Hierarchical assembly of tryptophan zipper peptides into stress-relaxing bioactive hydrogels.

Soft materials in nature are formed through reversible supramolecular assembly of biological polymers into dynamic hierarchical networks. Rational design has led to self-assembling peptides with structural similarities to natural materials. However, recreating the dynamic functional properties inherent to natural systems remains challenging. Here we report the discovery of a short peptide based on the tryptophan zipper (trpzip) motif, that shows multiscale hierarchical ordering that leads to emergent dynamic properties. Trpzip hydrogels are antimicrobial and self-healing, with tunable viscoelasticity and unique yield-stress properties that allow immediate harvest of embedded cells through a flick of the wrist. This characteristic makes Trpzip hydrogels amenable to syringe extrusion, which we demonstrate with examples of cell delivery and bioprinting. Trpzip hydrogels display innate bioactivity, allowing propagation of human intestinal organoids with apical-basal polarization. Considering these extensive attributes, we anticipate the Trpzip motif will prove a versatile building block for supramolecular assembly of soft materials for biotechnology and medicine.

Small and Large Extracellular Vesicles Derived from Pleural Mesothelioma Cell Lines Offer Biomarker Potential.

Pleural mesothelioma, previously known as malignant pleural mesothelioma, is an aggressive and fatal cancer of the pleura, with one of the poorest survival rates. Pleural mesothelioma is in urgent clinical need for biomarkers to aid early diagnosis, improve prognostication, and stratify patients for treatment. Extracellular vesicles (EVs) have great potential as biomarkers; however, there are limited studies to date on their role in pleural mesothelioma. We conducted a comprehensive proteomic analysis on different EV populations derived from five pleural mesothelioma cell lines and an immortalized control cell line. We characterized three subtypes of EVs (10 K, 18 K, and 100 K), and identified a total of 4054 unique proteins. Major differences were found in the cargo between the three EV subtypes. We show that 10 K EVs were enriched in mitochondrial components and metabolic processes, while 18 K and 100 K EVs were enriched in endoplasmic reticulum stress. We found 46 new cancer-associated proteins for pleural mesothelioma, and the presence of mesothelin and PD-L1/PD-L2 enriched in 100 K and 10 K EV, respectively. We demonstrate that different EV populations derived from pleural mesothelioma cells have unique cancer-specific proteomes and carry oncogenic cargo, which could offer a novel means to extract biomarkers of interest for pleural mesothelioma from liquid biopsies.

Molecular and Functional Characteristics of Airway Epithelium under Chronic Hypoxia.

Localized and chronic hypoxia of airway mucosa is a common feature of progressive respiratory diseases, including cystic fibrosis (CF). However, the impact of prolonged hypoxia on airway stem cell function and differentiated epithelium is not well elucidated. Acute hypoxia alters the transcription and translation of many genes, including the CF transmembrane conductance regulator (CFTR). CFTR-targeted therapies (modulators) have not been investigated in vitro under chronic hypoxic conditions found in CF airways in vivo. Nasal epithelial cells (hNECs) derived from eight CF and three non-CF participants were expanded and differentiated at the air-liquid interface (26-30 days) at ambient and 2% oxygen tension (hypoxia). Morphology, global proteomics (LC-MS/MS) and function (barrier integrity, cilia motility and ion transport) of basal stem cells and differentiated cultures were assessed. hNECs expanded at chronic hypoxia, demonstrating epithelial cobblestone morphology and a similar proliferation rate to hNECs expanded at normoxia. Hypoxia-inducible proteins and pathways in stem cells and differentiated cultures were identified. Despite the stem cells' plasticity and adaptation to chronic hypoxia, the differentiated epithelium was significantly thinner with reduced barrier integrity. Stem cell lineage commitment shifted to a more secretory epithelial phenotype. Motile cilia abundance, length, beat frequency and coordination were significantly negatively modulated. Chronic hypoxia reduces the activity of epithelial sodium and CFTR ion channels. CFTR modulator drug response was diminished. Our findings shed light on the molecular pathophysiology of hypoxia and its implications in CF. Targeting hypoxia can be a strategy to augment mucosal function and may provide a means to enhance the efficacy of CFTR modulators.

dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data.

