In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR

BACKGROUND: Clinical specimens are routinely fixed in 10% buffered formalin and paraffin embedded. Although DNA is commonly extracted from fixed tissues and amplified by PCR, the effects of formalin fixation are relatively unknown. Formalin fixation is known to impair PCR, presumably through damage that blocks polymerase elongation, but an insidious possibility is error prone translesion synthesis across sites of damage, producing in vitro artifactual mutations during PCR. METHODS: To better understand the consequences of fixation, DNA specimens extracted from fresh or fixed tissues were amplified with Taq DNA polymerase, and their PCR products were cloned and sequenced. RESULTS: Significantly more (3- to 4-fold) mutations were observed with fixed DNA specimens. The majority of mutations were transitions, predominantly at A:T base pairs, randomly distributed along the template. CONCLUSIONS: Formalin fixation appears to cause random base damage, which can be bridged during PCR by Taq DNA polymerase through error prone translesion synthesis. Fixed DNA is a damaged but "readable" template

The Carbon-Rich Gas in the Beta Pictoris Circumstellar Disk

The edge-on disk surrounding the nearby young star Beta Pictoris is the archetype of the "debris disks", which are composed of dust and gas produced by collisions and evaporation of planetesimals, analogues of Solar System comets and asteroids. These disks provide a window on the formation and early evolution of terrestrial planets. Previous observations of Beta Pic concluded that the disk gas has roughly solar abundances of elements [1], but this poses a problem because such gas should be rapidly blown away from the star, contrary to observations of a stable gas disk in Keplerian rotation [1, 2]. Here we report the detection of singly and doubly ionized carbon (CII, CIII) and neutral atomic oxygen (OI) gas in the Beta Pic disk; measurement of these abundant volatile species permits a much more complete gas inventory. Carbon is extremely overabundant relative to every other measured element. This appears to solve the problem of the stable gas disk, since the carbon overabundance should keep the gas disk in Keplerian rotation [3]. New questions arise, however, since the overabundance may indicate the gas is produced from material more carbon-rich than the expected Solar System analogues.Comment: Accepted for publication in Nature. PDF document, 12 pages. Supplementary information may be found at http://www.dtm.ciw.edu/akir/Documents/roberge_supp.pdf *** Version 2 : Removed extraneous publication information, per instructions from the Nature editor. No other changes mad

Substrate specificity of bacterial oligosaccharyltransferase suggests a common transfer mechanism for the bacterial and eukaryotic systems

The PgIB oligosaccharyltransferase (OTase) of Campylobacter jejuni can be functionally expressed in Escherichia coli, and its relaxed oligosaccharide substrate specificity allows the transfer of different glycans from the lipid carrier undecaprenyl pyrophosphate to an acceptor protein. To investigate the substrate specificity of PgIB, we tested the transfer of a set of lipid-linked polysaccharides in E. coli and Salmonella enterica serovar Typhimurium. A hexose linked to the C-6 of the monosaccharide at the reducing end did not inhibit the transfer of the O antigen to the acceptor protein. However, PgIB required an acetamido group at the C-2. A model for the mechanism of PgIB involving this functional group was proposed. Previous experiments have shown that eukaryotic OTases have the same requirement, suggesting that eukaryotic and prokaryotic OTases catalyze the transfer of oligosaccharides by a conserved mechanism. Moreover, we demonstrated the functional transfer of the C. jejuni glycosylation system into S. enterica. The elucidation of the mechanism of action and the substrate specificity of PgIB represents the foundation for engineering glycoproteins that will have an impact on biotechnology

Alcohol Production as an Adaptive Livelihood Strategy for Women Farmers in Tanzania and Its Potential for Unintended Consequences on Women's Reproductive Health.

