Emulsion PCR-coupled target enrichment: an effective fishing method for high-throughput sequencing of poorly preserved ancient DNA

Due to the difficulties in deep sequencing, high-throughput sequencing of ancient DNA has been limited to exceptionally well-preserved ancient materials. The primary factor is microbial attack popularly observed in the buried materials, and it causes drastic increase in relative ratio of microbial DNA in the extracted DNA. We present a unified strategy in which emulsion PCR is coupled with target enrichment followed by next-generation sequencing. The method made it possible to obtain efficiently non-duplicated reads mapped to target sequences of interest, and this can achieve deep and reliable sequencing of ancient DNA from typical materials, even though poorly preserved.

Deep venous thrombosis among disaster shelter inhabitants following the March 2011 earthquake and tsunami in Japan: a descriptive study

Objectives

A retrospective analysis of data collected during subject screening following Japan's March 2011 earthquake and tsunami was performed. We aimed to determine the incidence of deep venous thrombosis (DVT) among screened subjects and to identify risk factors associated with the development of DVT as independent variables.

Methods

Calf ultrasonography was undertaken in 269 subjects living in 21 shelters in Miyagi prefecture during the one-month period immediately following the March 2011 disaster. Information regarding the health and risk factors of subjects was collected by questionnaire and assessment of physical signs.

Results

Of the 269 evacuees screened, 65 (24%) met the criteria for calf DVT. We found lower limb trauma, reduced frequency of urination and sleeping in a vehicle to be independent positive predictors of DVT.

Conclusions

Evacuees had an increased risk of developing DVT, associated with tsunami-related lower limb injury, immobility and dehydration.

Ras-related C3 botulinum toxin substrate 1 (RAC1) regulates glucose-stimulated insulin secretion via modulation of F-actin

AIMS/HYPOTHESIS

The small G-protein ras-related C3 botulinum toxin substrate 1 (RAC1) plays various roles in mammalian cells, such as in the regulation of cytoskeletal organisation, cell adhesion, migration and morphological changes. The present study examines the effects of RAC1 ablation on pancreatic beta cell function.

METHODS

Isolated islets from pancreatic beta cell-specific Rac1-knockout (betaRac1(-/-)) mice and RAC1 knockdown INS-1 insulinoma cells treated with small interfering RNA were used to investigate insulin secretion and cytoskeletal organisation in pancreatic beta cells.

RESULTS

BetaRac1(-/-) mice showed decreased glucose-stimulated insulin secretion, while there were no apparent differences in islet morphology. Isolated islets from the mice had blunted insulin secretion in response to high glucose levels. In RAC1 knockdown INS-1 cells, insulin secretion was also decreased in response to high glucose levels, consistent with the phenotype of betaRac1(-/-) mice. Even under high glucose levels, RAC1 knockdown INS-1 cells remained intact with F-actin, which inhibits the recruitment of the insulin granules, resulting in an inhibition of insulin secretion.

CONCLUSIONS/INTERPRETATION

In RAC1-deficient pancreatic beta cells, F-actin acts as a barrier for insulin granules and reduces glucose-stimulated insulin secretion.

Abstract P4-02-04: Tissue oxyhemoglobin dynamics measured with functional optical imaging immediately after starting chemotherapy correlates with markers of cellular proliferation and inflammation in a rat breast tumor model

We have reported that a transient increase of oxyhemoglobin level measured 24 hours after the start of neoadjuvant chemotherapy using noninvasive Diffuse Optical Spectroscopic Imaging (DOSI) may be useful in discriminating nonresponding from reponding breast cancer patients (PNAS. 2011 Aug 30;108(35):14626–31). To elucidate the underlying biological mechanism, we compared optical measured hemoglobin levels to tissue biomarkers in a rat tumor model.

Method: An orthotopic mammary tumor model using Fischer 344 rats and MAT3B cells was used for this experiment. 16 mg of cyclophosphamide was administered (i.p.) in 15 rats after tumors had grown to a significant size. A wide-field functional imaging device that utilizes structured near-infrared light was used to measure superficial absolute concentrations of oxyhemoglobin (ctO2Hb) and deoxyhemoglobin (ctHHb) of the tumors. Rats were imaged and sacrificed (two per timepoint) at each of the following timepoints: baseline, 2, 6, 12, 24, 48, 96 hours, and day 8 following the injection. Resected tumors were sectioned after paraffin-embedding and representative slides were used for immunohistochemistry. Cellular markers of proliferation (measured by Ki67), apoptosis (Caspase3), NK cells (ANK61), and macrophages (MAC387) were counted in each slide using Image J software.

Result: Average tumors baseline values of ctO2Hb and ctHHb were 81.4 µM (±9.2 SD) and 22.4 µM (±4.1 SD) respectively. In most rats, both levels gradually increased from baseline to 24 hours after the injection and reached a maximum at 48 hours and then declined until Day 8. At 24 hours, ctO2Hb was significantly higher than baseline [96.8 µM (±8.8 SD) vs. 81.4µM (±9.2 SD), p = 0.003 using Student's t-test]. This trend was mimicked in the tissue markers of cellular proliferation and apoptosis, which peaked at 24 through 48 hours and then dropped. The average NK cell count was also found to rise consistently through the course of monitoring and reached the highest at day 8, while macrophage counts reached a peak at 48 hours and then declined. The differences between baseline and 24 hours for these were statistically significant: Ki67 [294 (±107 SD) vs. 115 (±68 SD), p = 0.0002], Caspase3 [2916 (±1383 SD) vs. 136 (±150 SD), p < 0.0001], NK cells [635 (±329 SD) vs. 159 (±110 SD), p = 0.0001], and macrophage markers [281 (±260 SD) vs. 39 (±31 SD), p = 0.01].

