Surface passivation of crystalline silicon by Cat-CVD amorphous and nanocrystalline thin silicon films

In this work, we study the electronic surface passivation of crystalline silicon with intrinsic thin silicon films deposited by Catalytic CVD. The contactless method used to determine the effective surface recombination velocity was the quasi-steady-state photoconductance technique. Hydrogenated amorphous and nanocrystalline silicon films were evaluated as passivating layers on n- and p-type float zone silicon wafers. The best results were obtained with amorphous silicon films, which allowed effective surface recombination velocities as low as 60 and 130 cms -1 on p- and n-type silicon, respectively. To our knowledge, these are the best results ever reported with intrinsic amorphous silicon films deposited by Catalytic CVD. The passivating properties of nanocrystalline silicon films strongly depended on the deposition conditions, especially on the filament temperature. Samples grown at lower filament temperatures (1600 °C) allowed effective surface recombination velocities of 450 and 600 cms -1 on n- and p-type silicon.

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

Combined CSL and p53 downregulation promotes cancer-associated fibroblast activation.

Stromal fibroblast senescence has been linked to ageing-associated cancer risk. However, density and proliferation of cancer-associated fibroblasts (CAFs) are frequently increased. Loss or downmodulation of the Notch effector CSL (also known as RBP-Jκ) in dermal fibroblasts is sufficient for CAF activation and ensuing keratinocyte-derived tumours. We report that CSL silencing induces senescence of primary fibroblasts from dermis, oral mucosa, breast and lung. CSL functions in these cells as a direct repressor of multiple senescence- and CAF-effector genes. It also physically interacts with p53, repressing its activity. CSL is downmodulated in stromal fibroblasts of premalignant skin actinic keratosis lesions and squamous cell carcinomas, whereas p53 expression and function are downmodulated only in the latter, with paracrine FGF signalling as the probable culprit. Concomitant loss of CSL and p53 overcomes fibroblast senescence, enhances expression of CAF effectors and promotes stromal and cancer cell expansion. The findings support a CAF activation-stromal co-evolution model under convergent CSL-p53 control.

Understanding Optical Trapping Phenomena: a Simulation for Undergraduates

Optical trapping is an attractive and multidisciplinary topic that has become the center of attention to a large number of researchers. Moreover, it is a suitable subject for advanced students that requires a knowledge of a wide range of topics. As a result, it has been incorporated into some syllabuses of both undergraduate and graduate programs. In this paper, basic concepts in laser trapping theory are reviewed. To provide a better understanding of the underlying concepts for students, a Java application for simulating the behavior of a dielectric particle trapped in a highly focused beam has been developed. The program illustrates a wide range of theoretical results and features, such as the calculation of the force exerted by a beam in the Mie and Rayleigh regimes or the calibration of the trap stiffness. Some examples that are ready to be used in the classroom or in the computer lab are also supplied.

Optical trapping: a review of essential concepts

Optical tweezers are an innovative technique for the non-contact, all-optical manipulation of small material samples, which has extraordinarily expanded and evolved since its inception in the mid-80s of the last century. Nowadays, the potential of optical tweezers has been clearly proven and a wide range of applications both from the physical and biological sciences have solidly emerged, turning the early ideas and techniques into a powerful paradigm for experimentation in the micro- and nanoworld. This review aims at highlighting the fundamental concepts that are essential for a thorough understanding of optical trapping, making emphasis on both its manipulation and measurement capabilities, as well as on the vast array of important biological applications appeared in the last years.

