Biology subjects

Martin, A.

Publications and source records attributed to Martin, A..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

A large-scale retrospective study in metastatic breast cancer patients using circulating tumor DNA and machine learning to predict treatment outcome and progression-free survival

PurposeMonitoring levels of circulating tumor-derived DNA (ctDNA) represents a non-invasive snapshot of tumor burden and potentially clonal evolution. Here we describe how a novel statistical model that uses serial ctDNA measurements from shallow whole genome sequencing (sWGS) in metastatic breast cancer patients produces a rapid and inexpensive assessment that is predictive of treatment response and progression-free survival. Patients and MethodsA cohort of 188 metastatic breast cancer patients had DNA extracted from serial plasma samples (total 1098, median=4, mean=5.87). Plasma DNA was assessed using sWGS and the tumor fraction in total cell free DNA estimated using ichorCNA. This approach was compared with ctDNA targeted sequencing and serial CA 15-3 measurements. The longitudinal ichorCNA values were used to develop a Bayesian learning model to predict subsequent treatment response. ResultsWe identified a transition point of 7% estimated tumor fraction to stratify patients into different categories of progression risk using ichorCNA estimates and a time-dependent Cox model, validated across different breast cancer subtypes and treatments, outperforming the alternative methods. We then developed a Bayesian learning model to predict subsequent treatment response with a sensitivity of 0.75 and a specificity of 0.66. ConclusionIn patients with metastatic breast cancer, sWGS of ctDNA and ichorCNA provide prognostic and predictive real-time valuable information on treatment response across subtypes and therapies. A prospective large-scale clinical trial to evaluate clinical benefit of early treatment changes based on ctDNA levels is now warranted.

genomics↗

bioRxiv2023

Genetics of continuous colour variation in a pair of sympatric sulphur butterflies

Continuous colour polymorphisms can serve as a tractable model for the genetic and developmental architecture of traits, but identification of the causative genetic loci is complex due to the number of individuals needed, and the challenges of scoring continuously varying traits. Here we investigated continuous colour variation in Colias eurytheme and C. philodice, two sister species of sulphur butterflies that hybridise in sympatry. Using Quantitative Trait Locus (QTL) analysis of 483 individuals from interspecific crosses and an high-throughput method of colour quantification, we found that two interacting large effect loci explain around 70% of the heritable variation in orange-to-yellow chromaticity. Knockouts of red Malphighian tubules (red), a candidate gene at the primary QTL likely involved in endosomal maturation, resulted in depigmented wing scales showing disorganised pterin granules. The Z sex chromosome contains a large secondary colour QTL that includes the transcription factor bric-a-brac (bab), which we show can act as a modulator of orange pigmentation in addition to its previously-described role in specifying UV-iridescence. We also describe the QTL architecture of other continuously varying traits, and that wing size maps to the Z chromosome, supporting a Large-X effect model where the genetic control of species-defining traits is enriched on sex chromosomes. This study sheds light on the genetic architecture of a continuously varying trait, and illustrates the power of using automated measurement to score phenotypes that are not always conspicuous to the human eye. ForewordThe colour phenotypes in this article involve nuanced gradations of yellow and orange that may be difficult to perceive for people who are colour vision deficient. Hue-shifted versions of all main figures are accessible online for dichromat readers (BioRxiv preprint: Supplementary Material).

genetics↗

bioRxiv2023

A general strategy to develop fluorogenic polymethine dyes for bioimaging

Fluorescence imaging is an invaluable tool to study biological processes and further progress depends on the development of advanced probes. Fluorogenic dyes are crucial to reach intracellular targets and label them with high specificity. Excellent fluorogenic rhodamine dyes have been reported, but they often require a long and low-yielding synthesis and are spectrally limited to the visible range. Here, we present a general strategy to transform polymethine compounds into fluorogenic dyes using an intramolecular ring closure approach. We illustrate the generality of this method by creating both spontaneously blinking and no-wash, turn-on polymethine dyes with emissions across the visible and near-infrared spectrum. These probes are compatible with self-labeling proteins and small-molecule targeting ligands and can be combined with rhodamine-based dyes for multicolor and fluorescence lifetime multiplexing imaging. This strategy provides access to bright, fluorogenic dyes that emit at wavelengths that are significantly more red-shifted than those of existing rhodamine-based dyes.

biochemistry↗

bioRxiv2023

A harmonized public resource of deeply sequenced diverse human genomes

Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftover and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.

