Biology subjects

Moore, D.

Publications and source records attributed to Moore, D..

31 records · Page 2Linked to original sources

bioRxiv2022

Evaluation of the broth microdilution methodology for susceptibility testing of Mycobacterium tuberculosis in Peru

Peru is amongst the 30 countries with the highest burden of multidrug-resistant tuberculosis worldwide. In the fight against drug-resistant tuberculosis, the UKMYC6 microtiter plate was developed and validated by the CRyPTIC project. Our objective was to evaluate the use of the broth microdilution UKMYC6 plate for susceptibility testing of drug-resistant Mycobacterium tuberculosis (MTB) strains in Peru. 496 nationally-representative MTB strains determined drug-resistant by the routine agar proportion method (APM) were selected. MICs of 13 anti-tuberculosis drugs were determined for each strain using the microdilution UKMYC6 plates and compared with the APM result. MIC distributions for APM-susceptible and APM-resistant strains were demonstrated for rifampicin, isoniazid, kanamycin, and levofloxacin, with reasonable agreement (0.64[≤]k[≤]0.79) for rifampicin, ethambutol, ethionamide and kanamycin and the best agreement for isoniazid and levofloxacin (k>0.8). No strain presented MICs higher than the CRyPTIC Epidemiological cut-off values for the new (bedaquiline, delamanid) or repurposed (clofazimine, linezolid) drugs. The microbroth dilution method using the UKMYC6 microtiter plate allowed the complete susceptibility characterization, through the determination of MICs, of drug-resistant Mycobacterium tuberculosis strains in Peru. This methodology showed a good diagnostic performance for the drugs rifampicin, isoniazid, kanamycin and levofloxacin drugs.

microbiology↗

bioRxiv2020

The Role of Colony Temperature in the Entrainment of Circadian Rhythms of Honey Bee Foragers

Honey bees utilize their circadian rhythms to accurately predict the time of day. This ability allows foragers to remember the specific timing of food availability and its location for several days. Previous studies have provided strong evidence toward light/dark cycles being the primary Zeitgeber for honey bees. Work in our laboratory described large individual variation in the endogenous period length of honey bee foragers from the same colony and differences in the endogenous rhythms under different constant temperatures. In this study, we further this work by examining temperature inside the honey bee colony. By placing temperature and light data loggers at different locations inside the colony we measured temperature at various locations within the colony. We observed significant oscillations of temperature inside the hive, that show seasonal patterns. We then simulated the observed temperature oscillations in the laboratory and found that using the temperature cycle as a Zeitgeber, foragers present large individual differences in the phase of locomotor rhythms with respect to temperature. Moreover, foragers successfully synchronize their locomotor rhythms to these simulated temperature cycles. Advancing the cycle by six hours, resulted in changes in the phase of activity in some foragers in the assay. The results shown in this study highlight the importance of temperature as a potential Zeitgeber in the field. Future studies will examine the possible functional and evolutionary role of the observed phase differences of circadian rhythms.

animal behavior and cognition↗

bioRxiv2020

Neonicotinoids Disrupt Circadian Rhythms and Sleep in Honey Bees

Honey bees are critical pollinators in ecosystems and agriculture, but their numbers have significantly declined. Declines in pollinator populations are thought to be due to multiple factors including habitat loss, climate change, increased vulnerability to disease and parasites, and pesticide use. Neonicotinoid pesticides are agonists of insect nicotinic cholinergic receptors, and sub-lethal exposures are linked to reduced honey bee hive survival. Honey bees are highly dependent on circadian clocks to regulate critical behaviors, such as foraging orientation and navigation, time-memory for food sources, sleep, and learning/ memory processes. Because circadian clock neurons in insects receive light input through cholinergic signaling we tested for effects of neonicotinoids on honey bee circadian rhythms and sleep. Neonicotinoid ingestion by feeding over several days results in neonicotinoid accumulation in the bee brain, disrupts circadian rhythmicity in many individual bees, shifts the timing of behavioral circadian rhythms in bees that remain rhythmic, and impairs sleep. Neonicotinoids and light input act synergistically to disrupt bee circadian behavior, and neonicotinoids directly stimulate wake-promoting clock neurons in the fruit fly brain. Neonicotinoids disrupt honey bee circadian rhythms and sleep, likely by aberrant stimulation of clock neurons, to potentially impair honey bee navigation, time-memory, and social communication.

