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Dive into the research topics where Berat Z. Haznedaroglu is active.

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Featured researches published by Berat Z. Haznedaroglu.


BMC Genomics | 2011

Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels

Hamid Rismani-Yazdi; Berat Z. Haznedaroglu; Kyle Bibby; Jordan Peccia

BackgroundBiodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production.ResultsNext generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) identifiers. These analyses identified the majority of lipid and starch biosynthesis and catabolism pathways in D. tertiolecta.ConclusionsThe construction of metabolic pathways involved in the biosynthesis and catabolism of fatty acids, triacylglycrols, and starch in D. tertiolecta as well as the assembled transcriptome provide a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock.


Biotechnology for Biofuels | 2012

Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation

Hamid Rismani-Yazdi; Berat Z. Haznedaroglu; Carol Hsin; Jordan Peccia

BackgroundThe lack of sequenced genomes for oleaginous microalgae limits our understanding of the mechanisms these organisms utilize to become enriched in triglycerides. Here we report the de novo transcriptome assembly and quantitative gene expression analysis of the oleaginous microalga Neochloris oleoabundans, with a focus on the complex interaction of pathways associated with the production of the triacylglycerol (TAG) biofuel precursor.ResultsAfter growth under nitrogen replete and nitrogen limiting conditions, we quantified the cellular content of major biomolecules including total lipids, triacylglycerides, starch, protein, and chlorophyll. Transcribed genes were sequenced, the transcriptome was assembled de novo, and the expression of major functional categories, relevant pathways, and important genes was quantified through the mapping of reads to the transcriptome. Over 87 million, 77 base pair high quality reads were produced on the Illumina HiSeq sequencing platform. Metabolite measurements supported by genes and pathway expression results indicated that under the nitrogen-limiting condition, carbon is partitioned toward triglyceride production, which increased fivefold over the nitrogen-replete control. In addition to the observed overexpression of the fatty acid synthesis pathway, TAG production during nitrogen limitation was bolstered by repression of the β-oxidation pathway, up-regulation of genes encoding for the pyruvate dehydrogenase complex which funnels acetyl-CoA to lipid biosynthesis, activation of the pentose phosphate pathway to supply reducing equivalents to inorganic nitrogen assimilation and fatty acid biosynthesis, and the up-regulation of lipases—presumably to reconstruct cell membranes in order to supply additional fatty acids for TAG biosynthesis.ConclusionsOur quantitative transcriptome study reveals a broad overview of how nitrogen stress results in excess TAG production in N. oleoabundans, and provides a variety of genetic engineering targets and strategies for focused efforts to improve the production rate and cellular content of biofuel precursors in oleaginous microalgae.


Trends in Biotechnology | 2013

Nitrogen supply is an important driver of sustainable microalgae biofuel production

Jordan Peccia; Berat Z. Haznedaroglu; James Gutierrez; Julie B. Zimmerman

Favorable growth characteristics continue to generate interest in using triacylglycerides (TAGs) produced from microalgae for biodiesel feedstocks. In this opinion article, we suggest that due to the energy consumption associated with the production of external nitrogen fertilizers, the manner in which nitrogen is supplied to microalgae biorefineries will be an important driver of energy yields, sustainability, and commercial success. Schemes including the reuse of urban wastewater represent improvements on the overall energy balance, but will not allow for significant production of biofuels unless the nitrogen from the non-TAG portions of microalgae is recycled. Approaches to recycling nitrogen require an improved understanding of the tradeoffs between the different potential uses of the non-TAG microalgal portion (i.e., energy production via anaerobic digestion or thermal catalytic processes), and the development of nitrogen separation technologies.


Bioresource Technology | 2014

Evaluating microalgal integrated biorefinery schemes: empirical controlled growth studies and life cycle assessment.

Lindsay Soh; Mahdokht Montazeri; Berat Z. Haznedaroglu; Cuchulain Kelly; Jordan Peccia; Matthew J. Eckelman; Julie B. Zimmerman

Two freshwater and two marine microalgae species were grown under nitrogen replete and deplete conditions evaluating the impact on total biomass yield and biomolecular fractions (i.e. starch, protein, and lipid). A life cycle assessment was performed to evaluate varying species/growth conditions considering each biomass fraction and final product substitution based on energy consumption, greenhouse gas emissions (GHG), and eutrophication potential. Lipid for biodiesel was assumed as the primary product. Protein and carbohydrate fractions were processed as co-products. Composition of the non-lipid fraction presented significant trade-offs among biogas production, animal feed substitution, nutrient recycling, and carbon sequestration. Maximizing total lipid productivity rather than lipid content yielded the least GHG emissions. A marine, N-deplete case with relatively low lipid productivity but effective nutrient recycling had the lowest eutrophication impacts. Tailoring algal species/growth conditions to optimize the mix of biomolecular fractions matched to desired products and co-products can enable a sustainable integrated microalgal biorefinery.