Bulk electronic structure of the dilute magnetic semiconductor Ga(1-x)Mn(x)As through hard X-ray angle-resolved photoemission

A detailed understanding of the origin of the magnetism in dilute magnetic semiconductors is crucial to their development for applications. Using hard X-ray angle-resolved photoemission (HARPES) at 3.2 keV, we investigate the bulk electronic structure of the prototypical dilute magnetic semiconductor Ga(0.97)Mn(0.03)As, and the reference undoped GaAs. The data are compared to theory based on the coherent potential approximation and fully relativistic one-step-model photoemission calculations including matrix-element effects. Distinct differences are found between angle-resolved, as well as angle-integrated, valence spectra of Ga(0.97)Mn(0.03)As and GaAs, and these are in good agreement with theory. Direct observation of Mn-induced states between the GaAs valence-band maximum and the Fermi level, centred about 400 meV below this level, as well as changes throughout the full valence-level energy range, indicates that ferromagnetism in Ga(1-x)Mn(x)As must be considered to arise from both p-d exchange and double exchange, thus providing a more unifying picture of this controversial material.

Comparative aspects of polyglutamine binding domain in PQBP-1 among Vertebrata

We investigated the evolutionary conservation of polyglutamine binding protein-1 (PQBP-1) among Vertebrata. PQBP-1s were highly conserved and shared the same domain features including a WW domain, a polar amino acid rich domain (PRD), a nuclear localization signal (NLS), and a C-terminal domain (CTD) among Eutheria, but not always among Vertebrata. PQBP-1s of Vertebrata contained a variable region in the middle portion corresponding to the position of PRD. The full form of PRD including both 7aa and DR/ER repeats was specific to Eutheria. PRD of non-eutherian Amniota was minimal. Amphibia had no PRD. The DR/ER repeat was solo in fishes. Agnatha PRD was also rich in polar amino acids, but contained no repetitive sequence. We investigated 3 polyQ-containing proteins known to interact with PQBP-1: BRN-2, Huntingtin, and ATAXIN-1, and showed a diverse nature of protein-protein interaction in Vertebrata. There appears to be no interaction between PQBP-1 and BRN-2, Huntingtin, or ATAXIN-1 in Amphibia, while the interaction between PQBP-1 and BRN-2 is expected to be conserved among Mammalia, and the interaction between PQBP-1 and Huntingtin or ATAXIN-1 depends on the lineage in Eutheria.

Electronic structure changes across the metamagnetic transition in FeRh via hard X-ray photoemission

Stoichiometric FeRh undergoes a temperature-induced antiferromagnetic (AFM) to ferromagnetic (FM) transition at ~350 K. In this Letter, changes in the electronic structure accompanying this transition are investigated in epitaxial FeRh thin films via bulk-sensitive valence-band and core-level hard x-ray photoelectron spectroscopy with a photon energy of 5.95 keV. Clear differences between the AFM and FM states are observed across the entire valence-band spectrum and these are well reproduced using density-functional theory. Changes in the 2p core levels of Fe are also observed and interpreted using Anderson impurity model calculations. These results indicate that significant electronic structure changes over the entire valence-band region are involved in this AFM-FM transition.

The unstable CCTG repeat responsible for myotonic dystrophy type 2 originates from an AluSx element insertion into an early primate genome

Myotonic dystrophy type 2 (DM2) is a subtype of the myotonic dystrophies, caused by expansion of a tetranucleotide CCTG repeat in intron 1 of the zinc finger protein 9 (ZNF9) gene. The expansions are extremely unstable and variable, ranging from 75–11,000 CCTG repeats. This unprecedented repeat size and somatic heterogeneity make molecular diagnosis of DM2 difficult, and yield variable clinical phenotypes. To better understand the mutational origin and instability of the ZNF9 CCTG repeat, we analyzed the repeat configuration and flanking regions in 26 primate species. The 3′-end of an AluSx element, flanked by target site duplications (5′-ACTRCCAR-3′or 5′-ACTRCCARTTA-3′), followed the CCTG repeat, suggesting that the repeat was originally derived from the Alu element insertion. In addition, our results revealed lineage-specific repetitive motifs: pyrimidine (CT)-rich repeat motifs in New World monkeys, dinucleotide (TG) repeat motifs in Old World monkeys and gibbons, and dinucleotide (TG) and tetranucleotide (TCTG and/or CCTG) repeat motifs in great apes and humans. Moreover, these di- and tetra-nucleotide repeat motifs arose from the poly (A) tail of the AluSx element, and evolved into unstable CCTG repeats during primate evolution. Alu elements are known to be the source of microsatellite repeats responsible for two other repeat expansion disorders: Friedreich ataxia and spinocerebellar ataxia type 10. Taken together, these findings raise questions as to the mechanism(s) by which Alu-mediated repeats developed into the large, extremely unstable expansions common to these three disorders.