Biotechnology Commons^™

Identification Of Genes Encoding Enzymes Catalyzing The Early Steps Of Carrot Polyacetylene Biosynthesis, Lucas Busta, Won Cheol Yim, Evan William Labrant, Peng Wang, Lindsey Grimes, Kiah Malyszka, John C. Cushman, Patricia Santos, Dylan K. Kosma, Edgar B. Cahoon

Department of Biochemistry: Faculty Publications

Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is largely unknown. To begin filling this gap and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp. sativus). Using gas chromatography and mass spectrometry, we identified three known polyacetylenes and assigned provisional structures to two novel polyacetylenes. We …

Role Of Selenof As A Gatekeeper Of Secreted Disulfide-Rich Glycoproteins, Sun Hee Yim, Robert A. Everley, Frank A. Schildberg, Sang-Goo Lee, Andrea Orsi, Zachary R. Barbati, Kutay Karatepe, Dmitry E. Fomenko, Petra A. Tsuji, Hongbo R. Luo, Steven P. Gygi, Roberto Sitia, Arlene H. Sharpe, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Selenof (15-kDa selenoprotein; Sep15) is an endoplasmic reticulum (ER)-resident thioredoxin-like oxidoreductase that occurs in a complex with UDPglucose: glycoprotein glucosyltransferase. We found that Selenof deficiency in mice leads to elevated levels of non-functional circulating plasma immunoglobulins and increased secretion of IgM during in vitro splenic B cell differentiation. However, Selenof knockout animals show neither enhanced bacterial killing capacity nor antigen-induced systemic IgM activity, suggesting that excess immunoglobulins are not functional. In addition, ER-to-Golgi transport of a target glycoprotein was delayed in Selenof knockout embryonic fibroblasts, and proteomic analyses revealed that Selenof deficiency is primarily associated with antigen presentation and ER-to-Golgi …

Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle E. Howell, Karin V. Van Dijk, Christine S. Booth, Tomáš Helikar, Brian A. Couch, Rebecca Roston

Department of Biochemistry: Faculty Publications

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7).

Structural Basis For The Substrate Inhibition Of Proline Utilization A By Proline, David A. Korasick, Travis A. Pemberton, Benjamin W. Arentson, Donald F. Becker, John J. Tanner

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) is a bifunctional flavoenzyme that catalyzes the two-step oxidation of L-proline to L-glutamate using spatially separated proline dehydrogenase (PRODH) and L-glutamate-y-semialdehyde dehydrogenase (GSALDH) active sites. Substrate inhibition of the coupled PRODH-GSALDH reaction by proline is a common kinetic feature of PutAs, yet the structural basis for this phenomenon remains unknown. To understand the mechanism of substrate inhibition, we determined the 2.15 Å resolution crystal structure of Bradyrhizobium japonicum PutA complexed with proline. Proline was discovered in five locations remote from the PRODH active site. Most notably, strong electron density indicated that proline bound tightly to the …

Lncrna Meg3 Protects Endothelial Function By Regulating The Dna Damage Response, Mohamed Sham Shihabudeen Haider Ali, Xiao Cheng, Matthew Moran, Stefan Haemmig, Michael J. Naldrett, Sophie Alvarez, Mark W. Feinberg, Xinghui Sun

Department of Biochemistry: Faculty Publications

The role of long non-coding RNAs (lncRNAs) in regulating endothelial function through the DNA damage response (DDR) remains poorly understood. In this study, we demonstrate that lncRNA maternally expressed gene 3 (Meg3) interacts with the RNA binding protein polypyrimidine tract binding protein 3 (PTBP3) to regulate gene expression and endothelial function through p53 signaling a major coordinator of apoptosis and cell proliferation triggered by the DDR. Meg3 expression is induced in endothelial cells (ECs) upon p53 activation. Meg3 silencing induces DNA damage, activates p53 signaling, increases the expression of p53 target genes, promotes EC apoptosis, and inhibits EC proliferation. Mechanistically, …

