The current threats of climate change are driving attention away from the petrochemical industry towards more sustainable and bio‐based production processes for fuels and speciality chemicals. These ...processes require suitable low‐cost starting material. One potential material assessed here is the oat hull. Its overall chemical composition has so far not been fully characterized. Furthermore, it is not known how it is affected by extreme weather events.
Oat hulls (Kerstin and Galant varieties) grown during ‘normal’ weather years (2016 and 2017) are compared to the harvest of the warmer and drier year (2018). Standard methods for determination of plant chemical composition, with focus on carbohydrate composition, are utilized.
Oat hulls grown in ‘normal’ weather conditions (2017) are rich in lignocellulose (84%), consisting of 35% hemicellulose, 25% lignin and 23% cellulose. Arabinoxylan was found to be the major biopolymer (32%). However, this composition is greatly influenced by weather variations during the oat growth phase. A lignocellulose reduction of 25% was recorded in the warmer and drier 2018 harvest. Additionally, a 6.6‐fold increase in starch content, a four‐fold increase in protein content and a 60% decrease in phenolic content was noted.
Due to its high lignocellulose composition, with an exceptionally large hemicellulose fraction, the chemical composition of oat hulls is unique among agricultural by‐products. However, this characteristic is significantly reduced when grown in warmer and drier weather, which could compromise its suitability for use in a successful biorefinery.
The chemical composition of oat hulls is unique among agricultural side streams and significantly altered by warmer and drier weather.
Urinary extracellular vesicles (EVs) are a promising source of biomarkers, which can be obtained in a non-invasive manner. However, the yield of EVs from urine samples may be insufficient for various ...analyses due to the entrapment of EVs by the Tamm-Horsfall protein (THP) meshwork.
Here, we developed a simple dilution protocol to increase the urinary EV yield by disrupting the interaction between THP filaments and EVs with the help of alkaline pH and lowered ionic concentration. The integrity of the EVs and THP was assessed by electron microscopy. The effect of the protocol on the EV yield was quantified against an undiluted control by western blotting of four EV markers, nanoparticle tracking analysis and measuring of the RNA/miRNA concentration of the EV samples.
The average EV yield from the dilution protocol was 2–7 fold the yield from the undiluted control i.e. increased by 130–624% as measured by western blotting and NTA. The yield increased most from samples with a high THP to EV ratio. The morphology and size range of the EVs were unaltered by the protocol. However, RNA/miRNA yields were the same as from the undiluted control and THP filaments could still be detected in EV samples.
The dilution protocol, that we named KeepEX, provides a simple and efficient way to prevent loss of EVs thus increasing their yield from urine. Since KeepEX does not require individual adjustment of sample pH nor extra centrifugation steps, it could be used on its own or in combination with other EV purification protocols to improve EV isolation particularly from small urine volumes.
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Injuries are common and on increase in most developing countries, including sub-Saharan Africa. A large proportion of the injuries are caused by road traffic accidents, falls, burns, assaults, bites, ...stings and other animal-related injuries, poisonings, drownings/near-drownings and suicide. Globally, injuries are responsible for about five per cent of the total mortality, and the overall global annual costs were estimated in the late 1980s at around 500 billion US dollars. The burden and pattern of injuries in Africa and other developing areas are poorly known and not well studied. The incidence is on the increase, partly due to rapid growth of motorised transport and to expansion of industrial production without adequate safety precautions. This is a review of data on various kinds of injuries in developing countries with a focus on sub-Saharan Africa. A computerised search of the relevant literature published between 1985 and 1998 was conducted and a manual search of journals publishing texts on health in low-income countries and in tropical environments was also done. A few studies on injury prevention policy and on research related to injury epidemiology and prevention have also been identified and included. It is concluded that in a relatively typical East African area with a total mortality rate of 1,300/100,000/year, injuries are likely to cause around 100 of these deaths. The corresponding total rate of significant injuries is estimated at 40,000/100,000/year with a breakdown as tabulated below. table: see text Although a few surveys and other investigations of injuries have been conducted over the years, injury epidemiology and control remain under-researched and relatively neglected subject areas. Much needs to be done. Collection and analysis of injury data need to be standardised, for example regarding age groups, gender disaggregation and severity. Injuries and accidents should be subdivided in at least road traffic injury, fall, burn, assault, poisoning, drowning, suicide, homicide and others, and details regarding time and place, victim and main cause should be noted. Morbidity survey field staff should be informed that injuries are part of the illness concept and that questions should be asked accordingly. Details regarding the circumstances surrounding different injuries must be known to those who develop preventive