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Cancer Jun 2024The mechanisms underlying alcohol-induced breast carcinogenesis are not fully understood but may involve hormonal changes.
BACKGROUND
The mechanisms underlying alcohol-induced breast carcinogenesis are not fully understood but may involve hormonal changes.
METHODS
Cross-sectional associations were investigated between self-reported alcohol intake and serum or plasma concentrations of estradiol, estrone, progesterone (in premenopausal women only), testosterone, androstenedione, dehydroepiandrosterone sulfate, and sex hormone binding globulin (SHBG) in 45 431 premenopausal and 173 476 postmenopausal women. Multivariable linear regression was performed separately for UK Biobank, European Prospective Investigation into Cancer and Nutrition, and Endogenous Hormones and Breast Cancer Collaborative Group, and meta-analyzed the results. For testosterone and SHBG, we also conducted Mendelian randomization and colocalization using the ADH1B (alcohol dehydrogenase 1B) variant (rs1229984).
RESULTS
Alcohol intake was positively, though weakly, associated with all hormones (except progesterone in premenopausal women), with increments in concentrations per 10 g/day increment in alcohol intake ranging from 1.7% for luteal estradiol to 6.6% for postmenopausal dehydroepiandrosterone sulfate. There was an inverse association of alcohol with SHBG in postmenopausal women but a small positive association in premenopausal women. Two-sample randomization identified positive associations of alcohol intake with total testosterone (difference per 10 g/day increment: 4.1%; 95% CI, 0.6-7.6) and free testosterone (7.8%; 4.1-11.5), and an inverse association with SHBG (-8.1%; -11.3% to -4.9%). Colocalization suggested a shared causal locus at ADH1B between alcohol intake and higher free testosterone and lower SHBG (posterior probability for H4, 0.81 and 0.97, respectively).
CONCLUSIONS
Alcohol intake was associated with small increases in sex hormone concentrations, including bioavailable fractions, which may contribute to its effect on breast cancer risk.
PubMed: 38824654
DOI: 10.1002/cncr.35391 -
Genomic deletions in Aureobasidium pullulans by an AMA1 plasmid for gRNA and CRISPR/Cas9 expression.Fungal Biology and Biotechnology Jun 2024Aureobasidium pullulans is a generalist polyextremotolerant black yeast fungus. It tolerates temperatures below 0 °C or salt concentrations up to 18%, among other...
BACKGROUND
Aureobasidium pullulans is a generalist polyextremotolerant black yeast fungus. It tolerates temperatures below 0 °C or salt concentrations up to 18%, among other stresses. A. pullulans genome sequencing revealed a high potential for producing bioactive metabolites. Only few molecular tools exist to edit the genome of A. pullulans, hence it is important to make full use of its potential. Two CRISPR/Cas9 methods have been proposed for the protoplast-based transformation of A. pullulans. These methods require the integration of a marker gene into the locus of the gene to be deleted, when the deletion of this gene does not yield a selectable phenotype. We present the adaptation of a plasmid-based CRISPR/Cas9 system developed in Aspergillus niger for A. pullulans to create deletion strains.
RESULTS
The A. niger CRISPR/Cas9 plasmid led to efficient genomic deletions in A. pullulans. In this study, strains with deletions ranging from 30 to 862 bp were obtained by using an AMA1 plasmid-based genome editing strategy.
CONCLUSION
The CRISPR/Cas9 transformation system presented in this study provides new opportunities for strain engineering of A. pullulans. This system allows expression of Cas9 and antibiotic resistance while being easy to adapt. This strategy could open the path to intensive genomic engineering in A. pullulans.
PubMed: 38824542
DOI: 10.1186/s40694-024-00175-4 -
Scientific Reports Jun 2024Pulse wave encephalopathy (PWE) is hypothesised to initiate many forms of dementia, motivating its identification and risk assessment. As candidate pulsatility based...
