Value added processing of dehydrated and suncured alfalfa

Non-Peer ReviewedA pilot scale pellet mill was used to produce pellets using ground alfalfa leaf and stem fractions. Both suncured and dehydrated alfalfa chops were used in the experiments. The moisture content of the suncured and dehydrated chops was 8.4 and 9.6% (wb), respectively. A stack of two square sieves with different opening sizes and a pan were used to separate leaf and stem fractions. The leaf and stem fractions were further segregated into two sample lots and ground in a hammer mill using two screen sizes of 3.20 mm (1/8 in.) and 1.98 mm (5/64 in.). The leaf and stem fractions from each sample lot of same grind sizes were combined to get five different samples with leaf content ranging from 0% to 100% in 25% increments. The moisture content and temperature of the samples were raised to 10-11% (wb) and 76oC, respectively, in a double chamber steam conditioner prior to the pelleting operation. The temperature of material was further raised to 95oC in the pellet mill due to the friction between its roller-die assembly. Average particle sizes of sample lots were determined. Temperature and moisture content of samples after various pelleting stages were recorded. High durability pellets were produced using fractionated suncured alfalfa irrespective of grind size (except for 100% stems, which was low). Durability fluctuated between high and medium range for dehydrated alfalfa (except for 100% stems, which was low). Dehydrated alfalfa produced pellets with greener color, while suncured alfalfa produced harder pellets

Recent developments in the disinfestation of Hessian fly puparia in baled hay

Non-Peer ReviewedTo comply with phytosanitary and quarantine regulations, baled hay has to be disinfested of Hessian fly [Mayetiola destructor (Say)] puparia before exporting to Japan. Several laboratory and field trials to destroy Hessian fly puparia in baled hay were either successful or unsuccessful. After the unsuccessful attempt to destroy Hessian fly puparia in the last confirmatory field test, laboratory tests were performed to identify any problem areas and validate the possible causes of insect survival during the field trials. Three different quantities of infested wheat seedlings contained in mesh bags designated types “A”, “B” and “C” test cages were used in the tests. Moisture content of the infested wheat seedlings contained in test cages was determined by the oven method. A recirculating forced-air dryer unit was used to determine the time required for the temperatures within the bulk of the infested wheat seedling to reach 60oC, and to confirm the thermal kill temperature for the Hessian fly puparia when the puparia were still located in the seedlings intact. Three thermocouple sensors were inserted into the bulk of the wheat seedlings to monitor the temperature. Three replicates were conducted for each test cage size. Heat disinfestation and control (unheated and heated) tests were conducted in a heat treatment unit on timothy hay bales. Thermocouple sensors were inserted into the bales and the wheat seedlings to monitor their temperature profiles. The heating time was influenced by the packing density of the infested wheat seedlings contained in the test cages. The survival of the Hessian fly puparia was influenced by the moisture content and the packing density of the infested wheat seedlings

Accelerated search for biomolecular network models to interpret high-throughput experimental data

<p>Abstract</p> <p>Background</p> <p>The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control protein expression. Models of biomolecular network structure and dynamics can be inferred from high-throughput measurements of gene and protein expression. We build on our previously developed fuzzy logic method for bridging quantitative and qualitative biological data to address the challenges of noisy, low resolution high-throughput measurements, i.e., from gene expression microarrays. We employ an evolutionary search algorithm to accelerate the search for hypothetical fuzzy biomolecular network models consistent with a biological data set. We also develop a method to estimate the probability of a potential network model fitting a set of data by chance. The resulting metric provides an estimate of both model quality and dataset quality, identifying data that are too noisy to identify meaningful correlations between the measured variables.</p> <p>Results</p> <p>Optimal parameters for the evolutionary search were identified based on artificial data, and the algorithm showed scalable and consistent performance for as many as 150 variables. The method was tested on previously published human cell cycle gene expression microarray data sets. The evolutionary search method was found to converge to the results of exhaustive search. The randomized evolutionary search was able to converge on a set of similar best-fitting network models on different training data sets after 30 generations running 30 models per generation. Consistent results were found regardless of which of the published data sets were used to train or verify the quantitative predictions of the best-fitting models for cell cycle gene dynamics.</p> <p>Conclusion</p> <p>Our results demonstrate the capability of scalable evolutionary search for fuzzy network models to address the problem of inferring models based on complex, noisy biomolecular data sets. This approach yields multiple alternative models that are consistent with the data, yielding a constrained set of hypotheses that can be used to optimally design subsequent experiments.</p