The role of MAR elements in DNA recombination

The untargeted integration of foreign DNA into the mammalian cell genome, extensively used in gene therapy and biotechnology, remains an incompletely understood process. It is believed to be based on cellular DNA double strand break (DSB) repair machinery and to involve two major steps: i) the formation of long gene arrays (concatemers), and ii) recombination of the resulting concatemer with the genome. The main DSB repair pathways in eukaryotes include non-homologous end-joining (NHEJ), homologous recombination (HR), and microhomology-mediated end-joining (MMEJ). However, it is still not clear, which of these pathways are responsible for transgene integration. Here, we show that NHEJ is not the primary pathway used by mammalian cells in the transgene integration process, while the components of the HR pathway seem to be important for genomic integration but not concatemerization. Instead, concatemer formation appears to be mediated by a subset of the MMEJ pathway, termed synthesis-dependent MMEJ (SD-MMEJ). This mechanism also seems to be preferentially used for plasmid integration into the genome, as confirmed by the analysis of plasmid-to-genome junction sequences, which were found to display an SD-MMEJ pattern. Therefore, we propose the existence of two distinct SD-MMEJ subpathways, relying on different subsets of enzymes. One of these mechanisms appears to be responsible for concatemerization, while the other mechanism, partially dependent in HR enzymes, seems to mediate recombination with the genome. Previous studies performed by our group suggested that matrix attachment regions (MARs), which are epigenetic regulatory DNA elements that participate in the formation of chromatin boundaries and augment transcription, may mediate increased plasmid integration into the genome of CHO cells by stimulating DNA recombination. In the present work, we demonstrate that MAR-mediated plasmid integration results from the enhanced SD-MMEJ pathway. Analysis of transgene integration loci and junction DNA sequences validated the prevalent use of this pathway by the MAR elements to target plasmid DNA into gene-rich areas of the CHO genome. We propose that this finding should in the future help to engineer cells for improved recombinant protein production. In addition to investigating the process of transgene integration, we designed recombination assays to better characterize the components of the MMEJ and SD-MMEJ pathways. We also used CHO cells expressing cycle-sensitive reporter genes to demonstrate a potential role of HR proteins in the cell cycle regulation.

A role for homologous recombination proteins in cell cycle regulation.

Eukaryotic cells respond to DNA breaks, especially double-stranded breaks (DSBs), by activating the DNA damage response (DDR), which encompasses DNA repair and cell cycle checkpoint signaling. The DNA damage signal is transmitted to the checkpoint machinery by a network of specialized DNA damage-recognizing and signal-transducing molecules. However, recent evidence suggests that DNA repair proteins themselves may also directly contribute to the checkpoint control. Here, we investigated the role of homologous recombination (HR) proteins in normal cell cycle regulation in the absence of exogenous DNA damage. For this purpose, we used Chinese Hamster Ovary (CHO) cells expressing the Fluorescent ubiquitination-based cell cycle indicators (Fucci). Systematic siRNA-mediated knockdown of HR genes in these cells demonstrated that the lack of several of these factors alters cell cycle distribution, albeit differentially. The knock-down of MDC1, Rad51 and Brca1 caused the cells to arrest in the G2 phase, suggesting that they may be required for the G2/M transition. In contrast, inhibition of the other HR factors, including several Rad51 paralogs and Rad50, led to the arrest in the G1/G0 phase. Moreover, reduced expression of Rad51B, Rad51C, CtIP and Rad50 induced entry into a quiescent G0-like phase. In conclusion, the lack of many HR factors may lead to cell cycle checkpoint activation, even in the absence of exogenous DNA damage, indicating that these proteins may play an essential role both in DNA repair and checkpoint signaling.

A chromosomal insertion toolbox for promoter probing, mutant complementation and pathogenicity studies in Ralstonia solanacearum

We describe here the construction of a delivery system for stable and directed insertion of gene constructs in a permissive chromosomal site of the bacterial wilt pathogen Ralstonia solanacearum. The system consists of a collection of suicide vectors the Ralstonia chromosome (pRC) series that carry an integration element flanked by transcription terminators and two sequences of homology to the chromosome of strain GMI1000, where the integration element is inserted through a double recombination event. Unique restriction enzyme sites and a GATEWAY cassette enable cloning of any promoter::gene combination in the integration element. Variants endowed with different selectable antibiotic resistance genes and promoter::gene combinations are described. We show that the system can be readily used in GMI1000 and adapted to other R. solanacearum strains using an accessory plasmid. We prove that the pRC system can be employed to complement a deletion mutation with a single copy of the native gene, and to measure transcription of selected promoters in monocopy both in vitro and in planta. Finally, the system has been used to purify and study secretion type III effectors. These novel genetic tools will be particularly useful for the construction of recombinant bacteria that maintain inserted genes or reporter fusions in competitive situations (i.e., during plant infection).

