Duplication Time Research Articles

Phylogenetic analysis of STK gene family and Usp domain in maize.

Serine and threonine kinase STK1 and STK2 play an important regulatory role in the process of pollen development in maize. Six homologous sequences which were similar with STK1 and STK2 having more than 80 % similarity were found at NCBI, and they all belong to STK gene family. Phylogenetic analysis showed that STK family in maize might belong to RLK family. In STK family, gene duplication event was occurred during evolutionary process, and experienced purifying selection after gene duplication and the time of gene duplication was about 12 million years ago. The domains of STK family belongs to single transmembrane protein, which have intracellular conserved kinase catalytic domain and extracellular receptor domain on N-terminal. The evolution of intracellular selection was faster than extracellular selection, and positive selection or weak purifying selection play an important role. Analyzing its unique Usp domain we found that it was located between sensor domain at N-terminal and catalytic domain at C-terminal, which belongs to hydrophobic protein with several phosphorylation sites, acting on serine and threonine protein phosphorylation. The kinship of Usp domain in STK family was close to 35-like protein containing U-box domain, predicting that they might belong to the same family with a similar structure and function, so that we can predict the function of Usp domain in STK family.

Abstract 2099: Cellular and molecular determinants of retinoic acid sensitivity in breast cancer

Abstract All-trans-retinoic acid (ATRA) is the primary metabolite of vitamin A and a promising agent in the treatment/prevention of solid tumors, including breast cancer. Breast cancer is a very heterogeneous disease that can be classified according to the global gene-expression profiles into various subgroups. A rational use of ATRA in the clinics requires definition of the breast cancer subtypes characterized by sensitivity/natural-resistance to this compound and derived retinoids. In addition, it is fundamental to define the cellular and molecular mechanisms underlying the sensitivity/resistance to ATRA. As a first step in this direction, 44 breast cancer cell lines, belonging to the Cancer Cell Line Encyclopedia (CCLE) of the Broad Institute and recapitulating the heterogeneity of this tumor, were evaluated for their sensitivity to the anti-proliferative activity of ATRA. Individual cell lines were challenged with increasing concentrations of the retinoid for 3, 6 and 9 days. The concentrations of ATRA causing 50% of the maximal growth inhibition (IC50) and the maximal effect observed were calculated. The two parameters, along with the duplication time of the cell lines, were used to define a novel algorithm (ATRA SCORE). The ATRA score is a continuous parameter which defines the sensitivity of the cell lines to ATRA in a quantitative fashion. The lower the ATRA score the higher the sensitivity of the cell to the anti-proliferative action of ATRA. Using this score, an enrichment in cell lines characterized by a luminal phenotype and/or estrogen receptor (ER)-positivity was observed in the group showing sensitivity to ATRA. In contrast an enrichment in cell lines with a basal phenotype and/or ER-negativity was evident in the group characterized by natural resistance to the retinoid. Measurement of the mRNAs corresponding to various isoforms of the retinoid receptors belonging to the RAR and RXR family in the 44 cell lines allowed us to establish correlations between the expression of these transcripts and ATRA sensitivity. With respect to this, we found a significant and direct correlation with the expression levels of RARalpha1. This indicates that the receptor represents a determinant and a predictor of ATRA- sensitivity in breast cancer cells. The correlation was confirmed also at the protein level using specific RARalpha antibodies. Most of these findings were validated with the use of short-term cultures of breast cancer tissue slices obtained from surgical specimens. The availability of the global gene-expression profiles of each cell line permitted the construction of a gene fingerprint consisting of approximately 130 elements that has the potential to predict sensitivity to ATRA not only in breast cancer cell lines, but also in tumor samples. In addition, the identified gene fingerprint allowed the identification of various and unexpected molecular determinants of sensitivity which do not belong to the classic retinoid pathway. Citation Format: Enrico Garattini, Floriana Centritto, Silvio K. Garattini, Gabriela Paroni, Marco Bolis, Maddalena Fratelli, Mineko Terao. Cellular and molecular determinants of retinoic acid sensitivity in breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2099. doi:10.1158/1538-7445.AM2014-2099

