An interplay of structure and intrinsic disorder in the functionality of peptidylarginine deiminases, a family of key autoimmunity-related enzymes

Citrullination is a post-translation modification of proteins, where the proteinaceous arginine residues are converted to non-coded citrulline residues. The immune tolerance to such citrullinated protein can be lost, leading to inflammatory and autoimmune diseases. Citrullination is a chemical reaction mediated by peptidylarginine deiminase enzymes (PADs), which are a family of calcium-dependent cysteine hydrolase enzymes that includes five isotypes: PAD1, PAD2, PAD3, PAD4, and PAD6. Each PAD has specific substrates and tissue distribution, where it modifies the arginine to produce a citrullinated protein with altered structure and function. All mammalian PADs have a sequence similarity of about 70-95%, whereas in humans, they are 50-55% homologous in their structure and amino acid sequences. Being calcium-dependent hydrolases, PADs are inactive under the physiological level of calcium, but could be activated due to distortions in calcium homeostasis, or when the cellular calcium levels are increased. In this article, we analyze some of the currently available data on the structural properties of human PADs, the mechanisms of their calcium-induced activation, and show that these proteins contain functionally important regions of intrinsic disorder. Citrullination represents an important trigger of multiple physiological and pathological processes, and as a result, PADs are recognized to play a number of important roles in autoimmune diseases, cancer, and neurodegeneration. Therefore, we also review the current state of the art in the development of PAD inhibitors with good potency and selectivity.

Highly Efficient Spin-Orbit Torque and Switching of Layered Ferromagnet Fe3GeTe2

Among van der Waals (vdW) layered ferromagnets, Fe₃GeTe₂ (FGT) is an excellent candidate material to form FGT/heavy metal heterostructures for studying the effect of spin-orbit torques (SOT). Its metallicity, strong perpendicular magnetic anisotropy built in the single atomic layers, relatively high Curie temperature (T_c ∼ 225 K), and electrostatic gate tunability offer a tantalizing possibility of achieving the ultimate high SOT limit in monolayer all-vdW nanodevices. In this study, we fabricate heterostructures of FGT/Pt with 5 nm of Pt sputtered onto the atomically flat surface of ∼15-23 nm exfoliated FGT flakes. The spin current generated in Pt exerts a damping-like SOT on FGT magnetization. At ∼2.5 × 10¹¹ A/m² current density, SOT causes the FGT magnetization to switch, which is detected by the anomalous Hall effect of FGT. To quantify the SOT effect, we measure the second harmonic Hall responses as the applied magnetic field rotates the FGT magnetization in the plane. Our analysis shows that the SOT efficiency is comparable with that of the best heterostructures containing three-dimensional (3D) ferromagnetic metals and much larger than that of heterostructures containing 3D ferrimagnetic insulators. Such large efficiency is attributed to the atomically flat FGT/Pt interface, which demonstrates the great potential of exploiting vdW heterostructures for highly efficient spintronic nanodevices.

Probing Magnetism in Insulating Cr2Ge2Te6 by Induced Anomalous Hall Effect in Pt

Two-dimensional ferromagnet Cr₂Ge₂Te₆ (CGT) is so resistive below its Curie temperature that probing its magnetism by electrical transport becomes extremely difficult. By forming heterostructures with Pt, however, we observe clear anomalous Hall effect (AHE) in 5 nm thick Pt deposited on thin (<50 nm) exfoliated flakes of CGT. The AHE hysteresis loops persist to ∼60 K, which matches well to the Curie temperature of CGT obtained from the bulk magnetization measurements. The slanted AHE loops with a narrow opening indicate magnetic domain formation, which is confirmed by low-temperature magnetic force microscopy (MFM) imaging. These results clearly demonstrate that CGT imprints its magnetization in the AHE signal of the Pt layer. Density functional theory calculations of CGT/Pt heterostructures suggest that the induced ferromagnetism in Pt may be primarily responsible for the observed AHE. Our results establish a powerful way of investigating magnetism in 2D insulating ferromagnets, which can potentially work for monolayer devices.

Health risk associated with airborne particulate matter and its components in Jeddah, Saudi Arabia

Samples of PM_2.5 and PM₁₀ have been collected in all of four seasons at seven sites within the city of Jeddah, Saudi Arabia. The samples have been analysed for a range of trace elements. There is a large loading of wind-blown dust and the majority of elements are predominantly associated with coarse particles. Enrichment factors, however, show that some elements are markedly enriched above crustal abundance. Using mean data for the PM_2.5 and PM₁₀ fractions from each of the seven sampling sites, health risks have been estimated for particulate matter mass, the elements Cr, Mn, Ni, Pb, As, Cd and V measured in this study, and polycyclic aromatic hydrocarbons using data from an earlier study within Jeddah. Cancer risks are calculated from mean airborne concentrations and cancer slope factors for the carcinogenic metals and PAH, but the cancer risks are relatively modest compared to the lifetime risk of mortality due to PM_2.5 exposure. The risks associated with exposure to V and Mn are considered to be small, while concentrations of cadmium far exceed the European Union Limit Value and World Health Organisation guideline. Cadmium shows a very high crustal enrichment factor but is present predominantly in the coarse particle fraction suggesting that local soils and surface dusts are unusually enriched in Cd relative to the global average. Using national data for mortality rates, the excess mortality due to PM_2.5 exposure has been calculated and amounts to over 1100 deaths annually for the city of Jeddah.