High-resolution computed tomography and histopathological findings in hypersensitivity pneumonitis: a pictorial essay

Abstract Hypersensitivity pneumonitis is a diffuse interstitial and granulomatous lung disease caused by the inhalation of any one of a number of antigens. The objective of this study was to illustrate the spectrum of abnormalities in high-resolution computed tomography and histopathological findings related to hypersensitivity pneumonitis. We retrospectively evaluated patients who had been diagnosed with hypersensitivity pneumonitis (on the basis of clinical-radiological or clinical-radiological-pathological correlations) and had undergone lung biopsy. Hypersensitivity pneumonitis is clinically divided into acute, subacute, and chronic forms; high-resolution computed tomography findings correlate with the time of exposure; and the two occasionally overlap. In the subacute form, centrilobular micronodules, ground-glass opacities, and air trapping are characteristic high-resolution computed tomography findings, whereas histopathology shows lymphocytic inflammatory infiltrates, bronchiolitis, variable degrees of organizing pneumonia, and giant cells. In the chronic form, high-resolution computed tomography shows traction bronchiectasis, honeycombing, and lung fibrosis, the last also being seen in the biopsy sample. A definitive diagnosis of hypersensitivity pneumonitis can be made only through a multidisciplinary approach, by correlating clinical findings, exposure history, high-resolution computed tomography findings, and lung biopsy findings.

Chromosomal polymorphism of D. subobscura: no differences between wild males and sons of wild females

When analyzing the chromosomal polymorphism of D. subobscura natural populations it is assumed that the information provided by wild males and sons of wild females is equivalent. Thus, using both in the analysis it is possible to increase the sample size. However, it is important to verify whether there are significant differences between both groups or not. The aim of this research has been to statistically compare the results of chromosomal polymorphism of both groups. We have used data from Avala Mountain (Serbia) where D. subobscura flies were collected from the 30th May to the 5th June 2011. Avala is located 18 km south of Belgrade and the trapping place is a forest with polydominant communities of Fagetum submontanum Table 1. Number and percentage of adult flies collected in Font Groga (Barcelona, Spain) on 9th October 2013. Males and sons of wild females were crossed with virgin females of the Küsnacht strain. Third instar larvae from F1 were dissected to obtain the salivary glands and the polytene chromosomes were stained and squashed in aceto-orcein solution. No significant differences were observed for any chromosome of the karyotype: A (p-value = 0.485), J (p-value = 0.230), U (p-value =0.572), E (p-value = 0.536), and O (p-value = 0.338). Thus, it seems that the two groups can be grouped together to obtain the chromosomal polymorphism of the population.

Study of linkage between miniature and singed genes in Drosophila melanogaster

We have developed a practical exercise for undergraduate students whose main aim is to identify, using genetic crosses, a pair of D. melanogaster mutations (miniature and singed). Each student receives a vial with the problem strain containing two unknown mutations. The first step is to observe and describe both mutations. Then, the students carry out genetic crosses between mutant and normal strains: (P) ♀ mutant strain × ♂ normal strain (P) ♀ normal strain × ♂ mutant strain A different offspring is expected in these crosses: in the first one we will obtain normal females and m sn males, whereas in the second all individuals will present normal phenotype. It is possible to deduce that both are sex linked mutations. With this information and to simplify the amount of work, only F1 individuals from the first cross will be used (m+sn+ / m sn × m sn / Y chrom.) to obtain the F2 generation. By counting the number of miniature (recombinant type), singed (recombinant type), miniature-singed (parental type) and normal (parental type) flies it is possible to estimate the recombination frequency between both genes. Knowing the phenotype, their chromosomal location (X chromosome) and the genetic distance between both mutations, it is possible to identify them by finding all this information in a Drosophila melanogaster genetic map. Additionally, a statistical analysis can be carried out to compare the number of expected F2 individuals with those observed in the experiment. As the distance between both genes is 15.1 m.u., then the expected percentages for each phenotype would be: normal (42.45%), miniature-signed (42.45%), miniature (7.55%) and singed (7.55%). Multiplying the frequency of each class by the total number of individuals obtained in the F2 it is possible to estimate the expected number of flies for each class. Finally, a χ2 test can be computed to ascertain whether there are significant differences between expected and observed number of individuals.