genomics↗

bioRxiv2022

HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes

Existing methods for simulating synthetic genotype and phenotype datasets have limited scalability, constraining their usability for large-scale analyses. Moreover, a systematic approach for evaluating synthetic data quality and a benchmark synthetic dataset for developing and evaluating methods for polygenic risk scores are lacking. We present HAPNEST, a novel approach for efficiently generating diverse individual-level genotypic and phenotypic data. In comparison to alternative methods, HAPNEST shows faster computational speed and a lower degree of relatedness with reference panels, while generating datasets that preserve key statistical properties of real data. These desirable synthetic data properties enabled us to generate 6.8 million common variants and nine phenotypes with varying degrees of heritability and polygenicity across 1 million individuals. We demonstrate how HAPNEST can facilitate biobank-scale analyses through the comparison of seven methods to generate polygenic risk scoring across multiple ancestry groups and different genetic architectures.

bioinformatics↗

bioRxiv2022

Targeted chromosomal barcoding establishes direct genotype-phenotype associations for antibiotic resistance in Mycobacterium abscessus

A bedaquiline resistant Mycobacterium abscessus isolate was sequenced and a candidate mutation in the atpE gene was identified as responsible for the antibiotic resistance phenotype. To establish a direct genotype-phenotype relationship of this D29A mutation, we developed a recombineering-based method consisting of the specific replacement of the desired mutation in the bacterial chromosome. As surrogate bacteria, we used two M. abscessus antibiotic susceptible strains: ATCC19977, and the SL541 clinical isolate. The allelic exchange substrates used in recombineering carried either the sole D29A mutation, or a genetic barcode of silent mutations in codons flanking the D29A mutation. After selection of bedaquiline resistant M. abscessus colonies, transformed with both substrates, we obtained equivalent numbers of recombinants. These resistant colonies were analyzed by allele-specific PCR, and Sanger sequencing, demonstrating that the presence of the genetic barcode is linked to the targeted incorporation of the desired mutation in its chromosomal location. All recombinants displayed the same minimal inhibitory concentration to bedaquiline than the original isolate, from which the D29A mutation was identified. Finally, to demonstrate the broad applicability of this method, we confirmed the association of bedaquiline resistance with the atpE A64P mutation, performed in independent M. abscessus strains and by independent researchers.

microbiology↗

bioRxiv2022

Compensation and conversation in autism: atypical connectivity supports typical behavior

BackgroundIt is well-established that individuals with autism show atypical functional brain connectivity. However, the role this plays in behavior, especially in naturalistic social settings, has remained unclear. Some atypical patterns may reflect core deficits, while others may instead compensate for deficits and promote adaptive behavior. Distinguishing these possibilities requires measuring the typicality of spontaneous behavior and determining which connectivity patterns correlate with it. MethodsThirty-nine male participants (19 autism, 20 typically-developed) engaged in 115 spontaneous conversations with an experimenter during fMRI scanning (Jasmin, et al., 2019, Brain). A classifier algorithm was trained to distinguish participants by diagnosis based on 81 semantic, affective and linguistic dimensions derived from their use of language. The algorithms certainty that a participant was in either the autism or typical group was used as a measure of task performance and compared with functional connectivity levels. ResultsThe algorithm accurately classified participants (74%, P = .002), and its scores correlated with clinician-observed autism signs (ADOS) (rs = .56, P = .03). In support of a compensatory role, greater functional connectivity, most prominently between left-hemisphere social communication regions and right inferior frontal cortex, correlated with more typical language behaviour, only for the autism group (rs = .56, P = .01). ConclusionWe report a simple and highly generalizable method for quantifying behavioral performance and neural compensation during complex spontaneous social behavior, without the need for an a priori benchmark. The findings suggest that functional connectivity increases in autism during communication reflect a neural compensation strategy.

neuroscience↗

bioRxiv2022

Prefrontal-Parietal-cTBS effects on metacognitive awareness: real or illusory?

