Homo and heteroassembly of amide-based [2]rotaxanes using α,α'-dimethyl-p-xylylenediamines.

The formation of [2]rotaxanes via a fumaramide-templated clipping reaction using α,α'-dimethyl-p-xylylenediamines is described. This process selectively affords two out of seven possible interlocked isomers due to a noticeable effect of the methyl groups on the in/out disposition of the amide CO groups.

ABPSE: Alineador de ADN Basado en Paralelismo a Nivel de Bit y la Estrategia Siembra y Extiende / ABPSE: DNA Aligner Based on Bit-level Parallelism and the Seed and Extend Strategy

Resumen La alineación de ADN es un proceso clave para la reconstrucción de genomas, a partir de los millones de lecturas cortas producidas por las máquinas de secuenciación paralela masiva. Tal proceso suele realizarse mediante algoritmos con elevada complejidad espacial y temporal, requiriendo varias horas para entregar los resultados, así como decenas de GB de RAM. Esto ha motivado la búsqueda de nuevos algoritmos y/o estrategias que permitan disminuir los tiempos de ejecución, mientras se utilizan recursos mínimos de memoria. En este artículo se presenta ABPSE, un nuevo alineador de ADN que combina el algoritmo de Ferragina y Manzini (o índices de FM) y el algoritmo de Myers, mediante la estrategia siembra y extiende. En la siembra, los índices de FM permiten calcular de manera rápida regiones con alta probabilidad de alineación; mientras que en la extensión, el algoritmo de Myers refina la alineación utilizando operaciones basadas en vectores de bits, calculando simultáneamente varias celdas de la matriz de programación dinámica. Los resultados muestran un 96.1% de lecturas alineadas correctamente, un factor de aceleración de 2.45x en relación a BWA-SW y un uso de memoria de apenas 7.6 GB, cuando se alinea el genoma humano completo.

Abstract DNA alignment is a key process in the assembly of genomes from the millions of short reads that are produced by massive parallel sequencing machines. Such a process is usually done by means of high spatial and temporal complexity algorithms, which takes hours to deliver the results as well as tens of GB of RAM. This has prompted the search for new algorithms and/or strategies that allow shorter runtimes, while using minimal memory footprint. In this article, we present ABPSE, a new DNA aligner that combines the Ferragina and Manzini algorithm (or FM indexes) and the Myers algorithm, by means of the seed and extend strategy. In the seeding, the FM indices allow a rapid calculation of the regions with high probability of alignment. In the extension, the Myers algorithm refines the alignment using operations based on bit vectors. It simultaneously calculates several cells of the dynamic programming matrix. The results show 96.1% of correctly aligned reads, an acceleration factor of 2.45x in relation to BWA-SW and a memory footprint of only 7.6 GB when aligning the entire human genome.

Computational Study of the Binding Modes of Diverse DPN Analogues on Estrogen Receptors (ER) and the Biological Evaluation of a New Potential Antiestrogenic Ligand.

Estrogen (17ß-estradiol) is essential for normal growth and differentiation in the mammary gland. In the last three decades, previous investigations have revealed that Estrogen Receptor Alpha (ERα) plays a critical role in breast cancer. More recently, observations regarding the widespread expression of ERß-like proteins in normal and neoplastic mammary tissues have suggested that ERß is also involved in the mentioned pathology. Design of new drugs both steroidal and nonsteroidal that target any of these receptors represents a promise to treat breast cancer although it remains a challenge due to the sequence similarity between their catalytic domains. In this work, we propose a new set of compounds that could effectively target the estrogen receptors ERα and ERß. These ligands were designed based on the chemical structure of the ERß-selective agonist Diarylpropionitrile (DPN). The designed ligands were submitted to in silico ADMET studies, yielding in a filtered list of ligands that showed better drug-like properties. Molecular dynamics simulations of both estrogen receptors and docking analysis were carried-out employing the designed compounds, from which two were chosen due to their promising characteristics retrieved from theoretical results (docking analysis or targeting receptor predictions). They were chemically synthetized and during the process, two precursor ligands were also obtained. These four ligands were subjected to biological studies from which it could be detected that compound mol60b dislplayed inhibitory activity and its ability to activate the transcription via an estrogenic mechanism of action was also determined. Interestinly, this observation can be related to theoretical binding free energy calculations, where the complex: ERß-mol60b showed the highest energy ΔGbind value in comparison to others.

