Nanostructured 3C-SiC on Si by a network of (111) platelets: a fully textured film generated by intrinsic growth anisotropy.

In this paper, we address the unique nature of fully textured, high surface-to-volume 3C-SiC films, as produced by intrinsic growth anisotropy, in turn generated by the high velocity of the stacking fault growth front in two-dimensional (111) platelets. Structural interpretation of high resolution scanning electron microscopy and transmission electron microscopy data is carried out for samples grown in a hot-wall low-pressure chemical vapour deposition reactor with trichlorosilane and ethylene precursors, under suitable deposition conditions. By correlating the morphology and the X-ray diffraction analysis we also point out that twinning along (111) planes is very frequent in such materials, which changes the free-platelet configuration.

TRPML1 links lysosomal calcium to autophagosome biogenesis through the activation of the CaMKKß/VPS34 pathway.

The lysosomal calcium channel TRPML1, whose mutations cause the lysosomal storage disorder (LSD) mucolipidosis type IV (MLIV), contributes to upregulate autophagic genes by inducing the nuclear translocation of the transcription factor EB (TFEB). Here we show that TRPML1 activation also induces autophagic vesicle (AV) biogenesis through the generation of phosphatidylinositol 3-phosphate (PI3P) and the recruitment of essential PI3P-binding proteins to the nascent phagophore in a TFEB-independent manner. Thus, TRPML1 activation of phagophore formation requires the calcium-dependent kinase CaMKKß and AMPK, which increase the activation of ULK1 and VPS34 autophagic protein complexes. Consistently, cells from MLIV patients show a reduced recruitment of PI3P-binding proteins to the phagophore during autophagy induction, suggesting that altered AV biogenesis is part of the pathological features of this disease. Together, we show that TRPML1 is a multistep regulator of autophagy that may be targeted for therapeutic purposes to treat LSDs and other autophagic disorders.

Ultra-wideband Ge-rich silicon germanium mid-infrared polarization rotator with mode hybridization flattening.

In this work we investigate the implementation of ultra-wideband polarization rotator in the mid-infrared spectral region. A new design method of the rotation section is proposed, yielding a polarization rotator with an extinction ratio of at least 15 dB in a wavelength range of 2 µm. For a spectral range wider than 3.8 µm, an extinction ratio of at least 10 dB is achieved for this design. The device is 1660 µm long and the associated insertion loss is below 1.2 dB on the full operational wavelength range. The influence of geometrical parameters with respect to the design method to obtain such a broadband behavior is discussed. Finally, to increase the tolerance to fabrication errors, a tapered rotator design is proposed. Such a device can support up to ± 100 nm fabrication errors and still guarantees remarkable broadband behavior. To the best of our knowledge, this is the first time an integrated polarization rotator is designed to operate for the wavelength range of 4 to 9 µm with a bandwidth exceeding 2 µm.

Voltage-tunable dual-band Ge/Si photodetector operating in VIS and NIR spectral range.

Extending and controlling the spectral range of light detectors is very appealing for several sensing and imaging applications. Here we report on a normal incidence dual band photodetector operating in the visible and near infrared with a bias tunable spectral response. The device architecture is a germanium on silicon epitaxial structure made of two back-to-back connected photodiodes. The photodetectors show a broad photoresponse extending from 390nm to 1600nm with the capability to electronically select the shorter (400-1100 nm) or the longer (1000-1600 nm) portion with a relatively low applied voltage. Devices exhibit peak VIS and NIR responsivities of 0.33 and 0.63 A/W, respectively, a low optical crosstalk (<-30dB), a wide dynamic range (>120dB) and, thanks to their low voltage operation, maximum specific detectivities of 7·1011cmHz1/2/W and 2·1010cmHz1/2/W in the VIS and NIR, respectively.

Composition determination of semiconductor alloys towards atomic accuracy by HAADF-STEM.

