A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis.

The gut microbiota contributes to the development of normal immunity but, when dysregulated, can promote autoimmunity through various non-antigen-specific effects on pathogenic and regulatory lymphocytes. Here, we show that an integrase expressed by several species of the gut microbial genus Bacteroides encodes a low-avidity mimotope of the pancreatic ß cell autoantigen islet-specific glucose-6-phosphatase-catalytic-subunit-related protein (IGRP206-214). Studies in germ-free mice monocolonized with integrase-competent, integrase-deficient, and integrase-transgenic Bacteroides demonstrate that the microbial epitope promotes the recruitment of diabetogenic CD8+ T cells to the gut. There, these effectors suppress colitis by targeting microbial antigen-loaded, antigen-presenting cells in an integrin ß7-, perforin-, and major histocompatibility complex class I-dependent manner. Like their murine counterparts, human peripheral blood T cells also recognize Bacteroides integrase. These data suggest that gut microbial antigen-specific cytotoxic T cells may have therapeutic value in inflammatory bowel disease and unearth molecular mimicry as a novel mechanism by which the gut microbiota can regulate normal immune homeostasis. PAPERCLIP.

BRAF and RET polymorphism association with thyroid cancer risk, a preliminary study from Khyber Pakhtunkhwa population.

BACKGROUND: Thyroid cancer, originating in the neck's thyroid gland, encompasses various types. Genetic mutations, particularly in BRAF and RET genes are crucial in its development. This study investigates the association between BRAF (rs113488022) and RET (rs77709286) polymorphisms and thyroid cancer risk in the Khyber Pakhtunkhwa (KP) population. METHODS: Blood samples from 100 thyroid cancer patients and 100 healthy controls were genotyped using ARMS-PCR followed by gel electrophoresis and statistical analysis. RESULTS: Analysis revealed a significant association between the minor allele T of BRAF (rs113488022) and thyroid cancer risk (P = 0.0001). Both genotypes of BRAF (rs113488022) showed significant associations with thyroid cancer risk (AT; P = 0.0012 and TT; P = 0.045). Conversely, the minor allele G of RET (rs77709286) exhibited a non-significant association with thyroid cancer risk (P = 0.2614), and neither genotype showed significant associations (CG; P = 0.317, GG; P = 0.651). Demographic and clinical parameters analysis using SPSS showed a non-significant association between BRAF and RET variants and age group (P = 0.878 and P = 0.536), gender (P = 0.587 and P = 0.21), tumor size (P = 0.796 and P = 0.765), or tumor localization (P = 0.689 and P = 0.727). CONCLUSION: In conclusion, this study emphasizes the significant association between BRAF polymorphism and thyroid cancer risk, while RET polymorphism showed a less pronounced impact. Further validation using larger and specific datasets is essential to establish conclusive results.

Optimizing liquid fermentation for Wolfiporia cocos: gene expression and biosynthesis of pachymic acid and mycelial biomass.

Wolfiporia cocos, a versatile fungus acclaimed for its nutritional and therapeutic benefits in Traditional Chinese Medicine, holds immense potential for pharmaceutical and industrial applications. In this study, we aimed to optimize liquid fermentation techniques and culture medium composition to maximize mycelial biomass (MB) yield, pachymic acid (PA) concentration, and overall PA production. Additionally, we investigated the molecular basis of our findings by quantifying the expression levels of genes associated with PA and MB biosynthesis using quantitative real-time polymerase chain reaction. Under the optimized fermentation conditions, significant results were achieved, with maximum MB reaching 6.68 g l-1, PA content peaking at 1.25 mg g-1, and a total PA yield of 4.76 g l-1. Notably, among the four examined genes, squalene monooxygenase, exhibited enhanced expression at 0.06 ratio under the optimized conditions. Furthermore, within the realm of carbohydrate-active enzymes, the glycoside hydrolases 16 family displayed elevated expression levels at 21 ratios, particularly during MB production. This study enhances understanding of genetic mechanism governing MB and PA production in W. cocos, highlighting the roles of squalene monooxygenase and glycoside hydrolases 16 carbohydrate-active enzymes.

Palliative Therapies in Metastatic Pancreatic Cancer: Does Medicaid Expansion Make a Difference?