Combination of p53-DC vaccine and rAd-p53 gene therapy induced CTLs cytotoxic against p53-deleted human prostate cancer cells in vitro.

Recently, the US FDA approved sipuleucel-T, which is composed of autologous DCs stimulated with a recombinant fusion protein of prostatic acid phosphatase (PAP) and granulocyte-macrophage colony-stimulating factor (GM-CSF), as the first immunotherapeutic agent for metastatic castration resistant prostate cancer (mCRPC). However, sipuleucel-T demonstrated only modest efficacy in mCPRC patients. Researchers are now investigating the potential of p53 protein as a tumor-associated antigen (TAA) loaded in DC-based cancer vaccine. Approximately half of all tumors overexpress p53, and up to 20% of prostate cancer cells overexpresses p53. In this study, we evaluated the feasibility of combining p53-DC vaccine and rAd-p53 gene therapy, using the p53-overexpressing and non-expressing prostate cancer cells in vitro. We successfully generated the p53-DC vaccine by culturing autologous DCs infected with rAd-p53. This p53-DC vaccine can differentiate CTLs specifically cytotoxic to p53-overexpressing prostate cancer cells. In addition, rAd-p53 infection can induce overexpression of p53 and thus the cytotoxicity of CTLs differentiated by the p53-DC vaccine in p53 non-expressing prostate cancer cells. These findings suggest that this combination therapy using p53-DC vaccine and rAd-p53 gene therapy together may represent a new paradigm for the treatment of mCRPC.

Single administration of recombinant IL-6 restores the gene expression of lipogenic enzymes in liver of fasting IL-6-deficient mice.

BACKGROUND AND PURPOSE: Lipogenesis is intimately controlled by hormones and cytokines as well as nutritional conditions. IL-6 participates in the regulation of fatty acid metabolism in the liver. We investigated the role of IL-6 in mediating fasting/re-feeding changes in the expression of hepatic lipogenic enzymes. EXPERIMENTAL APPROACH: Gene and protein expression of lipogenic enzymes were examined in livers of wild-type (WT) and IL-6-deficient (IL-6(-/-) ) mice during fasting and re-feeding conditions. Effects of exogenous IL-6 administration on gene expression of these enzymes were evaluated in vivo. The involvement of STAT3 in mediating these IL-6 responses was investigated by using siRNA in human HepG2 cells. KEY RESULTS: During feeding, the up-regulation in the hepatic expression of lipogenic genes presented similar time kinetics in WT and IL-6(-/-) mice. During fasting, expression of lipogenic genes decreased gradually over time in both strains, although the initial drop was more marked in IL-6(-/-) mice. Protein levels of hepatic lipogenic enzymes were lower in IL-6(-/-) than in WT mice at the end of the fasting period. In WT, circulating IL-6 levels paralleled gene expression of hepatic lipogenic enzymes. IL-6 administration in vivo and in vitro showed that IL-6-mediated signalling was associated with the up-regulation of hepatic lipogenic enzyme genes. Moreover, silencing STAT3 in HepG2 cells attenuated IL-6 mediated up-regulation of lipogenic gene transcription levels. CONCLUSIONS AND IMPLICATIONS: IL-6 sustains levels of hepatic lipogenic enzymes during fasting through activation of STAT3. Our findings indicate that clinical use of STAT3-associated signalling cytokines, particularly against steatosis, should be undertaken with caution.

Automated anthropometric phenotyping with novel Kinect-based three-dimensional imaging method: comparison with a reference laser imaging system.

BACKGROUND/OBJECTIVES: Anthropometry for measuring body composition, shape, surface area and volume is important for human clinical research and practice. Although training and technical skills are required for traditional tape and caliper anthropometry, a new opportunity exists for automated measurement using newly developed relatively low-cost three-dimensional (3D) imaging devices. The aim of this study was to compare results provided by a Kinect-based device to a traditional laser 3D reference system. SUBJECTS/METHODS: Measurements made by the evaluated device, a hybrid of commercially purchased hardware (KX-16; TC(2), Cary, NC, USA) with our additional added software, were compared with those derived by a high-resolution laser scanner (Vitus Smart XXL; Human Solutions North America, Cary, NC, USA). Both imaging systems were compared with additional linear (stadiometer-derived height) and volumetric (total volume, air-displacement plethysmography) measurements. Subjects (n=101) were healthy children (age ≥5 years) and adults varying in body mass index. RESULTS: Representative linear (4), circumferential (6), volumetric (3) and surface area (1) measurements made by the Kinect-based device showed a consistent pattern relative to the laser system: high correlations (R(2)s= 0.70-0.99, all P<0.001); 1-3% differences for large linear (for example, height, X±s.d., -1.4±0.5%), circumferential (for example, waist circumference, -2.1±1.8%), volume (for example, total body, -0.8±2.2%) and surface area (whole-body, -1.7±2.0%) estimates. By contrast, mean measurement differences were substantially larger for small structures (for example, forearm volume, 31.3±31.4%). CONCLUSIONS: Low-cost 3D Kinect-based imaging systems have the potential for providing automated accurate anthropometric and related body measurements for relatively large components; further hardware and software developments may be able to improve system small-component resolution.

