The rockefeller university

Early work on de novo gene discovery in Drosophila was consistent with the idea that many such genes have male-biased patterns of expression, including a large number expressed in the testis. However, there has been little formal analysis of variation in the abundance and properties of de novo genes expressed in different tissues. Here, we investigate the population biology of recently evolved de novo genes expressed in the Drosophila melanogaster accessory gland, a somatic male tissue that plays an important role in male and female fertility and the post mating response of females, using the same collection of inbred lines used previously to identify testis-expressed de novo genes, thus allowing for direct cross tissue comparisons of these genes in two tissues of male reproduction. Using RNA-seq data, we identify candidate de novo genes located in annotated intergenic and intronic sequence and determine the properties of these genes including chromosomal location, expression, abundance, and coding capacity. Generally, we find major differences between the tissues in terms of gene abundance and expression, though other properties such as transcript length and chromosomal distribution are more similar. We also explore differences between regulatory mechanisms of de novo genes in the two tissues and how such differences may interact with selection to produce differences in D. melanogaster de novo genes expressed in the two tissues.

CRISPR-Cas systems have the ability to integrate invasive DNA sequences to build adaptive immunity in bacteria. In this issue Dimitriu et al. show bacteriostatic antibiotics prompt CRISPR acquisition events, illustrating how environmental conditions affect complex dynamics between host and virus and the corresponding biological and genetic arms race.

BACKGROUND & AIMS: Desmosomes are intercellular junctions connecting keratin intermediate filaments of neighboring cells. The cadherins desmoglein 2 (Dsg2) and desmocollin 2 mediate cell-cell adhesion, whereas desmoplakin (Dsp) provides the attachment of desmosomes to keratins. Although the importance of the desmosome-keratin network is well established in mechanically challenged tissues, we aimed to assess the currently understudied function of desmosomal proteins in intestinal epithelia.& nbsp;METHODS: We analyzed the intestine-specific villin-Cre DSP (DSP delta IEC) and the combined intestine-specific DSG2/DSP delta IEC (delta Dsg2/Dsp) knockout mice. Cross-breeding with keratin 8-yellow fluorescent protein knock-in mice and generation of organoids was performed to visualize the keratin network. A Dsp-deficient colorectal carcinoma HT29-derived cell line was generated and the role of Dsp in adhesion and mechanical stress was studied in dispase assays, after exposure to uniaxial cell stretching and during scratch assay.& nbsp;RESULTS: The intestine of DSP delta IEC mice was histopathologically inconspicuous. Intestinal epithelial cells, however, showed an accelerated migration along the crypt and an enhanced shedding into the lumen. Increased intestinal permeability and altered levels of desmosomal proteins were detected. An inconspicuous phenotype also was seen in delta Dsg2/Dsp mice. After dextran sodium sulfate treatment, DSP delta IEC mice developed more pronounced colitis. A retracted keratin network was seen in the intestinal epithelium of DSP delta IEC/keratin 8-yellow fluorescent protein mice and organoids derived from these mice presented a collapsed keratin network. The level, phosphorylation status, and solubility of keratins were not affected. Dsp-deficient HT29 cells had an impaired cell adhesion and suffered from increased cellular damage after stretch.& nbsp;CONCLUSIONS: Our results show that Dsp is required for proper keratin network architecture in intestinal epithelia, mechanical resilience, and adhesion, thereby protecting from injury.