BACKGROUND: The aim of this study was to evaluate the impact of medicaid expansion (ME) on receipt of palliative therapies in metastatic pancreatic cancer patients. PATIENTS AND METHODS: A difference-in-differences (DID) approach was used to analyze patients with metastatic pancreatic cancer identified from the National Cancer Database diagnosed during two time periods: pre-expansion (2010-2012) and post-expansion (2014-2016). Patients diagnosed while residing in ME states were compared with those in non-ME states. Multivariable logistic regression was used to identify predictors of receipt of palliative therapies. RESULTS: Of 87,738 patients overall, 7483(18.1%) received palliative therapies in the pre-expansion, while 10,211(21.5%) received palliative therapies in the post-expansion period. In the pre-expansion period, treatment at a high-volume facility (HVF) (odds ratio [OR] 1.10, 95% confidence interval [CI] 1.02-1.18) and non-west geographic location were predictive of increased palliative therapies. In the post-expansion period, treatment at an HVF (OR 1.09, 95% CI 1.02-1.16), geographic location, and living in an ME state at the time of diagnosis (OR 1.14, 95% CI 1.06-1.22) were predictive of increased palliative therapies. Older age, highest quartile median income (zip-code based), and treatment at a nonacademic facility were independently associated with decreased palliative therapies in both periods. DID analysis demonstrated that patients with metastatic pancreatic cancer living in ME states had increased receipt of palliative therapies relative to those in non-ME states (DID = 2.68, p < 0.001). CONCLUSIONS: The overall utilization of palliative therapies in metastatic pancreatic cancer is low. Multiple sociodemographic disparities exist in the receipt of palliative therapies. ME is associated with increased receipt of palliative therapies in patients with metastatic pancreatic cancer.

pfeRNAs-A Novel Class of Small Non-coding RNAs With Real Translational Potential.

Small non-coding RNAs (sncRNAs) are defined by being less than 200 nucleotides (nt) in length, and consequently, have been divided into many different subclasses including mature microRNA (miRNA), small interfering RNA (siRNA), piwi-interacting RNA (piRNA), protein functional effector sncRNA (pfeRNA), precursor miRNA (pre-miRNA), small nucleolar RNA (snoRNA), 5S ribosome RNA (5SrRNA), 5.8SrRNA, and small nuclear RNA (snRNA). Except for the class of pfeRNAs, the discovery, identification, biogenesis, characterization, and function of other sncRNAs have been well documented. Herein, we provide a review, written especially for clinicians, of the least understood class of functional sncRNAs, the pfeRNAs, focusing on their initial discovery, identification, unique features, function, as well as their exciting clinical translational potential.

The COVID-19 Era Is Associated With Delays in Esophageal Cancer Diagnosis and Treatment.

INTRODUCTION: The coronavirus disease-2019 (COVID-19) pandemic has substantially affected the delivery of healthcare globally. The purpose of this study was to evaluate the association of this era with the timeline of care in esophageal cancer patients. METHODS: We performed a retrospective chart-review of patients presenting to a single high-volume tertiary care center with the diagnosis of esophageal cancer. COVID era was defined as March 2020-December 2020 and compared with the year before (3/2019-12/2019). RESULTS: In total, 117 patients presented in the COVID-era versus 190 in pre-COVID. Stage 3 + 4 disease was found in 77.8% of the patients in the COVID-era compared to 68.9% in the pre-COVID era (P = 0.34). Diagnoses through emergency department admission were 35.5% in the COVID versus 26.7% in the pre-COVID group (P = 0.15). In the COVID era it took a median of 78 d to visit primary care provider (versus 52 d, P = 0.12 in pre-COVID), 45 d to endoscopy (versus 18 d, P = 0.004) and 38 d to treatment initiation (versus 36 d, P = 0.48). Thirty-five percent of the patients underwent esophagectomy compared to 26% in the pre-COVID-era. Median days of intensive-care-unit (ICU) (2 versus 3, P = 0.16) and hospital stay (14 versus 15, P = 0.28) were similar in both groups as well as postoperative 30-day morbidities (63 versus 63%, P = 0.48). One-year follow-up showed 83.7% (95% confidence interval [CI]: 73.8%-90.1%) survival in the COVID-group compared to 76.4% (95% CI: 66.9%-83.5%) in the pre-COVID-group (P = 0.58). Only three patients had a positive COVID result. CONCLUSIONS: Our institution treated fewer esophageal cancer patients during COVID-19 accompanied by a delay in endoscopic diagnosis. Postoperative outcomes and 1-year survival remained similar.

Tumor deposits are associated with a higher risk of peritoneal disease in non-metastatic colorectal cancer patients.

