Volume 18. Article 3. Studies on two skates: Raja erinacea Mitchill, Raja eglanteria Bosc.

https://elischolar.library.yale.edu/bulletin_yale_bingham_oceanographic_collection/1164/thumbnail.jp

A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing.

Background. Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the genetic changes in a human papillomavirus- (HPV-)positive and an HPV-negative head and neck tumor. Methods. DNA was extracted from the blood and primary tumor of a patient with an HPV-positive tonsillar cancer and those of a patient with an HPV-negative oral tongue tumor. Exome enrichment was performed using the Agilent SureSelect All Exon Kit, followed by sequencing on the ABI SOLiD platform. Results. Exome sequencing revealed slightly more mutations in the HPV-negative tumor (73) in contrast to the HPV-positive tumor (58). Multiple mutations were noted in zinc finger genes (ZNF3, 10, 229, 470, 543, 616, 664, 638, 716, and 799) and mucin genes (MUC4, 6, 12, and 16). Mutations were noted in MUC12 in both tumors. Conclusions. HPV-positive HNSCC is distinct from HPV-negative disease in terms of evidence of viral infection, p16 status, and frequency of mutations. Next-generation sequencing has the potential to identify novel therapeutic targets and biomarkers in HNSCC

The mycobacterial glycoside hydrolase LamH enables capsular arabinomannan release and stimulates growth

Mycobacterial glycolipids are important cell envelope structures that drive host-pathogen interactions. Arguably, the most important are lipoarabinomannan (LAM) and its precursor, lipomannan (LM), which are trafficked from the bacterium to the host via unknown mechanisms. Arabinomannan is thought to be a capsular derivative of these molecules, lacking a lipid anchor. However, the mechanism by which this material is generated has yet to be elucidated. Here, we describe the identification of a glycoside hydrolase family 76 enzyme that we term LamH (Rv0365c in Mycobacterium tuberculosis) which specifically cleaves α−1,6-mannoside linkages within LM and LAM, driving its export to the capsule releasing its phosphatidyl-myo-inositol mannoside lipid anchor. Unexpectedly, we found that the catalytic activity of this enzyme is important for efficient exit from stationary phase cultures, potentially implicating arabinomannan as a signal for growth phase transition. Finally, we demonstrate that LamH is important for M. tuberculosis survival in macrophages

Effect of fungi associated with foliar diseases of Ficus capensis on the proximate, anti-nutrient and mineral composition of leaves

 The Ficus capensis Thunb leaves are affected by some foliar diseases, which could reduce the nutrient benefits from these leaves. This study aimed at isolation and characterization of fungal pathogens associated with the plant's foliar diseases, analysis of the proximate and phytochemical composition of healthy and diseased fruits and leaves. The effect of isolated fungal species on these proximate and phytochemical contents of leaves was also investigated. Hendersonula sp., Didymeria conferta, Rhizopus stolonifer and Fusarium oxysporium were isolated and characterized as fungi associated with the leaves. Proximate analysis revealed the presence of protein, carbohydrate, lipid, ash, fiber, and moisture. Mineral nutrient analysis revealed the presence of copper, zinc, lead, manganese, magnesium, potassium, sodium, calcium, while that of anti-nutrients revealed saponin, alkaloid, flavonoid, tannin and cyanogenic glycoside, both in the diseased and the healthy leaves and fruits of the plant. The values of the food nutrients and minerals in healthy leaves were significantly different from those of the infected fruits and leaves, with the value of non-nutrients in infected leaves were higher than those in health ones. The non-nutrients in the infected leaves were higher than those in the healthy leaves and fruits of the plants, while the proximate and mineral composition of the supposedly healthy leaves was greater than those of diseased leaves.  &nbsp

Political parties and democratic consolidation in post-communist societies

Political parties have a central role to play in democratic consolidation, yet we know comparatively little about how effectively they represent social cleavages in newly emerging democracies. Using the Lipset–Rokkan framework, this article examines the role of parties in articulating social cleavages in 14 established and 6 emerging democracies using the Comparative Study of Electoral Systems datasets. The results show that the social cleavages in the emerging democracies are similar to those of the established democracies, with religion and class predominating. Parties appear to be less effective in representing social cleavages in the emerging than in the established democracies

Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples

Identification of d -arabinan-degrading enzymes in mycobacteria

Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the D-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arabinogalactan-degrading activities and identified four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using one of these isolates with exo-D-galactofuranosidase activity, we generated enriched D-arabinan and used it to identify a strain of Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan, including members of the DUF2961 family (GH172) and a family of glycoside hydrolases (DUF4185/GH183) that display endo-D-arabinofuranase activity and are conserved in mycobacteria and other microbes. Mycobacterial genomes encode two conserved endo-D-arabinanases with different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall

Eu-Social Science: The Role of Internet Social Networks in the Collection of Bee Biodiversity Data

Background Monitoring change in species diversity, community composition and phenology is vital to assess the impacts of anthropogenic activity and natural change. However, monitoring by trained scientists is time consuming and expensive. Methodology/Principal Findings Using social networks, we assess whether it is possible to obtain accurate data on bee distribution across the UK from photographic records submitted by untrained members of the public, and if these data are in sufficient quantity for ecological studies. We used Flickr and Facebook as social networks and Flickr for the storage of photographs and associated data on date, time and location linked to them. Within six weeks, the number of pictures uploaded to the Flickr BeeID group exceeded 200. Geographic coverage was excellent; the distribution of photographs covered most of the British Isles, from the south coast of England to the Highlands of Scotland. However, only 59% of photographs were properly uploaded according to instructions, with vital information such as ‘tags’ or location information missing from the remainder. Nevertheless, this incorporation of information on location of photographs was much higher than general usage on Flickr (∼13%), indicating the need for dedicated projects to collect spatial ecological data. Furthermore, we found identification of bees is not possible from all photographs, especially those excluding lower abdomen detail. This suggests that giving details regarding specific anatomical features to include on photographs would be useful to maximise success. Conclusions/Significance The study demonstrates the power of social network sites to generate public interest in a project and details the advantages of using a group within an existing popular social network site over a traditional (specifically-designed) web-based or paper-based submission process. Some advantages include the ability to network with other individuals or groups with similar interests, and thus increasing the size of the dataset and participation in the project