Pulse wave encephalopathy (PWE) is hypothesised to initiate many forms of dementia, motivating its identification and risk assessment. As candidate pulsatility based biomarkers for PWE, pulsatility index and pulsatility damping have been studied and, currently, do not adequately stratify risk due to variability in pulsatility and spatial bias. Here, we propose a locus-independent pulsatility transmission coefficient computed by spatially tracking pulsatility along vessels to characterise the brain pulse dynamics at a whole-organ level. Our preliminary analyses in a cohort of 20 subjects indicate that this measurement agrees with clinical observations relating blood pulsatility with age, heart rate, and sex, making it a suitable candidate to study the risk of PWE. We identified transmission differences between vascular regions perfused by the basilar and internal carotid arteries attributed to the identified dependence on cerebral blood flow, and some participants presented differences between the internal carotid perfused regions that were not related to flow or pulsatility burden, suggesting underlying mechanical differences. Large populational studies would benefit from retrospective pulsatility transmission analyses, providing a new comprehensive arterial description of the hemodynamic state in the brain. We provide a publicly available implementation of our tools to derive this coefficient, built into pre-existing open-source software.
Topics: Humans; Female; Male; Cerebrovascular Circulation; Pulsatile Flow; Magnetic Resonance Imaging; Aged; Middle Aged; Brain; Pulse Wave Analysis; Carotid Artery, Internal; Basilar Artery; Adult
PubMed: 38824230
DOI: 10.1038/s41598-024-63312-4 -
Legal Medicine (Tokyo, Japan) May 2024Closely linked groups of markers on the X chromosome are very useful for testing complex kinship relationships involving X-STR transmission. The Argus X-12 kit, a...
Closely linked groups of markers on the X chromosome are very useful for testing complex kinship relationships involving X-STR transmission. The Argus X-12 kit, a unique commercially available kit, can obtain haplotypes of 4 linkage groups (LGs) consisting of 3 markers. Although many population data have been reported for forensic purposes, differences in discrimination ability exist between LG1 and LG2, 3, and 4 in East Asian populations, and the data of this kit would become more useful if the discrimination ability of the latter groups were increased. Therefore, for matches found using this kit for some linkage group data, then to increase the identification ability, we additionally introduced 13 X-STR loci and established a method allowing comparison using data from 25 loci. The 13X-STRs add two locus data to each of LG2, 3, and 4, and also add two closely linked group (CLG) data between LG2 and 3 and LG3 and 4 in one multiplex PCR. Assessment of this method for a Malay population for which data by Argus X-12 had already been reported showed that the frequencies of distinct haplotypes in LG2, 3, and 4 were increased by 33.0-42.6 %, and frequencies of unique haplotypes increased by 45.4-59.2 %. The respective haplotype diversity values of the additional 3-locus and 4-locus CLGs were 0.9838 and 0.9939, which helps to improve discriminatory power and to predict recombination locations on the X chromosome. Although we have been testing these loci with Japanese subjects, this system would also be useful for the Malay population.
PubMed: 38823287
DOI: 10.1016/j.legalmed.2024.102463 -
TAG. Theoretical and Applied Genetics.... Jun 2024qLA3.1, controlling leaf angle in tomato, was fine-mapped to an interval of 4.45 kb on chromosome A03, and one gene encoding auxin response factor was identified as a...
qLA3.1, controlling leaf angle in tomato, was fine-mapped to an interval of 4.45 kb on chromosome A03, and one gene encoding auxin response factor was identified as a candidate gene. Leaf angle is a crucial trait in plant architecture that plays an important role in achieving optimal plant structure. However, there are limited reports on gene localization, cloning, and the function of plant architecture in horticultural crops, particularly regarding leaf angle. In this study, we selected 'Z3' with erect leaves and 'Heinz1706' with horizontal leaves as the phenotype and cytological observation. We combined bulked segregant analysis and fine genetic mapping to identify a candidate gene, known as, i.e., qLA3.1, which was related to tomato leaf angle. Through multiple analyses, we found that Solyc03g113410 was the most probably candidate for qLA3.1, which encoded the auxin response factor SlARF11 in tomato and was homologous to OsARF11 related to leaf angle in rice. We discovered that silencing SlARF11 resulted in upright leaves, while plants with over-expressed SlARF11 exhibited horizontal leaves. We also found that cultivars with erect leaves had a mutation from base G to base A. Moreover, quantitative analysis of plants treated with hormones indicated that SlARF11 might participate in cell elongation and the activation of genes related to auxin and brassinosteroid pathways. Transcriptome analysis further validated that SlARF11 may regulate leaf angle through hormone signaling pathways. These data support the idea that the auxin response factor SlARF11 may have an important function in tomato leaf petiole angles.
