Integrated micro fuel cells with on-board hydride reactors and autonomous control schemes

Miniaturization of power generators to the MEMS scale, based on the hydrogen-air fuel cell, is the object of this research. The micro fuel cell approach has been adopted for advantages of both high power and energy densities. On-board hydrogen production/storage and an efficient control scheme that facilitates integration with a fuel cell membrane electrode assembly (MEA) are key elements for micro energy conversion. Millimeter-scale reactors (ca. 10 µL) have been developed, for hydrogen production through hydrolysis of CaH2 and LiAlH4, to yield volumetric energy densities of the order of 200 Whr/L. Passive microfluidic control schemes have been implemented in order to facilitate delivery, self-regulation, and at the same time eliminate bulky auxiliaries that run on parasitic power. One technique uses surface tension to pump water in a microchannel for hydrolysis and is self-regulated, based on load, by back pressure from accumulated hydrogen acting on a gas-liquid microvalve. This control scheme improves uniformity of power delivery during long periods of lower power demand, with fast switching to mass transport regime on the order of seconds, thus providing peak power density of up to 391.85 W/L. Another method takes advantage of water recovery by backward transport through the MEA, of water vapor that is generated at the cathode half-cell reaction. This regulation-free scheme increases available reactor volume to yield energy density of 313 Whr/L, and provides peak power density of 104 W/L. Prototype devices have been tested for a range of duty periods from 2-24 hours, with multiple switching of power demand in order to establish operation across multiple regimes. Issues identified as critical to the realization of the integrated power MEMS include effects of water transport and byproduct hydrate swelling on hydrogen production in the micro reactor, and ambient relative humidity on fuel cell performance.

Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes

The exocarp, or skin, of fleshy fruit is a specialized tissue that protects the fruit, attracts seed dispersing fruit eaters, and has large economical relevance for fruit quality. Development of the exocarp involves regulated activities of many genes. This research analyzed global gene expression in the exocarp of developing sweet cherry (Prunus avium L., 'Regina'), a fruit crop species with little public genomic resources. A catalog of transcript models (contigs) representing expressed genes was constructed from de novo assembled short complementary DNA (cDNA) sequences generated from developing fruit between flowering and maturity at 14 time points. Expression levels in each sample were estimated for 34 695 contigs from numbers of reads mapping to each contig. Contigs were annotated functionally based on BLAST, gene ontology and InterProScan analyses. Coregulated genes were detected using partitional clustering of expression patterns. The results are discussed with emphasis on genes putatively involved in cuticle deposition, cell wall metabolism and sugar transport. The high temporal resolution of the expression patterns presented here reveals finely tuned developmental specialization of individual members of gene families. Moreover, the de novo assembled sweet cherry fruit transcriptome with 7760 full-length protein coding sequences and over 20 000 other, annotated cDNA sequences together with their developmental expression patterns is expected to accelerate molecular research on this important tree fruit crop.

Next-generation sequencing of hereditary hemochromatosis-related genes: novel likely pathogenic variants found in the Portuguese population

Hereditary hemochromatosis (HH) is an autosomal recessive disorder characterized by excessive iron absorption resulting in pathologically increased body iron stores. It is typically associated with common HFE gene mutation (p.Cys282Tyr and p.His63Asp). However, in Southern European populations up to one third of HH patients do not carry the risk genotypes. This study aimed to explore the use of next-generation sequencing (NGS) technology to analyse a panel of iron metabolism-related genes (HFE, TFR2, HJV, HAMP, SLC40A1, and FTL) in 87 non-classic HH Portuguese patients. A total of 1241 genetic alterations were detected corresponding to 53 different variants, 13 of which were not described in the available public databases. Among them, five were predicted to be potentially pathogenic: three novel mutations in TFR2 [two missense (p.Leu750Pro and p.Ala777Val) and one intronic splicing mutation (c.967-1GNC)], one missense mutation in HFE (p.Tyr230Cys), and one mutation in the 5′-UTR of HAMP gene(c.-25GNA). The results reported here illustrate the usefulness of NGS for targeted iron metabolism-related gene panels, as a likely cost-effective approach for molecular genetics diagnosis of non-classic HH patients. Simultaneously, it has contributed to the knowledge of the pathophysiology of those rare iron metabolism-related disorders.