Environmental Science & Technology | 2010

Correlating Transport Behavior with Cell Properties for Eight Porcine Escherichia coli Isolates

Carl H. Bolster; Kimberly L. Cook; Ian M. Marcus; Berat Z. Haznedaroglu; Sharon L. Walker

In this study we investigate how growth stage and depositional environment affect variability of cell properties and transport behavior of eight porcine E. coli isolates. We compared the surface properties for cells harvested during exponential and stationary growth phase and their transport behavior through columns packed with either uncoated or Fe-coated quartz sand. We then investigated correlations between measured cell properties and fitted bacterial attachment efficiencies. For both growth stages we found that bacterial attachment efficiencies in the uncoated quartz sand varied among the eight different isolates by over an order of magnitude whereas attachment efficiencies in the Fe-coated sands varied by a factor of less than two. With the exception of one isolate, growth condition had minimal impact on attachment efficiencies to the uncoated sands. A strong and statistically significant inverse relationship was observed between bacterial attachment efficiencies in the uncoated quartz sand columns and log-transformed zeta potential, whereas a mild yet statistically significant relationship between bacterial attachment efficiencies in the Fe-coated sands and cell width was observed. For the experimental conditions used in our study, we found that variability in E. coli transport was more dependent on the depositional environment than on growth conditions.


Critical Reviews in Oncology Hematology | 2012

Pleiotropic cellular, hemostatic, and biological actions of Ankaferd hemostat

Berat Z. Haznedaroglu; Yavuz Beyazit; Sharon L. Walker; Ibrahim C. Haznedaroglu

Sustaining hemostasis in clinical hemorrhages is a challenging task and requires extensive effort to stabilize medically hard-to-treat traumatic injuries. Several hemostatic agents are preferred to control external and internal bleedings, yet commercially available products are not sufficiently effective or fast-acting to achieve hemostasis in extreme cases. Ankaferd Blood Stopper (ABS) is a herbal extract traditionally used as a hemostatic agent. Recent studies have shown that ABS could be utilized successfully as a hemostatic agent for the management of clinical hemorrhages when conventional methods were ineffective. This review serves as a basis to provide recent findings on several applications of ABS, specifically preclinical, biological, and clinical studies both in vitro and in vivo. Another section focuses on the ultrastructural morphology and protein network formation of ABS in an effort to understand the hemostatic mechanisms of this unique agent at tissue level.


BMC Bioinformatics | 2012

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Berat Z. Haznedaroglu; Darryl Reeves; Hamid Rismani-Yazdi; Jordan Peccia

BackgroundThe k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA) were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs) were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog identifiers (KOIs), and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly.ResultsAnalyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63). For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs) in the assemblies of individual k-mers (k-19 to k-63) that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented.ConclusionsThis study demonstrated that different k-mer choices result in various quantities of unique contigs per single k-mer assembly which affects biological information that is retrievable from the transcriptome. This undesirable effect can be minimized, but not eliminated, with clustering of multi-k assemblies with redundancy removal. The complete extraction of biological information in de novo transcriptomics studies requires both the production of a CA and efforts to identify unique contigs that are present in individual k-mer assemblies but not in the CA.


Soft Matter | 2013

Carbon nanotube bundling: influence on layer-by-layer assembly and antimicrobial activity

Seyma Aslan; Jukka Määttä; Berat Z. Haznedaroglu; Jesse P. M. Goodman; Lisa D. Pfefferle; Menachem Elimelech; Emmanuel Pauthe; Maria Sammalkorpi; Paul R. Van Tassel

