Changes in Dry State Hemoglobin over Time Do Not Increase the Potential for Oxidative DNA Damage in Dried Blood

BACKGROUND: Hemoglobin (Hb) is the iron-containing oxygen transport protein present in the red blood cells of vertebrates. Ancient DNA and forensic scientists are particularly interested in Hb reactions in the dry state because both regularly encounter aged, dried bloodstains. The DNA in such stains may be oxidatively damaged and, in theory, may be deteriorated by the presence of Hb. To understand the nature of the oxidative systems potentially available to degrade DNA in the presence of dried Hb, we need to determine what molecular species Hb forms over time. These species will determine what type of iron (i.e. Fe(2+)/Fe(3+)/Fe(4+)) is available to participate in further chemical reactions. The availability of "free" iron will affect the ability of the system to undergo Fenton-type reactions which generate the highly reactive hydroxyl radical (OH*). The OH* can directly damage DNA. METHODOLOGY/PRINCIPAL FINDINGS: Oxygenated Hb (oxyHb) converts over time to oxidized Hb (metHb), but this happens more quickly in the dry state than in the hydrated state, as shown by monitoring stabilized oxyHb. In addition, dry state oxyHb converts into at least one other unknown species other than metHb. Although "free" iron was detectable as both Fe(2+) and Fe(3+) in dry and hydrated oxyHb and metHb, the amount of ions detected did not increase over time. There was no evidence that Hb becomes more prone to generating OH* as it ages in either the hydrated or dry states. CONCLUSIONS: The Hb molecule in the dried state undergoes oxidative changes and releases reactive Fe(II) cations. These changes, however, do not appear to increase the ability of Hb to act as a more aggressive Fenton reagent over time. Nevertheless, the presence of Hb in the vicinity of DNA in dried bloodstains creates the opportunity for OH*-induced oxidative damage to the deoxyribose sugar and the DNA nucleobases

Sedimentary context and palaeoecology of Gigantoproductus shell beds in the Mississippian Eyam Limestone Formation, Derbyshire carbonate platform, central England

A sedimentological study was conducted at two localities exposing the Mississippian Eyam Limestone Formation of the Derbyshire carbonate platform, UK. Ricklow Quarry comprises seven facies with diverse skeletal assemblages, representing deposition on the inner to middle ramp within open marine waters. Once-a-Week Quarry comprises four facies, dominated by crinoidal debris representing deposition on the inner ramp. Both localities expose Gigantoproductus shell beds. Palaeoecological analysis of a single shell bed from each locality enabled investigation of the rapid colonization and success of this taxon on the platform. At Ricklow Quarry, on the eastern side of a localized mud mound, both life (>72% of thin and thick-shelled brachiopods in life position) and neighbourhood assemblages are present. A low-moderate diversity community (<1.37 and <0.8 Shannon diversity index) rapidly established over relict Brigantian mud mounds. Shell beds are preluded by intervals of decreased energy that allowed larvae to settle. Once established, the dominance of thick-shelled individuals enabled baffling, potentially providing localized shelter for larvae and nearby individuals. At Once-a-Week Quarry, where no mud mound is present, only thick-shelled Gigantoproductus species and a low diversity community (<1.07 Shannon diversity index) exclusively comprising neighbourhood assemblages (37% in life position) is present. The presence of inactive mud mounds at Ricklow Quarry appears to have been the key to the success of Gigantoproductus species enabling the onset of stable communities in the shelter provided by the relict mound. Once the first palaeocommunities were established, larvae dispersed and colonized higher energy settings, such as at Once-a-Week Quarry

Directing Differentiation of Pluripotent Stem Cells Toward Retinal Pigment Epithelium Lineage

