ANKRD54 preferentially selects Bruton's Tyrosine Kinase (BTK) from a Human Src-Homology 3 (SH3) domain library

Bruton's Tyrosine Kinase (BTK) is a cytoplasmic protein tyrosine kinase with a fundamental role in B-lymphocyte development and activation. The nucleocytoplasmic shuttling of BTK is specifically modulated by the Ankyrin Repeat Domain 54 (ANKRD54) protein and the interaction is known to be exclusively SH3-dependent. To identify the spectrum of the ANKRD54 SH3-interactome, we applied phage-display screening of a library containing all the 296 human SH3 domains. The BTK-SH3 domain was the prime interactor. Quantitative western blotting analysis demonstrated the accuracy of the screening procedure. Revealing the spectrum and specificity of ANKRD54-interactome is a critical step toward functional analysis in cells and tissues.Peer reviewe

Predicting the Need for Therapeutic Intervention and Mortality in Acute Pancreatitis: A Two-Center International Study Using Machine Learning

BackgroundCurrent approaches to predicting intervention needs and mortality have reached 65-85% accuracy, which falls below clinical decision-making requirements in patients with acute pancreatitis (AP). We aimed to accurately predict therapeutic intervention needs and mortality on admission, in AP patients, using machine learning (ML).MethodsData were obtained from three databases of patients admitted with AP: one retrospective (Chengdu) and two prospective (Liverpool and Chengdu) databases. Intervention and mortality differences, as well as potential predictors, were investigated. Univariate analysis was conducted, followed by a random forest ML algorithm used in multivariate analysis, to identify predictors. The ML performance matrix was applied to evaluate the model's performance.ResultsThree datasets of 2846 patients included 25 potential clinical predictors in the univariate analysis. The top ten identified predictors were obtained by ML models, for predicting interventions and mortality, from the training dataset. The prediction of interventions includes death in non-intervention patients, validated with high accuracy (96%/98%), the area under the receiver-operating-characteristic curve (0.90/0.98), and positive likelihood ratios (22.3/69.8), respectively. The post-test probabilities in the test set were 55.4% and 71.6%, respectively, which were considerably superior to existing prognostic scores. The ML model, for predicting mortality in intervention patients, performed better or equally with prognostic scores.ConclusionsML, using admission clinical predictors, can accurately predict therapeutic interventions and mortality in patients with AP

One-Step Synthesis of Monodisperse In-Doped ZnO Nanocrystals

A method for the synthesis of high quality indium-doped zinc oxide (In-doped ZnO) nanocrystals was developed using a one-step ester elimination reaction based on alcoholysis of metal carboxylate salts. The resulting nearly monodisperse nanocrystals are well-crystallized with typically crystal structure identical to that of wurtzite type of ZnO. Structural, optical, and elemental analyses on the products indicate the incorporation of indium into the host ZnO lattices. The individual nanocrystals with cubic structures were observed in the 5% In–ZnO reaction, due to the relatively high reactivity of indium precursors. Our study would provide further insights for the growth of doped oxide nanocrystals, and deepen the understanding of doping process in colloidal nanocrystal syntheses

Identification of a novel homozygous nonsense mutation in EYS in a Chinese family with autosomal recessive retinitis pigmentosa

<p>Abstract</p> <p>Background</p> <p>Retinitis pigmentosa is the most important hereditary retinal degenerative disease, which has a high degree of clinical and genetic heterogeneity. More than half of all cases of retinitis pigmentosa are autosomal recessive (arRP), but the gene(s) causing arRP in most families has yet to be identified. The purpose of this study is to identify the genetic basis of severe arRP in a consanguineous Chinese family.</p> <p>Methods</p> <p>Linkage and haplotype analyses were used to define the chromosomal location of the pathogenic gene in the Chinese arRP family. Direct DNA sequence analysis of the entire coding region and exon-intron boundaries of <it>EYS </it>was used to determine the disease-causing mutation, and to demonstrate that the mutation co-segregates with the disease in the family.</p> <p>Results</p> <p>A single nucleotide substitution of G to T at nucleotide 5506 of EYS was identified in the Chinese arRP family. This change caused a substitution of a glutamic acid residue at codon 1,836 by a stop codon TAA (p.E1836X), and resulted in a premature truncated EYS protein with 1,835 amino acids. Three affected siblings in the family were homozygous for the p.E1836X mutation, while the other unaffected family members carried one mutant allele and one normal EYS allele. The nonsense mutation p.E1836X was not detected in 200 unrelated normal controls.</p> <p>Conclusions</p> <p>The <it>EYS </it>gene is a recently identified disease-causing gene for retinitis pigmentosa, and encodes the orthologue of <it>Drosophila </it>spacemaker. To date, there are only eight mutations in <it>EYS </it>that have been identified to cause arRP. Here we report one novel homozygous nonsense mutation of <it>EYS </it>in a consanguineous Chinese arRP family. Our study represents the first independent confirmation that mutations in <it>EYS </it>cause arRP. Additionally, this is the first <it>EYS </it>mutation identified in the Chinese population.</p