Infection triggers a dynamic cascade of reciprocal events between host and pathogen wherein the host activates complex mechanisms to recognise and kill pathogens while the pathogen often adjusts its virulence and fitness to avoid eradication by the host. The interaction between the pathogen and the host results in large-scale changes in gene expression in both organisms. Dual RNA-seq, the simultaneous detection of host and pathogen transcripts, has become a leading approach to unravelling complex molecular interactions between the host and the pathogen and is particularly informative for intracellular organisms. The amount of in vitro and in vivo dual RNA-seq data is rapidly growing, which demands computational pipelines to effectively analyse such data. In particular, holistic, systems-level, and temporal analyses of dual RNA-seq data are essential to enable further insights into the host-pathogen transcriptional dynamics and potential interactions. Here, we developed an integrative network-driven bioinformatics pipeline, dRNASb, a systems biology-based computational pipeline to analyse temporal transcriptional clusters, incorporate molecular interaction networks (e.g. protein-protein interactions), identify topologically and functionally key transcripts in host and pathogen, and associate host and pathogen temporal transcriptome to decipher potential between-species interactions. The pipeline is applicable to various dual RNA-seq data from different species and experimental conditions. As a case study, we applied dRNASb to analyse temporal dual RNA-seq data of Salmonella-infected human cells, which enabled us to uncover genes contributing to the infection process and their potential functions and to identify putative associations between host and pathogen genes during infection. Overall, dRNASb has the potential to identify key genes involved in bacterial growth or host defence mechanisms for future uses as therapeutic targets.

Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods.

Liquid biopsy has shown promise for cancer diagnosis due to its minimally invasive nature and the potential for novel biomarker discovery. However, the low concentration of relevant blood-based biosources and the heterogeneity of samples (i.e. the variability of relative abundance of molecules identified), pose major challenges to biomarker discovery. Moreover, the number of molecular measurements or features (e.g. transcript read counts) per sample could be in the order of several thousand, whereas the number of samples is often substantially lower, leading to the curse of dimensionality. These challenges, among others, elucidate the importance of a robust biomarker panel identification or feature extraction step wherein relevant molecular measurements are identified prior to classification for cancer detection. In this work, we performed a benchmarking study on 12 feature extraction methods using transcriptomic profiles derived from different blood-based biosources. The methods were assessed both in terms of their predictive performance and the robustness of the biomarker panels in diagnosing cancer or stratifying cancer subtypes. While performing the comparison, the feature extraction methods are categorized into feature subset selection methods and transformation methods. A transformation feature extraction method, namely partial least square discriminant analysis, was found to perform consistently superior in terms of classification performance. As part of the benchmarking study, a generic pipeline has been created and made available as an R package to ensure reproducibility of the results and allow for easy extension of this study to other datasets (https://github.com/VafaeeLab/bloodbased-pancancer-diagnosis).

Disentangling single-cell omics representation with a power spectral density-based feature extraction.

Emerging single-cell technologies provide high-resolution measurements of distinct cellular modalities opening new avenues for generating detailed cellular atlases of many and diverse tissues. The high dimensionality, sparsity, and inaccuracy of single cell sequencing measurements, however, can obscure discriminatory information, mask cellular subtype variations and complicate downstream analyses which can limit our understanding of cell function and tissue heterogeneity. Here, we present a novel pre-processing method (scPSD) inspired by power spectral density analysis that enhances the accuracy for cell subtype separation from large-scale single-cell omics data. We comprehensively benchmarked our method on a wide range of single-cell RNA-sequencing datasets and showed that scPSD pre-processing, while being fast and scalable, significantly reduces data complexity, enhances cell-type separation, and enables rare cell identification. Additionally, we applied scPSD to transcriptomics and chromatin accessibility cell atlases and demonstrated its capacity to discriminate over 100 cell types across the whole organism and across different modalities of single-cell omics data.

