MetaDamage Tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

2021 ◽  
Author(s):  
Rosie Everett ◽  
Becky Cribdon ◽  
Logan Kistler ◽  
Roselyn Ware ◽  
Robin Allaby
Keyword(s):  
Ancient Dna ◽  
Simulated Data ◽  
Initial Assessment ◽  
Post Mortem ◽  
Cytosine Deamination ◽  
Modern Material ◽  
Depositional Process ◽  
Palaeoecological Reconstruction ◽  
Key Questions

<p>Authentication of ancient sedimentary DNA (sedaDNA) remains central to the interpretation of the proxy for wider understanding of palaeoecological archives. Distinguishing between in-situ, endogenous sedaDNA from that of contamination or modern material also allows for a wider understanding of taphonomy in the deposition and post-depositional process in the formation of the sedaDNA archive. At current, tools for authentication are reliant on single-taxon input and require a significant number of input sequences to identify an established cytosine deamination rate consistent with ancient DNA. We present the MetaDamage tool: a tool that examines cytosine deamination on a metagenomic scale. In this paper we outline the process of and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data in order to demonstrate the resolution in which MetaDamage can observe deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for initial assessment of the presence of ancient sedaDNA and provides a method for a wider understanding of key questions of preservation for palaeoecological reconstruction.</p>

scholarly journals Can post-mortem MRI be used as a proxy for in vivo? A case study

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Baayla D C Boon ◽  
Petra J W Pouwels ◽  
Laura E Jonkman ◽  
Matthijs J Keijzer ◽  
Paolo Preziosa ◽  
...  
Keyword(s):  
White Matter ◽  
Rating Scales ◽  
Brain Volume ◽  
Brain Mri ◽  
Post Mortem ◽  
Early Onset Alzheimer’S Disease ◽  
And Diffusion

Abstract Post-mortem in situ MRI has been used as an intermediate between brain histo(patho)logy and in vivo imaging. However, it is not known how comparable post-mortem in situ is to ante-mortem imaging. We report the unique situation of a patient with familial early-onset Alzheimer’s disease due to a PSEN1 mutation, who underwent ante-mortem brain MRI and post-mortem in situ imaging only 4 days apart. T1-weighted and diffusion MRI was performed at 3-Tesla at both time points. Visual atrophy rating scales, brain volume, cortical thickness and diffusion measures were derived from both scans and compared. Post-mortem visual atrophy scores decreased 0.5–1 point compared with ante-mortem, indicating an increase in brain volume. This was confirmed by quantitative analysis; showing a 27% decrease of ventricular and 7% increase of whole-brain volume. This increase was more pronounced in the cerebellum and supratentorial white matter than in grey matter. Furthermore, axial and radial diffusivity decreased up to 60% post-mortem whereas average fractional anisotropy of white matter increased approximately 10%. This unique case study shows that the process of dying affects several imaging markers. These changes need to be taken into account when interpreting post-mortem MRI to make inferences on the in vivo situation.

scholarly journals Central role of nitric oxide in ozone production in the upper tropical troposphere over the Atlantic Ocean and western Africa

2021 ◽  
Vol 21 (10) ◽  
pp. 8195-8211
Author(s):  
Ivan Tadic ◽  
Clara M. Nussbaumer ◽  
Birger Bohn ◽  
Hartwig Harder ◽  
Daniel Marno ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Atlantic Ocean ◽  
General Circulation ◽  
Simulated Data ◽  
Ozone Production ◽  
Mixing Ratios ◽  
Western Africa ◽  
Tropical Troposphere