BACKGROUND AND OBJECTIVES: Tumor deposit (TD) is a poor prognostic factor in colorectal cancer (CRC) patients. This study aimed to determine whether TD carry the same risk of peritoneal recurrence as known high-risk (HR) features in CRC patients. METHODS: A retrospective cohort-study of stage I-III CRC patients from 2010 to 2015 was conducted. TD group was defined by the presence of TD on histopathology whereas HR group was defined by the presence of obstruction, perforation, or T4-stage. RESULTS: A total of 151 patients with CRC were identified, of which 50 had TD and 101 had a HR feature. The overall risk of peritoneal recurrence was higher in the TD group versus HR group (36.0% vs. 19.8%, p = 0.03). The risk of peritoneum as the site of first recurrence was also higher in the TD group (22.0% vs. 12.9%, p = 0.03). Overall cancer recurrence at any site was also higher in the TD group (56.0% vs. 34.7%, p = 0.01). Median time to first recurrence was 1.2 (0.7-1.9) years in the TD group compared to 1.4 (0.8-2.1) years in the HR group (p = 0.31). CONCLUSIONS: In non-metastatic CRC patients, TD might have a higher risk of tumor recurrence versus their HR counterparts. Alternative strategies for surveillance and treatment should be considered.

Knowledge and perception of medical students towards the use of artificial intelligence in healthcare.

OBJECTIVE: To assess the knowledge and perception of medical students regarding the utility and applications of artificial intelligence in medicine. METHODS: The cross-sectional study was conducted at the Shifa College of Medicine, Islamabad, Pakistan, from February to August 2021, and comprised medical students regardless of gender or year of studies. Data was collected using a pretested questionnaire. Differences in perceptions were explored relative to gender and the year of studies. Data was analysed using SPSS 23. RESULTS: Of the 390 participants, 168(43.1%) were males and 222(56.9%) were females. The overall mean age was 20±1.65 years. There were 121(31%) students from the first year of studies, 122(31.3%) second year, 30(7.7%) from third year, 73(18.7%) from fourth year, and 44(11.3%) from the fifth year. Most participants 221(56.7%) had a good familiarity with artificial intelligence, and 226(57.9%) agreed that the biggest advantage of using artificial intelligence in healthcare was its ability to speed up the processes. In terms of gender of year of studies, there were no significant differences on both counts (p>0.05). CONCLUSIONS: Medical students, regardless of age and year of studies, were found to have a good understanding of the usage and application of artificial intelligence in medicine.

Confronted With Death: Factors Affecting End of Life Decisions in the Intensive Care Unit.

To determine how often care is limited at the end of life and the factors that are associated with this decision, we reviewed the medical records of all patients that passed away in the intensive care units (ICU) of Aga Khan University. We found that a majority of patients had Do-Not-Resuscitate orders in place at the time of death. Our analysis yielded 6 variables that were associated with the decision to limit care. These are patient age, sex, duration of mechanical ventilation, Glasgow Coma Scale (GCS) ≤8 at any point during ICU stay, GCS ≤8 in the first 24 hours following ICU admission, and mean arterial pressure <65 mm of Hg while on vasopressors in the first 24 hours following ICU admission. These variables require further study and should be carefully considered during end of life discussions to allow for optimal management at the end of life.

Investigation of the effect of addition of Momordica charantia to glibenclamide on amelioration of endothelial dysfunction in diabetic rats by activating Takeda G protein-coupled receptor 5.

Endothelial dysfunction (ED) is a significant risk factor of blood vessel related diseases of diabetes and this study evaluate the effect of adding Momordica charantia (Mc) to glibenclamide (GLB) on ED markers in diabetic rats. Streptozotocin (STZ-40mg/kg b. w.) induced diabetic rats were randomly put into 3 groups with 10 rats/group; diabetic control [DC] group, glibenclamide treated group (GLB -2.5mg/kg) and GLB-Mc treated group (2.5mg/kg + 400mg/kg). Serum glucose was measured weekly for eight weeks whereas insulin, sVCAM-1, vWF-Ag and interleukin-6 [IL-6] were measured at week 0 and week 8. Luciferase assay was performed to determine luminescence. At week 8, GLB and GLB-Mc groups revealed improvements in blood glucose and insulin concentrations (P≤0.05) when compared to corresponding baseline values with GLB-Mc group showing slightly greater improvements. GLB-M c group also revealed improvement (P≤0.05) in vWF-Ag, sVCAM-1 and IL-6 concentrations but was non-significant in GLB group when compared to corresponding baseline values. Comparison between GLB and GLB-Mc group showed significantly high concentration of sVCAM-1 in GLB group (P≤0.05) due to its minimal effect on TGR5 activation. We conclude that adding M. charantia to GLB may be a useful choice for modulating diabetes induced ED due to its stimulatory effect on TGR5 receptors.