Topics: Solanum lycopersicum; Plant Leaves; Quantitative Trait Loci; Phenotype; Chromosome Mapping; Plant Proteins; Gene Expression Regulation, Plant; Genes, Plant
PubMed: 38822827
DOI: 10.1007/s00122-024-04657-2 -
The New Phytologist Jun 2024In the early 1900s, Erwin Baur established Antirrhinum majus as a model system, identifying and characterising numerous flower colour variants. This included...
In the early 1900s, Erwin Baur established Antirrhinum majus as a model system, identifying and characterising numerous flower colour variants. This included Picturatum/Eluta, which restricts the accumulation of magenta anthocyanin pigments, forming bullseye markings on the flower face. We identified the gene underlying the Eluta locus by transposon-tagging, using an Antirrhinum line that spontaneously lost the nonsuppressive el phenotype. A candidate MYB repressor gene at this locus contained a CACTA transposable element. We subsequently identified plants where this element excised, reverting to a suppressive Eluta phenotype. El alleles inhibit expression of anthocyanin biosynthetic genes, confirming it to be a regulatory locus. The modes of action of Eluta were investigated by generating stable transgenic tobacco lines, biolistic transformation of Antirrhinum petals and promoter activation/repression assays. Eluta competes with MYB activators for promoter cis-elements, and also by titrating essential cofactors (bHLH proteins) to reduce transcription of target genes. Eluta restricts the pigmentation established by the R2R3-MYB factors, Rosea and Venosa, with the greatest repression on those parts of the petals where Eluta is most highly expressed. Baur questioned the origin of heredity units determining flower colour variation in cultivated A. majus. Our findings support introgression from wild species into cultivated varieties.
PubMed: 38822654
DOI: 10.1111/nph.19866 -
The Plant Genome May 2024Aggressive strains of Neopestalotiopsis sp. have recently emerged as devastating pathogens of strawberry (Fragaria × ananassa Duchesne ex Rozier), infecting nearly all...
Aggressive strains of Neopestalotiopsis sp. have recently emerged as devastating pathogens of strawberry (Fragaria × ananassa Duchesne ex Rozier), infecting nearly all plant parts and causing severe outbreaks of leaf spot and fruit rot in Florida and globally. The development of host resistance is imperative due to the absence of fungicides that effectively inhibit Neopestalotiopsis sp. growth on an infected strawberry crop. Here, we analyzed 1578 individuals from the University of Florida's (UF) strawberry breeding program to identify and dissect genetic variation for resistance to Neopestalotiopsis sp. and to explore the feasibility of genomic selection. We found that less than 12% of elite UF germplasm exhibited resistance, with narrow-sense heritability estimates ranging from 0.28 to 0.69. Through genome-wide association studies (GWAS), we identified two loci accounting for 7%-16% of phenotypic variance across four trials and 3 years. Several candidate genes encoding pattern recognition receptors, intra-cellular nucleotide-binding leucine-rich repeats, and downstream components of plant defense pathways co-localized with the Neopestalotiopsis sp. resistance loci. Interestingly, favorable alleles at the largest-effect locus were rare in elite UF material and had previously been unintentionally introduced from an exotic cultivar. The array-based markers and candidate genes described herein provide the foundation for targeting this locus through marker-assisted selection. The predictive abilities of genomic selection models, with and without explicitly modeling peak GWAS markers as fixed effects, ranged between 0.25 and 0.59, suggesting that genomic selection holds promise for enhancing resistance to Neopestalotiopsis sp. in strawberry.
