Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores.

BACKGROUND: Nonsyndromic cleft lip with/without cleft palate (nsCL/P) is a congenital malformation of multifactorial etiology. Research has identified >40 genome-wide significant risk loci, which explain less than 40% of nsCL/P heritability. Studies show that some of the hidden heritability is explained by rare penetrant variants. METHODS: To identify new candidate genes, we searched for highly penetrant de novo variants (DNVs) in 50 nsCL/P patient/parent-trios with a low polygenic risk for the phenotype (discovery). We prioritized DNV-carrying candidate genes from the discovery for resequencing in independent cohorts of 1010 nsCL/P patients of diverse ethnicities and 1574 population-matched controls (replication). Segregation analyses and rare variant association in the replication cohort, in combination with additional data (genome-wide association data, expression, protein-protein-interactions), were used for final prioritization. CONCLUSION: In the discovery step, 60 DNVs were identified in 60 genes, including a variant in the established nsCL/P risk gene CDH1. Re-sequencing of 32 prioritized genes led to the identification of 373 rare, likely pathogenic variants. Finally, MDN1 and PAXIP1 were prioritized as top candidates. Our findings demonstrate that DNV detection, including polygenic risk score analysis, is a powerful tool for identifying nsCL/P candidate genes, which can also be applied to other multifactorial congenital malformations.

Extending the allelic spectrum at noncoding risk loci of orofacial clefting.

Genome-wide association studies (GWAS) have generated unprecedented insights into the genetic etiology of orofacial clefting (OFC). The moderate effect sizes of associated noncoding risk variants and limited access to disease-relevant tissue represent considerable challenges for biological interpretation of genetic findings. As rare variants with stronger effect sizes are likely to also contribute to OFC, an alternative approach to delineate pathogenic mechanisms is to identify private mutations and/or an increased burden of rare variants in associated regions. This report describes a framework for targeted resequencing at selected noncoding risk loci contributing to nonsyndromic cleft lip with/without cleft palate (nsCL/P), the most frequent OFC subtype. Based on GWAS data, we selected three risk loci and identified candidate regulatory regions (CRRs) through the integration of credible SNP information, epigenetic data from relevant cells/tissues, and conservation scores. The CRRs (total 57 kb) were resequenced in a multiethnic study population (1061 patients; 1591 controls), using single-molecule molecular inversion probe technology. Combining evidence from in silico variant annotation, pedigree- and burden analyses, we identified 16 likely deleterious rare variants that represent new candidates for functional studies in nsCL/P. Our framework is scalable and represents a promising approach to the investigation of additional congenital malformations with multifactorial etiology.

Short exposure to cadmium disrupts the olfactory system of zebrafish (Danio rerio) - Relating altered gene expression in the olfactory organ to behavioral deficits.

Fish strongly rely on olfaction as a variety of essential behaviors such as foraging and predator avoidance are mediated by the olfactory system. Cadmium (Cd) is known to impair olfaction and accumulate in the olfactory epithelium (OE) and bulb (OB) of fishes. In the present study, the acute toxicity of Cd on olfaction in zebrafish (Danio rerio) was characterized on the molecular and behavioral level. To this end, quantitative real-time PCR was performed in order to analyze the expression of selected genes in both the OE and OB. Moreover, the response of zebrafish to an alarm cue was investigated. Following 24 h of exposure to Cd, the expression of genes associated with olfactory sensory neurons was reduced in the OE. Furthermore, the antioxidant genes peroxiredoxin 1 (prdx1) and heme oxygenase 1 (hmox1), as well as the metallothionein 2 gene (mt2) were upregulated in the OE, whereas hmox1 and the stress-inducible heat shock protein 70 gene (hsp70) were upregulated in the OB upon exposure to Cd. Following stimulation with a conspecific skin extract, zebrafish displayed a considerable disruption of the antipredator behavior with increasing Cd concentration. Taken together, Cd impaired olfaction in zebrafish, thereby disrupting the antipredator response, which is crucial for the survival of individuals. Cellular stress followed by disruption of olfactory sensory neurons may have contributed to the observed behavioral deficits.

Do you smell the danger? Effects of three commonly used pesticides on the olfactory-mediated antipredator response of zebrafish (Danio rerio).

Fish are warned about the presence of predators via an alarm cue released from the skin of injured conspecifics. The detection of this odor inherently initiates an antipredator response, which increases the chance of survival for the individual. In the present study, we assessed the effect of three commonly used pesticides on the antipredator response of zebrafish (Danio rerio). For this, we analyzed the behavioral response of zebrafish to a conspecific skin extract following 24 h of exposure to the respective contaminants. Results demonstrate that fish exposed to 20 µg/L of the organophosphate insecticide chlorpyrifos significantly reduced bottom-dwelling and freezing behavior, suggesting an impairment of the antipredator response. For the urea-herbicide linuron and the pyrethroid insecticide permethrin, no statistically significant effects could be detected. However, linuron-exposed fish appeared to respond in an altered manner to the skin extract; some individuals failed to perform the inherent behaviors such as erratic movements and instead merely increased their velocity. Furthermore, we determined whether zebrafish would avoid the pesticides in a choice maze. While fish avoided permethrin, they behaved indifferently to chlorpyrifos and linuron. The study demonstrates that pesticides may alter the olfactory-mediated antipredator response of zebrafish in distinct ways, revealing that particularly fish exposed to chlorpyrifos may be more prone to predation.

