DNA/RNA Degradation Rate in Long Term Fixed Museum Specimens

In today’s research driven society, it has become commonplace for institutions to rely upon DNA and RNA extraction techniques to help obtain genomic data from old specimens. Generally, specimens were commonly preserved for future gross examination and/or teaching. Using histological examination of specimens from museum jars from the Pathology Department at the Indiana University School of Medicine, the sequential and chronological degradation of DNA and RNA has been studied. We examined gross specimens from nine decades from 1920 until 2000. We evaluated histologic preservation of kidney, liver, heart, lung, spleen, uterus, and brain for nuclear structure in these samples. Nuclear preservation was based on amount of nuclei per 20x microscopic field and the crispness of the nuclear membrane and internal features. The nuclei in high lipid tissues such as the brain were found to degrade at a quicker rate than dense tissues such as the heart and uterus. Our study has shown specimens preserved beyond fifty years were likely to have little to no nuclei left, thus indicating that there was little to no DNA and RNA remaining. This technique of histologic evaluation first is an important finding and a general guideline which may save research institutions from the expensive process of DNA and RNA extraction

DNA/RNA Degradation Rate in Fixed Tissue

poster abstractIn today’s research driven society, it has become commonplace for institutions to rely upon DNA and RNA extraction techniques to help obtain genomic data from old specimens. Generally, specimens were commonly preserved for future gross examination and/or teaching. Using histological examination of specimens from museum jars from the Pathology Department at the Indiana University School of Medicine, the sequential and chronological degradation of DNA and RNA has been studied. We examined gross specimens from nine decades from 1920 until 2000. We evaluated histologic preservation of nuclear structure in these samples. Nuclear preservation was based on amount of nuclei per 20x microscopic field, the crispness of the nuclear membrane and internal features. The nuclei in high lipid tissues such as the brain were found to degrade at a quicker rate than dense proteinaceous structures such as the heart and uterus. Our study has shown specimens preserved beyond roughly fifty years are likely to have little to no nuclei left, thus indicating that there was little to no DNA and RNA remaining. This technique of histologic evaluation is an important finding and general guideline which may save research institutions from the expensive process of DNA and RNA extractio

A retrospective cohort pilot study to evaluate a triage tool for use in a pandemic

Abstract Introduction The objective of this pilot study was to assess the usability of the draft Ontario triage protocol, to estimate its potential impact on patient outcomes, and ability to increase resource availability based on a retrospective cohort of critically ill patients cared for during a non-pandemic period. Methods Triage officers applied the protocol prospectively to 2 retrospective cohorts of patients admitted to 2 academic medical/surgical ICUs during an 8 week period of peak occupancy. Each patient was assigned a treatment priority (red -- 'highest', yellow -- 'intermediate', green -- 'discharge to ward', or blue/black -- 'expectant') by the triage officers at 3 separate time points (at the time of admission to the ICU, 48, and 120 hours post admission). Results Overall, triage officers were either confident or very confident in 68.4% of their scores; arbitration was required in 54.9% of cases. Application of the triage protocol would potentially decrease the number of required ventilator days by 49.3% (568 days) and decrease the total ICU days by 52.6% (895 days). On the triage protocol at ICU admission the survival rate in the red (93.7%) and yellow (62.5%) categories were significantly higher then that of the blue category (24.6%) with associated P values of < 0.0001 and 0.0003 respectively. Further, the survival rate of the red group was significantly higher than the overall survival rate of 70.9% observed in the cohort (P < 0.0001). At 48 and 120 hours, survival rates in the blue group increased but remained lower then the red or yellow groups. Conclusions Refinement of the triage protocol and implementation is required prior to future study, including improved training of triage officers, and protocol modification to minimize the exclusion from critical care of patients who may in fact benefit. However, our results suggest that the triage protocol can help to direct resources to patients who are most likely to benefit, and help to decrease the demands on critical care resources, thereby making available more resources to treat other critically ill patients

Analysis of Neptune's 2017 Bright Equatorial Storm

We report the discovery of a large ($\sim$8500 km diameter) infrared-bright storm at Neptune's equator in June 2017. We tracked the storm over a period of 7 months with high-cadence infrared snapshot imaging, carried out on 14 nights at the 10 meter Keck II telescope and 17 nights at the Shane 120 inch reflector at Lick Observatory. The cloud feature was larger and more persistent than any equatorial clouds seen before on Neptune, remaining intermittently active from at least 10 June to 31 December 2017. Our Keck and Lick observations were augmented by very high-cadence images from the amateur community, which permitted the determination of accurate drift rates for the cloud feature. Its zonal drift speed was variable from 10 June to at least 25 July, but remained a constant $237.4 \pm 0.2$ m s$^{-1}$ from 30 September until at least 15 November. The pressure of the cloud top was determined from radiative transfer calculations to be 0.3-0.6 bar; this value remained constant over the course of the observations. Multiple cloud break-up events, in which a bright cloud band wrapped around Neptune's equator, were observed over the course of our observations. No "dark spot" vortices were seen near the equator in HST imaging on 6 and 7 October. The size and pressure of the storm are consistent with moist convection or a planetary-scale wave as the energy source of convective upwelling, but more modeling is required to determine the driver of this equatorial disturbance as well as the triggers for and dynamics of the observed cloud break-up events.Comment: 42 pages, 14 figures, 6 tables; Accepted to Icaru

