Freshwater savings from marine protein consumption

NASA Astrophysics Data System (ADS)

Gephart, Jessica A.; Pace, Michael L.; D'Odorico, Paolo

2014-01-01

Marine fisheries provide an essential source of protein for many people around the world. Unlike alternative terrestrial sources of protein, marine fish production requires little to no freshwater inputs. Consuming marine fish protein instead of terrestrial protein therefore represents freshwater savings (equivalent to an avoided water cost) and contributes to a low water footprint diet. These water savings are realized by the producers of alternative protein sources, rather than the consumers of marine protein. This study quantifies freshwater savings from marine fish consumption around the world by estimating the water footprint of replacing marine fish with terrestrial protein based on current consumption patterns. An estimated 7 600 km3 yr-1 of water is used for human food production. Replacing marine protein with terrestrial protein would require an additional 350 km3 yr-1 of water, meaning that marine protein provides current water savings of 4.6%. The importance of these freshwater savings is highly uneven around the globe, with savings ranging from as little as 0 to as much as 50%. The largest savings as a per cent of current water footprints occur in Asia, Oceania, and several coastal African nations. The greatest national water savings from marine fish protein occur in Southeast Asia and the United States. As the human population increases, future water savings from marine fish consumption will be increasingly important to food and water security and depend on sustainable harvest of capture fisheries and low water footprint growth of marine aquaculture.

A transdisciplinary approach to the initial validation of a single cell protein as an alternative protein source for use in aquafeeds

USDA-ARS?s Scientific Manuscript database

The human population is growing and, globally, we must meet the challenge of increased protein needs required to feed this population. Single cell proteins (SCP), when coupled to aquaculture production, offers a means to ensure future protein needs can be met without direct competition with food for...

Termite Proteins Cross-React with Cockroach Allergens

USDA-ARS?s Scientific Manuscript database

Shrimp are among a group of 8 foods that commonly cause food allergy, and shrimp allergens have been demonstrated to cross-react with arthropod proteins, such as those from cockroaches. Edible insects are beginning to be popularized as an alternate source of protein and have a high nutrition value....

Laticiferous taxa as a source of energy and hydrocarbon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marimuthu, S.; Subramanian, R.B.; Kothari, I.L.

Twenty-nine laticiferous taxa of Apocynaceae, Asclepiadaceae, and Sapotaceae were screened for suitability as alternative sources of renewable energy, rubber, and phytochemicals and to select the most promising ones for large-scale cultivation. Of these, Allamanda violacea (14.9% protein, 13.8% polyphenol, 8.6% oil, 3.2% hydrocarbon), Catharanthus roseus (15.4% protein, 10.4% polyphenol, 11.5% oil, 1.9% hydrocarbon), and Holarrhena antidysenterica (14.2% protein, 16.4% polyphenol, 5,4% oil, 4.8% hydrocarbon) of Apocynaceae; Asclepias curassavica (19.3% protein, 6.5% polyphenol, 3.9% oil, 2.0% hydrocarbon), Calotropis gigantea (18.5% protein, 6.8% polyphenol, 7.0% oil, 2.8% hydrocarbon) of Asclepiadaceae; Mimusops elengi (11.3% protein, 9.7% polyphenol, 7.2% oil, 4.0% hydrocarbon) of Sapotaceaemore » show promising potential for future petrochemical plantations; of all these taxa, Holarrhena antidysenterica yielded an unusually high percentage (4.8%) of hydrocarbon fraction followed by Mimusops elengi (4.0%). NMR spectra confirmed the presence of cis-polyisoprene in all species studied except Nerium indicum (white-flowered var.). These data indicate that the majority of the species under investigation may be considered for large-scale cultivation as an alternative source of rubber, intermediate energy, and other phytochemicals.« less

Dietary purines in vegetarian meat analogues.

PubMed

Havlik, Jaroslav; Plachy, Vladimir; Fernandez, Javier; Rada, Vojtech

2010-11-01

The meat alternatives market offers a wide range of products resembling meat in taste, flavour or texture but based on vegetable protein sources. These high protein-low purine foods may find application in a low purine or purine-free diet, which is sometimes suggested for subjects with increased serum urate levels, i.e. hyperuricaemia. We determined purine content (uric acid, adenine, guanine, hypoxanthine, xanthine) in 39 commercially available meat substitutes and evaluated them in relation to their protein content. Some of the products contained a comparable sum of adenine and hypoxanthine per protein as meat. Analysis of variance showed an influence of protein source used. Mycoprotein-based products had significantly higher contents (2264 mg kg(-1)) of adenine and hypoxanthine per kg of 100% protein than soybean-based products (1648 mg kg(-1)) or mixtures consisting of soybean protein and wheat protein (1239 mg kg(-1)). Protein-rich vegetable-based meat substitutes might be generally accepted as meat alternatives for individuals on special diets. The type of protein used to manufacture these products determines the total content of purines, which is relatively higher in the case of mycoprotein or soybean protein, while appearing lower in wheat protein and egg white-based products. These are therefore more suitable for dietary considerations in a low-purine diet for hyperuricaemic subjects. 2010 Society of Chemical Industry

Protein for Life: Review of Optimal Protein Intake, Sustainable Dietary Sources and the Effect on Appetite in Ageing Adults

PubMed Central

Hooker, Emma; Green, Mark A.; Stevenson, Emma J.; Penson, Simon; Johnstone, Alexandra M.

2018-01-01

With an ageing population, dietary approaches to promote health and independence later in life are needed. In part, this can be achieved by maintaining muscle mass and strength as people age. New evidence suggests that current dietary recommendations for protein intake may be insufficient to achieve this goal and that individuals might benefit by increasing their intake and frequency of consumption of high-quality protein. However, the environmental effects of increasing animal-protein production are a concern, and alternative, more sustainable protein sources should be considered. Protein is known to be more satiating than other macronutrients, and it is unclear whether diets high in plant proteins affect the appetite of older adults as they should be recommended for individuals at risk of malnutrition. The review considers the protein needs of an ageing population (>40 years old), sustainable protein sources, appetite-related implications of diets high in plant proteins, and related areas for future research. PMID:29547523

Navy bean flour particle size and protein content affect cake baking and batter quality

USDA-ARS?s Scientific Manuscript database

There is a great demand for wheat alternatives in foods, particularly baked goods, as gluten sensitivity increases. Baked goods such as cakes have wheat flour as a major ingredient, which is rich in gluten protein. Bean proteins do not have gluten, and are a good source of soluble fiber, B-vitamins,...

Trichoderma Reesei single cell protein production from rice straw pulp in solid state fermentation

NASA Astrophysics Data System (ADS)

Zaki, M.; Said, S. D.

2018-04-01

The dependency on fish meal as a major protein source for animal feed can lead toit priceinstability in line with the increasing in meat production and consumption in Indonesia. In order todeal with this problem, an effort to produce an alternative protein sources production is needed. This scenario is possible due to the abundantavailability of agricultural residues such as rice straw whichcould be utilized as substrate for production of single cell proteins as an alternative proteinsource. This work investigated the potential utilization of rice straw pulp and urea mixture as substrate for the production of local Trichoderma reesei single cell protein in solid state fermentation system. Some parameters have been analyzed to evaluate the effect of ratio of rice straw pulp to urea on mixed single cell protein biomass (mixed SCP biomass) composition, such as total crude protein (analyzed by kjedhal method) and lignin content (TAPPI method).The results showed that crude protein content in mixed SCP biomassincreases with the increasing in fermentation time, otherwise it decreases with the increasing insubstrate carbon to nitrogen (C/N) ratio. Residual lignin content in mixed SCP biomass decreases from 7% to 0.63% during fermentationproceeded of 21 days. The highest crude protein content in mixed SCP biomasswas obtained at substrate C/N ratio 20:1 of 25%.

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

PubMed Central

Vanderperre, Benoît; Lucier, Jean-François; Bissonnette, Cyntia; Motard, Julie; Tremblay, Guillaume; Vanderperre, Solène; Wisztorski, Maxence; Salzet, Michel; Boisvert, François-Michel; Roucou, Xavier

2013-01-01

A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome. PMID:23950983

Edible insects are the future?

PubMed

van Huis, Arnold

2016-08-01

The global increase in demand for meat and the limited land area available prompt the search for alternative protein sources. Also the sustainability of meat production has been questioned. Edible insects as an alternative protein source for human food and animal feed are interesting in terms of low greenhouse gas emissions, high feed conversion efficiency, low land use, and their ability to transform low value organic side streams into high value protein products. More than 2000 insect species are eaten mainly in tropical regions. The role of edible insects in the livelihoods and nutrition of people in tropical countries is discussed, but this food source is threatened. In the Western world, there is an increasing interest in edible insects, and examples are given. Insects as feed, in particular as aquafeed, have a large potential. Edible insects have about the same protein content as conventional meat and more PUFA. They may also have some beneficial health effects. Edible insects need to be processed and turned into palatable dishes. Food safety may be affected by toxicity of insects, contamination with pathogens, spoilage during conservation and allergies. Consumer attitude is a major issue in the Western world and a number of strategies are proposed to encourage insect consumption. We discuss research pathways to make insects a viable sector in food and agriculture: an appropriate disciplinary focus, quantifying its importance, comparing its nutritional value to conventional protein sources, environmental benefits, safeguarding food safety, optimising farming, consumer acceptance and gastronomy.

Studies on the incorporation of velvet bean (Mucuna pruriens var. utilis) as an alternative protein source in poultry feed and its effect on growth performance of broiler chickens.

PubMed

Vadivel, Vellingiri; Pugalenthi, Muthiah

2010-10-01

The effect of replacement of soybean meal by the velvet bean meal as an alternative protein ingredient on the growth performance of broiler chickens was investigated. The raw seeds of velvet bean [Mucuna pruriens (L.) DC. var. utilis (Wall. ex Wight) Baker ex Burck], an under-utilized food legume collected from South India, was found to contain appreciable levels of crude protein (273.2 g/kg DM), lipid (60.61 g/kg DM), neutral detergent fiber (84.3 g/kg DM), and ash content (56.04 g/kg DM). Soaking in 0.2% sodium bicarbonate solution + autoclaving treatment caused a substantial reduction on the levels of various antinutritional compounds such as tannins (84%), L: -Dopa (79%), phytic acid (87%), raffinose (93%), stachyose (83%), verbascose (73%), haemagglutinating activity (84%), trypsin inhibitor activity (77%), and alpha-amylase inhibitor activity (78%) without affecting the nutritional quality of velvet bean seeds. The processed velvet bean meal was incorporated as an alternative protein source by replacing soybean meal protein at 0, 20%, 40%, 60%, 80%, and 100% levels in the broiler diets. Replacement of soybean meal protein up to 40% level, which corresponds to the inclusion of velvet bean meal up to 15.7% and 11% in the starter and finisher phase poultry feeds, respectively, exhibited better growth performance of broiler birds without any adverse effects.

Bioactivities of alternative protein sources and their potential health benefits.

PubMed

Pihlanto, A; Mattila, P; Mäkinen, S; Pajari, A-M

2017-10-18

Increasing the utilisation of plant proteins is needed to support the production of protein-rich foods that could replace animal proteins in the human diet so as to reduce the strain that intensive animal husbandry poses to the environment. Lupins, quinoa and hempseed are significant sources of energy, high quality proteins, fibre, vitamins and minerals. In addition, they contain compounds such as polyphenols and bioactive peptides that can increase the nutritional value of these plants. From the nutritional standpoint, the right combination of plant proteins can supply sufficient amounts of essential amino acids for human requirements. This review aims at providing an overview of the current knowledge of the nutritional properties, beneficial and non-nutritive compounds, storage proteins, and potential health benefits of lupins, quinoa and hempseed.

Evaluation of genetically-improved (glandless) and genetically-modified low-gossypol cottonseed meal as alternative protein sources in the diet of juvenile southern flounder Paralichthys lethostigma reared in a recirculating

USDA-ARS?s Scientific Manuscript database

Cottonseed meal (CSM) proteins from genetically-improved (glandless) seed (GI-CSM, 52.1% crude protein, CP), genetically-modified low-gossypol seed (GMO-CSM, 56.0% CP) and from an untreated regular (glanded) seed (R-CSM 49.9% CP) were evaluated to replace fish meal (FM) protein (59.5% CP) in juvenil...

Allergenicity assessment strategy for novel food proteins and protein sources.

PubMed

Verhoeckx, Kitty; Broekman, Henrike; Knulst, André; Houben, Geert

2016-08-01

To solve the future food insecurity problem, alternative and sustainable protein sources (e.g. insects, rapeseed, fava bean and algae) are now being explored for the production of food and feed. To approve these novel protein sources for future food a comprehensive risk assessment is needed according to the European food legislation. Allergenicity risk assessment might pose some major difficulties, since detailed guidance on how to assess the allergenic potential of novel foods is not available. At present, the approach relies mostly on the guidance of allergenicity assessment for genetically modified (GM) plant foods. The most recent one was proposed by EFSA (2010 and 2011); "weight-of-evidence approach". However this guidance is difficult to interpret, not completely applicable or validated for novel foods and therefore needs some adjustments. In this paper we propose a conceptual strategy which is based on the "weight-of-evidence approach" for food derived from GM plants and other strategies that were previously published in the literature. This strategy will give more guidance on how to assess the allergenicity of novel food proteins and protein sources. Copyright © 2016 Elsevier Inc. All rights reserved.

Future Protein Supply and Demand: Strategies and Factors Influencing a Sustainable Equilibrium

PubMed Central

Henchion, Maeve; Hayes, Maria; Mullen, Anne Maria; Fenelon, Mark; Tiwari, Brijesh

2017-01-01

A growing global population, combined with factors such as changing socio-demographics, will place increased pressure on the world’s resources to provide not only more but also different types of food. Increased demand for animal-based protein in particular is expected to have a negative environmental impact, generating greenhouse gas emissions, requiring more water and more land. Addressing this “perfect storm” will necessitate more sustainable production of existing sources of protein as well as alternative sources for direct human consumption. This paper outlines some potential demand scenarios and provides an overview of selected existing and novel protein sources in terms of their potential to sustainably deliver protein for the future, considering drivers and challenges relating to nutritional, environmental, and technological and market/consumer domains. It concludes that different factors influence the potential of existing and novel sources. Existing protein sources are primarily hindered by their negative environmental impacts with some concerns around health. However, they offer social and economic benefits, and have a high level of consumer acceptance. Furthermore, recent research emphasizes the role of livestock as part of the solution to greenhouse gas emissions, and indicates that animal-based protein has an important role as part of a sustainable diet and as a contributor to food security. Novel proteins require the development of new value chains, and attention to issues such as production costs, food safety, scalability and consumer acceptance. Furthermore, positive environmental impacts cannot be assumed with novel protein sources and care must be taken to ensure that comparisons between novel and existing protein sources are valid. Greater alignment of political forces, and the involvement of wider stakeholders in a governance role, as well as development/commercialization role, is required to address both sources of protein and ensure food security. PMID:28726744

Future Protein Supply and Demand: Strategies and Factors Influencing a Sustainable Equilibrium.

PubMed

Henchion, Maeve; Hayes, Maria; Mullen, Anne Maria; Fenelon, Mark; Tiwari, Brijesh

2017-07-20

A growing global population, combined with factors such as changing socio-demographics, will place increased pressure on the world's resources to provide not only more but also different types of food. Increased demand for animal-based protein in particular is expected to have a negative environmental impact, generating greenhouse gas emissions, requiring more water and more land. Addressing this "perfect storm" will necessitate more sustainable production of existing sources of protein as well as alternative sources for direct human consumption. This paper outlines some potential demand scenarios and provides an overview of selected existing and novel protein sources in terms of their potential to sustainably deliver protein for the future, considering drivers and challenges relating to nutritional, environmental, and technological and market/consumer domains. It concludes that different factors influence the potential of existing and novel sources. Existing protein sources are primarily hindered by their negative environmental impacts with some concerns around health. However, they offer social and economic benefits, and have a high level of consumer acceptance. Furthermore, recent research emphasizes the role of livestock as part of the solution to greenhouse gas emissions, and indicates that animal-based protein has an important role as part of a sustainable diet and as a contributor to food security. Novel proteins require the development of new value chains, and attention to issues such as production costs, food safety, scalability and consumer acceptance. Furthermore, positive environmental impacts cannot be assumed with novel protein sources and care must be taken to ensure that comparisons between novel and existing protein sources are valid. Greater alignment of political forces, and the involvement of wider stakeholders in a governance role, as well as development/commercialization role, is required to address both sources of protein and ensure food security.

Diversification of the muscle proteome through alternative splicing.

PubMed

Nakka, Kiran; Ghigna, Claudia; Gabellini, Davide; Dilworth, F Jeffrey

2018-03-06

Skeletal muscles express a highly specialized proteome that allows the metabolism of energy sources to mediate myofiber contraction. This muscle-specific proteome is partially derived through the muscle-specific transcription of a subset of genes. Surprisingly, RNA sequencing technologies have also revealed a significant role for muscle-specific alternative splicing in generating protein isoforms that give specialized function to the muscle proteome. In this review, we discuss the current knowledge with respect to the mechanisms that allow pre-mRNA transcripts to undergo muscle-specific alternative splicing while identifying some of the key trans-acting splicing factors essential to the process. The importance of specific splicing events to specialized muscle function is presented along with examples in which dysregulated splicing contributes to myopathies. Though there is now an appreciation that alternative splicing is a major contributor to proteome diversification, the emergence of improved "targeted" proteomic methodologies for detection of specific protein isoforms will soon allow us to better appreciate the extent to which alternative splicing modifies the activity of proteins (and their ability to interact with other proteins) in the skeletal muscle. In addition, we highlight a continued need to better explore the signaling pathways that contribute to the temporal control of trans-acting splicing factor activity to ensure specific protein isoforms are expressed in the proper cellular context. An understanding of the signal-dependent and signal-independent events driving muscle-specific alternative splicing has the potential to provide us with novel therapeutic strategies to treat different myopathies.

Protein enrichment of brewery spent grain from Rhizopus oligosporus by solid-state fermentation.

PubMed

Canedo, Marianny Silva; de Paula, Fernanda Gomes; da Silva, Flávio Alves; Vendruscolo, Francielo

2016-07-01

Brewery spent grain represents approximately 85 % of total by-products generated in a brewery. Consisting of carbohydrates, fiber, minerals and low amounts of protein, the use of brewery spent grain is limited to the feeding of ruminants; however, its potential use should be investigated. The reuse of this by-product using microorganisms by solid-state fermentation process as the case of protein enrichment by single-cell protein incorporation is an alternative to ensure sustainability and generate commercially interesting products. In this context, the aim of this study was to grow Rhizopus oligosporus in brewery spent grain under different initial moisture contents and nitrogen sources to increase the protein content of the fermented material. After 7 days of fermentation, increase of 2-4 times in the crude protein and soluble protein content was verified, respectively, compared to unfermented brewery spent grain. The kinetics of protein enrichment demonstrated the possibility of application of this technique, which can be a great alternative for use in diets for animals.

Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis

USDA-ARS?s Scientific Manuscript database

Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteriti...

Food Products Made With Glycomacropeptide, a Low Phenylalanine Whey Protein, Provide a New Alternative to Amino Acid-Based Medical Foods for Nutrition Management of Phenylketonuria

PubMed Central

Van Calcar, Sandra C.; Ney, Denise M.

2012-01-01

Phenylketonuria (PKU), an inborn error in phenylalanine (phe) metabolism, requires lifelong nutrition management with a low-phe diet, which includes a phe-free amino acid-based medical formula to provide the majority of an individual’s protein needs. Compliance with this diet is often difficult for older children, adolescents and adults with PKU. The whey protein glycomacropeptide (GMP) is ideally suited for the PKU diet since it is naturally low in phe. Nutritionally complete, acceptable medical foods and beverages can be made with GMP to increase the variety of protein sources for the PKU diet. As an intact protein, GMP improves protein utilization and increases satiety compared with amino acids. Thus, GMP provides a new, more physiologic source of low-phe dietary protein for those with PKU. PMID:22818728

Physical, Chemical and Biochemical Modifications of Protein-Based Films and Coatings: An Extensive Review

PubMed Central

Zink, Joël; Wyrobnik, Tom; Prinz, Tobias; Schmid, Markus

2016-01-01

Protein-based films and coatings are an interesting alternative to traditional petroleum-based materials. However, their mechanical and barrier properties need to be enhanced in order to match those of the latter. Physical, chemical, and biochemical methods can be used for this purpose. The aim of this article is to provide an overview of the effects of various treatments on whey, soy, and wheat gluten protein-based films and coatings. These three protein sources have been chosen since they are among the most abundantly used and are well described in the literature. Similar behavior might be expected for other protein sources. Most of the modifications are still not fully understood at a fundamental level, but all the methods discussed change the properties of the proteins and resulting products. Mastering these modifications is an important step towards the industrial implementation of protein-based films. PMID:27563881

Validation of alternate light sources for detection of bruises in non-embalmed and embalmed cadavers.

PubMed

Olds, Kelly; Byard, Roger W; Winskog, Calle; Langlois, Neil E I

2017-03-01

Bruising is frequently documented in cases of violence for use as forensic evidence. However, bruises can be overlooked if they are not visible to the naked eye. Alternate light sources such as ultraviolet, narrow band, and infrared have been used in an attempt to reveal the presence of bruising that is not otherwise apparent. However, there is a significant gap in knowledge surrounding this technique as it has not been validated against histology to confirm that bruising is genuinely being enhanced. A recent study evaluated the ability of alternate light sources to enhance visibility of bruises using a pigskin model. However, histological confirmation of bruising in humans using these light sources has not yet been performed. In this study, embalmed and non-embalmed human cadavers were used. Bodies were surveyed with alternate light sources, and enhanced regions that were unapparent under white light were photographed with the alternate light sources and sampled for histological assessment. Immunohistochemical staining for the red blood cell surface protein glycophorin was used determine if the enhanced area was a bruise (defined by the presence of extravasated erythrocytes). Photographs of areas confirmed to be bruises were analyzed using the program Fiji to measure enhancement, which was defined as an increase in the measured transverse diameter. In the non-embalmed and the embalmed cadavers violet alternate light produced the greatest enhancement of histologically confirmed bruises, followed by blue (both p < 0.0001). Regions that were not confirmed as bruises also enhanced, indicating that light sources may not be specific. This suggests that the use of light sources to enhance the visibility of bruising should be undertaken with caution and further studies are required.

Alternative Splicing as a Target for Cancer Treatment.

PubMed

Martinez-Montiel, Nancy; Rosas-Murrieta, Nora Hilda; Anaya Ruiz, Maricruz; Monjaraz-Guzman, Eduardo; Martinez-Contreras, Rebeca

2018-02-11

Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.

Algal Proteins: Extraction, Application, and Challenges Concerning Production

PubMed Central

Bleakley, Stephen; Hayes, Maria

2017-01-01

Population growth combined with increasingly limited resources of arable land and fresh water has resulted in a need for alternative protein sources. Macroalgae (seaweed) and microalgae are examples of under-exploited “crops”. Algae do not compete with traditional food crops for space and resources. This review details the characteristics of commonly consumed algae, as well as their potential for use as a protein source based on their protein quality, amino acid composition, and digestibility. Protein extraction methods applied to algae to date, including enzymatic hydrolysis, physical processes, and chemical extraction and novel methods such as ultrasound-assisted extraction, pulsed electric field, and microwave-assisted extraction are discussed. Moreover, existing protein enrichment methods used in the dairy industry and the potential of these methods to generate high value ingredients from algae, such as bioactive peptides and functional ingredients are discussed. Applications of algae in human nutrition, animal feed, and aquaculture are examined. PMID:28445408

A physical mechanism of cancer heterogeneity

NASA Astrophysics Data System (ADS)

Chen, Cong; Wang, Jin

2016-02-01

We studied a core cancer gene regulatory network motif to uncover possible source of cancer heterogeneity from epigenetic sources. When the time scale of the protein regulation to the gene is faster compared to the protein synthesis and degradation (adiabatic regime), normal state, cancer state and an intermediate premalignant state emerge. Due to the epigenetics such as DNA methylation and histone remodification, the time scale of the protein regulation to the gene can be slower or comparable to the protein synthesis and degradation (non-adiabatic regime). In this case, many more states emerge as possible phenotype alternations. This gives the origin of the heterogeneity. The cancer heterogeneity is reflected from the emergence of more phenotypic states, larger protein concentration fluctuations, wider kinetic distributions and multiplicity of kinetic paths from normal to cancer state, higher energy cost per gene switching, and weaker stability.

[Plants as an alternative source of therapeutic proteins].

PubMed

Łucka, Marta; Kowalczyk, Tomasz; Szemraj, Janusz; Sakowicz, Tomasz

2015-03-22

In recent years, there has been an increased interest of researchers in developing efficient plant heterologous expression systems of proteins for a wide range of applications. It represents an alternative to the traditional strategy utilizing bacterial, yeast, insect or mammalian cells. New techniques of identification and characterization and effective methods of plant genetic transformation allow the range of recombinant protein products to be expanded. Great expectations are associated with the use of plants as bioreactors for the production of specific proteins of therapeutic interest. This strategy offers a number of advantages, the most important being: the possibility of a significant reduction in production costs, the safety of the products obtained and full eukaryotic post-translational modifications of proteins. A group of proteins of special interest is pharmaceuticals, and a number of successful experiments have confirmed the possibility of obtaining heterogeneous proteins with therapeutic potential: monoclonal antibodies, vaccine antigens, and a variety of cytokines. This work is focused on selected recombinant proteins belonging to those groups expression of which was achieved in plant cells. These proteins may be used in the future for therapy or prevention of viral, bacterial or cancer diseases.

Comparison of femtosecond laser and continuous wave UV sources for protein-nucleic acid crosslinking.

PubMed

Fecko, Christopher J; Munson, Katherine M; Saunders, Abbie; Sun, Guangxing; Begley, Tadhg P; Lis, John T; Webb, Watt W

2007-01-01

Crosslinking proteins to the nucleic acids they bind affords stable access to otherwise transient regulatory interactions. Photochemical crosslinking provides an attractive alternative to formaldehyde-based protocols, but irradiation with conventional UV sources typically yields inadequate product amounts. Crosslinking with pulsed UV lasers has been heralded as a revolutionary technique to increase photochemical yield, but this method had only been tested on a few protein-nucleic acid complexes. To test the generality of the yield enhancement, we have investigated the benefits of using approximately 150 fs UV pulses to crosslink TATA-binding protein, glucocorticoid receptor and heat shock factor to oligonucleotides in vitro. For these proteins, we find that the quantum yields (and saturating yields) for forming crosslinks using the high-peak intensity femtosecond laser do not improve on those obtained with low-intensity continuous wave (CW) UV sources. The photodamage to the oligonucleotides and proteins also has comparable quantum yields. Measurements of the photochemical reaction yields of several small molecules selected to model the crosslinking reactions also exhibit nearly linear dependences on UV intensity instead of the previously predicted quadratic dependence. Unfortunately, these results disprove earlier assertions that femtosecond pulsed laser sources provide significant advantages over CW radiation for protein-nucleic acid crosslinking.