Neurochemical Properties of the Synapses in the Pathways of Orofacial Nociceptive Reflexes

The brainstem premotor neurons of the facial nucleus (VII) and hypoglossal (XII) nucleus can integrate orofacial nociceptive input from the caudal spinal trigeminal nucleus (Vc) and coordinate orofacial nociceptive reflex (ONR) responses. However, the synaptoarchitectures of the ONR pathways are still unknown. In the current study, we examined the distribution of GABAergic premotor neurons in the brainstem local ONR pathways, their connections with the Vc projections joining the brainstem ONR pathways and the neurochemical properties of these connections. Retrograde tracer fluoro-gold (FG) was injected into the VII or XII, and anterograde tracer biotinylated dextran amine (BDA) was injected into the Vc. Immunofluorescence histochemical labeling for inhibitory/excitatory neurotransmitters combined with BDA/FG tracing showed that GABAergic premotor neurons were mainly distributed bilaterally in the ponto-medullary reticular formation with an ipsilateral dominance. Some GABAergic premotor neurons made close appositions to the BDA-labeled fibers coming from the Vc, and these appostions were mainly distributed in the parvicellular reticular formation (PCRt), dorsal medullary reticular formation (MdD), and supratrigeminal nucleus (Vsup). We further examined the synaptic relationships between the Vc projecting fibers and premotor neurons in the VII or XII under the confocal laser-scanning microscope and electron microscope, and found that the BDA-labeled axonal terminals that made asymmetric synapses on premotor neurons showed vesicular glutamate transporter 2 (VGluT2) like immunoreactivity. These results indicate that the GABAergic premotor neurons receive excitatory neurotransmission from the Vc and may contribute to modulating the generation of the tonic ONR

Clear Genetic Distinctiveness between Human- and Pig-Derived Trichuris Based on Analyses of Mitochondrial Datasets

The whipworm, Trichuris trichiura, causes trichuriasis in ∼600 million people worldwide, mainly in developing countries. Whipworms also infect other animal hosts, including pigs (T. suis), dogs (T. vulpis) and non-human primates, and cause disease in these hosts, which is similar to trichuriasis of humans. Although Trichuris species are considered to be host specific, there has been considerable controversy, over the years, as to whether T. trichiura and T. suis are the same or distinct species. Here, we characterised the entire mitochondrial genomes of human-derived Trichuris and pig-derived Trichuris, compared them and then tested the hypothesis that the parasites from these two host species are genetically distinct in a phylogenetic analysis of the sequence data. Taken together, the findings support the proposal that T. trichiura and T. suis are separate species, consistent with previous data for nuclear ribosomal DNA. Using molecular analytical tools, employing genetic markers defined herein, future work should conduct large-scale studies to establish whether T. trichiura is found in pigs and T. suis in humans in endemic regions

Expression of CDX2 and Hepatocyte Antigen in Benign and Malignant Lesions of Gallbladder and Its Correlation with Histopathologic Type and Clinical Outcome

