondrial isocitrate dehydrogenase, NAD-malate dehydrogenase, succinate dehydrogenase, pyruvate dehydrogenase, and α-ketoglutarate dehydrogenase, which then increased the output of ATP and NADH. Furthermore, amino acid and protein biosynthesis was boosted by enhanced glutamine synthetase and glutamate synthase. In particular, GSH increased with increased H. illucens larvae meal. Unsaturated fatty acid biosynthesis was stimulated by higher levels of fatty acid synthase and acetyl CoA carboxylase. Additionally, there was no significant change in lipase levels. Thus, the higher acetyl Co-A content was primarily involved in fatty acid biosynthesis and energy metabolism. Flavor substances, such as nonanal and 2-methyl-3-furanthiol, also accumulated with the addition of H. illucens larvae meal, which increased the umami taste and meat flavor. Additionally, the flavor of tilapia was improved owing to a decrease in trimethylamine content, which causes an earthy and fishy taste. This study uncovers a previously unknown metabolic effect of dietary H. illucens larvae meal on Nile tilapia.


Zebrafish (Danio rerio) larva as an in vivo vertebrate model to study renal function.

  • Jan Stephan Bolten‎ et al.
  • American journal of physiology. Renal physiology‎
  • 2022‎

There is an increasing interest in using zebrafish (Danio rerio) larva as a vertebrate screening model to study drug disposition. As the pronephric kidney of zebrafish larvae shares high similarity with the anatomy of nephrons in higher vertebrates including humans, we explored in this study whether 3- to 4-day-old zebrafish larvae have a fully functional pronephron. Intravenous injection of fluorescent polyethylene glycol and dextran derivatives of different molecular weight revealed a cutoff of 4.4-7.6 nm in hydrodynamic diameter for passive glomerular filtration, which is in agreement with corresponding values in rodents and humans. Distal tubular reabsorption of a FITC-folate conjugate, covalently modified with PEG2000, via folate receptor 1 was shown. Transport experiments of fluorescent substrates were assessed in the presence and absence of specific inhibitors in the blood systems. Thereby, functional expression in the proximal tubule of organic anion transporter oat (slc22) multidrug resistance-associated protein mrp1 (abcc1), mrp2 (abcc2), mrp4 (abcc4), and zebrafish larva p-glycoprotein analog abcb4 was shown. In addition, nonrenal clearance of fluorescent substrates and plasma protein binding characteristics were assessed in vivo. The results of transporter experiments were confirmed by extrapolation to ex vivo experiments in killifish (Fundulus heteroclitus) proximal kidney tubules. We conclude that the zebrafish larva has a fully functional pronephron at 96 h postfertilization and is therefore an attractive translational vertebrate screening model to bridge the gap between cell culture-based test systems and pharmacokinetic experiments in higher vertebrates.NEW & NOTEWORTHY The study of renal function remains a challenge. In vitro cell-based assays are approved to study, e.g., ABC/SLC-mediated drug transport but do not cover other renal functions such as glomerular filtration. Here, in vivo studies combined with in vitro assays are needed, which are time consuming and expensive. In view of these limitations, our proof-of-concept study demonstrates that the zebrafish larva is a translational in vivo test model that allows for mechanistic investigations to study renal function.


Development and neural organization of the tornaria larva of the Hawaiian hemichordate, Ptychodera flava.

  • Yoko Nakajima‎ et al.
  • Zoological science‎
  • 2004‎

We report scanning and transmission electron microscopic studies of the early development of the Hawaiian acorn worm, Ptychodera flava. In addition, we provide an immunohistochemical identification of the larval nervous system. Development occurs and is constrained within the stout chorion and fertilization envelope that forms upon the release of the cortical granules in the cytoplasm of the egg. The blastula consists of tall columnar blastomeres encircling a small blastocoel. Typical gastrulation occurs and a definitive tornaria is formed compressed within the fertilization envelope. The young tornaria hatches at 44 hr and begins to expand. The major circumoral ciliary band that crosses the dorsal surface and passes preorally and postorally is well developed. In addition, we find a nascent telotroch, as well as a midventral ciliary band that is already clearly developed. The epithelium of tornaria is a mosaic of monociliated and multiciliated cells. Immunohistochemistry with a novel neural marker, monoclonal antibody 1E11, first detects nerve cells at the gastrula stage. In tornaria, 1E11 staining nerve cells occur throughout the length of the ciliary bands, in the apical organ, in a circle around the mouth, in the esophageal epithelium and in circumpylorus regions. Axon(s) and apical processes extend from the nerve cell bodies and run in tracks along the ciliary bands. Axons extending from the preoral and postoral bands extend into the oral field and form a network. The tornaria nervous system with ciliary bands and an apical organ is rather similar to the echinoderm bipinnaria larvae.