De la Secuenciación a la Aceleración Hardware de los Programas de Alineación de ADN, una Revisión Integral / From sequencing to hardware acceleration of DNA alignment software: A integral review

En los últimos años ha ocurrido un avance impresionante en las máquinas de secuenciación paralela masiva, también llamadas de secuenciación de siguiente generación (NGS), por ejemplo, máquinas recientes como Illumina Hiseq son capaces de generar millones de lecturas en una sola corrida. No obstante, estas tecnologías están limitadas a secuenciar solo fragmentos pequeños de material genético (entre 35 y 1100 nucleótidos), por lo que para secuenciar un genoma completo es necesario dividir la cadena, secuenciar y posteriormente ensamblar las lecturas cortas obtenidas. En este trabajo se revisan y comparan las tecnologías de secuenciación recientes, se estudia el proceso de ensamble de genomas completos y se establece formalmente el problema de la alineación. También se incluye un resumen de los principales programas de alineación y sus algoritmos que lo soportan. Finalmente, después de concluir que las tecnologías de secuenciación han superado en velocidad por un factor mayor a 10x a los programas de alineación, se revisa la aceleración Hardware como alternativa para acelerar tales programas. Este trabajo al ser una revisión integral pretende contribuir al desarrollo de investigación en el área de bioinformática en el país.

In recent years, impressive progress has occurred in the machines of massively parallel sequencing, also called of next-generation sequencing (NGS), for example, recent machines like Illumina HiSeq are capable of generating millions of reads in a single run. However, these technologies are limited to sequence only small fragments of genetic material (35 to 1100 nucleotides), so that for complete-genome sequencing, it is necessary to divide the chain, to sequence the fragments, and, subsequently, to assemble the obtained short readings. In this paper, the recent NGS sequencing technologies are reviewed and compared, analyzing the problem of sequence assembly, and formally establishing the problem of alignment. Also, it is examined the main alignment programs and the algorithms that support them. Finally, after concluding that sequencing technologies have speed that exceeds 10 times to the speed of the alignment programs, the hardware acceleration is reviewed as an alternative to accelerate these programs. This work, which is a comprehensive analysis and review, aims to contribute to the development of the research in the area of bioinformatics in the country.

Effect of Bacillus Subtilis-based Direct-fed Microbials on Immune Status in Broiler Chickens Raised on Fresh or Used Litter.

Type of dietary direct-fed microbials (DFMs) or poultry litter could directly influence the composition of gut microbiota. Gut microbiota plays an important role in shaping the developing immune system and maintaining the homeostasis of the mature immune system in mammal and chickens. The present study was carried out to investigate the interaction among litter, DFMs and immunity in broiler chickens exposed to a field-simulated environment. Immune status of broiler chickens was assessed by serum antibodies against Eimeria spp. and Clostridium spp. and intestinal cytokine mRNA expression. The current experimental design had a 3 ×2 factorial arrangement of treatments with three types of litter, i.e., fresh litter or used litter that was obtained from a farm with no disease outbreak (used litter) or a farm with history of a gangrenous dermatitis outbreak (GD litter), and two dietary treatments with or without DFMs. It was found that either DFM addition or type of litter significantly affected anticoccidial antibody levels of broiler chickens at d 42. In general, dietary DFMs increased the anticoccidial antibodies in the fresh-litter raised chickens, but lowered the levels in the GD-litter raised chickens. Serum antibodies against Clostridium perfringens α-toxin were significantly (p<0.05) higher in chickens raised on GD litter compared with those raised on fresh litter. Cytokine mRNA expression was significantly (p<0.05) altered by either the type of litter or DFMs. Of interest, dietary DFMs lowered interferon-γ, interleukin 1beta, and CXCLi2 cytokine mRNA expression in chickens raised on fresh litter but increased them in GD-litter raised chickens. In conclusion, dietary DFMs modulate various immune parameters of broiler chickens, but the DFM-mediated effects were dependent upon the type of litter on which chickens were raised.