programmes. Injury is a public health problem affecting some people more than others. Our ordinary environment--the home, the work-site, the street or road--represents various kinds of risk, and some of these are difficult to eliminate. Not only do we have to accept much of our environment with its existing houses, equipment, vehicles, transport systems, energy supply, toxic substances etcetera, many also suffer from various inherited or acquired conditions that increase the risk. We therefore need to develop safer and more "forgiving" living environments where ordinary people can live and move around safely. Injury control activities may focus on different categories of injury. Road safety measures often include information and education campaigns, improved driver training, road design and maintenance, regular vehicle safety checks, separation of pedestrians from vehicle traffic, speed limits, safety belt, air-bag and helmet use, special training and control of public service vehicle drivers, bicycle lane separation, road lighting, reflectorised materials on clothing, review of the road traffic related legislation and law enforcement, and emergency medical services improvement. Domestic injuries can be prevented for example with window guards, child barriers at stairs, smoke detectors, clothes and furniture in less flammable materials, replacement of open stoves, stabilising of open lamps, fire-fighting equipment and practice, child-proof poison packaging and storage, safe disposal of toxic waste, home safety education of parents, and strict building code enforcement. Occupational injuries can largely be prevented if well adapted to the work environment. Research is required in several areas. An improved facility-based injury recording and reporting system needs to be developed and tested. There is need to combine data collection methods, such as interview surveys, hospital records, police records, focus group discussions and key informant interviews. The outcome of emergency medical care and of different forms of transport and referral needs to be determined. Different combinations of preventive interventions needs to be evaluated. This review is intended as guidance for those who need a broad overview of the subject of injury occurrence and prevention in Africa, for example in preparation for the development of injury control programmes or to help identify issues requiring further research in this field.
Motivation: Selecting oligonucleotide probes for use in microarray design, and other applications requiring signature sequences, involves identifying sequences which will bind strongly to their ...intended target, while binding only weakly (or preferably, not at all) to non-target sequences which may be present in the hybridization reaction. While many tools to assist in selection of such sequences exist, all the ones we examined lack important oligo design and software features. Results: YODA is an application for assisting biological researchers in selecting signature sequences. It incorporates a custom sequence similarity search to find potential cross-hybridizing non-target sequences. For this task, most oligo design tools rely on BLAST, which is ill suited for it due to an unacceptable risk of false negatives. YODA supports multiple probe design goals including single-genome, multiple-genome, pathogen-host and species/strain-identification. A graphical interface is provided as well as a command-line interface, both of which support many user-controlled parameters. YODA is easy to install and use and runs on Windows, Mac OS X and Linux platforms. Availability: Freely available (LGLP) along with source code and additional documentation at http://pathport.vbi.vt.edu/YODA Contact: enordber@vbi.vt.edu
The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a ...data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: 'breadth first' beginning with whole-genome and proteome curation using standardized protocols, a 'targeted' approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website (https://patric.vbi.vt.edu) will continually grow with the addition of data, analysis and functionality over the course of the project.
Affibody molecules specific for the epidermal growth factor receptor (EGFR) have been selected by phage display technology from a combinatorial protein library based on the 58-residue, protein ...A-derived Z domain. EGFR is overexpressed in various malignancies and is frequently associated with poor patient prognosis, and the information provided by targeting this receptor could facilitate both patient diagnostics and treatment. Three selected Affibody variants were shown to selectively bind to the extracellular domain of EGFR (EGFR-ECD). Kinetic biosensor analysis revealed that the three monomeric Affibody molecules bound with similar affinity, ranging from 130 to 185 nM. Head-to-tail dimers of the Affibody molecules were compared for their binding to recombinant EGFR-ECD in biosensor analysis and in human epithelial cancer A431 cells. Although the dimeric Affibody variants were found to bind in a range of 25–50 nM affinities in biosensor analysis, they were found to be low nanomolar binders in the cellular assays. Competition assays using radiolabeled Affibody dimers confirmed specific EGFR-binding and demonstrated that the three Affibody molecules competed for the same epitope. Immunofluorescence microscopy demonstrated that the selected Affibody dimers were initially binding to EGFR at the cell surface of A431, and confocal microscopy analysis showed that the Affibody dimers could thereafter be internalized. The potential use of the described Affibody molecules as targeting agents for radionuclide based imaging applications in various carcinomas is discussed.
