225 research outputs found
Evaluating pathway enumeration algorithms in metabolic engineering case studies
The design of cell factories for the production of compounds involves the search for suitable heterologous pathways. Different strategies have been proposed to infer such pathways, but most are optimization approaches with specific objective functions, not suited to enumerate multiple pathways. In this work, we analyze two pathway enumeration algorithms based on graph representations: the Solution Structure Generation and the Find Path algorithms. Both are capable of enumerating exhaustively multiple pathways using network topology. We study their capabilities and limitations when designing novel heterologous pathways, by applying these methods on two case studies of synthetic metabolic engineering related to the production of butanol and vanillin
Paternal effect on genomic activation, clinical pregnancy and live birth rate after ICSI with cryopreserved epididymal versus testicular spermatozoa
<p>Abstract</p> <p>Background</p> <p>This study takes an in depth look at embryonic development, implantation, pregnancy and live birth rates with frozen epididymal and testicular sperm from obstructed (OA) and non-obstructed (NOA) patients.</p> <p>Methods</p> <p>Paternal effect of sperm source on zygote formation, embryonic cleavage, and genomic activation were examined. Additional outcome parameters monitored were clinical pregnancy rate (CPR), implantation rate (IR) and live birth rate.</p> <p>Results</p> <p>In this report, we retrospectively analyzed 156 ICSI cycles using cryopreserved epididymal sperm (ES; n = 77) or testicular sperm (TESE; n = 79). The developmental potential of embryos did not appear to be influenced by the type of surgically retrieved sperm. The average number of blastomeres observed on Day 3 was not different among different groups; 7.5 +/- 1.7 (ES), 7.6 +/- 2.1 (TESE-OA) and 6.5 +/- 2.3 (TESE-NOA). Compaction and blastulation rates, both indicators of paternal genomic activation, were similar in embryos derived from ICSI with ES or TESE from OA as well as NOA men. The only parameter significantly affected in NOA-TESE cases was the fertilization rate. CPR and IR with cryopreserved TESE (TESE-OA 59%, 34%, and TESE-NOA 37%, 20%) were also not statistically different, from that achieved with cryopreserved ES (61% and 39%). Live birth rates also appeared to be independent of sperm type. The 87 clinical pregnancies established using cryopreserved TESE and ES, resulted in the birth of 115 healthy infants. No congenital anomalies were noted.</p> <p>Conclusion</p> <p>Zygotic activation seems to be independent of sperm origin and type of azoospermia.</p
The effects of augmented reality on students' academic achievement and motivation in a biology course
Assessment of endometrial and ovarian characteristics using three dimensional power Doppler ultrasound to predict response in frozen embryo transfer cycles
<p>Abstract</p> <p>Objective</p> <p>To evaluate whether endometrial or ovarian parameters as measured using 3D power Doppler ultrasound would predict the outcome in frozen embryo transfer (FET) cycles.</p> <p>Methods</p> <p>Thirty women with no known gynecological pathology undergoing FET were recruited. The FET was carried out in the natural menstrual cycle 3-4 days after the first positive LH test result. Blood samples for hormonal analysis were collected, and three-dimensional (3D) ultrasonographic examination was performed on the day of the FET and repeated with analysis of the total hCG one week later.</p> <p>Results</p> <p>The demographic, clinical, and embryological characteristics were similar between the pregnant (15/30) and nonpregnant groups (15/30). There were no differences between the groups in endometrial/subendometrial thickness, volume, or vascularization index (VI). The endometrial triple-line pattern was more often present in the pregnant group on the day of the FET (93.3% vs. 40.0%, 95% CI 25.5-81.2%). No differences in the ovaries were observed on the day of the FET. At the second visit, the triple-line pattern was still more often present in those patients who had conceived (91.7% vs. 42.9%, 95% CI 18.5-79.1%), and their corpus luteum was more active as judged by the rise in 17-hydroxyprogesterone and estradiol levels. No differences were observed in the dominant ovarian vasculature.</p> <p>Conclusions</p> <p>According to our results, measurement of power Doppler indices using 3D ultrasound on the day of the FET does not provide any additional information concerning the outcome of the cycle. The existence of the triple-line pattern on the day of the FET seems to be a prognostic sign of a prosperous outcome after FET. The dominant ovary in the pregnant group seems to be already activated one week after the FET.</p
Specific Recognition of p53 Tetramers by Peptides Derived from p53 Interacting Proteins