Asymptomatic Brain Abscess Following Decompressive Craniotomy for Stroke - A Report of Two Cases and Review of the Literature.

Stroke is a significant health problem in both developed and developing nations. The treatment strategies of stroke differ among various centers depending on the available expertise. Nevertheless, stroke contributes to a major economic burden for patients and health institutions. The recovery period after stroke is a critical period wherein various complications can develop in survivors. Among these multiple complications, the formation of brain abscess in the infarcted brain tissue is rare and less well described in the literature. Fever or signs of raised intracranial pressure are the usual manifestation of poststroke brain abscess. We present two unique cases of large brain abscess in patients who survived a malignant stroke. Both the patients were recuperating well after decompressive craniectomy for stroke without any signs of intracranial infection or raised intracranial pressure. Both the patients underwent open drainage of brain abscess, followed by delayed cranioplasty. There are only a few cases of brain abscess reported in the literature in patients who underwent decompressive craniectomy for stroke.

Chronic Subdural Hematoma: A Questionnaire Survey of Management Practice in India and Review of Literature.

OBJECTIVE: To identify the current management modalities practiced by neurosurgeons in India for chronic subdural hematoma. METHODS: A questionnaire was prepared for the survey and sent via e-mail to neurosurgeons. It covered the following aspects of managing chronic subdural hematoma: 1) demographic and institutional details; 2) choice of surgical procedure; 3) surgical adjutants such as placing a subdural drain; 4) pre- and postoperative care; and 5) recurrences and management. Responses obtained were entered in a SPSS data sheet and analyzed. RESULTS: Response rate of the survey was 9.3%. The majority of neurosurgeons (75%) preferred to do burr whole drainage for primary chronic subdural hematoma and also for recurrences. Only one third of routinely placed a subdural drain. Considerable practice variations exist for medical and perioperative management. CONCLUSIONS: Bedside twist drill drainage, which is effective and less costly than operative room procedures, has not gained popularity in practice. The present survey points towards the importance of making management guidelines for this common neurosurgical entity.

Pearl in interhemispheric fissure: A rare phenomenon.

Epidermoid cysts (Keratin pearls) are benign congenital lesions, found commonly in cerebello-pontine angle, suprasellar cistern, sylvian cistern, pineal region, but they are very rare in interhemispheric fissure. Approaching these lesions are challenging to neurosurgeons because of narrow and deep fissure with surrounding vital structures. The present study constitutes an analysis of interhemispheric epidermoid managed at our hospital in last 10 years (Jan 2001-Dec 2010). Total 187 cases of intracranial epidermoid operated in our institute; eight of them were interhemispheric epidermoid making about 4.27% of all epidermoids. The patients were presented with seizures (50%), headache (37%), and weakness (25%). On examination, the common findings were decreased Mini mental score (MMSE) in 50%, motor deficit in 25%, and decreased visual acuity in 25% of cases. All patients underwent craniotomy across the midline as per the location of the lesions. In seven patients, tumors were resected by interhemispheric approach but in one by transcortical. Lesion were excised with microscope and endoscopic assistance with measures to prevent spillage of epidermoid tissue while excision. Post excision tumor bed was irrigated with hydrocortisone diluted saline. All patients except one improved after surgery and non-developed chemical meningitis. One patient of parietal interhemispheric epidermoid with transcortical approach developed weakness in immediate post-operative period. Patients were followed for average 6.8 year without any recurrence. Interhemispheric epidermoids are rare tumors. Achieving safe complete excision without spillage is surgical goal to prevent chemical meningitis and recurrence. Endoscope assists in achieving complete excision so decrease incidence of chemical meningitis and recurrence.