This paper presents a comprehensive investigation of an extended method to determine composition of materials by scanning transmission electron microscopy (STEM) high angle annular darkfield (HAADF) images and using complementary multislice simulations. The main point is to understand the theoretical capabilities of the algorithm and address the intrinsic limitations of using STEM HAADF intensities for composition determination. A special focus is the potential of the method regarding single-atom accuracy. All-important experimental parameters are included into the multislice simulations to ensure the best possible fit between simulation and experiment. To demonstrate the capabilities of the extended method, results for three different technical important semiconductor samples are presented. Overall the method shows a high lateral resolution combined with a high accuracy towards single-atom accuracy.

Graded SiGe waveguides with broadband low-loss propagation in the mid infrared.

Mid-infrared (mid-IR) silicon photonics is expected to lead key advances in different areas including spectroscopy, remote sensing, nonlinear optics or free-space communications, among others. Still, the inherent limitations of the silicon-on-insulator (SOI) technology, namely the early mid-IR absorption of silicon oxide and silicon at λ~3.6 µm and at λ ~8.5 µm respectively, remain the main stumbling blocks that prevent this platform to fully exploit the mid-IR spectrum (λ ~2-20 µm). Here, we propose using a compact Ge-rich graded-index Si1-xGex platform to overcome this constraint. A flat propagation loss characteristic as low as 2-3 dB/cm over a wavelength span from λ = 5.5 µm to 8.5 µm is demonstrated in Ge-rich Si1-xGex waveguides of only 6 µm thick. The comparison of three different waveguides design with different vertical index profiles demonstrates the benefit of reducing the fraction of the guided mode that overlaps with the Si substrate to obtain such flat low loss behavior. Such Ge-rich Si1-xGex platforms may open the route towards the implementation of mid-IR photonic integrated circuits with low-loss beyond the Si multi-phonon absorption band onset, hence truly exploiting the full Ge transparency window up to λ ~15 µm.

Ge-rich graded-index Si1-xGex waveguides with broadband tight mode confinement and flat anomalous dispersion for nonlinear mid-infrared photonics.

This work explores the use of Ge-rich graded-index Si1-xGex rib waveguides as building blocks to develop integrated nonlinear optical devices for broadband operation in the mid-IR. The vertical Ge gradient concentration in the waveguide core renders unique properties to the guided optical mode, providing tight mode confinement over a broadband mid-IR wavelength range from λ = 3 µm to 8 µm. Additionally, the gradual vertical confinement pulls the optical mode upwards in the waveguide core, overlapping with the Ge-rich area where the nonlinear refractive index is larger. Moreover, the Ge-rich graded-index Si1-xGex waveguides allow efficient tailoring of the chromatic dispersion curves, achieving flat anomalous dispersion for the quasi-TM optical mode with D ≤ 14 ps/nm/km over a ~1.4 octave span while retaining an optimum third-order nonlinear parameter, γeff. These results confirm the potential of Ge-rich graded-index Si1-xGex waveguides as an attractive platform to develop mid-IR nonlinear approaches requiring broadband dispersion engineering.

Methods to Monitor and Manipulate TFEB Activity During Autophagy.

Macroautophagy is a catabolic process deputed to the turnover of intracellular components. Recent studies have revealed that transcriptional regulation is a major mechanism controlling autophagy. Currently, more than 20 transcription factors have been shown to modulate cellular autophagy levels. Among them, the transcription factor EB (TFEB) appears to have the broadest proautophagy role, given its capacity to control the biogenesis of lysosomes and autophagosomes, the two main organelles required for the autophagy pathway. TFEB has attracted major attention owing to its ability to enhance cellular clearance of pathogenic substrates in a variety of animal models of disease, such as lysosomal storage disorders, Parkinson's, Alzheimer's, α1-antitrypsin, obesity as well as others, suggesting that the TFEB pathway represents an extraordinary possibility for future development of innovative therapies. Importantly, the subcellular localization and activity of TFEB are regulated by its phosphorylation status, suggesting that TFEB activity can be pharmacologically targeted. Given the growing list of common and rare diseases in which manipulation of autophagy may be beneficial, in this chapter we describe a set of validated protocols developed to modulate and analyze TFEB-mediated enhancement of autophagy both in vitro and in vivo conditions.

Analysis of Ge micro-cavities with in-plane tensile strains above 2.

