Quantum cascade lasers monolithically integrated on germanium

Silicon (Si) photonics can have a major impact on the development of mid-IR photonics by leveraging on the reliable and high-volume fabrication technologies already developed for microelectronic integrated circuits. Germanium (Ge), already used in Si photonics, is a prime candidate to extend the operating wavelength of Group IV-based photonic integrated circuits beyond 8 µm, and potentially up to 15 µm. High performance quantum cascade lasers (QCLs) and interband cascade lasers grown on Si have been demonstrated, whereas no QCLs monolithically integrated on Ge have been reported yet. In this work, we present InAs-based QCLs directly grown on Ge by molecular beam epitaxy. The lasers emitting near 14 µm exhibited threshold current densities as low as 0.8-0.85 kA/cm² at room temperature.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

III-V-on-silicon integrated micro - spectrometer for the 3 μm wavelength range

A compact (1.2 mm²) fully integrated mid-IR spectrometer operating in the 3 μm wavelength range is presented. To our knowledge this is the longest wavelength integrated spectrometer operating in the important wavelength window for spectroscopy of organic compounds. The spectrometer is based on a silicon-on-insulator arrayed waveguide grating filter. An array of InAs_0.91Sb_0.09 p-i-n photodiodes is heterogeneously integrated on the spectrometers output grating couplers using adhesive bonding. The spectrometer insertion loss is less than 3 dB and the waveguide-referred responsivity of the integrated photodiodes at room temperature is 0.3 A/W.

Silicon-on-insulator shortwave infrared wavelength meter with integrated photodiodes for on-chip laser monitoring

This paper demonstrates a very compact wavelength meter for on-chip laser monitoring in the shortwave infrared wavelength range based on an optimized arrayed waveguide grating (AWG) filter with an integrated photodiode array. The AWG response is designed to obtain large nearest neighbor crosstalk (i.e. large overlap) between output channels, which allows accurately measuring the wavelength of a laser under test using the centroid detection technique. The passive AWG is fabricated on a 220 nm silicon-on-insulator (SOI) platform and is combined with GaInAsSb-based photodiodes. The photodiodes are heterogeneously integrated on the output grating couplers of the AWG using DVS-BCB adhesive bonding. The complete device with AWG and detectors has a footprint of only 2 mm(2) while the measured accuracy and resolution of the detected wavelength is better than 20pm.

Silicon-on-insulator spectrometers with integrated GaInAsSb photodiodes for wide-band spectroscopy from 1510 to 2300 nm

We present a silicon-on-insulator (SOI) based spectrometer platform for a wide operational wavelength range. Both planar concave grating (PCG, also known as echelle grating) and arrayed waveguide grating (AWG) spectrometer designs are explored for operation in the short-wave infrared. In addition, a total of four planar concave gratings are designed to cover parts of the wavelength range from 1510 to 2300 nm. These passive wavelength demultiplexers are combined with GaInAsSb photodiodes. These photodiodes are heterogeneously integrated on SOI with benzocyclobutene (DVS-BCB) as an adhesive bonding layer. The uniformity of the photodiode characteristics and high processing yield, indicate a robust fabrication process. We demonstrate good performance of the miniature spectrometers over all operational wavelengths which paves the way to on-chip absorption spectroscopy in this wavelength range.

Specific molecular targets to control tropical diseases

Chagas' disease or American trypanosomiasis is considered by the Word Health Organization to be one of the important tropical parasitic diseases worldwide together with malaria and schistosomiasis. The etiologic agent of this illness is the kinetoplastid protozoon Trypanosoma cruzi. The present chemotherapy for the treatment of Chagas' disease remains unsolved. The drugs currently in use are old, ineffective and toxic. Bearing in mind the metabolic differences between the parasite and the mammalian host, some attractive interesting molecular targets for drug design are presented.

Bisphosphonates derived from fatty acids are potent growth inhibitors of Trypanosoma cruzi

We have investigated the effect of a series of bisphosphonates derived from fatty acids against Trypanosoma cruzi proliferation in in vitro assays. Some of these drugs proved to be potent inhibitors against the intracellular form of the parasite exhibiting IC50 values at the low micromolar level. As bisphosphonates are FDA clinically approved for treatment of bone resorption, their potential innocuousness makes them good candidates to control tropical diseases.

Design and synthesis of aryloxyethyl thiocyanate derivatives as potent inhibitors of Trypanosoma cruzi proliferation