Withaferin A Inhibits Prostate Carcinogenesis in a PTEN-deficient Mouse Model of Prostate Cancer

We recently demonstrated that AKT activation plays a role in prostate cancer progression and inhibits the pro-apoptotic function of FOXO3a and Par-4. AKT inhibition and Par-4 induction suppressed prostate cancer progression in preclinical models. Here, we investigate the chemopreventive effect of the phytonutrient Withaferin A (WA) on AKT-driven prostate tumorigenesis in a Pten conditional knockout (Pten-KO) mouse model of prostate cancer. Oral WA treatment was carried out at two different doses (3 and 5 mg/kg) and compared to vehicle over 45 weeks. Oral administration of WA for 45 weeks effectively inhibited primary tumor growth in comparison to vehicle controls. Pathological analysis showed the complete absence of metastatic lesions in organs from WA-treated mice, whereas discrete metastasis to the lungs was observed in control tumors. Immunohistochemical analysis revealed the down-regulation of pAKT expression and epithelial-to-mesenchymal transition markers, such as β-catenin and N-cadherin, in WA-treated tumors in comparison to controls. This result corroborates our previous findings from both cell culture and xenograft models of prostate cancer. Our findings demonstrate that the daily administration of a phytonutrient that targets AKT activation provides a safe and effective treatment for prostate cancer in a mouse model with strong potential for translation to human disease.

A substitution mutation in cardiac ubiquitin ligase, FBXO32, is associated with an autosomal recessive form of dilated cardiomyopathy

Background

Familial dilated cardiomyopathy (DCM) is genetically heterogeneous. Mutations in more than 40 genes have been identified in familial cases, mostly inherited in an autosomal dominant pattern. DCM due to recessive mutations is rarely observed. In consanguineous families, homozygosity mapping and whole exome sequencing (WES) can be utilized to identify the genetic defects in recessively inherited DCM.

Methods

In a consanguineous family with four affected siblings with severe DCM, we combined homozygosity mapping, linkage analysis and WES, to uncover the genetic defect.

Results

A region of homozygosity (ROH) on chromosome 8q24.13–24.23 was found to be shared by all of the four affected siblings. WES detected ~47,000 variants that were filtered to a homozygous mutation (p.Gly243Arg) in the FBXO32 gene, located within the identified ROH. The mutation segregated with the phenotype, replaced a highly-conserved amino acid, and was not detected in 1986 ethnically-matched chromosomes. FBXO32, which encodes a muscle-specific ubiquitin ligase, has been implicated in the pathogenesis of cardiomyopathy through the ubiquitin proteasome system (UPS). In addition, FBXO32-knockout mice manifest with cardiomyopathy. Screening the index patient for all of the WES variants in 48 genes known to be implicated in hypertrophic and dilated cardiomyopathy was negative.

Conclusions

Our data suggest that FBXO32 is a candidate gene for recessive DCM. Acting as a cardiac ubiquitin ligase, mutated FBXO32 could perturb the degradation of target proteins in the UPS, the impairment of which has been observed in cardiomyopathy. Our work proposes that genes encoding other ubiquitin ligases could also be implicated in familial cardiomyopathy.

Electronic supplementary material

The online version of this article (doi:10.1186/s12881-016-0267-5) contains supplementary material, which is available to authorized users.

Educational crowdsourcing to support the learning of computer programming

Recent advancements in technology have enabled a shift to occur in teaching and learning. We are living in a connected world where physical boundaries of attending an institution to gain an education no longer apply. There are currently thousands of courses available online that do not require formal attendance. As such, this era of "open learning" pioneers an innovative research, across multiple disciplines. One domain of knowledge where open learning can be advantageous is within computer science. This industry is now highly in demand and can benefit from open learning platforms, where students may not have the opportunity to formally attend courses but still want to enhance their skills. However, there are some significant limitations in open learning applications: how they assess the quality of learning (i.e., was it just copying or at best learning by rote) or considering individual differences among learners. In this emerging research paper, we posit the idea of an adaptive, crowdsourced, and primarily educational technology, targeted at software development students. The proposed technology caters for either individual or group learning. It differentiates itself from other tutoring and programming support technologies as it will continually monitor and assess students' performance in each phase of the education process.

