The complete mitochondrial genome of Yarrowia lipolytica

We here report the complete nucleotide sequence of the 47.9 kb mitochondrial (mt) genome from the obligate aerobic yeast Yarrowia lipolytica. It encodes, all on the same strand, seven subunits of NADH: ubiquinone oxidoreductase (ND1-6, ND4L), apocytochrome b (COB), three subunits of cytochrome oxidase (COX1, 2, 3), three subunits of ATP synthetase (ATP6, 8 and 9), small and large ribosomal RNAs and an incomplete set of tRNAs. The Y. lipolytica mt genome is very similar to the Hansenula wingei mt genome, as judged from blocks of conserved gene order and from sequence homology. The extra DNA in the Y. lipolytica mt genome consists of 17 group 1 introns and stretches of A+Trich sequence, interspersed with potentially transposable GC clusters. The usual mould mt genetic code is used. Interestingly, there is no tRNA able to read CGN (arginine) codons. CGN codons could not be found in exonic open reading frames, whereas they do occur in intronic open reading frames. However, several of the intronic open reading frames have accumulated mutations and must be regarded as pseudogenes. We propose that this may have been triggered by the presence of untranslatable CGN codons. This sequence is available under EMBL Accession No. AJ307410

Yarrowia lipolytica: a model organism for protein secretion studies

This paper reviews the advantages of the yeast Yarrowia lipolytica as a tool in the study of protein secretion. Work has been focused on the early steps leading the polypeptide, from the cytoplasmic ribosomes where it is synthesized, to the lumen of the endoplasmic reticulum. Using a thermosensitive allele of the 7SL RNA, the first in vivo evidence for a co-translational translocation was shown. Genetic screens allowed the identification of several new components of the translocation apparatus: Sls1p, an ER lumenal component involved in both translocation and lumenal transit; Tsr1p, involved in SRP-ribosome targeting; Tsr3p. Major translocation partners were also identified by reverse genetics (Sec61p, Sec62p, Kar2p, Srp54p, Sec65p)

Radiation Effects in CMOS Isolation Oxides: Differences and Similarities With Thermal Oxides

Radiation effects in thick isolation oxides of modern CMOS technologies are investigated using dedicated test structures designed using two commercial foundries. Shallow Trench Isolation and Pre-Metal Dielectric are studied using electrical measurements performed after X-ray irradiations and isochronal annealing cycles. This paper shows that trapping properties of such isolation oxides can strongly differ from those of traditional thermal oxides usually used to process the gate oxide of Metal Oxide Semiconductor Field Effect Transistors. Buildup and annealing of both radiation-induced oxide-trap charge and radiation-induced interface traps are discussed as a function of the oxide type, foundry and bias condition during irradiation. Radiation-induced interface traps in such isolation oxides are shown to anneal below 100°C contrary to what is usually observed in thermal oxides. Implications for design hardening and radiation tests of CMOS Integrated Circuits are discussed

Deciphering the Hybridisation History Leading to the Lager Lineage Based on the Mosaic Genomes of Saccharomyces bayanus Strains NBRC1948 and CBS380T

Saccharomyces bayanus is a yeast species described as one of the two parents of the hybrid brewing yeast S. pastorianus. Strains CBS380T and NBRC1948 have been retained successively as pure-line representatives of S. bayanus. In the present study, sequence analyses confirmed and upgraded our previous finding: S. bayanus type strain CBS380T harbours a mosaic genome. The genome of strain NBRC1948 was also revealed to be mosaic. Both genomes were characterized by amplification and sequencing of different markers, including genes involved in maltotriose utilization or genes detected by array-CGH mapping. Sequence comparisons with public Saccharomyces spp. nucleotide sequences revealed that the CBS380T and NBRC1948 genomes are composed of: a predominant non-cerevisiae genetic background belonging to S. uvarum, a second unidentified species provisionally named S. lagerae, and several introgressed S. cerevisiae fragments. The largest cerevisiae-introgressed DNA common to both genomes totals 70kb in length and is distributed in three contigs, cA, cB and cC. These vary in terms of length and presence of MAL31 or MTY1 (maltotriose-transporter gene). In NBRC1948, two additional cerevisiae-contigs, cD and cE, totaling 12kb in length, as well as several smaller cerevisiae fragments were identified. All of these contigs were partially detected in the genomes of S. pastorianus lager strains CBS1503 (S. monacensis) and CBS1513 (S. carlsbergensis) explaining the noticeable common ability of S. bayanus and S. pastorianus to metabolize maltotriose. NBRC1948 was shown to be inter-fertile with S. uvarum CBS7001. The cross involving these two strains produced F1 segregants resembling the strains CBS380T or NRRLY-1551. This demonstrates that these S. bayanus strains were the offspring of a cross between S. uvarum and a strain similar to NBRC1948. Phylogenies established with selected cerevisiae and non-cerevisiae genes allowed us to decipher the complex hybridisation events linking S. lagerae/S. uvarum/S. cerevisiae with their hybrid species, S. bayanus/pastorianus

Identification and typing of the yeast strains isolated from bili bili, a traditional sorghum beer of Chad

