ORCID Profile
0000-0001-7602-8366
Current Organisations
University of Southern Denmark
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SDU
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Publisher: Springer Science and Business Media LLC
Date: 09-04-2022
DOI: 10.1186/S13104-022-06013-3
Abstract: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses. These data include raw sequences from four separate sequencing runs of the metagenome of a single in idual of Halichondria panicea —one Illumina MiSeq (2 × 300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the ‘best’ assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.
Publisher: American Society for Microbiology
Date: 24-02-2015
Abstract: The oceans have an uncertain future due to anthropogenic stressors and an uncertain past that is becoming clearer with advances in biogeochemistry. Both past and future oceans were, or will be, deoxygenated in comparison to present conditions.
Publisher: eLife Sciences Publications, Ltd
Date: 06-02-2018
DOI: 10.7554/ELIFE.31176
Abstract: Animals have a carefully orchestrated relationship with oxygen. When exposed to low environmental oxygen concentrations, and during periods of increased energy expenditure, animals maintain cellular oxygen homeostasis by enhancing internal oxygen delivery, and by enabling the anaerobic production of ATP. These low-oxygen responses are thought to be controlled universally across animals by the hypoxia-inducible factor (HIF). We find, however, that sponge and ctenophore genomes lack key components of the HIF pathway. Since sponges and ctenophores are likely sister to all remaining animal phyla, the last common ancestor of extant animals likely lacked the HIF pathway as well. Laboratory experiments show that the marine sponge Tethya wilhelma maintains normal transcription under oxygen levels down to 0.25% of modern atmospheric saturation, the lowest levels we investigated, consistent with the predicted absence of HIF or any other HIF-like pathway. Thus, the last common ancestor of all living animals could have metabolized aerobically under very low environmental oxygen concentrations.
Publisher: Elsevier BV
Date: 03-2013
Publisher: Springer Science and Business Media LLC
Date: 13-06-2018
DOI: 10.1038/S41380-018-0078-5
Abstract: The 22q11.2 deletion (22q11DS) is a common chromosomal microdeletion and a potent risk factor for psychotic illness. Prior studies reported widespread cortical changes in 22q11DS, but were generally underpowered to characterize neuroanatomic abnormalities associated with psychosis in 22q11DS, and/or neuroanatomic effects of variability in deletion size. To address these issues, we developed the ENIGMA (Enhancing Neuro Imaging Genetics Through Meta-Analysis) 22q11.2 Working Group, representing the largest analysis of brain structural alterations in 22q11DS to date. The imaging data were collected from 10 centers worldwide, including 474 subjects with 22q11DS (age = 18.2 ± 8.6 46.9% female) and 315 typically developing, matched controls (age = 18.0 ± 9.2 45.9% female). Compared to controls, 22q11DS in iduals showed thicker cortical gray matter overall (left/right hemispheres: Cohen’s d = 0.61/0.65), but focal thickness reduction in temporal and cingulate cortex. Cortical surface area (SA), however, showed pervasive reductions in 22q11DS (left/right hemispheres: d = −1.01/−1.02). 22q11DS cases vs. controls were classified with 93.8% accuracy based on these neuroanatomic patterns. Comparison of 22q11DS-psychosis to idiopathic schizophrenia (ENIGMA-Schizophrenia Working Group) revealed significant convergence of affected brain regions, particularly in fronto-temporal cortex. Finally, cortical SA was significantly greater in 22q11DS cases with smaller 1.5 Mb deletions, relative to those with typical 3 Mb deletions. We found a robust neuroanatomic signature of 22q11DS, and the first evidence that deletion size impacts brain structure. Psychotic illness in this highly penetrant deletion was associated with similar neuroanatomic abnormalities to idiopathic schizophrenia. These consistent cross-site findings highlight the homogeneity of this single genetic etiology, and support the suitability of 22q11DS as a biological model of schizophrenia.