PubMed: 38822520
DOI: 10.1002/tpg2.20477 -
Alzheimer's Research & Therapy May 2024Autopsy work reported that neuronal density in the locus coeruleus (LC) provides neural reserve against cognitive decline in dementia. Recent neuroimaging and...
BACKGROUND
Autopsy work reported that neuronal density in the locus coeruleus (LC) provides neural reserve against cognitive decline in dementia. Recent neuroimaging and pharmacological studies reported that left frontoparietal network functional connectivity (LFPN-FC) confers resilience against beta-amyloid (Aβ)-related cognitive decline in preclinical sporadic and autosomal dominant Alzheimer's disease (AD), as well as against LC-related cognitive changes. Given that the LFPN and the LC play important roles in attention, and attention deficits have been observed early in the disease process, we examined whether LFPN-FC and LC structural health attenuate attentional decline in the context of AD pathology.
METHODS
142 participants from the Harvard Aging Brain Study who underwent resting-state functional MRI, LC structural imaging, PiB(Aβ)-PET, and up to 5 years of cognitive follow-ups were included (mean age = 74.5 ± 9.9 years, 89 women). Cross-sectional robust linear regression associated LC integrity (measured as the average of five continuous voxels with the highest intensities in the structural LC images) or LFPN-FC with Digit Symbol Substitution Test (DSST) performance at baseline. Longitudinal robust mixed effect analyses examined associations between DSST decline and (i) two-way interactions of baseline LC integrity (or LFPN-FC) and PiB or (ii) the three-way interaction of baseline LC integrity, LFPN-FC, and PiB. Baseline age, sex, and years of education were included as covariates.
RESULTS
At baseline, lower LFPN-FC, but not LC integrity, was related to worse DSST performance. Longitudinally, lower baseline LC integrity was associated with a faster DSST decline, especially at PiB > 10.38 CL. Lower baseline LFPN-FC was associated with a steeper decline on the DSST but independent of PiB. At elevated PiB levels (> 46 CL), higher baseline LFPN-FC was associated with an attenuated decline on the DSST, despite the presence of lower LC integrity.
CONCLUSIONS
Our findings demonstrate that the LC can provide resilience against Aβ-related attention decline. However, when Aβ accumulates and the LC's resources may be depleted, the functioning of cortical target regions of the LC, such as the LFPN-FC, can provide additional resilience to sustain attentional performance in preclinical AD. These results provide critical insights into the neural correlates contributing to individual variability at risk versus resilience against Aβ-related cognitive decline.
Topics: Humans; Female; Male; Alzheimer Disease; Aged; Locus Coeruleus; Magnetic Resonance Imaging; Parietal Lobe; Aged, 80 and over; Attention; Frontal Lobe; Positron-Emission Tomography; Cross-Sectional Studies; Neural Pathways; Cognitive Dysfunction; Neuropsychological Tests
PubMed: 38822365
DOI: 10.1186/s13195-024-01485-w -
Heredity May 2024Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with...
Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.
PubMed: 38822132
DOI: 10.1038/s41437-024-00688-z -
Biological Psychology May 2024Altered automatic attention cueing has been reported in autistic children. Yet less is known about how autistic children would respond when the social cue that directs...
BACKGROUND
Altered automatic attention cueing has been reported in autistic children. Yet less is known about how autistic children would respond when the social cue that directs attention occurs in an implied social interaction.
METHODS
By using eye-tracking, the current study examined orienting responses to a socially-relevant target or a nonsocial target cued by a goal-directed social gesture in autistic children. Saccadic reaction time and pupillary responses were employed to measure gaze behavior and physiological arousal of autistic children.
RESULTS
Both groups of children showed reflexive orienting to the target regardless of its sociality, whereas typically developing (TD) children exhibited faster gaze shift than autistic children when the target was a social stimulus. An increased pupil dilation was observed in autistic children in response to stimuli relative to TD children. Further, autistic children showed larger baseline pupil response.
CONCLUSIONS
Autistic children show attenuated sensitivity to social targets and atypical pupil responses, which may be due to the dysfunction of locus coeruleus (LC) - norepinephrine (NE) system.
PubMed: 38821466
DOI: 10.1016/j.biopsycho.2024.108822