Disparities in Access to Oncologic Care in Pancreatic Cancer: A Systematic Review.

BACKGROUND: Pancreatic cancer care is complex, and multiple disparities in receipt of therapies have been documented. The authors aimed to conduct a systematic review of the literature to critically assess and summarize disparities in access to oncologic therapies for pancreatic cancer. METHODS: A search of PubMed, Scopus, Web of Science, and Cochrane databases were performed for studies reporting disparities in access to oncologic care for pancreatic cancer. Primary research articles published in the United States from 2000 to 2020 were included. Data were independently extracted, and risk of bias was assessed using the modified Newcastle-Ottawa scale. RESULTS: The inclusion criteria were met by 47 studies. All the studies used retrospective data, with 70 % involving national database studies, 41 assessing the impact of race/ethnicity, 22 assessing the impact of socioeconomic status, 18 assessing the impact of insurance status, 23 assessing the impact of gender, 26 assessing the impact of age, and 3 assessing the impact of location on the delivery of cancer-directed therapies. Race, socioeconomic status, insurance status, gender, and age- based disparities in receipt of surgical resection, treatment at high-volume facilities and multimodal therapy for resectable pancreatic cancer, receipt of systemic chemotherapy for metastatic cancer, and receipt of expected standard-of-care treatment are reported. CONCLUSION: Significant sociodemographic disparities in access to equitable oncologic care exist along the continuum of pancreatic cancer care. Multiple patient, provider, and systemic factors contribute to these disparities. The ongoing study of these disparities is important to elucidate processes that may be targeted to improve access to equitable oncologic care for patients with pancreatic cancer.

Current role for cytoreduction and HIPEC for gastric cancer with peritoneal disease.

Gastric cancer (GC) is an aggressive malignancy with a high burden of peritoneal disease. Evidence regarding the use of cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) to improve outcomes has been growing. However, given multiple limitations, there remains a lack of international consensus regarding the optimal treatment paradigm. This review article discusses the burden of peritoneal disease in GC patients and the role of CRS + HIPEC in all treatment intents-curative, prophylactic, and palliative.

Feasibility of cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) for advanced peritoneal surface tumors during the COVID-19 pandemic: A single-institution experience.

BACKGROUND AND OBJECTIVES: Cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) is a complex treatment used in selected patients with peritoneal surface malignancies. HIPEC procedures are time and resource intensive. The primary aim of this analysis was to compare the experience of treating advanced abdominal tumors with CRS-HIPEC before and during the coronavirus disease 2019 (COVID-19) pandemic. METHODS: Patients included in this analysis received CRS-HIPEC at a single center during either a prepandemic (March 18, 2019-March 17, 2020) or pandemic (March 18, 2020-February 5, 2021) interval. A retrospective chart review was performed. RESULTS: Our analysis included 67 patients: 30 (45%) treated prepandemic and 37 (55%) treated during the pandemic. Median age at the time of operation was 58 years (interquartile range: [49-65]); 53% of patients were women. Patients treated during the pandemic presented with higher peritoneal cancer index (PCI) scores with 32% (n = 12) having a PCI > 20 at the time of surgery (p = 0.01). Five patients had delays in surgery due to the pandemic. Rates of overall postoperative morbidity, reoperation, and readmission were not different between the cohorts. CONCLUSIONS: Despite presenting with more extensive disease, patients treated with CRS-HIPEC during the height of the COVID-19 pandemic had comparable perioperative outcomes to patients treated prepandemic.

Soft hybrid intrinsically motile robot for wireless small bowel enteroscopy.