Although women occupy a central position in agriculture in many developing countries, they face numerous constraints to achieving their full potential including unequal access to assets and limited decision-making authority. We explore the intersection of agricultural livelihoods, food and economic security, and women's sexual and reproductive health in Iringa Region, Tanzania. Our goal was to understand whether the benefits of supporting women in the agricultural sector might also extend to more distal outcomes, including sexual and reproductive health. Using the Sustainable Livelihoods Framework to guide data collection, we conducted 13 focus group discussions (FGD) with female (n = 11) and male farmers (n = 2) and 20 in-depth interviews with agricultural extension officers (n = 10) and village agro-dealers (n = 10). Despite providing the majority of agricultural labor, women have limited control over land and earned income and have little bargaining power. In response to these constraints, women adopt adaptive livelihood strategies, such as alcohol production, that allow them to retain control over income and support their households. However, women's central role in alcohol production, in concert with the ubiquitous nature of alcohol consumption, places them at risk by enhancing their vulnerability to unsafe or transactional sex. This represents a dangerous confluence of risk for female farmers, in which alcohol plays an important role in income generation and also facilitates high-risk sexual behavior. Alcohol production and consumption has the potential to both directly and indirectly place women at risk for undesirable sexual and reproductive health outcomes. Group formation, better access to finance, and engaging with agricultural extension officers were identified as potential interventions for supporting women farmers and challenging harmful gender norms. In addition, joint, multi-sectoral approaches from health and agriculture and alternative income-generating strategies for women might better address the complexities of achieving safe and sustainable livelihoods for women in this context

Quantum Hall effect and Landau level crossing of Dirac fermions in trilayer graphene

We investigate electronic transport in high mobility (\textgreater 100,000 cm$^2$/V$\cdot$s) trilayer graphene devices on hexagonal boron nitride, which enables the observation of Shubnikov-de Haas oscillations and an unconventional quantum Hall effect. The massless and massive characters of the TLG subbands lead to a set of Landau level crossings, whose magnetic field and filling factor coordinates enable the direct determination of the Slonczewski-Weiss-McClure (SWMcC) parameters used to describe the peculiar electronic structure of trilayer graphene. Moreover, at high magnetic fields, the degenerate crossing points split into manifolds indicating the existence of broken-symmetry quantum Hall states.Comment: Supplementary Information at http://jarilloherrero.mit.edu/wp-content/uploads/2011/04/Supplementary_Taychatanapat.pd

Vitamin D in the general population of young adults with autism in the Faroe Islands

Vitamin D deficiency has been proposed as a possible risk factor for developing autism spectrum disorder (ASD). 25-Hydroxyvitamin D3 (25(OH)D3) levels were examined in a cross-sectional population-based study in the Faroe Islands. The case group consisting of a total population cohort of 40 individuals with ASD (aged 15–24 years) had significantly lower 25(OH)D3 than their 62 typically-developing siblings and their 77 parents, and also significantly lower than 40 healthy age and gender matched comparisons. There was a trend for males having lower 25(OH)D3 than females. Effects of age, month/season of birth, IQ, various subcategories of ASD and Autism Diagnostic Observation Schedule score were also investigated, however, no association was found. The very low 25(OH)D3 in the ASD group suggests some underlying pathogenic mechanism

Does the biomarker search paradigm need re-booting?

The clinical problem of bladder cancer is its high recurrence and progression, and that the most sensitive and specific means of monitoring is cystoscopy, which is invasive and has poor patient compliance. Biomarkers for recurrence and progression could make a great contribution, but in spite of decades of research, no biomarkers are commercially available with the requisite sensitivity and specificity. In the post-genomic age, the means to search the entire genome for biomarkers has become available, but the conventional approaches to biomarker discovery are entirely inadequate to yield results with the new technology. Finding clinically useful biomarker panels with sensitivity and specificity equal to that of cystoscopy is a problem of systems biology

