Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis

Background

Advanced intercross lines (AIL) are segregating populations created using a multi-generation breeding protocol for fine mapping complex trait loci (QTL) in mice and other organisms. Applying QTL mapping methods for intercross and backcross populations, often followed by naïve permutation of individuals and phenotypes, does not account for the effect of AIL family structure in which final generations have been expanded and leads to inappropriately low significance thresholds. The critical problem with naïve mapping approaches in AIL populations is that the individual is not an exchangeable unit.

Methodology/Principal Findings

The effect of family structure has immediate implications for the optimal AIL creation (many crosses, few animals per cross, and population expansion before the final generation) and we discuss these and the utility of AIL populations for QTL fine mapping. We also describe Genome Reshuffling for Advanced Intercross Permutation, (GRAIP) a method for analyzing AIL data that accounts for family structure. GRAIP permutes a more interchangeable unit in the final generation crosses – the parental genome – and simulating regeneration of a permuted AIL population based on exchanged parental identities. GRAIP determines appropriate genome-wide significance thresholds and locus-specific P-values for AILs and other populations with similar family structures. We contrast GRAIP with naïve permutation using a large densely genotyped mouse AIL population (1333 individuals from 32 crosses). A naïve permutation using coat color as a model phenotype demonstrates high false-positive locus identification and uncertain significance levels, which are corrected using GRAIP. GRAIP also detects an established hippocampus weight locus and a new locus, Hipp9a.

Conclusions and Significance

GRAIP determines appropriate genome-wide significance thresholds and locus-specific P-values for AILs and other populations with similar family structures. The effect of family structure has immediate implications for the optimal AIL creation and we discuss these and the utility of AIL populations.     

Suppression of RhoA activity by focal adhesion kinase-induced activation of p190RhoGAP: role in regulation of endothelial permeability

The interaction of endothelial cells with extracellular matrix proteins at focal adhesions sites contributes to the integrity of vascular endothelial barrier. Although focal adhesion kinase (FAK) activation is required for the recovery of the barrier function after increased endothelial junctional permeability, the basis for the recovery remains unclear. We tested the hypothesis that FAK activates p190RhoGAP and, thus, negatively regulates RhoA activity and promotes endothelial barrier restoration in response to the permeability-increasing mediator thrombin. We observed that thrombin caused a transient activation of RhoA but a more prolonged FAK activation temporally coupled to the recovery of barrier function. Thrombin also induced tyrosine phosphorylation of p190RhoGAP, which coincided with decrease in RhoA activity. We further showed that FAK was associated with p190RhoGAP, and importantly, recombinant FAK phosphorylated p190RhoGAP in vitro. Inhibition of FAK by adenoviral expression of FRNK (a dominant negative FAK construct) in monolayers prevented p190RhoGAP phosphorylation, increased RhoA activity, induced actin stress fiber formation, and produced an irreversible increase in endothelial permeability in response to thrombin. We also observed that p190RhoGAP was unable to attenuate RhoA activation in the absence of FAK activation induced by FRNK. The inhibition of RhoA by the C3 toxin (Clostridium botulinum toxin) restored endothelial barrier function in the FRNK-expressing cells. These findings in endothelial cells were recapitulated in the lung microcirculation in which FRNK expression in microvessel endothelia increased vascular permeability. Our studies demonstrate that FAK-induced down-modulation of RhoA activity via p190RhoGAP is a crucial step in signaling endothelial barrier restoration after increased endothelial permeability.     

Scram1 is a modifier of spinal cord resistance for astrocytoma on mouse Chr 5

Tumor location can profoundly affect morbidity and patient prognosis, even for the same tumor type. Very little is known about whether tumor location is determined stochastically or whether genetic risk factors can affect where tumors arise within an organ system. We have taken advantage of the Nf1-/+;Trp53-/+cis mouse model of astrocytoma/glioblastoma to map genetic loci affecting whether astrocytomas are found in the spinal cord. We identify a locus on distal Chr 5, termed Scram1 for spinal cord resistance to astrocytoma modifier 1, with a LOD score of 5.0 and a genome-wide significance of P?相似文献   

Isolation and Characterization of Campylobacter jejuni subsp. jejuni from Macaroni Penguins (Eudyptes chrysolophus) in the Subantarctic Region

On Bird Island, South Georgia, albatrosses (n = 140), penguins (n = 100), and fur seals (n = 206) were sampled for Campylobacter jejuni. C. jejuni subsp. jejuni was recovered from three macaroni penguins (Eudyptes chrysolophus). These isolates, the first reported for the subantarctic region, showed low genetic diversity and high similarity to Northern Hemisphere C. jejuni isolates, possibly suggesting recent introduction to the area.     