Background: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease presenting with diverse manifestations ranging from nodules and abscesses to draining tunnels. Whether the underlying inflammation from lesions extends to relatively healthy-appearing adjacent perilesional and distant nonlesional skin has not been systematically evaluated. Objective: We sought to characterize lesional, perilesional, and nonlesional skin in patients with HS. Methods: Skin biopsy samples were collected under ultrasound guidance from patients with active, untreated moderate-tosevere HS. Site-matched control biopsy samples from healthy volunteers were used for comparison. Results: RNA sequencing demonstrated that HS skin clustered separately from healthy control skin, with perilesional and lesion skin clustering together and away from nonlesional skin. Immunohistochemistry analysis identified psoriasiform hyperplasia with keratin 16 positivity in both perilesional and lesional skin, with comparable levels of CD3(+), CD11c(+), and neutrophil elastase-positive cellular infiltration. There was a marked upregulation of IL-17 signaling in perilesional and lesional skin. HS samples clustered on the basis of expression of lipocalin-2 (LCN2), with samples characterized by high LCN2 expression in the skin exhibiting a differing transcriptomic profile with significantly higher overall inflammation than that of skin characterized by low LCN2 levels. Conclusions: Perilesional HS skin has a transcriptomic and molecular profile comparable to that of lesional skin. HS can be grouped into 2 distinct subtypes based on molecular levels of LCN2 in the skin, with the LCN2-high subtype exhibiting an overall higher inflammatory burden and an upregulation of targetable cytokines. To our knowledge, this is the first study to characterize a unique HS subtype (and a potential endotype) that may guide future therapeutic targets.

Elective single embryo transfer (eSET) was first introduced to IVF in 1999, and its subsequent integration into mainstream reproductive endocrinology and infertility has been hugely consequential. It can be viewed as the first (among many since) 'add-ons' to IVF that has significantly and adversely affected how IVF is practised, resulting in astonishing declines in live birth rates after fresh non-donor IVF cycles worldwide. We propose that, like most 'addons' to IVF over recent years, the almost universal use of eSET worldwide lacks proper validation of its underlying hypothesis and is based on statistically incorrect assumptions and incorrect data interpretation. As with most recent 'add-ons' to IVF, eSET lacks evidentiary support, and, therefore, its remarkable success in the marketplace must be based on expert opinions, the lowest level of evidence in medicine and widely recognized as frequently biased. Like other 'add-ons' to IVF, eSET-practice must be reassessed because it does not offer the benefits it has widely claimed to provide, prolongs time to conception and adversely affects live birth chances for many women. Moreover, by ignoring that infertile women value quick conception over most other considerations, provider-insistence on eSET frequently deprives them of the right to self-determination.

Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.

Background Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. Results We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. Conclusion We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.

Mirman et al. report that the primary function of the shieldin complex in double-strand break repair in BRCA1-deficient cells is the recruitment of the CST-Pol alpha-primase complex to conduct fill-in synthesis. The efficacy of poly(ADP)-ribose polymerase 1 inhibition (PARPi) in BRCA1-deficient cells depends on 53BP1 and shieldin, which have been proposed to limit single-stranded DNA at double-strand breaks (DSBs) by blocking resection and/or through CST-Pol alpha-primase-mediated fill-in. We show that primase (like 53BP1-shieldin and CST-Pol alpha) promotes radial chromosome formation in PARPi-treated BRCA1-deficient cells and demonstrate shieldin-CST-Pol alpha-primase-dependent incorporation of BrdU at DSBs. In the absence of 53BP1 or shieldin, radial formation in BRCA1-deficient cells was restored by the tethering of CST near DSBs, arguing that in this context, shieldin acts primarily by recruiting CST. Furthermore, a SHLD1 mutant defective in CST binding (SHLD1 Delta) was non-functional in BRCA1-deficient cells and its function was restored after reconnecting SHLD1 Delta to CST. Interestingly, at dysfunctional telomeres and at DNA breaks in class switch recombination where CST has been implicated, SHLD1 Delta was fully functional, perhaps because these DNA ends carry CST recognition sites that afford SHLD1-independent binding of CST. These data establish that in BRCA1-deficient cells, CST-Pol alpha-primase is the major effector of shieldin-dependent DSB processing.

This essay critiques the fiercely utilitarian allocation scheme of Cameron et al. Children have no hope of recovery if their lives are cut short based on administrative protocols that misrepresent the nature of their conditions. Unilateral futility judgements - especially those based on a false predicate - are discriminatory. When considering the best interests of children, we should see possibility in disability and not advance ill-informed utilitarianism.