BackgroundNeuroimaging and lesion studies suggested that the dorsolateral prefrontal and posterior parietal cortices mediate visual metacognitive awareness. The causal evidence provided by non-invasive brain stimulation, however, is inconsistent. Objective/HypothesisHere we revisit a major figure discrimination experiment adding a new Kanizsa figure task trying to resolve whether bilateral continuous theta-burst transcranial magnetic stimulation (cTBS) over these regions affects perceptual metacognition. Specifically, we tested whether subjective visibility ratings and/or metacognitive efficiency are lower when cTBS is applied to these two regions in comparison to an active control region. MethodsA within-subjects design including three sessions spaced by one-week intervals was implemented. In each session, every participant was administered bilateral cTBS to either prefrontal, control or parietal cortices. Two concurrent tasks were performed, a real and an illusory figure task, stabilising objective performance with use of an adaptive staircase procedure. ResultsWhen performing the replicated task, cTBS was found insufficient to disrupt neither visibility ratings nor metacognitive efficiency. However, with use of Kanizsa style illusory figures, cTBS over the dorsolateral prefrontal, but not over the posterior parietal cortex, was observed to significantly diminish metacognitive efficiency. Conclusion(s)Real and illusory figure tasks demonstrated different cTBS effects. A possible explanation is the involvement of the prefrontal cortex in the creation of expectations, which is necessary for efficient metacognition. Failure to replicate previous findings for the real figure task, however, cannot be said to support, conclusively, the notion that these brain regions have a causal role in metacognitive awareness. This inconsistent finding may result from certain limitations of our study, thereby suggesting the need for yet further investigation.

neuroscience↗

bioRxiv2022

A common neural code for representing imagined and inferred tastes

Inferences about the taste of foods are a key aspect of our everyday experience of food choice. Despite this, gustatory mental imagery is a relatively under-studied aspect of our mental lives. In the present study, we examined subjects during high-field fMRI as they actively imagined basic tastes and subsequently viewed pictures of foods dominant in those specific taste qualities. Imagined tastes elicited activity in the bilateral dorsal mid-insula, one of the primary cortical regions responsive to the experience of taste. In addition, within this region we reliably decoded imagined tastes according to their dominant quality - sweet, sour, or salty - thus indicating that, like actual taste, imagined taste activates distinct quality-specific neural patterns. Using a cross-task decoding analysis, we found that the neural patterns for imagined tastes and food pictures in the mid-insula were reliably similar and quality-specific, suggesting a common code for representing taste quality regardless of whether explicitly imagined or automatically inferred when viewing food. These findings have important implications for our understanding of the mechanisms of mental imagery and the multimodal nature of presumably primary sensory brain regions like the dorsal mid-insula.

neuroscience↗

bioRxiv2022

Efficient hyperactive piggyBac transgenesis in Plodia pantry moths

While piggyBac transposon-based transgenesis is widely used in various emerging model organisms, its relatively low transposition rate in butterflies and moths has hindered its use for routine genetic transformation in Lepidoptera. Here, we tested the suitability of a codon-optimized hyperactive piggyBac transposase (hyPBase) in mRNA form to deliver and integrate transgenic cassettes into the genome of the pantry moth Plodia interpunctella. Co-injection of hyPBase mRNA with donor plasmids successfully integrated 1.5-4.4 kb expression cassettes driving the fluorescent markers EGFP, DsRed, or EYFP in eyes and glia with the 3xP3 promoter. Somatic integration and expression of the transgene in the G0 injected generation was detectable from 72-hr embryos and onward in larvae, pupae and adults carrying a recessive white-eyed mutation. Overall, 2.5% of injected eggs survived into transgene-bearing adults with mosaic fluorescence. Subsequent outcrossing of fluorescent G0 founders transmitted single-insertion copies of 3xP3::EGFP and 3xP3::EYFP and generated stable isogenic lines. Random in-crossing of a small cohort of G0 founders expressing 3xP3::DsRed yielded a stable transgenic line segregating for more than one transgene insertion site. We discuss how hyPBase can be used to generate stable transgenic resources in Plodia and other moths.

genetics↗

bioRxiv2022

Signaling pathways involved in the repression of root nitrate uptake by nitrate in Arabidopsis thaliana