An alternative animal protein source: cultured beef.

PubMed

Post, Mark J

2014-11-01

Alternative sources of animal proteins are needed that can be produced efficiently, thereby providing food security with diminished ecological burden. It is feasible to culture beef from bovine skeletal muscle stem cells, but the technology is still under development. The aim is to create a beef mimic with equivalent taste, texture, and appearance and with the same nutritional value as livestock-produced beef. More specifically, there is a need for optimization of protein content and fat content. In addition, scalability of production requires modification of current small-scale bioreactors to the largest possible scale. The necessary steps and current progress suggest that this aim is achievable, but formal evidence is still required. Similarly, we can be optimistic about consumer acceptance based on initial data, but detailed studies are needed to gain more insight into potential psychological obstacles that could lead to rejection. These challenges are formidable but likely surmountable. The severity of upcoming food-security threats warrants serious research and development efforts to address the challenges that come with bringing cultured beef to the market. © 2014 New York Academy of Sciences.

Alternative Protein Sources in the Diet Modulate Microbiota and Functionality in the Distal Intestine of Atlantic Salmon (Salmo salar)

PubMed Central

Jaramillo-Torres, Alexander; Kortner, Trond M.; Merrifield, Daniel L.; Tinsley, John; Bakke, Anne Marie; Krogdahl, Åshild

2016-01-01

ABSTRACT The present study aimed to investigate whether alternative dietary protein sources modulate the microbial communities in the distal intestine (DI) of Atlantic salmon, and whether alterations in microbiota profiles are reflected in modifications in host intestinal function and health status. A 48-day feeding trial was conducted, in which groups of fish received one of five diets: a reference diet in which fishmeal (diet FM) was the only protein source and four experimental diets with commercially relevant compositions containing alternative ingredients as partial replacements of fishmeal, i.e., poultry meal (diet PM), a mix of soybean meal and wheat gluten (diet SBMWG), a mix of soy protein concentrate and poultry meal (diet SPCPM), and guar meal and wheat gluten (diet GMWG). Samples were taken of DI digesta and mucosa for microbial profiling using high-throughput sequencing and from DI whole tissue for immunohistochemistry and expression profiling of marker genes for gut health. Regardless of diet, there were significant differences between the microbial populations in the digesta and the mucosa in the salmon DI. Microbial richness was higher in the digesta than the mucosa. The digesta-associated bacterial communities were more affected by the diet than the mucosa-associated microbiota. Interestingly, both legume-based diets (SBMWG and GMWG) presented high relative abundance of lactic acid bacteria in addition to alteration in the expression of a salmon gene related to cell proliferation (pcna). It was, however, not possible to ascertain the cause-effect relationship between changes in bacterial communities and the host's intestinal responses to the diets. IMPORTANCE The intestine of cultivated Atlantic salmon shows symptoms of compromised function, which are most likely caused by imbalances related to the use of new feed ingredients. Intestinal microbiota profiling may become in the future a valuable endpoint measurement in order to assess fish intestinal health status and effects of diet. The present study aimed to gain information about whether alternative dietary protein sources modulate the microbial communities in the Atlantic salmon intestine and whether alterations in microbiota profiles are reflected in alterations in host intestinal function and health status. We demonstrate here that there are substantial differences between the intestinal digesta and mucosa in the presence and abundance of bacteria. The digesta-associated microbiota showed clear dependence on the diet composition, whereas mucosa-associated microbiota appeared to be less affected by diet composition. Most important, the study identified bacterial groups associated with diet-induced gut dysfunction that may be utilized as microbial markers of gut health status in fish. PMID:27986728

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

Advances in the study on nutrient requirements of grouper (Epinephelus sp.): a review

NASA Astrophysics Data System (ADS)

Luo, Zhi; Liu, Yongjian; Mai, Kangsen; Tian, Lixia

2005-04-01

The paper reviews the recent advances in studying grouper nutrition requirement for the development of cost-effective and environmentally friendly artificial diets. It consists of seven parts: protein and amino acid, lipid and essential fatty acid, carbohydrate, vitamin, mineral, alternative protein source, broodstock and larval nutrition. The review provides some basic information for further investigation of nutrient requirements of groupers.

Yeast derived from lignocellulosic biomass as a sustainable feed resource for use in aquaculture.

PubMed

Øverland, Margareth; Skrede, Anders

2017-02-01

The global expansion in aquaculture production implies an emerging need of suitable and sustainable protein sources. Currently, the fish feed industry is dependent on high-quality protein sources of marine and plant origin. Yeast derived from processing of low-value and non-food lignocellulosic biomass is a potential sustainable source of protein in fish diets. Following enzymatic hydrolysis, the hexose and pentose sugars of lignocellulosic substrates and supplementary nutrients can be converted into protein-rich yeast biomass by fermentation. Studies have shown that yeasts such as Saccharomyces cerevisiae, Candida utilis and Kluyveromyces marxianus have favourable amino acid composition and excellent properties as protein sources in diets for fish, including carnivorous species such as Atlantic salmon and rainbow trout. Suitable downstream processing of the biomass to disrupt cell walls is required to secure high nutrient digestibility. A number of studies have shown various immunological and health benefits from feeding fish low levels of yeast and yeast-derived cell wall fractions. This review summarises current literature on the potential of yeast from lignocellulosic biomass as an alternative protein source for the aquaculture industry. It is concluded that further research and development within yeast production can be important to secure the future sustainability and economic viability of intensive aquaculture. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Unveiling the potential of novel yeast protein extracts in white wines clarification and stabilization

PubMed Central

Fernandes, Joana P.; Neto, Rodrigo; Centeno, Filipe; De Fátima Teixeira, Maria; Gomes, Ana Catarina

2015-01-01

Fining agents derived from animal and mineral sources are widely used to clarify and stabilize white wines. Nevertheless, health and environmental problems are being raised, concerning the allergenic and environmental impact of some of those fining products. In this study, our aim is to validate the potential of yeast protein extracts, obtained from an alternative and safe source, naturally present in wine: oenological yeasts. Three untreated white wines were used in this work in order to evaluate the impact of these novel yeast protein extracts (YPE) in terms of the wine clarification and stabilization improvement. Two separated fining trials were thus conducted at laboratory scale and the yeast alternatives were compared with reference fining agents, obtained from mineral, animal and vegetable origins. Our results indicate that YPE were capable to promote (i) brilliance/color improvement, (ii) turbidity reduction (76–89% comparing with the untreated wines), and (iii) production of compact and homogeneous lees (44% smaller volume than obtained with bentonite). Additionally, after submitting wines to natural and forced oxidations, YPE treatments revealed (iv) different forms of colloidal stabilization, by presenting comparable or superior effects when particularly compared to casein. Altogether, this study reveals that YPE represent a promising alternative for white wine fining, since they are resultant from a natural and more sustainable origin, at present not regarded as potential allergenic according to Regulation (EC) No. 1169/2011. PMID:25853122

Evaluation of black soldier fly (Hermetia illucens) larvae meal as partial or total replacement of marine fish meal in practical diets for Pacific white shrimp (Litopenaeus vannamei)

USDA-ARS?s Scientific Manuscript database

Black soldier fly larvae (BSFL) meal, produced from the larvae of Hermetia illucens, has shown promise as a fish meal (FM) replacement in diets for rainbow trout, catfish and tilapia, but has not been examined as an alternative protein source in shrimp diets. Six isonitrogenous (35% crude protein, a...

Liquid egg as an alternative protein source in calf milk replacers.

PubMed

Touchette, K J; O'Brien, M L; Coalson, J A

2003-08-01

The use of alternative proteins in milk replacer has been evaluated for their ability to decrease the cost of milk replacers without negatively impacting performance of the calf. Three studies were conducted to evaluate the performance of calves fed milk replacer utilizing liquid egg as an alternative protein and to determine the optimal concentration of liquid egg to include in milk replacers. Calves in trials 1 and 2 were assigned to a control diet of all milk protein replacer (MILK) or a diet formulated to contain 5% of the diet (13.5% of the protein) from liquid egg (5% EGG). Calves in trial 3 were assigned to one of four diets: the control (MILK) and 5% EGG diets fed in trials 1 and 2, or diets formulated to contain either 10 or 15% of the diet (27 or 40.5% of the protein) from liquid egg (10% EGG, 15% EGG). For all experiments, milk replacers were formulated to contain 20% protein, 20% fat and were fed at 454 g/d reconstituted to 12% DM. Production of the diets containing egg protein utilized breaker eggs that were pasteurized during manufacturing. Holstein bull calves (n = 44 for experiment 1, n = 38 for experiment 2, and n = 120 for experiment 3), were purchased from an area sale barn. Calves were housed in individual hutches with water available free choice starting on d 0. A commercially available calf starter was offered free choice beginning on d 7 for experiments 1 and 2 and on d 1 for experiment 3. Feed intake, scour scores, and antibiotic treatments were recorded daily. For experiment 1, calves fed 5% EGG had greater weight gains than calves fed MILK. No differences in average daily feed intake were observed. For experiment 2, weight gains tended to be lower with 5% EGG, whereas feed intakes and gain to feed ratios were similar between calves fed MILK or 5% EGG. For experiment 3, as the amount of egg in the diet increased, weight gain decreased in a linear fashion during the milk replacer feeding period, but the decrease in gain was significant only with the 15% EGG diet. These results indicate that egg is an effective alternative protein source to milk protein in calf milk replacers when fed at levels up to 10% of the diet in a conventional feeding program of 0.45 kg per head per day.

Splice Variant Biomarkers for Parkinson’s Disease

DTIC Science & Technology

2014-05-01

reactions where they are a major source of energy and are critical for carbohydrate, fat and protein metabolism (Massey, 2000). It has been suggested... fat in the diet, saturated or unsat- urated, which is not always specified. Nor is the amount of animal protein consumed to supply the fat intake...neurotoxins, such as those possibly present in milk . Alternatively, saturated fat could modify the risk of PD by affecting PUFA metabolism and inducing adverse

Genome-based analysis of heme biosynthesis and uptake in prokaryotic systems.

PubMed

Cavallaro, Gabriele; Decaria, Leonardo; Rosato, Antonio

2008-11-01

Heme is the prosthetic group of many proteins that carry out a variety of key biological functions. In addition, for many pathogenic organisms, heme (acquired from the host) may constitute a very important source of iron. Organisms can meet their heme demands by taking it up from external sources, by producing the cofactor through a dedicated biosynthetic pathway, or both. Here we analyzed the distribution of proteins specifically involved in the processes of heme biosynthesis and heme uptake in 474 prokaryotic organisms. These data allowed us to identify which organisms are capable of performing none, one, or both processes, based on the similarity to known systems. Some specific instances where one or more proteins along the pathways had unusual modifications were singled out. For two key protein domains involved in heme uptake, we could build a series of structural models, which suggested possible alternative modes of heme binding. Future directions for experimental work are given.

Alternative Protein Sources in the Diet Modulate Microbiota and Functionality in the Distal Intestine of Atlantic Salmon (Salmo salar).

PubMed

Gajardo, Karina; Jaramillo-Torres, Alexander; Kortner, Trond M; Merrifield, Daniel L; Tinsley, John; Bakke, Anne Marie; Krogdahl, Åshild

2017-03-01

The present study aimed to investigate whether alternative dietary protein sources modulate the microbial communities in the distal intestine (DI) of Atlantic salmon, and whether alterations in microbiota profiles are reflected in modifications in host intestinal function and health status. A 48-day feeding trial was conducted, in which groups of fish received one of five diets: a reference diet in which fishmeal (diet FM) was the only protein source and four experimental diets with commercially relevant compositions containing alternative ingredients as partial replacements of fishmeal, i.e., poultry meal (diet PM), a mix of soybean meal and wheat gluten (diet SBMWG), a mix of soy protein concentrate and poultry meal (diet SPCPM), and guar meal and wheat gluten (diet GMWG). Samples were taken of DI digesta and mucosa for microbial profiling using high-throughput sequencing and from DI whole tissue for immunohistochemistry and expression profiling of marker genes for gut health. Regardless of diet, there were significant differences between the microbial populations in the digesta and the mucosa in the salmon DI. Microbial richness was higher in the digesta than the mucosa. The digesta-associated bacterial communities were more affected by the diet than the mucosa-associated microbiota. Interestingly, both legume-based diets (SBMWG and GMWG) presented high relative abundance of lactic acid bacteria in addition to alteration in the expression of a salmon gene related to cell proliferation ( pcna ). It was, however, not possible to ascertain the cause-effect relationship between changes in bacterial communities and the host's intestinal responses to the diets. IMPORTANCE The intestine of cultivated Atlantic salmon shows symptoms of compromised function, which are most likely caused by imbalances related to the use of new feed ingredients. Intestinal microbiota profiling may become in the future a valuable endpoint measurement in order to assess fish intestinal health status and effects of diet. The present study aimed to gain information about whether alternative dietary protein sources modulate the microbial communities in the Atlantic salmon intestine and whether alterations in microbiota profiles are reflected in alterations in host intestinal function and health status. We demonstrate here that there are substantial differences between the intestinal digesta and mucosa in the presence and abundance of bacteria. The digesta-associated microbiota showed clear dependence on the diet composition, whereas mucosa-associated microbiota appeared to be less affected by diet composition. Most important, the study identified bacterial groups associated with diet-induced gut dysfunction that may be utilized as microbial markers of gut health status in fish. Copyright © 2017 Gajardo et al.

Alternative splicing in plant immunity.

PubMed

Yang, Shengming; Tang, Fang; Zhu, Hongyan

2014-06-10

Alternative splicing (AS) occurs widely in plants and can provide the main source of transcriptome and proteome diversity in an organism. AS functions in a range of physiological processes, including plant disease resistance, but its biological roles and functional mechanisms remain poorly understood. Many plant disease resistance (R) genes undergo AS, and several R genes require alternatively spliced transcripts to produce R proteins that can specifically recognize pathogen invasion. In the finely-tuned process of R protein activation, the truncated isoforms generated by AS may participate in plant disease resistance either by suppressing the negative regulation of initiation of immunity, or by directly engaging in effector-triggered signaling. Although emerging research has shown the functional significance of AS in plant biotic stress responses, many aspects of this topic remain to be understood. Several interesting issues surrounding the AS of R genes, especially regarding its functional roles and regulation, will require innovative techniques and additional research to unravel.

Effects of graded taurine levels on juvenile cobia

USDA-ARS?s Scientific Manuscript database

Taurine, which has multiple important physiological roles in teleost fish and mammals, is an amino acid not found in alternative protein sources not derived from animals. Although taurine is found in fish-meal-based feeds, its high water solubility leads to lower taurine levels in reduction-process-...

Family differences related to carbohydrate utilization in rainbow trout Oncorhynchus mykiss

USDA-ARS?s Scientific Manuscript database

Rainbow trout utilize protein as an energy source much more efficiently than carbohydrates. Alternative diets utilizing plant material typically contain higher levels of carbohydrate than standard fish meal diets. The goal of this study was to determine if there are molecular and physiological diffe...

DEVELOPMENT OF NOVEL PROTEINS TO ENHANCE CELLULOSE DECONSTRUCTION FOR ETHANOL PRODUCTION - PHASE I

EPA Science Inventory

Fuels derived from cellulosic biomass offer an alternative to conventional energy sources that supports national economic growth, national energy security, and environmental goals. In the 2007 State of the Union address, President Bush called for 35 billion gallons of alternat...

Recovery of soluble proteins from migratory locust (Locusta migratoria) and characterisation of their compositional and techno-functional properties.

PubMed

Purschke, Benedict; Tanzmeister, Helene; Meinlschmidt, Pia; Baumgartner, Sabine; Lauter, Kathrin; Jäger, Henry

2018-04-01

Edible insects emerged as an alternative source of high-quality proteins. Therefore, the effect of an extraction procedure for the recovery of migratory locust (Locusta migratoria) protein concentrate (MLPC) on the compositional characteristics and techno-functional properties was studied. The influence of pH value (2-10) and salt concentration (0, 1 and 3% w/v) on techno-functional properties was evaluated. Proteins were identified and characterized by RP-HPLC, SDS-PAGE and LC-MS/MS. The initial crude protein content of the whole locusts (65.9% on dry base) could be enhanced to 82.3% (MLPC). Solubility profiles of MLPC showed maximum solubility at pH9 (100%). Promising functionality comparable to egg white protein in terms of emulsifying activity at pH5, foamability at pH3 and 3% NaCl, and foam stability at pH9 were found. Consequently, MLPC offers a nutritious protein source with good functional properties at certain conditions, which could be used as food ingredient in a variety of food systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Protein Hydrolysates from Non-bovine and Plant Sources Replaces Tryptone in Microbiological Media

NASA Astrophysics Data System (ADS)

Ranganathan, Yamini; Patel, Shifa; Pasupuleti, Vijai K.; Meganathan, R.

Tryptone (pancreatic digest of casein) is a common ingredient in laboratory and fermentation media for growing wild-type and genetically modified microorganisms. Many of the commercially manufactured products such as human growth hormone, antibiotics, insulin, etc. are produced by recombinant strains grown on materials derived from bovine sources. With the emergence of Bovine Spongiform Encephalopathy (BSE) and the consequent increase in Food and Drug Administration (FDA) regulations, elimination of materials of bovine origin from fermentation media is of paramount importance. To achieve this objective, a number of protein hydrolysates derived from non-bovine animal and plant sources were evaluated. Tryptone in Luria-Bertani (LB) broth was replaced with an equal quantity of alternate protein hydrolysates. Four of the six hydrolysates (one animal and three from plants) were found to efficiently replace the tryptone present in LB-medium as measured by growth rate and growth yield of a recombinant Escherichia coli strain. In addition, we have determined plasmid stability, inducibility and activity of the plasmid encoded β-galactosidase in the recombinant strain grown in the presence of various protein hydrolysates.

Alternative Pre-mRNA Splicing in Mammals and Teleost Fish: A Effective Strategy for the Regulation of Immune Responses Against Pathogen Infection.

PubMed

Chang, Ming Xian; Zhang, Jie

2017-07-15

Pre-mRNA splicing is the process by which introns are removed and the protein coding elements assembled into mature mRNAs. Alternative pre-mRNA splicing provides an important source of transcriptome and proteome complexity through selectively joining different coding elements to form mRNAs, which encode proteins with similar or distinct functions. In mammals, previous studies have shown the role of alternative splicing in regulating the function of the immune system, especially in the regulation of T-cell activation and function. As lower vertebrates, teleost fish mainly rely on a large family of pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs) from various invading pathogens. In this review, we summarize recent advances in our understanding of alternative splicing of piscine PRRs including peptidoglycan recognition proteins (PGRPs), nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs), retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and their downstream signaling molecules, compared to splicing in mammals. We also discuss what is known and unknown about the function of splicing isoforms in the innate immune responses against pathogens infection in mammals and teleost fish. Finally, we highlight the consequences of alternative splicing in the innate immune system and give our view of important directions for future studies.

Seaweed as a source of novel nutraceuticals: sulfated polysaccharides and peptides.

PubMed

Jiménez-Escrig, A; Gómez-Ordóñez, E; Rupérez, P

2011-01-01

Seaweeds and seaweed-derived products are underexploited marine bioresources and a source of natural ingredients for functional foods. Nutritional studies on seaweeds indicate that brown and red seaweeds possess a good nutritional quality and could be used as an alternative source of dietary fiber, protein, and minerals. Moreover, bioactive sulfated polysaccharides are the main components of soluble fiber in seaweeds and also bioactive peptides can be prepared from seaweed protein. This chapter gives an overview of the main biological properties of sulfated polysaccharides and peptides from brown and red seaweeds. Recent studies have provided evidence that sulfated polysaccharides from seaweeds can play a vital role in human health and nutrition. Besides, peptides derived from algal protein are most promising as antihypertensive agents. Further research work, especially in vivo studies, are needed in order to gain a better knowledge of the relation structure-function by which bioactive compounds from seaweeds exert their bioactivity. Copyright © 2011 Elsevier Inc. All rights reserved.

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

PubMed Central

Holden, Brian J; Pinney, John W; Lovell, Simon C; Amoutzias, Grigoris D; Robertson, David L

2007-01-01

Background Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix (bHLH) family of transcription factors as an example. Results Network representations that arrange nodes (proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available. PMID:17683601

Nitrogen-to-Protein Conversion Factors for Three Edible Insects: Tenebrio molitor, Alphitobius diaperinus, and Hermetia illucens.

PubMed

Janssen, Renske H; Vincken, Jean-Paul; van den Broek, Lambertus A M; Fogliano, Vincenzo; Lakemond, Catriona M M

2017-03-22

Insects are considered a nutritionally valuable source of alternative proteins, and their efficient protein extraction is a prerequisite for large-scale use. The protein content is usually calculated from total nitrogen using the nitrogen-to-protein conversion factor (Kp) of 6.25. This factor overestimates the protein content, due to the presence of nonprotein nitrogen in insects. In this paper, a specific Kp of 4.76 ± 0.09 was calculated for larvae from Tenebrio molitor, Alphitobius diaperinus, and Hermetia illucens, using amino acid analysis. After protein extraction and purification, a Kp factor of 5.60 ± 0.39 was found for the larvae of three insect species studied. We propose to adopt these Kp values for determining protein content of insects to avoid overestimation of the protein content.

Nitrogen-to-Protein Conversion Factors for Three Edible Insects: Tenebrio molitor, Alphitobius diaperinus, and Hermetia illucens

PubMed Central

2017-01-01

Insects are considered a nutritionally valuable source of alternative proteins, and their efficient protein extraction is a prerequisite for large-scale use. The protein content is usually calculated from total nitrogen using the nitrogen-to-protein conversion factor (Kp) of 6.25. This factor overestimates the protein content, due to the presence of nonprotein nitrogen in insects. In this paper, a specific Kp of 4.76 ± 0.09 was calculated for larvae from Tenebrio molitor, Alphitobius diaperinus, and Hermetia illucens, using amino acid analysis. After protein extraction and purification, a Kp factor of 5.60 ± 0.39 was found for the larvae of three insect species studied. We propose to adopt these Kp values for determining protein content of insects to avoid overestimation of the protein content. PMID:28252948

Cell-free unnatural amino acid incorporation with alternative energy systems and linear expression templates.

PubMed

Shrestha, Prashanta; Smith, Mark Thomas; Bundy, Bradley Charles

2014-01-25

Site-specific incorporation of unnatural amino acids (uAAs) during protein synthesis expands the proteomic code through the addition of unique residue chemistry. This field provides a unique tool to improve pharmacokinetics, cancer treatments, vaccine development, proteomics and protein engineering. The limited ability to predict the characteristics of proteins with uAA-incorporation creates a need for a low-cost system with the potential for rapid screening. Escherichia coli-based cell-free protein synthesis is a compelling platform for uAA incorporation due to the open and accessible nature of the reaction environment. However, typical cell-free systems can be expensive due to the high cost of energizing reagents. By employing alternative energy sources, we reduce the cost of uAA-incorporation in CFPS by 55%. While alternative energy systems reduce cost, the time investment to develop gene libraries can remain cumbersome. Cell-free systems allow the direct use of PCR products known as linear expression templates, thus alleviating tedious plasmid library preparations steps. We report the specific costs of CFPS with uAA incorporation, demonstrate that LETs are suitable expression templates with uAA-incorporation, and consider the substantial reduction in labor intensity using LET-based expression for CFPS uAA incorporation. Copyright © 2013 Elsevier B.V. All rights reserved.

Polarizing the Neuron through Sustained Co-expression of Alternatively Spliced Isoforms.

PubMed

Yap, Karen; Xiao, Yixin; Friedman, Brad A; Je, H Shawn; Makeyev, Eugene V

2016-05-10

Alternative splicing (AS) is an important source of proteome diversity in eukaryotes. However, how this affects protein repertoires at a single-cell level remains an open question. Here, we show that many 3'-terminal exons are persistently co-expressed with their alternatives in mammalian neurons. In an important example of this scenario, cell polarity gene Cdc42, a combination of polypyrimidine tract-binding, protein-dependent, and constitutive splicing mechanisms ensures a halfway switch from the general (E7) to the neuron-specific (E6) alternative 3'-terminal exon during neuronal differentiation. Perturbing the nearly equimolar E6/E7 ratio in neurons results in defects in both axonal and dendritic compartments and suggests that Cdc42E7 is involved in axonogenesis, whereas Cdc42E6 is required for normal development of dendritic spines. Thus, co-expression of a precise blend of functionally distinct splice isoforms rather than a complete switch from one isoform to another underlies proper structural and functional polarization of neurons. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Acceptable low-phenylalanine foods and beverages can be made with glycomacropeptide from cheese whey for individuals with PKU

PubMed Central

Lim, Kyungwha; van Calcar, Sandra C.; Nelson, Kathryn L.; Gleason, Sally T.; Ney, Denise M.