Cloning of the ω-secalin gene family in a wheat 1BL/1RS translocation line using BAC clone sequencing

Background: Wheat 1BL/1RS translocation lines are planted around the world for their disease resistance and high yield. Most of them are poor in bread making, which is partially caused by ω-secalins that are encoded by the ω-secalin gene family, which is located on the short arm of rye chromosome 1R (1RS). However, information on the structure and evolution of the ω-secalin gene family is still limited. Results: We first generated a physicalmap of the ω-secalin gene family covering 195 kb of the Sec-1 locus based on sequencing three bacterial artificial chromosome (BAC) clones of the 1BL/1RS translocation wheat cultivar Shimai 15. A BAC contig was constructed spanning 168 kb of the Sec-1 locus on 1RS. Twelve ω-secalin genes were arranged in a head-to-tail fashion, separated by 8.2–21.6 kb spacers on the contig, whereas six other ω-secalin genes were arranged head-to-tail, separated by 8.2–8.4 kb of spacers on clone BAC125. The 18 ω-secalin genes can be classified into six types among which eight ω-secalin genes were expressed during seed development. The ω-secalin genes with the 1074-bp open reading frame (ORF) represented the main population. Except for two pseudogenes, the N-terminal of the ω-secalin gene was conserved, whereas variations in the C-terminal led to a change in ORF length. The spacers can be sorted into two classes. Class-1 spacers contained conserved and non-conservative sequences. Conclusion: The ω-secalin gene family consisted of at least 18 members in the 1BL/1RS translocation line cv. Shimai 15. Eight ω-secalin genes were expressed during seed development. Eighteen members may originate from a progenitor with a 1,074-bp ORF. The spacers differed in length and sequence conservation.

PCR-Internal Transcribed Spacer (ITS) genes sequencing and phylogenetic analysis of clinical and environmental Aspergillus species associated with HIV-TB co infected patients in a hospital in Abeokuta, southwestern Nigeria.

Background: Aspergillosis has been identified as one of the hospital acquired infections but the contribution of water and inhouse air as possible sources of Aspergillus infection in immunocompromised individuals like HIV-TB patients have not been studied in any hospital setting in Nigeria. Objective: To identify and investigate genetic relationship between clinical and environmental Aspergillus species associated with HIV-TB co infected patients. Methods: DNA extraction, purification, amplification and sequencing of Internal Transcribed Spacer (ITS) genes were performed using standard protocols. Similarity search using BLAST on NCBI was used for species identification and MEGA 5.0 was used for phylogenetic analysis. Results: Analyses of sequenced ITS genes of selected fourteen (14) Aspergillus isolates identified in the GenBank database revealed Aspergillus niger (28.57%), Aspergillus tubingensis (7.14%), Aspergillus flavus (7.14%) and Aspergillus fumigatus (57.14%). Aspergillus in sputum of HIV patients were Aspergillus niger, A. fumigatus, A. tubingensis and A. flavus. Also, A. niger and A. fumigatus were identified from water and open-air. Phylogenetic analysis of sequences yielded genetic relatedness between clinical and environmental isolates. Conclusion: Water and air in health care settings in Nigeria are important sources of Aspergillus sp. for HIV-TB patients.

Evolution of genome sequencing techniques

The quality and the speed for genome sequencing has advanced at the same time that technology boundaries are stretched. This advancement has been divided so far in three generations. The first-generation methods enabled sequencing of clonal DNA populations. The second-generation massively increased throughput by parallelizing many reactions while the third-generation methods allow direct sequencing of single DNA molecules. The first techniques to sequence DNA were not developed until the mid-1970s, when two distinct sequencing methods were developed almost simultaneously, one by Alan Maxam and Walter Gilbert, and the other one by Frederick Sanger. The first one is a chemical method to cleave DNA at specific points and the second one uses ddNTPs, which synthesizes a copy from the DNA chain template. Nevertheless, both methods generate fragments of varying lengths that are further electrophoresed. Moreover, it is important to say that until the 1990s, the sequencing of DNA was relatively expensive and it was seen as a long process. Besides, using radiolabeled nucleotides also compounded the problem through safety concerns and prevented the automation. Some advancements within the first generation include the replacement of radioactive labels by fluorescent labeled ddNTPs and cycle sequencing with thermostable DNA polymerase, which allows automation and signal amplification, making the process cheaper, safer and faster. Another method is Pyrosequencing, which is based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation. By the end of the last millennia, parallelization of this method started the Next Generation Sequencing (NGS) with 454 as the first of many methods that can process multiple samples, calling it the 2º generation sequencing. Here electrophoresis was completely eliminated. One of the methods that is sometimes used is SOLiD, based on sequencing by ligation of fluorescently dye-labeled di-base probes which competes to ligate to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. The widely used Solexa/Illumina method uses modified dNTPs containing so called “reversible terminators” which blocks further polymerization. The terminator also contains a fluorescent label, which can be detected by a camera. Now, the previous step towards the third generation was in charge of Ion Torrent, who developed a technique that is based in a method of “sequencing-by-synthesis”. Its main feature is the detection of hydrogen ions that are released during base incorporation. Likewise, the third generation takes into account nanotechnology advancements for the processing of unique DNA molecules to a real time synthesis sequencing system like PacBio; and finally, the NANOPORE, projected since 1995, also uses Nano-sensors forming channels obtained from bacteria that conducts the sample to a sensor that allows the detection of each nucleotide residue in the DNA strand. The advancements in terms of technology that we have nowadays have been so quick, that it makes wonder: ¿How do we imagine the next generation?