Morphological dataset of aboveground macrofungal communities within different forest conversion stages in the Eifel National Park in Germany.

This dataset includes 235 aboveground macrofungal species observed at 15 sampling sites, which are associated with five different forest conversion stages. We used a space-for-time substitution approach to represent a forest conversion from Norway spruce (Picea abies) to European beech (Fagus sylvatica) through three different, widely used management practices. In addition to the results of 75 macrofungal field surveys, this data article includes information about site characteristics, vegetation structure, and observation frequencies. A multivariate statistic and myco-ecological interpretation of the macrofungal dataset is presented in an associated research article entitled "Forest conversion from Norway spruce to European beech increases species richness and functional structure of aboveground macrofungal communities" (Heine et al., 2019) [1].

Fishing for contaminants: identification of three mechanism specific transcriptome signatures using Danio rerio embryos.

In ecotoxicology, transcriptomics is an effective way to detect gene expression changes in response to environmental pollutants. Such changes can be used to identify contaminants or contaminant classes and can be applied as early warning signals for pollution. To do so, it is important to distinguish contaminant-specific transcriptomic changes from genetic alterations due to general stress. Here we present a first step in the identification of contaminant class-specific transcriptome signatures. Embryos of zebrafish (Danio rerio) were exposed to three substances (methylmercury, chlorpyrifos and Aroclor 1254, each from 24 to 48 hpf exposed) representing sediment typical contaminant classes. We analyzed the altered transcriptome to detect discriminative genes significantly regulated in reaction to the three applied contaminants. By comparison of the results of the three contaminants, we identified transcriptome signatures and biologically important pathways (using Cytoscape/ClueGO software) that react significantly to the contaminant classes. This approach increases the chance of finding genes that play an important role in contaminant class-specific pathways rather than more general processes.

Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse.

Database URL: Edaphostat is part of the Edaphobase Web Application available at https://portal.edaphobase.org.

Fighting for the web: competition between female feather-legged spiders (Uloborus plumipes).

Most spider species are solitary, and among the few social interactions among them, resource competition between females has received little attention. We discovered that females of the feather-legged spider Uloborus plumipes invade the orb webs of conspecifics and compete for webs. Following observations in the wild, intruder-defender interactions were studied in a terrarium and in controlled laboratory experiments. We found that contests for orb webs occurred spontaneously between adult females. Competitive interactions in U. plumipes were characterized by an escalation of ritualized behaviors. In 27% of the contests the winner was determined by interactions at a distance, which involved behaviors that caused vibratory signaling on the web. The remaining interactions escalated to physical contact, and in 78% of these a fight occurred between the contestants. Using multivariate logistic regression we determined the factors that predicted the outcome of the contests: (i) Web ownership did not give the defender a competitive advantage. (ii) The difference in physical size between the competing spiders was the most important predictor for the outcome of web contests. (iii) Independent of body size, the display of certain behaviors, specifically the ability to reach the hub before the contestant and the frequency of attacks, increased the probability of winning. (iv) Winning or losing a fight did not affect the chances of winning subsequent contests. The interactions reported here provide a promising approach to investigate communication in spiders and to test theoretical models of intraspecific competition.

Fold-change threshold screening: a robust algorithm to unmask hidden gene expression patterns in noisy aggregated transcriptome data.

Transcriptomics is often used to investigate changes in an organism's genetic response to environmental contamination. Data noise can mask the effects of contaminants making it difficult to detect responding genes. Because the number of genes which are found differentially expressed in transcriptome data is often very large, algorithms are needed to reduce the number down to a few robust discriminative genes. We present an algorithm for aggregated analysis of transcriptome data which uses multiple fold-change thresholds (threshold screening) and p values from Bayesian generalized linear model in order to assess the robustness of a gene as a potential indicator for the treatments tested. The algorithm provides a robustness indicator (ROBI) as well as a significance profile, which can be used to assess the statistical significance of a given gene for different fold-change thresholds. Using ROBI, eight discriminative genes were identified from an exemplary dataset (Danio rerio FET treated with chlorpyrifos, methylmercury, and PCB) which could be potential indicators for a given substance. Significance profiles uncovered genetic effects and revealed appropriate fold-change thresholds for single genes or gene clusters. Fold-change threshold screening is a powerful tool for dimensionality reduction and feature selection in transcriptome data, as it effectively reduces the number of detected genes suitable for environmental monitoring. In addition, it is able to unmask patterns in altered genetic expression hidden by data noise and reduces the chance of type II errors, e.g., in environmental screening.