2007-01-01

Glycomacropeptide (GMP) is a whey protein that contains no aromatic amino acids including phenylalanine (phe). The objective of this study was to make a variety of palatable, low-phe foods and beverages with GMP and to assess their acceptability by conducting consumer sensory studies in individuals with PKU. Results demonstrate acceptability of products made with GMP. GMP supplemented with limiting indispensable amino acids could provide an alternative protein source for individuals with PKU. PMID:17644019

Meat Quality Derived from High Inclusion of a Micro-Alga or Insect Meal as an Alternative Protein Source in Poultry Diets: A Pilot Study

PubMed Central

Neumann, Carmen; Velten, Susanne; Liebert, Frank

2018-01-01

The effects on meat quality resulting from alternative dietary protein sources (Spirulina and Hermetia meal) in poultry diets are studied to determine the overall suitability of these ingredients considering state-of-the-art packaging practices—highly oxygenated modified atmosphere packaging (HiOx MAP). We monitored standard slaughterhouse parameters, such as live weight, carcass weight, dressed yield, and pH at 20 min and 24 h post mortem. In addition, we studied the effects that 3 and 7-day storage in HiOx MAP has on the overall product physico-chemical and sensory properties. In addition to previously supported effects of HiOx MAP, we found that meat quality could be improved when Spirulina replaces 50% of the soy protein in broiler diets; however, this substitution results in a dark reddish-yellowish meat colour. On the other hand, the substitution with Hermetia larval meal results in a product that does not differ from the standard fed control group, with the exception that the breast filet has a more intense flavour that decreases over storage time. All-in-all Spirulina and Hermetia meal have the potential to replace soybean meal in broiler diets without deteriorating meat quality. PMID:29518048

Physicochemical and Functional Properties of Vegetable and Cereal Proteins as Potential Sources of Novel Food Ingredients

PubMed Central

Soria-Hernández, Cintya; Serna-Saldívar, Sergio

2015-01-01

Summary Proteins from vegetable and cereal sources are an excellent alternative to substitute animal-based counterparts because of their reduced cost, abundant supply and good nutritional value. The objective of this investigation is to study a set of vegetable and cereal proteins in terms of physicochemical and functional properties. Twenty protein sources were studied: five soya bean flour samples, one pea flour and fourteen newly developed blends of soya bean and maize germ (five concentrates and nine hydrolysates). The physicochemical characterization included pH (5.63 to 7.57), electrical conductivity (1.32 to 4.32 mS/cm), protein content (20.78 to 94.24% on dry mass basis), free amino nitrogen (0.54 to 2.87 mg/g) and urease activity (0.08 to 2.20). The functional properties showed interesting differences among proteins: water absorption index ranged from 0.41 to 18.52, the highest being of soya and maize concentrates. Nitrogen and water solubility ranged from 10.14 to 74.89% and from 20.42 to 95.65%, respectively. Fat absorption and emulsification activity indices ranged from 2.59 to 4.72 and from 3936.6 to 52 399.2 m2/g respectively, the highest being of pea flour. Foam activity (66.7 to 475.0%) of the soya and maize hydrolysates was the best. Correlation analyses showed that hydrolysis affected solubility-related parameters whereas fat-associated indices were inversely correlated with water-linked parameters. Foam properties were better of proteins treated with low heat, which also had high urease activity. Physicochemical and functional characterization of the soya and maize protein concentrates and hydrolysates allowed the identification of differences regarding other vegetable and cereal protein sources such as pea or soya bean. PMID:27904358

Kansas Food Service Employee. Short Courses.

ERIC Educational Resources Information Center

Kansas State Dept. of Education, Topeka. Div. of Vocational Education.

This is a series of five modules, each of which consists of six 3-hour classes in food preparation for nonmanagement personnel from institutional food services. Topics of the modules are breads and breakfasts, meats, vegetables and salads, extended meats and meat alternatives as sources of protein, and desserts. Included in each module are…

The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems

USDA-ARS?s Scientific Manuscript database

The reliance on fishmeal as a primary protein source is among the chief economic and environmental concerns in aquaculture today. Fishmeal-based feeds often require harvest from wild fish stocks, placing pressure on natural ecosystems and promoting price instability. Advances in alternative diet for...

Collagen from Marine Biological Sources and Medical Applications.

PubMed

Felician, Fatuma Felix; Xia, Chunlei; Qi, Weiyan; Xu, Hanmei

2018-05-01

Collagen is the most studied protein with a wide range of applications including pharmaceutical, biomedical, cosmetics, leather, and film industries due to its special characteristics that are high biocompatibility, good bioactivity, and weak antigenicity. Although collagen sources are abundant, the outbreak of varied diseases among land animals posed threat to its utilization in our daily life. Thus, a probe for an alternative source began, which in turn revealed the immense untapped marine sources, such as fish, jellyfish, and some marine Mammals. The present article deals with a brief description of collagen, its characteristics, marine sources, extraction, collagen peptides and their biological activities, potential use and application in various field. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

Dual potential of microalgae as a sustainable biofuel feedstock and animal feed

PubMed Central

2013-01-01

The rise in global population has led to explorations of alternative sources of energy and food. Because corn and soybean are staple food crops for humans, their common use as the main source of dietary energy and protein for food-producing animals directly competes with their allocation for human consumption. Alternatively, de-fatted marine microalgal biomass generated from the potential biofuel production may be a viable replacement of corn and soybean meal due to their high levels of protein, relatively well-balanced amino acid profiles, and rich contents of minerals and vitamins, along with unique bioactive compounds. Although the full-fatted (intact) microalgae represent the main source of omega-3 (n-3) polyunsaturated fatty acids including docohexaenoic acid (DHA) and eicosapentaenoic acid (EPA), the de-fatted microalgal biomass may still contain good amounts of these components for enriching DHA/EPA in eggs, meats, and milk. This review is written to highlight the necessity and potential of using the de-fatted microalgal biomass as a new generation of animal feed in helping address the global energy, food, and environmental issues. Nutritional feasibility and limitation of the biomass as the new feed ingredient for simple-stomached species are elaborated. Potential applications of the biomass for generating value-added animal products are also explored. PMID:24359607

Modular electron transfer circuits for synthetic biology

PubMed Central

Agapakis, Christina M

2010-01-01

Electron transfer is central to a wide range of essential metabolic pathways, from photosynthesis to fermentation. The evolutionary diversity and conservation of proteins that transfer electrons makes these pathways a valuable platform for engineered metabolic circuits in synthetic biology. Rational engineering of electron transfer pathways containing hydrogenases has the potential to lead to industrial scale production of hydrogen as an alternative source of clean fuel and experimental assays for understanding the complex interactions of multiple electron transfer proteins in vivo. We designed and implemented a synthetic hydrogen metabolism circuit in Escherichia coli that creates an electron transfer pathway both orthogonal to and integrated within existing metabolism. The design of such modular electron transfer circuits allows for facile characterization of in vivo system parameters with applications toward further engineering for alternative energy production. PMID:21468209

Reduction of nitrogen excretion and emission in poultry: A review for organic poultry.

PubMed

Chalova, Vesela I; Kim, Jihyuk; Patterson, Paul H; Ricke, Steven C; Kim, Woo K

2016-01-01

Organic poultry is an alternative to conventional poultry which is rapidly developing as a response to customers' demand for better food and a cleaner environment. Although organic poultry manure can partially be utilized by organic horticultural producers, litter accumulation as well as excessive nitrogen still remains a challenge to maintain environment pureness, animal, and human health. Compared to conventional poultry, diet formulation without nitrogen overloading in organic poultry is even more complicated due to specific standards and regulations which limit the application of some supplements and imposes specific criteria to the ingredients in use. This is especially valid for methionine provision which supplementation as a crystalline form is only temporarily allowed. This review is focused on the utilization of various protein sources in the preparation of a diet composed of 100% organic ingredients which meet the avian physiology need for methionine, while avoiding protein overload. The potential to use unconventional protein sources such as invertebrates and microbial proteins to achieve optimal amino acid provision is also discussed.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

PubMed

Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

White clover fractions as protein source for monogastrics: dry matter digestibility and protein digestibility-corrected amino acid scores.

PubMed

Stødkilde, Lene; Damborg, Vinni K; Jørgensen, Henry; Laerke, Helle N; Jensen, Søren K

2018-05-01

The present study aimed to evaluate the use of white clover as an alternative protein source for monogastrics. White clover plant and leaves were processed using a screw-press resulting in a solid pulp and a juice from which protein was acid-precipitated. The chemical composition of all fractions was determined and digestibility of dry matter (DM) and protein was assessed in an experiment with growing rats. Protein concentrates were produced with crude protein (CP) contents of 451 g kg -1 and 530 g kg -1 DM for white clover plant and leaves, respectively, and a pulp with CP contents of 313 and 374 g kg -1 DM from plant and leaves, respectively. The amino acid composition ranged from 4.72 to 6.49 g per 16 g of nitrogen (N) for lysine, 1.82-2.6 g per 16 g N for methionine and cysteine, and 3.66-5.24 g per 16 g N for threonine. True faecal digestibility of protein varied from 0.81 to 0.88, whereas DM digestibility was in the range 0.72-0.80. Methionine and cysteine were found to be limiting in all fractions, regardless of the reference group used. A high digestibility of white clover protein was found irrespective of the physical fractionation. Together with a well-balanced amino acid composition, this makes white clover a promising protein source for monogastrics. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Potential use of the invasive European green crab (Carcinus maenas) as an ingredient in Atlantic Salmon (Salmo salar) diets; a preliminary analysis

USDA-ARS?s Scientific Manuscript database

Atlantic salmon (Salmo salar) is an important cultured carnivorous species with wide comsumer acceptance. With the finite supply of available fishmeal and fish oil available for aquafeeds, research on and utilization of alternative protein and lipid sources is expandingWe examined the nutritional p...

Recent developments in L-asparaginase discovery and its potential as anticancer agent.

PubMed

Shrivastava, Abhinav; Khan, Abdul Arif; Khurshid, Mohsin; Kalam, Mohd Abul; Jain, Sudhir K; Singhal, Pradeep K

2016-04-01

L-Asparaginase (EC3.5.1.1) is an enzyme, which is used for treatment of acute lymphoblastic leukaemia (ALL) and other related blood cancers from a long time. This enzyme selectively hydrolyzes the extracellular amino acid L-asparagine into L-aspartate and ammonia, leading to nutritional deficiencies, protein synthesis inhibition, and ultimately death of lymphoblastic cells by apoptosis. Currently, bacterial asparaginases are used for treatment purpose but offers scepticism due to a number of toxicities, including thrombosis, pancreatitis, hyperglycemia, and hepatotoxicity. Resistance towards bacterial asparaginase is another major disadvantage during cancer management. This situation attracted attention of researchers towards alternative sources of L-asparaginase, including plants and fungi. Present article discusses about potential of L-asparaginase as an anticancer agent, its mechanism of action, and adverse effects related to current asparaginase formulations. This article also provides an outlook for recent developments in L-asparaginase discovery from alternative sources and their potential as a less toxic alternative to current formulations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

House dust mite (Der p 10) and crustacean allergic patients may react to food containing Yellow mealworm proteins.

PubMed

Verhoeckx, Kitty C M; van Broekhoven, Sarah; den Hartog-Jager, Constance F; Gaspari, Marco; de Jong, Govardus A H; Wichers, Harry J; van Hoffen, Els; Houben, Geert F; Knulst, André C

2014-03-01

Due to the imminent growth of the world population, shortage of protein sources for human consumption will arise in the near future. Alternative and sustainable protein sources (e.g. insects) are being explored for the production of food and feed. In this project, the safety of Yellow mealworms (Tenebrio molitor L.) for human consumption was tested using approaches as advised by the European Food Safety Authority for allergenicity risk assessment. Different Yellow mealworm protein fractions were prepared, characterised, and tested for cross-reactivity using sera from patients with an inhalation or food allergy to biologically related species (House dust mite (HDM) and crustaceans) by immunoblotting and basophil activation. Furthermore, the stability was investigated using an in vitro pepsin digestion test. IgE from HDM- and crustacean allergic patients cross-reacted with Yellow mealworm proteins. This cross-reactivity was functional, as shown by the induction of basophil activation. The major cross-reactive proteins were identified as tropomyosin and arginine kinase, which are well known allergens in arthropods. These proteins were moderately stable in the pepsin stability test. Based on these cross-reactivity studies, there is a realistic possibility that HDM- and crustacean allergic patients may react to food containing Yellow mealworm proteins. Copyright © 2014 Elsevier Ltd. All rights reserved.

A probabilistic model for detecting rigid domains in protein structures.

PubMed

Nguyen, Thach; Habeck, Michael

2016-09-01

Large-scale conformational changes in proteins are implicated in many important biological functions. These structural transitions can often be rationalized in terms of relative movements of rigid domains. There is a need for objective and automated methods that identify rigid domains in sets of protein structures showing alternative conformational states. We present a probabilistic model for detecting rigid-body movements in protein structures. Our model aims to approximate alternative conformational states by a few structural parts that are rigidly transformed under the action of a rotation and a translation. By using Bayesian inference and Markov chain Monte Carlo sampling, we estimate all parameters of the model, including a segmentation of the protein into rigid domains, the structures of the domains themselves, and the rigid transformations that generate the observed structures. We find that our Gibbs sampling algorithm can also estimate the optimal number of rigid domains with high efficiency and accuracy. We assess the power of our method on several thousand entries of the DynDom database and discuss applications to various complex biomolecular systems. The Python source code for protein ensemble analysis is available at: https://github.com/thachnguyen/motion_detection : mhabeck@gwdg.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Physics and evolution of thermophilic adaptation.

PubMed

Berezovsky, Igor N; Shakhnovich, Eugene I

2005-09-06

Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their thermostabilization. The first mechanism is "structure-based," whereby some hyperthermostable proteins are significantly more compact than their mesophilic homologues, while no particular interaction type appears to cause stabilization; rather, a sheer number of interactions is responsible for thermostability. Other hyperthermostable proteins employ an alternative, "sequence-based" mechanism of their thermal stabilization. They do not show pronounced structural differences from mesophilic homologues. Rather, a small number of apparently strong interactions is responsible for high thermal stability of these proteins. High-throughput comparative analysis of structures and complete genomes of several hyperthermophilic archaea and bacteria revealed that organisms develop diverse strategies of thermophilic adaptation by using, to a varying degree, two fundamental physical mechanisms of thermostability. The choice of a particular strategy depends on the evolutionary history of an organism. Proteins from organisms that originated in an extreme environment, such as hyperthermophilic archaea (Pyrococcus furiosus), are significantly more compact and more hydrophobic than their mesophilic counterparts. Alternatively, organisms that evolved as mesophiles but later recolonized a hot environment (Thermotoga maritima) relied in their evolutionary strategy of thermophilic adaptation on "sequence-based" mechanism of thermostability. We propose an evolutionary explanation of these differences based on physical concepts of protein designability.

Protein engineering in designing tailored enzymes and microorganisms for biofuels production

PubMed Central

Wen, Fei; Nair, Nikhil U; Zhao, Huimin

2009-01-01

Summary Lignocellulosic biofuels represent a sustainable, renewable, and the only foreseeable alternative energy source to transportation fossil fuels. However, the recalcitrant nature of lignocellulose poses technical hurdles to an economically viable biorefinery. Low enzymatic hydrolysis efficiency and low productivity, yield, and titer of biofuels are among the top cost contributors. Protein engineering has been used to improve the performances of lignocellulose-degrading enzymes, as well as proteins involved in biofuel synthesis pathways. Unlike its great success seen in other industrial applications, protein engineering has achieved only modest results in improving the lignocellulose-to-biofuels efficiency. This review will discuss the unique challenges that protein engineering faces in the process of converting lignocellulose to biofuels and how they are addressed by recent advances in this field. PMID:19660930

Arabidopsis-derived shrimp viral-binding protein, PmRab7 can protect white spot syndrome virus infection in shrimp.

PubMed

Thagun, Chonprakun; Srisala, Jiraporn; Sritunyalucksana, Kallaya; Narangajavana, Jarunya; Sojikul, Punchapat

2012-09-15

White spot syndrome virus is currently the leading cause of production losses in the shrimp industry. Penaeus monodon Rab7 protein has been recognized as a viral-binding protein with an efficient protective effect against white spot syndrome infection. Plant-derived recombinant PmRab7 might serve as an alternative source for in-feed vaccination, considering the remarkable abilities of plant expression systems. PmRab7 was introduced into the Arabidopsis thaliana T87 genome. Arabidopsis-derived recombinant PmRab7 showed high binding activity against white spot syndrome virus and a viral envelope, VP28. The growth profile of Arabidopsis suspension culture expressing PmRab7 (ECR21# 35) resembled that of its counterpart. PmRab7 expression in ECR21# 35 reached its maximum level at 5 mg g(-1) dry weight in 12 days, which was higher than those previously reported in Escherichia coli and in Pichia. Co-injection of white spot syndrome virus and Arabidopsis crude extract containing PmRab7 in Litopenaeus vannamei showed an 87% increase in shrimp survival rate at 5 day after injection. In this study, we propose an alternative PmRab7 source with higher production yield, and cheaper culture media costs, that might serve the industry's need for an in-feed supplement against white spot syndrome infection. Copyright © 2012 Elsevier B.V. All rights reserved.

Antioxidant Effectiveness of Vegetable Powders on the Lipid and Protein Oxidative Stability of Cooked Turkey Meat Patties: Implications for Health

PubMed Central

Duthie, Garry; Campbell, Fiona; Bestwick, Charles; Stephen, Sylvia; Russell, Wendy

2013-01-01

Lipid and protein oxidation decreases the shelf-life of foods and may result in formation of end-products potentially detrimental for health. Consumer pressure to decrease the use of synthetic phenolic antioxidants has encouraged identification of alternative compounds or extracts from natural sources. We have assessed whether inclusion of dried vegetable powders improves the oxidative stability of turkey meat patties. Such powders are not only potentially-rich sources of phenolic antioxidants, but also may impart additional health benefits, as inadequate vegetable consumption is a risk factor for heart disease and several cancers. In an accelerated oxidation system, six of eleven vegetable powders significantly (p < 0.05) improved oxidative stability of patties by 20%–30% (spinach < yellow pea < onion < red pepper < green pea < tomato). Improved lipid oxidative stability was strongly correlated with the decreased formation of protein carbonyls (r = 0.747, p < 0.01). However, improved lipid stability could not be ascribed to phenolic acids nor recognized antioxidants, such as α- and γ-tocopherol, despite their significant (p < 0.01) contribution to the total antioxidant capacity of the patties. Use of chemically complex vegetable powders offers an alternative to individual antioxidants for increasing shelf-life of animal-based food products and may also provide additional health benefits associated with increased vegetable intake. PMID:23595133

Rice protein-based infant formula: current status and future development.

PubMed

Koo, W W K; Lasekan, J B

2007-02-01

Rice is the world's leading staple cereal food and is the major source of protein for many parts of the world. Rice is among the first solid foods fed to infants in many cultures, in part because of its hypoallergenicity from lack of gluten. Nutritional quality of rice protein compares favorably with other cereal proteins including wheat, oat and barley. It is rich in methionine and cystine, although as is the case for other cereals, it is an incomplete protein source for human infants with lysine and threonine being the primary limiting amino acids. Fortification of rice proteins with these two limiting amino acids improves its protein quality. Rice protein-based infant formulas (RPF) were initially based on high protein rice flours, but more recently are based on rice protein concentrates, isolates or hydrolysates, fortified with lysine and threonine. Hypoallergenicity efficacy, particularly for hydrolyzed rice protein-based formulas, has been reported, and limited data indicated that rice protein based infant formula may provide potentially adequate alternative if standard milk- or soy protein-based formulas are not tolerated. Unlike the rice-protein based infant formula, rice beverage formulas made from rice flour are nutritionally inadequate for infants. Reports have indicated stunted growth in infants/children fed rice beverage formulas. Future development for the RPF include those based on genetically improved rice with high lysine and threonine content, supplementation with appropriate mineral and fat blend, and long-term clinical studies in infants to confirm its efficacy and safety.

Protein-intrinsic and signaling network-based sources of resistance to EGFR- and ErbB family-targeted therapies in head and neck cancer

PubMed Central

Mehra, Ranee; Serebriiskii, Ilya G.; Dunbrack, Roland L.; Robinson, Matthew K.; Burtness, Barbara; Golemis, Erica A.

2011-01-01

Agents targeting EGFR and related ErbB family proteins are valuable therapies for the treatment of many cancers. For some tumor types, including squamous cell carcinomas of the head and neck (SCCHN), antibodies targeting EGFR were the first protein-directed agents to show clinical benefit, and remain a standard component of clinical strategies for management of the disease. Nevertheless, many patients display either intrinsic or acquired resistance to these drugs; hence, major research goals are to better understand the underlying causes of resistance, and to develop new therapeutic strategies that boost the impact of EGFR/ErbB inhibitors. In this review, we first summarize current standard use of EGFR inhibitors in the context of SCCHN, and described new agents targeting EGFR currently moving through pre-clinical and clinical development. We then discuss how changes in other transmembrane receptors, including IGF1R, c-Met, and TGF-β, can confer resistance to EGFR-targeted inhibitors, and discuss new agents targeting these proteins. Moving downstream, we discuss critical EGFR-dependent effectors, including PLC-γ; PI3K and PTEN; SHC, GRB2, and RAS and the STAT proteins, as factors in resistance to EGFR-directed inhibitors and as alternative targets of therapeutic inhibition. We summarize alternative sources of resistance among cellular changes that target EGFR itself, through regulation of ligand availability, post-translational modification of EGFR, availability of EGFR partners for hetero-dimerization and control of EGFR intracellular trafficking for recycling versus degradation. Finally, we discuss new strategies to identify effective therapeutic combinations involving EGFR-targeted inhibitors, in the context of new system level data becoming available for analysis of individual tumors. PMID:21920801

Effect of different tryptophan sources on amino acids availability to the brain and mood in healthy volunteers.

PubMed

Markus, C Rob; Firk, Christine; Gerhardt, Cindy; Kloek, Joris; Smolders, Gertjan F

2008-11-01

Reduced brain serotonin function is acknowledged as a vulnerability factor for affective disturbances. Since the production of serotonin is limited by the availability of its plasma dietary amino acid precursor tryptophan (TRP), the beneficial effects of tryptophan-rich alpha-lactalbumin whey protein (ALAC) have recently been studied. The effects of ALAC remain rather modest, and alternative protein sources of tryptophan may be more effective. We tested whether hydrolyzed protein (HPROT) has greater effects on the plasma TRP/large neutral amino acids (LNAA) ratio and mood than intact ALAC protein in healthy volunteers. In a double-blind, randomized cross-over study, plasma amino acids and mood were repeatedly measured in 18 healthy subjects before and after intake of ALAC and HPROT as well as after placebo protein, pure tryptophan, and a tryptophan-containing synthetic peptide. Except for the placebo protein, all interventions contained 0.8 g TRP. Significantly faster and greater increases in plasma TRP/LNAA were found after HPROT than after ALAC. In addition, the effects of HPROT on plasma TRP/LNAA were comparable with the effects of the tryptophan-containing synthetic peptide and even exceeded the effect of pure tryptophan. Sixty minutes after intake, mood was improved only following intake of HPROT and pure tryptophan, whereas longer-lasting mood effects were only found after intake of HPROT. The use of a tryptophan-rich hydrolyzed protein source may be more adequate to increase brain tryptophan and 5-HT function compared with intact alpha-lactalbumin protein or pure tryptophan.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiser, C.; McIntosh, L.

The rise in alternative respiratory capacity upon aging of potato (Solanum tuberosum) tuber slices is correlated with changes in mitochondrial membrane protein composition and a requirement for cytoplasmic protein synthesis. However, the lack of an antibody specific to the alternative oxidase has, until recently, prevented examination of the alternative oxidase protein(s) itself. We have employed a monoclonal antibody raised against the Sauromatum guttatum alternative oxidase to investigate developmental changes in the alternative pathway of aging potato slice mitochondria and to characterize the potato alternative oxidase by one- and two-dimensional gel electrophoresis. The relative levels of a 36 kilodalton protein parallelmore » the rise in alternative path capacity. A plausible interpretation is that this alternative oxidase protein is synthesized de novo during aging of potato slices.« less

Net Flux of Amino Acids Across the Portal-drained Viscera and Liver of the Ewe During Abomasal Infusion of Protein and Glucose

USDA-ARS?s Scientific Manuscript database

Decreasing the fraction of amino acids metabolized by the mucosal cells may increase the fraction of AA being released into the blood. A potential mechanism to reduce AA catabolism by mucosal cells is to provide an alternative source of energy. We hypothesized that increasing glucose flow to the s...

Probing Protein Sequences as Sources for Encrypted Antimicrobial Peptides

PubMed Central

Brand, Guilherme D.; Magalhães, Mariana T. Q.; Tinoco, Maria L. P.; Aragão, Francisco J. L.; Nicoli, Jacques; Kelly, Sharon M.; Cooper, Alan; Bloch, Carlos

2012-01-01

Starting from the premise that a wealth of potentially biologically active peptides may lurk within proteins, we describe here a methodology to identify putative antimicrobial peptides encrypted in protein sequences. Candidate peptides were identified using a new screening procedure based on physicochemical criteria to reveal matching peptides within protein databases. Fifteen such peptides, along with a range of natural antimicrobial peptides, were examined using DSC and CD to characterize their interaction with phospholipid membranes. Principal component analysis of DSC data shows that the investigated peptides group according to their effects on the main phase transition of phospholipid vesicles, and that these effects correlate both to antimicrobial activity and to the changes in peptide secondary structure. Consequently, we have been able to identify novel antimicrobial peptides from larger proteins not hitherto associated with such activity, mimicking endogenous and/or exogenous microorganism enzymatic processing of parent proteins to smaller bioactive molecules. A biotechnological application for this methodology is explored. Soybean (Glycine max) plants, transformed to include a putative antimicrobial protein fragment encoded in its own genome were tested for tolerance against Phakopsora pachyrhizi, the causative agent of the Asian soybean rust. This procedure may represent an inventive alternative to the transgenic technology, since the genetic material to be used belongs to the host organism and not to exogenous sources. PMID:23029273

Standardized ileal digestibility of proteins and amino acids in sesame expeller and soya bean meal in weaning piglets.

PubMed

Aguilera, A; Reis de Souza, T C; Mariscal-Landín, G; Escobar, K; Montaño, S; Bernal, M G

2015-08-01

Apparent ileal digestibility (AID) of diets containing sesame expeller (SE) and soya bean meal (SBM) was determined using 15 piglets (Genetiporc(®)), weaned at 17 ± 0.4 days with average body weight of 6.4 ± 0.7 kg (Fertilis 20 × G Performance, Genetiporc(®), PIC México, Querétaro, México). Piglets were randomly assigned to three treatments: (i) a reference diet with casein as the sole protein source; (ii) a mixed diet of casein-SE; and (iii) a mixed diet of casein-SBM. The chemical composition of SE and SBM was determined, and AID and standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AAs) were determined for each protein source. SE contained greater quantities of ether extract, neutral detergent fibre, phytic acid, methionine and arginine than SBM. Lysine and proline contents and trypsin inhibitor activity were higher in SBM than in SE. The AID and SID of CP and AA (except for lysine and proline) were similar in SE and SBM. The AID of lysine and proline was higher in SBM than in SE (p < 0.05), and the SID of proline was higher in SE than in SBM (p < 0.05). These findings indicate that SE is an appropriate alternative protein source for early weaned pigs. Journal of Animal Physiology and Animal Nutrition © 2014 Blackwell Verlag GmbH.

Physicochemical and functional properties of protein concentrate from by-product of coconut processing.