Antimicrobial surfaces are needed for many health care applications. Single walled carbon nanotubes (SWNT) have shown promise as antimicrobial agents, but important questions persist concerning the effects of tube bundling, a common phenomenon owing to strong hydrophobicity. We investigate here the influence of bundling on the layer-by-layer (LbL) assembly of SWNT with charged polymers, and on the antimicrobial properties of the resultant films. We employ a poly(ethylene glycol) functionalized phospholipid (PL-PEG) to disperse SWNT in aqueous solution, and consider cases where SWNT are dispersed (i) as essentially isolated objects and (ii) as small bundles. Quartz crystal microgravimetry with dissipation (QCMD) and ellipsometry measurements show the bundled SWNT system to adsorb in an unusually strong fashion – with layers twice (when hydrated) and three times (when dried) as thick as those of isolated SWNT. Molecular dynamics simulation reveals a lower PL-PEG density and degree of solution extension on bundled versus isolated SWNT, suggesting thicker adsorbed layers may result from suppressed steric repulsion between bundled nanotubes. Enhanced van der Waals attraction in the bundled system may also play a role. Scanning electron micrographs reveal Escherichia coli on films with bundled SWNT to be essentially engulfed by the nanotubes, whereas the bacteria rest upon films with isolated SWNT. While both systems inactivate 90% of bacteria in 24 h, the bundled SWNT system is “fast-acting,” reaching this inactivation rate in 1 h. This study demonstrates the significant impact of SWNT bundling on LbL assembly and antimicrobial activity, explores the molecular basis of nanotube–nanotube interactions, and demonstrates the possibility of bacteria-engulfing, fast-acting, SWNT-based antimicrobial coatings.


Biofuels | 2018

Effects of macro and micronutrients on neutral lipid accumulation in oleaginous microalgae

Mohsen Ghafari; Behzad Rashidi; Berat Z. Haznedaroglu

ABSTRACT In this study, effects of key macro and micronutrients on neutral lipid accumulation of six oleaginous microalgae species were investigated. For each nutrient, three different concentrations (0.5×, 1×, and 2×) were tested individually and compared to the most commonly utilized growth medium recipes. Neutral lipid accumulation was quantified using specific nonpolar dyes with long-wavelength absorption and fluorescence. Tested microalgae species showed different lipid accumulation responses to changes in nutrient concentrations. Optimum concentrations of nutrients were selected for each species based on either the most lipid productive case or no significant difference to the lipid contents. Selected optimal conditions were also validated where Chlorella sorokiniana, Chlorella vulgaris, Dunaliella tertiolecta, and Tetraselmis suecica showed 4, 10, 34, and 39% higher lipid productivities per unit volume, respectively. Botryococcus sudeticus and Ettlia oleoabundans did not show improved lipid productivities. Extensive optimization of macro and micronutrient concentrations offers several benefits of decreased material inputs and waste generation, improved biomass productivity, and overall cost savings.


Biotechnology for Biofuels | 2018

Time-series lipidomic analysis of the oleaginous green microalga species Ettlia oleoabundans under nutrient stress

Eryn K. Matich; Mohsen Ghafari; E. Camgoz; E. Caliskan; Blaine A. Pfeifer; Berat Z. Haznedaroglu; G. E. Atilla-Gokcumen

BackgroundMicroalgae are uniquely advantageous organisms cultured and harvested for several value-added biochemicals. A majority of these compounds are lipid-based, such as triacylglycerols (TAGs), which can be used for biofuel production, and their accumulation is most affected under nutrient stress conditions. As such, the balance between cellular homeostasis and lipid metabolism becomes more intricate to achieve efficiency in bioproduct synthesis. Lipidomics studies in microalgae are of great importance as biochemical diversity also plays a major role in lipid regulation among oleaginous species.MethodsThe aim of this study was to analyze time-series changes in lipid families produced by microalga under different nutrient conditions and growth phases to gain comprehensive information at the cellular level. For this purpose, we worked with a highly adaptable, oleaginous, non-model green microalga species, Ettlia oleoabundans (a.k.a. Neochloris oleoabundans). Using a mass spectrometry-based untargeted and targeted metabolomics’ approach, we analyzed the changes in major lipid families under both replete and deplete nitrogen and phosphorus conditions at four different time points covering exponential and stationary growth phases.ResultsComprehensive analysis of the lipid metabolism highlighted the accumulation of TAGs, which can be utilized for the production of biodiesel via transesterification, and depletion of chlorophylls and certain structural lipids required for photosynthesis, under nutrient deprived conditions. We also found a correlation between the depletion of digalactosyldiacylglycerols (DGDGs) and sulfoquinovosyldiacylglycerols (SQDGs) under nutrient deprivation.ConclusionsHigh accumulation of TAGs under nutrient limitation as well as a depletion of other lipids of interest such as phosphatidylglycerols (PGs), DGDGs, SQDGs, and chlorophylls seem to be interconnected and related to the microalgal photosynthetic efficiency. Overall, our results provided key biochemical information on the lipid regulation and physiology of a non-model green microalga, along with optimization potential for biodiesel and other value-added product synthesis.

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Mohsen Ghafari

State University of New York System

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Scott A. Bradford

Agricultural Research Service

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Hyunjung Kim

Chonbuk National University

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Blaine A. Pfeifer

State University of New York System

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Eryn K. Matich

State University of New York System

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