Long-Chain Omega-3 Polyunsaturated Fatty Acids Modulate Mammary Gland Composition And Inflammation, Saraswoti Khadge, Geoffrey M. Thiele, J. Graham Sharp, Timothy R. Mcguire, Lynell W. Klassen, Paul N. Black, Concetta Dirusso, James Talmadge

Department of Biochemistry: Faculty Publications

Studies in rodents have shown that dietary modifications as mammary glands (MG) develop, regulates susceptibility to mammary tumor initiation. However, the effects of dietary PUFA composition on MGs in adult life, remains poorly understood. This study investigated morphological alterations and inflammatory microenvironments in the MGs of adult mice fed isocaloric and isolipidic liquid diets with varying compositions of omega (ω)-6 and long-chain (Lc)-ω3FA that were pair-fed. Despite similar consumption levels of the diets, mice fed the ω-3 diet had significantly lower body-weight gains, and abdominal-fat and mammary fat pad (MFP) weights. Fatty acid analysis showed significantly higher levels of Lc-ω-3FAs …

Dietary Omega-3 And Omega-6 Polyunsaturated Fatty Acids Modulate Hepatic Pathology, Saraswoti Khadge, J. Graham Sharp, Geoffrey M. Thiele, Timothy R. Mcguire, Lynell W. Klassen, Michael J. Duryee, Holly C. Britton, Jordan Beck, Paul N. Black, Concetta Dirusso, James Talmadge

Department of Biochemistry: Faculty Publications

Recent evidence has suggested that dietary polyunsaturated fatty acids (PUFAs) modulate inflammation; however, few studies have focused on the pathobiology of PUFA using isocaloric and isolipidic diets and it is unclear if the associated pathologies are due to dietary PUFA composition, lipid metabolism or obesity, as most studies compare diets fed ad libitum. Our studies used isocaloric and isolipidic liquid diets (35% of calories from fat), with differing compositions of omega (ω)-6 or long chain (Lc) ω-3 PUFA that were pair-fed and assessed hepatic pathology, inflammation and lipid metabolism. Consistent with an isocaloric, pair-fed model we observed no significant difference …

Adenosine Has Two Faces: Regionally Dichotomous Adenosine Tone In A Model Of Epilepsy With Comorbid Sleep Disorders, Ted J. Warren, Timothy A. Simeone, D. David Smith, Ryan Grove, Jiri Adamec, Kaeli K. Samson, Harrison M. Roundtree, Deepak Madhavan, Kristina A. Simeone

Department of Biochemistry: Faculty Publications

Objective: Adenosine participates in maintaining the excitatory/inhibitory balance in neuronal circuits. Studies indicate that adenosine levels in the cortex and hippocampus increase and exert sleep pressure in sleep-deprived and control animals, whereas in epilepsy reduced adenosine tone promotes hyperexcitability. To date, the role of adenosine in pathological conditions that result in both seizures and sleep disorders is unknown. Here, we determined adenosine tone in sleep and seizure regulating brain regions of Kv1.1 knockout (KO) mice, a model of temporal epilepsy with comorbid sleep disorders.

Methods: 1) Reverse phase-high performance liquid chromatography (RP-HPLC) was performed on brain tissue to determine levels …

Multiple Factors Drive Variation Of Forest Root Biomass In Southwestern China, Hao Zhang, Kelin Wang, Zhaoxia Zeng, Zhigang Zou, Yanfang Xu, Fuping Zeng

Nebraska Center for Biotechnology: Faculty and Staff Publications

The roots linking the above-ground organs and soil are key components for estimating net primary productivity and carbon sequestration of forests. The patterns and drivers of root biomass in forest have not been examined well at the regional scale, especially for the widely distributed forest ecosystems in southwestern China. We attempted to determine the spatial patterns of root biomass (RB, Mg/ha), annual increment root biomass (AIRB, Mg/ha/year), ratio of root and above-ground (RRA), and the relative contributions of abiotic and biotic factors that drive the variation of root biomass. Forest biomass and multiple factors (climate, soil, forest types, and stand …

Diversity And Functional Evolution Of Terpene Synthases In Dictyostelid Social Amoebae, Xinlu Chen, Tobias G. Kollner, Gad Shaulsky, Qidong Jia, Jeroen S. Dickschat, Jonathan Gershenzon, Feng Chen