animal behavior and cognition↗

bioRxiv2019

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

genomics↗

bioRxiv2019

Minimal and mild hearing loss in children: Association with auditory perception, cognition, and communication problems

Objectives Minimal and mild hearing loss are the most common but least understood forms of hearing loss in children. Children with better ear hearing level as low as 30 dB HL have a global language impairment and, according to the World Health Organization, a \"disabling level of hearing loss\". We examined in a population of 6 - 11 year olds how hearing level [≤] 40.0 dB HL (1 and 4 kHz pure tone average, PTA, threshold) related to auditory perception, cognition and communication.\n\nDesignSchool children (n=1638) were recruited in four centres across the UK. They completed a battery of hearing (audiometry, filter width, temporal envelope, speech-in-noise) and cognitive (IQ, attention, verbal memory, receptive language, reading) tests. Caregivers assessed their childrens communication and listening skills. Children included in this study (702 male; 752 female) had four reliable tone thresholds (1, 4 kHz each ear), and no caregiver reported medical or intellectual disorder. Normal hearing children (n=1124, 77.1%) had all four thresholds and PTA < 15 dB HL. Children with [≥] 15 dB HL for at least one threshold, and PTA < 20 dB (n=245, 16.8%) had Minimal hearing loss. Children with 20 [≤] PTA < 40 dB HL (n=88, 6.0%) had Mild hearing loss. Interaural Asymmetric hearing loss (|Left PTA - Right PTA| [≥] 10 dB) was found in 28.9% of those with Minimal and 39.8% of those with Mild hearing loss.\n\nResultsSpeech perception in noise, indexed by VCV pseudoword repetition in speech modulated noise, was impaired in children with Minimal and Mild hearing loss, relative to Normal hearing children. Effect size was largest (d=0.63) in Asymmetric Mild hearing loss and smallest (d=0.21) in Symmetric Minimal hearing loss. Spectral (filter width) and temporal (backward masking) perception were impaired in children with both forms of hearing loss, but supra-threshold perception generally related only weakly to PTA. Speech-in-noise (nonsense syllables) and language (pseudoword repetition) were also impaired in both forms of hearing loss and correlated more strongly with PTA. Children with Mild hearing loss were additionally impaired in working memory (digit span) and reading, and generally performed more poorly than those with Minimal loss. Asymmetric hearing loss produced as much impairment overall on both auditory and cognitive tasks as Symmetric hearing loss. Nonverbal IQ, attention and caregiver-rated listening and communication were not significantly impaired in children with hearing loss. Modelling suggested that 15 dB HL is objectively an appropriate lower audibility limit for diagnosis of hearing loss.\n\nConclusionsHearing loss between 15 - 30 dB PTA is, at ~20%, much more prevalent in 6-11 y.o. children than most current estimates. Key aspects of auditory and cognitive skills are impaired in both symmetric and asymmetric minimal and mild hearing loss. Hearing loss < 30 dB HL is most closely related to speech perception in noise, and to cognitive abilities underpinning language and reading. The results suggest wider use of speech-in-noise measures to diagnose and assess management of hearing loss and reduction of the clinical hearing loss threshold for children to 15 dB HL.