Dinoflagellate Genomic Organization and Phylogenetic Marker Discovery Utilizing Deep Sequencing Data

Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The Suessiales were found to be sister to the Peridinales. The Prorocentrales formed a monophyletic group with the Dinophysiales that was sister to the Gonyaulacales. The Gymnodinales was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets.

In situ differentiation of labile/inert metal species in Brazilian tropical rivers by means of a time-controlled batch-procedure based on TEPHA resin

The present study deals with a new analytical procedure based on a cellulose diffusion membrane and immobilised tetraethylene-pentamine-hexaacetate chelator (DM-TEPHA) for an in situ differentiation of labile and inert metal species in aquatic systems. The DM-TEPHA system was prepared by placing TEPHA chelator in pre-purified cellulose bags and in situ applied immersing the system in two Brazilian rivers to study the relative lability of metal species (Cu, Pb, Fe, Mn and Ni) as a function of the time and the quantity of exchanger, respectively. The procedure is simple and enables a new perspective for understanding the complexation, transport, stability and lability of metal species in aquatic systems rich in organic matter.

Genes found in partial sequencing od Phytophthora cinnamomi

Members of the oomycete cause extensive losses in agriculture and widespread degradation in natural plant communities, being responsible for the death of thousands of trees every year. Two of the representative species are Phytophthora infestans, which causes late blight of potato, and Phytophthora cinnamomi, which causes chestnut ink disease, responsible for losses on sweet chestnut production in Europe. Genome sequencing efforts have been focused on the study of three species: P. infestans, P. sojae and P. ramorum. Phytophthora infestans has been developed as the model specie for the genus, possessing excellent genetic and genomics resources including genetic maps, BAC libraries, and EST sequences. Our research team is trying to sequence the genome of P. cinnamomi in order to gain a better understanding of this oomycete, to study changes in plant-pathogen relationships including those resulting from climate change and trying to decrease the pathogen’s impact on crops and plants in natural ecosystems worldwide. We present here a preliminary report of partially sequenced genomic DNA from P. cinnamomi encoding putative protein-coding sequences and tRNAs. Database analysis reveals the presence of genes conserved in oomycetes.

Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era

The class Kinetoplastea encompasses both free-living and parasitic species from a wide range of hosts. Several representatives of this group are responsible for severe human diseases and for economic losses in agriculture and livestock. While this group encompasses over 30 genera, most of the available information has been derived from the vertebrate pathogenic genera Leishmania and Trypanosoma. Recent studies of the previously neglected groups of Kinetoplastea indicated that the actual diversity is much higher than previously thought. This article discusses the known segment of kinetoplastid diversity and how gene-directed Sanger sequencing and next-generation sequencing methods can help to deepen our knowledge of these interesting protists.

Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples

Gastric (GC) and breast (BrC) cancer are two of the most common and deadly tumours. Different lines of evidence suggest a possible causative role of viral infections for both GC and BrC. Wide genome sequencing (WGS) technologies allow searching for viral agents in tissues of patients with cancer. These technologies have already contributed to establish virus-cancer associations as well as to discovery new tumour viruses. The objective of this study was to document possible associations of viral infection with GC and BrC in Mexican patients. In order to gain idea about cost effective conditions of experimental sequencing, we first carried out an in silico simulation of WGS. The next-generation-platform IlluminaGallx was then used to sequence GC and BrC tumour samples. While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV) sequences were found in GC tissues. An end-point polymerase chain reaction confirmed an enrichment of EBV sequences in one of the GC samples sequenced, validating the next-generation sequencing-bioinformatics pipeline.