Abstract. Mechanisms of tropospheric ozone (O3) formation are generally well understood. However, studies reporting on net ozone production rates (NOPRs) directly derived from in situ observations are challenging and are sparse in number. To analyze the role of nitric oxide (NO) in net ozone production in the upper tropical troposphere above the Atlantic Ocean and western Africa, we present in situ trace gas observations obtained during the CAFE-Africa (Chemistry of the Atmosphere: Field Experiment in Africa) campaign in August and September 2018. The vertical profile of in situ measured NO along the flight tracks reveals lowest NO mixing ratios of less than 20 pptv between 2 and 8 km altitude and highest mixing ratios of 0.15–0.2 ppbv above 12 km altitude. Spatial distribution of tropospheric NO above 12 km altitude shows that the sporadically enhanced local mixing ratios (>0.4 ppbv) occur over western Africa, which we attribute to episodic lightning events. Measured O3 shows little variability in mixing ratios at 60–70 ppbv, with slightly decreasing and increasing tendencies towards the boundary layer and stratosphere, respectively. Concurrent measurements of CO, CH4, OH, HO2 and H2O enable calculations of NOPRs along the flight tracks and reveal net ozone destruction at −0.6 to −0.2 ppbv h−1 below 6 km altitude and balance of production and destruction around 7–8 km altitude. We report vertical average NOPRs of 0.2–0.4 ppbv h−1 above 12 km altitude with NOPRs occasionally larger than 0.5 ppbv h−1 over western Africa coincident with enhanced NO. We compare the observational results to simulated data retrieved from the general circulation model ECHAM/MESSy Atmospheric Chemistry (EMAC). Although the comparison of mean vertical profiles of NO and O3 indicates good agreement, local deviations between measured and modeled NO are substantial. The vertical tendencies in NOPRs calculated from simulated data largely reproduce those from in situ experimental data. However, the simulation results do not agree well with NOPRs over western Africa. Both measurements and simulations indicate that ozone formation in the upper tropical troposphere is NOx limited.

scholarly journals PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11845
Author(s):  
Maxime Borry ◽  
Alexander Hübner ◽  
Adam B. Rohrlach ◽  
Christina Warinner
Keyword(s):  
Dna Damage ◽  
Functional Diversity ◽  
Ancient Dna ◽  
Damage Identification ◽  
De Novo ◽  
Metagenomic Data ◽  
Cytosine Deamination ◽  
High Data ◽  
Manual Inspection ◽  
Gene Catalogue

DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.

Development of an In-Situ Nanoindentation Specimen Holder for the High Voltage Electron Microscope

1997 ◽  
Vol 3 (S2) ◽  
pp. 593-594 ◽  
Author(s):  
M.A. Wall ◽  
U. Dahmen
Keyword(s):  
In Situ Tem ◽  
Post Mortem ◽  
Delamination Wear ◽  
Voltage Electron ◽  
Specimen Holder ◽  
Tem Characterization ◽  
Natural Sampling ◽  
Sampling Volume ◽  
Considerable Work

Progress on the development of an in-situ nanoindentation specimen holder for the Kratos 1.5MeV HVEM located at the National Center for Electron Microscopy, Berkeley, CA, USA, is reported. There is currently considerable work being reported on the mechanical properties (i.e., hardness, delamination, wear, etc.) of single and multicomponent thin films, nanoclusters and fibers by techniques such as nanoindenting, ref. [1] are recent examples. However, with all of these tests there has not been direct, unambiguous observation of the response or evolution of the microstructure. With many of these reports, there has been little “post-mortem” TEM characterization and there has been no real attempts to simulate these dynamically in the TEM. For the case of nano-testing of the materials the interaction volumes are often on the scale of the natural sampling volume of the HVEM. It seems natural that post-mortem and in-situ TEM characterization techniques be applied.

Expression of PD-L1 and IDO in hormone receptor negative DCIS.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e14116-e14116
Author(s):  
Sneha Deepak Phadke ◽  
Gerald H. Clamon ◽  
Amani Bashir ◽  
Matthew Keeney ◽  
Timothy Ginader
Keyword(s):  
Monoclonal Antibody ◽  
Hormone Receptor ◽  
Ductal Carcinoma ◽  
Mouse Monoclonal Antibody ◽  
Initial Assessment ◽  
Low Grade ◽  
University Of Iowa ◽  
Clinicopathologic Characteristics ◽  
Formalin Fixed Paraffin Embedded