PubMed

Rodsamran, Pattrathip; Sothornvit, Rungsinee

2018-02-15

Coconut cake, a by-product from milk and oil extractions, contains a high amount of protein. Protein extraction from coconut milk cake and coconut oil cake was investigated. The supernatant and precipitate protein powders from both coconut milk and oil cakes were compared based on their physicochemical and functional properties. Glutelin was the predominant protein fraction in both coconut cakes. Protein powders from milk cake presented higher water and oil absorption capacities than those from oil cake. Both protein powders from oil cake exhibited better foaming capacity and a better emulsifying activity index than those from milk cake. Coconut proteins were mostly solubilized in strong acidic and alkaline solutions. Minimum solubility was observed at pH 4, confirming the isoelectric point of coconut protein. Therefore, the coconut residues after extractions might be a potential alternative renewable plant protein source to use asa food ingredient to enhance food nutrition and quality. Copyright © 2017 Elsevier Ltd. All rights reserved.

Optimisation of a cheap and residential small-scale production of edible crickets with local by-products as an alternative protein-rich human food source in Ratanakiri Province, Cambodia.

PubMed

Caparros Megido, Rudy; Alabi, Taofic; Nieus, Clément; Blecker, Christophe; Danthine, Sabine; Bogaert, Jan; Haubruge, Éric; Francis, Frédéric

2016-01-30

The health status of the indigenous people of Ratanakiri Province, Cambodia, is significantly lower compared with that of the rest of the nation. The domestication and mass production of insects may represent a sustainable, cost effective and high quality alternative source of protein to traditional livestock. This study aimed to optimise a cheap and residential cricket breeding system based on unused wild resources. The development of crickets, Teleogryllus testaceus (Walker), under seven diets composed of taro aerial parts, young cassava leaves, young cashew leaves and brown rice flour (with or without banana slices), versus a traditionally used broiler feed diet was studied. Cricket mortality was low in all diets, except the two cashew-based diets. Total biomass was significantly higher under the broiler feed, in addition to the two diets containing a combination of cassava leaf powder and brown rice. Yet, crickets fed with the taro diet had the highest percentage of protein. Concerning the breeding system cost, units using cassava leaves were the cheapest. Diets based on cassava leaves seem to be the most promising. Nevertheless, to produce crickets with a high body mass and a high protein level, a new experiments must be devised in which cassava leaf maturity will be adapted to fit with the cricket growth stage. Moreover, to reduce the cost of the breeding units, handmade local products should be used instead of purchased components. © 2015 Society of Chemical Industry.

Sorbitol Can Fuel Mouse Sperm Motility and Protein Tyrosine Phosphorylation via Sorbitol Dehydrogenase1

PubMed Central

Cao, Wenlei; Aghajanian, Haig K.; Haig-Ladewig, Lisa A.; Gerton, George L.

2008-01-01

Energy sources that can be metabolized to yield ATP are essential for normal sperm functions such as motility. Two major monosaccharides, sorbitol and fructose, are present in semen. Furthermore, sorbitol dehydrogenase (SORD) can convert sorbitol to fructose, which can then be metabolized via the glycolytic pathway in sperm to make ATP. Here we characterize Sord mRNA and SORD expression during mouse spermatogenesis and examine the ability of sorbitol to support epididymal sperm motility and tyrosine phosphorylation. Sord mRNA levels increased during the course of spermatogenic differentiation. SORD protein, however, was first detected at the condensing spermatid stage. By indirect immunofluorescence, SORD was present along the length of the flagella of caudal epididymal sperm. Furthermore, immunoelectron microscopy showed that SORD was associated with mitochondria and the plasma membranes of sperm. Sperm incubated with sorbitol maintained motility, indicating that sorbitol was utilized as an energy source. Sorbitol, as well as glucose and fructose, were not essential to induce hyperactive motility. Protein tyrosine phosphorylation increased in a similar manner when sorbitol was substituted for glucose in the incubation medium used for sperm capacitation. These results indicate that sorbitol can serve as an alternative energy source for sperm motility and protein tyrosine phosphorylation. PMID:18799757

Multi-Instance Metric Transfer Learning for Genome-Wide Protein Function Prediction.

PubMed

Xu, Yonghui; Min, Huaqing; Wu, Qingyao; Song, Hengjie; Ye, Bicui

2017-02-06

Multi-Instance (MI) learning has been proven to be effective for the genome-wide protein function prediction problems where each training example is associated with multiple instances. Many studies in this literature attempted to find an appropriate Multi-Instance Learning (MIL) method for genome-wide protein function prediction under a usual assumption, the underlying distribution from testing data (target domain, i.e., TD) is the same as that from training data (source domain, i.e., SD). However, this assumption may be violated in real practice. To tackle this problem, in this paper, we propose a Multi-Instance Metric Transfer Learning (MIMTL) approach for genome-wide protein function prediction. In MIMTL, we first transfer the source domain distribution to the target domain distribution by utilizing the bag weights. Then, we construct a distance metric learning method with the reweighted bags. At last, we develop an alternative optimization scheme for MIMTL. Comprehensive experimental evidence on seven real-world organisms verifies the effectiveness and efficiency of the proposed MIMTL approach over several state-of-the-art methods.

To meat or not to meat? New perspectives on Neanderthal ecology.

PubMed

Fiorenza, Luca; Benazzi, Stefano; Henry, Amanda G; Salazar-García, Domingo C; Blasco, Ruth; Picin, Andrea; Wroe, Stephen; Kullmer, Ottmar

2015-02-01

Neanderthals have been commonly depicted as top predators who met their nutritional needs by focusing entirely on meat. This information mostly derives from faunal assemblage analyses and stable isotope studies: methods that tend to underestimate plant consumption and overestimate the intake of animal proteins. Several studies in fact demonstrate that there is a physiological limit to the amount of animal proteins that can be consumed: exceeding these values causes protein toxicity that can be particularly dangerous to pregnant women and newborns. Consequently, to avoid food poisoning from meat-based diets, Neanderthals must have incorporated alternative food sources in their daily diets, including plant materials as well. © 2014 American Association of Physical Anthropologists.

ROLES OF ADIPOCYTES AND FIBROBLASTS IN ACTIVATION OF THE ALTERNATIVE PATHWAY OF COMPLEMENT IN INFLAMMATORY ARTHRITIS IN MICE

PubMed Central

Arend, William P.; Mehta, Gaurav; Antonioli, Alexandra H.; Takahashi, Minoru; Takahashi, Kazue; Stahl, Gregory L.; Holers, V. Michael; Banda, Nirmal K.

2013-01-01

The complement system is involved in mediation of joint damage in rheumatoid arthritis, with evidence suggesting activation of both the classical and alternative pathways (AP). The AP is both necessary and sufficient to mediate collagen antibody-induced arthritis (CAIA), an experimental animal model of immune complex (IC)-induced joint disease. The AP in mice is dependent on MASP-1/3 cleavage of pro-factor D (pro-FD) into mature FD. The objectives of the present study were to determine the cells synthesizing MASP-1/3 and pro-FD in synovial tissue. CAIA was studied in wild-type C57BL/6 mice, and the localization of mRNA and protein for FD and MASP-1/3 in synovial adipose tissue (SAT) and fibroblast-like synoviocytes (FLS) was determined using various techniques, including laser capture micro-dissection (LCM). SAT was the sole source of mRNA for pro-FD. Cultured differentiated 3T3 adipocytes, a surrogate for SAT, produced pro-FD but no mature FD. FLS were the main source of MASP-1/3 mRNA and protein. Using cartilage micro-particles (CMP) coated with anti-collagen mAb and serum from MASP-1/3−/− mice as a source of factor B, pro-FD in 3T3 supernatants was cleaved into mature FD by MASP-1/3 in FLS supernatants. The mature FD was eluted from the CMP, and was not present in the supernatants from the incubation with CMP, indicating that cleavage of pro-FD into mature FD by MASP-1 occurred on the CMP. These results demonstrate that pathogenic activation of the AP may occur in the joint through IC adherent to cartilage and the local production of necessary AP proteins by adipocytes and FLS. PMID:23650618

Quality of eggs from Lohmann Brown Classic laying hens fed black soldier fly meal as substitute for soya bean.

PubMed

Secci, G; Bovera, F; Nizza, S; Baronti, N; Gasco, L; Conte, G; Serra, A; Bonelli, A; Parisi, G

2018-01-08

Soya bean is the main protein source in poultry feed but rising prices make an alternative protein source necessary. Insects, such as the black soldier fly (Hermetia illucens), may be an attractive solution for hens, although little information is available on their effect on egg quality. The present study aims to fill this gap by testing the effect of 100% replacement of soya bean with H. illucens larva meal in the diet of Lohmann Brown Classic laying hens for 21 weeks. At the end of the trial, the eggs were characterized for parameters such as weight, colour, proximate composition of albumen and yolk, and content of carotenoids, tocopherols and cholesterol. The fatty acid profile of yolks was also determined. Hens fed the insect-based diet produced eggs (HIM group) with a higher proportion of yolk than the group fed the soya bean-based diet (SBM group). HIM was associated with redder yolks (red index 5.63 v. 1.36) than SBM. HIM yolks were richer in γ-tocopherol (4.0 against 2.4 mg/kg), lutein (8.6 against 4.9 mg/kg), β-carotene (0.33 against 0.19 mg/kg) and total carotenoids (15 against 10.5 mg/kg) than SBM yolks. The fatty acid composition of HIM yolks was almost identical to that of SBM yolks. Finally, HIM yolks contained 11% less cholesterol than SBM yolks. These results suggest that H. illucens larva meal is a suitable total substitute for soya bean meal in the diet of Lohmann Brown Classic laying hens. A sustainable alternative to the plant protein source therefore seems feasible.

Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions.

PubMed

Raman, Babu; Nandakumar, M P; Muthuvijayan, Vignesh; Marten, Mark R

2005-11-05

Proteome analysis was used to compare global protein expression changes in Escherichia coli fermentation between exponential and glucose-limited fed-batch phase. Two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry were used to separate and identify 49 proteins showing >2-fold difference in expression. Proteins upregulated during exponential phase include ribonucleotide biosynthesis enzymes and ribosomal recycling factor. Proteins upregulated during fed-batch phase include those involved in high-affinity glucose uptake, transport and degradation of alternate carbon sources and TCA cycle, suggesting an enhanced role of the cycle under glucose- and energy-limited conditions. We report the upregulation of several putative proteins (ytfQ, ygiS, ynaF, yggX, yfeX), not identified in any previous study under carbon-limited conditions. Copyright (c) 2005 Wiley Periodicals, Inc.

A novel expression system for intracellular production and purification of recombinant affinity-tagged proteins in Aspergillus niger.

PubMed

Roth, Andreas H F J; Dersch, Petra

2010-03-01

A set of different integrative expression vectors for the intracellular production of recombinant proteins with or without affinity tag in Aspergillus niger was developed. Target genes can be expressed under the control of the highly efficient, constitutive pkiA promoter or the novel sucrose-inducible promoter of the beta-fructofuranosidase (sucA) gene of A. niger in the presence or absence of alternative carbon sources. All expression plasmids contain an identical multiple cloning sequence that allows parallel construction of N- or C-terminally His6- and StrepII-tagged versions of the target proteins. Production of two heterologous model proteins, the green fluorescence protein and the Thermobifida fusca hydrolase, proved the functionality of the vector system. Efficient production and easy detection of the target proteins as well as their fast purification by a one-step affinity chromatography, using the His6- or StrepII-tag sequence, was demonstrated.

[Alternative splicing regulation: implications in cancer diagnosis and treatment].

PubMed

Martínez-Montiel, Nancy; Rosas-Murrieta, Nora; Martínez-Contreras, Rebeca

2015-04-08

The accurate expression of the genetic information is regulated by processes like mRNA splicing, proposed after the discoveries of Phil Sharp and Richard Roberts, who demonstrated the existence of intronic sequences, present in almost every structural eukaryotic gene, which should be precisely removed. This intron removal is called "splicing", which generates different proteins from a single mRNA, with different or even antagonistic functions. We currently know that alternative splicing is the most important source of protein diversity, given that 70% of the human genes undergo splicing and that mutations causing defects in this process could originate up to 50% of genetic diseases, including cancer. When these defects occur in genes involved in cell adhesion, proliferation and cell cycle regulation, there is an impact on cancer progression, rising the opportunity to diagnose and treat some types of cancer according to a particular splicing profile. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

Cassava chip (Manihot esculenta Crantz) as an energy source for ruminant feeding.

PubMed

Wanapat, Metha; Kang, Sungchhang

2015-12-01

Cassava ( Manihot esculenta Crantz) is widely grown in sub-tropical and tropical areas, producing roots as an energy source while the top biomass including leaves and immature stems can be sun-dried and used as cassava hay. Cassava roots can be processed as dried chip or pellet. It is rich in soluble carbohydrate (75 to 85%) but low in crude protein (2 to 3%). Its energy value is comparable to corn meal but has a relatively higher rate of rumen degradation. Higher levels of non-protein nitrogen especially urea (1 to 4%) can be successfully incorporated in concentrates containing cassava chip as an energy source. Cassava chip can also be processed with urea and other ingredients (tallow, sulfur, raw banana meal, cassava hay, and soybean meal) to make products such as cassarea, cassa-ban, and cassaya. Various studies have been conducted in ruminants using cassava chip to replace corn meal in the concentrate mixtures and have revealed satisfactory results in rumen fermentation efficiency and the subsequent production of meat and milk. In addition, it was advantageous when used in combination with rice bran in the concentrate supplement. Practical home-made-concentrate using cassava chip can be easily prepared for use on farms. A recent development has involved enriching protein in cassava chips, yielding yeast fermented cassava chip protein (YEFECAP) of up to 47.5% crude protein, which can be used to replace soybean meal. It is therefore, recommended to use cassava chip as an alternative source of energy to corn meal when the price is economical and it is locally available.

Sequence co-evolution gives 3D contacts and structures of protein complexes

PubMed Central

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

2014-01-01

Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

Purine derivate content and amino acid profile in larval stages of three edible insects.

PubMed

Bednářová, Martina; Borkovcová, Marie; Komprda, Tomáš

2014-01-15

Considering their high content of protein, insects are a valuable alternative protein source. However, no evaluation of their purine content has so far been done. High content of purine derivates may lead to the exclusion of such food from the diet of people with specific diseases. The aim of this study was to analyse the content of selected purine derivates and amino acid profile in the three insect species most often used for entomophagy in Europe and compare them with the purine content in egg white and chicken breast. The content of individual purine derivates and their total content were significantly dependent on insect species. The purine content in all three species was significantly higher (P < 0.05) than in egg white, but some values were significantly lower (P < 0.05) than in chicken breast. The total protein content was 548.9 g kg(-1) dry matter (DM) in mealworm (Tenebrio molitor), 551.6 g kg(-1) DM in superworm (Zophobas atratus) and 564.9 g kg(-1) DM in cricket (Gryllus assimilis). Larvae of mealworm and superworm are protein-rich and purine-low meat alternatives. In contrast, cricket nymphs are protein-rich and purine-rich and cannot be recommended for people with hyperuricemia or gout. © 2013 Society of Chemical Industry.

Toxic compound, anti-nutritional factors and functional properties of protein isolated from detoxified Jatropha curcas seed cake.

PubMed

Saetae, Donlaporn; Suntornsuk, Worapot

2010-12-28

Jatropha curcas is a multipurpose tree, which has potential as an alternative source for biodiesel. All of its parts can also be used for human food, animal feed, fertilizer, fuel and traditional medicine. J. curcas seed cake is a low-value by-product obtained from biodiesel production. The seed cake, however, has a high amount of protein, with the presence of a main toxic compound: phorbol esters as well as anti-nutritional factors: trypsin inhibitors, phytic acid, lectin and saponin. The objective of this work was to detoxify J. curcas seed cake and study the toxin, anti-nutritional factors and also functional properties of the protein isolated from the detoxified seed cake. The yield of protein isolate was approximately 70.9%. The protein isolate was obtained without a detectable level of phorbol esters. The solubility of the protein isolate was maximal at pH 12.0 and minimal at pH 4.0. The water and oil binding capacities of the protein isolate were 1.76 g water/g protein and 1.07 mL oil/g protein, respectively. The foam capacity and stability, including emulsion activity and stability of protein isolate, had higher values in a range of basic pHs, while foam and emulsion stabilities decreased with increasing time. The results suggest that the detoxified J. curcas seed cake has potential to be exploited as a novel source of functional protein for food applications.

Toxic Compound, Anti-Nutritional Factors and Functional Properties of Protein Isolated from Detoxified Jatropha curcas Seed Cake

PubMed Central

Saetae, Donlaporn; Suntornsuk, Worapot

2011-01-01

Jatropha curcas is a multipurpose tree, which has potential as an alternative source for biodiesel. All of its parts can also be used for human food, animal feed, fertilizer, fuel and traditional medicine. J. curcas seed cake is a low-value by-product obtained from biodiesel production. The seed cake, however, has a high amount of protein, with the presence of a main toxic compound: phorbol esters as well as anti-nutritional factors: trypsin inhibitors, phytic acid, lectin and saponin. The objective of this work was to detoxify J. curcas seed cake and study the toxin, anti-nutritional factors and also functional properties of the protein isolated from the detoxified seed cake. The yield of protein isolate was approximately 70.9%. The protein isolate was obtained without a detectable level of phorbol esters. The solubility of the protein isolate was maximal at pH 12.0 and minimal at pH 4.0. The water and oil binding capacities of the protein isolate were 1.76 g water/g protein and 1.07 mL oil/g protein, respectively. The foam capacity and stability, including emulsion activity and stability of protein isolate, had higher values in a range of basic pHs, while foam and emulsion stabilities decreased with increasing time. The results suggest that the detoxified J. curcas seed cake has potential to be exploited as a novel source of functional protein for food applications. PMID:21339978

Iron management and production of electricity by microorganisms.

PubMed

Folgosa, Filipe; Tavares, Pedro; Pereira, Alice S

2015-10-01

The increasing dependency on fossil fuels has driven researchers to seek for alternative energy sources. Renewable energy sources such as sunlight, wind, or water are the most common. However, since the 1990s, other sources for energy production have been studied. The use of microorganisms such as bacteria or archaea to produce energy is currently in great progress. These present several advantages even when compared with other renewable energy sources. Besides the energy production, they are also involved in bioremediation such as the removal of heavy metal contaminants from soils or wastewaters. Several research groups have demonstrated that these organisms are able to interact with electrodes via heme and non-heme iron proteins. Therefore, the role of iron as well as iron metabolism in these species must be of enormous relevance. Recently, the influence of cellular iron regulation by Fur in the Geobacter sulfurreducens growth and ability to produce energy was demonstrated. In this review, we aim to briefly describe the most relevant proteins involved in the iron metabolism of bacteria and archaea and relate them and their biological function with the ability of selected organisms to produce energy.

Chemical composition, true nutrient digestibility, and true metabolizable energy of novel pet food protein sources using the precision-fed cecectomized rooster assay.

PubMed

Deng, P; Utterback, P L; Parsons, C M; Hancock, L; Swanson, K S

2016-08-01

A wide variety of animal protein-based ingredients is commonly used in the pet food products. The raw ingredients and processing procedures used may greatly affect protein quality. Testing the quality of alternative protein sources is necessary and contributes to the sustainability of pet foods. The objective of this study was to test the chemical composition of 8 protein sources intended for use in dog and cat foods (calamari meal, pork peptone, alligator meal, lamb meal, venison meal, chicken meal, and 2 duck meals), and evaluate their true nutrient digestibility and nitrogen-corrected true ME (TMEn) using the precision-fed cecectomized rooster assay. Calamari meal and pork peptone had lower ash (4.4 and 3.6% of DM, respectively) but greater CP (88.1 and 80.5% of DM, respectively) and either greater or similar GE (5.6 and 5.3 kcal/g of DM, respectively) compared with alligator, lamb, venison, chicken, and duck meals (11.8 to 24.5% ash, 58.7 to 65.9% CP, and 4.6 to 5.3 kcal GE/g). Acid-hydrolyzed fat (AHF) was lower in calamari meal (8.7% of DM) compared with the other proteins tested (15.5-22.1% of DM). True nutrient digestibility was variable among the protein sources (52 to 79% of DM, 60 to 83% of OM, 78 to 92% of AHF, and 70 to 89% of GE) with pork peptone having the highest DM, AHF, and GE digestibility and calamari meal having the highest OM digestibility. True indispensable AA digestibility was highest for calamari meal, with all AA having a digestibility greater than 90%. Except for histidine, all indispensable AA had a digestibility over 85% for pork peptone. In contrast, true indispensable AA digestibility was lowest for lamb meal, with histidine having digestibility less than 70% and the other entire indispensable AA having digestibility between 72 and 88%. The TMEn of calamari meal (4.82 kcal/g DM and 86.9% of GE) was greater ( < 0.05) than the other protein sources. The lamb meal had the lowest TMEn value (3.12 kcal/g DM and 66.9% of GE), with others being intermediate (3.46-4.09 kcal/g DM and 71.2-77.9% of GE). This study demonstrates the considerable variability that exists not only in the chemical composition but also in the true nutrient digestibility among protein sources intended for use in dog and cat foods and justifies further in vivo testing of novel protein sources.

The sialotranscriptome of Antricola delacruzi female ticks is compatible with non-hematophagous behavior and an alternative source of food

PubMed Central

Ribeiro, José Marcos C.; Labruna, Marcelo B.; Mans, Ben J.; Maruyama, Sandra Regina; Francischetti, Ivo M. B.; Barizon, Gustavo Canavaci; de Miranda Santos, Isabel K. F.

2012-01-01

The hosts for Antricola delacruzi ticks are insectivorous, cave-dwelling bats on which only larvae are found. The mouthparts of nymphal and adult A. delacruzi are compatible with scavenging feeding because the hypostome is small and toothless. How a single blood meal of a larva provides energy for several molts as well as for oviposition by females is not known. Adults of A. delacruzi possibly feed upon an unknown food source in bat guano, a substrate on which nymphal and adult stages are always found. Guano produced by insectivorous bats contains twice the amount of protein and 60 times the amount of iron as beef. In addition, bacteria and chitin-rich fungi proliferate on guano. Comparative data on the transcriptome of the salivary glands of A. delacruzi is nonexistent and would help to understand the physiological adaptations of salivary glands that accompany different sources of food as well as the steps taken by the Acari towards haematophagy, believed to have evolved from scavenging dead animals. Annotation of the transcriptome of salivary glands from female instars of A. delacruzi collected on guano categorized 5.7% of the clusters of expressed genes as putative secreted proteins. They included abundantly expressed TIL domain-containing proteins (possible anti-microbials), an abundantly expressed protein similar to a serum amyloid found in the sialotranscriptomes of Ornithodoros spp., a savignygrin, a family of mucin/peritrophin/cuticle-like proteins, antimicrobials and an HIV envelope-like glycoprotein also found in soft ticks. When comparing the transcriptome of A. delacruzi with those of blood-feeding female soft and hard ticks some notable differences were observed; they consisted of the following transcripts over- or under-represented or absent in the sialotranscriptome of A. delacuzi that may reflect its source of food: ferritin, mucins with chitin-binding domains and TIL domain-containing proteins versus lipocalins, basic tail proteins, metalloproteases, glycine-rich proteins and Kunitz protease inhibitors, respectively. PMID:22306723

Nutritional aspects of second generation soy foods.

PubMed

Alezandro, Marcela Roquim; Granato, Daniel; Lajolo, Franco Maria; Genovese, Maria Inés

2011-05-25

Samples of 15 second generation soy-based products (n = 3), commercially available, were analyzed for their protein and isoflavone contents and in vitro antioxidant activity, by means of the Folin-Ciocalteu reducing ability, DPPH radical scavenging capacity, and oxygen radical absorbance capacity. Isoflavone identification and quantification were performed by high-performance liquid chromatography. Products containing soy and/or soy-based ingredients represent important sources of protein in addition to the low fat amounts. However, a large variation in isoflavone content and in vitro antioxidant capacity was observed. The isoflavone content varied from 2.4 to 18.1 mg/100 g (FW), and soy kibe and soy sausage presented the highest amounts. Chocolate had the highest antioxidant capacity, but this fact was probably associated with the addition of cocoa liquor, a well-known source of polyphenolics. This study showed that the soy-based foods do not present a significant content of isoflavones when compared with the grain, and their in vitro antioxidant capacity is not related with these compounds but rather to the presence of other phenolics and synthetic antioxidants, such as sodium erythorbate. However, they may represent alternative sources and provide soy protein, isoflavones, and vegetable fat for those who are not ready to eat traditional soy foods.

Angiotensin-converting enzyme-inhibitory activity in protein hydrolysates from normal and anthracnose disease-damaged Phaseolus vulgaris seeds.

PubMed

Hernández-Álvarez, Alan Javier; Carrasco-Castilla, Janet; Dávila-Ortiz, Gloria; Alaiz, Manuel; Girón-Calle, Julio; Vioque-Peña, Javier; Jacinto-Hernández, Carmen; Jiménez-Martínez, Cristian

2013-03-15

Bean seeds are an inexpensive source of protein. Anthracnose disease caused by the fungus Colletotrichum lindemuthianum results in serious losses in common bean (Phaseolus vulgaris L.) crops worldwide, affecting any above-ground plant part, and protein dysfunction, inducing the synthesis of proteins that allow plants to improve their stress tolerance. The aim of this study was to evaluate the use of beans damaged by anthracnose disease as a source of peptides with angiotensin-converting enzyme (ACE-I)-inhibitory activity. Protein concentrates from beans spoiled by anthracnose disease and from regular beans as controls were prepared by alkaline extraction and precipitation at isolelectric pH and hydrolysed using Alcalase 2.4 L. The hydrolysates from spoiled beans had ACE-I-inhibitory activity (IC(50) 0.0191 mg protein mL(-1)) and were very similar to those from control beans in terms of ACE-I inhibition, peptide electrophoretic profile and kinetics of hydrolysis. Thus preparation of hydrolysates using beans affected by anthracnose disease would allow for revalorisation of this otherwise wasted product. The present results suggest the use of spoiled bean seeds, e.g. anthracnose-damaged beans, as an alternative for the isolation of ACE-I-inhibitory peptides to be further introduced as active ingredients in functional foods. © 2012 Society of Chemical Industry.

Function of alternative splicing

PubMed Central

Kelemen, Olga; Convertini, Paolo; Zhang, Zhaiyi; Wen, Yuan; Shen, Manli; Falaleeva, Marina; Stamm, Stefan

2017-01-01

Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in ‘splicing programs’, which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed. PMID:22909801

Effect of dietary alternative lipid sources on haematological parameters and serum constituents of Heterobranchus longifilis fingerlings.