In Arabidopsis thaliana, root high-affinity nitrate (NO3-) uptake depends mainly on NRT2.1, 2.4 and 2.5, which are repressed by high NO3- supply at the transcript level. For NRT2.1, this regulation is due to the action of (i) feedback downregulation by N metabolites and (ii) repression by NO3- itself mediated by the transceptor NRT1.1(NPF6.3). However, for NRT2.4 and NRT2.5 the signaling pathway(s) remain unknown along with the molecular elements involved. Here we show that unlike NRT2.1, NRT2.4 and NRT2.5 are not induced in a NO3- reductase mutant but are strongly upregulated following replacement of NO3- by ammonium (NH4+) as the N source. Moreover, increasing NO3- concentration in a mixed nutrient solution with constant NH4+ concentration results in a gradual repression of NRT2.4 and NRT2.5, which is suppressed in a nrt1.1 mutant. This indicates that NRT2.4 and NRT2.5 are subjected to repression by NRT1.1-mediated NO3- sensing, and not to feedback repression by reduced N metabolites. We further show that key regulators of NRT2s transporters, such as HHO1, HRS1, PP2C, LBD39, BT1 and BT2, are also regulated by NRT1.1-mediated NO3- sensing, and that several are involved in NO3- repression of NRT2.1, 2.4 and 2.5. Finally, we provide evidence that it is the phosphorylated form of NRT1.1 at the T101 residue, which is most active in triggering the NRT1.1-mediated NO3- regulation of all these genes. Altogether, these data led to propose a regulatory model for high-affinity NO3- uptake in Arabidopsis, highlighting several NO3- transduction cascades downstream the phosphorylated form of the NRT1.1 transceptor. One sentence summaryCharacterisation and identification of molecular elements involved in the signaling pathways repressing NRT2s transporters and root nitrate uptake in response to nitrate.

plant biology↗

bioRxiv2022

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Heliconius butterflies, a speciose genus of Mullerian mimics, represent a classic example of an adaptive radiation that includes a range of derived dietary, life history, physiological and neural traits. However, key lineages within the genus, and across the broader Heliconiini tribe, lack genomic resources, limiting our understanding of how adaptive and neutral processes shaped genome evolution during their radiation. We have generated highly contiguous genome assemblies for nine new Heliconiini, 29 additional reference-assembled genomes, and improve 10 existing assemblies. Altogether, we provide a major new dataset of annotated genomes for a total of 63 species, including 58 species within the Heliconiini tribe. We use this extensive dataset to generate a robust and dated heliconiine phylogeny, describe major patterns of introgression, explore the evolution of genome architecture, and the genomic basis of key innovations in this enigmatic group, including an assessment of the evolution of putative regulatory regions at the Heliconius stem. Our work illustrates how the increased resolution provided by such dense genomic sampling improves our power to generate and test gene-phenotype hypotheses, and precisely characterize how genomes evolve.

evolutionary biology↗

bioRxiv2022

VALPROIC ACID AFFECTS NEURONAL SPECIFICATION AND DIFFERENTIATION DURING EARLY OPTIC TECTUM DEVELOPMENT OF ZEBRAFISH

The mammalian superior colliculus and its non-mammalian homolog, the optic tectum (OT), are midbrain structures that integrate multimodal sensory inputs and guide non-voluntary movements in response to prevalent stimuli. Recent studies have implicated this structure as a possible site affected in Autism Spectrum Disorder (ASD). Interestingly, fetal exposure to valproic acid (VPA) has also been associated with an increased risk of ASD in humans and animal models. Therefore, we took the approach of determining the effects of VPA treatment on zebrafish OT development as a first step in identifying the mechanisms that allow its formation. We describe the normal OT development during the first 5 days of development and show that in VPA treated embryos, while proliferation of the OT neuroepithelium continued, neuronal specification stalled. This was followed by impairment of neurite extension and complexity, suggesting that in addition to neurogenesis, VPA treatment affects axonogenesis and dendritogenesis. VPA treatment was most detrimental during the first three days of development and did not appear to be linked to oxidative stress. In conclusion, our work provides a foundation for research into mechanisms driving OT development, as well as the relationship between the OT, VPA, and ASD.

developmental biology↗

bioRxiv2022

The Nucleocapsid Protein Of SARS-CoV-2, Combined With ODN-39M, Is A Potential Component For An Intranasal Bivalent Pancorona Vaccine

Despite the rapid development of vaccines and their reported efficacy for controlling the COVID-19 waves, two key challenges remain: the scope of the immunity against upcoming variants and zoonosis events, and the induction of mucosal immunity able to clear the virus in the upper respiratory tract for halting the transmission. The present study is aiming at assessing a potential component for a new generation of vaccines so as to overcome such limitations. The recombinant nucleocapsid (N) protein from SARS-CoV-2 Delta variant was combined with a phosphodiester backbone CpG ODN (ODN-39M), forming high molecular weight aggregates. The evaluation of its immunogenicity in Balb/C mice revealed that only administration by intranasal route induced a systemic cross-reactive Cell-Mediated-Immunity (CMI). In turn, this combination was able to induce anti-N IgA in lungs, which along with the specific IgG in sera and CMI in spleen, resulted cross-reactive against the nucleocapsid protein of SARS-CoV-1. Furthermore, the nasal administration of the N+ODN-39M preparation combined with the RBD Delta protein, as inductor of neutralizing Abs, enhanced the local and systemic immune response against RBD with a modulation toward a Th1 pattern. Taken together, these results make the N+ODN-39M preparation a suitable component for a future intranasal pancorona vaccine against Sarbecoviruses. Particularly, the bivalent vaccine formulation N+ODN-39M+RBD could be used as an effective nasal booster in previously vaccinated population.