BACKGROUND: Difficulties in establishing diagnosis of small bowel (SB) disorders, prevented their effective treatment. This problem was largely resolved by wireless capsule endoscopy (WCE), which has since become the first line investigation for suspected SB disorders. Several types of WCE pills are now used in clinical practice, despite their limitations and complications. WCE pills are large, rigid and immotile capsules. When swallowed, they provide SB enteroscopy downloaded to a data logger carried by the patient. Most of the complications of WCEs result from lack of intrinsic locomotion: incomplete examination, capsule retention and impaction within strictures. In addition, the rigid nature and size of current generation of WCE pills is accompanied by 0.1% inability to swallow the pill by patients with normal esophageal motility. METHODS: The aim of this communication is to describe the initial prototype, P1, which is thinner and slightly longer than the current generation of WCEs. In addition, it exhibits intrinsic active locomotion, produced by vibrating silicon legs. These generate a controlled-skid locomotion on the small bowel mucosal surface, rendered slippery by surface mucus and intraluminal surfactant bile salts. We demonstrate the mechanism responsible for the active locomotion of P1, which we consider translatable into a working prototype, suitable for further R&D for eventual clinical translation. RESULTS: The shape and attachment of the rubber vibrating legs to vibrating actuators, have been designed specifically to produce a tight clockwise circular motion. When inserted inside a circular tube in vitro of equivalent diameter to human small intestine, the intrinsic circular clockwise motion of P1 translates into a linear locomotion by the constraints imposed by the surrounding circular walls of SB and rest of the gastrointestinal tract. This design ensures device stability during transit, essential for imaging and targeting lesions encountered during the enteroscopy. We preformed two experiments: (i) transit of P1 through a phantom consisting of a segment of PVC tube placed on a horizontal surface and (ii) transit through a transparent slippery nylon sleeve insufflated with air. In the PVC tube, its transit rate averages 15.6 mm/s, which is too fast for endoscopy: whereas inside the very slippery nylon sleeve insufflated with air, the average transit rate of P1 is reduced to 5.9 mm/s, i.e., ideal for inspection endoscopy. CONCLUSIONS: These in-vitro experiments indicate that the P1 hybrid soft robot prototype has the potential specifically for clinical translation for SB enteroscopy.

Inadequate Bowel Preparation in Pediatric Colonoscopy-Prospective Study of Potential Causes.

OBJECTIVES: Inadequate bowel preparation (IBP) for colonoscopy leads to missed diagnosis, longer anesthesia time, higher chance of complications and increased costs. Adult studies have demonstrated that patient characteristics such as male gender and obesity are associated with IBP. Little is known about factors affecting bowel preparation in children. Our aim was to determine factors associated with IBP in children. METHODS: We prospectively enrolled children undergoing outpatient colonoscopy. Quality of bowel preparation was assessed using Boston Bowel Preparation Scale (BBPS) score (range 0-9). Data collected included patient demographics, indication, and type of insurance. Patients were divided into two groups based on BBPS score-adequate (BBPS score > 5) and inadequate (BBPS score < 5) and groups were compared using Student t-test and chi-square test. Possible predictors were analyzed using multivariate logistic regression models. RESULTS: A total of 334 children were prospectively enrolled of whom 321 were studied further (age range 2-18 years; mean age 12.4 years; 60.4% female; 85.9% Caucasian). The mean BBPS score was 6.8 (standard deviation of ±2). IBP was reported in 12.8% (41/321). Multivariable logistic regression analysis did not show statistical differences between the groups in studied patient factors including age, gender, obesity, race, insurance type, and indication for colonoscopy. CONCLUSION: Contrary to several adult studies, the results of our prospective study did not show any relationship between examined patient factors and IBP in children. Interestingly, IBP was less prevalent in our pediatric study compared to published adult data (12.8% vs 20-40%).

Changes in Lifestyle, Health Practices, and Perceived Anxiety amidst the COVID-19 Pandemic: A Cross-Sectional Study Conducted on the General Population of Pakistan.

Background: The emergence of the coronavirus disease 2019 (COVID-19) pandemic has created unprecedented challenges across the globe. In addition to its debilitating impacts on health, the pandemic has also resulted in sudden changes in the quality of life. Our study aims to assess and highlight the alterations in lifestyle, health practices, and perceived anxiety in amongst the Pakistani denizens during the categorical lockdown across the country. Methods: A cross-sectional study was conducted during April 2020 through an online self-administered questionnaire using the snowball sampling technique. The online survey included a diversified set of questions ranging from the demographics, participants' sleeping routine, physical activity, hygiene habits, daily routine, and dietary habits during the quarantine period. It also assessed their anxiety through a series of questions, stretching from their own apprehension of their mental health to their assumption regarding the uncertainty of the future. SPSS v23 was used for data analysis, and chi-square test was applied. Results: A total of 384 respondents were included in the study. The mean age of the participants was 21.26 ± 4.267 years. It was observed that 203 (52.9%) individuals spent most of their time in self-isolation on social media, and 167 (43.5%) of participants claimed to be undertaking online classes or watching television. Furthermore, half of the participants noted that their sleep duration had increased 194 (50.5%), along with increased levels of perceived anxiety 242 (63%). Conclusion: The imposed nationwide lockdown due to COVID-19 has extensively affected the daily routine of the people living in Pakistan, eliciting profound changes in their sleeping patterns, dietary habits, mental health, and physical activity. Therefore, addressing the issues that arise amidst the lockdown remains pivotal.