PubMed

Babalola, T O O; Adebayo, M A; Apata, D F; Omotosho, J S

2009-03-01

The worldwide increase in aquaculture production and the decrease of wild fish stocks has made the replacement of fish oil (FO) in aquafeed industry a priority. Therefore, the use of terrestrial animal fats and vegetable oils, which has lower cost and larger supplies, may be good as substitute for FO. This study investigate the effects of total replacement of FO by two terrestrial animal fats (pork lard and poultry fat) and three vegetable oils (palm kernel oil, sheabutter oil and sunflower oil) on haematological and serum biochemical profile of Heterobranchus longifilis over 70 days. FO-diet was used as the control. The haematological parameters were significantly affected by dietary lipid sources. Serum total protein was not influenced by the dietary lipids. However, serum cholesterol was significantly higher in fish fed diet containing sunflower oil. Glucose and activities of liver enzymes in blood serum were significantly reduced in fish fed alternative lipids when compared with the control. These results indicate that FO can be replaced completely with alternative lipids without any serious negative health impacts.

Fluorescence Reporter-Based Genome-Wide RNA Interference Screening to Identify Alternative Splicing Regulators.

PubMed

Misra, Ashish; Green, Michael R

2017-01-01

Alternative splicing is a regulated process that leads to inclusion or exclusion of particular exons in a pre-mRNA transcript, resulting in multiple protein isoforms being encoded by a single gene. With more than 90 % of human genes known to undergo alternative splicing, it represents a major source for biological diversity inside cells. Although in vitro splicing assays have revealed insights into the mechanisms regulating individual alternative splicing events, our global understanding of alternative splicing regulation is still evolving. In recent years, genome-wide RNA interference (RNAi) screening has transformed biological research by enabling genome-scale loss-of-function screens in cultured cells and model organisms. In addition to resulting in the identification of new cellular pathways and potential drug targets, these screens have also uncovered many previously unknown mechanisms regulating alternative splicing. Here, we describe a method for the identification of alternative splicing regulators using genome-wide RNAi screening, as well as assays for further validation of the identified candidates. With modifications, this method can also be adapted to study the splicing regulation of pre-mRNAs that contain two or more splice isoforms.

Cheese whey: A cost-effective alternative for hyaluronic acid production by Streptococcus zooepidemicus.

PubMed

Amado, Isabel R; Vázquez, José A; Pastrana, Lorenzo; Teixeira, José A

2016-05-01

This study focuses on the optimisation of cheese whey formulated media for the production of hyaluronic acid (HA) by Streptococcus zooepidemicus. Culture media containing whey (W; 2.1g/L) or whey hydrolysate (WH; 2.4 g/L) gave the highest HA productions. Both W and WH produced high yields on protein consumed, suggesting cheese whey is a good nitrogen source for S. zooepidemicus production of HA. Polysaccharide concentrations of 4.0 g/L and 3.2g/L were produced in W and WH in a further scale-up to 5L bioreactors, confirming the suitability of the low-cost nitrogen source. Cheese whey culture media provided high molecular weight (>3000 kDa) HA products. This study revealed replacing the commercial peptone by the low-cost alternative could reduce HA production costs by up to a 70% compared to synthetic media. Copyright © 2015 Elsevier Ltd. All rights reserved.

General introduction: recombinant protein production and purification of insoluble proteins.

PubMed

Ferrer-Miralles, Neus; Saccardo, Paolo; Corchero, José Luis; Xu, Zhikun; García-Fruitós, Elena

2015-01-01

Proteins are synthesized in heterologous systems because of the impossibility to obtain satisfactory yields from natural sources. The production of soluble and functional recombinant proteins is among the main goals in the biotechnological field. In this context, it is important to point out that under stress conditions, protein folding machinery is saturated and this promotes protein misfolding and, consequently, protein aggregation. Thus, the selection of the optimal expression organism and the most appropriate growth conditions to minimize the formation of insoluble proteins should be done according to the protein characteristics and downstream requirements. Escherichia coli is the most popular recombinant protein expression system despite the great development achieved so far by eukaryotic expression systems. Besides, other prokaryotic expression systems, such as lactic acid bacteria and psychrophilic bacteria, are gaining interest in this field. However, it is worth mentioning that prokaryotic expression system poses, in many cases, severe restrictions for a successful heterologous protein production. Thus, eukaryotic systems such as mammalian cells, insect cells, yeast, filamentous fungus, and microalgae are an interesting alternative for the production of these difficult-to-express proteins.

Alternative splicing of mutually exclusive exons--a review.

PubMed

Pohl, Martin; Bortfeldt, Ralf H; Grützmann, Konrad; Schuster, Stefan

2013-10-01

Alternative splicing (AS) of pre-mRNAs in higher eukaryotes and several viruses is one major source of protein diversity. Usually, the following major subtypes of AS are distinguished: exon skipping, intron retention, and alternative 3' and 5' splice sites. Moreover, mutually exclusive exons (MXEs) represent a rare subtype. In the splicing of MXEs, two (or more) splicing events are not independent anymore, but are executed or disabled in a coordinated manner. In this review, several bioinformatics approaches for analyzing MXEs are presented and discussed. In particular, we revisit suitable definitions and nomenclatures, and bioinformatics tools for finding MXEs, adjacent and non-adjacent MXEs, clustered and grouped MXEs. Moreover, the molecular mechanisms for splicing MXEs proposed in the literature are reviewed and discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Identification of the alternative terminal oxidase of higher plant mitochondria

PubMed Central

Elthon, Thomas E.; McIntosh, Lee

1987-01-01

In addition to cytochrome oxidase, plant mitochondria have a second terminal oxidase called the alternative oxidase. The alternative oxidase is of great interest in that energy is not conserved when electrons flow through it. The potential energy of the system is thus lost as heat, and, in plants with high levels of the alternative oxidase, this results in thermogenesis. We have purified the alternative oxidase from mitochondria of the thermogenic spadix of Sauromatum guttatum and have identified its polypeptide constituents by using polyclonal antibodies. A 166-fold purification was achieved through a combination of cation-exchange (carboxymethyl-Sepharose) and hydrophobic-interaction (phenyl-Sepharose) chromatography. Polyclonal antibodies raised to the CM-Sepharose fractions readily immunoprecipitated alternative oxidase activity and immunoprecipitated four of the proteins that copurify with the activity. These proteins have apparent molecular masses of 37, 36, 35.5, and 35 kDa. Polyclonal antibodies raised individually to the 37-, 36-, and 35.5- plus 35-kDa proteins cross-reacted with all of these proteins, indicating the presence of common antigenic sites. The 37-kDa protein appears to be constitutive in Sauromatum, whereas expression of the 36- and 35-kDa proteins was correlated with presence of alternative pathway activity. The 35.5-kDa protein appears with loss of alternative pathway activity during senescence, indicating that this protein may be a degradation product of the 36-kDa protein. Binding of anti-36-kDa protein antibodies to total mitochondrial protein blots of five plant species indicated that similar proteins were always present when alternative pathway activity was observed. Images PMID:16593898

7 CFR Appendix A to Part 225 - Alternate Foods for Meals

Code of Federal Regulations, 2011 CFR

2011-01-01

... Used in the Summer Food Service Program? 1. An alternate protein product used in meals planned under..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How Are Alternate Protein Products Used in the Summer Food Service Program? 1...

7 CFR Appendix A to Part 225 - Alternate Foods for Meals

Code of Federal Regulations, 2014 CFR

2014-01-01

... Used in the Summer Food Service Program? 1. An alternate protein product used in meals planned under..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How Are Alternate Protein Products Used in the Summer Food Service Program? 1...

7 CFR Appendix A to Part 225 - Alternate Foods for Meals

Code of Federal Regulations, 2010 CFR

2010-01-01

... Used in the Summer Food Service Program? 1. An alternate protein product used in meals planned under..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How Are Alternate Protein Products Used in the Summer Food Service Program? 1...

7 CFR Appendix A to Part 225 - Alternate Foods for Meals

Code of Federal Regulations, 2012 CFR

2012-01-01

... Used in the Summer Food Service Program? 1. An alternate protein product used in meals planned under..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How Are Alternate Protein Products Used in the Summer Food Service Program? 1...

7 CFR Appendix A to Part 225 - Alternate Foods for Meals

Code of Federal Regulations, 2013 CFR

2013-01-01

... Used in the Summer Food Service Program? 1. An alternate protein product used in meals planned under..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How Are Alternate Protein Products Used in the Summer Food Service Program? 1...

Dynamics of the Escherichia coli proteome in response to nitrogen starvation and entry into the stationary phase.

PubMed

Sanchuki, Heloisa B S; Gravina, Fernanda; Rodrigues, Thiago E; Gerhardt, Edileusa C M; Pedrosa, Fábio O; Souza, Emanuel M; Raittz, Roberto T; Valdameri, Glaucio; de Souza, Gustavo A; Huergo, Luciano F

2017-03-01

Nitrogen is needed for the biosynthesis of biomolecules including proteins and nucleic acids. In the absence of fixed nitrogen prokaryotes such as E. coli immediately ceases growth. Ammonium is the preferred nitrogen source for E. coli supporting the fastest growth rates. Under conditions of ammonium limitation, E. coli can use alternative nitrogen sources to supply ammonium ions and this reprogramming is led by the induction of the NtrC regulon. Here we used label free proteomics to determine the dynamics of E. coli proteins expression in response to ammonium starvation in both the short (30min) and the longer (60min) starvation. Protein abundances and post-translational modifications confirmed that activation of the NtrC regulon acts as the first line of defense against nitrogen starvation. The ribosome inactivating protein Rmf was induced shortly after ammonium exhaustion and this was preceded by induction of other ribosome inactivating proteins such as Hpf and RaiA supporting the hypothesis that ribosome shut-down is a key process during nitrogen limitation stress. The proteomic data revealed that growth arrest due to nitrogen starvation correlates with the accumulation of proteins involved in DNA condensation, RNA and protein catabolism and ribosome hibernation. Collectively, these proteome adaptations will result in metabolic inactive cells which are likely to exhibit multidrug tolerance. Copyright © 2016 Elsevier B.V. All rights reserved.

Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources.

PubMed

Rimoldi, Simona; Terova, Genciana; Ascione, Chiara; Giannico, Riccardo; Brambilla, Fabio

2018-01-01

Animal by-product meals from the rendering industry could provide a sustainable and commercially viable alternative to fishmeal (FM) in aquaculture, as they are rich in most essential amino acids and contain important amounts of water-soluble proteins that improve feed digestibility and palatability. Among them, poultry by-product meal (PBM) have given encouraging results in rainbow trout (Oncorhynchus mykiss). However, the introduction of new ingredients in the diet needs to be carefully evaluated since diet is one of the main factors affecting the gut microbiota, which is a complex community that contributes to host metabolism, nutrition, growth, and disease resistance. Accordingly, we investigated the effects of partial replacement of dietary FM with a mix of animal by-product meals and plant proteins on intestinal microbiota composition of rainbow trout in relation to growth and feeding efficiency parameters. We used 1540 trout with an initial mean body weight of 94.6 ± 14.2 g. Fish were fed for 12 weeks with 7 different feed formulations. The growth data showed that trout fed on diets rich in animal by-product meals grew as well as fish fed on control diet, which was rich in FM (37.3%) and PBM-free. High-throughput 16S rRNA gene amplicon sequencing (MiSeq platform, Illumina) was utilised to study the gut microbial community profile. After discarding Cyanobacteria (class Chloroplast) and mitochondria reads a total of 2,701,274 of reads taxonomically classified, corresponding to a mean of 96,474 ± 68,056 reads per sample, were obtained. Five thousand three hundred ninety-nine operational taxonomic units (OTUs) were identified, which predominantly mapped to the phyla of Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. The ratio between vegetable and animal proteins proved to play a central role in determining microbiome profiles and Firmicutes and Proteobacteria phyla were particularly discriminatory for diet type in trout. Plant ingredients favoured a higher Firmicutes:Proteobacteria ratio than animal proteins. Acceptable abundance of Firmicutes was guaranteed by including at least 25% of vegetable proteins in the diet regardless of animal protein source and percentage. In summary animal by-product meals, as replacements to FM, gave good results in terms of growth performances and did not induce significant changes in gut microbial richness, thus proving to be a suitable protein source for use in rainbow trout aqua feed.

Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources

PubMed Central

Rimoldi, Simona; Ascione, Chiara; Giannico, Riccardo; Brambilla, Fabio

2018-01-01

Animal by-product meals from the rendering industry could provide a sustainable and commercially viable alternative to fishmeal (FM) in aquaculture, as they are rich in most essential amino acids and contain important amounts of water-soluble proteins that improve feed digestibility and palatability. Among them, poultry by-product meal (PBM) have given encouraging results in rainbow trout (Oncorhynchus mykiss). However, the introduction of new ingredients in the diet needs to be carefully evaluated since diet is one of the main factors affecting the gut microbiota, which is a complex community that contributes to host metabolism, nutrition, growth, and disease resistance. Accordingly, we investigated the effects of partial replacement of dietary FM with a mix of animal by-product meals and plant proteins on intestinal microbiota composition of rainbow trout in relation to growth and feeding efficiency parameters. We used 1540 trout with an initial mean body weight of 94.6 ± 14.2 g. Fish were fed for 12 weeks with 7 different feed formulations. The growth data showed that trout fed on diets rich in animal by-product meals grew as well as fish fed on control diet, which was rich in FM (37.3%) and PBM-free. High-throughput 16S rRNA gene amplicon sequencing (MiSeq platform, Illumina) was utilised to study the gut microbial community profile. After discarding Cyanobacteria (class Chloroplast) and mitochondria reads a total of 2,701,274 of reads taxonomically classified, corresponding to a mean of 96,474 ± 68,056 reads per sample, were obtained. Five thousand three hundred ninety-nine operational taxonomic units (OTUs) were identified, which predominantly mapped to the phyla of Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. The ratio between vegetable and animal proteins proved to play a central role in determining microbiome profiles and Firmicutes and Proteobacteria phyla were particularly discriminatory for diet type in trout. Plant ingredients favoured a higher Firmicutes:Proteobacteria ratio than animal proteins. Acceptable abundance of Firmicutes was guaranteed by including at least 25% of vegetable proteins in the diet regardless of animal protein source and percentage. In summary animal by-product meals, as replacements to FM, gave good results in terms of growth performances and did not induce significant changes in gut microbial richness, thus proving to be a suitable protein source for use in rainbow trout aqua feed. PMID:29509788

Metaproteomic analysis of biocake proteins to understand membrane fouling in a submerged membrane bioreactor.

PubMed

Zhou, Zhongbo; Meng, Fangang; He, Xiang; Chae, So-Ryong; An, Yujia; Jia, Xiaoshan

2015-01-20

Metaproteomic analyses, including two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) separation and matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)/TOF mass spectrometer (MS) detection, were used to trace and identify biocake proteins on membranes in a bench-scale submerged membrane bioreactor (MBR). 2D-PAGE images showed that proteins in the biocake (S3) at a low transmembrane pressure (TMP) level (i.e., before the TMP jump) had larger gray intensities in the pH 5.5–7.0 region regardless of the membrane flux, similar to soluble microbial product (SMP) proteins. However, the biocake (S2 and S4) at a high TMP level (i.e., after the TMP jump) had many more proteins in the pH range of 4.0–5.5, similar to extracellular polymeric substance (EPS) proteins. Such similarities between biocake proteins and SMP or EPS proteins can be useful for tracing the sources of proteins resulting in membrane fouling. In total, 183 differentially abundant protein spots were marked in the three biocakes (S2, S3, and S4). However, only 32 protein spots co-occurred in the 2D gels of the three biocakes, indicating that membrane fluxes and TMP evolution levels had significant effects on the abundance of biocake proteins. On the basis of the MS and MS/MS data, 23 of 71 protein spots were successfully identified. Of the 23 proteins, outer membrane proteins (Omp) were a major contributor (60.87%). These Omps were mainly from potential surface colonizers such as Aeromonas, Enterobacter, Pseudomonas, and Thauera. Generally, the metaproteomic analysis is a useful alternative to trace the sources and compositions of biocake proteins on the levels of molecules and bacteria species that can provide new insight into membrane fouling.

Red Meat Intake and Risk of ESRD

PubMed Central

Lew, Quan-Lan Jasmine; Jafar, Tazeen Hasan; Koh, Hiromi Wai Ling; Jin, Aizhen; Chow, Khuan Yew; Yuan, Jian-Min

2017-01-01

Randomized controlled trials suggest that protein restriction may retard the progression of CKD toward ESRD. However, the effects of dietary protein intake level and the food sources of dietary protein on the risk of ESRD in the general population remain unclear. We investigated these effects in the Singapore Chinese Health Study, a prospective population-based cohort that recruited 63,257 Chinese adults aged 45–74 years from 1993 to 1998. We collected habitual diet information via a validated semiquantitative food frequency questionnaire and identified ESRD via record linkage with a nationwide registry. In all, 951 cases of ESRD occurred over a mean follow-up of 15.5 years. Regarding total protein intake, compared with the lowest quartile, the three higher quartiles combined had a hazard ratio for ESRD of 1.24 (95% confidence interval [95% CI], 1.05 to 1.46), but the dose-dependent association across the quartiles was not statistically significant (Ptrend=0.16). Red meat intake strongly associated with ESRD risk in a dose-dependent manner (hazard ratio for highest quartile versus lowest quartile,1.40 [95% CI, 1.15 to 1.71; Ptrend<0.001]). Intake of poultry, fish, eggs, or dairy products did not associate with risk of ESRD. In substitution analysis, replacing one serving of red meat with other food sources of protein associated with a maximum relative risk reduction of 62.4% (95% CI, 33.1 to 78.9; P<0.01). Our study shows that red meat intake may increase the risk of ESRD in the general population and substituting alternative sources of protein may reduce the incidence of ESRD. PMID:27416946

Gene and protein nomenclature in public databases

PubMed Central

Fundel, Katrin; Zimmer, Ralf

2006-01-01

Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. Results We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. Conclusion In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of combined dictionaries considerably increases size and decreases ambiguity. The entries of the curated synonym dictionary are available for manual querying, editing, and PubMed- or Google-search via the ProThesaurus-wiki. For automated querying via custom software, we offer a web service and an exemplary client application. PMID:16899134

Histone and RNA-binding protein interaction creates crosstalk network for regulation of alternative splicing.

PubMed

Kim, Yong-Eun; Park, Chungoo; Kim, Kyoon Eon; Kim, Kee K

2018-04-30

Alternative splicing is an essential process in eukaryotes, as it increases the complexity of gene expression by generating multiple proteins from a single pre-mRNA. However, information on the regulatory mechanisms for alternative splicing is lacking, because splicing occurs over a short period via the transient interactions of proteins within functional complexes of the spliceosome. Here, we investigated in detail the molecular mechanisms connecting alternative splicing with epigenetic mechanisms. We identified interactions between histone proteins and splicing factors such as Rbfox2, Rbfox3, and splicing factor proline and glutamine rich protein (SFPQ) by in vivo crosslinking and immunoprecipitation. Furthermore, we confirmed that splicing factors were bound to specific modified residues of histone proteins. Additionally, changes in histone methylation due to histone methyltransferase inhibitor treatment notably affected alternative splicing in selected genes. Therefore, we suggested that there may be crosstalk mechanisms connecting histone modifications and RNA-binding proteins that increase the local concentration of RNA-binding proteins in alternative exon loci of nucleosomes by binding specific modified histone proteins, leading to alternative splicing. This crosstalk mechanism may play a major role in epigenetic processes such as histone modification and the regulation of alternative splicing. Copyright © 2018 Elsevier Inc. All rights reserved.

7 CFR Appendix A to Part 226 - Alternate Foods for Meals

Code of Federal Regulations, 2010 CFR

2010-01-01

... used in the Child and Adult Care Food Program? 1. An alternate protein product used in meals planned..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How are alternate protein products used in the Child and Adult Care Food Program? 1...

7 CFR Appendix A to Part 226 - Alternate Foods for Meals

Code of Federal Regulations, 2013 CFR

2013-01-01

... used in the Child and Adult Care Food Program? 1. An alternate protein product used in meals planned..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How are alternate protein products used in the Child and Adult Care Food Program? 1...

7 CFR Appendix A to Part 226 - Alternate Foods for Meals

Code of Federal Regulations, 2012 CFR

2012-01-01

... used in the Child and Adult Care Food Program? 1. An alternate protein product used in meals planned..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How are alternate protein products used in the Child and Adult Care Food Program? 1...

7 CFR Appendix A to Part 226 - Alternate Foods for Meals

Code of Federal Regulations, 2011 CFR

2011-01-01

... used in the Child and Adult Care Food Program? 1. An alternate protein product used in meals planned..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How are alternate protein products used in the Child and Adult Care Food Program? 1...

7 CFR Appendix A to Part 226 - Alternate Foods for Meals

Code of Federal Regulations, 2014 CFR

2014-01-01

... used in the Child and Adult Care Food Program? 1. An alternate protein product used in meals planned..., manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the... meat alternates. B. How are alternate protein products used in the Child and Adult Care Food Program? 1...

Effect of legume grains as a source of dietary protein on the quality of organic lamb meat.

PubMed

Bonanno, Adriana; Tornambè, Gabriele; Di Grigoli, Antonino; Genna, Vincenzo; Bellina, Vincenzo; Di Miceli, Giuseppe; Giambalvo, Dario

2012-11-01

This study evaluated the effects on lamb growth, carcass traits and meat quality of replacing conventional soybean meal in the diet with alternative legume grains. Twenty-eight male lambs of Comisana breed weighing 16.9 ± 2.7 kg at weaning (66 ± 6 days old) were assigned to one of four diets. Until slaughter at 129 ± 6 days of age, each group received ad libitum pelleted alfalfa hay and concentrates differing in the source of protein: chickpea, faba bean, pea or soybean meal. Lambs fed chickpea showed higher dry matter and protein intakes from concentrate than those fed soybean. Lambs' growth, carcass weight and net dressing percentage did not vary by protein source, although chickpea lambs had more perirenal and pelvic fat than those in the soybean group. Diet did not affect chemical composition, colour, thawing and cooking losses, tenderness, and sensory properties of meat. Chickpea increased trans-vaccenic and linoleic acid, and chickpea and faba bean increased the isomers of conjugated linoleic acid. Legume grains can completely replace soybean meal in concentrate, resulting in lamb carcasses and meat of comparable quality. Chickpea leads to an increase in feed intake of lambs and in fat depots in the carcass, and a more beneficial fatty acid profile. Copyright © 2012 Society of Chemical Industry.

Hemp as an Agricultural Commodity

DTIC Science & Technology

2014-02-14

yarns and raw or processed spun fibers, paper, carpeting, home furnishings, construction and insulation materials, auto parts, and composites. The...interior stalk (hurd) is used in various applications such as animal bedding, raw material inputs, low-quality papers, and composites. Hemp seed and...oilcake are used in a range of foods and beverages, and can be an alternative food protein source. Oil from the crushed hemp seed is an ingredient in a

Cultured meat from stem cells: challenges and prospects.

PubMed

Post, Mark J

2012-11-01

As one of the alternatives for livestock meat production, in vitro culturing of meat is currently studied. The generation of bio-artificial muscles from satellite cells has been ongoing for about 15 years, but has never been used for generation of meat, while it already is a great source of animal protein. In order to serve as a credible alternative to livestock meat, lab or factory grown meat should be efficiently produced and should mimic meat in all of its physical sensations, such as visual appearance, smell, texture and of course, taste. This is a formidable challenge even though all the technologies to create skeletal muscle and fat tissue have been developed and tested. The efficient culture of meat will primarily depend on culture conditions such as the source of medium and its composition. Protein synthesis by cultured skeletal muscle cells should further be maximized by finding the optimal combination of biochemical and physical conditions for the cells. Many of these variables are known, but their interactions are numerous and need to be mapped. This involves a systematic, if not systems, approach. Given the urgency of the problems that the meat industry is facing, this endeavor is worth undertaking. As an additional benefit, culturing meat may provide opportunities for production of novel and healthier products. Copyright © 2012 Elsevier Ltd. All rights reserved.

Intestinal Fluid Permeability in Atlantic Salmon (Salmo salar L.) Is Affected by Dietary Protein Source.

PubMed

Hu, Haibin; Kortner, Trond M; Gajardo, Karina; Chikwati, Elvis; Tinsley, John; Krogdahl, Åshild

2016-01-01

In Atlantic salmon (Salmo salar L.), and also in other fish species, certain plant protein ingredients can increase fecal water content creating a diarrhea-like condition which may impair gut function and reduce fish growth. The present study aimed to strengthen understanding of the underlying mechanisms by observing effects of various alternative plant protein sources when replacing fish meal on expression of genes encoding proteins playing key roles in regulation of water transport across the mucosa of the distal intestine (DI). A 48-day feeding trial was conducted with five diets: A reference diet (FM) in which fish meal (72%) was the only protein source; Diet SBMWG with a mix of soybean meal (30%) and wheat gluten (22%); Diet SPCPM with a mix of soy protein concentrate (30%) and poultry meal (6%); Diet GMWG with guar meal (30%) and wheat gluten (14.5%); Diet PM with 58% poultry meal. Compared to fish fed the FM reference diet, fish fed the soybean meal containing diet (SBMWG) showed signs of enteritis in the DI, increased fecal water content of DI chyme and higher plasma osmolality. Altered DI expression of a battery of genes encoding aquaporins, ion transporters, tight junction and adherens junction proteins suggested reduced transcellular transport of water as well as a tightening of the junction barrier in fish fed the SBMWG diet, which may explain the observed higher fecal water content and plasma osmolality. DI structure was not altered for fish fed the other experimental diets but alterations in target gene expression and fecal water content were observed, indicating that alterations in water transport components may take place without clear effects on intestinal structure.

The greenhouse emissions footprint of free-range eggs.

PubMed

Taylor, R C; Omed, H; Edwards-Jones, G

2014-01-01

Eggs are an increasingly significant source of protein for human consumption, and the global poultry industry is the single fastest-growing livestock sector. In the context of international concern for food security and feeding an increasingly affluent human population, the contribution to global greenhouse-gas (GHG) emissions from animal protein production is of critical interest. We calculated the GHG emissions footprint for the fastest-growing sector of the UK egg market: free-range production in small commercial units on mixed farms. Emissions are calculated to current Intergovernmental Panel on Climate Change and UK standards (PAS2050): including direct, indirect, and embodied emissions from cradle to farm gate compatible with a full product life-cycle assessment. We present a methodology for the allocation of emissions between ruminant and poultry enterprises on mixed farms. Greenhouse gas emissions averaged a global warming potential of 2.2 kg of CO2e/dozen eggs, or 1.6 kg of CO2equivalent (e)/kg (assuming average egg weight of 60 g). One kilogram of protein from free-range eggs produces 0.2 kg of CO2e, lower than the emissions from white or red meat (based on both kg of meat and kg of protein). Of these emissions, 63% represent embodied carbon in poultry feed. A detailed GHG emissions footprint represents a baseline for comparison with other egg production systems and sources of protein for human consumption. Eggs represent a relatively low-carbon supply of animal protein, but their production is heavily dependent on cereals and soy, with associated high emissions from industrial nitrogen production, land-use change, and transport. Alternative sources of digestible protein for poultry diets are available, may be produced from waste processing, and would be an effective tool for reducing the industry's GHG emissions and dependence on imported raw materials.

