Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs. Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the unitigs against a reference genome. By applying the method on 35-fold human resequencing data, we showed that in comparison to the standard pipeline, our approach yields similar accuracy for SNP calling and better results for INDEL calling. It has higher sensitivity than other de novo assembly based methods for variant calling. Our work suggests that variant calling with de novo assembly be a beneficial complement to the standard variant calling pipeline for whole-genome resequencing. In the methodological aspects, we proposed FMD-index for forward-backward extension of DNA sequences, a fast algorithm for finding all super-maximal exact matches and one-pass construction of unitigs from an FMD-index. Availability: http://github.com/lh3/fermi Contact: [email protected]: Rev2: submitted version with minor improvements; 7 page

Saphenous vein graft aneurysm with graft-enteric fistula after renal artery bypass

A 65-year-old female presented with upper gastrointestinal hemorrhage thirty years following an aorta-to-right renal artery bypass constructed with saphenous vein. Upper endoscopy demonstrated a duodenal ulcer, and a CAT scan demonstrated aneurysmal degeneration of her renal artery bypass with duodenal impingement. Laparotomy demonstrated erosion of the aneurysm through the posterior wall of the duodenum; extra-anatomic renovascular reconstruction and primary duodenal repair was performed. Although aneurysmal degeneration of intraabdominal saphenous vein grafts is well described and rupture likewise reported, this report represents the first description of an intraabdominal autogenous vein graft aneurysm presenting with gastrointestinal erosion and fistula

All-Optical Quantum Random Bit Generation from Intrinsically Binary Phase of Parametric Oscillators

True random number generators (RNGs) are desirable for applications ranging from cryptogra- phy to computer simulations. Quantum phenomena prove to be attractive for physical RNGs due to their fundamental randomness and immunity to attack [1]- [5]. Optical parametric down conversion is an essential element in most quantum optical experiments including optical squeezing [9], and generation of entangled photons [10]. In an optical parametric oscillator (OPO), photons generated through spontaneous down conversion of the pump initiate the oscillation in the absence of other inputs [11, 12]. This quantum process is the dominant effect during the oscillation build-up, leading to selection of one of the two possible phase states above threshold in a degenerate OPO [13]. Building on this, we demonstrate a novel all-optical quantum RNG in which the photodetection is not a part of the random process, and no post processing is required for the generated bit sequence. We implement a synchronously pumped twin degenerate OPO, which comprises two identical independent OPOs in a single cavity, and measure the relative phase states of the OPO outputs above threshold as a bit value. We show that the outcome is statistically random with 99% confidence. With the use of micro- and nanoscale OPO resonators, this technique offers a promise for simple, robust, and high-speed on-chip all-optical quantum random number generators

Chalcogenide optical parametric oscillator

We demonstrate the first optical parametric oscillator (OPO) based on chalcogenide glass. The parametric gain medium is an As2Se3 chalcogenide microwire coated with a layer of polymer. The doubly-resonant OPO oscillates simultaneously at a Stokes and an anti Stokes wavelength shift of >50 nm from the pump wavelength that lies at {\lambda}P = 1552 nm. The oscillator has a peak power threshold of 21.6 dBm and a conversion efficiency of >19 %. This OPO experiment provides an additional application of the chalcogenide microwire technology; and considering the transparency of As2Se3 glass extending far in the mid-infrared (mid-IR) wavelengths, the device holds promise for realizing mid IR OPOs utilizing existing optical sources in the telecommunications wavelength region

In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes.

Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant–bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant–bacteria interaction

Interpersonal sources of conflict in young people with and without mild to moderate intellectual disabilities at transition from adolescence to adulthood

<p><b>Background:</b> Interpersonal conflict is a source of stress and contributes to poor mental health in people with mild to moderate intellectual disabilities. Understanding the contexts in which conflict typically occurs can better equip services to help people with such difficulties. However, existing studies into the contexts of conflict have included participants with wide-ranging ages and may not reflect the experiences of young adults in particular.</p> <p><b>Materials and Methods:</b> Twenty-six young adults (16-20 years) with intellectual disabilities and 20 non-disabled young adults completed a semi-structured interview about a recent experience of interpersonal conflict. Participants were asked to describe their beliefs and feelings about the event and their subsequent response.</p> <p><b>Results:</b> Participants with intellectual disabilities were more likely to encounter conflict with strangers or peers outside their friendship group and to describe incidents of aggression than non-disabled participants. They were also more likely to characterize the other person globally as 'bad' and to perceive the other's actions as being personally directed at them. Young women with intellectual disabilities were less likely to describe responding aggressively to incidents.</p> <p><b>Conclusions:</b> Findings suggest that young adults with intellectual disabilities are often the target of overt aggression from those outside their inner social sphere, while their non-disabled peers are more likely to experience conflict with people close to them. Young adults with intellectual disabilities may also be more likely to feel victimized by interpersonal conflict. Implications of these findings and limitations of the study are discussed.</p&gt