Abstract 1952: Notch-1 regulated stemness and EMT in colorectal cancer

Abstract Colorectal cancer (CRC) is the second leading cause of cancer death nationwide. In 2013, nearly 156,000 patients will be diagnosed with CRC. Surgical resection for early stage disease offers the best chance for cure; however, up to 30% of patients will relapse. Current models of CRC progression hold that tumor development is driven by a small subpopulation of cancer initiating (CIC) or cancer stem (CSC) cells that share many properties of stem cells. These cells have the capacity to drive tumor growth, are largely responsible for relapse and have been implicated in metastasis via epithelial to mesenchymal transition (EMT), similar to normal counterparts in organogenesis. Notch-1 is the major receptor for a highly conserved signaling pathway that is well-documented to control stem cell and lineage commitment in various organs, including the colon. The function of Notch signaling in colorectal cancer, however, is not well-defined. Based on preliminary data in which colon tumor samples from CRC patients expressed Notch-1 but surrounding benign tissue did not, we sought to test the hypothesis that Notch-1 signaling in colon cells promotes tumorigenesis by enhancing stem cell and EMT characteristics of tumor cells. The human colon tumor line HCT-116 was transduced with a retroviral construct that expresses constitutively active Notch-1 (ICN1). Hes-1 protein levels were increased in the activated Notch-1 transduced cells, indicating that the construct was functional in activating Notch-signaling. These HCT116/ICN1 cells exhibited higher plating efficiency than the parental cell line. The average colony size of the HCT116/ICN1 cells was about two-fold smaller than the parental cell line (p<0.001). In addition, cells with constitutively active Notch-1 (HCT116/ICN1) had a longer duplication time than parental HCT-116 cells (p<0.03). Consistent with longer duplication time, HCT116/ICN1 cells were two-fold slower in completing wound healing as compared with the parental HCT-116 cell line (p<0.001). Transwell migration assays revealed a two-fold increase in migration of HCT116/ICN1 cells as compared with the parental control (p<0.03). Western blot analysis demonstrated that the HCT116/ICN1 cells with activated Notch-1 expressed highly increased levels of the EMT associated proteins Smad3, CD44 and Slug. This was accompanied by a four-fold decreased expression of E-cadherin. Meanwhile, E-cadherin was not altered in HCT116 cells transduced with a Notch-1 shRNA lentiviral construct that inactivated Notch-1 signaling. Finally, levels of the numb protein, a Notch-1 antagonist, appeared to be significantly reduced (five-fold decrease) by constitutive Notch-1 signaling. Alternatively, inactivation of Notch-1 resulted in a four-fold increased expression of the numb protein. Collectively, our data point to the Notch-1 pathway as being a potential key regulator of EMT in colorectal tumors and as such, may be of therapeutic or prognostic utility. Citation Format: Alex Fender, Makenzie Nutter, Timothy Fitzgerald, Fred Bertrand, George Sigounas. Notch-1 regulated stemness and EMT in colorectal cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1952. doi:10.1158/1538-7445.AM2014-1952

Isolation of cancer stem cells from three human glioblastoma cell lines: characterization of two selected clones.

Cancer stem cells (CSC) were isolated via a non-adherent neurosphere assay from three glioma cell lines: LI, U87, and U373. Using a clonal assay, two clones (D2 and F11) were selected from spheres derived from LI cells and were characterized for the: expression of stem cell markers (CD133, Nestin, Musashi-1 and Sox2); proliferation; differentiation capability (determined by the expression of GalC, βIII-Tubulin and GFAP); Ca2+ signaling and tumorigenicity in nude mice. Both D2 and F11 clones expressed higher levels of all stem cell markers with respect to the parental cell line. Clones grew more slowly than LI cells with a two-fold increase in duplication time. Markers of differentiation (βIII-Tubulin and GFAP) were expressed at high levels in both LI cells and in neurospheres. The expression of Nestin, Sox2, and βIII-Tubulin was down-regulated in D2 and F11 when cultured in serum-containing medium, whereas Musashi-1 was increased. In this condition, duplication time of D2 and F11 increased without reaching that of LI cells. D2, F11 and parental cells did not express voltage-dependent Ca2+-channels but they exhibited increased intracellular Ca2+ levels in response to ATP. These Ca2+ signals were larger in LI cells and in spheres cultured in serum-containing medium, while they were smaller in serum-free medium. The ATP treatment did not affect cell proliferation. Both D2 and F11 induced the appearance of tumors when ortotopically injected in athymic nude mice at a density 50-fold lower than that of LI cells. All these data indicate that both clones have characteristics of CSC and share the same stemness properties. The findings regarding the expression of differentiation markers and Ca2+-channels show that both clones are unable to reach the terminal differentiation. Both D2 and F11 might represent a good model to improve the knowledge on CSC in glioblastoma and to identify new therapeutic approaches.