Ge on Si micro-disk, ring and racetrack cavities are fabricated and strained using silicon nitride stressor layers. Photoluminescence measurements demonstrate emission at wavelengths ≥ 2.3 µm, and the highest strained samples demonstrate in-plane, tensile strains of > 2 %, as measured by Raman spectroscopy. Strain analysis of the micro-disk structures demonstrate that shear strains are present in circular cavities, which can detrimentally effect the carrier concentration for direct band transitions. The advantages and disadvantages of each type of proposed cavity structure are discussed.

Disease pathogenesis explained by basic science: lysosomal storage diseases as autophagocytic disorders.

Lysosomal storage diseases (LSDs) are characterized by intra-lysosomal accumulation of undegraded metabolites due to the defective activity of lysosomal enzymes. There is a paucity of data, however, relating to the mechanisms that link this accumulation with disease pathology. Several LSDs can be attributed to deficiencies in the activity of sulfatase enzymes. The gene responsible for the post-translational modification that activates sulfatases, sulfatase modifying factor 1 (SUMF1), is defective in the rare autosomal recessive disorder multiple sulfatase deficiency (MSD). A mouse model of MSD (Sumf1 knockout mouse) exhibits a similar phenotype to patients with MSD, with marked lysosomal storage of undegraded metabolites, and increased expression of inflammatory markers and apoptotic markers. Investigation of disease pathology in mouse models of two LSDs (MSD and mucopolysaccharidosis (MPS) Type IIIA) has revealed an increased number of autophagosomes in these animals compared with wild-type mice. This appears to result from impaired autophagosome-lysosome fusion, which may in turn lead to an absence of autophagy. The suggestion that LSDs can be defined as disorders of autophagy implies that there may be some overlap between pathological mechanisms of LSDs and more common neurodegenerative diseases, and this may help provide direction for future therapeutic strategies.

Safety of arylsulfatase A overexpression for gene therapy of metachromatic leukodystrophy.

Successful gene therapy approaches for metachromatic leukodystrophy (MLD), based either on hematopoietic stem/progenitor cells (HSPCs) or direct central nervous system (CNS) gene transfer, highlighted a requirement for high levels of arylsulfatase A (ARSA) expression to achieve correction of disease manifestations in the mouse model. Full assessment of the safety of ARSA expression above physiological levels thus represents a prerequisite for clinical translation of these approaches. Here, using lentiviral vectors (LVs), we generated two relevant models for the stringent evaluation of the consequences of ARSA overexpression in transduced cells. We first demonstrated that ARSA overexpression in human HSPCs does not affect their clonogenic and multilineage differentiation capacities in clonogenic assays and in a neonatal hematochimeric mouse model. Further, we studied ARSA overexpression in all body tissues by generating transgenic mice overexpressing the ARSA enzyme by LV up to 15-fold above the normal range and carrying multiple copies of LV in their genome. Characterization of these mice demonstrated the safety of ARSA overexpression in two main gene therapy targets, HSPCs and neurons, with maintenance of the complex functions of the hematopoietic and nervous system in the presence of supraphysiological enzyme levels. The activity of other sulfatases dependent on the same common activator, sulfatase-modifying factor-1 (SUMF1), was tested in ARSA-overexpressing HSPCs and in transgenic mice, excluding the occurrence of saturation phenomena. Overall, these data indicate that from the perspective of clinical translation, therapeutic levels of ARSA overexpression can be safely achieved. Further, they demonstrate an experimental platform for the preclinical assessment of the safety of new gene therapy approaches.

Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship.