N-terminal Sumoylation of Centromeric Histone H3 Variant Cse4 Regulates Its Proteolysis To Prevent Mislocalization to Non-centromeric Chromatin

Stringent regulation of cellular levels of evolutionarily conserved centromeric histone H3 variant (CENP-A in humans, CID in flies, Cse4 in yeast) prevents its mislocalization to non-centromeric chromatin. Overexpression and mislocalization of CENP-A has been observed in cancers and leads to aneuploidy in yeast, flies, and human cells. Ubiquitin-mediated proteolysis of Cse4 by E3 ligases such as Psh1 and Sumo-Targeted Ubiquitin Ligase (STUbL) Slx5 prevent mislocalization of Cse4. Previously, we identified Siz1 and Siz2 as the major E3 ligases for sumoylation of Cse4. In this study, we have identified lysine 65 (K65) in Cse4 as a site that regulates sumoylation and ubiquitin-mediated proteolysis of Cse4 by Slx5. Strains expressing cse4 K65R exhibit reduced levels of sumoylated and ubiquitinated Cse4 in vivo. Furthermore, co-immunoprecipitation experiments reveal reduced interaction of cse4 K65R with Slx5, leading to increased stability and mislocalization of cse4 K65R under normal physiological conditions. Based on the increased stability of cse4 K65R in psh1 strains but not in slx5 strains, we conclude that Slx5 targets sumoylated Cse4 K65 for ubiquitination-mediated proteolysis independent of Psh1. In summary, we have identified and characterized the physiological role of Cse4 K65 in sumoylation, ubiquitin-mediated proteolysis, and localization of Cse4 for genome stability

SUMO targeting of a stress-tolerant Ulp1 SUMO protease

SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1. We find that the catalytic UD domains of both ScUlp1 and KmUlp1 show a high degree of sequence conservation, complement a ulp1 Delta mutant in vivo, and process a SUMO precursor in vitro. Next, to compare the SUMO-trapping features of both SUMO proteases we produced catalytically inactive recombinant fragments of the UD domains of ScUlp1 and KmUlp1, termed ScUTAG and KmUTAG respectively. Both ScUTAG and KmUTAG were able to efficiently bind a variety of purified SUMO isoforms and bound immobilized SUMO1 with nanomolar affinity. However, KmUTAG showed a greatly enhanced ability to bind SUMO and SUMO-modified proteins in the presence of oxidative, temperature and other stressors that induce protein misfolding. We also investigated whether a SUMO-interacting motif (SIM) in the UD domain of KmULP1 that is not conserved in ScUlp1 may contribute to the SUMO-binding properties of KmUTAG. In summary, our data reveal important details about how SUMO proteases target and bind their sumoylated substrates, especially under stress conditions. We also show that the robust pan-SUMO binding features of KmUTAG can be exploited to detect and study SUMO-modified proteins in cell culture systems

SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin

Cell viability and gene expression profiles are altered in cellular models of neurodegenerative disorders such as Huntington\u27s Disease (HD). Using the yeast model system, we show that the SUMO-targeted ubiquitin ligase (STUbL) Slx5 reduces the toxicity and abnormal transcriptional activity associated with a mutant, aggregation-prone fragment of huntingtin (Htt), the causative agent of HD. We demonstrate that expression of an aggregation-prone Htt construct with 103 glutamine residues (103Q), but not the non-expanded form (25Q), results in severe growth defects in slx5Delta and slx8Delta cells. Since Slx5 is a nuclear protein and because Htt expression affects gene transcription, we assessed the effect of STUbLs on the transcriptional properties of aggregation-prone Htt. Expression of Htt 25Q and 55Q fused to the Gal4 activation domain (AD) resulted in reporter gene auto-activation. Remarkably, the auto-activation of Htt constructs was abolished by expression of Slx5 fused to the Gal4 DNA-binding domain (BD-Slx5). In support of these observations, RNF4, the human ortholog of Slx5, curbs the aberrant transcriptional activity of aggregation-prone Htt in yeast and a variety of cultured human cell lines. Functionally, we find that an extra copy of SLX5 specifically reduces Htt aggregates in the cytosol as well as chromatin-associated Htt aggregates in the nucleus. Finally, using RNA sequencing, we identified and confirmed specific targets of Htt\u27s transcriptional activity that are modulated by Slx5. In summary, this study of STUbLs uncovers a conserved pathway that counteracts the accumulation of aggregating, transcriptionally active Htt (and possibly other poly-glutamine expanded proteins) on chromatin in both yeast and in mammalian cells

Driven depinning of strongly disordered media and anisotropic mean-field limits

Extended systems driven through strong disorder are modeled generically using coarse-grained degrees of freedom that interact elastically in the directions parallel to the driving force and that slip along at least one of the directions transverse to the motion. A realization of such a model is a collection of elastic channels with transverse viscous couplings. In the infinite range limit this model has a tricritical point separating a region where the depinning is continuous, in the universality class of elastic depinning, from a region where depinning is hysteretic. Many of the collective transport models discussed in the literature are special cases of the generic model.Comment: 4 pages, 2 figure