Structure and evolution analysis of pollen receptor-like kinase in Zea mays and Arabidopsis thaliana

Receptor-like kinase (RLKs) is an important member in protein kinase family which is widely involved in plant growth, development and defense responses. It is significant to analyze the kinase structure and evolution of pollen RLKs in order to study their mechanisms. In our study, 64 and 73 putative pollen RLKs were chosen from maize and Arabidopsis. Phylogenetic analysis showed that the pollen RLKs were conservative and might had existed before divergence between monocot and dicot which were mainly concentrated in RLCK-VII and LRR-III two subfamilies. Chromosomal localization and gene duplication analysis showed the expansion of pollen RLKs were mainly caused by segmental duplication. By calculating Ka/Ks value of extracellular domain, intracellular domain and kinase domain in pollen RLKs, we found that the pollen RLKs duplicated genes had mainly experienced the purifying selection, while maize might have experienced weaker purifying selection. Meanwhile, extracellular domain might have experienced stronger diversifying selection than intracellular domain in both species. Estimation of duplication time showed that the duplication events of Arabidopsis have occurred approximately between 18 and 69 million years ago, compared to 0.67–170 million years ago of maize.

Isolation, Culture, and Characterization of Human Dental Pulp Mesenchymal Stem Cells

Introduction Based on previous researches, dental pulp stem cells (DPSCs) are easily accessible with limited morbidity after collection. Their embryonic origin, from neural crests, explains their multipotency. DPSCs are primarily derived from the pulp tissues of the teeth.Objective: This study was undertaken to isolate, culture, and characterize two different third molar and first premolar human dental pulp mesenchymal stem cells. Methods: To obtain DPSCs, pulp tissues were removed from human third molar and first premolar teeth. They were digested by treating with collagenase type I. The extracted cells were passaged from primary culture up to passage 8. To enumerate the cells, the specified number of the cells were seeded into 24-well culture plates and the number of cells were counted to determine the growth curves of isolated cells from both type of teeth and the population duplication time (PDT) was determined. PCR and karyotype assays were performed to determine the cell surface mesenchymal markers and demonstrate the genetic stability of DPSCs, respectively. Results: The human DPSCs from both the third molar and the first premolar teeth were spindle-shaped in morphology. As growth curves showed, the proliferation rate of DPSCs in passage 8 among both teeth was different denoting to an increase in doubling time in the first premolar when compared to the third molar teeth. Normal karyotype of DPSCs derived from both the third molar and the first premolar teeth were exhibited. The isolated dental pulp stem cells expressed mesenchymal stem cell surface antigen. These cells were positive for CD73 but were negative for CD45 (hematopoietic stem cell marker). Conclusion: DPSCs can be an attractive candidate in regenerative medicine. As growth curves revealed, the first premolar teeth are suggested as a better source of MSC isolation. Keywords: Dental pulp, Growth curve, Mesenchymal stem cell, Molar tooth, Premolar tooth.

Genome tailoring powered production of isobutanol in continuous CO2/H2 blend fermentation using engineered acetogen biocatalyst

The cell energy fraction that powered maintenance and expression of genes encoding pro-phage elements, pta-ack cluster, early sporulation, sugar ABC transporter periplasmic proteins, 6-phosphofructokinase, pyruvate kinase, and fructose-1,6-disphosphatase in acetogen Clostridium sp. MT871 was re-directed to power synthetic operon encoding isobutanol biosynthesis at the expense of these genes achieved via their elimination. Genome tailoring decreased cell duplication time by 7.0 ± 0.1 min (p < 0.05) compared to the parental strain, with intact genome and cell duplication time of 68 ± 1 min (p < 0.05). Clostridium sp. MT871 with tailored genome was UVC-mutated to withstand 6.1 % isobutanol in fermentation broth to prevent product inhibition in an engineered commercial biocatalyst producing 5 % (674.5 mM) isobutanol during two-step continuous fermentation of CO2/H2 gas blend. Biocatalyst Clostridium sp. MT871RG- 11IBR6 was engineered to express six copies of synthetic operon comprising optimized synthetic format dehydrogenase, pyruvate formate lyase, acetolactate synthase, acetohydroxyacid reductoisomerase, 2,3-dihydroxy-isovalerate dehydratase, branched-chain alpha-ketoacid decarboxylase gene, aldehyde dehydrogenase, and alcohol dehydrogenase, regaining cell duplication time of 68 ± 1 min (p < 0.05) for the parental strain. This is the first report on isobutanol production by an engineered acetogen biocatalyst suitable for commercial manufacturing of this chemical/fuel using continuous fermentation of CO2/H2 blend thus contributing to the reversal of global warming.