Un-oriented Quiver Theories for Majorana Neutrons

In the context of un-oriented open string theories, we identify quivers whereby a Majorana mass for the neutron is indirectly generated by exotic instantons. We discuss two classes of (Susy) Standard Model like quivers, depending on the embedding of SU(2)_W in the Chan-Paton group. In both cases, the main mechanism involves a vector-like pair mixing through a non-perturbative mass term. We also discuss possible relations between the phenomenology of Neutron-Antineutron oscillations and LHC physics in these models. In particular, a vector-like pair of color-triplet scalars or color-triplet fermions could be directly detected at LHC, compatibly with n-\bar{n} limits. Finally we briefly comment on Pati-Salam extensions of our models.Comment: More comments on phenomenology and fluxes, Re-discussion of SM-quivers compatible with n-cycles conditions Version accepted by JHE

Large infrapatellar ganglionic cyst of the knee fat pad: a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p>Large ganglionic cystic formations arising from the infrapatellar fat pad are quite uncommon and only a few are mentioned in the literature. An open excision in these cases is mandatory.</p> <p>Case presentation</p> <p>We report the case of a large infrapatellar fat pad ganglion in a 37-year-old Greek man with chronic knee discomfort. The ganglionic cyst originated from the infrapatellar fat pad and had no intrasynovial extension. The final diagnosis was determined with magnetic resonance imaging of the knee, and the lesion was treated with surgery.</p> <p>Conclusions</p> <p>These lesions are asymptomatic in most cases but often are misdiagnosed as meniscal or ligamentous lesions of the knee joint. Nowadays, the therapeutic trend for such lesions is arthroscopic excision, but when there is a large ganglion, as in this case report, the treatment should be an open and thorough resection. This report is intended mostly but not exclusively for clinical physicians and radiologists.</p

Algorithm for identifying and separating beats from arterial pulse records

BACKGROUND: This project was designed as an epidemiological aid-selecting tool for a small country health center with the general objective of screening out possible coronary patients. Peripheral artery function can be non-invasively evaluated by impedance plethysmography. Changes in these vessels appear as good predictors of future coronary behavior. Impedance plethysmography detects volume variations after simple occlusive maneuvers that may show indicative modifications in arterial/venous responses. Averaging of a series of pulses is needed and this, in turn, requires proper determination of the beginning and end of each beat. Thus, the objective here is to describe an algorithm to identify and separate out beats from a plethysmographic record. A secondary objective was to compare the output given by human operators against the algorithm. METHODS: The identification algorithm detected the beat's onset and end on the basis of the maximum rising phase, the choice of possible ventricular systolic starting points considering cardiac frequency, and the adjustment of some tolerance values to optimize the behavior. Out of 800 patients in the study, 40 occlusive records (supradiastolic- subsystolic) were randomly selected without any preliminary diagnosis. Radial impedance plethysmographic pulse and standard ECG were recorded digitizing and storing the data. Cardiac frequency was estimated with the Power Density Function and, thereafter, the signal was derived twice, followed by binarization of the first derivative and rectification of the second derivative. The product of the two latter results led to a weighing signal from which the cycles' onsets and ends were established. Weighed and frequency filters are needed along with the pre-establishment of their respective tolerances. Out of the 40 records, 30 seconds strands were randomly chosen to be analyzed by the algorithm and by two operators. Sensitivity and accuracy were calculated by means of the true/false and positive/negative criteria. Synchronization ability was measured through the coefficient of variation and the median value of correlation for each patient. These parameters were assessed by means of Friedman's ANOVA and Kendall Concordance test. RESULTS: Sensitivity was 97% and 91% for the two operators, respectively, while accuracy was cero for both of them. The synchronism variability analysis was significant (p < 0.01) for the two statistics, showing that the algorithm produced the best result. CONCLUSION: The proposed algorithm showed good performance as expressed by its high sensitivity. The correlation analysis demonstrated that, from the synchronism point of view, the algorithm performed the best detection. Patients with marked arrhythmic processes are not good candidates for this kind of analysis. At most, they would be singled out by the algorithm and, thereafter, to be checked by an operator