The growing field of biotechnology is in constant need of binding proteins with novel properties. Not just binding specificities and affinities but also structural stability and productivity are ...important characteristics for the purpose of large‐scale applications. In order to find such molecules, libraries are created by diversifying naturally occurring binding proteins, which in those cases serve as scaffolds. In this study, we investigated the use of a thermostable carbohydrate binding module, CBM4‐2, from a xylanase found in Rhodothermus marinus, as a diversity‐carrying scaffold. A combinatorial library was created by introducing restricted variation at 12 positions in the carbohydrate binding site of the CBM4‐2. Despite the small size of the library (1.6×106 clones), variants specific towards different carbohydrate polymers (birchwood xylan, Avicel and ivory nut mannan) as well as a glycoprotein (human IgG4) were successfully selected for, using the phage display method. Investigated clones showed a high productivity (on average 69 mg of purified protein/l shake flask culture) when produced in Escherichia coli and they were all stable molecules displaying a high melting transition temperature (75.7 ± 5.3°C). All our results demonstrate that the CBM4‐2 molecule is a suitable scaffold for creating variants useful in different biotechnological applications.
Objective: To assess female sex hormone related variables in a group of women with biopsy positive giant cell arteritis and a control group. Methods: 49 women with biopsy positive giant cell ...arteritis, aged 50 to 69 years at the time of diagnosis, answered a questionnaire on hormonal and reproductive factors. The same questions were answered by a large population of women from the same geographical area in connection with routine mammograms. The results were tested statistically, using logistic regression analysis of each variable adjusted for age, and a multivariate logistic regression analysis including age and the variables which differed significantly between giant cell arteritis and controls. Results: From the multivariate logistic regression analysis, three independent variables were associated with an increased risk of having giant cell arteritis: smoking and being an ex-smoker (odds ratio (OR) = 6.324 (95% confidence interval (CI), 3.503 to 11.418), p<0.0001); body mass index (a reduction of 1.0 kg/m2 increased the risk by 10% (OR = 0.898 (0.846 to 0.952), p = 0.0003); and menopause before the age of 43 (OR = 3.521 (1.717 to 7.220), p = 0.0006). Conclusions: There was a significant association between hormonal and reproduction related factors and the risk of developing giant cell arteritis in women given the diagnosis before the age of 70. The results suggest a possible role of oestrogen deficiency in the pathogenesis of giant cell arteritis. To confirm the results, an extended study will be needed, including women older than 70.
Effects on intracellular signaling were studied in cells treated with the affibody molecule (ZEGFR:955)2 that targets the epithelial growth factor receptor (EGFR). EGFR is overexpressed in many types ...of cancers and plays a fundamental role in cell signaling and it is of interest to find targeting agents capable of blocking the receptor. The clinically approved antibody cetuximab (Erbitux) and the natural ligand EGF were included as reference molecules. Two EGFR-rich cell lines, A-431 and U-343, were exposed to the three targeting agents and lysed. The cell lysates were immunoprecipitated with the receptors, or directly separated by SDS-Page. Autophosphorylation of the receptors and phosphorylation of the downstream signaling proteins Erk and Akt, were evaluated by Western blotting. Although the three different agents compete for the same binding site on EGFR, they influenced the signaling differently. The affibody molecule did not induce autophosphorylation of EGFR or any other receptor in the EGFR-family but, in spite of this, induced phosphorylation of Erk in both cell lines and Akt in the A-431 cells. Thus, the results suggest that the signaling pattern induced by (ZEGFR:955)2 is only partly similar to that induced by cetuximab. This makes the affibody molecule a potentially interesting alternative to cetuximab for EGFR-targeted therapy since it might give different therapy-related effects on tumor cells and different side effects on normal tissues.
Metabolic stress is a phenomenon often discussed in conjunction with recombinant protein production in Escherichia coli. This investigation shows how heterologous protein production and the presence ...of host cell proteases is related to: (1) Isopropyl-beta-D-thiogalactopyranoside (IPTG) induction, (2) cell-mass concentration at the time of induction, and (3) the presence of metabolites (glutamic acid or those from tryptone soy broth) during the post-induction phase of high cell density fed-batch cultivations. Two thermostable xylanase variants and one thermostable cellulase, all originating from Rhodothermus marinus, were expressed in E. coli strain BL21 (DE3). A three-fold difference in the specific activity of both xylanase variants between 7,000 and 21,000 U/(g cell dry weight), was observed under the different conditions tested. Upon induction at high cell-mass concentrations employing a nutrient feed devoid of the metabolites above, the specific activity of the xylanase variants, was initially higher but decreased 2-3 h into the post-induction phase and simultaneously protease activity was detected. Furthermore, protease activity was detected in all induced cultivations employing this nutrient feed, but was undetected in uninduced control cultivations (final cell-mass concentration of 40 g/l-1), as well as in induced cultivations employing metabolite-supplemented nutrient feeds. By contrast, maximum specific cellulase activity between 700 and 900 U/(g cell dry weight) remained relatively unaffected in all cases. The results demonstrate that detectable host cell proteases was not the primary reason for the decrease in post-induction activity observed under certain conditions, and possible causes for the differing production levels of heterologous proteins are discussed.
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