Biology subjects

Lane, C.

Publications and source records attributed to Lane, C..

7 recordsLinked to original sources

bioRxiv2025

Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health

Major mental disorders are increasingly understood as disorders of brain development. Large and heterogeneous samples are required to define generalizable links between brain development and psychopathology. To this end, we introduce the Reproducible Brain Charts (RBC), an open data resource that integrates data from 5 large studies of brain development in youth from three continents (N=6,346; 45% Female). Confirmatory bifactor models were used to create harmonized psychiatric phenotypes that capture major dimensions of psychopathology. Following rigorous quality assurance, neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner with DataLad, the Configurable Pipeline for the Analysis of Connectomes (C-PAC), and FreeSurfer. Initial analyses of RBC data emphasize the benefit of careful quality assurance and data harmonization in delineating developmental effects and associations with psychopathology. Critically, all RBC data - including harmonized psychiatric phenotypes, unprocessed images, and fully processed imaging derivatives - are openly shared without a data use agreement via the International Neuroimaging Data-sharing Initiative. Together, RBC facilitates large-scale, reproducible, and generalizable research in developmental and psychiatric neuroscience.

neuroscience↗

bioRxiv2024

Analyses of transposable elements in arbuscular mycorrhizal fungi support evolutionary parallels with fungal plant pathogens

Transposable elements (TEs) are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi (AMF) are beneficial plant symbionts with large, TE-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model AMF strains. Here, we aimed to obtain a more comprehensive understanding of TE function and evolution in AMF by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing TE activity contributing to the diversification of AMF lineages. We also found that TEs are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of TEs in promoting the diversity in proteins involved in molecular dialogues with hosts and, more generally, in driving gene regulation. The mechanisms of TEs evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.

genomics↗

bioRxiv2024

Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics

Ochrophyta is a vast and morphologically diverse group of algae with complex plastids, including familiar taxa with fundamental ecological importance (diatoms or kelp), and a wealth of lesser-known and obscure organisms. The sheer diversity of ochrophytes poses a challenge for reconstructing their phylogeny, with major gaps in sampling and an unsettled placement of particular taxa yet to be tackled. We sequenced transcriptomes from 25 strategically selected representatives and used these data to build the most taxonomically comprehensive ochrophyte-centered phylogenomic supermatrix to date. We employed a combination of approaches to reconstruct and critically evaluate the relationships among ochrophytes. While generally congruent with previous analyses, the updated ochrophyte phylogenomic tree resolved the position of several taxa with previously uncertain placement, and supported a redefinition of the class Synchromophyceae. Our results indicated that the heterotrophic plastid-lacking heliozoan Actinophrys sol is not a sister lineage of ochrophytes, as proposed recently, but rather phylogenetically nested among them. In addition, we found Picophagus flagellatus to be a secondarily heterotrophic ochrophyte lacking all hallmark plastid genes, yet exhibiting mitochondrial proteins that seem to be genetic footprints of lost plastid organelle. We thus document, for the first time, plastid loss in two separate ochrophyte lineages. Altogether, our study provides a new framework for reconstructing trait evolution in ochrophytes and demonstrates that plastid loss is more common than previously thought. Issue Section: Discoveries

evolutionary biology↗

bioRxiv2019

Genomics, evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes

The Alternaria section alternaria (A. alternata species group) represents a diverse group of saprophytes, human allergens and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear and strawberry pathotypes, providing new tools for pathogen diagnostics.

microbiology↗

bioRxiv2018

A double dissociation in sensitivity to verb and noun semantics across cortical networks.

What is the neural organization of the mental lexicon? Previous research suggests that partially distinct cortical networks are active during verb and noun processing. Are these networks preferentially involved in representing the meanings of verbs as opposed to nouns? We used multivoxel pattern analysis (MVPA) to investigate whether brain regions that are more active during verb than noun processing are also more sensitive to distinctions among their preferred lexical class. Participants heard four types of verbs (light emission, sound emission, hand-related actions, mouth-related actions) and four types of nouns (birds, mammals, manmade places, natural places). As previously shown, the left posterior middle temporal gyrus (LMTG) and inferior frontal gyrus (LIFG) responded more to verbs, whereas areas in the inferior parietal lobule (LIP), precuneus (LPC), and inferior temporal (LIT) cortex responded more to nouns. MVPA revealed a double-dissociation in semantic sensitivity: classification was more accurate among verbs than nouns in the LMTG, and among nouns than verbs in the LIP, LPC, and LIT. However, classification was similar for verbs and nouns in the LIFG, and above chance for the non-preferred category in all regions. These results suggest that the meanings of verbs and nouns are represented in partially non-overlapping networks.

neuroscience↗

bioRxiv2017

Real-time genomic and epidemiological investigation of a multi-institution outbreak of KPC-producing Enterobacteriaceae: a translational study

BackgroundUntil recently, KPC-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks.\n\nMethods and FindingsAll KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing (WGS) was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids. Initial investigations indicated the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012-2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation.\n\nConclusionsA real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase producing Enterobacteriaceae management.

genomics↗

bioRxiv2017

Salmonella enterica Serovar Typhimurium ST313 Responsible For Gastroenteritis In The UK Are Genetically Distinct From Isolates Causing Bloodstream Infections In Africa

The ST313 sequence type of Salmonella enterica serovar Typhimurium causes invasive non-typhoidal salmonellosis amongst immunocompromised people in sub-Saharan Africa (sSA). Previously, two distinct phylogenetic lineages of ST313 have been described which have rarely been found outside sSA. Following the introduction of routine whole genome sequencing of Salmonella enterica by Public Health England in 2014, we have discovered that 2.7% (79/2888) of S. Typhimurium from patients in England and Wales are ST313. Of these isolates, 59/72 originated from stool and 13/72 were from extra-intestinal sites. The isolation of ST313 from extra-intestinal sites was significantly associated with travel to Africa (OR 12 [95% CI: 3,53]). Phylogenetic analysis revealed previously unsampled diversity of ST313, and distinguished UK-linked isolates causing gastroenteritis from African-associated isolates causing invasive disease. Bayesian evolutionary investigation suggested that the two African lineages diverged from their most recent common ancestors independently, circa 1796 and 1903. The majority of genome degradation of African ST313 lineage 2 is conserved in the UK ST313 lineages and only 10/44 pseudogenes were lineage 2-specific. The African lineages carried a characteristic prophage and antibiotic resistance gene repertoire, suggesting a strong selection pressure for these horizontally-acquired genetic elements in the sSA setting. We identified an ST313 isolate associated with travel to Kenya that carried a chromosomally-located blaCTX-M-15, demonstrating the continual evolution of this sequence type in Africa in response to selection pressure exerted by antibiotic usage.\n\nThe S. Typhimurium ST313 sequence type has been primarily associated with invasive disease in Africa. Here, we highlight the power of routine whole-genome-sequencing by public health agencies to make epidemiologically-significant deductions that would be missed by conventional microbiological methods. The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. We speculate that the niche specialization of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.

microbiology↗