Influence of the shear stress and salinity on Anammox biofilms formation: modelling results

Anammox biomass has a long duplication time and low yield, thus the process must be operated in reactors with good sludge retention, such as biofilm systems. Therefore, it would be important to research the ability of Anammox biomass to form biofilms under different conditions. The effects of shear stress and salinity (NaCl and CaCl2) on Anammox biofilm formation were studied. Anammox bacteria showed good attachment capacity, with an initial adhesion phase lasting for 5-7days at the different flow rates tested (Reynolds numbers 54, 63, 188 and 400). A four-parameter model was developed and the experimental data fitted well into the model. The presence of 5g/L of each of the two salts favoured the formation of Anammox biofilm. The effects of CaCl2 were stronger than those caused by NaCl. 15g/L of NaCl was detrimental for the biofilm, probably due to an inhibitory effect.

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.

Post-fire recovery of savanna vegetation from rocky outcrops

The degree of stability of the Cerrado following burning is widely discussed in literature. However, little is known about the effects of fire on the resilience of savanna formations from rocky outcrops, known as “cerrado rupestre”. We tested the hypothesis that floristic, structural, and dynamics parameters of a tree–shrub cerrado rupestre community have high stability following fire. We sampled the woody vegetation (plants with trunk diameter equal or larger than 3cm as measured 30cm above ground) in ten 20m×50m plots before (2008) and after (2009, 2010, 2011, and 2012) an accidental burning in September 2008. Species richness and composition did not change. However, plant density and basal area were reduced after the fire, but began to increase in the second year after the fire. Recruitment rate was higher than mortality. Basal areal and half-life also increased, while time of duplication decreased. The community recovered relatively well from the fire, presenting high resilience to burning. However, it seemed not to have attained a complete restoration to the state prior to the fire after four years.

Evolution of the Relaxin/Insulin-Like Gene Family in Anthropoid Primates

The relaxin/insulin-like gene family includes signaling molecules that perform a variety of physiological roles mostly related to reproduction and neuroendocrine regulation. Several previous studies have focused on the evolutionary history of relaxin genes in anthropoid primates, with particular attention on resolving the duplication history of RLN1 and RLN2 genes, which are found as duplicates only in apes. These studies have revealed that the RLN1 and RLN2 paralogs in apes have a more complex history than their phyletic distribution would suggest. In this regard, alternative scenarios have been proposed to explain the timing of duplication, and the history of gene gain and loss along the organismal tree. In this article, we revisit the question and specifically reconstruct phylogenies based on coding and noncoding sequence in anthropoid primates to readdress the timing of the duplication event giving rise to RLN1 and RLN2 in apes. Results from our phylogenetic analyses based on noncoding sequence revealed that the duplication event that gave rise to the RLN1 and RLN2 occurred in the last common ancestor of catarrhine primates, between ∼44.2 and 29.6 Ma, and not in the last common ancestor of apes or anthropoids, as previously suggested. Comparative analyses based on coding and noncoding sequence suggests an event of convergent evolution at the sequence level between co-ortholog genes, the single-copy RLN gene found in New World monkeys and the RLN1 gene of apes, where changes in a fraction of the convergent sites appear to be driven by positive selection.

UVC-mutagenesis in acetogens: resistance to methanol, ethanol, acetone, or n-butanol in recombinants with tailored genomes as the step in engineering of commercial biocatalysts for continuous CO2/H2 blend fermentations