e14116 Background: Although outcomes from ductal carcinoma in situ (DCIS) are generally excellent, hormone receptor (HR) negative DCIS is associated with a higher rate of recurrence. There is no chemopreventative agent that has been effective in this subgroup. The aim of our study was to evaluate expression of PD-L1 and IDO (Indoleamine 2,3-Dioxygenase) in HR negative DCIS, in an effort to identify a possible target for prevention using immunotherapy. Methods: Using pathology databases at the University of Iowa, we identified 60 cases of HR negative DCIS from 1995-2017, and 41 of these cases had adequate DCIS tissue for immunostaining. Immunohistochemical staining with antibodies against PD-L1 and IDO was performed on slides prepared from formalin-fixed paraffin-embedded tissue blocks retrieved from pathology archives. IDO was assessed by IHC using the mouse monoclonal antibody clone 10.1 (Millipore Sigma). An initial assessment for PD-L1 (M3653 mouse monoclonal antibody clone 22C3, DAKO) was negative. A repeat assessment for PD-L1 on a smaller sample in a different laboratory was also negative. Clinical data was abstracted from the medical record of each patient. Results: Of the 41 subjects with enough tissue for staining, the median age at diagnosis was 56.76 years, and median BMI was 26.59 kg/m2. Most common method of DCIS detection was screening mammogram (80.5%) versus a patient detected breast finding (19.5%). Most subjects had high grade DCIS (92.7%) and none had low grade DCIS. Six subjects (16.7%) had an ipsilateral in situ recurrence while another 6 subjects developed ipsilateral invasive cancer. Most of the subjects had HER2+ DCIS (63.9%). None of the 41 cases stained positive for IDO or PD-L1, thus no statistical analysis was done to analyze associations with clinicopathologic characteristics. Conclusions: Our sample of HR negative DCIS tumors did not express PD-L1 or IDO, making these receptors unlikely targets for immunopreventative efforts. It is still possible that tumor mutation burden, expression of PD-L2, PD-L1 or IDO expression on TILs, or expression of CTLA-4 may be future considerations for work in the DCIS microenvironment.

Inhibition of post-mortem muscle softening following in situ perfusion of protease inhibitors in tilapia

2003 ◽  
Vol 69 (3) ◽  
pp. 632-638 ◽  
Author(s):  
Noriko ISHIDA ◽  
Michiaki YAMASHITA ◽  
Naoko KOIZUMI ◽  
Makoto TERAYAMA ◽  
Toshinao INENO ◽  
...  
Keyword(s):  
Protease Inhibitors ◽  
Post Mortem ◽  
In Situ Perfusion

Fusion Technology related studies at JET: Post-mortem tile analysis with MKII-HD geometry, In situ laser detritiation and Molecular Sieve Bed detritiation

2011 ◽  
Vol 417 (1-3) ◽  
pp. 1356-1360 ◽  
Author(s):  
N. Bekris ◽  
J.P. Coad ◽  
C. Grisolia ◽  
J. Likonen ◽  
A. Semerok ◽  
...  
Keyword(s):  
Molecular Sieve ◽  
Post Mortem ◽  
Fusion Technology

scholarly journals Architecture and functional morphology of the skeletal apparatus of ozarkodinid conodonts

1997 ◽  
Vol 352 (1361) ◽  
pp. 1545-1564 ◽  
Author(s):  
Mark A. Purnell ◽  
Philip C. J. Donoghue
Keyword(s):  
Functional Morphology ◽  
Food Item ◽  
Anterior Part ◽  
The Body ◽  
Scale Model ◽  
Post Mortem ◽  
Feeding Apparatus ◽  
Food Acquisition ◽  
Anterior Edge

Ozarkodinid conodonts were one of the most successful groups of agnathan vertebrates. Only the oropharyngeal feeding apparatus of conodonts was mineralized, and the skeletal elements were generally disarticulated on the death and decay of the body. Occasionally, however, they were preserved in association as ‘natural assemblages’, fossilized in situ after post–mortem collapse of the apparatus. From analysis of element arrangement in natural assemblages of Idiognathodus from the Pennsylvanian of Illinois we have produced a precise scale model of the feeding apparatus of ozarkodinid conodonts. At the front lay an axial Sa element, flanked by two groups of four close-set elongate Sb and Sc elements which were inclined obliquely inwards and forwards; above these elements lay a pair of arched and inward pointing M elements. Behind the S-M array lay transversely oriented and bilaterally opposed Pb and Pa elements. Our model sheds new light on food acquisition in conodonts. We propose that the anterior S and M elements of ozarkodinid conodonts were attached to cartilaginous plates. In order for the animal to feed, these plates were first everted, and then drawn back and upward over the anterior edge of an underlying cartilage. These movements produced a highly effective grasping action, the cusps and denticles of the elements converging to grab and impale any food item that lay anterior to the open array. According to this hypothesis, the anterior part of the conodont apparatus is comparable to, and possibly homologous with, the lingual apparatus of extant agnathans; the elements themselves, however, have no direct homologues.

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