neuroscience↗

bioRxiv2019

Pathognomonic and epistatic genetic alterations in B-cell non-Hodgkin lymphoma

B-cell non-Hodgkins lymphoma (B-NHL) encompasses multiple clinically and phenotypically distinct subtypes of malignancy with unique molecular etiologies. Common subtypes of B-NHL such as diffuse large B-cell lymphoma (DLBCL) have been comprehensively interrogated at the genomic level. But rarer subtypes such as mantle cell lymphoma (MCL) remain sparsely characterized. Furthermore, multiple B-NHL subtypes have thus far not been comprehensively compared using the same methodology to identify conserved or subtype-specific patterns of genomic alterations. Here, we employed a large targeted hybrid-capture sequencing approach encompassing 380 genes to interrogate the genomic landscapes of 685 B-NHL tumors at high depth; including DLBCL, MCL, follicular lymphoma (FL), and Burkitt lymphoma (BL). We identified conserved hallmarks of B-NHL that were deregulated in the majority of tumor from each subtype, including the frequent genetic deregulation of the ubiquitin proteasome system (UPS). In addition, we identified subtype-specific patterns of genetic alterations, including clusters of co-occurring mutations and DNA copy number alterations. The cumulative burden of mutations within a single cluster were more discriminatory of B-NHL subtypes than individual mutations, implicating likely patterns of genetic cooperation that contribute to disease etiology. We therefore provide the first cross-sectional analysis of mutations and DNA copy number alterations across major B-NHL subtypes and a framework of co-occurring genetic alterations that deregulate genetic hallmarks and likely cooperate in lymphomagenesis.

genomics↗

bioRxiv2019

Development of the first low nanomolar Liver Receptor Homolog-1 agonist through structure-guided design

As a key regulator of metabolism and inflammation, the orphan nuclear hormone receptor, Liver Receptor Homolog-1 (LRH-1), has potential as a therapeutic target for diabetes, nonalcoholic fatty liver disease, and inflammatory bowel diseases. Discovery of LRH-1 modulators has been difficult, in part due to the tendency for synthetic compounds to bind unpredictably within the lipophilic binding pocket. Using a structure-guided approach, we exploited a newly-discovered polar interaction to lock agonists in a consistent orientation. This enabled the discovery of the first low nanomolar LRH-1 agonist, one hundred times more potent than the best previous modulator. We elucidate a novel mechanism of action that relies upon specific polar interactions deep in the LRH-1 binding pocket. In an organoid model of inflammatory bowel disease, the new agonist increases expression of LRH-1-conrolled steroidogenic genes and promotes anti-inflammatory gene expression changes. These studies constitute major progress in developing LRH-1 modulators with potential clinical utility.

pharmacology and toxicology↗

bioRxiv2019

De novo mutations in fetal brain specific enhancers play a significant role in severe intellectual disability

PurposeThe genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood.\n\nMethodsWe sequenced 70 whole genomes from 24 ID probands and their unaffected parents and analyzed 30 previously sequenced genomes from exome-negative ID probands.\n\nResultsWe found that DNVs were selectively enriched in fetal brain-specific enhancers that show purifying selection in human population. DNV containing enhancers were associated with genes that show preferential expression in the pre-frontal cortex, have been previously implicated in ID or related disorders, and exhibit intolerance to loss of function variants. DNVs from ID probands preferentially disrupted putative binding sites of neuronal transcription factors, as compared to DNVs from healthy individuals and most showed allele-specific enhancer activity. In addition, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1 and POU3F3). Moreover, CRISPR-based perturbation of a DNV-containing enhancer caused CSMD1 overexpression and abnormal expression of neurodevelopmental regulators.\n\nConclusionOur results, therefore, provide new evidence to indicate that DNVs in constrained fetal brain-specific enhancers play a role in the etiology of ID.

genomics↗

bioRxiv2019

Versatile proteome labelling in fruit flies with SILAF

Drosophila melanogaster has been a working horse of genetics and cell biology for more than a century. However, proteomic-based methods have been limited due to technical obstacles, especially the lack of reliable labelling methods. Here, we advanced a chemically defined food source into stable-isotope labelling of amino acids in flies (SILAF). It allows for the rapid generation of a large number of flies with full incorporation of lysine-6. SILAF followed by fractionation and enrichment gave proteomic insights at a depth of 5,966 proteins and 7,496 phosphorylation sites, which substantiated metabolic regulation on enzymatic level. Furthermore, the label can be traced and predicts protein turnover rates during different developmental stages. The ease and versatility of the method actuates the fruit fly as an appealing model in proteomic and post-translational modification studies and it enlarges potential metabolic applications based on heavy amino acid diets.