Time- and cost-efficient six-step UVC-mutagenesis was developed and validated to generate acetogen mutants with preliminary reduced genomes to prevent product inhibition in the to-be-engineered commercial biocatalysts. Genome reduction was performed via elimination of pta, ack, spo0A, spo0J and some pro-phage genes. UVC-mutants such as Clostridium sp. MT1784RG, Clostridium sp. MT653RG, Clostridium sp. MT896RG, and Clostridium sp. MT1962RG (all 4 share 97 % DNA homology with Clostridium ljungdahlii ATCC 55383) were selected based on resistance to methanol (3 M), ethanol (3.6 M), acetone (2.5 M), or n-butanol (0.688 M), respectively. As a part of the biocatalyst engineering algorithm, genome reduction step was associated with integration of attTn7 recognition sequence to the chromosomes of each of the above strains to prepare the defined integration sites for future integration of multi-copy synthetic operons encoding biosynthesis of methanol, ethanol, acetone or n-butanol. Reduced genome mutants had cell duplication times decreased compared to the same for the respective parental strains. All groups of mutants had decreased share of palmitic (C16:0) and increased share of oleic (C18:1) acids along with detection of isopropylstearate (C20) compared to the parental strains. Mutants resistant to acetone and n-butanol also had monounsaturated fatty acid (C20:1) not found in parental strains. Cyclopropane fatty acid (C21) was identified only in n-butanol resistant mutants.

Development of a low cost medium for Tetraselmis sp. growth and biochemical profile improvement

Event Abstract Back to Event Development of a low cost medium for Tetraselmis sp. growth and biochemical profile improvement Catarina Rosado Correia1*, Inês Póvoa2, Daniel F. Marques1, Carla Tecelão1, Victória Del Pino2 and Sérgio Miguel Leandro1 1 GIRM -Group of Investigation on Marine Resources, School of Tourism and Marine Technology, Campus 4 - Polytechnic Institute of Leiria, Portugal 2 Necton, S.A. - Portuguese Marine Cultures: Microalgae business Unit, Belamandil, Portugal In aquaculture, food quality improvement – especially microalgae – is mandatory. Despite having many applications in this industry, few genera of microalgae are actively used and exploited, mainly because of its lack of requirements, such as digestibility, size and lack of toxicity. Tetraselmis sp. is one of the most commonly used microalgae on aquaculture. Despite their nutritional profile, this is a highly demanding industry that requires constant improvement concerning cost production and productivity, and a biochemical profile for end usage. Improvements can be achieved through culture condition manipulation, changing, for instance, culture media’s composition. In order to achieve better biochemical profiles, productivity and lower production costs, three mediums were tested – NutriBloom [NB] (commercial medium used at Necton’s facilities), Simplex [S] (no addition of iron or any micronutrient) and Sea Mineral Solution [SMS], and Tetraselmis’s level of protein, carbohydrates, total lipid and PUFA’s profile were controlled at logarithmic and stationary phase, using classical techniques, according to Lowry (1951), Dubois (1956), Bligh and Dyer (1959) and Lepage & Roy (1986). SMS revealed better results than the others, achieving higher cell numbers, productivity and less duplication time. In logarithmic phase, this medium also had the higher lipid and PUFAs percentage. S medium showed higher protein content. In stationary phase, NB medium presented more proteins, lipid and sugars. S medium had better PUFAs percentage. Differences between micronutrient concentrations explain the verified variations in microalgae’s biochemical profile, developing a low-cost medium for Tetraselmis sp. culture. Keywords: Aquaculture, Biochemical profile, micronutrient, PUFA, Microalgae mass cultivation, Tetraselmis sp. Conference: IMMR | International Meeting on Marine Research 2014, Peniche, Portugal, 10 Jul - 11 Jul, 2014. Presentation Type: Poster Presentation Topic: BLUE BIOTECH Citation: Rosado Correia C, Póvoa I, Marques DF, Tecelão C, Del Pino V and Leandro S (2014). Development of a low cost medium for Tetraselmis sp. growth and biochemical profile improvement. Front. Mar. Sci. Conference Abstract: IMMR | International Meeting on Marine Research 2014. doi: 10.3389/conf.fmars.2014.02.00049 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 10 May 2014; Published Online: 18 Jul 2014. * Correspondence: Dr. Catarina Rosado Correia, GIRM -Group of Investigation on Marine Resources, School of Tourism and Marine Technology, Campus 4 - Polytechnic Institute of Leiria, 2520–641 Peniche, Portugal, catarinasrcorreia@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Catarina Rosado Correia Inês Póvoa Daniel F Marques Carla Tecelão Victória Del Pino Sérgio Miguel Leandro Google Catarina Rosado Correia Inês Póvoa Daniel F Marques Carla Tecelão Victória Del Pino Sérgio Miguel Leandro Google Scholar Catarina Rosado Correia Inês Póvoa Daniel F Marques Carla Tecelão Victória Del Pino Sérgio Miguel Leandro PubMed Catarina Rosado Correia Inês Póvoa Daniel F Marques Carla Tecelão Victória Del Pino Sérgio Miguel Leandro Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Why is Mycobacterium Tuberculosis Hard to Grow? The Principle of Biorelativity Explains