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.SCHRES.2014.01.020
Abstract: 22q11.2 deletion syndrome (22q11.2DS) is associated with high rates of psychotic disorder, particularly schizophrenia. The deletion is considered to be a biological model for understanding this debilitating psychiatric disorder. It is unclear whether the psychotic manifestations in 22q11.2DS are similar to those in schizophrenia patients without the deletion. Catechol-O-methyltransferase (COMT), a positional candidate gene for schizophrenia, resides within the 22q11.2 region. It remains unknown whether hemizygosity for this gene is associated with risk of psychotic disorder. This study includes 83 adults with 22q11.2DS, 90 non-deleted in iduals with schizophrenia, and 316 normal controls. Psychopathology was assessed using the Schedules for Clinical Assessment in Neuropsychiatry, the Schedules for the Assessment of Positive and Negative Symptoms and the Global Assessment Scale. Schizotypy was assessed with the Kings Schizotypy Questionnaire and Oxford Liverpool Inventory of Feelings and Emotions. IQ estimates were also obtained. Adults with 22q11.2DS were genotyped for a number of COMT polymorphisms as well as the Ashkenazi risk haplotype. This study confirms high rates of psychotic disorder (29%) in in iduals with 22q11.2DS of which the majority had schizophrenia (22%). There does not appear to be a differential expression of schizophrenic symptom clusters in 22q11.2DS in relation to sporadic schizophrenia, though schizophrenia in 22q11.2DS seems to be less severe in terms of global assessment scores. Psychosis proneness seems to be of genetic origin in 22q11.2DS as in iduals with 22q11.2DS without schizophrenia had higher schizotypy scores than normal controls. Finally, COMT was not associated with schizophrenia status or schizotypy.
Publisher: Springer Science and Business Media LLC
Date: 03-2001
DOI: 10.1038/35065071
Publisher: Elsevier BV
Date: 11-2016
Publisher: Public Library of Science (PLoS)
Date: 25-06-2014
Publisher: Wiley
Date: 10-2018
DOI: 10.1002/AJMG.A.40359
Publisher: Elsevier BV
Date: 03-2019
Publisher: Cold Spring Harbor Laboratory
Date: 18-09-2018
DOI: 10.1101/420778
Abstract: The last decade has seen the development of services for adults presenting with symptoms of autism spectrum disorder (ASD) in the UK. Compared to children, little is known about the phenotypic and genetic characteristics of these patients. This e-cohort study aimed to examine the phenotypic and genetic characteristics of a clinically-presenting s le of adults diagnosed with ASD by specialist services. In iduals diagnosed with ASD as adults were recruited by the National Centre for Mental Health and completed self-report questionnaires, interviews and provided DNA. 105 eligible in iduals were matched to 76 healthy controls. We investigated the demographics, social history, comorbid psychiatric and physical disorders. S les were genotyped, copy number variants (CNVs) were called and polygenic risk scores calculated. 89.5% of in iduals with ASD had at least one comorbid psychiatric diagnosis with comorbid depression (62.9%) and anxiety (55.2%) the most common. The ASD group experienced more neurological comorbidities than healthy controls, particularly migraine headache. They were less likely to have married or be in work and had more alcohol-related problems. There was a significantly higher load of autism common genetic variants in the adult ASD group compared to controls, but there was no difference in the rate of rare CNVs. This study provides important information about psychiatric comorbidity in adult ASD which may be used to inform clinical practice and patient counselling. It also suggests that the polygenic load of common ASD-associated variants may be important in conferring risk within non-intellectually disabled population of adults with ASD.
Publisher: Cold Spring Harbor Laboratory
Date: 21-01-2022
DOI: 10.1101/2022.01.18.22269463
Abstract: Current psychiatric diagnoses, although heritable, have not been clearly mapped onto distinct underlying pathogenic processes. The same symptoms often occur in multiple disorders, and a substantial proportion of both genetic and environmental risk factors are shared across disorders. However, the relationship between shared symptomatology and shared genetic liability is still poorly understood. Well-characterised, cross-disorder s les are needed to investigate this matter, but currently few exist, and severe mental disorders are poorly represented in existing biobanking efforts. Purposely curated and aggregated data from in idual research groups can fulfil this unmet need, resulting in rich resources for psychiatric research. As part of the Cardiff MRC Mental Health Data Pathfinder, we have curated and harmonised phenotypic and genetic information from 15 studies within the MRC Centre for Neuropsychiatric Genetics and Genomics to create a new data repository, DRAGON-DATA. To date, DRAGON-DATA includes over 45,000 in iduals: adults or children with psychiatric diagnoses, affected probands with family members and in iduals who carry a known neurodevelopmental copy number variant (ND-CNV). We have processed the available phenotype information to derive core variables that can be reliably analysed across groups. In addition, all datasets with genotype information have undergone rigorous quality control, imputation, CNV calling and polygenic score generation. DRAGON-DATA combines genetic and non-genetic information and is available as a resource for research across traditional psychiatric diagnostic categories. Its structure and governance follow standard UK ethical requirements (at the level of participating studies and the project as a whole) and conforms to principles reflected in the EU data protection scheme (GDPR). Algorithms and pipelines used for data harmonisation are currently publicly available for the scientific community, and an appropriate data sharing protocol will be developed as part of ongoing projects (DATAMIND) in partnership with HDR UK.