Development of efficient and reproducible conditions for directed differentiation of pluripotent stem cells into specific cell types is important not only to understand early human development but also to enable more practical applications, such as in vitro disease modeling, drug discovery, and cell therapies. The differentiation of stem cells to retinal pigment epithelium (RPE) in particular holds promise as a source of cells for therapeutic replacement in age-related macular degeneration. Here we show development of an efficient method for deriving homogeneous RPE populations in a period of 45 days using an adherent, monolayer system and defined xeno-free media and matrices. The method utilizes sequential inhibition and activation of the Activin and bone morphogenetic protein signaling pathways and can be applied to both human embryonic stem cells and induced pluripotent stem cells as the starting population. In addition, we use whole genome transcript analysis to characterize cells at different stages of differentiation that provides further understanding of the developmental dynamics and fate specification of RPE. We show that with the described method, RPE develop through stages consistent with their formation during embryonic development. This characterization- together with the absence of steps involving embryoid bodies, three-dimensional culture, or manual dissections, which are common features of other protocols-makes this process very attractive for use in research as well as for clinical applications. SIGNIFICANCE: This report describes a novel method of directed differentiation to generate retinal pigment epithelium (RPE) cells from pluripotent stem cells. The employed method is based on adherent monolayer culture using xeno-free conditions and manipulation of the Activin and bone morphogenetic protein signaling pathway using small molecules and recombinant proteins. Whole genome microarray analysis was performed to characterize the differentiation process and understand the developmental path of RPE generation in vitro. This method can be applied for generation of RPE for research as well as for clinical applications

H3F3A (Histone 3.3) G34W Immunohistochemistry: A Reliable Marker Defining Benign and Malignant Giant Cell Tumor of Bone

Giant cell tumor of bone (GCTB) is a locally aggressive subarticular tumor. Having recently reported that H3.3 G34W mutations are characteristic of this tumor type, we have now investigated the sensitivity and specificity of the anti-histone H3.3 G34W rabbit monoclonal antibody in a wide variety of tumors including histologic mimics of GCTB to assess its value as a diagnostic marker. We also determined the incidence of H3.3 G34 mutations in primary malignant bone tumors as assessed by genotype and H3.3 G34W immunostaining. A total of 3163 tumors were tested. Totally, 213/235 GCTB (90.6%) showed nuclear H3.3 p.G34W immunoreactivity. This was not the case for the rare variants, p.G34L, M, and V, which occurred most commonly in the small bones of the hands, patella, and the axial skeleton. If these sites were excluded from the analysis, H3.3 G34W expression was found in 97.8% of GCTB. Malignant bone tumors initially classified as osteosarcomas were the only other lesions (n=11) that showed G34W expression. Notably an additional 2 previously reported osteosarcomas with a p.G34R mutation were not immunoreactive for the antibody. A total of 11/13 of these malignant H3.3-mutant tumors exhibited an osteoclast-rich component: when imaging was available all but one presented at a subarticular site. We propose that subarticular primary malignant bone sarcoma with H3.3 mutations represent true malignant GCTB, even in the absence of a benign GCTB component

Enhancing the early student experience

This paper is concerned with identifying how the early student experience can be enhanced in order to improve levels of student retention and achievement. The early student experience is the focus of this project as the literature has consistently declared the first year to be the most critical in shaping persistence decisions. Programme managers of courses with high and low retention rates have been interviewed to identify activities that appear to be associated with good retention rates. The results show that there are similarities in the way programmes with high retention are run, with these features not being prevalent on programmes with low retention. Recommendations of activities that appear likely to enhance the early student experience are provided

Digital PCR analysis of circulating tumor DNA: a biomarker for chondrosarcoma diagnosis, prognostication, and residual disease detection