molecular biology↗

bioRxiv2018

Dynamics of microRNA expression during mouse prenatal development

MicroRNAs (miRNAs) play a critical role as post-transcriptional regulators of gene expression. The ENCODE project profiled the expression of miRNAs in a comprehensive set of tissues during a time-course of mouse embryonic development and captured the expression dynamics of 785 miRNAs. We found distinct tissue and developmental stage specific miRNA expression clusters, with an overall pattern of increasing tissue specific expression as development proceeds. Comparative analysis of conserved miRNAs in mouse and human revealed stronger clustering of expression patterns by tissue types rather than by species. An analysis of messenger RNA gene expression clusters compared with miRNA expression clusters identifies the potential role of specific miRNA expression clusters in suppressing the expression of mRNAs specific to other developmental programs in the tissue where these microRNAs are expressed during embryonic development. Our results provide the most comprehensive timecourse of miRNA expression as an integrated part of the ENCODE reference dataset for mouse embryonic development.

genomics↗

bioRxiv2018

Foxp1 controls neural stem cell competence and bias towards deep layer cortical fate.

SUMMARYThe laminar architecture of the mammalian neocortex depends on the orderly generation of distinct neuronal subtypes by apical radial glia (aRG) during embryogenesis. We identify critical roles for Foxp1 in maintaining RG identity and gating the temporal competency for early neurogenesis. High levels of Foxp1 are associated with early aRG and are required to promote proliferation and influence cell division symmetry, favoring aRG expansion and production of early born neurons. The potent pro-progenitor functions of Foxp1 are revealed through its ability to preserve a population of cells with aRG identity throughout development and extend the early neurogenic period into postnatal life. Foxp1 further promotes the formation of cells resembling basal RG (bRG), a progenitor group implicated in the increased size and complexity of the human cortex. Consistent with this role, we show that FOXP1 is associated with the initial formation and expansion of bRG during human corticogenesis.\n\nHIGHLIGHTSO_LIFoxp1 is transiently expressed by aRG during the early phase of corticogenesis\nC_LIO_LIFoxp1 promotes self-renewing vertical cell divisions and aRG maintenance\nC_LIO_LIFoxp1 gates the time window of deep layer neurogenesis\nC_LIO_LIEctopic Foxp1 expression can elicit bRG formation\nC_LI

developmental biology↗

bioRxiv2018

Quantitative Real-Time Imaging of Glutathione with Sub-Cellular Resolution

Quantitative imaging of glutathione with high spatial and temporal resolution is essential for studying the roles of glutathione in redox biology. We developed a fluorescent glutathione probe--HaloRT--that targets organelles of interest through expressing organelle-specific HaloTag proteins. Using HaloRT, we quantitatively measure the glutathione concentrations in the nucleus and the cytosol and find no appreciable concentration gradient between these two organelles, challenging the view of nuclear compartmentalization of glutathione.

cell biology↗

bioRxiv2017

DNA copy number gains of TCF4 (E2-2) are associated with poor outcome and the activated B-cell-like subtype of diffuse large B-cell lymphoma

The activated B-cell (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) is characterized by the chronic activation of signaling initiated by immunoglobulin- (IgM). By analyzing DNA copy profiles of 1,000 DLBCLs, we identified gains of 18q21.2 as the most frequent genetic alteration in ABC-like DLBCL. We show that these alterations target the TCF4 (E2-2) transcription factor, and that over-expression of TCF4 leads to its occupancy on immunoglobulin gene enhancers and increased expression of IgM at the transcript and protein level. The TCF4 gene is one of the top BRD4-regulated genes in DLBCL. Using a BET proteolysis-targeting chimera (PROTAC) we show that TCF4 and IgM expression can be extinguished, and ABC-like DLBCL cells can be killed in vitro and in vivo. This highlights a novel genetic mechanism for promoting immunoglobulin signaling in ABC-like DLBCL and provides a functional rationale for the use of BET inhibitors in this disease.

genomics↗