Publisher: Elsevier BV
Date: 05-2020
Publisher: Springer Science and Business Media LLC
Date: 04-09-2003
DOI: 10.1007/S00253-003-1422-4
Abstract: Recently, two fresh water species, " Candidatus Brocadia anammoxidans" and " Candidatus Kuenenia stuttgartiensis", and one marine species, " Candidatus Scalindua sorokinii", of planctomycete anammox bacteria have been identified. " Candidatus Scalindua sorokinii" was discovered in the Black Sea, and contributed substantially to the loss of fixed nitrogen. All three species contain a unique organelle--the anammoxosome--in their cytoplasm. The anammoxosome contains the hydrazine/hydroxylamine oxidoreductase enzyme, and is thus the site of anammox catabolism. The anammoxosome is surrounded by a very dense membrane composed almost exclusively of linearly concatenated cyclobutane-containing lipids. These so-called 'ladderanes' are connected to the glycerol moiety via both ester and ether bonds. In natural and man-made ecosystems, anammox bacteria can cooperate with aerobic ammonium-oxidising bacteria, which protect them from harmful oxygen, and provide the necessary nitrite. The cooperation of these two groups of ammonium-oxidising bacteria is the microbial basis for a sustainable one reactor system, CANON (completely autotrophic nitrogen-removal over nitrite) to remove ammonia from high strength wastewater.
Publisher: American Chemical Society (ACS)
Date: 26-09-0002
Publisher: American Psychiatric Association Publishing
Date: 11-2017
Publisher: Cold Spring Harbor Laboratory
Date: 10-09-2020
DOI: 10.1101/2020.09.09.290791
Abstract: Climate change is expanding marine oxygen minimum zones (OMZs), while anthropogenic nutrient input depletes oxygen concentrations locally. The effects of deoxygenation on animals are generally detrimental however, some sponges (Porifera) exhibit hypoxic and anoxic tolerance through currently unknown mechanisms. Sponges harbor highly specific microbiomes, which can include microbes with anaerobic capabilities. Sponge-microbe symbioses must also have persisted through multiple anoxic/hypoxic periods throughout Earth history. Since sponges lack key components of the hypoxia-inducible factor (HIF) pathway responsible for hypoxic responses in other animals, it was hypothesized that sponge tolerance to deoxygenation may be facilitated by its microbiome. To test this hypothesis, we determined the microbial composition of sponge species tolerating seasonal anoxia and hypoxia in situ in a semi-enclosed marine lake, using 16S rRNA licon sequencing. We discovered a high degree of cryptic ersity among sponge species tolerating seasonal deoxygenation, including at least nine encrusting species of the orders Axinellida and Poecilosclerida. Despite significant changes in microbial community structure in the water, sponge microbiomes were species specific and remarkably stable under varied oxygen conditions, though some symbiont sharing occurred under anoxia. At least three symbiont combinations, all including large populations of Thaumarchaeota , corresponded with deoxygenation tolerance, and some combinations were shared between distantly related hosts. We propose hypothetical host-symbiont interactions following deoxygenation that could confer deoxygenation tolerance. The oceans have an uncertain future due to anthropogenic stressors and an uncertain past that is becoming clearer with advances in biogeochemistry. Both past and future oceans were, or will be, deoxygenated compared to present conditions. Studying how sponges and their associated microbes tolerate deoxygenation provides insights into future marine ecosystems. Moreover, sponges form the earliest branch of the animal evolutionary tree and they likely resemble some of the first animals. We determined the effects of variable environmental oxygen concentrations on the microbial communities of several demosponge species during seasonal anoxia in the field. Our results indicate that anoxic tolerance in some sponges may depend on their symbionts, but anoxic tolerance was not universal in sponges. Therefore, some sponge species could likely outcompete benthic organisms like corals in future, reduced-oxygen ecosystems. Our results support the molecular evidence that sponges and other animals have a Neoproterozoic origin, and that animal evolution was not limited by low-oxygen conditions.