S1 is associated with chronic low back pain: a functional and structural MRI study

A fundamental characteristic of neural circuits is the capacity for plasticity in response to experience. Neural plasticity is associated with the development of chronic pain disorders. In this study, we investigated 1) brain resting state functional connectivity (FC) differences between patients with chronic low back pain (cLBP) and matched healthy controls (HC); 2) FC differences within the cLBP patients as they experienced different levels of endogenous low back pain evoked by exercise maneuvers, and 3) morphometric differences between cLBP patients and matched HC. We found the dynamic character of FC in the primary somatosensory cortex (S1) in cLBP patients, i.e., S1 FC decreased when the patients experienced low intensity LBP as compared with matched healthy controls, and FC at S1 increased when cLBP patients experienced high intensity LBP as compared with the low intensity condition. In addition, we also found increased cortical thickness in the bilateral S1 somatotopically associated with the lower back in cLBP patients as compared to healthy controls. Our results provide evidence of structural plasticity co-localized with areas exhibiting FC changes in S1 in cLBP patients

Genome-wide MicroRNA profiling of mantle cell lymphoma reveal a distinct subgroup with poor prognosis

MicroRNA (miRNA) deregulation has been implicated in the pathogenesis of mantle cell lymphoma (MCL). Using a high-throughput quantitative real-time PCR platform, we performed miRNA profiling on cyclin D1- positive MCL (n=30) and cyclin D1-negative MCL (n=7) and compared them with small lymphocytic leukemia/lymphoma (SLL, n=12), aggressive B-cell lymphomas (n=138), normal B-cell subsets and stromal cells. We identified a 19-miRNA classifier which included six upregulated miRNAs (miR-135a, miR-708, miR-150, miR-363, miR-184, miR-342-5p) and 13 downregulated miRNAs, that was able to distinguish MCL from other aggressive lymphomas with \u3e90% probability. Some of these upregulated miRNAs are highly expressed in naïve B-cells. MicroRNA classifier showed consistent results in FFPE tissues and was able to distinguish cyclin D1-negative MCL from other lymphomas. A 26-miRNA classifier could distinguish MCL from SLL, dominated by 23 upregulated miRNAs in MCL. Unsupervised hierarchical clustering of MCL cases demonstrated a cluster characterized by high expression of miRNAs from polycistronic miR17~92 cluster and its paralogs miR-106a-363 and miR-106b-25, which was distinct from the other clusters showing enrichment of stroma associated miRNAs. The corresponding gene-expressionprofiling (GEP) data showed that the former cluster of MCL had significantly higher proliferation genesignature (PS), while the other subsets had higher expression of stroma associated genes. Clinical outcome analysis suggests that miRNAs can serve as prognosticators

Loss of signalling via Gα13 in germinal center B-cell-derived lymphoma

Germinal centre B-cell-like diffuse large B-cell lymphoma (GCB-DLBCL) is a common malignancy, yet the signalling pathways that are deregulated and the factors leading to its systemic dissemination are poorly defined1,2. Work in mice showed that sphingosine-1-phosphate receptor-2 (S1PR2), a Gα12 and Gα13 coupled receptor, promotes growth regulation and local confinement of germinal centre B cells3,4. Recent deep sequencing studies of GCB-DLBCL have revealed mutations in many genes in this cancer, including in GNA13 (encoding Gα13) and S1PR2 (refs 5,6, 7). Here we show, using in vitro and in vivo assays, that GCB-DLBCL-associated mutations occurring in S1PR2 frequently disrupt the receptor's Akt and migration inhibitory functions. Gα13-deficient mouse germinal centre B cells and human GCB-DLBCL cells were unable to suppress pAkt and migration in response to S1P, and Gα13-deficient mice developed germinal centre B-cell-derived lymphoma. Germinal centre B cells, unlike most lymphocytes, are tightly confined in lymphoid organs and do not recirculate. Remarkably, deficiency in Gα13, but not S1PR2, led to germinal centre B-cell dissemination into lymph and blood. GCB-DLBCL cell lines frequently carried mutations in the Gα13 effector ARHGEF1, and Arhgef1 deficiency also led to germinal centre B-cell dissemination. The incomplete phenocopy of Gα13- and S1PR2 deficiency led us to discover that P2RY8, an orphan receptor that is mutated in GCB-DLBCL and another germinal centre B-cell-derived malignancy, Burkitt's lymphoma, also represses germinal centre B-cell growth and promotes confinement via Gα13. These findings identify a Gα13-dependent pathway that exerts dual actions in suppressing growth and blocking dissemination of germinal centre B cells that is frequently disrupted in germinal centre B-cell-derived lymphoma