Evaluation of various types of supplemental food for two species of predatory mites, Amblyseius swirskii and Neoseiulus cucumeris (Acari: Phytoseiidae).

PubMed

Delisle, J F; Brodeur, J; Shipp, L

2015-04-01

Although phytoseiids are best known as predators of phytophagous mites and other small arthropods, several species can also feed and reproduce on pollen. In laboratory assays, we assessed the profitability of two types of dietary supplements (three pollen species-cattail, maize and apple-and eggs of the Mediterranean flour moth, Ephestia kuehniella) for the two species of predatory mites most commonly used as biocontrol agents in horticulture in Canada, Neoseiulus cucumeris and Amblyseius swirskii. We measured the effects of each diet on phytoseiid fitness parameters (survival, development, sex ratio, fecundity) and, as a means of comparison, when fed larvae of the common targeted pest species, western flower thrips Frankliniella occidentalis. A soluble protein assay was also performed on the alternative food sources as protein content is often linked to high nutritive value according to the literature. All food sources tested were suitable for N. cucumeris and A. swirskii, both species being able to develop from egg to adult. The dietary supplements had a beneficial impact on biological parameters, mostly resulting in shorter development times and higher survival rates when compared to thrips larvae. Amblyseius swirskii exhibited a wider dietary range than N. cucumeris. Overall, flour moth eggs, cattail pollen and apple pollen are food sources of equal quality for A. swirskii, whereas apple and cattail pollen are better when it comes to N. cucumeris. In contrast, maize pollen is a less suitable food source for N. cucumeris and A. swirskii. Soluble protein content results did not match the prediction under which the most beneficial food source would contain the highest concentration in protein.

Supplying the energy and fiber needs of dairy cows from alternate feed sources.

PubMed

Coppock, C E

1987-05-01

Alternate feeds are a major resource of the dairy industry. The major issue involving them is a method to predict accurately nutritive value from laboratory analyses. Variation in nutrient content of most alternate feeds is greater than in feed grains. Another issue is which depression factors to use in adjusting values for TDN from maintenance to production intakes. The NRC uses an average depression of 8% for all feeds; others think each feedstuff should be depressed individually, and discount factors have been proposed. For some alternate feeds, large differences in net energy estimates occur. Neutral detergent fiber has been proposed as an indicator of productive energy, but it has several deficiencies with alternate feeds high in fat, molasses, or ash. A summative equation based on fat, ash, protein, NDF, and lignin has wider application for predicting NE1 for all feeds. A roughage value index reflects a feed's property to stimulate chewing and rumination. Its use has special relevance for alternate feeds with small particle sizes, which may induce little chewing. Supplemental fat may increase the metabolizable energy converted to milk, but respiration experiments are needed.

7 CFR Appendix A to Part 220 - Alternate Foods for Meals

Code of Federal Regulations, 2014 CFR

2014-01-01

... in the School Breakfast Program? 1. An alternate protein product used in meals planned under the food... an alternate protein product mix, manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the package; (2) Hydration instructions; and (3) instructions...

7 CFR Appendix A to Part 220 - Alternate Foods for Meals

Code of Federal Regulations, 2013 CFR

2013-01-01

... in the School Breakfast Program? 1. An alternate protein product used in meals planned under the food... an alternate protein product mix, manufacturers should provide information on: (1) The amount by weight of dry alternate protein product in the package; (2) Hydration instructions; and (3) instructions...

Protein quality of insects as potential ingredients for dog and cat foods.

PubMed

Bosch, Guido; Zhang, Sheng; Oonincx, Dennis G A B; Hendriks, Wouter H

2014-01-01

Insects have been proposed as a high-quality, efficient and sustainable dietary protein source. The present study evaluated the protein quality of a selection of insect species. Insect substrates were housefly pupae, adult house cricket, yellow mealworm larvae, lesser mealworm larvae, Morio worm larvae, black soldier fly larvae and pupae, six spot roach, death's head cockroach and Argentinean cockroach. Reference substrates were poultry meat meal, fish meal and soyabean meal. Substrates were analysed for DM, N, crude fat, ash and amino acid (AA) contents and for in vitro digestibility of organic matter (OM) and N. The nutrient composition, AA scores as well as in vitro OM and N digestibility varied considerably between insect substrates. For the AA score, the first limiting AA for most substrates was the combined requirement for Met and Cys. The pupae of the housefly and black soldier fly were high in protein and had high AA scores but were less digestible than other insect substrates. The protein content and AA score of house crickets were high and similar to that of fish meal; however, in vitro N digestibility was higher. The cockroaches were relatively high in protein but the indispensable AA contents, AA scores and the in vitro digestibility values were relatively low. In addition to the indices of protein quality, other aspects such as efficiency of conversion of organic side streams, feasibility of mass-production, product safety and pet owner perception are important for future dog and cat food application of insects as alternative protein source.

PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting.

PubMed

Radifar, Muhammad; Yuniarti, Nunung; Istyastono, Enade Perdana

2013-01-01

Structure-based virtual screening (SBVS) methods often rely on docking score. The docking score is an over-simplification of the actual ligand-target binding. Its capability to model and predict the actual binding reality is limited. Recently, interaction fingerprinting (IFP) has come and offered us an alternative way to model reality. IFP provides us an alternate way to examine protein-ligand interactions. The docking score indicates the approximate affinity and IFP shows the interaction specificity. IFP is a method to convert three dimensional (3D) protein-ligand interactions into one dimensional (1D) bitstrings. The bitstrings are subsequently employed to compare the protein-ligand interaction predicted by the docking tool against the reference ligand. These comparisons produce scores that can be used to enhance the quality of SBVS campaigns. However, some IFP tools are either proprietary or using a proprietary library, which limits the access to the tools and the development of customized IFP algorithm. Therefore, we have developed PyPLIF, a Python-based open source tool to analyze IFP. In this article, we describe PyPLIF and its application to enhance the quality of SBVS in order to identify antagonists for estrogen α receptor (ERα). PyPLIF is freely available at http://code.google.com/p/pyplif.

Mitochondria are an early target of oxidative modifications in senescing legume nodules.

PubMed

Matamoros, Manuel A; Fernández-García, Nieves; Wienkoop, Stefanie; Loscos, Jorge; Saiz, Ana; Becana, Manuel

2013-02-01

Legume nodule senescence is a poorly understood process involving a decrease in N(2) fixation and an increase in proteolytic activity. Some physiological changes during nodule aging have been reported, but scarce information is available at the subcellular level. Biochemical, immunological and proteomic approaches were used to provide insight into the effects of aging on the mitochondria and cytosol of nodule host cells. In the mitochondria, the oxidative modification of lipids and proteins was associated with a marked decline in glutathione, a reduced capacity to regenerate ascorbate, and upregulation of alternative oxidase and manganese superoxide dismutase. In the cytosol, there were consistent reductions in the protein concentrations of carbon metabolism enzymes, inhibition of protein synthesis and increase in serine proteinase activity, disorganization of cytoskeleton, and a sharp reduction of cytosolic proteins, but no detectable accumulation of oxidized molecules. We conclude that nodule mitochondria are an early target of oxidative modifications and a likely source of redox signals. Alternative oxidase and manganese superoxide dismutase may play important roles in controlling ROS concentrations and the redox state of mitochondria. The finding that specific methionine residues of a cytosolic glutamine synthetase isoform are sulfoxidized suggests a regulatory role of this enzyme in senescing nodules. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Physical properties of ice cream containing milk protein concentrates.

PubMed

Alvarez, V B; Wolters, C L; Vodovotz, Y; Ji, T

2005-03-01

Two milk protein concentrates (MPC, 56 and 85%) were studied as substitutes for 20 and 50% of the protein content in ice cream mix. The basic mix formula had 12% fat, 11% nonfat milk solids, 15% sweetener, and 0.3% stabilizer/emulsifier blend. Protein levels remained constant, and total solids were compensated for in MPC mixes by the addition of polydextrose. Physical properties investigated included apparent viscosity, fat globule size, melting rate, shape retention, and freezing behavior using differential scanning calorimetry. Milk protein concentrate formulations had higher mix viscosity, larger amount of fat destabilization, narrower ice melting curves, and greater shape retention compared with the control. Milk protein concentrates did not offer significant modifications of ice cream physical properties on a constant protein basis when substituted for up to 50% of the protein supplied by nonfat dry milk. Milk protein concentrates may offer ice cream manufacturers an alternative source of milk solids non-fat, especially in mixes reduced in lactose or fat, where higher milk solids nonfat are needed to compensate other losses of total solids.

Lower growth temperature increases alternative pathway capacity and alternative oxidase protein in tobacco.

PubMed

Vanlerberghe, G C; McIntosh, L

1992-09-01

Suspension cells of NT1 tobacco (Nicotiana tabacum L. cv bright yellow) have been used to study the effect of growth temperature on the CN-resistant, salicylhydroxamic acid-sensitive alternative pathway of respiration. Mitochondria isolated from cells maintained at 30 degrees C had a low capacity to oxidize succinate via the alternative pathway, whereas mitochondria isolated from cells 24 h after transfer to 18 degrees C displayed, on average, a 5-fold increase in this capacity (from 7 to 32 nanoatoms oxygen per milligram protein per minute). This represented an increase in alternative pathway capacity from 18 to 45% of the total capacity of electron transport. This increased capacity was lost upon transfer of cells back to 30 degrees C. A monoclonal antibody to the terminal oxidase of the alternative pathway (the alternative oxidase) from Sauromatum guttatum (T.E. Elthon, R.L. Nickels, L. McIntosh [1989] Plant Physiology 89: 1311-1317) recognized a 35-kilodalton mitochondrial protein in tobacco. There was an excellent correlation between the capacity of the alternative path in isolated tobacco mitochondria and the levels of this 35-kilodalton alternative oxidase protein. Cycloheximide could inhibit both the increased level of the 35-kilodalton alternative oxidase protein and the increased alternative pathway capacity normally seen upon transfer to 18 degrees C. We conclude that transfer of tobacco cells to the lower temperature increases the capacity of the alternative pathway due, at least in part, to de novo synthesis of the 35-kilodalton alternative oxidase protein.

Biochemical characteristics of four marine fish skins in Korea.

PubMed

Cho, Jae-Kwon; Jin, Young-Guk; Rha, Sung-Ju; Kim, Seon-Jae; Hwang, Jae-Ho

2014-09-15

In this study, we investigated the biochemical characteristics of the fish skins of four industrial species: olive flounder (Paralichthys olivaceus), black rockfish (Sebastes schlegeli), sea bass (Lateolabrax maculatus) and red sea bream (Pagrus major). There is high domestic demand in Korea for farming of these fish for human consumption. Crude protein contents in the skin of these fish ranged from 73% to 94% by dry weight; this was in part due to a high content of the structural protein, collagen. Among the four species, olive flounder had the thickest dermal and epidermal layers in the dorsal skin. This species was also associated with the highest extraction ratio of acid-soluble collagen. We also examined whether fish skin could be a cost-effective alternative to current fish meal sources. Our analysis indicates that, when supplemented with additional fish oils and essential amino acids, fish skin is a viable alternative for fish meal formulations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Protein nanoparticles as drug delivery carriers for cancer therapy.

PubMed

Lohcharoenkal, Warangkana; Wang, Liying; Chen, Yi Charlie; Rojanasakul, Yon

2014-01-01

Nanoparticles have increasingly been used for a variety of applications, most notably for the delivery of therapeutic and diagnostic agents. A large number of nanoparticle drug delivery systems have been developed for cancer treatment and various materials have been explored as drug delivery agents to improve the therapeutic efficacy and safety of anticancer drugs. Natural biomolecules such as proteins are an attractive alternative to synthetic polymers which are commonly used in drug formulations because of their safety. In general, protein nanoparticles offer a number of advantages including biocompatibility and biodegradability. They can be prepared under mild conditions without the use of toxic chemicals or organic solvents. Moreover, due to their defined primary structure, protein-based nanoparticles offer various possibilities for surface modifications including covalent attachment of drugs and targeting ligands. In this paper, we review the most significant advancements in protein nanoparticle technology and their use in drug delivery arena. We then examine the various sources of protein materials that have been used successfully for the construction of protein nanoparticles as well as their methods of preparation. Finally, we discuss the applications of protein nanoparticles in cancer therapy.

[Ribonucleic acids and proteins of influenza A/USSR/90/77 viruses].

PubMed

Vorkunova, G K; Dotsenko, G N; Bukrinskaia, A G; Zhdanov, V M

1979-01-01

The "return" of influenza A (HINI) virus after 20 years of absence raised the question of the sources and mechanisms of emergence of epidemic influenza viruses and, particularly, of a new HINI virus (A/USSR/90/77). Two alternative hypotheses answer this question differently: the new HINI virus is the progeny of old HINI viruses retained in the human population or is a newly arising recombinant between numerous human and animal influenza viruses circulation in the biosphere. For the acceptance of one or the other hypothesis further accumulation of facts is required and, first of all, comparative investigations of RNAs and proteins of various influenza viruses. This paper presents the results of comparative studies of RNAs and proteins of old and new influenza A (HINI) viruses.

Extraction, integration and analysis of alternative splicing and protein structure distributed information

PubMed Central

D'Antonio, Matteo; Masseroli, Marco

2009-01-01

Background Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structures. This suggests possible correlations between alternative splicing and protein structure. In order to support the investigation of such relationships, we have developed the Alternative Splicing and Protein Structure Scrutinizer (PASS), a Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank. Primary data from these databases have been integrated and analyzed using the Protein Identifier Cross-Reference, BLAST, CLUSTALW and FeatureMap3D software tools. Results A database has been developed to store the considered primary data and the results from their analysis; a system of Perl scripts has been implemented to automatically create and update the database and analyze the integrated data; a Web interface has been implemented to make the analyses easily accessible; a database has been created to manage user accesses to the PASS Web application and store user's data and searches. Conclusion PASS automatically integrates data from the Alternative Splicing Database with protein structure data from the Protein Data Bank. Additionally, it comprehensively analyzes the integrated data with publicly available well-known bioinformatics tools in order to generate structural information of isoform pairs. Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different functions. PMID:19828075

Red Meat Intake and Risk of ESRD.

PubMed

Lew, Quan-Lan Jasmine; Jafar, Tazeen Hasan; Koh, Hiromi Wai Ling; Jin, Aizhen; Chow, Khuan Yew; Yuan, Jian-Min; Koh, Woon-Puay

2017-01-01

Randomized controlled trials suggest that protein restriction may retard the progression of CKD toward ESRD. However, the effects of dietary protein intake level and the food sources of dietary protein on the risk of ESRD in the general population remain unclear. We investigated these effects in the Singapore Chinese Health Study, a prospective population-based cohort that recruited 63,257 Chinese adults aged 45-74 years from 1993 to 1998. We collected habitual diet information via a validated semiquantitative food frequency questionnaire and identified ESRD via record linkage with a nationwide registry. In all, 951 cases of ESRD occurred over a mean follow-up of 15.5 years. Regarding total protein intake, compared with the lowest quartile, the three higher quartiles combined had a hazard ratio for ESRD of 1.24 (95% confidence interval [95% CI], 1.05 to 1.46), but the dose-dependent association across the quartiles was not statistically significant (P trend =0.16). Red meat intake strongly associated with ESRD risk in a dose-dependent manner (hazard ratio for highest quartile versus lowest quartile,1.40 [95% CI, 1.15 to 1.71; P trend <0.001]). Intake of poultry, fish, eggs, or dairy products did not associate with risk of ESRD. In substitution analysis, replacing one serving of red meat with other food sources of protein associated with a maximum relative risk reduction of 62.4% (95% CI, 33.1 to 78.9; P<0.01). Our study shows that red meat intake may increase the risk of ESRD in the general population and substituting alternative sources of protein may reduce the incidence of ESRD. Copyright © 2016 by the American Society of Nephrology.

Progress in Top-Down Proteomics and the Analysis of Proteoforms

PubMed Central

Toby, Timothy K.; Fornelli, Luca; Kelleher, Neil L.

2017-01-01

From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research. PMID:27306313

Evolution and Biological Roles of Alternative 3'UTRs.

PubMed

Mayr, Christine

2016-03-01

More than half of human genes use alternative cleavage and polyadenylation to generate alternative 3' untranslated region (3'UTR) isoforms. Most efforts have focused on transcriptome-wide mapping of alternative 3'UTRs and on the question of how 3'UTR isoform ratios may be regulated. However, it remains less clear why alternative 3'UTRs have evolved and what biological roles they play. This review summarizes our current knowledge of the functional roles of alternative 3'UTRs, including mRNA localization, mRNA stability, and translational efficiency. Recent work suggests that alternative 3'UTRs may also enable the formation of protein-protein interactions to regulate protein localization or to diversify protein functions. These recent findings open an exciting research direction for the investigation of new biological roles of alternative 3'UTRs. Copyright © 2015 Elsevier Ltd. All rights reserved.

The sialotranscriptome of Antricola delacruzi female ticks is compatible with non-hematophagous behavior and an alternative source of food.

PubMed

Ribeiro, José Marcos C; Labruna, Marcelo B; Mans, Ben J; Maruyama, Sandra Regina; Francischetti, Ivo M B; Barizon, Gustavo Canavaci; de Miranda Santos, Isabel K F

2012-05-01

The hosts for Antricola delacruzi ticks are insectivorous, cave-dwelling bats on which only larvae are found. The mouthparts of nymphal and adult A. delacruzi are compatible with scavenging feeding because the hypostome is small and toothless. How a single blood meal of a larva provides energy for several molts as well as for oviposition by females is not known. Adults of A. delacruzi possibly feed upon an unknown food source in bat guano, a substrate on which nymphal and adult stages are always found. Guano produced by insectivorous bats contains twice the amount of protein and 60 times the amount of iron as beef. In addition, bacteria and chitin-rich fungi proliferate on guano. Comparative data on the transcriptome of the salivary glands of A. delacruzi is nonexistent and would help to understand the physiological adaptations of salivary glands that accompany different sources of food as well as the steps taken by the Acari toward haematophagy, believed to have evolved from scavenging dead animals. Annotation of the transcriptome of salivary glands from female instars of A. delacruzi collected on guano categorized 5.7% of the clusters of expressed genes as putative secreted proteins. They included abundantly expressed TIL-domain-containing proteins (possible anti-microbials), an abundantly expressed protein similar to a serum amyloid found in the sialotranscriptomes of Ornithodoros spp., a savignygrin, a family of mucin/peritrophin/cuticle-like proteins, anti-microbials and an HIV envelope-like glycoprotein also found in soft ticks. When comparing the transcriptome of A. delacruzi with those of blood-feeding female soft and hard ticks some notable differences were observed; they consisted of the following transcripts over- or under-represented or absent in the sialotranscriptome of A. delacruzi that may reflect its source of food: ferritin, mucins with chitin-binding domains and TIL-domain-containing proteins versus lipocalins, basic tail proteins, metalloproteases, glycine-rich proteins and Kunitz protease inhibitors, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

From Genomes to Protein Models and Back

NASA Astrophysics Data System (ADS)

Tramontano, Anna; Giorgetti, Alejandro; Orsini, Massimiliano; Raimondo, Domenico

2007-12-01

The alternative splicing mechanism allows genes to generate more than one product. When the splicing events occur within protein coding regions they can modify the biological function of the protein. Alternative splicing has been suggested as one way for explaining the discrepancy between the number of human genes and functional complexity. We analysed the putative structure of the alternatively spliced gene products annotated in the ENCODE pilot project and discovered that many of the potential alternative gene products will be unlikely to produce stable functional proteins.

Alternative promoter usage generates novel shorter MAPT mRNA transcripts in Alzheimer's disease and progressive supranuclear palsy brains.

PubMed

Huin, Vincent; Buée, Luc; Behal, Hélène; Labreuche, Julien; Sablonnière, Bernard; Dhaenens, Claire-Marie

2017-10-03

Alternative promoter usage is an important mechanism for transcriptome diversity and the regulation of gene expression. Indeed, this alternative usage may influence tissue/subcellular specificity, protein translation and function of the proteins. The existence of an alternative promoter for MAPT gene was considered for a long time to explain differential tissue specificity and differential response to transcription and growth factors between mRNA transcripts. The alternative promoter usage could explain partly the different tau proteins expression patterns observed in tauopathies. Here, we report on our discovery of a functional alternative promoter for MAPT, located upstream of the gene's second exon (exon 1). By analyzing genome databases and brain tissue from control individuals and patients with Alzheimer's disease or progressive supranuclear palsy, we identified novel shorter transcripts derived from this alternative promoter. These transcripts are increased in patients' brain tissue as assessed by 5'RACE-PCR and qPCR. We suggest that these new MAPT isoforms can be translated into normal or amino-terminal-truncated tau proteins. We further suggest that activation of MAPT's alternative promoter under pathological conditions leads to the production of truncated proteins, changes in protein localization and function, and thus neurodegeneration.

Chondrogenic induction of mesenchymal stromal/stem cells from Wharton's jelly embedded in alginate hydrogel and without added growth factor: an alternative stem cell source for cartilage tissue engineering.

PubMed

Reppel, Loïc; Schiavi, Jessica; Charif, Naceur; Leger, Léonore; Yu, Hao; Pinzano, Astrid; Henrionnet, Christel; Stoltz, Jean-François; Bensoussan, Danièle; Huselstein, Céline

2015-12-30

Due to their intrinsic properties, stem cells are promising tools for new developments in tissue engineering and particularly for cartilage tissue regeneration. Although mesenchymal stromal/stem cells from bone marrow (BM-MSC) have long been the most used stem cell source in cartilage tissue engineering, they have certain limits. Thanks to their properties such as low immunogenicity and particularly chondrogenic differentiation potential, mesenchymal stromal/stem cells from Wharton's jelly (WJ-MSC) promise to be an interesting source of MSC for cartilage tissue engineering. In this study, we propose to evaluate chondrogenic potential of WJ-MSC embedded in alginate/hyaluronic acid hydrogel over 28 days. Hydrogels were constructed by the original spraying method. Our main objective was to evaluate chondrogenic differentiation of WJ-MSC on three-dimensional scaffolds, without adding growth factors, at transcript and protein levels. We compared the results to those obtained from standard BM-MSC. After 3 days of culture, WJ-MSC seemed to be adapted to their new three-dimensional environment without any detectable damage. From day 14 and up to 28 days, the proportion of WJ-MSC CD73(+), CD90(+), CD105(+) and CD166(+) decreased significantly compared to monolayer marker expression. Moreover, WJ-MSC and BM-MSC showed different phenotype profiles. After 28 days of scaffold culture, our results showed strong upregulation of cartilage-specific transcript expression. WJ-MSC exhibited greater type II collagen synthesis than BM-MSC at both transcript and protein levels. Furthermore, our work highlighted a relevant result showing that WJ-MSC expressed Runx2 and type X collagen at lower levels than BM-MSC. Once seeded in the hydrogel scaffold, WJ-MSC and BM-MSC have different profiles of chondrogenic differentiation at both the phenotypic level and matrix synthesis. After 4 weeks, WJ-MSC, embedded in a three-dimensional environment, were able to adapt to their environment and express specific cartilage-related genes and matrix proteins. Today, WJ-MSC represent a real alternative source of stem cells for cartilage tissue engineering.

Lower Growth Temperature Increases Alternative Pathway Capacity and Alternative Oxidase Protein in Tobacco 1

PubMed Central

Vanlerberghe, Greg C.; McIntosh, Lee

1992-01-01

Suspension cells of NT1 tobacco (Nicotiana tabacum L. cv bright yellow) have been used to study the effect of growth temperature on the CN-resistant, salicylhydroxamic acid-sensitive alternative pathway of respiration. Mitochondria isolated from cells maintained at 30°C had a low capacity to oxidize succinate via the alternative pathway, whereas mitochondria isolated from cells 24 h after transfer to 18°C displayed, on average, a 5-fold increase in this capacity (from 7 to 32 nanoatoms oxygen per milligram protein per minute). This represented an increase in alternative pathway capacity from 18 to 45% of the total capacity of electron transport. This increased capacity was lost upon transfer of cells back to 30°C. A monoclonal antibody to the terminal oxidase of the alternative pathway (the alternative oxidase) from Sauromatum guttatum (T.E. Elthon, R.L. Nickels, L. McIntosh [1989] Plant Physiology 89: 1311-1317) recognized a 35-kilodalton mitochondrial protein in tobacco. There was an excellent correlation between the capacity of the alternative path in isolated tobacco mitochondria and the levels of this 35-kilodalton alternative oxidase protein. Cycloheximide could inhibit both the increased level of the 35-kilodalton alternative oxidase protein and the increased alternative pathway capacity normally seen upon transfer to 18°C. We conclude that transfer of tobacco cells to the lower temperature increases the capacity of the alternative pathway due, at least in part, to de novo synthesis of the 35-kilodalton alternative oxidase protein. Images Figure 3 Figure 4 PMID:16652932

Diet-dependent gene expression in honey bees: honey vs. sucrose or high fructose corn syrup.

PubMed

Wheeler, Marsha M; Robinson, Gene E

2014-07-17

Severe declines in honey bee populations have made it imperative to understand key factors impacting honey bee health. Of major concern is nutrition, as malnutrition in honey bees is associated with immune system impairment and increased pesticide susceptibility. Beekeepers often feed high fructose corn syrup (HFCS) or sucrose after harvesting honey or during periods of nectar dearth. We report that, relative to honey, chronic feeding of either of these two alternative carbohydrate sources elicited hundreds of differences in gene expression in the fat body, a peripheral nutrient-sensing tissue analogous to vertebrate liver and adipose tissues. These expression differences included genes involved in protein metabolism and oxidation-reduction, including some involved in tyrosine and phenylalanine metabolism. Differences between HFCS and sucrose diets were much more subtle and included a few genes involved in carbohydrate and lipid metabolism. Our results suggest that bees receive nutritional components from honey that are not provided by alternative food sources widely used in apiculture.