Oligomerization plays a major role in regulating the activity of many proteins, and in modulating their interactions. p53 is a homotetrameric transcription factor that has a pivotal role in tumor suppression. Its tetramerization domain is contained within its C-terminal domain, which is a site for numerous protein-protein interactions. Those can either depend on or regulate p53 oligomerization. Here we screened an array of peptides derived from proteins known to bind the tetrameric p53 C-terminal domain (p53CTD) and identified ten binding peptides. We quantitatively characterized their binding to p53CTD using fluorescence anisotropy. The peptides bound tetrameric p53CTD with micromolar affinities. Despite the high charge of the binding peptides, electrostatics contributed only mildly to the interactions. NMR studies indicated that the peptides bound p53CTD at defined sites. The most significant chemical shift deviations were observed for the peptides WS100B(81–92), which bound directly to the p53 tetramerization domain, and PKCα(281–295), which stabilized p53CTD in circular dichroism thermal denaturation studies. Using analytical ultracentrifugation, we found that several of the peptides bound preferentially to p53 tetramers. Our results indicate that the protein-protein interactions of p53 are dependent on the oligomerization state of p53. We conclude that peptides may be used to regulate the oligomerization of p53
Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype
<p>Abstract</p> <p>Background</p> <p>A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level.</p> <p>Results</p> <p>We propose a new finite state machine able to detect and correct aberrant molecular phenotype given by mutated genetic transcripts. The aberrant mutations trigger a cascade reaction: specific molecular markers as input are released and induce a spontaneous self-assembly of a wild type protein or peptide, while the mutational disease phenotype is silenced. We experimentally demostrated in <it>in vitro </it>translation system that a viable protein can be autonomously assembled.</p> <p>Conclusion</p> <p>Our work demostrates the basic principles of computational genes and particularly, their potential to detect mutations, and as a response thereafter administer an output that suppresses the aberrant disease phenotype and/or restores the lost physiological function.</p
ASPP: a new family of oncogenes and tumour suppressor genes
The apoptosis stimulating proteins of p53 (ASPP) family consists of three members, ASPP1, ASPP2 and iASPP. They bind to proteins that are key players in controlling apoptosis (p53, Bcl-2 and RelA/p65) and cell growth (APCL, PP1). So far, the best-known function of the ASPP family members is their ability to regulate the apoptotic function of p53 and its family members, p63 and p73. Biochemical and genetic evidence has shown that ASPP1 and ASPP2 activate, whereas iASPP inhibits, the apoptotic but not the cell-cycle arrest function of p53. The p53 tumour suppressor gene, one of the most frequently mutated genes in human cancer, is capable of suppressing tumour growth through its ability to induce apoptosis or cell-cycle arrest. Thus, the ASPP family of proteins helps to determine how cells choose to die and may therefore be a novel target for cancer therapy
Cassava processing wastewater as a platform for third generation biodiesel production
ABSTRACT This study aimed to evaluate third generation biodiesel production by microalgae Phormidium autumnale using cassava processing wastewater as a platform. Experiments were performed in a heterotrophic bubble column bioreactor. The study focused on the evaluation of the bioreactor (batch and fed-batch) of different operational modes and the analysis of biofuel quality. Results indicate that fed-batch cultivations improved system performance, elevating biomass and oil productions to 12.0 g L−1 and 1.19 g L−1, respectively. The composition of this oil is predominantly saturated (60 %) and monounsaturated (39 %), resulting in a biodiesel that complys with U.S., European and Brazilian standards. The technological route developed indicates potential for sustainable production of bulk oil and biodiesel, through the minimization of water and chemical demands required to support such a process
CP-31398, a putative p53-stabilizing molecule tested in mammalian cells and in yeast for its effects on p53 transcriptional activity
BACKGROUND: CP-31398 is a small molecule that has been reported to stabilize the DNA-binding core domain of the human tumor suppressor protein p53 in vitro. The compound was also reported to function as a potential anti-cancer drug by rescuing the DNA-binding activity and, consequently, the transcription activation function of mutant p53 protein in mammalian tissue culture cells and in mice. RESULTS: We performed a series of gene expression experiments to test the activity of CP-31398 in yeast and in human cell cultures. With these cell-based assays, we were unable to detect any specific stimulation of mutant p53 activity by this compound. Concentrations of CP-31398 that were reported to be active in the published work were highly toxic to the human H1299 lung carcinoma and Saos-2 cell lines in our experiments. CONCLUSION: In our experiments, the small molecule CP-31398 was unable to reactivate mutant p53 protein. The results of our in vivo experiments are in agreement with the recently published biochemical analysis of CP-31398 showing that this molecule does not bind p53 as previously claimed, but intercalates into DNA
Elimination, reversal, and directional bias of optical diffraction
We experimentally demonstrate the manipulation of optical diffraction,
utilizing the atomic thermal motion in a hot vapor medium of
electromagnetically-induced transparency (EIT). By properly tuning the EIT
parameters, the refraction induced by the atomic motion may completely
counterbalance the paraxial free-space diffraction and by that eliminates the
effect of diffraction for arbitrary images. By further manipulation, the
diffraction can be doubled, biased asymmetrically to induced deflection, or
even reversed. The latter allows an experimental implementation of an analogy
to a negative-index lens
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