Endothelial specific isoform of type XVIII collagen (COL-18N): A marker of vascular integrity in haemophilic arthropathy.

BACKGROUND: Haemophilic arthropathy (HA) is a major complication in haemophilia. Collagens IV, XV and XVIII are responsible for maintaining the integrity of the vessel wall in the joint. Following joint remodelling and damage, the short isoform of collagen type XVIII (COL-18N) is degraded, releasing measurable fragments. Our goal was to quantify the specific isoform COL-18N in haemophilia A patients and to assess its relation to the clinical and radiological data as well as haemophilia joint health score (HJHS), functional independence score for haemophilia (FISH), and haemophilia quality of life (Haemo-Qol). METHODS: This cross-sectional study included 50 haemophilia A patients recruited from the Paediatric Haematology and Oncology unit, Ain Shams University, Cairo, Egypt. Quantification of COL-18N was done by ELISA. Assessment of joint state clinically using FISH and HJH scores and radiologically by X-rays and ultrasound. RESULTS: Haemophilia A patients had significantly higher median COL-18N levels compared to the control group. Inhibitor positive and negative haemophilia A patients as well as those on non-steroidal anti-inflammatory drug and those not had comparable COL-18N levels. Patients with ≥2 target joints had significantly higher COL-18N level compared to those with one or those without target joints. There were significant positive correlations between COL-18N level and the total HJHS, Haemo-Qol, the HEAD-US score and annual bleeding rate. CONCLUSION: Our results demonstrated a high level of COL-18N in haemophilia A patients and argued its benefit as a potential marker for monitoring the development of haemophilic arthropathy and tailoring the optimal treatment to prevent further joint damage.

Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases.

Adjusting DNA structure via epigenetic modifications, and altering polyadenylation (pA) sites at which precursor mRNA is cleaved and polyadenylated, allows cells to quickly respond to environmental stress. Since polyadenylation occurs co-transcriptionally, and specific patterns of nucleosome positioning and chromatin modifications correlate with pA site usage, epigenetic factors potentially affect alternative polyadenylation (APA). We report that the histone H3K4 methyltransferase Set1, and the histone H3K36 methyltransferase Set2, control choice of pA site in Saccharomyces cerevisiae, a powerful model for studying evolutionarily conserved eukaryotic processes. Deletion of SET1 or SET2 causes an increase in serine-2 phosphorylation within the C-terminal domain of RNA polymerase II (RNAP II) and in the recruitment of the cleavage/polyadenylation complex, both of which could cause the observed switch in pA site usage. Chemical inhibition of TOR signaling, which causes nutritional stress, results in Set1- and Set2-dependent APA. In addition, Set1 and Set2 decrease efficiency of using single pA sites, and control nucleosome occupancy around pA sites. Overall, our study suggests that the methyltransferases Set1 and Set2 regulate APA induced by nutritional stress, affect the RNAP II C-terminal domain phosphorylation at Ser2, and control recruitment of the 3' end processing machinery to the vicinity of pA sites.

COVID-19 in Children With Cancer: A Single Low-Middle Income Center Experience.

BACKGROUND: Coronavirus disease-2019 (COVID-19) could be associated with morbidity and mortality in immunocompromised children. OBJECTIVE: The objective of this study was to measure the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among hospitalized children with cancer and to detect the associated clinical manifestations and outcomes. METHODOLOGY: A prospective noninterventional study including all hospitalized children with cancer conducted between mid-April and mid-June 2020 in Ain Shams University Hospital, Egypt. Clinical, laboratory, and radiologic data were collected. SARS-CoV-2 infection was diagnosed by reverse transcription polymerase chain reaction tests in nasopharyngeal swabs. RESULTS: Fifteen of 61 hospitalized children with cancer were diagnosed with SARS-CoV-2. Their mean age was 8.3±3.5 years. Initially, 10 (66.7%) were asymptomatic and 5 (33.3%) were symptomatic with fever and/or cough. Baseline laboratory tests other than SARS-CoV-2 reverse transcription polymerase chain reaction were not diagnostic; the mean absolute lymphocyte count was 8.7±2.4×109/L. C-reactive protein was mildly elevated in most of the patients. Imaging was performed in 10 (66.7%) patients with significant radiologic findings detected in 4 (40%) patients. Treatment was mainly supportive with antibiotics as per the febrile neutropenia protocol and local Children Hospital guidance for management of COVID-19 in children. CONCLUSIONS: Pediatric cancer patients with COVID-19 were mainly asymptomatic or with mild symptoms. A high index of suspicion and regular screening with nasopharyngeal swab in asymptomatic hospitalized cancer patients is recommended.