Sulfatases catalyze the hydrolysis of sulfate ester bonds from a wide variety of substrates. Several human inherited diseases are caused by the deficiency of individual sulfatases, while in patients with multiple sulfatase deficiency mutations in the Sulfatase Modifying Factor 1 (SUMF1) gene cause a defect in the post-translational modification of a cysteine residue into C(alpha)-formylglycine (FGly) at the active site of all sulfatases. This unique modification mechanism, which is required for catalytic activity, has been highly conserved during evolution. Here, we used a genomic approach to investigate the relationship between sulfatases and their modifying factors in humans and several model systems. First, we determined the complete catalog of human sulfatases, which comprises 17 members (versus 14 in rodents) including four novel ones (ARSH, ARSI, ARSJ and ARSK). Secondly, we showed that the active site, which is the target of the post-translational modification, is the most evolutionarily constrained region of sulfatases and shows intraspecies sequence convergence. Exhaustive sequence analyses of available proteomes indicate that sulfatases are the only likely targets of their modifying factors. Thirdly, we showed that sulfatases and ectonucleotide pyrophosphatases share significant homology at their active sites, suggesting a common evolutionary origin as well as similar catalytic mechanisms. Most importantly, gene association studies performed on prokaryotes suggested the presence of at least two additional mechanisms of cysteine-to-FGly conversion, which do not require SUMF1. These results may have important implications in the study of diseases caused by sulfatase deficiencies and in the development of therapeutic strategies.

Molecular cloning and characterization of NEU4, the fourth member of the human sialidase gene family.

Several mammalian sialidases have been cloned so far and here we describe the identification and expression of a new member of the human sialidase gene family. The NEU4 gene, identified by searching sequence databases for entries showing homologies to the human cytosolic sialidase NEU2, maps in 2q37 and encodes a 484-residue protein. The polypeptide contains all the typical sialidase amino acid motifs and, apart from an amino acid stretch that appears unique among mammalian sialidases, shows a high degree of homology for NEU2 and the plasma membrane-associated (NEU3) sialidases. RNA dot-blot analysis showed a low but wide expression pattern, with the highest level in liver. Transient transfection in COS7 cells allowed the detection of a sialidase activity toward the artificial substrate 4MU-NeuAc in the acidic range of pH. Immunofluorescence staining and Western blot analysis demonstrated the association of NEU4 with the inner cell membranes.

Amplification and overexpression of PRUNE in human sarcomas and breast carcinomas-a possible mechanism for altering the nm23-H1 activity.

PRUNE, the human homologue of the Drosophila gene, is located in 1q21.3, a region highly amplified in human sarcomas, malignant tumours of mesenchymal origin. Prune protein interacts with the metastasis suppressor nm23-H1, but shows impaired affinity towards the nm23-H1 S120G mutant associated with advanced neuroblastoma. Based on these observations, we previously suggested that prune may act as a negative regulator of nm23-H1 activity. We found amplification of PRUNE in aggressive sarcoma subtypes, such as leiomyosarcomas and malignant fibrous histiocytomas (MFH) as well as in the less malignant liposarcomas. PRUNE amplification was generally accompanied by high mRNA and moderate to high protein levels. The sarcoma samples expressed nm23-H1 mostly at low or moderate levels, whereas mRNA and protein levels were moderate to high in breast carcinomas. For the more aggressive sarcoma subtypes, 9/13 patients with PRUNE amplification developed metastases. A similar situation was observed in all breast carcinomas with amplification of PRUNE. Infection of NIH3T3 cells with a PRUNE recombinant retrovirus increased cell proliferation. Possibly, amplification and overexpression of PRUNE has the same effect in the tumours. We suggest that amplification and overexpression of PRUNE could be a mechanism for inhibition of nm23-H1 activity that affect the development or progression of these tumours.

Linkage mapping of a nonspecific form of X-linked mental retardation (MRX53) in a large Pakistani family.

Nonspecific X-linked mental retardation is a nonprogressive, genetically heterogeneous condition that affects cognitive function in the absence of other distinctive clinical manifestations. We report here linkage data on a large Pakistani family affected by a form of X-linked nonspecific mental retardation. X chromosome genotyping of family members and linkage analysis allowed the identification of a new disease locus, MRX53. The defined critical region spans approximately 15 cM between DXS1210 and DXS1047 in Xq22.2-26. A LOD score value of 3.34 at no recombination was obtained with markers DXS1072 and DXS8081.

The tripartite motif family identifies cell compartments.