Recent studies have shown that both CDX2 and Hepatocyte antigen (Hep) are detected in different types of cancer and associated with clinical prognosis. However, fever studies have examined gallbladder cancer specimens, and little is known about the clinicopathological significance of both CDX2 and Hep expression in gallbladder adenocarcinomas. In present study, we examined the expression frequencies of CDX2 and Hepatocyte antigen (Hep), and explored their clinicopathologic significances in gallbladder adenocarcinoma. Immunohistochemistry was used to detect and compare the frequencies of CDX2 and Hep expression in 108 samples of gallbladder adenocarcinoma, 46 peri-tumor tissues and 35 chronic cholecystitis. The expression frequencies for CDX2 and Hep were 49/108 (45.4%) and 45/108 (41.7%) in gallbladder carcinoma; 13/46 (28.3%) and 11/46 (23.9) in peri-tumor tissues; 5/35 (14.3%) and 2/35 (5.7%) in chronic cholecystitis. The positive staining of CDX2 or Hep in gallbladder adenocarcinoma was significantly higher than that in peritumoral tissues (both, P < 0.05), and chronic cholecystits (both, P < 0.01). The expression of CDX2 or Hep was negatively correlated to grade of differentiation, tumor size and lymph node metastasis (P < 0.01 or P < 0.05). Elevated expression frequency of CDX2 or Hep was associated with increased overall survival (P = 0.003 or P = 0.002). Multivariate Cox regression analysis showed that CDX2 (P = 0.014) or Hep (P = 0.026) expression was an independent prognostic predictor in gallbladder adenocarcinoma. CDX2 and Hep might function as important biological markers in the development and prognosis of gallbladder adenocarcinoma

A Single-Photon Imager Based on Microwave Plasmonic Superconducting Nanowire

Detecting spatial and temporal information of individual photons by using single-photon-detector (SPD) arrays is critical to applications in spectroscopy, communication, biological imaging, astronomical observation, and quantum-information processing. Among the current SPDs1,detectors based on superconducting nanowires have outstanding performance2, but are limited in their ability to be integrated into large scale arrays due to the engineering difficulty of high-bandwidth cryogenic electronic readout3-8. Here, we address this problem by demonstrating a scalable single-photon imager using a single continuous photon-sensitive superconducting nanowire microwave-plasmon transmission line. By appropriately designing the nanowire's local electromagnetic environment so that the nanowire guides microwave plasmons, the propagating voltages signals generated by a photon-detection event were slowed down to ~ 2% of the speed of light. As a result, the time difference between arrivals of the signals at the two ends of the nanowire naturally encoded the position and time of absorption of the photon. Thus, with only two readout lines, we demonstrated that a 19.7-mm-long nanowire meandered across an area of 286 {\mu}m * 193 {\mu}m was capable of resolving ~590 effective pixels while simultaneously recording the arrival times of photons with a temporal resolution of 50 ps. The nanowire imager presents a scalable approach to realizing high-resolution photon imaging in time and space

GPS-ARM: Computational Analysis of the APC/C Recognition Motif by Predicting D-Boxes and KEN-Boxes

Anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase incorporated with Cdh1 and/or Cdc20 recognizes and interacts with specific substrates, and faithfully orchestrates the proper cell cycle events by targeting proteins for proteasomal degradation. Experimental identification of APC/C substrates is largely dependent on the discovery of APC/C recognition motifs, e.g., the D-box and KEN-box. Although a number of either stringent or loosely defined motifs proposed, these motif patterns are only of limited use due to their insufficient powers of prediction. We report the development of a novel GPS-ARM software package which is useful for the prediction of D-boxes and KEN-boxes in proteins. Using experimentally identified D-boxes and KEN-boxes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted. By extensive evaluation and comparison, the GPS-ARM performance was found to be much better than the one using simple motifs. With this powerful tool, we predicted 4,841 potential D-boxes in 3,832 proteins and 1,632 potential KEN-boxes in 1,403 proteins from H. sapiens, while further statistical analysis suggested that both the D-box and KEN-box proteins are involved in a broad spectrum of biological processes beyond the cell cycle. In addition, with the co-localization information, we predicted hundreds of mitosis-specific APC/C substrates with high confidence. As the first computational tool for the prediction of APC/C-mediated degradation, GPS-ARM is a useful tool for information to be used in further experimental investigations. The GPS-ARM is freely accessible for academic researchers at: http://arm.biocuckoo.org