Involvement of K-RAS mutations and amino acid substitutions in the survival of metastatic colorectal cancer patients.

The efficacy of epidermal growth factor-targeting therapies has been found to be limited in tumors with the wild-type K-RAS gene, suggesting a predictive value of K-RAS gene analysis in tumoral response. However, the prognostic value of K-RAS is controversial. This study included patients diagnosed with metastatic colorectal cancer. The presence of K-RAS mutations was analyzed, and the tumors positive for a K-RAS mutation were further analyzed to identify the mutation type. Similarly, the following clinical and pathological variables were also collected. The study was composed of 53.3 % of patients with wild-type K-RAS and 46.7 % of patients with mutated K-RAS (mutated codon 12 was the most frequent). With a mean follow-up of 15 months (range, 1-45), the median survival of patients with wild-type K-RAS was 31.6 months. The median survival was 24.8 months for patients with K-RAS mutated in codon 12 and 17.8 months for patients with mutated codon 13 (p = 0.37). In a univariate analysis, K-RAS was associated with stage IV at diagnosis (p < 0.005). When K-RAS was mutated, a lower overall survival was observed in cases of G → A transition compared with G → T transversion (19.5 vs. 24.2 months, respectively; p = 0.47). When the amino acid change resulted in an acidic substitution, survival was lower, but it increased when the substitution resulted in a polar or nonpolar amino acid (19.5 vs. 23.2 vs. 24.4 months, p = 0.79). The type of K-RAS mutation or amino acid changes may have prognostic implications in metastatic colon cancer patients. Further research is needed in patients treated in prospective controlled trials.

Characterization of infectious bursal disease viruses isolated in 2007 from Delmarva commercial broiler chickens.

A study was performed in 2007 to isolate and characterize infectious bursal disease viruses (IBDVs) in commercial broilers grown in the Delmarva (DMV) Peninsula region of the United States. Bursae of Fabricius were collected weekly from 1 to 4 wk of age from broilers on 10 farms with a history of poor performance. Microscopic pathology was used to determine the infectious bursal disease (IBD) status of the broilers. Bursae from 1- and 2-wk-old broilers did not show IBD microscopic lesions. Moreover, broilers on 1 of the 10 farms were IBD lesion free at 3 and 4 wk of age. However, 3 of 9 and 9 of 9 farms yielded broilers with IBD-affected bursae from 3- and 4-wk-old commercial broilers, respectively. Ten IBDV isolates were recovered from 3 of 3 lesion-positive bursal pools at 3 wk of age and 7 of 9 lesion-positive bursal pools at 4 wk of age. Analysis of the viral protein (VP) 2 genes identified all isolates as serotype 1 Delaware (Del) variant viruses. Five field isolates, each representing different molecular clades of the Delaware variant viruses, were selected for further study. Experimental infection of specific-pathogen-free white leghorn chickens with isolates DMV/4813/07, DMV/4947/07, DMV/4955/07, DMV/5038/07, and DMV/5041/07 produced gross and microscopic pathology of the bursa consistent with Delaware variant infection. Monoclonal antibody testing showed DMV/4813/07, DMV/4947/07, DMV/ 4955/07, and DMV/5041/07 to be similar to previous recognized variant viruses. However, DMV/5038/07 was found to be unreactive with the monoclonal antibodies that typically recognize reference strains STC, Del E, GLS, RS593, and AL2. In a challenge of immunity study, 10-day-old progeny from breeders immunized with a commercially available inactivated IBDV vaccine containing the Del E and classic strains were protected to a lesser degree against isolate DMV/5038/07 compared to Del E challenge based on microscopic lesion scores (P < 0.01) of the bursa. This result suggests the virus is antigenically different from the Del E strain contained in the vaccine. Collectively, the monoclonal antibody and progeny challenge of immunity findings suggest DMV/5038/07 is antigenically different from the Del E strain contained in the vaccine.

Effect of dietary antimicrobials on immune status in broiler chickens.