Conventional chondrosarcoma is the most common primary bone tumor in adults. Prognosis corresponds with tumor grade but remains variable, especially for individuals with grade (G) II disease. There are currently no biomarkers available for monitoring or prognostication of chondrosarcoma. Circulating tumor DNA (ctDNA) has recently emerged as a promising biomarker for a broad range of tumor types. To date, little has been done to study the presence of ctDNA and its potential utility in the management of sarcomas, including chondrosarcoma. In this study, we have assessed ctDNA levels in a cohort of 71 patients, 32 with sarcoma, including 29 individuals with central chondrosarcoma (CS) and 39 with locally aggressive and benign bone and soft tissue tumors, using digital PCR. In patients with CS, ctDNA was detected in pretreatment samples in 14/29 patients, which showed clear correlation with tumor grade as demonstrated by the detection of ctDNA in all patients with GIII and dedifferentiated disease (n = 6) and in 8/17 patients with GII disease, but never associated with GI CS. Notably detection of ctDNA preoperatively in GII disease was associated with a poor outcome. A total of 14 patients with CS had ctDNA levels assessed at multiple time points and in most patients there was a clear reduction following surgical removal. This research lays the foundation for larger studies to assess the utility of ctDNA for chondrosarcoma diagnosis, prognostication, early detection of residual disease and monitoring disease progression

Using a new video rating tool to crowd-source analysis of behavioural reaction to stimuli

Quantifying the intensity of animals’ reaction to stimuli is notoriously difficult as classic unidimensional measures of responses such as latency or duration of looking can fail to capture the overall strength of behavioural responses. More holistic rating can be useful but have the inherent risks of subjective bias and lack of repeatability. Here, we explored whether crowdsourcing could be used to efficiently and reliably overcome these potential flaws. A total of 396 participants watched online videos of dogs reacting to auditory stimuli and provided 23,248 ratings of the strength of the dogs’ responses from zero (default) to 100 using an online survey form. We found that raters achieved very high inter-rater reliability across multiple datasets (although their responses were affected by their sex, age, and attitude towards animals) and that as few as 10 raters could be used to achieve a reliable result. A linear mixed model applied to PCA components of behaviours discovered that the dogs’ facial expressions and head orientation influenced the strength of behaviour ratings the most. Further linear mixed models showed that that strength of behaviour ratings was moderately correlated to the duration of dogs’ reactions but not to dogs’ reaction latency (from the stimulus onset). This suggests that observers’ ratings captured consistent dimensions of animals’ responses that are not fully represented by more classic unidimensional metrics. Finally, we report that overall participants strongly enjoyed the experience. Thus, we suggest that using crowdsourcing can offer a useful, repeatable tool to assess behavioural intensity in experimental or observational studies where unidimensional coding may miss nuance, or where coding multiple dimensions may be too time-consuming

Limitations to recording larger mammalian predators in savannah using camera traps and spoor

Traditionally, spoor (tracks, pug marks) have been used as a cost effective tool to assess the presence of larger mammals. Automated camera traps are now increasingly utilized to monitor wildlife, primarily as the cost has greatly declined and statistical approaches to data analysis have improved. While camera traps have become ubiquitous, we have little understanding of their effectiveness when compared to traditional approaches using spoor in the field. Here, we a) test the success of camera traps in recording a range of carnivore species against spoor; b) ask if simple measures of spoor size taken by amateur volunteers is likely to allow individual identification of leopards and c) for a trained tracker, ask if this approach may allow individual leopards to be followed with confidence in savannah habitat. We found that camera traps significantly under-recorded mammalian top and meso-carnivores, with camera traps more likely under-record the presence of smaller carnivores (civet 64%; genet 46%, Meller’s mongoose 45%) than larger (jackal sp. 30%, brown hyena 22%), while leopard was more likely to be recorded by camera trap (all recorded by camera trap only). We found that amateur trackers could be beneficial in regards to collecting presence data; however the large variance in measurements of spoor taken in the field by volunteers suggests that this approach is unlikely to add further data. Nevertheless, the use of simple spoor measurements in the field by a trained field researcher increases their ability to reliably follow a leopard trail in difficult terrain. This allows researchers to glean further data on leopard behaviour and habitat utilisation without the need for complex analysis

Intra-patient comparison of reduced-dose model-based iterative reconstruction with standard-dose adaptive statistical iterative reconstruction in the CT diagnosis and follow-up of urolithiasis

The final publication is available at link.springer.co