Comparing the lifespan and the proliferative potential of E. coli and MTB, we see a reverse relationship. E. coli live short, and grow fast. It just takes 18-20 minutes for them to duplicate. Conversely, MTBs live long, are quite tolerant to different environments, and grow so slowly that their duplication time exceeds 18 hrs. The duplication time of mycobacterium leprae is even longer, so that all the cultivation efforts have failed. Although nobody knows exactly how long these bacteria can live since they cannot be cultivated, it can be postulated that they live very long. That explains why leprosy is so difficult to cure.

Modified PEHPS medium as an alternative for the in vitro culture of Giardia lamblia.

Commercial culture media present interlot variations in biological activity. We have previously designed a homemade and economic culture medium, PEHPS medium, for the axenic cultivation of Entamoeba histolytica and Trichomonas vaginalis. Trophozoites of amoebae and trichomonads grow well in this medium. Furthermore, the medium is stable for several months when stored frozen or refrigerated. The objective of this work was to modify PEHPS medium to support the in vitro growth of Giardia lamblia. Inocula of 5 × 103 trophozoites/mL of G. lamblia were incubated at 36.5°C in modified PEHPS or TYI-S-33 medium. Then, the growths of the three Giardia strains in both media were compared. The logarithmic growth phase lasted 72 h; the mean yield of the strains ranged from 10.06 to 11.43 × 105 Giardia trophozoites/mL, and the range of duplication time in the three strains was from 5.67 to 6.06 in modified PEHPS medium. These growth characteristics were not significantly different from those obtained with TYI-S-33 medium. We conclude that modified PEHPS medium might be used for the axenic cultivation of G. lamblia.

Second-generation bioethanol production from water hyacinth and duckweed in Izmir: A case study

Water hyacinth and duckweed are both aquatic plants that live in clean water and wastewater. They have excellent filtration ability of nitrogen and supply oxygen to water while cleaning it up. The vegetative reproduction rates of these two plants are really high and it is about 8 days that of duplication time. Because of these features, water hyacinth and duckweed are useful for wastewater treatment. Also production of second-generation bioethanol from these plants is proper due to their cellulose ratios and carbohydrate potentials. In this study, the process of bioethanol production from water hyacinth and duckweed was studied by taking into account the potential of cultivation values and usability in wastewater treatment procedures in Izmir. Different microorganisms, yeast and bacteria (Saccharomyces cerevisiae, Pichia stipitis, and Clostridium thermocellum) have been considered to identify the best process of ethanol production, considering Turkey's policy regarding biofuels.

Evolution after whole-genome duplication: a network perspective.

Gene duplication plays an important role in the evolution of genomes and interactomes. Elucidating how evolution after gene duplication interplays at the sequence and network level is of great interest. In this work, we analyze a data set of gene pairs that arose through whole-genome duplication (WGD) in yeast. All these pairs have the same duplication time, making them ideal for evolutionary investigation. We investigated the interplay between evolution after WGD at the sequence and network levels and correlated these two levels of divergence with gene expression and fitness data. We find that molecular interactions involving WGD genes evolve at rates that are three orders of magnitude slower than the rates of evolution of the corresponding sequences. Furthermore, we find that divergence of WGD pairs correlates strongly with gene expression and fitness data. Because of the role of gene duplication in determining redundancy in biological systems and particularly at the network level, we investigated the role of interaction networks in elucidating the evolutionary fate of duplicated genes. We find that gene neighborhoods in interaction networks provide a mechanism for inferring these fates, and we developed an algorithm for achieving this task. Further epistasis analysis of WGD pairs categorized by their inferred evolutionary fates demonstrated the utility of these techniques. Finally, we find that WGD pairs and other pairs of paralogous genes of small-scale duplication origin share similar properties, giving good support for generalizing our results from WGD pairs to evolution after gene duplication in general.