A rare cause of asymptomatic solitary pulmonary nodule: adult Schistosoma worm

Solitary pulmonary nodule due to various pathologies has been reported in the medical literature. We report a case of solitary pulmonary nodule in an asymptomatic 60-year-old male smoker, who had a positive family history of pulmonary tuberculosis. His routine screening chest X-ray revealed a 2 × 1.5 cm nodule in the right lung upper zone. A CT scan of the thorax confirmed the finding. Bronchoscopy, lavage, biopsy and screening for tuberculosis were negative. Owing to its technical difficulty, a CT-guided biopsy was deferred by the radiologist, hence we decided to perform segmentectomy that showed granuloma harbouring an adult Schistosoma worm. This is the first case of asymptomatic solitary pulmonary nodule due to adult Schistosoma worm 26 years after the exposure.

Echo-Doppler assessment of the biophysical properties of the aorta in children with chronic kidney disease

Chronic kidney disease (CKD) is known to cause increased arterial stiffness, which is an important independent risk factor for adverse cardiovascular events. The purpose of this study was to assess the vascular properties of the aorta (AO) in a group of children with CKD using a noninvasive echocardiography (echo)-Doppler method. We studied 24 children with stages 2 through 5 CKD and 48 age-matched controls. Detailed echocardiographic assessment and echo-Doppler pulse wave velocity (PWV) was performed. Indices of arterial stiffness, including characteristic (Zc) and input (Zi) impedances, elastic pressure-strain modulus (Ep), and arterial wall stiffness index, were calculated. CKD patients underwent full nephrology assessment, and an iohexol glomerular filtration rate was performed, which allowed for accurate assignment of the CKD stage. CKD patients had greater median systolic blood pressure (114 vs. 110 mmHg; p < 0.04) and pulse pressure (51 vs. 40 mmHg; p < 0.001) compared with controls. PWV was similar between groups (358 vs. 344 cm s(-1); p = 0.759), whereas Zi (182 vs. 131 dyne s cm(-5); p < 0.001), Zc (146 vs. 138 dyne s cm(-5); p = 0.05), and Ep (280 vs. 230 mmHg; p < 0.02) were significantly greater in CKD than in controls. Although load-dependent measures of arterial stiffness were greater in non-dialysis dependent CKD patients, PWV was not increased compared with controls. This suggests that the increased arterial stiffness may not be permanent in these pediatric patients with kidney disease.

Recurrent hepatocellular carcinoma after transplantation: use of a pathological score on explanted livers to predict recurrence

Milan and University of California at San Francisco (UCSF) criteria are used to select patients with hepatocellular carcinoma (HCC) for liver transplantation (LT). Recurrent HCC is a significant cause of death. There is no widely accepted pathological assessment strategy to predict recurrent HCC after transplantation. This study compares the pathology of patients meeting Milan and UCSF criteria and develops a pathological score and nomogram to assess the risk of recurrent HCC after transplantation. All explanted livers with HCC from our center over the 18-yr period 1985 to 2003 were assessed for multiple pathological features and relevant clinical data were recorded; multivariate analysis was performed to determine features associated with recurrent HCC. Using pathological variables that independently predicted recurrent HCC, a pathological score and nomogram were developed to determine the probability of recurrent HCC. Of 75 cases analyzed, 50 (67%) met Milan criteria, 9 (12%) met only UCSF criteria and 16 (21%) met neither criteria based on explant pathology. There were 20 cases of recurrent HCC and the mean follow-up was 8 yr. Recurrent HCC was more common (67 vs. 12%; P < 0.001) and survival was lower (15 vs. 83% at 5 yr; 15 vs. 55% at 8 yr; P < 0.001) with those who met only UCSF criteria, compared to those who met Milan criteria. Cryptogenic cirrhosis (25 vs. 5%; P = 0.015), preoperative AFP >1,000 ng/mL (20 vs. 0%; P < 0.001) and postoperative OKT3 use (40 vs. 15%; P = 0.017) were more common among patients with recurrent HCC. While microvascular invasion was the strongest pathological predictor of recurrent HCC, tumor size >or=3 cm (P = 0.004; odds ratio [OR] = 7.42), nuclear grade (P = 0.044; OR = 3.25), microsatellitosis (P = 0.020; OR = 4.82), and giant/bizarre cells (P = 0.028; OR = 4.78) also predicted recurrent HCC independently from vascular invasion. The score and nomogram stratified the risk of recurrent HCC into 3 tiers: low (<5%), intermediate (40-65%), and high (>95%). In conclusion, compared to patients meeting Milan criteria, patients who meet only UCSF criteria have a worse survival and an increased rate of recurrent HCC with long-term follow-up, as well as more frequent occurrence of adverse histopathological features, such as microvascular invasion. Application of a pathological score and nomogram could help identify patients at increased risk for tumor recurrence, who may benefit from increased surveillance or adjuvant therapy.