Evidence of oxygenic phototrophy in ancient phosphatic stromatolites from the Paleoproterozoic Vindhyan and Aravalli Supergroups,India

Fossil microbiotas are rare in the early rock record, limiting the type of ecological information extractable from ancient microbialites. In the absence of body fossils, emphasis may instead be given to microbially derived features, such as microbialite growth patterns, microbial mat morphologies, and the presence of fossilized gas bubbles in lithified mats. The metabolic affinity of micro‐organisms associated with phosphatization may reveal important clues to the nature and accretion of apatite‐rich microbialites. Stromatolites from the 1.6 Ga Chitrakoot Formation (Semri Group, Vindhyan Supergroup) in central India contain abundant fossilized bubbles interspersed within fine‐grained in situ‐precipitated apatite mats with average δ¹³C_org indicative of carbon fixation by the Calvin cycle. In addition, the mats hold a synsedimentary fossil biota characteristic of cyanobacterial and rhodophyte morphotypes. Phosphatic oncoid cone‐like stromatolites from the Paleoproterozoic Aravalli Supergroup (Jhamarkotra Formation) comprise abundant mineralized bubbles enmeshed within tufted filamentous mat fabrics. Construction of these tufts is considered to be the result of filamentous bacteria gliding within microbial mats, and as fossilized bubbles within pristine mat laminae can be used as a proxy for oxygenic phototrophy, this provides a strong indication for cyanobacterial activity in the Aravalli mounds. We suggest that the activity of oxygenic phototrophs may have been significant for the formation of apatite in both Vindhyan and Aravalli stromatolites, mainly by concentrating phosphate and creating steep diurnal redox gradients within mat pore spaces, promoting apatite precipitation. The presence in the Indian stromatolites of alternating apatite‐carbonate lamina may result from local variations in pH and oxygen levels caused by photosynthesis–respiration in the mats. Altogether, this study presents new insights into the ecology of ancient phosphatic stromatolites and warrants further exploration into the role of oxygen‐producing biotas in the formation of Paleoproterozoic shallow‐basin phosphorites.     

Disturbed sleep in shift workers, day workers, and insomniacs

Very little is known about differences in sleep between day and shift workers in representative samples of the population. This study compared a national representative sample (N=3400) of shift (with night shifts) and day workers regarding the different types of sleep disturbances and also the level of sleep symptoms with that of insomnia patients. The results showed very few differences between shift and day workers; only "too little sleep" and "nodding off at work" were marginally higher among shift workers. The results also showed that the complaints of insomnia patients for most sleep disturbances corresponded to the 2nd-16th percentile of the shift workers' levels of complaints. The results suggest, at least with the present questionnaire methodology, that shift work does not appear to be a major source of sleep disturbances and that their complaint levels bear no resemblance to those seen in insomniac patients.     

An ADAMTSL2 Founder Mutation Causes Musladin-Lueke Syndrome,a Heritable Disorder of Beagle Dogs,Featuring Stiff Skin and Joint Contractures

Background

Musladin-Lueke Syndrome (MLS) is a hereditary disorder affecting Beagle dogs that manifests with extensive fibrosis of the skin and joints. In this respect, it resembles human stiff skin syndrome and the Tight skin mouse, each of which is caused by gene defects affecting fibrillin-1, a major component of tissue microfibrils. The objective of this work was to determine the genetic basis of MLS and the molecular consequence of the identified mutation.

Methodology and Principal Findings

We mapped the locus for MLS by genome-wide association to a 3.05 Mb haplotype on canine chromosome 9 (CFA9 (50.11–54.26; p_raw <10⁻⁷)), which was homozygous and identical-by-descent among all affected dogs, consistent with recessive inheritance of a founder mutation. Sequence analysis of a candidate gene at this locus, ADAMTSL2, which is responsible for the human TGFβ dysregulation syndrome, Geleophysic Dysplasia (GD), uncovered a mutation in exon 7 (c.660C>T; p.R221C) perfectly associated with MLS (p-value = 10⁻¹²). Murine ADAMTSL2 containing the p.R221C mutation formed anomalous disulfide-bonded dimers when transiently expressed in COS-1, HEK293F and CHO cells, and was present in the medium of these cells at lower levels than wild-type ADAMTSL2 expressed in parallel.