immunology↗

bioRxiv2022

A role for the anterior hippocampus in autobiographical memory construction regardless of temporal distance

Mounting evidence suggests distinct functional contributions of the anterior and posterior hippocampus to autobiographical memory retrieval, but how these subregions function under different retrieval demands as memories age is not yet understood. Specifically, autobiographical memory retrieval is not a homogenous process, rather, it is thought to consist of multiple stages: an early stage of memory construction and a later stage of detailed elaboration, which may differently engage the hippocampus over time. In the present study, we analyzed data from 40 participants who constructed and overtly elaborated upon recent and remote memories in response to picture cues in the fMRI scanner. We previously reported a temporal gradient in the posterior hippocampus during the elaboration period of autobiographical retrieval, with posterior hippocampal activation observed for recent but not remote timepoints. Here, we consider the previously unanalyzed construction stage of retrieval, where participants searched for and selected a memory. We found no evidence of a temporal gradient during memory construction, instead observing strong anterior hippocampus activity regardless of memory remoteness. Our findings suggest a unique contribution of the anterior hippocampus to the construction process of autobiographical retrieval over time. These findings highlight that retrieval processes, which have yet to be considered in current models of systems consolidation, offer novel insights to hippocampal subregion function over time.

neuroscience↗

bioRxiv2022

Restriction of dietary fat, but not carbohydrate, alters brain reward circuitry in adults with obesity

Weight loss diets often target restriction of dietary fat or carbohydrate, macronutrients that are sensed via distinct gut-brain pathways and differentially affect peripheral hormones and metabolism. However, the effects of such diet changes on human brain are unclear. We investigated whether selective isocaloric reductions in dietary fat or carbohydrate altered dopamine D2/3 receptor binding potential (D2BP) and neural activity in brain reward regions in response to visual food cues in 17 inpatient adults with obesity as compared to a eucaloric baseline diet. On the fifth day of dietary fat restriction, but not carbohydrate restriction, both D2BP and neural activity to food cues were decreased in brain reward regions. After the reduced fat diet, ad libitum intake shifted towards foods high in both fat and carbohydrates. These results suggest that dietary fat restriction increases tonic dopamine in brain reward regions and affects food choice in ways that may hamper diet adherence.

neuroscience↗

bioRxiv2022

Genotypic sex shapes maternal care in the African Pygmy mouse, Mus minutoides

AO_SCPLOWBSTRACTC_SCPLOWSexually dimorphic behaviours, such as parental care, have long been thought to be driven mostly, if not exclusively, by gonadal hormones. In the past two decades, a few studies have challenged this view, highlighting the direct influence of the sex chromosome complement (XX vs XY or ZZ vs ZW). The African pygmy mouse, Mus minutoides, is a wild mouse species with naturally occurring XY sex reversal induced by a third, feminizing X* chromosome, leading to three female genotypes: XX, XX* and X*Y. Here, we show that sex reversal in X*Y females shapes a divergent maternal care strategy from both XX and XX* females, rather than altering care quality. In addition, we show that sex reversal may also impact the dopaminergic system in the anteroventral periventricular nucleus of the hypothalamus, consistent with one component of maternal care: pup retrieval. Combining behavioural ecology and neurobiology in a rodent subject to natural selection, we evaluate potential candidates for the neural basis of maternal behaviours and strengthen the underestimated role of the sex chromosomes in shaping sex differences in brain and behaviours. All things considered, we further highlight the emergence of a third sexual phenotype, challenging the binary view of phenotypic sexes.

evolutionary biology↗

bioRxiv2022

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders, but attempts to assess constraint for non-protein-coding regions have proven more difficult. Here we aggregate, process, and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD), the largest public open-access human genome reference dataset, and use this dataset to build a mutational constraint map for the whole genome. We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation across the genome. As expected, proteincoding sequences overall are under stronger constraint than non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association, and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, while non-coding constraint captures additional functional information underrecognized by gene constraint metrics. We demonstrate that this genome-wide constraint map provides an effective approach for characterizing the non-coding genome and improving the identification and interpretation of functional human genetic variation.

genetics↗