Electroluminescence of silicon- and some metal oxides

In the present work electroluminescence in Si-SiO2 structures has been investigated. Electroluminescence has been recorded in the range of 250-900 nm in a system of electrolyte-insulator-semiconductor at the room temperature. The heating process of electrons in SiO2 was studied and possibility of separation it into two phases has been shown. The nature of luminescence centers and the model of its formation were proposed. This paper also includes consideration of oxide layer formation. Charge transfer mechanisms have been attended as well. The nature of electroluminescence is understood in detail. As a matter of fact, electron traps in silicon are the centers of luminescence. Electroluminescence occurs when electrons move from one trap to another. Thus the radiation of light quantum occurs. These traps appear as a result of the oxide growth. At the same time the bonds deformation of silicon atoms with SiOH groups is not excludes. As a result, dangling bonds are appeared, which are the trapping centers or the centers of luminescence.

Traditional and transgenic strategies for controlling tomato-infecting begomoviruses

Viruses of to the family Geminiviridae are considered some of the most important pathogens in tropical and subtropical regions of the world. Members of one Geminiviridae genus, Begomovirus, have been causing severe losses, particularly in tomato (Lycopersicon esculentum) production in the Americas and the Caribbean. Several new begomoviruses have been reported in the region and, at least one, Tomato yellow leaf curl virus (TYLCV), has been brought in from the Old World via infected transplants. In addition, the recombination events that are playing an important role in Begomovirus diversity have increased the complexity of their control. This scenario has led to the search for control measures that go beyond traditional host genetic resistance, chemical controls and cultural practices. In this review, besides the recommended classical control measures, transgenic approaches will be discussed, as well as the mechanisms involved in their successful control of viruses.

Time-Resolved Photoluminescence in Antimonide and Dilute Nitride Quantum Well Structures

This Master's thesis is devoted to semiconductor samples study using time-resolved photoluminescence. This method allows investigating recombination in semiconductor samples in order to develop quality of optoelectronic device. An additional goal was the method accommodation for low-energy-gap materials. The first chapter gives a brief intercourse into the basis of semiconductor physics. The key features of the investigated structures are noted. The usage area of the results covers saturable semiconductor absorber mirrors, disk lasers and vertical-external-cavity surface-emittinglasers. The experiment set-up is described in the second chapter. It is based on up-conversion procedure using a nonlinear crystal and involving the photoluminescent emission and the gate pulses. The limitation of the method was estimated. The first series of studied samples were grown at various temperatures and they suffered rapid thermal annealing. Further, a latticematched and metamorphically grown samples were compared. Time-resolved photoluminescence method was adapted for wavelengths up to 1.5 µm. The results allowed to specify the optimal substrate temperature for MBE process. It was found that the lattice-matched sample and the metamorphically grown sample had similar characteristics.

Spin-Dynamics in Cold Gases of 87Rb and Atomic Hydrogen. The spins they are a-changin’

In this thesis the dynamics of cold gaseous atoms is studied. Two different atomic species and two different experimental techniques have been used. In the first part of the thesis experiments with Bose-Einstein condensates of Rb-87 are presented. In these experiments the methods of laser cooling and magnetic trapping of atoms were utilized. An atom chip was used as the experimental technique for implementation of magnetic trapping. The atom chip is a small integrated instrument allowing accurate and detailed manipulation of the atoms. The experiments with Rb-87 probed the behaviour of a falling beam of atoms outcoupled from the Bose-Einstein condensate by electromagnetic field induced spin flips. In the experiments a correspondence between the phases of the outcoupling radio frequency field and the falling beam of atoms was found. In the second part of the thesis experiments of spin dynamics in cold atomic hydrogen gas are discussed. The experiments with atomic hydrogen are conducted in a cryostat using a dilution refrigerator as the cooling method. These experiments concentrated on explaining and quantifying modulations in the electron spin resonance spectra of doubly polarized atomic hydrogen. The modifications to the previous experimental setup are described and the observation of electron spin waves is presented. The observed spin wave modes were caused by the identical spin rotation effect. These modes have a strong dependence on the spatial profile of the polarizing magnetic field. We also demonstrated confinement of these modes in regions of strong magnetic field and manipulated their spatial distribution by changing the position of the field maximum.