Nebraska Center for Biotechnology: Faculty and Staff Publications

Dictyostelids, or social amoebae, have a unique life style in forming multicellular fruiting bodies from unicellular amoeboids upon starvation. Recently, dictyostelids were found to contain terpene synthase (TPS) genes, a gene type of secondary metabolism previously known to occur only in plants, fungi and bacteria. Here we report an evolutionary functional study of dictyostelid TPS genes. The number of TPS genes in six species of dictyostelids examined ranges from 1 to 19; and the model species Dictyostelium purpureum contains 12 genes. Using in vitro enzyme assays, the 12 TPS genes from D. purpureum were shown to encode functional enzymes with …

Non-Targeted Colonization By The Endomycorrhizal Fungus, Serendipita Vermifera, In Three Weeds Typically Co-Occurring With Switchgrass, Prasun Ray, Yingqing Guo, Jaydeep Kolape

Nebraska Center for Biotechnology: Faculty and Staff Publications

Serendipita vermifera (=Sebacina vermifera; isolate MAFF305830) is a mycorrhizal fungus originally isolated from the roots of an Australian orchid that we have previously shown to be beneficial in enhancing biomass yield and drought tolerance in switchgrass, an important bioenergy crop for cellulosic ethanol production in the United States. However, almost nothing is known about how this root-associated fungus proliferates and grows through the soil matrix. Such information is critical to evaluate the possibility of non-target effects, such as unintended spread to weedy plants growing near a colonized switchgrass plant in a field environment. A microcosm experiment was conducted …

Effect Of Substrate Feeding Concentration On Initial Biofilm Development In Anaerobic Hybrid Reactor, Suraraksa B., Nopharatana A., Chaiprasert P., Bhumiratana S., Tanticharoen M.

ASEAN Journal on Science and Technology for Development

To elucidate the effect of substrate concentration on biofilm development, glucose concentrations of 500 and 1,000 mg/L were used. At an early stage, biofilm development at both concentrations was not significantly different (P=0.621). After removing suspended biomass at 24 operational hours, the biofilm development at high substrate concentration was higher than at lower concentration. At 72 operational hours, the amounts of attached biomass at low and high glucose feeding were 9.04±1.17 and 28.58±2.72 g VSS/m2, respectively. The activities of acidogens, acetogens, and methanogens at the low glucose concentration were 0.334, 0.016 and 0.003 g COD/g VSS/h, and those at the …

Empirical Models For Power And Energy Requirements Ii : A Powered Implement Operation In Serdang Sandy Clay Loam, Malaysia, Kheiralla A. F., Yahya A., Zohadie M., Ishak W.

ASEAN Journal on Science and Technology for Development

Power and energy requirements were measured with an instrumented tractor for rotary tilling in Serdang sandy clay loam soil. The effects of travel speed and rotor speed upon the measured data were investigated. Power model from orthogonal regression analysis was formulated based on linear and quadratic functions of travel speed and bite length. Fuel consumption model from regression analysis was formulated based on linear tractor PTO power as well as linear equivalent tractor PTO power. Fuel consumption rates predicted by ASAE D497.3 were found to be 25% to 28% overestimates of the values predicted by the model developed. However, fuel …

Design Of A Hvdc-Based Controller For Load Change Compensation And Stabilization Of Inter-Area Oscillations, Ngamroo I.

ASEAN Journal on Science and Technology for Development

As an interconnected power system via a High-Voltage Direct Current (HVDC) link is subjected to a rapid load change with the frequency of inter-area oscillation mode, system frequency and tie line power may be severely disturbed and oscillate. To compensate for the rapid load change and stabilize both frequency and tie line power oscillations due to the inter-area mode, the dynamic power flow control via a HVDC link can be exploited. To implement this concept, a new design method of HVDC-based controller is proposed. To grasp a physical characteristic of the inter-area oscillation frequency, the technique of overlapping decompositions is …

Application Of Deswirl Device In Cyclone Dust Separator, Abdullah M. Z., Husain Z., Fraser S. M.