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.

The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps toward elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depend on robustly assembled sequences. In the span of a single decade, the sequence throughput of leading DNA sequencing instruments has increased drastically, and coupled with established and planned large-scale, personalized medicine initiatives to sequence genomes in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft genomes is timely. With ABySS 1.0, we originally showed that assembling the human genome using short 50-bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using a standardized message-passing system (MPI). We present here its redesign, which departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements. We benchmarked ABySS 2.0 human genome assembly using a Genome in a Bottle data set of 250-bp Illumina paired-end and 6-kbp mate-pair libraries from a single individual. Our assembly yielded a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using <35 GB of RAM. This is a modest memory requirement by today's standards and is often available on a single computer. We also investigate the use of BioNano Genomics and 10x Genomics' Chromium data to further improve the scaffold NG50 (NGA50) of this assembly to 42 (15) Mbp.

Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey.

Diversity-generating retroelements (DGRs) are novel genetic elements that use reverse transcription to generate vast numbers of sequence variants in specific target genes. Here, we present a detailed comparative bioinformatic analysis that depicts the landscape of DGR sequences in nature as represented by data in GenBank. Over 350 unique DGRs are identified, which together form a curated reference set of putatively functional DGRs. We classify target genes, variable repeats and DGR cassette architectures, and identify two new accessory genes. The great variability of target genes implies roles of DGRs in many undiscovered biological processes. There is much evidence for horizontal transfers of DGRs, and we identify lineages of DGRs that appear to have specialized properties. Because GenBank contains data from only 10% of described species, the compilation may not be wholly representative of DGRs present in nature. Indeed, many DGR subtypes are present only once in the set and DGRs of the candidate phylum radiation bacteria, and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea archaea, are exceptionally diverse in sequence, with little information available about functions of their target genes. Nonetheless, this study provides a detailed framework for classifying and studying DGRs as they are uncovered and studied in the future.

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Motivation: Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques, when the species and closely related species lack high quality reference resources. For certain applications such as de novo annotation, information on putative exons and alternative splicing may be desirable. Results: Here we present ChopStitch, a new method for finding putative exons de novo and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-Seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm also accounts for base substitutions in transcript sequences that may be derived from sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are represented as splice graphs in DOT output format. Availability and implementation: ChopStitch is written in Python and C++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ChopStitch. Contact: hkhan@bcgsc.ca or ibirol@bcgsc.ca. Supplementary information: Supplementary data are available at Bioinformatics online.

Combined treatment with GSNO and CAPE accelerates functional recovery via additive antioxidant activities in a mouse model of TBI.

Traumatic brain injury (TBI) is the major cause of physical disability and emotional vulnerability. Treatment of TBI is lacking due to its multimechanistic etiology, including derailed mitochondrial and cellular energy metabolism. Previous studies from our laboratory show that an endogenous nitric oxide (NO) metabolite S-nitrosoglutathione (GSNO) provides neuroprotection and improves neurobehavioral function via anti-inflammatory and anti-neurodegenerative mechanisms. To accelerate the rate and enhance the degree of recovery, we investigated combining GSNO with caffeic acid phenethyl ester (CAPE), a potent antioxidant compound, using a male mouse model of TBI, controlled cortical impact in mice. The combination therapy accelerated improvement of cognitive and depressive-like behavior compared with GSNO or CAPE monotherapy. Separately, both GSNO and CAPE improved mitochondrial integrity/function and decreased oxidative damage; however, the combination therapy had greater effects on Drp1 and MnSOD. Additionally, while CAPE alone activated AMPK, this activation was heightened in combination with GSNO. CAPE treatment of normal animals also significantly increased the expression levels of pAMPK, pACC (activation of AMPK substrate ACC), and pLKB1 (activation of upstream to AMPK kinase LKB1), indicating that CAPE activates AMPK via LKB1. These results show that while GSNO and CAPE provide neuroprotection and improve functional recovery separately, the combination treatment invokes greater recovery by significantly improving mitochondrial functions and activating the AMPK enzyme. Both GSNO and CAPE are in human consumption without any known adverse effects; therefore, a combination therapy-based multimechanistic approach is worthy of investigation in human TBI.