A functional genomic approach, based on systematic data gathering, was used to characterize a family of proteins containing a tripartite motif (TRIM). A total of 37 TRIM genes/proteins were studied, 21 of which were novel. The results demonstrate that TRIM proteins share a common function: by means of homo-multimerization they identify specific cell compartments.

WBSCR14, a gene mapping to the Williams--Beuren syndrome deleted region, is a new member of the Mlx transcription factor network.

Williams-Beuren syndrome (WBS) is a developmental disorder associated with haploinsufficiency of multiple genes at 7q11.23. Here, we report the functional characterization of WBS critical region gene 14 (WBSCR14), a gene contained in the WBS commonly deleted region. It encodes a basic-helix--loop--helix leucine zipper (bHLHZip) transcription factor of the Myc/Max/Mad superfamily. WBSCR14 is expressed in multiple tissues, including regions of the brain and the intestinal tract. WBSCR14 forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence CACGTG. Like Max, Mlx has no intrinsic transcriptional activity, but its association with Mad1, Mad4, Mnt or WBSCR14 can repress E-box-dependent transcription. Preliminary results suggest a possible role of WBSCR14 in growth control. Our data support the view that the Max-like bHLHZip protein, Mlx, is a key element of a transcription factor network. We thus suggest that WBSCR14 may contribute to some aspects of the WBS pathology.

Identification of the gene for oral-facial-digital type I syndrome.

Oral-facial-digital type 1 syndrome (OFD1 [MIM 311200]) is transmitted as an X-linked dominant condition with lethality in males and is characterized by malformations of the face, oral cavity, and digits, and by a highly variable expressivity even within the same family. Malformation of the brain and polycystic kidneys are commonly associated with this disorder. The locus for OFD1 was mapped by linkage analysis to a 12-Mb interval, flanked by markers DXS85 and DXS7105 in the Xp22 region. To identify the gene responsible for this syndrome, we analyzed several transcripts mapping to the region and found mutations in OFD1 (formerly named "Cxorf5/71-7a"), encoding a protein containing coiled-coil alpha-helical domains. Seven patients with OFD1, including three with familial and four with sporadic cases, were analyzed. Analysis of the familial cases revealed a missense mutation, a 19-bp deletion, and a single base-pair deletion leading to a frameshift. In the sporadic cases, we found a missense (de novo), a nonsense, a splice, and a frameshift mutation. RNA in situ studies on mouse embryo tissue sections show that Ofd1 is developmentally regulated and is expressed in all tissues affected in OFD1 syndrome. The involvement of OFD1 in oral-facial-digital type I syndrome demonstrates an important role of this gene in human development.

Functional analysis of mutations in SLC7A9, and genotype-phenotype correlation in non-Type I cystinuria.

Cystinuria (OMIM 220100) is a common recessive disorder of renal reabsorption of cystine and dibasic amino acids that results in nephrolithiasis of cystine. Mutations in SLC3A1, which encodes rBAT, cause Type I cystinuria, and mutations in SLC7A9, which encodes a putative subunit of rBAT (b(o,+)AT), cause non-Type I cystinuria. Here we describe the genomic structure of SLC7A9 (13 exons) and 28 new mutations in this gene that, together with the seven previously reported, explain 79% of the alleles in 61 non-Type I cystinuria patients. These data demonstrate that SLC7A9 is the main non-Type I cystinuria gene. Mutations G105R, V170M, A182T and R333W are the most frequent SLC7A9 missense mutations found. Among heterozygotes carrying these mutations, A182T heterozygotes showed the lowest urinary excretion values of cystine and dibasic amino acids. Functional analysis of mutation A182T after co-expression with rBAT in HeLa cells revealed significant residual transport activity. In contrast, mutations G105R, V170M and R333W are associated to a complete or almost complete loss of transport activity, leading to a more severe urinary phenotype in heterozygotes. SLC7A9 mutations located in the putative transmembrane domains of b(o,+)AT and affecting conserved amino acid residues with a small side chain generate a severe phenotype, while mutations in non-conserved residues give rise to a mild phenotype. These data provide the first genotype-phenotype correlation in non-Type I cystinuria, and show that a mild urinary phenotype in heterozygotes may associate with mutations with significant residual transport activity.