Publisher: Cold Spring Harbor Laboratory
Date: 16-01-2020
DOI: 10.1101/2020.01.14.20017426
Abstract: Certain copy number variants (CNVs) greatly increase risk of autism. We conducted a genetics-first study to investigate whether heterogeneity in the clinical presentation of autism is underpinned by specific genotype-phenotype relationships. This international study included 547 in iduals (12.3 years (SD=4.2), 54% male) who were ascertained on the basis of having a genetic diagnosis of a rare CNV associated with high risk of autism (82 16p11.2 deletion carriers, 50 16p11.2 duplication carriers, 370 22q11.2 deletion carriers and 45 22q11.2 duplication carriers), as well as 2027 in iduals (9.1 years (SD=4.9), 86% male) with autism of heterogeneous aetiology. The Autism Diagnostic Interview-Revised (ADI-R) and IQ testing were conducted. The four genetic variant groups differed in autism severity, autism subdomain profile as well as IQ profile. However, we found substantial variability in phenotypic outcome within in idual genetic variant groups (74% to 97% of the variance depending on the trait), whereas variability between groups was low (1% to 21% depending on trait). We compared CNV carriers who met autism criteria, to in iduals with heterogeneous autism, and a range of profile differences were identified. Using clinical cut-offs, we found that 54% of in iduals with one of the 4 CNVs who did not meet full autism diagnostic criteria nonetheless had elevated levels of autistic traits. Many CNV carriers do not meet full diagnostic criteria for autism, but nevertheless meet clinical cut-offs for autistic traits. Although we find profile differences between variants, there is considerable variability in clinical symptoms within the same variant.
Publisher: Wiley
Date: 24-09-2015
DOI: 10.1002/AJMG.B.32378
Publisher: Royal College of Psychiatrists
Date: 10-2017
DOI: 10.1192/BJP.BP.116.195651
Abstract: 22q11.2 deletion syndrome (22q11.2DS) is associated with a high risk of childhood as well as adult psychiatric disorders, in particular schizophrenia. Childhood cognitive deterioration in 22q11.2DS has previously been reported, but only in studies lacking a control s le. To compare cognitive trajectories in children with 22q11.2DS and unaffected control siblings. A longitudinal study of neurocognitive functioning (IQ, executive function, processing speed and attention) was conducted in children with 22q11.2DS ( n = 75, mean age time 1 ( T 1 ) 9.9, time 2 ( T 2 ) 12.5) and control siblings ( n = 33, mean age T 1 10.6, T 2 134). Children with 22q11.2DS exhibited deficits in all cognitive domains. However, mean scores did not indicate deterioration. When in idual trajectories were examined, some participants showed significant decline over time, but the prevalence was similar for 22q11.2DS and control siblings. Findings are more likely to reflect normal developmental fluctuation than a 22q11.2DS-specific abnormality. Childhood cognitive deterioration is not associated with 22q11.2DS. Contrary to previous suggestions, we believe it is premature to recommend repeated monitoring of cognitive function to identifying in idual children with 22q11.2DS at high risk of developing schizophrenia.
Publisher: American Psychiatric Association Publishing
Date: 06-2014
Publisher: Wiley
Date: 05-07-2021
DOI: 10.1111/GBI.12462
Publisher: Wiley
Date: 20-12-2016
DOI: 10.1111/GBI.12220
Abstract: The geochemical behavior of molybdenum (Mo) in the oceans is closely linked to the presence of sulfide species in anoxic environments, where Fe availability may play a key role in the Mo scavenging. Here, we show that Mo(VI) is reduced in the presence of particulate organic matter (represented by sulfate-reducing bacteria). Molybdenum was immobilized at the surface of both living cells and dead/lysed cells, but not in cell-free control experiments. Experiments were carried out at four different Mo concentrations (0.1 to 2 mm) to yield cell-associated Mo precipitates with little or no Fe, consisting of mainly Mo(IV)-sulfide compounds with molecular structures similar to Mo enzymes and to those found in natural euxinic sediments. Therefore, we propose that Mo removal in natural sulfidic waters can proceed via a non-Fe-assisted pathway that requires particulate organic matter (dead or living sulfate-reducing bacteria). This pathway has implications for global marine Mo cycling and the current use of Mo-based proxies for paleo-environmental investigations.