Analysis of five simulated straw harvest scenarios

. Analysis of five simulated straw harvest scenarios. Canadian Biosystems Engineering/Le ge´nie des biosyste`ms au Canada 50: 2.27Á2.35. Almost 36 million tonnes (t) of cereal grains are harvested annually on more than 16 million hectares (ha) on the Canadian prairies. The net straw production varies year by year depending upon weather patterns, crop fertility, soil conservation measures, harvest method, and plant variety. The net yield of straw, after discounting for soil conservation, averages approximately 2.5 dry (d)t ha (1 . Efficient equipment is needed to collect and package the material as a feedstock for industrial applications. This paper investigates the costs, energy input, and emissions from power equipment used for harvesting straw. Five scenarios were investigated: (1) large square bales, (2) round bales, (3) large compacted stacks (loafs), (4) dried chops, and (5) wet chops. The baled or loafed biomass is stacked next to the farm. Dry chop is collected in a large pile and wet chop is ensiled. The baling and stacking cost was $21.47 dt (1 (dry tonne), with little difference between round and large square baling. Loafing was the cheapest option at$17.08 dt (1 and wet chop followed by ensiling was $59.75 dt -1 . A significant portion of the wet chop cost was in ensiling. Energy input and emissions were proportional to the costs for each system, except for loafing, which required more energy input than the baling systems. As a fraction of the energy content of biomass (roughly 16 GJ dt (1 ), the energy input ranged from 1.2% for baling to 3.2% for ensiling. Emissions from the power equipment ranged from 20.3 kg CO 2 e dt (1 to more than 40 kg CO 2 e dt (1 . A sensitivity analysis on the effect of yield on collection costs showed that a 33% increase in yield reduced the cost by 20%. Similarly a sensitivity analysis on weather conditions showed that a 108C cooler climate extended the harvest period by 5Á10 days whereas a 108C warmer climate shortened the harvest period by 2Á3 days

Corn Stover Availability and Collection Efficiency Using Typical Hay Equipment

Corn stover has been identified as a potential feedstock for the production of fermentable sugars and thermochemical processes. The availability and efficiency of typical hay equipment for collecting corn stover has not been well quantified. Corn stover was collected for two years on a central Kentucky farm near Louisville. Six different harvesting treatments, using traditional hay equipment, were used to harvest corn stover. A rotary mower, rotary scythe (flail-type mower with windrow-forming shields), parallel bar rake, and a round baler were utilized. The average stover moisture content prior to grain harvest was above 40%, and field drying was required before baling. All treatments were analyzed for collection efficiency and corn stover yield. The stover collection yields varied from 1.93 to 5.34 dry t/ha, with collection efficiencies (ratio of stover collected to the total above-ground stover excluding grain) between 32.1% and 94.5%. The most promising collection strategy was disengaging the straw chopper and spreader to produce a windrow behind the combine. This windrow could then be baled in a separate operation that resulted in a collection efficiency of 74.1%

An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces

Abasic (AP) sites in DNA arise through both endogenous and exogenous mechanisms. Since AP sites can prevent replication and transcription, the cell contains systems for their identification and repair. AP endonuclease (APEX1) cleaves the phosphodiester backbone 5′ to the AP site. The cleavage, a key step in the base excision repair pathway, is followed by nucleotide insertion and removal of the downstream deoxyribose moiety, performed most often by DNA polymerase beta (pol-β). While yeast two-hybrid studies and electrophoretic mobility shift assays provide evidence for interaction of APEX1 and pol-β, the specifics remain obscure. We describe a theoretical study designed to predict detailed interacting surfaces between APEX1 and pol-β based on published co-crystal structures of each enzyme bound to DNA. Several potentially interacting complexes were identified by sliding the protein molecules along DNA: two with pol-β located downstream of APEX1 (3′ to the damaged site) and three with pol-β located upstream of APEX1 (5′ to the damaged site). Molecular dynamics (MD) simulations, ensuring geometrical complementarity of interfaces, enabled us to predict interacting residues and calculate binding energies, which in two cases were sufficient (∼−10.0 kcal/mol) to form a stable complex and in one case a weakly interacting complex. Analysis of interface behavior during MD simulation and visual inspection of interfaces allowed us to conclude that complexes with pol-β at the 3′-side of APEX1 are those most likely to occur in vivo. Additional multiple sequence analyses of APEX1 and pol-β in related organisms identified a set of correlated mutations of specific residues at the predicted interfaces. Based on these results, we propose that pol-β in the open or closed conformation interacts and makes a stable interface with APEX1 bound to a cleaved abasic site on the 3′ side. The method described here can be used for analysis in any DNA-metabolizing pathway where weak interactions are the principal mode of cross-talk among participants and co-crystal structures of the individual components are available