Cleavage and polyadenylation factors are potential regulators of adipogenesis.

OBJECTIVE: Alternative polyadenylation (APA) is a co-transcriptional process that leads to isoform diversity in the 3' ends of mRNAs. APA is known to occur during differentiation, and its dysregulation is observed in diseases like cancer and autoimmune disorders. It has been previously reported that differentiation of 3T3-L1 cells to adipocytes leads to an overall lengthening of mRNAs, but the proteins involved in this regulation have not been identified. The expression levels of subunits of the cleavage and polyadenylation (C/P) complex can regulate the choice of poly(A) site, which in turn can affect different cellular activities. In this paper, we studied the change in levels of C/P proteins during 3T3-L1 differentiation. RESULTS: We observed that while the RNA expression of these proteins is unchanged during differentiation, the protein levels of some subunits do change, including a decrease in levels of CPSF73, the nuclease that cuts at the poly(A) site. However, overexpression of CPSF73 alone does not affect the efficiency and rate of differentiation.

Transcriptomic analysis reveals regulation of adipogenesis via long non-coding RNA, alternative splicing, and alternative polyadenylation.

Obesity is characterized by dysregulated adipogenesis that leads to increased number and/or size of adipocytes. Understanding the molecular mechanisms governing adipogenesis is therefore key to designing therapeutic interventions against obesity. In our study, we analyzed 3'-end sequencing data that we generated from human preadipocytes and adipocytes, as well as previously published RNA-seq datasets, to elucidate mechanisms of regulation via long non-coding RNA (lncRNA), alternative splicing (AS) and alternative polyadenylation (APA). We discovered lncRNAs that have not been previously characterized but may be key regulators of white adipogenesis. We also detected 100 AS events and, using motif enrichment analysis, identified RNA binding proteins (RBPs) that could mediate exon skipping-the most prevalent AS event. In addition, we show that usage of alternative poly(A) sites in introns or 3'-UTRs of key adipogenesis genes leads to isoform diversity, which can have significant biological consequences on differentiation efficiency. We also identified RBPs that may modulate APA and defined how 3'-UTR APA can regulate gene expression through gain or loss of specific microRNA binding sites. Taken together, our bioinformatics-based analysis reveals potential therapeutic avenues for obesity through manipulation of lncRNA levels and the profile of mRNA isoforms via alternative splicing and polyadenylation.

Recombinant origin and interspecies transmission of a HERV-K(HML-2)-related primate retrovirus with a novel RNA transport element.

HERV-K(HML-2), the youngest clade of human endogenous retroviruses (HERVs), includes many intact or nearly intact proviruses, but no replication competent HML-2 proviruses have been identified in humans. HML-2-related proviruses are present in other primates, including rhesus macaques, but the extent and timing of HML-2 activity in macaques remains unclear. We have identified 145 HML-2-like proviruses in rhesus macaques, including a clade of young, rhesus-specific insertions. Age estimates, intact open reading frames, and insertional polymorphism of these insertions are consistent with recent or ongoing infectious activity in macaques. 106 of the proviruses form a clade characterized by an ~750 bp sequence between env and the 3' long terminal repeat (LTR), derived from an ancient recombination with a HERV-K(HML-8)-related virus. This clade is found in Old World monkeys (OWM), but not great apes, suggesting it originated after the ape/OWM split. We identified similar proviruses in white-cheeked gibbons; the gibbon insertions cluster within the OWM recombinant clade, suggesting interspecies transmission from OWM to gibbons. The LTRs of the youngest proviruses have deletions in U3, which disrupt the Rec Response Element (RcRE), required for nuclear export of unspliced viral RNA. We show that the HML-8-derived region functions as a Rec-independent constitutive transport element (CTE), indicating the ancestral Rec-RcRE export system was replaced by a CTE mechanism.