Optimal surgical timing and treatment of thumb duplication in children

To investigate the optimal surgical timing and treatment of congenital duplication of the thumb in children. A clinical study was performed on 154 fingers of the 132 patients (including 85 males, 47 females;mean age (1.53 +/- 2.47) years; ranged from 2 months to 13 years). Duplicated thumbs were surgically treated from December 2007 to February 2012. All patients underwent detailed physical examination and radiological assessment. Surgical methods should be selected according to the age, Wassel classification and deformity. The operation steps included resection of the most hypoplastic thumb, followed by skin flap plasty, tendon shift (transplantation) , reconstruction of collateral ligament and articular capsule. 11 cases over the age of 6 underwent osteotomy discretion as appropriate. A total of 117 fingers of the 104 patients were followed up for an average 36. 7 months (range,6-55 months). We adopted upgrade Tada standard to evaluate the follow-up results as excellent in 77 thumbs, good in 21 thumbs, fair in 15 thumbs and poor in 4 thumbs. Three thumbs appeared secondary angular deformity 2 years after operation and one thumb appeared residual osteoepiphysis in the radial side of metacarpophalangeal joint 3 years after operation. The appearance and the function were almost normal after second operation. The optimal surgical timing of congenital duplication of thumb should be based on the appearance of thumb ossification center. The surgical timing of Wassel type- I and II should be chosen at 1. 5 years old when the ossification center of distal phalanx appears, Wassel type-III and IV should be chosen at 1 year old when the ossification center of proximal phalanx appears, Wassel type-V and VI should be chosen at 2. 5 years old when the ossification center of metacarpal appears, and Wassel type-VII should be chosen at 2. 5 years old. The surgical method should be selected on individualized principle. The key points are reconstruction of collateral ligament, tendon and articular capsule and correction of ulnar deviation (or radial deviation).

In vitro selection of bacteria with potential for use as probiotics in marine shrimp culture

The objective of this work was to isolate strains of lactic acid bacteria with probiotic potential from the digestive tract of marine shrimp (Litopenaeus vannamei), and to carry out in vitro selection based on multiple characters. The ideotype (ideal proposed strain) was defined by the highest averages for the traits maximum growth velocity, final count of viable cells, and inhibition halo against nine freshwater and marine pathogens, and by the lowest averages for the traits duplication time and resistance of strains to NaCl (1.5 and 3%), pH (6, 8, and 9), and biliary salts (5%). Mahalanobis distance (D²) was estimated among the evaluated strains, and the best ones were those with the shortest distances to the ideotype. Ten bacterial strains were isolated and biochemically identified as Lactobacillus plantarum (3), L. brevis (3), Weissella confusa (2), Lactococcus lactis (1), and L. delbrueckii (1). Lactobacillus plantarum strains showed a wide spectrum of action and the largest inhibition halos against pathogens, both Gram-positive and negative, high growth rate, and tolerance to all evaluated parameters. In relation to ideotype, L. plantarum showed the lowest Mahalanobis (D²) distance, followed by the strains of W. confusa, L. brevis, L. lactis, and L. delbrueckii. Among the analyzed bacterial strains, those of Lactobacillus plantarum have the greatest potential for use as a probiotic for marine shrimp.

ZrFsy1, a High-Affinity Fructose/H+ Symporter from Fructophilic Yeast Zygosaccharomyces rouxii

Zygosaccharomyces rouxii is a fructophilic yeast than can grow at very high sugar concentrations. We have identified an ORF encoding a putative fructose/H+ symporter in the Z. rouxii CBS 732 genome database. Heterologous expression of this ORF in a S. cerevisiae strain lacking its own hexose transporters (hxt-null) and subsequent kinetic characterization of its sugar transport activity showed it is a high-affinity low-capacity fructose/H+ symporter, with Km 0.45±0.07 mM and Vmax 0.57±0.02 mmol h−1 (gdw) −1. We named it ZrFsy1. This protein also weakly transports xylitol and sorbose, but not glucose or other hexoses. The expression of ZrFSY1 in Z. rouxii is higher when the cells are cultivated at extremely low fructose concentrations (<0.2%) and on non-fermentable carbon sources such as mannitol and xylitol, where the cells have a prolonged lag phase, longer duplication times and change their microscopic morphology. A clear phenotype was determined for the first time for the deletion of a fructose/H+ symporter in the genome where it occurs naturally. The effect of the deletion of ZrFSY1 in Z. rouxii cells is only evident when the cells are cultivated at very low fructose concentrations, when the ZrFsy1 fructose symporter is the main active fructose transporter system.