Identification and Characterization of Inhibitors of Human Apurinic/apyrimidinic Endonuclease APE1

APE1 is the major nuclease for excising abasic (AP) sites and particular 3′-obstructive termini from DNA, and is an integral participant in the base excision repair (BER) pathway. BER capacity plays a prominent role in dictating responsiveness to agents that generate oxidative or alkylation DNA damage, as well as certain chain-terminating nucleoside analogs and 5-fluorouracil. We describe within the development of a robust, 1536-well automated screening assay that employs a deoxyoligonucleotide substrate operating in the red-shifted fluorescence spectral region to identify APE1 endonuclease inhibitors. This AP site incision assay was used in a titration-based high-throughput screen of the Library of Pharmacologically Active Compounds (LOPAC1280), a collection of well-characterized, drug-like molecules representing all major target classes. Prioritized hits were authenticated and characterized via two high-throughput screening assays – a Thiazole Orange fluorophore-DNA displacement test and an E. coli endonuclease IV counterscreen – and a conventional, gel-based radiotracer incision assay. The top, validated compounds, i.e. 6-hydroxy-DL-DOPA, Reactive Blue 2 and myricetin, were shown to inhibit AP site cleavage activity of whole cell protein extracts from HEK 293T and HeLa cell lines, and to enhance the cytotoxic and genotoxic potency of the alkylating agent methylmethane sulfonate. The studies herein report on the identification of novel, small molecule APE1-targeted bioactive inhibitor probes, which represent initial chemotypes towards the development of potential pharmaceuticals

Systems Biology by the Rules: Hybrid Intelligent Systems for Pathway Modeling and Discovery

Background: Expert knowledge in journal articles is an important source of data for reconstructing biological pathways and creating new hypotheses. An important need for medical research is to integrate this data with high throughput sources to build useful models that span several scales. Researchers traditionally use mental models of pathways to integrate information and development new hypotheses. Unfortunately, the amount of information is often overwhelming and these are inadequate for predicting the dynamic response of complex pathways. Hierarchical computational models that allow exploration of semi-quantitative dynamics are useful systems biology tools for theoreticians, experimentalists and clinicians and may provide a means for cross-communication. Results: A novel approach for biological pathway modeling based on hybrid intelligent systems or soft computing technologies is presented here. Intelligent hybrid systems, which refers to several related computing methods such as fuzzy logic, neural nets, genetic algorithms, and statistical analysis, has become ubiquitous in engineering applications for complex control system modeling and design. Biological pathways may be considered to be complex control systems, which medicine tries to manipulate to achieve desired results. Thus, hybrid intelligent systems may provide a useful tool for modeling biological system dynamics and computational exploration of new drug targets. A new modeling approach based on these methods is presented in the context of hedgehog regulation of the cell cycle in granule cells. Code and input files can be found at the Bionet website: www.chip.ord/~wbosl/Software/Bionet. Conclusion: This paper presents the algorithmic methods needed for modeling complicated biochemical dynamics using rule-based models to represent expert knowledge in the context of cell cycle regulation and tumor growth. A notable feature of this modeling approach is that it allows biologists to build complex models from their knowledge base without the need to translate that knowledge into mathematical form. Dynamics on several levels, from molecular pathways to tissue growth, are seamlessly integrated. A number of common network motifs are examined and used to build a model of hedgehog regulation of the cell cycle in cerebellar neurons, which is believed to play a key role in the etiology of medulloblastoma, a devastating childhood brain cancer