This study evaluated the effects of dietary anticoccidial drugs plus antibiotic growth promoters (AGPs) on parameters of immunity in commercial broiler chickens. Day-old chicks were raised on used litter from a farm with endemic gangrenous dermatitis to simulate natural pathogen exposure and provided with diets containing decoquinate (DECX) or monensin (COBN) as anticoccidials plus bacitracin methylene disalicylate and roxarsone as AGPs. As a negative control, the chickens were fed with a non-supplemented diet. Immune parameters examined were concanavalin A (ConA)-stimulated spleen cell proliferation, intestine intraepithelial lymphocyte (IEL) and spleen cell subpopulations, and cytokine/chemokine mRNA levels in IELs and spleen cells. ConA-induced proliferation was decreased at 14 d post-hatch in DECX-treated chickens, and increased at 25 and 43 d in COBN-treated animals, compared with untreated controls. In DECX-treated birds, increased percentages of MHC2(+) and CD4(+) IELS were detected at 14 d, but decreased percentages of these cells were seen at 43 d, compared with untreated controls, while increased TCR2(+) IELs were evident at the latter time. Dietary COBN was associated with decreased fractions of MHC2(+) and CD4(+) IELs and reduced percentages of MHC2(+), BU1(+), and TCR1(+) spleen cells compared with controls. The levels of transcripts for interleukin-4 (IL-4), IL-6, IL-17F, IL-13, CXCLi2, interferon-γ (IFN-γ), and transforming growth factorß4 were elevated in IELs, and those for IL-13, IL-17D, CXCLi2, and IFN-γ were increased in spleen cells, of DECX- and/or COBN-treated chickens compared with untreated controls. By contrast, IL-2 and IL-12 mRNAs in IELs, and IL-4, IL-12, and IL-17F transcripts in spleen cells, were decreased in DECX- and/or COBN-treated chickens compared with controls. These results suggest that DECX or COBN, in combination with bacitracin and roxarsone, modulate the development of the chicken post-hatch immune system.

Impact of fresh or used litter on the posthatch immune system of commercial broilers.

This study was carried out to investigate the effects of exposure of growing broiler chickens of commercial origin to used poultry litter on intestinal and systemic immune responses. The litter types evaluated were fresh wood shavings or used litter obtained from commercial poultry farms with or without a history of gangrenous dermatitis (GD). Immune parameters measured were serum nitric oxide (NO) levels, serum antibody titers against Eimeria or Clostridium perfringens, mitogen-induced spleen cell proliferation, and intestinal intraepithelial lymphocyte or splenic lymphocyte subpopulations. At 43 days posthatch, birds raised on used litter from a GD farm had higher serum NO levels and greater Eimeria or C. perfringens antibody levels compared with chickens raised on fresh litter or used, non-GD litter. Birds raised on non-GD and GD used litter had greater spleen cell mitogenic responses compared with chickens raised on fresh litter. Finally, spleen and intestinal lymphocyte subpopulations were increased or decreased depending on the litter type and the surface marker analyzed. Although it is likely that the presence of Eimeria oocysts and endemic viruses varies qualitatively and quantitatively between flocks and, by extension, varies between different used litter types, we believe that these data provide evidence that exposure of growing chicks to used poultry litter stimulates humoral and cell-mediated immune responses, presumably due to contact with contaminating enteric pathogens.

Massachusetts live vaccination protects against a novel infectious bronchitis virus S1 genotype DMV/5642/06.

Four infectious bronchitis virus (IBV) isolates were recovered from commercial broiler chicken flocks located on the Delmarva Peninsula (east coast of the United States) in the spring of 2006. Sequence analysis of the S1 subunit of the spike glycoprotein gene showed the four isolates were highly related to each other (> or = 99.6% nucleotide identity; > or = 98.9% amino acid identity). Basic local alignment search tool analysis indicated the highest S1 amino acid identity of isolate DMV/5642/06, typical of the four Delmarva (DMV) isolates, was to CA/1737/04, an isolate obtained from broilers in California in 2004. A pathogenicity study conducted, using two-week-old commercial broilers, showed that DMV/5642/06 caused respiratory but not renal (kidney) disease. A vaccination-challenge study in three-week-old specific-pathogen-free leghorn chickens demonstrated that a commercial live attenuated IBV vaccine containing the Massachusetts strain conferred protection against challenge with DMV/5642/06 based on virus reisolation attempts and microscopic pathology.