As a part of our project directed at the search of new chemotherapeutic agents against American trypanosomiasis (Chagas' disease), several drugs possessing the 4-phenoxyphenoxy skeleton and other closely related structures employing the thiocyanate moiety as polar end group were designed, synthesized, and evaluated as antiproliferative agents against Trypanosoma cruzi, the parasite responsible for this disease. These thiocyanate analogues were envisioned bearing in mind the potent activity shown by 4-phenoxyphenoxyethyl thiocyanate (compound 8) taken as lead drug. This compound had previously proved to be an extremely active growth inhibitor against T. cruzi with IC(50) values ranging from the very low micromolar level in epimastigotes to the low nanomolar level in the intracellular form of the parasite. Of the designed compounds, the ethyl thiocyanate drugs connected to nonpolar skeletons, namely, arylthio, 2,4-dichlorophenoxy, ortho-substituted aryloxy, and 2-methyl-4-phenoxyphenoxy (compounds 15, 34, 47, 52, 72, respectively), were shown to be very potent antireplicative agents against T. cruzi. On the other hand, conformationally restricted analogues as well as branched derivatives at the aliphatic side chain were shown to be moderately active against T. cruzi growth. The biological activity of drugs bearing the thiocyanate group correlated quite well with the activity exhibited by their normal precursors, the tetrahydropyranyl ether derivatives, when bonded to the same nonpolar skeleton. Compounds having the tetrahydropyranyl moeity as polar end were proportionally much less active than sulfur-containing derivatives in all cases. Drugs 47 and 72 also resulted to be very active against the amastigote form of the parasite growing in myoblasts; however, they were slightly less active than the lead drug 8. On the other hand, compounds 34 and 52 were almost devoid of activity against myoblasts. Surprisingly, the dithio derivative 15 was toxic for myoblasts.

Sulphur-containing derivatives structurally related to fenoxycarb are potent growth inhibitors against the intracellular form of Trypanosoma cruzi

Sulphur-containing derivatives structurally related to the insect growth regulator fenoxycarb were shown to be extremely active antiproliferative agents against the amastigote form of Trypanosoma cruzi in in vitro assays. All of these drugs had previously been proved to be remarkably potent growth inhibitors against the epimastigote form of the parasite.

Synthesis of C-5'-nor-dideoxycarbanucleosides structurally related to neplanocin C

Purine carbanucleosides built on a 6-oxabicyclo[3.1.0]hexane template were synthesized from readily available 2-cyclopentenone employing a Mitsunobu reaction to incorporate the base onto the carbocyclic ring. Both adenosine and guanosine analogues exhibited moderate antiviral activity.

Growth inhibitory effect of juvenile hormone analogues on epimastigotes of Trypanosoma cruzi

Several compounds, structurally related to the insect growth regulator Fenoxycarb, exhibited interesting inhibition action to control proliferation of Trypanosoma cruzi, the parasite responsible for Chagas' disease. Some of these drugs were shown to be potent growth inhibitors of this parasite. All of these drugs had previously presented juvenoid activity on several non-related bug species such as Tenebrio molitor, Galleria mellonella, Dysdercus cingulatos, and Pyrrhocoris apterus.

Structure-activity relationship of new growth inhibitors of Trypanosoma cruzi

Several drugs bearing the 4-phenoxyphenoxy skeleton and other closely related structures were designed, synthesized, and evaluated as antiproliferative agents against Trypanosoma cruzi, the etiologic agent of Chagas' disease. The new class of drugs was envisioned by modifying the nonpolar 4-phenoxyphenoxy moiety replacing selected aromatic protons by different groups via electrophilic aromatic substitution reactions as well as introducing a sulfur atom at the polar extreme. Of the designed compounds, sulfur-containing derivatives were shown to be potent antireplicative agents against T. cruzi. Among these drugs, 4-phenoxyphenoxyethyl thiocyanate (compound 56) proved to be an extremely active growth inhibitor of the epimastigote forms of T. cruzi and displayed an IC50 of 2.2 microM. Under the same assay conditions, this drug was much more active than Nifurtimox, one of the drugs currently in clinical use to control this disease. This thiocyanate derivative was also a very active inhibitor against the intracellular form of the parasite at the nanomolar level. Other sulfur derivatives prepared also exhibited very potent antiproliferative action against T. cruzi. The presence of a sulfur atom at the polar extreme for this family of compounds seems to be very important for biological action because this atom was always associated with high inhibition values. 4-Phenoxyphenoxyethyl thiocyanate presents very good prospective not only as a lead drug but also as a potential chemotherapeutic agent.

Design, synthesis, and biological evaluation of new growth inhibitors of Trypanosoma cruzi (epimastigotes)

As a continuation of our project aimed at the search for new chemotherapeutic agents against Chagas' disease, several drugs structurally related to the insect growth regulator Fenoxycarb and the naturally occurring juvenile hormone of insects were designed, synthesized, and evaluated as antiproliferative agents against the parasite responsible of this disease. Isoprenoid derivatives (compounds 33, 34, 36, and 37) were potent growth inhibitors of Trypanosoma cruzi epimastigotes. In addition, taking into account the high activity observed for compound 30 and the inhibitory action of related compounds, the allyl ether moiety bonded at the polar extreme of these inhibitors proved to be a promising group for the design of new drugs.

The sterols of Cucurbita moschata ("calabacita") seed oil

From the sterol fraction of seed oil from commercial Cucurbita moschata Dutch ("calabacita") delta 5 and delta 7 sterols having saturated and unsaturated side chain were isolated by chromatographic procedures and characterized by spectroscopic (1H and 13C-nuclear magnetic resonance, mass spectrometry) methods. The main components were identified as 24S-ethyl 5 alpha-cholesta-7,22E-dien-3 beta-ol (alpha-spinasterol); 24S-ethyl 5 alpha-cholesta-7,22E,25-trien-3 beta-ol (25-dehydrochondrillasterol); 24S-ethyl 5 alpha-cholesta-7,25-dien-3 beta-ol; 24R-ethyl-cholesta-7-en-3 beta-ol (delta 7-stigmastenol) and 24-ethyl-cholesta-7, 24(28)-dien-3 beta-ol (delta 7,24(28)-stigmastadienol).