Diet-dependent gene expression in honey bees: honey vs. sucrose or high fructose corn syrup

PubMed Central

Wheeler, Marsha M.; Robinson, Gene E.

2014-01-01

Severe declines in honey bee populations have made it imperative to understand key factors impacting honey bee health. Of major concern is nutrition, as malnutrition in honey bees is associated with immune system impairment and increased pesticide susceptibility. Beekeepers often feed high fructose corn syrup (HFCS) or sucrose after harvesting honey or during periods of nectar dearth. We report that, relative to honey, chronic feeding of either of these two alternative carbohydrate sources elicited hundreds of differences in gene expression in the fat body, a peripheral nutrient-sensing tissue analogous to vertebrate liver and adipose tissues. These expression differences included genes involved in protein metabolism and oxidation-reduction, including some involved in tyrosine and phenylalanine metabolism. Differences between HFCS and sucrose diets were much more subtle and included a few genes involved in carbohydrate and lipid metabolism. Our results suggest that bees receive nutritional components from honey that are not provided by alternative food sources widely used in apiculture. PMID:25034029

TGFβ1-mediated expression and alternative splicing of Fibronectin Extra Domain A in human podocyte culture.

PubMed

Madne, Tarunkumar Hemraj; Dockrell, Mark Edward Carl

2018-02-28

Alternative splicing is a fundamental phenomenon to build protein diversity in health and diseases. Extra Domain A+ Fibronectin (EDA+Fn) is an alternatively spliced form of fibronectin protein present in the extra cellular matrix (ECM) in renal fibrosis. Podocytes are spectacular cell type and play a key role in filtration and synthesise ECM proteins in renal physiology and pathology. TGFβ1 is a strong stimulator of ECM proteins in renal injury. In this study, we have investigated alternative splicing of EDA+ Fn in human podocytes in response to TGFβ1. We have performed western blotting and immunofluorescence to characterise the expression of the EDA+Fn protein, real-time PCR for RNA expression and RT-PCR to look for alternative splicing of EDA+Fn in conditionally immortalised human podocytes culture.We used TGFβ1 as a stimulator and SB431542 and SRPIN340 for inhibitory studies. In this work, for the first time we have demonstrated in human podocytes culture EDA+Fn is expressed in the basal condition and TGFβ1 2.5ng/ml induced the Fn mRNA and EDA+Fn protein expression demonstrated by real-time PCR, western blotting and immunofluorescence. TGFβ1 2.5ng/ml induced the alternative splicing of EDA+Fn shown by conventional RT-PCR. Studies with ALK5 inhibitor SB431542 and SRPIN340 show that TGFβ1 induced alternative splicing of EDA+Fn was by the ALK5 receptor and the SR proteins.  In human podocytes culture, alternative splicing of EDA+Fn occurs at basal conditions and TGFβ1 further induced the alternative splicing of EDA+Fn via ALK5 receptor activation and SR proteins. This is the first evidence of basal and TGFβ1 mediated alternative splicing of EDA+Fn in human podocytes culture.

An automated method for detecting alternatively spliced protein domains.

PubMed

Coelho, Vitor; Sammeth, Michael

2018-06-01

Alternative splicing (AS) has been demonstrated to play a role in shaping eukaryotic gene diversity at the transcriptional level. However, the impact of AS on the proteome is still controversial. Studies that seek to explore the effect of AS at the proteomic level are hampered by technical difficulties in the cumbersome process of casting forth and back between genome, transcriptome and proteome space coordinates, and the naïve prediction of protein domains in the presence of AS suffers many redundant sequence scans that emerge from constitutively spliced regions that are shared between alternative products of a gene. We developed the AstaFunk pipeline that computes for every generic transcriptome all domains that are altered by AS events in a systematic and efficient manner. In a nutshell, our method employs Viterbi dynamic programming, which guarantees to find all score-optimal hits of the domains under consideration, while complementary optimisations at different levels avoid redundant and other irrelevant computations. We evaluate AstaFunk qualitatively and quantitatively using RNAseq in well-studied genes with AS, and on large-scale employing entire transcriptomes. Our study confirms complementary reports that the effect of most AS events on the proteome seems to be rather limited, but our results also pinpoint several cases where AS could have a major impact on the function of a protein domain. The JAVA implementation of AstaFunk is available as an open source project on http://astafunk.sammeth.net. micha@sammeth.net. Supplementary data are available at Bioinformatics online.

49 CFR 7.46 - Alternative sources of information.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Alternative sources of information. 7.46 Section 7... § 7.46 Alternative sources of information. In the interest of making documents of general interest publicly available at as low a cost as possible, alternative sources will be arranged whenever possible. In...

Protein purification and crystallization artifacts: The tale usually not told.

PubMed

Niedzialkowska, Ewa; Gasiorowska, Olga; Handing, Katarzyna B; Majorek, Karolina A; Porebski, Przemyslaw J; Shabalin, Ivan G; Zasadzinska, Ewelina; Cymborowski, Marcin; Minor, Wladek

2016-03-01

The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non-reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources. If the contaminated or misidentified sample is used for crystallization, in many cases the problem may not be detected until structures are determined. In the case of functional studies, the problem may not be detected for years. Here several procedures that can be successfully used for the identification of crystallized protein contaminants, including: (i) a lattice parameter search against known structures, (ii) sequence or fold identification from partially built models, and (iii) molecular replacement with common contaminants as search templates have been presented. A list of common contaminant structures to be used as alternative search models was provided. These methods were used to identify four cases of purification and crystallization artifacts. This report provides troubleshooting pointers for researchers facing difficulties in phasing or model building. © 2016 The Protein Society.

Chemical Utilization of Albizia lebbeck Leaves for Developing Protein Concentrates as a Dietary Supplement.

PubMed

Khan, Lutful Haque; Varshney, V K

2017-08-17

In search of nonconventional sources of protein to combat widespread malnutrition, the possibility of developing a protein concentrate as an alternative dietary supplement from abundantly available yet poorly valorized leaves of Albizia lebbeck (siris) was examined. A process for recovery of leaf protein concentrate (LPC) from these leaves was optimized and applied for isolation of LPCs from lower, middle, and upper canopies of the tree. The optimized conditions (leaves to water 1:9, coagulation at pH 4.0 using 1 N citric acid at 90°C for 11 minutes) afforded LPCs containing protein 37.15%, 37.57%, and 37.76% in 5.99%, 5.97%, and 6.07% yield, respectively. The proximate nutritional composition, pigments, minerals, in vitro digestibility, and antinutritional factors of these LPCs were determined. Analysis of variance of these data revealed no significant difference with respect to canopy. Use of Albizia lebbeck leaves for development of LPC as a food/feed supplement was revealed.

Functional properties of tropical banded cricket (Gryllodes sigillatus) protein hydrolysates.

PubMed

Hall, Felicia G; Jones, Owen G; O'Haire, Marguerite E; Liceaga, Andrea M

2017-06-01

Recently, the benefits of entomophagy have been widely discussed. Due to western cultures' reluctance, entomophagy practices are leaning more towards incorporating insects into food products. In this study, whole crickets (Gryllodes sigillatus) were hydrolyzed with alcalase at 0.5, 1.5, and 3.0% (w/w) for 30, 60, and 90min. Degree of hydrolysis (DH), amino acid composition, solubility, emulsion and foaming properties were evaluated. Hydrolysis produced peptides with 26-52% DH compared to the control containing no enzyme (5% DH). Protein solubility of hydrolysates improved (p<0.05) over a range of pH's, exhibiting >30% soluble protein at pH 3 and 7 and 50-90% at alkaline pH, compared with the control. Emulsion activity index ranged from 7 to 32m 2 /g, while foamability ranged from 100 to 155% for all hydrolysates. These improved functional properties demonstrate the potential to develop cricket protein hydrolysates as a source of functional alternative protein in food ingredient formulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative study of the quality characteristics of defatted soy flour treated by supercritical carbon dioxide and organic solvent.

PubMed

Kang, Sung-Won; Rahman, M Shafiur; Kim, Ah-Na; Lee, Kyo-Yeon; Park, Chan-Yang; Kerr, William L; Choi, Sung-Gil

2017-07-01

Defatted soy flour is a potential source of food protein, amino acids, ash and isoflavones. The supercritical carbon dioxide (SC-CO 2 ) and a traditional organic solvent extraction methods were used to remove fat from soy flour, and the quality characteristics of a control soy flour (CSF), defatted soy flour by SC-CO 2 (DSFSC-CO 2 ) and defatted soy flour by an organic solvent (DSF-OS) were compared. The SC-CO 2 process was carried out at a constant temperature of 45 °C, and a pressure of 40 MPa for 3 h with a CO 2 flow rate of 30 g/min. The DSFSC-CO 2 had significantly higher protein, ash, and amino acids content than CSF and DSF-OS. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis demonstrated that CSF and DSFSC-CO 2 had protein bands of similar intensity and area that indicated no denaturation of protein, whereas DSF-OS showed diffuse bands or no bands due to protein denaturation. In addition to higher nutritional value and protein contents, DSFSC-CO 2 showed superior functional properties in terms of total soluble solids content, water and oil absorption, emulsifying and foaming capacity. The SC-CO 2 method offers a nutritionally and environmentally friendly alternative extraction processing approach for the removal of oil from high-protein food sources. It has a great potential for producing high-protein fat-free, and low-calorie content diet than the traditional organic solvent extraction method.

In Vitro Iron Availability from Insects and Sirloin Beef.

PubMed

Latunde-Dada, Gladys O; Yang, Wenge; Vera Aviles, Mayra

2016-11-09

Interest in the consumption of insects (entomophagy) as an alternative environmentally sustainable source of protein in the diet of humans has recently witnessed a surge. Knowledge of the nutrient composition and, in particular, the bioavailability of minerals from insects is currently sparse. This study evaluated the availability of Fe, Ca, Cu, Mg, Mn, and Zn from four commonly eaten insects and compared these to sirloin beef. Soluble iron from the samples was measured by inductively coupled plasma optical emission spectrometry (ICP-OES). Iron bioavailability was determined using an in vitro simulated peptic-pancreatic digestion, followed by measurement of ferritin (a surrogate marker for iron absorption) in Caco-2 cells. Cricket and sirloin beef had comparably higher levels of Fe, Ca, and Mn than grasshopper, meal, and buffalo worms. However, iron solubility was significantly higher from the insect samples than from beef. The complementation of whole-wheat flour with insect or beef protein resulted in overall decreases in mineral content and iron solubility in the composite mixtures. Collectively, the data show that grasshopper, cricket, and mealworms contain significantly higher chemically available Ca, Cu, Mg, Mn, and Zn than sirloin. However, buffalo worms and sirloin exhibited higher iron bioavailability comparable to that of FeSO 4 . Commonly consumed insect species could be excellent sources of bioavailable iron and could provide the platform for an alternative strategy for increased mineral intake in the diets of humans.

Disturbed expression of type 1 iodothyronine deiodinase splice variants in human renal cancer.

PubMed

Piekielko-Witkowska, Agnieszka; Master, Adam; Wojcicka, Anna; Boguslawska, Joanna; Brozda, Izabela; Tanski, Zbigniew; Nauman, Alicja

2009-10-01

Alternative splicing, one of the sources of protein diversity, is often disturbed in cancer. Type 1 iodothyronine deiodinase (DIO1) catalyzes deiodination of thyroxine generating triiodothyronine, an important regulator of cell proliferation and differentiation. The expression of DIO1 is disturbed in different types of cancer. The aim of the study was to analyze the alternative splicing of DIO1 and its possible disturbance in renal cancer. Using real-time PCR, we analyzed 19 tissue samples (T) of renal cancer and 19 matched control samples (C) of the opposite pole of the kidney, not infiltrated by tumor, and 6 control samples (N) (nonneoplastic kidney abnormalities). Cloning of DIO1 mRNA isoforms revealed 11 different transcripts, among them 7 new splice variants, not previously reported. The expression of all variants of DIO1 was dramatically (>90%) and significantly (p < or = 0.0003) lowered in samples T compared to control samples C. The ratio of mRNA isoforms encoding DIO1 protein variants possessing or lacking the active center was lowered in samples T compared with control samples C, suggesting disturbed alternative splicing of DIO1. The expression of mRNA of splicing factors SF2/ASF (splicing factor-2/alternative-splicing factor) and hnRNPA1 (heterogeneous ribonucleoprotein A1), regulating 5'-splice site selection, was significantly but not proportionally lowered in samples T compared to samples C. The mRNA ratio of splicing factors SF2/ASF and hnRNPA1 correlated with the ratio of mRNA isoforms encoding DIO1 protein variants possessing or lacking the active center in controls C but not in samples T. Our results show that the expression and alternative splicing of DIO1 mRNA is disturbed in renal cancer, possibly due to changes in expression of splicing factors SF2/ASF and hnRNPA1.

SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics

PubMed Central

2013-01-01

Background Alternative splicing is an important and widespread mechanism for generating protein diversity and regulating protein expression. High-throughput identification and analysis of alternative splicing in the protein level has more advantages than in the mRNA level. The combination of alternative splicing database and tandem mass spectrometry provides a powerful technique for identification, analysis and characterization of potential novel alternative splicing protein isoforms from proteomics. Therefore, based on the peptidomic database of human protein isoforms for proteomics experiments, our objective is to design a new alternative splicing database to 1) provide more coverage of genes, transcripts and alternative splicing, 2) exclusively focus on the alternative splicing, and 3) perform context-specific alternative splicing analysis. Results We used a three-step pipeline to create a synthetic alternative splicing database (SASD) to identify novel alternative splicing isoforms and interpret them at the context of pathway, disease, drug and organ specificity or custom gene set with maximum coverage and exclusive focus on alternative splicing. First, we extracted information on gene structures of all genes in the Ensembl Genes 71 database and incorporated the Integrated Pathway Analysis Database. Then, we compiled artificial splicing transcripts. Lastly, we translated the artificial transcripts into alternative splicing peptides. The SASD is a comprehensive database containing 56,630 genes (Ensembl gene IDs), 95,260 transcripts (Ensembl transcript IDs), and 11,919,779 Alternative Splicing peptides, and also covering about 1,956 pathways, 6,704 diseases, 5,615 drugs, and 52 organs. The database has a web-based user interface that allows users to search, display and download a single gene/transcript/protein, custom gene set, pathway, disease, drug, organ related alternative splicing. Moreover, the quality of the database was validated with comparison to other known databases and two case studies: 1) in liver cancer and 2) in breast cancer. Conclusions The SASD provides the scientific community with an efficient means to identify, analyze, and characterize novel Exon Skipping and Intron Retention protein isoforms from mass spectrometry and interpret them at the context of pathway, disease, drug and organ specificity or custom gene set with maximum coverage and exclusive focus on alternative splicing. PMID:24267658

Functional Properties and Genomics of Glucose Transporters

PubMed Central

Zhao, Feng-Qi; Keating, Aileen F

2007-01-01

Glucose is the major energy source for mammalian cells as well as an important substrate for protein and lipid synthesis. Mammalian cells take up glucose from extracellular fluid into the cell through two families of structurallyrelated glucose transporters. The facilitative glucose transporter family (solute carriers SLC2A, protein symbol GLUT) mediates a bidirectional and energy-independent process of glucose transport in most tissues and cells, while the NaM+/glucose cotransporter family (solute carriers SLC5A, protein symbol SGLT) mediates an active, Na+-linked transport process against an electrochemical gradient. The GLUT family consists of thirteen members (GLUT1-12 and HMIT). Phylogenetically, the members of the GLUT family are split into three classes based on protein similarities. Up to now, at least six members of the SGLT family have been cloned (SGLT1-6). In this review, we report both the genomic structure and function of each transporter as well as intra-species comparative genomic analysis of some of these transporters. The affinity for glucose and transport kinetics of each transporter differs and ranges from 0.2 to 17mM. The ability of each protein to transport alternative substrates also differs and includes substrates such as fructose and galactose. In addition, the tissue distribution pattern varies between species. There are different regulation mechanisms of these transporters. Characterization of transcriptional control of some of the gene promoters has been investigated and alternative promoter usage to generate different protein isoforms has been demonstrated. We also introduce some pathophysiological roles of these transporters in human. PMID:18660845

Detection of alternative splice variants at the proteome level in Aspergillus flavus.

PubMed

Chang, Kung-Yen; Georgianna, D Ryan; Heber, Steffen; Payne, Gary A; Muddiman, David C

2010-03-05

Identification of proteins from proteolytic peptides or intact proteins plays an essential role in proteomics. Researchers use search engines to match the acquired peptide sequences to the target proteins. However, search engines depend on protein databases to provide candidates for consideration. Alternative splicing (AS), the mechanism where the exon of pre-mRNAs can be spliced and rearranged to generate distinct mRNA and therefore protein variants, enable higher eukaryotic organisms, with only a limited number of genes, to have the requisite complexity and diversity at the proteome level. Multiple alternative isoforms from one gene often share common segments of sequences. However, many protein databases only include a limited number of isoforms to keep minimal redundancy. As a result, the database search might not identify a target protein even with high quality tandem MS data and accurate intact precursor ion mass. We computationally predicted an exhaustive list of putative isoforms of Aspergillus flavus proteins from 20 371 expressed sequence tags to investigate whether an alternative splicing protein database can assign a greater proportion of mass spectrometry data. The newly constructed AS database provided 9807 new alternatively spliced variants in addition to 12 832 previously annotated proteins. The searches of the existing tandem MS spectra data set using the AS database identified 29 new proteins encoded by 26 genes. Nine fungal genes appeared to have multiple protein isoforms. In addition to the discovery of splice variants, AS database also showed potential to improve genome annotation. In summary, the introduction of an alternative splicing database helps identify more proteins and unveils more information about a proteome.

Autophagy Deficiency Compromises Alternative Pathways of Respiration following Energy Deprivation in Arabidopsis thaliana.

PubMed

Barros, Jessica A S; Cavalcanti, João Henrique F; Medeiros, David B; Nunes-Nesi, Adriano; Avin-Wittenberg, Tamar; Fernie, Alisdair R; Araújo, Wagner L

2017-09-01

Under heterotrophic conditions, carbohydrate oxidation inside the mitochondrion is the primary energy source for cellular metabolism. However, during energy-limited conditions, alternative substrates are required to support respiration. Amino acid oxidation in plant cells plays a key role in this by generating electrons that can be transferred to the mitochondrial electron transport chain via the electron transfer flavoprotein/ubiquinone oxidoreductase system. Autophagy, a catabolic mechanism for macromolecule and protein recycling, allows the maintenance of amino acid pools and nutrient remobilization. Although the association between autophagy and alternative respiratory substrates has been suggested, the extent to which autophagy and primary metabolism interact to support plant respiration remains unclear. To investigate the metabolic importance of autophagy during development and under extended darkness, Arabidopsis ( Arabidopsis thaliana ) mutants with disruption of autophagy ( atg mutants) were used. Under normal growth conditions, atg mutants showed lower growth and seed production with no impact on photosynthesis. Following extended darkness, atg mutants were characterized by signatures of early senescence, including decreased chlorophyll content and maximum photochemical efficiency of photosystem II coupled with increases in dark respiration. Transcript levels of genes involved in alternative pathways of respiration and amino acid catabolism were up-regulated in atg mutants. The metabolite profiles of dark-treated leaves revealed an extensive metabolic reprogramming in which increases in amino acid levels were partially compromised in atg mutants. Although an enhanced respiration in atg mutants was observed during extended darkness, autophagy deficiency compromises protein degradation and the generation of amino acids used as alternative substrates to the respiration. © 2017 American Society of Plant Biologists. All Rights Reserved.

48 CFR 206.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Open Competition After Exclusion of Sources 206.202 Establishing or maintaining alternative sources. (a) Agencies may use this authority to totally or partially exclude a particular source from a contract action... maintaining alternative sources. 206.202 Section 206.202 Federal Acquisition Regulations System DEFENSE...

Comparison of Yeasts as Hosts for Recombinant Protein Production.

PubMed

Vieira Gomes, Antonio Milton; Souza Carmo, Talita; Silva Carvalho, Lucas; Mendonça Bahia, Frederico; Parachin, Nádia Skorupa

2018-04-29

Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts ranging from the bacteria Escherichia coli to mammalian cells. Recombinant protein importance is represented by its market size, which reached $1654 million in 2016 and is expected to reach $2850.5 million by 2022. Among the available hosts, yeasts have been used for producing a great variety of proteins applied to chemicals, fuels, food, and pharmaceuticals, being one of the most used hosts for recombinant production nowadays. Historically, Saccharomyces cerevisiae was the dominant yeast host for heterologous protein production. Lately, other yeasts such as Komagataella sp., Kluyveromyces lactis , and Yarrowia lipolytica have emerged as advantageous hosts. In this review, a comparative analysis is done listing the advantages and disadvantages of using each host regarding the availability of genetic tools, strategies for cultivation in bioreactors, and the main techniques utilized for protein purification. Finally, examples of each host will be discussed regarding the total amount of protein recovered and its bioactivity due to correct folding and glycosylation patterns.

Iron, ferritin, and nutrition.

PubMed

Theil, Elizabeth C

2004-01-01

Ferritin, a major form of endogenous iron in food legumes such as soybeans, is a novel and natural alternative for iron supplementation strategies where effectiveness is limited by acceptability, cost, or undesirable side effects. A member of the nonheme iron group of dietary iron sources, ferritin is a complex with Fe3+ iron in a mineral (thousands of iron atoms inside a protein cage) protected from complexation. Ferritin illustrates the wide range of chemical and biological properties among nonheme iron sources. The wide range of nonheme iron receptors matched to the structure of the iron complexes that occurs in microorganisms may, by analogy, exist in humans. An understanding of the chemistry and biology of each type of dietary iron source (ferritin, heme, Fe2+ ion, etc.), and of the interactions dependent on food sources, genes, and gender, is required to design diets that will eradicate global iron deficiency in the twenty-first century.

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

PubMed Central

Delcourt, Vivian; Lucier, Jean-François; Gagnon, Jules; Beaudoin, Maxime C; Vanderperre, Benoît; Breton, Marc-André; Motard, Julie; Jacques, Jean-François; Brunelle, Mylène; Gagnon-Arsenault, Isabelle; Fournier, Isabelle; Ouangraoua, Aida; Hunting, Darel J; Cohen, Alan A; Landry, Christian R; Scott, Michelle S

2017-01-01

Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many genes are multicoding genes and code for a large protein and one or several small proteins. PMID:29083303

Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals

PubMed Central

Shabalina, Svetlana A.; Ogurtsov, Aleksey Y.; Spiridonov, Nikolay A.; Koonin, Eugene V.

2014-01-01

Alternative splicing (AS), alternative transcription initiation (ATI) and alternative transcription termination (ATT) create the extraordinary complexity of transcriptomes and make key contributions to the structural and functional diversity of mammalian proteomes. Analysis of mammalian genomic and transcriptomic data shows that contrary to the traditional view, the joint contribution of ATI and ATT to the transcriptome and proteome diversity is quantitatively greater than the contribution of AS. Although the mean numbers of protein-coding constitutive and alternative nucleotides in gene loci are nearly identical, their distribution along the transcripts is highly non-uniform. On average, coding exons in the variable 5′ and 3′ transcript ends that are created by ATI and ATT contain approximately four times more alternative nucleotides than core protein-coding regions that diversify exclusively via AS. Short upstream exons that encompass alternative 5′-untranslated regions and N-termini of proteins evolve under strong nucleotide-level selection whereas in 3′-terminal exons that encode protein C-termini, protein-level selection is significantly stronger. The groups of genes that are subject to ATI and ATT show major differences in biological roles, expression and selection patterns. PMID:24792168

49 CFR 193.2915 - Alternative power sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Alternative power sources. 193.2915 Section 193.2915 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS... GAS FACILITIES: FEDERAL SAFETY STANDARDS Security § 193.2915 Alternative power sources. An alternative...

Alternative intronic promoters in development and disease.

PubMed

Vacik, Tomas; Raska, Ivan

2017-05-01

Approximately 20,000 mammalian genes are estimated to encode between 250 thousand and 1 million different proteins. This enormous diversity of the mammalian proteome is caused by the ability of a single-gene locus to encode multiple protein isoforms. Protein isoforms encoded by one gene locus can be functionally distinct, and they can even have antagonistic functions. One of the mechanisms involved in creating this proteome complexity is alternative promoter usage. Alternative intronic promoters are located downstream from their canonical counterparts and drive the expression of alternative RNA isoforms that lack upstream exons. These upstream exons can encode some important functional domains, and proteins encoded by alternative mRNA isoforms can be thus functionally distinct from the full-length protein encoded by canonical mRNA isoforms. Since any misbalance of functionally distinct protein isoforms is likely to have detrimental consequences for the cell and the whole organism, their expression must be precisely regulated. Misregulation of alternative intronic promoters is frequently associated with various developmental defects and diseases including cancer, and it is becoming increasingly clear that this phenomenon deserves more attention.

Mechanisms of Nutrient Acquisition by Rock Eating Microbes Revealed by Proteomics

NASA Astrophysics Data System (ADS)

Bryce, C. C.; Martin, S.; LeBihan, T.; Cockell, C.

2013-12-01

In nutrient poor terrestrial environments such as fresh lava flows, bioessential elements contained within surrounding rocks can be an important source of nutrients for the microbial community. The role of microbes in the alteration of rock surfaces, driven by this nutrient requirement, is widely accepted and is known to play an important role in CO2 drawdown as well as influencing nutrient flux to the biosphere. There is, however, limited knowledge of the biological processes which facilitate the uptake of bioessential elements from rocks. Using a technique known as 'shotgun' proteomics we have investigated the cellular processes involved in the uptake of iron, calcium and magnesium from fresh basalt in the heavy metal resistant bacterium Cupriavidus metallidurans CH34. Quantitative proteomics allows us to obtain a detailed snapshot of the protein complement of cells. By comparing cultures grown under normal growth conditions to cultures grown with basalt as an alternative iron, calcium or magnesium source, we can highlight proteins which are differentially expressed and therefore important for life in a rocky environment. We observe that the use of rock-bound nutrients induces a complex metabolic response in C.metallidurans which is distinct from the effects observed in the presence of rocks in normal growth medium. This is evidenced, for example, by the upregulation of a number of proteins involved in alternative energy-producing processes such as chemolithotrophy, sulphur oxidation and hydrogen oxidation compared to control cultures. This work has implications for the understanding of how microbes forge a life for themselves from the Earth's crust and highlights the importance of the field of proteomics for the study of life in terrestrial environments.