A 100-million-year old predator: a fossil neuropteran larva with unusually elongated mouthparts.

  • Joachim T Haug‎ et al.
  • Zoological letters‎
  • 2019‎

Biological diversity is a hot topic in current research, especially its observed decrease in modern times. Investigations of past ecosystems offer additional insights to help better understand the processes underlying biodiversity. The Cretaceous period is of special interest in this context, especially with respect to arthropods. During that period, representatives of many modern lineages appeared for the first time, while representatives of more ancient groups also co-occurred. At the same time, side branches of radiating groups with 'experimental morphologies' emerged that seemed to go extinct shortly afterwards. However, larval forms, with their morphological diversity, are largely neglected in such studies, but may provide important insights into morphological and ecological diversity and its changes in the past.


Endosymbionts Alter Larva-to-Nymph Transstadial Transmission of Babesia microti in Rhipicephalus haemaphysaloides Ticks.

  • Lan-Hua Li‎ et al.
  • Frontiers in microbiology‎
  • 2018‎

Maternally inherited endosymbionts inhabit a variety of arthropods. Some of them can protect the arthropod host against a wide range of pathogens. However, very little is known about the association between endosymbionts and pathogen susceptibility in ticks. The present study investigated the effect of endosymbionts on larva-to-nymph transstadial transmission of Babesia microti by Rhipicephalus haemaphysaloides ticks. Engorged female ticks were injected with PBS, ciprofloxacin or kanamycin. The offspring larvae were used to infest B. microti-positive mice. Prevalence of B. microti among the nymphs in different treatment groups and its association with endosymbiont density in the larvae were analyzed. The results showed that the prevalence of B. microti in the kanamycin-treated group (63.9%, 95% confidence interval (CI): 52.8-75.0%) was higher than that in the PBS (23.6%, 95% CI: 13.8-33.4%) or ciprofloxacin-treated (25.0%, 95% CI: 15.0-35.0%) groups. This increased prevalence was associated with reduced density of Coxiella-like endosymbiont but was not related to the density of Rickettsia-like endosymbiont. No direct evidence has previously been reported about the impact of Coxiella-like endosymbiont on pathogen susceptibility in ticks. This study reveals that endosymbionts are potentially important defensive symbionts of R. haemaphysaloides which may influence the colonization or susceptibility of B. microti in the tick host.


Allomyrina dichotoma larva extract attenuates free fatty acid-induced lipotoxicity in pancreatic beta cells.

  • Kyong Kim‎ et al.
  • Nutrition research and practice‎
  • 2021‎

Allomyrina dichotoma larva (ADL), one of the many edible insects recognized as future food resources, has a range of pharmacological activities. In a previous study, an ADL extract (ADLE) reduced the hepatic insulin resistance of high-fat diet (HFD)-induced diabetic mice. On the other hand, the associated molecular mechanisms underlying pancreatic beta-cell dysfunction remain unclear. This study examined the effects of ADLE on palmitate-induced lipotoxicity in a beta cell line of a rat origin, INS-1 cells.


Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens.

  • Rafael J Hernandez‎ et al.
  • PeerJ‎
  • 2019‎

Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize pathogens from coastal environments in the South West of the UK. Whole-genome sequencing of highly virulent isolates revealed amongst others a Proteus mirabilis strain carrying the Salmonella SGI1 genomic island not reported from the UK before and the recently described species Vibrio injenensis hitherto only reported from human patients in Korea. Our novel method has the power to detect bacterial pathogens in the environment that potentially pose a serious risk to public health.


LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.

  • Lucas Lochovsky‎ et al.
  • Nucleic acids research‎
  • 2015‎

In cancer research, background models for mutation rates have been extensively calibrated in coding regions, leading to the identification of many driver genes, recurrently mutated more than expected. Noncoding regions are also associated with disease; however, background models for them have not been investigated in as much detail. This is partially due to limited noncoding functional annotation. Also, great mutation heterogeneity and potential correlations between neighboring sites give rise to substantial overdispersion in mutation count, resulting in problematic background rate estimation. Here, we address these issues with a new computational framework called LARVA. It integrates variants with a comprehensive set of noncoding functional elements, modeling the mutation counts of the elements with a β-binomial distribution to handle overdispersion. LARVA, moreover, uses regional genomic features such as replication timing to better estimate local mutation rates and mutational hotspots. We demonstrate LARVA's effectiveness on 760 whole-genome tumor sequences, showing that it identifies well-known noncoding drivers, such as mutations in the TERT promoter. Furthermore, LARVA highlights several novel highly mutated regulatory sites that could potentially be noncoding drivers. We make LARVA available as a software tool and release our highly mutated annotations as an online resource (larva.gersteinlab.org).


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