ASEAN Journal on Science and Technology for Development

The experimental investigations of the vortex flow inside the vortex finder (outlet duct) of the cyclone dust separator have been carried out. Preliminary study from the visualization experiment has been performed and discovered vortex instability inside the conventional vortex finder. In order to minimize the instabilities, the streamlined entry shape was inserted at the vortex finder entrance and the results showed remarkable improvement of the vortex flow instability inside the vortex finder. The velocity measurements of two main components of velocity were performed using a laser-Doppler anemometry at the cyclone vortex finder outlet. The experiments were conducted at a constant …

The Use Of Artificial Neural Network To Optimize The Ph Response Range Of Chlorophenol Red, Wong F., Ahmad M., Heng L. Y.

ASEAN Journal on Science and Technology for Development

Artificial Neural Network (ANN) had been used in this study to extend the response range of the pH indicator. The input from absorbance values of the absorbance spectra of chlorophenol red at different pH was used to train the ANN. During the training process, the coefficient values of the ANN will be adjusted to obtain the desire output. In this research, back propagation algorithm had been used for optimizing the response range of the pH indicator chlorophenol red in solution. The result indicates that the use of ANN enable the pH response range to be extended from 4.8-6.8 to 1.0-10.0.

Genetic Diversity Of Introduced (Pomacea Canaliculata) And Native (Pila) Apple Snails In Thailand Revealed By Randomly Amplified Polymorphic Dna (Rapd) Analysis, Thaewnon-Ngiw B., Klinbunga S., Phanwichien K., Sangduen N., Lauhachinda N., Menasveta P.

ASEAN Journal on Science and Technology for Development

Genetic diversity of the introduced golden apple snail, Pomacea canaliculata (Lamarck, 1822) and four native apple snails; Pila ampullacea (Linneaus, 1758), P. angelica (Annandale, 1920), P. pesmei (Morelet, 1889) and P. polita (Deshayes, 1830) in Thailand were studied by RAPD analysis. Two hundred and two polymorphic fragments (180-1500 bp in length) were generated across overall investigated samples (N = 254) using three informative primers (OPA07, OPB10 and UBC122). The percentages of polymorphic bands were 98.86%, 94.56%, 90.91%, 96.94% and 95.51% for Pomacea canaliculata, P. ampullacea, P. angelica, P. pesmei and P. polita, respectively. This indicated high genetic polymorphism of these …

Entropy Learning In Neural Network, Ng Geok See, Shi D., Wahab A., Singh H.

ASEAN Journal on Science and Technology for Development

In this paper, entropy term is used in the learning phase of a neural network. As learning progresses, more hidden nodes get into saturation. The early creation of such hidden nodes may impair generalisation. Hence entropy approach is proposed to dampen the early creation of such nodes. The entropy learning also helps to increase the importance of relevant nodes while dampening the less important nodes. At the end of learning, the less important nodes can then be eliminated to reduce the memory requirements of the neural network.

Efficient Reactive Power Compensation Algorithm For Distribution Network, Jerome J.

ASEAN Journal on Science and Technology for Development

The use of automation and energy efficient equipment with electronic control would greatly improve industrial production. These new devices are more sensitive to supply voltage deviation and the characteristics of the power system that was previously ignored are now very important. Hence the benefits of distribution automation have been widely acknowledged in recent years. This paper proposes an efficient load flow solution technique extended to find optimum location for reactive power compensation and network reconfiguration for planning and day-to-day operation of distribution networks. This is required as a part of the distribution automation system (DAS) for taking various control and …

Direct Synthesis Of Ladder Wave Digital Filters With Tunable Parameters, Samad S.A.

ASEAN Journal on Science and Technology for Development

This paper proposes a method for the synthesis of ladder wave digital filters (WDFs) directly from the digital domain. This method avoids the need for the synthesis of analog reference filters conventionally required in WDF design. This direct method allows for the determination of the WDF coefficients from the digital domain transfer function. This is similar to conventional infinite impulse response (IIR) filter coefficient determination but the WDF will give a more efficient realization. Due to the WDFs power complementary properties, a first-order ladder WDF can simultaneously realize both lowpass and highpass responses using the same structure, while a second-order …