Conclusions/Significance

The genetic basis of MLS is a founder mutation in ADAMTSL2, previously shown to interact with latent TGF-β binding protein, which binds fibrillin-1. The molecular effect of the founder mutation on ADAMTSL2 is formation of disulfide-bonded dimers. Although caused by a distinct mutation, and having a milder phenotype than human GD, MLS nevertheless offers a new animal model for study of GD, and for prospective insights on mechanisms and pathways of skin fibrosis and joint contractures.     

Cyclic 3′,5′-Adenosine Monophosphate and N-Acetyl-glucosamine-6-Phosphate as Regulatory Signals in Catabolite Repression of the lac Operon in Escherichia coli

When an Escherichia coli mutant lacking the enzyme N-acetyl-glucosamine-6-phosphate (AcGN6P) deacetylase is grown in a succinate-mineral salts medium and exposed to an exogenous source of N-acetylglucosamine, approximately 20 to 30 pmoles of AcGN6P per mug of cell dry weight will accumulate in these cells. This accumulation occurs within 2 to 4 min after the addition of N-acetylglucosamine and is coincident with the production of a severe permanent catabolite repression of beta-galactosidase synthesis. This repression does not occur if adenosine 3',5'-cyclic phosphate (cyclic AMP) is added to the cells before AcGN6P accumulates. An immediate derepression occurs when cyclic AMP is added to cells that have already accumulated a large AcGN6P pool. These findings are consistent with the view that low-molecular-weight carbohydrate metabolites and cyclic AMP play key roles in the catabolite repression phenomenon, and that metabolites such as AcGN6P may participate in the represion mechanism by influencing either the formation or degradation of cyclic AMP in E. coli.     

Delayed sleep phase disorder in a Swedish cohort of adolescents and young adults: Prevalence and associated factors

A delayed sleep–wake and circadian rhythm often occurs during puberty. While some individuals only develop a delayed sleep phase (DSP), others will fulfill the criteria for the diagnosis of delayed sleep phase disorder (DSPD). All previous studies have however not separated DSP from DSPD, and, as a result, the prevalence and associated factors are largely unknown for the two conditions individually. We estimated the prevalence of DSP and DSPD in a Swedish cohort of adolescents and young adults. We also investigated associated factors in the two conditions relative to each other and individuals with no DSP. A questionnaire regarding sleep patterns, demographics, substance use/abuse and symptoms of depression, anxiety, worry and rumination was sent to 1000 randomly selected participants (16–26 years of age) in Uppsala, Sweden (response rate = 68%). DSP was defined as a late sleep onset and a preferred late wake-up time. The DSPD diagnosis was further operationalized according to the Diagnostic and Statistical Manual of Mental Disorders, Edition 5 (DSM-5) criteria including insomnia or excessive sleepiness, distress or dysfunction caused by the DSP and that the sleep problem had been evident for 3 months. DSP occurred at a frequency of 4.6% and DSPD at a frequency of 4% in the investigated cohort. DSP was more common in males and was associated with not attending educational activity or work, having shift work, nicotine and alcohol use and less rumination. DSPD was equally common in males and females and was associated with not attending educational activity or work and with elevated levels of anxiety. Both DSP and DSPD appear to be common in adolescents and young adults in this Swedish cohort. No educational activity or work was associated with both DSP and DSPD. However, there were also apparent differences between the two groups in shift work, substance use and mental health, relative to persons with no DSP. Thus, it seems reasonable to assess DSP and DSPD as distinct entities in future studies.     

The duplication of arginine catabolism and the meaning of the two ornithine carbamoyltransferases in Bacillus licheniformis.

Arginine deiminase and carbamate kinase activities are shown to be present in cell-free extracts of $\text{Bacillus licheniformis}$. This gives the rationale for the occurrence of an arginine-inducible ornithine carbamoyltransferase in this organism and suggests that, $\text{in vivo}$ and under the proper conditions, this enzyme is able to catalyze the phosphorolysis of citrulline. This also shows that this Bacillus species has two arginine catabolic pathways. This duplication appears to be under the control of O₂.