Effects of juvenile hormone analogues (JHA) on the development of Trypanosoma cruzi

Juvenile hormone analogues were tested for their lytic activity on Trypanosoma cruzi Chagas, 1909 blood tripomastigotes cultivated in vitro. The results indicated that the carbamate 4 and the phenoxyphenol derivative 1 are considered good candidates for blood sterilization. The compounds were also assayed for inhibition of development of parasites in infected mice showing a moderated degree of activity.

Conformationally locked nucleoside analogues. Synthesis of dideoxycarbocyclic nucleoside analogues structurally related to neplanocin C

The glycon moiety of nucleosides in solution is known to exist in a rapid dynamic equilibrium between extreme northern and southern conformations as defined by the pseudorotation cycle. The concept of preparing rigid nucleoside analogues with the glycon conformation locked in one of these two extremes was tested with the synthesis of some cyclopropane-fused dideoxycarbocyclic nucleosides, similar to the well-known class of anti-HIV active dideoxynucleosides. The new compounds described here are dideoxynucleoside analogues of the fermentation product neplanocin C (6) which exhibits a typical northern geometry for its 6-oxabicyclo[3.1.0]hexane pseudosugar moiety. However, in view of the lability of the epoxide ring in this system, the equivalent cyclopropane-fused bicyclo[3.1.0]hexane system was used instead to prepare the corresponding dideoxynucleoside analogues bearing all the common bases [(+/-)-9-13]. Due to the well-documented preference of unrestricted bicyclo[3.1.0]hexane systems to exist exclusively in a boat conformation, the resulting nucleosides are structurally locked in a typical northern conformation similar to that of neplanocin C. The locked northern conformation in these nucleosides remained unchanged in solution in the 20-80 degrees C temperature range according to variable temperature 1H NMR studies. For the synthesis of these compounds, racemic trans-1-[(benzyloxy)methyl]-4-hydroxybicyclo[3.1.0]hexane [(+/-)-18] was prepared by a samarium-promoted cyclopropanation reaction with the antecedent cyclopentenol. All of the bases were incorporated under Mitsunobu conditions and converted to the desired final products following a standard methodology. Anti-HIV evaluation revealed that only the adenosine analogue (+/-)-9 possessed enough activity to warrant resolution into its optical antipodes. This was realized by chiral HPLC chromatography to give the individual enantiomers (-)-32 and (+)-33. Adenosine deaminase was used to identify isomer (+)-33 as the enantiomer with the "natural" configuration which was solely responsible for the observed biological activity and toxicity of (+/-)-9. It is possible that the exclusive northern conformation adopted by these nucleosides reduces their substrate affinity for the various activating kinases, except in the case of the adenosine analogue.

Effects of juvenile hormone on mammalian steroidogenesis

The effects of juvenile hormone-III (JH-III) and the JH analogue 2-(4-phenoxyphenoxy)-ethoxyte-trahydropiran on testicular steroidogenesis were studied. By using cultured MA-10 Leydig tumor cells as a model, these compounds were found to be potent inhibitors of LH/hCG steroidogenic action in a dose-dependent manner. Scatchard plot analysis of the binding data indicated that the JH analogue did not significantly alter the affinity nor the number of hCG binding sites, as well as GTP binding to plasma membranes. JH analogue inhibited the stimulatory action of both cholera toxin and forskolin on cAMP production and the concomitant steroidogenic response. JH analogue inhibited (Bu)2cAMP-stimulated progesterone synthesis, indicating that a process downstream to the adenylyl cyclase in the steroidogenic pathway is also affected.

Gas chromatographic-mass spectrometric method for the assessment of oxidative damage to double-stranded dna by quantification of thymine glycol residues

A technique for the measurement of thymine glycol at parts per million concentrations in double-stranded polymeric DNA is described. The procedure utilizes base to ring-open DNA-bound thymine glycol in the presence of monomeric [(2)H4]thymine glycol as an internal standard, followed by reduction, solvolytic cleavage, and quantification of the characteristic methyl-2-methylglycerate released from polymeric DNA. Methyl-2-methyl-glycerate is derivatized to form the di-tert-butyldimethylsilyl [(TBDMS)2] ether to enhance its gas chromatographic properties and electron ionization detection. This assay was tested by measuring thymine gIyco1 levels in native, undamaged DNA (not purposefully oxidized). The measured quantities of thymine glycol are proportional to the amount of DNA analyzed. Components of DNA not containing oxidizable thymine do not contribute to the measured signal from methyl-2-methylglycerate-(TBDMS)2. These results indicate that there is approximately one thymine glycol per lo6 bases in undamaged DNA and that this value increases with storage of DNA in refrigerated aqueous solutions.