Just as we study fossils to understand how animals and plants have evolved, we can study ancient viruses to understand how diseases have emerged and changed over long periods. Unlike fossils, viruses do not leave visible traces in the ground but, instead, they leave viral genes known as endogenous viral elements (or EVEs) that become permanently incorporated in their host's DNA. HML-2s are the youngest known EVEs in the human genome. They have evolved gradually by accumulating lots of small genetic changes and no longer actively infect humans. But these virus remnants have long been suspected to play a role in prostate cancer, lupus and other human diseases. Rhesus macaques and other monkeys also have HML-2s but these are less well studied than human HML-2s. Monkeys are often used as models of human biology in research studies, therefore, understanding how HML-2s have evolved in rhesus macaques may enable researchers to establish this monkey as a model for investigating the role of HML-2s in humans. To investigate this possibility, Williams et al. searched for HML-like EVEs in rhesus macaque genomes published in previous studies. The experiments found that, unlike human HML-2s, the macaque HML-2s underwent a sudden genetic transformation millions of years ago. They acquired a new gene from another virus that completely changed how the macaque HML-2s leave a compartment within the cells of their host that contains most of the host's genome ­ a key step in the life cycle of viruses. The data also suggest that HML-2s may still be actively infecting macaques today and that these EVEs jumped from monkeys into gibbons. This is the first known example of HML-2s moving between different types of primates and it indicates there may be a risk that macaque HML-2s could infect humans. In the future, the findings of Williams et al. may help researchers develop new approaches to treat prostate cancer and other diseases linked with HML-2s in humans.

Alarming Situation of Spreading Enteric Viruses Through Sewage Water in Dhaka City: Molecular Epidemiological Evidences.

Global burden of acute viral gastroenteritis remains high, particularly in developing countries including Bangladesh. Sewage water (SW) is an important node to monitor enteric pathogens both in the environment and among the population. Analysis of SW in Dhaka city deems crucially important because a large number of urban-city dwellers live in Dhaka city, the capital of Bangladesh, under a constant threat of precarious sewerage system. In this study, we collected raw SW from five locations of Dhaka city every month from June 2016 to May 2017. It was concentrated with polyethylene glycol (PEG) and investigated for three major enteric viruses, rotavirus A (RVA), norovirus GII (NoV GII) and adenovirus (AdV) using polymerase chain reaction (PCR). Most of these SW samples collected from both hospitals and non-hospital areas yielded enteric viruses: 76% samples were positive for AdV, followed by 53% NoV GII and 38% RVA. Viral load was determined as much as 1 × 107 copies/ml for RVA and 3.5 × 103 copies/ml for NoV GII. Importantly, NoV GII and AdV that can affect people of all ages were predominated during monsoon also when SW overflows and spreads over a wide and crowded area. Genotypes G1, G2, G3, G8, and G9 for RVA, GII.4 for NoV, and type 41 for AdV were detected representing the current profile of circulating genotypes in the population. This study provides the first evidence of distribution of major diarrheal viruses in SW in Dhaka city which is alarming showing grave risk of impending outbreaks through exposure.

Direct label-free electrical immunodetection of transplant rejection protein biomarker in physiological buffer using floating gate AlGaN/GaN high electron mobility transistors.

Monokine induced by interferon gamma (MIG/CXCL9) is used as an immune biomarker for early monitoring of transplant or allograft rejection. This paper demonstrates a direct electrical, label-free detection method of recombinant human MIG with anti-MIG IgG molecules in physiologically relevant buffer environment. The sensor platform used is a biologically modified GaN-based high electron mobility transistor (HEMT) device. Biomolecular recognition capability was provided by using high affinity anti-MIG monoclonal antibody to form molecular affinity interface receptors on short N-hydroxysuccinimide-ester functionalized disulphide (DSP) self-assembled monolayers (SAMs) on the gold sensing gate of the HEMT device. A floating gate configuration has been adopted to eliminate the influences of external gate voltage. Preliminary test results with the proposed chemically treated GaN HEMT biosensor show that MIG can be detected for a wide range of concentration varying from 5 ng/mL to 500 ng/mL.