Seventy six yeast strains isolated form bili bili and others sample were identified and typed in purpose of selecting appropriate starter culture. Identification techniques included conventional phenetic method, PCR/RFLP of NTS2 rDNA region, partial sequencing of the D1/D2 region of 26S rDNA and karyotyping using contour clamped homogenous electric field (CHEF) technique. The Saccharomyces cereviseiae strains were also compared to industrial strains according to their fermentation profiles on maltose in the presence of 2- eoxy-D-glucose and to their karyotypes. We observed that the fermentation of bili bili was carried out by an indigenous natural flora predominantly represented by highly polymorphic S. cerevisiae strains whereas early steps in the process were carried out mainly by Kluyveromyces maxianus strains. All of the S. cerevisiae strains which were used in trial fermentation gave a good rate of fermentation suggesting that they may be used as starter cultures.African Journal of Biotechnology Vol. 4 (7), pp. 646-656, 00

Radiation Effects in Pinned Photodiode CMOS Image Sensors: Pixel Performance Degradation Due to Total Ionizing Dose

Several Pinned Photodiode (PPD) CMOS Image Sensors (CIS) are designed, manufactured, characterized and exposed biased to ionizing radiation up to 10 kGy(SiO2 ). In addition to the usually reported dark current increase and quantum efficiency drop at short wavelengths, several original radiation effects are shown: an increase of the pinning voltage, a decrease of the buried photodiode full well capacity, a large change in charge transfer efficiency, the creation of a large number of Total Ionizing Dose (TID) induced Dark Current Random Telegraph Signal (DC-RTS) centers active in the photodiode (even when the Transfer Gate (TG) is accumulated) and the complete depletion of the Pre-Metal Dielectric (PMD) interface at the highest TID leading to a large dark current and the loss of control of the TG on the dark current. The proposed mechanisms at the origin of these degradations are discussed. It is also demonstrated that biasing (i.e., operating) the PPD CIS during irradiation does not enhance the degradations compared to sensors grounded during irradiation

Genomic Exploration of the Hemiascomycetous Yeasts: 7. Saccharomyces servazzii

AbstractThe genome of Saccharomyces servazzii was analyzed with 2570 random sequence tags totalling 2.3 Mb. BLASTX comparisons revealed a minimum of 1420 putative open reading frames with significant homology to Saccharomyces cerevisiae (58% aa identity on average), two with Schizosaccharomyces pombe and one with a human protein, confirming that S. servazzii is closely related to S. cerevisiae. About 25% of the S. servazzii genes were identified, assuming that the gene complement is identical in both yeasts. S. servazzii carries very few transposable elements related to Ty elements in S. cerevisiae. Most of the mitochondrial genes were identified in eight contigs altogether spanning 25 kb for a predicted size of 29 kb. A significant match with the Kluyveromyces lactis linear DNA plasmid pGKL-1 encoded RF4 killer protein suggests that a related plasmid exists in S. servazzii. The sequences have been deposited with EMBL under the accession numbers AL402279–AL404848

Design of Radiation-Hardened Rare-Earth Doped Amplifiers Through a Coupled Experiment/Simulation Approach

We present an approach coupling a limited experimental number of tests with numerical simulations regarding the design of radiation-hardened (RH) rare earth (RE)-doped fiber amplifiers. Radiation tests are done on RE-doped fiber samples in order to measure and assess the values of the principal input parameters requested by the simulation tool based on particle swarm optimization (PSO) approach. The proposed simulation procedure is validated by comparing the calculation results with the measured degradations of two amplifiers made with standard and RH RE-doped optical fibers, respectively. After validation, the numerical code is used to theoretically investigate the influence of some amplifier design parameters on its sensitivity to radiations. Simulations show that the RE-doped fiber length used in the amplifier needs to be adjusted to optimize the amplifier performance over the whole space mission profile rather than to obtain the maximal amplification efficiency before its integration in the harsh environment. By combining this coupled approach with the newly-developed RH RE-doped fibers, fiber-based amplifiers nearly insensitive to space environment may be designed in the future

Genomic Exploration of the Hemiascomycetous Yeasts: 6. Saccharomyces exiguus

AbstractRandom sequence tags were obtained from a genomic DNA library of Saccharomyces exiguus. The mitochondrial genome appeared to be at least 25.7 kb in size, with a different organization compared to Saccharomyces cerevisiae. An unusual putative 953 bp long terminal repeated element associated to Ty3 was found. A set of 1451 genes was identified homologous to S. cerevisiae open reading frames. Only five genes were identified outside the S. cerevisiae taxon, confirming that S. exiguus is phylogenetically closely related to S. cerevisiae. Unexpectedly, numerous duplicated genes were found whereas they are unique in S. cerevisiae. The sequences are deposited at EMBL under the accession numbers: AL407377–AL409955

Investigations on the vulnerability of advanced CMOS technologies to MGy dose environments

This paper investigates the TID sensitivity of silicon-based technologies at several MGy irradiation doses to evaluate their potential for high TID-hardened circuits. Such circuits will be used in several specific applications suc as safety systems of current or future nuclear power plants considering various radiation environments including normal and accidental operating conditions, high energy physics instruments, fusion experiments or deep space missions. Various device designs implemented in well established bulk silicon and Partially Depleted SOI technologies are studied here up to 3 MGy. Furthermore, new insights are given on the vulnerability of more advanced technologies including planar Fully Depleted SOI and multiple-gate SOI transistors at such high dose. Potential of tested technologies are compared and discussed for stand-alone integrated circuits