Estudo de reatores eletroquímicos para remoção de Cu2+ , Zn2+, Fenol e BTEX em água produzida

The production of water has become one of the most important wastes in the petroleum industry, specifically in the up stream segment. The treatment of this kind of effluents is complex and normally requires high costs. In this context, the electrochemical treatment emerges as an alternative methodology for treating the wastewaters. It employs electrochemical reactions to increase the capability and efficiency of the traditional chemical treatments for associated produced water. The use of electrochemical reactors can be effective with small changes in traditional treatments, generally not representing a significant additional surface area for new equipments (due to the high cost of square meter on offshore platforms) and also it can use almost the same equipments, in continuous or batch flow, without others high costs investments. Electrochemical treatment causes low environmental impact, because the process uses electrons as reagent and generates small amount of wastes. In this work, it was studied two types of electrochemical reactors: eletroflocculation and eletroflotation, with the aim of removing of Cu2+, Zn2+, phenol and BTEX mixture of produced water. In eletroflocculation, an electrical potential was applied to an aqueous solution containing NaCl. For this, it was used iron electrodes, which promote the dissolution of metal ions, generating Fe2+ and gases which, in appropriate pH, promote also clotting-flocculation reactions, removing Cu2+ and Zn2+. In eletroflotation, a carbon steel cathode and a DSA type anode (Ti/TiO2-RuO2-SnO2) were used in a NaCl solution. It was applied an electrical current, producing strong oxidant agents as Cl2 and HOCl, increasing the degradation rate of BTEX and phenol. Under different flow rates, the Zn2+ was removed by electrodeposition or by ZnOH formation, due the increasing of pH during the reaction. To better understand the electrochemical process, a statistical protocol factor (22) with central point was conducted to analyze the sensitivity of operating parameters on removing Zn2+ by eletroflotation, confirming that the current density affected the process negatively and the flow rate positively. For economical viability of these two electrochemical treatments, the energy consumption was calculated, taking in account the kWh given by ANEEL. The treatment cost obtained were quite attractive in comparison with the current treatments used in Rio Grande do Norte state. In addition, it could still be reduced for the case of using other alternative energy source such as solar, wind or gas generated directly from the Petrochemical Plant or offshore platforms

Assessment of naproxen adsorption on bone char in aqueous solutions using batch and fixed-bed processes

An integrated analysis of naproxen adsorption on bone char in batch and packed-bed column conditions has been performed. Kinetic, thermodynamic and breakthrough parameters have been calculated using adsorption models and artificial neural networks. Results show that naproxen removal using bone char in batch conditions is a feasible and effective process, which could involve electrostatic and non-electrostatic interactions depending mainly on pH conditions. However, the application of packed-bed column for naproxen adsorption on bone char is not effective for the treatment of diluted solutions due to the low degree of adsorbent utilization (below 4%) at tested operating conditions. The proposed mechanism for naproxen removal using bone char could include a complexation process via phosphate and naproxen, hydrogen bonding and the possibility of hydrophobic interactions via π–π electron. This study highlights the relevance of performing an integrated analysis of adsorbent effectiveness in batch and dynamic conditions to establish the best process configuration for the removal of emerging water pollutants such as pharmaceuticals.

Removal of paracetamol on biomass-derived activated carbon: Modeling the fixed bed breakthrough curves using batch adsorption experiments

The remediation of paracetamol (PA), an emerging contaminant frequently found in wastewater treatment plants, has been studied in the low concentration range (0.3–10 mg L−1) using as adsorbent a biomass-derived activated carbon. PA uptake of up to 100 mg g−1 over the activated carbon has been obtained, with the adsorption isotherms being fairly explained by the Langmuir model. The application of Reichemberg and the Vermeulen equations to the batch kinetics experiments allowed estimating homogeneous and heterogeneous diffusion coefficients, reflecting the dependence of diffusion with the surface coverage of PA. A series of rapid small-scale column tests were carried out to determine the breakthrough curves under different operational conditions (temperature, PA concentration, flow rate, bed length). The suitability of the proposed adsorbent for the remediation of PA in fixed-bed adsorption was proven by the high PA adsorption capacity along with the fast adsorption and the reduced height of the mass transfer zone of the columns. We have demonstrated that, thanks to the use of the heterogeneous diffusion coefficient, the proposed mathematical approach for the numerical solution to the mass balance of the column provides a reliable description of the breakthrough profiles and the design parameters, being much more accurate than models based in the classical linear driving force.

Fouling in emulsion polymerization reactors

160 p.