Isolated photosystem I reaction centers on a functionalized gated high electron mobility transistor.

In oxygenic plants, photons are captured with high quantum efficiency by two specialized reaction centers (RC) called Photosystem I (PS I) and Photosystem II (PS II). The captured photon triggers rapid charge separation and the photon energy is converted into an electrostatic potential across the nanometer-scale (~6 nm) reaction centers. The exogenous photovoltages from a single PS I RC have been previously measured using the technique of Kelvin force probe microscopy (KFM). However, biomolecular photovoltaic applications require two-terminal devices. This paper presents for the first time, a micro-device for detection and characterization of isolated PS I RCs. The device is based on an AlGaN/GaN high electron mobility transistor (HEMT) structure. AlGaN/GaN HEMTs show high current throughputs and greater sensitivity to surface charges compared to other field-effect devices. PS I complexes immobilized on the floating gate of AlGaN/GaN HEMTs resulted in significant changes in the device characteristics under illumination. An analytical model has been developed to estimate the RCs of a major orientation on the functionalized gate surface of the HEMTs.

Low-power low-voltage current readout circuit for inductively powered implant system.

Low voltage and low power are two key requirements for on-chip realization of wireless power and data telemetry for applications in biomedical sensor instrumentation. Batteryless operation and wireless telemetry facilitate robust, reliable, and longer lifetime of the implant unit. As an ongoing research work, this paper demonstrates a low-power low-voltage sensor readout circuit which could be easily powered up with an inductive link. This paper presents two versions of readout circuits that have been designed and fabricated in bulk complementary metal-oxide semiconductor (CMOS) processes. Either version can detect a sensor current in the range of 0.2 µA to 2 µA and generate square-wave data signal whose frequency is proportional to the sensor current. The first version of the circuit is fabricated in a 0.35-µ m CMOS process and it can generate an amplitude-shift-keying (ASK) signal while consuming 400 µ W of power with a 1.5-V power supply. Measurement results indicate that the ASK chip generates 76 Hz to 500 Hz frequency of a square-wave data signal for the specified sensor current range. The second version of the readout circuit is fabricated in a 0.5-µ m CMOS process and produces a frequency-shift-keying (FSK) signal while consuming 1.675 mW of power with a 2.5-V power supply. The generated data frequency from the FSK chip is 1 kHz and 9 kHz for the lowest and the highest sensor currents, respectively. Measurement results confirm the functionalities of both prototype schemes. The prototype circuit has potential applications in the monitoring of blood glucose level, lactate in the bloodstream, and pH or oxygen in a physiological system/environment.

Wavelet packets-based blind watermarking for medical image management.

The last decade has witnessed an explosive use of medical images and Electronics Patient Record (EPR) in the healthcare sector for facilitating the sharing of patient information and exchange between networked hospitals and healthcare centers. To guarantee the security, authenticity and management of medical images and information through storage and distribution, the watermarking techniques are growing to protect the medical healthcare information. This paper presents a technique for embedding the EPR information in the medical image to save storage space and transmission overheads and to guarantee security of the shared data. In this paper a new method for protecting the patient information in which the information is embedded as a watermark in the discrete wavelet packet transform (DWPT) of the medical image using the hospital logo as a reference image. The patient information is coded by an error correcting code (ECC), BCH code, to enhance the robustness of the proposed method. The scheme is blind so that the EPR can be extracted from the medical image without the need of the original image. Therefore, this proposed technique is useful in telemedicine applications. Performance of the proposed method was tested using four modalities of medical images; MRA, MRI, Radiological, and CT. Experimental results showed no visible difference between the watermarked and the original image. Moreover, the proposed watermarking method is robust against a wide range of attacks such as JPEG coding, Gaussian noise addition, histogram equalization, gamma correction, contrast adjustment, and sharpen filter and rotation.