Publisher: Royal College of Psychiatrists
Date: 2014
DOI: 10.1192/BJP.BP.113.132324
Abstract: Children with 22q11.2 deletion syndrome (22q11.2DS) have been reported to have high rates of cognitive and psychiatric problems. To establish the nature and prevalence of psychiatric disorder and neurocognitive impairment in children with 22q11.2DS and test whether risk of psychopathology is mediated by the children's intellectual impairment. Neurocognition and psychopathology were assessed in 80 children with 22q11.2DS (mean age 10.2 years, s.d. = 2.1) and 39 sibling controls (mean age 10.9 years, s.d. = 2.0). More than half (54%) of children with 22q11.2DS met diagnostic criteria for one or more DSM-IV-TR psychiatric disorder. These children had lower IQ (mean 76.8, s.d. = 13.0) than controls (mean 108.6, s.d. = 15.2) ( P .001) and showed a range of neurocognitive impairments. Increased risk of psychopathology was not mediated by intellectual impairment. 22q11.2DS is not related to a specific psychiatric phenotype in children. Moreover, the deletion has largely independent effects on IQ and risk of psychopathology, indicating that psychopathology in 22q11.2DS is not a non-specific consequence of generalised cognitive impairment.
Publisher: Elsevier BV
Date: 02-2019
Publisher: Elsevier BV
Date: 08-2023
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8JA00231B
Abstract: Synchrotron-based X-ray spectroscopy is a powerful technique for investigating vanadium speciation in marine sediment.
Publisher: Geological Society of America
Date: 05-2021
DOI: 10.1130/GSATG484A.1
Publisher: Elsevier BV
Date: 10-2017
Publisher: Geological Society of America
Date: 2002
Publisher: Elsevier BV
Date: 09-2018
Publisher: Springer Science and Business Media LLC
Date: 20-10-2023
Publisher: Proceedings of the National Academy of Sciences
Date: 24-06-2015
Abstract: Combined Fe- and Nd-isotope signatures suggest that banded iron formations (BIFs) contain a major component of continentally derived iron that was mobilized by microbial iron reduction followed by transport through an iron shuttle to the site of BIF formation in deep basin environments. This Fe source is in addition to the widely accepted submarine hydrothermal source of Fe in BIFs, and the two sources of Fe may be comparable in importance, although their proportions change over time dependent on basin-scale circulation.
Publisher: Wiley
Date: 27-05-2014
DOI: 10.1002/AJMG.B.32245
Abstract: Children reporting psychotic experiences (PEs) are at increased risk of developing psychosis in adulthood. Cognitive deficits and anxiety disorders often precede psychotic disorders and are associated with higher risk of PEs. While the high activity alleles of variants within COMT have been associated with cognitive deficits, and the low activity alleles with higher risk of anxiety disorders, no associations of COMT with PEs have been found. One possible explanation is that the association between COMT and PEs is indirect, through cognitive function and anxiety disorders. We examined whether the association between PEs and COMT (four single nucleotide polymorphisms and three haplotypes) is indirect, through cognition or anxiety disorders. 6,784 in iduals from the Avon Longitudinal Study of Parents and Children (ALSPAC) were genotyped and completed neurocognitive assessments at ages 8 and 11, as well as semi-structured interviews for anxiety disorders and PEs at ages 10 and 12, respectively. Alleles rs2097603 and rs4680, and two COMT haplotypes, all indexing high activity, were indirectly associated with higher risk of PEs through impaired processing speed, IQ and attention. There was no evidence of a total effect of COMT on PEs, nor for an indirect effect through anxiety disorders. This is the first study to examine indirect effects of COMT on PEs. Evidence of an indirect association suggests a complex developmental pathway underlies the emergence of PEs in children, with possible implications for prevention/intervention strategies. Our findings provide additional support for processing speed and attention as endophenotypes in psychotic disorders.
Publisher: American Psychiatric Association Publishing
Date: 05-2013
No related grants have been discovered for Don Canfield.