Exponential Megapriming PCR (EMP) Cloning-Seamless DNA Insertion into Any Target Plasmid without Sequence Constraints

We present a fast, reliable and inexpensive restriction-free cloning method for seamless DNA insertion into any plasmid without sequence limitation. Exponential megapriming PCR (EMP) cloning requires two consecutive PCR steps and can be carried out in one day. We show that EMP cloning has a higher efficiency than restriction-free (RF) cloning, especially for long inserts above 2.5 kb. EMP further enables simultaneous cloning of multiple inserts.National Institutes of Health (U.S.) (Grant GM077537

Definitive hypofractionated radiotherapy for early glottic carcinoma: experience of 55Gy in 20 fractions

Introduction: A wide variety of fractionation schedules have been employed for the treatment of early glottic cancer. The aim is to report our 10-year experience of using hypofractionated radiotherapy with 55Gy in 20 fractions at 2.75Gy per fraction. Methods: Patients treated between 2004 and 2013 with definitive radiotherapy to a dose of 55Gy in 20 fractions over 4 weeks for T1/2 N0 squamous cell carcinoma of the glottis were retrospectively identified. Patients with prior therapeutic minor surgery (eg. laser stripping, cordotomy) were included. The probabilities of local control, ultimate local control (including salvage surgery), regional control, cause specific survival (CSS) and overall survival (OS) were calculated. Results: One hundred thirty-two patients were identified. Median age was 65 years (range 33–89). Median follow up was 72 months (range 7–124). 50 (38 %), 18 (14 %) and 64 (48 %) of patients had T1a, T1b and T2 disease respectively. Five year local control and ultimate local control rates were: overall - 85.6 % and 97.3 % respectively, T1a - 91.8 % and 100 %, T1b - 81.6 and 93.8 %, and T2 - 80.9 % and 95.8 %. Five year regional control, CSS and OS rates were 95.4 %, 95.7 % and 78.8 % respectively. There were no significant associations of covariates (e.g. T-stage, extent of laryngeal extension, histological grade) with local control on univariate analysis. Only increasing age and transglottic extension in T2 disease were significantly associated with overall survival (both p <0.01). Second primary cancers developed in 17 % of patients. 13 (9.8 %) of patients required enteral tube feeding support during radiotherapy; no patients required long term enteral nutrition. One patient required a tracheostomy due to a non-functioning larynx on long term follow up. Conclusions: Hypofractionated radiation therapy with a dose of 55Gy in 20 fractions for early stage glottic cancer provides high rates of local control with acceptable toxicity

Plantation vs. natural forest: Matrix quality determines pollinator abundance in crop fields

In terrestrial ecosystems, ecological processes and patterns within focal patches frequently depend on their matrix. Crop fields (focal patches) are often surrounded by a mosaic of other land-use types (matrix), which may act as habitats for organisms and differ in terms of the immigration activities of organisms to the fields. We examined whether matrix quality affects wild pollinator abundance in crop fields, given that the species (Apis cerana) generally nest in the cavities of natural trees. We examined fields of a pollination-dependent crop surrounded by plantations and natural forests, which comprised the matrix. Our analysis revealed a clear positive effect of the natural forest on the pollinator abundance, but the plantation forest had little effects. These indicate that agricultural patches are influenced by their matrix quality and the resulting crop pollinator abundance, suggesting the importance of matrix management initiatives such as forest restoration surrounding agricultural fields to improve crop production

Amyloid-Like Aggregates of the Yeast Prion Protein Ure2 Enter Vertebrate Cells by Specific Endocytotic Pathways and Induce Apoptosis

BACKGROUND: A number of amyloid diseases involve deposition of extracellular protein aggregates, which are implicated in mechanisms of cell damage and death. However, the mechanisms involved remain poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: Here we use the yeast prion protein Ure2 as a generic model to investigate how amyloid-like protein aggregates can enter mammalian cells and convey cytotoxicity. The effect of three different states of Ure2 protein (native dimer, protofibrils and mature fibrils) was tested on four mammalian cell lines (SH-SY5Y, MES23.5, HEK-293 and HeLa) when added extracellularly to the medium. Immunofluorescence using a polyclonal antibody against Ure2 showed that all three protein states could enter the four cell lines. In each case, protofibrils significantly inhibited the growth of the cells in a dose-dependent manner, fibrils showed less toxicity than protofibrils, while the native state had no effect on cell growth. This suggests that the structural differences between the three protein states lead to their different effects upon cells. Protofibrils of Ure2 increased membrane conductivity, altered calcium homeostasis, and ultimately induced apoptosis. The use of standard inhibitors suggested uptake into mammalian cells might occur via receptor-mediated endocytosis. In order to investigate this further, we used the chicken DT40 B cell line DKOR, which allows conditional expression of clathrin. Uptake into the DKOR cell-line was reduced when clathrin expression was repressed suggesting similarities between the mechanism of PrP uptake and the mechanism observed here for Ure2. CONCLUSIONS/SIGNIFICANCE: The results provide insight into the mechanisms by which amyloid aggregates may cause pathological effects in prion and amyloid diseases

Effects of Heparin and Enoxaparin on APP Processing and Aβ Production in Primary Cortical Neurons from Tg2576 Mice

Alzheimer's disease (AD) is caused by accumulation of Aβ, which is produced through sequential cleavage of β-amyloid precursor protein (APP) by the β-site APP cleaving enzyme (BACE1) and γ-secretase. Enoxaparin, a low molecular weight form of the glycosaminoglycan (GAG) heparin, has been reported to lower Aβ plaque deposition and improve cognitive function in AD transgenic mice

Constraints on the Physical Properties of GW190814 through Simulations Based on DECam Follow-up Observations by the Dark Energy Survey

On 2019 August 14, the LIGO and Virgo Collaborations detected gravitational waves from a black hole and a 2.6 solar mass compact object, possibly the first neutron star–black hole merger. In search of an optical counterpart, the Dark Energy Survey (DES) obtained deep imaging of the entire 90% confidence level localization area with Blanco/DECam 0, 1, 2, 3, 6, and 16 nights after the merger. Objects with varying brightness were detected by the DES Pipeline, and we systematically reduced the candidate counterparts through catalog matching, light-curve properties, host-galaxy photometric redshifts, Southern Astrophysical Research spectroscopic follow-up observations, and machine-learning-based photometric classification. All candidates were rejected as counterparts to the merger. To quantify the sensitivity of our search, we applied our selection criteria to full light-curve simulations of supernovae and kilonovae as they would appear in the DECam observations. Because the source class of the merger was uncertain, we utilized an agnostic, three-component kilonova model based on tidally disrupted neutron star (NS) ejecta properties to quantify our detection efficiency of a counterpart if the merger included an NS. We find that, if a kilonova occurred during this merger, configurations where the ejected matter is greater than 0.07 solar masses, has lanthanide abundance less than 10−8.56, and has a velocity between 0.18c and 0.21c are disfavored at the 2σ level. Furthermore, we estimate that our background reduction methods are capable of associating gravitational wave signals with a detected electromagnetic counterpart at the 4σ level in 95% of future follow-up observations