Adenylate Cyclase and the Cyclic AMP Receptor Protein Modulate Stress Resistance and Virulence Capacity of Uropathogenic Escherichia coli

PubMed Central

Donovan, Grant T.; Norton, J. Paul; Bower, Jean M.

2013-01-01

In many bacteria, the second messenger cyclic AMP (cAMP) interacts with the transcription factor cAMP receptor protein (CRP), forming active cAMP-CRP complexes that can control a multitude of cellular activities, including expanded carbon source utilization, stress response pathways, and virulence. Here, we assessed the role of cAMP-CRP as a regulator of stress resistance and virulence in uropathogenic Escherichia coli (UPEC), the principal cause of urinary tract infections worldwide. Deletion of genes encoding either CRP or CyaA, the enzyme responsible for cAMP synthesis, attenuates the ability of UPEC to colonize the bladder in a mouse infection model, dependent on intact innate host defenses. UPEC mutants lacking cAMP-CRP grow normally in the presence of glucose but are unable to utilize alternate carbon sources like amino acids, the primary nutrients available to UPEC within the urinary tract. Relative to the wild-type UPEC isolate, the cyaA and crp deletion mutants are sensitive to nitrosative stress and the superoxide generator methyl viologen but remarkably resistant to hydrogen peroxide (H2O2) and acid stress. In the mutant strains, H2O2 resistance correlates with elevated catalase activity attributable in part to enhanced translation of the alternate sigma factor RpoS. Acid resistance was promoted by both RpoS-independent and RpoS-dependent mechanisms, including expression of the RpoS-regulated DNA-binding ferritin-like protein Dps. We conclude that balanced input from many cAMP-CRP-responsive elements, including RpoS, is critical to the ability of UPEC to handle the nutrient limitations and severe environmental stresses present within the mammalian urinary tract. PMID:23115037

Identifying functionally informative evolutionary sequence profiles.

PubMed

Gil, Nelson; Fiser, Andras

2018-04-15

Multiple sequence alignments (MSAs) can provide essential input to many bioinformatics applications, including protein structure prediction and functional annotation. However, the optimal selection of sequences to obtain biologically informative MSAs for such purposes is poorly explored, and has traditionally been performed manually. We present Selection of Alignment by Maximal Mutual Information (SAMMI), an automated, sequence-based approach to objectively select an optimal MSA from a large set of alternatives sampled from a general sequence database search. The hypothesis of this approach is that the mutual information among MSA columns will be maximal for those MSAs that contain the most diverse set possible of the most structurally and functionally homogeneous protein sequences. SAMMI was tested to select MSAs for functional site residue prediction by analysis of conservation patterns on a set of 435 proteins obtained from protein-ligand (peptides, nucleic acids and small substrates) and protein-protein interaction databases. Availability and implementation: A freely accessible program, including source code, implementing SAMMI is available at https://github.com/nelsongil92/SAMMI.git. andras.fiser@einstein.yu.edu. Supplementary data are available at Bioinformatics online.

17β-estradiol regulates the RNA-binding protein Nova1, which then regulates the alternative splicing of estrogen receptor β in the aging female rat brain.

PubMed

Shults, Cody L; Dingwall, Caitlin B; Kim, Chun K; Pinceti, Elena; Rao, Yathindar S; Pak, Toni R

2018-01-01

Alternative RNA splicing results in the translation of diverse protein products arising from a common nucleotide sequence. These alternative protein products are often functional and can have widely divergent actions from the canonical protein. Studies in humans and other vertebrate animals have demonstrated that alternative splicing events increase with advanced age, sometimes resulting in pathological consequences. Menopause represents a critical transition for women, where the beneficial effects of estrogens are no longer evident; therefore, factors underlying increased pathological conditions in women are confounded by the dual factors of aging and declining estrogens. Estrogen receptors (ERs) are subject to alternative splicing, the spliced variants increase following menopause, and they fail to efficiently activate estrogen-dependent signaling pathways. However, the factors that regulate the alternative splicing of ERs remain unknown. We demonstrate novel evidence supporting a potential biological feedback loop where 17β-estradiol regulates the RNA-binding protein Nova1, which, in turn, regulates the alternative splicing of ERβ. These data increase our understanding of ER alternative splicing and could have potential implications for women taking hormone replacement therapy after menopause. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

PubMed Central

Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L.

2012-01-01

Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and strongly suggests that the translation of alternative transcripts may be subject to selective constraints. PMID:22446687

48 CFR 906.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 906.202 Section 906.202 Federal Acquisition Regulations System DEPARTMENT OF ENERGY COMPETITION ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 906.202 Establishing or maintaining alternative sources. (b)(1) Every proposed contract...

48 CFR 406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 406.202 Section 406.202 Federal Acquisition Regulations System DEPARTMENT OF AGRICULTURE COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 406.202 Establishing or maintaining alternative sources. The Senior Procurement...

48 CFR 1406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 1406.202 Section 1406.202 Federal Acquisition Regulations System DEPARTMENT OF THE INTERIOR COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 1406.202 Establishing or maintaining alternative sources. HCAs are...

48 CFR 1306.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 1306.202 Section 1306.202 Federal Acquisition Regulations System DEPARTMENT OF COMMERCE COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 1306.202 Establishing or maintaining alternative sources. The authority to...

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins

PubMed Central

Kalyna, Maria; Lopato, Sergiy; Voronin, Viktor; Barta, Andrea

2006-01-01

Alternative splicing is an important mechanism for fine tuning of gene expression at the post-transcriptional level. SR proteins govern splice site selection and spliceosome assembly. The Arabidopsis genome encodes 19 SR proteins, several of which have no orthologues in metazoan. Three of the plant specific subfamilies are characterized by the presence of a relatively long alternatively spliced intron located in their first RNA recognition motif, which potentially results in an extremely truncated protein. In atRSZ33, a member of the RS2Z subfamily, this alternative splicing event was shown to be autoregulated. Here we show that atRSp31, a member of the RS subfamily, does not autoregulate alternative splicing of its similarily positioned intron. Interestingly, this alternative splicing event is regulated by atRSZ33. We demonstrate that the positions of these long introns and their capability for alternative splicing are conserved from green algae to flowering plants. Moreover, in particular alternative splicing events the splicing signals are embedded into highly conserved sequences. In different taxa, these conserved sequences occur in at least one gene within a subfamily. The evolutionary preservation of alternative splice forms together with highly conserved intron features argues for additional functions hidden in the genes of these plant-specific SR proteins. PMID:16936312

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

PubMed Central

Takeda, Jun-ichi; Suzuki, Yutaka; Nakao, Mitsuteru; Barrero, Roberto A.; Koyanagi, Kanako O.; Jin, Lihua; Motono, Chie; Hata, Hiroko; Isogai, Takao; Nagai, Keiichi; Otsuki, Tetsuji; Kuryshev, Vladimir; Shionyu, Masafumi; Yura, Kei; Go, Mitiko; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Wiemann, Stefan; Nomura, Nobuo; Sugano, Sumio; Gojobori, Takashi; Imanishi, Tadashi

2006-01-01

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants. PMID:16914452

Antifungal-protein production in maize (Zea mays) suspension cultures.

PubMed

Perri, Fabio; Della Penna, Serena; Rufini, Francesca; Patamia, Maria; Bonito, Mariantonietta; Angiolella, Letizia; Vitali, Alberto

2009-04-01

The growing emergency due to the phenomenon of drug resistance to micro-organisms has pushed forward the search for new potential drug alternatives to those already in use. Plants represent a suitable source of new antifungal molecules, as they produce a series of defensive proteins. Among them are the PRPs (pathogenesis-related proteins), shown to be effective in vitro against human pathogens. An optimized and established cell-suspension culture of maize (Zea mays) was shown to constitutively secrete in the medium a series of PRPs comprising the antifungal protein zeamatin (P33679) with a final yield of approx. 3 mg/litre. The in-vitro-produced zeamatin possessed antifungal activity towards a clinical strain of the human pathogenic yeast Candida albicans, an activity comparable with the one reported for the same protein extracted from maize seeds. Along with zeamatin, other PRPs were expressed: a 9 kDa lipid-transfer protein, a 26 kDa xylanase inhibitor and a new antifungal protein, PR-5. A fast, two-step chromatographic procedure was set up allowing the complete purification of the proteins considered, making this cell line a valuable system for the production of potential antifungal agents in a reliable and easy way.

48 CFR 2406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... alternative sources. 2406.202 Section 2406.202 Federal Acquisition Regulations System DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 2406.202 Establishing or maintaining alternative sources. (b)(1) The...

48 CFR 606.202 - Establishing or maintaining alternate sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternate sources. 606.202 Section 606.202 Federal Acquisition Regulations System DEPARTMENT OF STATE COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 606.202 Establishing or maintaining alternate sources. The Procurement Executive is the...

The influence of Argonaute proteins on alternative RNA splicing.

PubMed

Batsché, Eric; Ameyar-Zazoua, Maya

2015-01-01

Alternative splicing of precursor RNAs is an important process in multicellular species because it impacts several aspects of gene expression: from the increase of protein repertoire to the level of expression. A large body of evidences demonstrates that factors regulating chromatin and transcription impact the outcomes of alternative splicing. Argonaute (AGO) proteins were known to play key roles in the regulation of gene expression at the post-transcriptional level. More recently, their role in the nucleus of human somatic cells has emerged. Here, we will discuss some of the nuclear functions of AGO, with special emphasis on alternative splicing. The AGO-mediated modulation of alternative splicing is based on several properties of these proteins: their binding to transcripts on chromatin and their interactions with many proteins, especially histone tail-modifying enzymes, HP1γ and splicing factors. AGO proteins may favor a decrease in the RNA-polymerase II kinetics at actively transcribed genes leading to the modulation of alternative splicing decisions. They could also influence alternative splicing through their interaction with core components of the splicing machinery and several splicing factors. We will discuss the modes of AGO recruitment on chromatin at active genes. We suggest that long intragenic antisense transcripts (lincRNA) might be an important feature of genes containing splicing events regulated by AGO. © 2014 John Wiley & Sons, Ltd.

Mineral Properties and Dietary Value of Raw and Processed Stinging Nettle (Urtica dioica L.).

PubMed

Rutto, Laban K; Xu, Yixiang; Ramirez, Elizabeth; Brandt, Michael

2013-01-01

Stinging nettle (Urtica dioica L.) has a long history of usage and is currently receiving attention as a source of fiber and alternative medicine. In many cultures, nettle is also eaten as a leafy vegetable. In this study, we focused on nettle yield (edible portion) and processing effects on nutritive and dietary properties. Actively growing shoots were harvested from field plots and leaves separated from stems. Leaf portions (200 g) were washed and processed by blanching (1 min at 96-98°C) or cooking (7 min at 98-99°C) with or without salt (5 g·L(-1)). Samples were cooled immediately after cooking and kept in frozen storage before analysis. Proximate composition, mineral, amino acid, and vitamin contents were determined, and nutritive value was estimated based on 100 g serving portions in a 2000 calorie diet. Results show that processed nettle can supply 90%-100% of vitamin A (including vitamin A as β-carotene) and is a good source of dietary calcium, iron, and protein. We recommend fresh or processed nettle as a high-protein, low-calorie source of essential nutrients, minerals, and vitamins particularly in vegetarian, diabetic, or other specialized diets.

48 CFR 3006.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 3006.202 Establishing or maintaining alternative sources. (b)(1) The HCA is delegated authority to approve a D&F in support of a... maintaining alternative sources. 3006.202 Section 3006.202 Federal Acquisition Regulations System DEPARTMENT...

Comparison of the principal proteins in bovine, caprine, buffalo, equine and camel milk.

PubMed

Hinz, Katharina; O'Connor, Paula M; Huppertz, Thom; Ross, R Paul; Kelly, Alan L

2012-05-01

Proteomic analysis of bovine, caprine, buffalo, equine and camel milk highlighted significant interspecies differences. Camel milk was found to be devoid of β-lactoglobulin, whereas β-lactoglobulin was the major whey protein in bovine, buffalo, caprine, and equine milk. Five different isoforms of κ-casein were found in camel milk, analogous to the micro-heterogeneity observed for bovine κ-casein. Several spots observed in 2D-electrophoretograms of milk of all species could tentatively be identified as polypeptides arising from the enzymatic hydrolysis of caseins. The understanding gained from the proteomic comparison of these milks may be of relevance both in terms of identifying sources of hypoallergenic alternatives to bovine milk and detection of adulteration of milk samples and products.

Carbon monoxide transport and actions in blood and tissues.

PubMed

Thom, Stephen R

2011-01-01

This chapter will discuss the transport of carbon monoxide (CO) from the environment to the tissues of the body and physiological effects on blood-borne cells and perivascular tissues. It will review the physiology of CO exchange between alveolar gas and pulmonary capillary blood, dynamics of hemoglobin transport, the effects of CO on blood elements, and the effects of CO on extravascular tissues at the capillary bed. Effects of CO from exogenous and endogenous sources on the activities of different proteins will be reviewed. Because CO binds competitively to heme-containing proteins its effects depend on CO concentration relative to alternative ligands. Therefore, some discussion is devoted to how nitric oxide and hydrogen sulfide influence CO effects. © 2011 American Physiological Society.

MHC structure and function − antigen presentation. Part 2

PubMed Central

Goldberg, Anna Carla; Rizzo, Luiz Vicente

2015-01-01

The second part of this review deals with the molecules and processes involved in the processing and presentation of the antigenic fragments to the T-cell receptor. Though the nature of the antigens presented varies, the most significant class of antigens is proteins, processed within the cell to be then recognized in the form of peptides, a mechanism that confers an extraordinary degree of precision to this mode of immune response. The efficiency and accuracy of this system is also the result of the myriad of mechanisms involved in the processing of proteins and production of peptides, in addition to the capture and recycling of alternative sources aiming to generate further diversity in the presentation to T-cells. PMID:25807243

Zein-based Nanocarriers as Potential Natural Alternatives for Drug and Gene Delivery: Focus on Cancer Therapy.

PubMed

Elzoghby, Ahmed; Freag, May; Mamdouh, Hadeer; Elkhodairy, Kadria

2017-01-01

Protein nanocarriers possess unique merits including minimal cytotoxicity, numerous renewable sources, and high drug-binding capability. In opposition to delivery carriers utilizing hydrophilic animal proteins, hydrophobic plant proteins (e.g, zein) have great tendency in fabricating controlled-release particulate carriers without additional chemical modification to stiffen them, which in turn evades the use of toxic chemical crosslinkers. Moreover, zein is related to a class of alcohol-soluble prolamins and generally recognized as safe (GRAS) carrier for drug delivery. Various techniques have been adopted to fabricate zein-based nanoparticulate systems including phase separation coacervation, spray-drying, supercritical anti-solvent approach, electrospinning and self-assembly. This manuscript reviews the recent advances in the zein-based colloidal nano-carrier systems such as nanospheres, nanocapsules, micelles and nanofibers with a special focus on their physicochemical characteristics and drug delivery applications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Efficient recovery of proteins from multiple source samples after TRIzol(®) or TRIzol(®)LS RNA extraction and long-term storage.

PubMed

Simões, André E S; Pereira, Diane M; Amaral, Joana D; Nunes, Ana F; Gomes, Sofia E; Rodrigues, Pedro M; Lo, Adrian C; D'Hooge, Rudi; Steer, Clifford J; Thibodeau, Stephen N; Borralho, Pedro M; Rodrigues, Cecília M P

2013-03-15

Simultaneous isolation of nucleic acids and proteins from a single biological sample facilitates meaningful data interpretation and reduces time, cost and sampling errors. This is particularly relevant for rare human and animal specimens, often scarce, and/or irreplaceable. TRIzol(®) and TRIzol(®)LS are suitable for simultaneous isolation of RNA, DNA and proteins from the same biological sample. These reagents are widely used for RNA and/or DNA isolation, while reports on their use for protein extraction are limited, attributable to technical difficulties in protein solubilisation. TRIzol(®)LS was used for RNA isolation from 284 human colon cancer samples, including normal colon mucosa, tubulovillous adenomas, and colon carcinomas with proficient and deficient mismatch repair system. TRIzol(®) was used for RNA isolation from human colon cancer cells, from brains of transgenic Alzheimer's disease mice model, and from cultured mouse cortical neurons. Following RNA extraction, the TRIzol(®)-chloroform fractions from human colon cancer samples and from mouse hippocampus and frontal cortex were stored for 2 years and 3 months, respectively, at -80°C until used for protein isolation.Simple modifications to the TRIzol(®) manufacturer's protocol, including Urea:SDS solubilization and sonication, allowed improved protein recovery yield compared to the TRIzol(®) manufacturer's protocol. Following SDS-PAGE and Ponceau and Coomassie staining, recovered proteins displayed wide molecular weight range and staining pattern comparable to those obtainable with commonly used protein extraction protocols. We also show that nuclear and cytosolic proteins can be easily extracted and detected by immunoblotting, and that posttranslational modifications, such as protein phosphorylation, are detectable in proteins recovered from TRIzol(®)-chloroform fractions stored for up to 2 years at -80°C. We provide a novel approach to improve protein recovery from samples processed for nucleic acid extraction with TRIzol(®) and TRIzol(®)LS compared to the manufacturer`s protocol, allowing downstream immunoblotting and evaluation of steady-state relative protein expression levels. The method was validated in large sets of samples from multiple sources, including human colon cancer and brains of transgenic Alzheimer's disease mice model, stored in TRIzol(®)-chloroform for up to two years. Collectively, we provide a faster and cheaper alternative to the TRIzol(®) manufacturer`s protein extraction protocol, illustrating the high relevance, and wide applicability, of the present protein isolation method for the immunoblot evaluation of steady-state relative protein expression levels in samples from multiple sources, and following prolonged storage.

Alternative transportation funding sources available to Virginia localities.

DOT National Transportation Integrated Search

2006-01-01

In 2003, the Virginia Department of Transportation developed a list of alternative transportation funding sources available to localities in Virginia. Alternative funding sources are defined as those that are not included in the annual interstate, pr...

Characterization and profiling of immunomodulatory genes of equine mesenchymal stromal cells from non-invasive sources

PubMed Central

2014-01-01

Introduction Mesenchymal stromal cells (MSCs) have been extensively studied for their promising capabilities in regenerative medicine. Although bone marrow is the best-known source for isolating equine MSCs, non-invasive alternative sources such as umbilical cord blood (UCB), umbilical cord matrix (UCM), and peripheral blood (PB) have also been reported. Methods Equine MSCs from three non-invasive alternative sources were isolated from six individual mares (PB) and their foals (UCB and UCM) at parturition. To minimize inter-horse variability, the samples from the three sources were matched within the same mare and for UCB and UCM even within the same foal from that specific mare. The following parameters were analyzed: (i) success rate of isolation, (ii) proliferation capacity, (iii) tri-lineage differentiation ability, (iv) immunophenotypical protein, and (v) immunomodulatory mRNA profiles. Linear regression models were fit to determine the association between the source of MSCs (UCB, UCM, PB) and (i) the moment of first observation, (ii) the moment of first passage, (iii) cell proliferation data, (iv) the expression of markers related to cell immunogenicity, and (v) the mRNA profile of immunomodulatory factors, except for hepatocyte growth factor (HGF) as no normal distribution could be obtained for the latter variable. To evaluate the association between the source of MSCs and the mRNA expression of HGF, the non-parametric Kruskal-Wallis test was performed instead. Results While equine MSCs could be isolated from all the UCB and PB samples, isolation from UCM was successful in only two samples because of contamination issues. Proliferation data showed that equine MSCs from all three sources could be easily expanded, although UCB-derived MSCs appeared significantly faster in culture than PB- or UCM-derived MSCs. Equine MSCs from both UCB and PB could be differentiated toward the osteo-, chondro-, and adipogenic lineage, in contrast to UCM-derived MSCs in which only chondro- and adipogenic differentiation could be confirmed. Regardless of the source, equine MSCs expressed the immunomodulatory genes CD40, CD80, HGF, and transforming growth factor-beta (TGFβ). In contrast, no mRNA expression was found for CD86, indoleamine 2,3-dioxygenase (IDO), and tumor necrosis factor-alpha (TNFα). Conclusions Whereas UCM seems less feasible because of the high contamination risks and low isolation success rates, UCB seems a promising alternative MSC source, especially when considering allogeneic MSC use. PMID:24418262

48 CFR 1806.202 - Establishing or maintaining alternative sources. (NASA supplements paragraphs (a) and (b))

Code of Federal Regulations, 2010 CFR

2010-10-01

... COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 1806.202 Establishing or maintaining alternative sources. (NASA supplements paragraphs (a) and (b)) (a) The authority of FAR 6.202 is... alternative sources. (NASA supplements paragraphs (a) and (b)) 1806.202 Section 1806.202 Federal Acquisition...

48 CFR 2406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2011 CFR

2011-10-01

... maintaining alternative sources. 2406.202 Section 2406.202 Federal Acquisition Regulations System DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 2406.202 Establishing or maintaining alternative...

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

PubMed

Teo, Guoshou; Kim, Sinae; Tsou, Chih-Chiang; Collins, Ben; Gingras, Anne-Claude; Nesvizhskii, Alexey I; Choi, Hyungwon

2015-11-03

Data independent acquisition (DIA) mass spectrometry is an emerging technique that offers more complete detection and quantification of peptides and proteins across multiple samples. DIA allows fragment-level quantification, which can be considered as repeated measurements of the abundance of the corresponding peptides and proteins in the downstream statistical analysis. However, few statistical approaches are available for aggregating these complex fragment-level data into peptide- or protein-level statistical summaries. In this work, we describe a software package, mapDIA, for statistical analysis of differential protein expression using DIA fragment-level intensities. The workflow consists of three major steps: intensity normalization, peptide/fragment selection, and statistical analysis. First, mapDIA offers normalization of fragment-level intensities by total intensity sums as well as a novel alternative normalization by local intensity sums in retention time space. Second, mapDIA removes outlier observations and selects peptides/fragments that preserve the major quantitative patterns across all samples for each protein. Last, using the selected fragments and peptides, mapDIA performs model-based statistical significance analysis of protein-level differential expression between specified groups of samples. Using a comprehensive set of simulation datasets, we show that mapDIA detects differentially expressed proteins with accurate control of the false discovery rates. We also describe the analysis procedure in detail using two recently published DIA datasets generated for 14-3-3β dynamic interaction network and prostate cancer glycoproteome. The software was written in C++ language and the source code is available for free through SourceForge website http://sourceforge.net/projects/mapdia/.This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Transcriptional regulation of the protein kinase a subunits in Saccharomyces cerevisiae during fermentative growth.

PubMed

Galello, Fiorella; Pautasso, Constanza; Reca, Sol; Cañonero, Luciana; Portela, Paula; Moreno, Silvia; Rossi, Silvia

2017-12-01

Yeast cells can adapt their growth in response to the nutritional environment. Glucose is the favourite carbon source of Saccharomyces cerevisiae, which prefers a fermentative metabolism despite the presence of oxygen. When glucose is consumed, the cell switches to the aerobic metabolism of ethanol, during the so-called diauxic shift. The difference between fermentative and aerobic growth is in part mediated by a regulatory mechanism called glucose repression. During glucose derepression a profound gene transcriptional reprogramming occurs and genes involved in the utilization of alternative carbon sources are expressed. Protein kinase A (PKA) controls different physiological responses following the increment of cAMP as a consequence of a particular stimulus. cAMP-PKA is one of the major pathways involved in the transduction of glucose signalling. In this work the regulation of the promoters of the PKA subunits during respiratory and fermentative metabolism are studied. It is demonstrated that all these promoters are upregulated in the presence of glycerol as carbon source through the Snf1/Cat8 pathway. However, in the presence of glucose as carbon source, the regulation of each PKA promoter subunits is different and only TPK1 is repressed by the complex Hxk2/Mig1 in the presence of active Snf1. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A cell-free translocation system using extracts of cultured insect cells to yield functional membrane proteins.

PubMed

Ezure, Toru; Nanatani, Kei; Sato, Yoko; Suzuki, Satomi; Aizawa, Keishi; Souma, Satoshi; Ito, Masaaki; Hohsaka, Takahiro; von Heijine, Gunnar; Utsumi, Toshihiko; Abe, Keietsu; Ando, Eiji; Uozumi, Nobuyuki

2014-01-01

Cell-free protein synthesis is a powerful method to explore the structure and function of membrane proteins and to analyze the targeting and translocation of proteins across the ER membrane. Developing a cell-free system based on cultured cells for the synthesis of membrane proteins could provide a highly reproducible alternative to the use of tissues from living animals. We isolated Sf21 microsomes from cultured insect cells by a simplified isolation procedure and evaluated the performance of the translocation system in combination with a cell-free translation system originating from the same source. The isolated microsomes contained the basic translocation machinery for polytopic membrane proteins including SRP-dependent targeting components, translocation channel (translocon)-dependent translocation, and the apparatus for signal peptide cleavage and N-linked glycosylation. A transporter protein synthesized with the cell-free system could be functionally reconstituted into a lipid bilayer. In addition, single and double labeling with non-natural amino acids could be achieved at both the lumen side and the cytosolic side in this system. Moreover, tail-anchored proteins, which are post-translationally integrated by the guided entry of tail-anchored proteins (GET) machinery, were inserted correctly into the microsomes. These results showed that the newly developed cell-free translocation system derived from cultured insect cells is a practical tool for the biogenesis of properly folded polytopic membrane proteins as well as tail-anchored proteins.

Regulation of human adenovirus alternative RNA splicing by the adenoviral L4-33K and L4-22K proteins.

PubMed

Biasiotto, Roberta; Akusjärvi, Göran

2015-01-28

Adenovirus makes extensive use of alternative RNA splicing to produce a complex set of spliced viral mRNAs. Studies aimed at characterizing the interactions between the virus and the host cell RNA splicing machinery have identified three viral proteins of special significance for the control of late viral gene expression: L4-33K, L4-22K, and E4-ORF4. L4-33K is a viral alternative RNA splicing factor that controls L1 alternative splicing via an interaction with the cellular protein kinases Protein Kinase A (PKA) and DNA-dependent protein kinase (DNA-PK). L4-22K is a viral transcription factor that also has been implicated in the splicing of a subset of late viral mRNAs. E4-ORF4 is a viral protein that binds the cellular protein phosphatase IIA (PP2A) and controls Serine/Arginine (SR)-rich protein activity by inducing SR protein dephosphorylation. The L4-33K, and most likely also the L4-22K protein, are highly phosphorylated in vivo. Here we will review the function of these viral proteins in the post-transcriptional control of adenoviral gene expression and further discuss the significance of potential protein kinases phosphorylating the L4-33K and/or L4-22K proteins.

Pine as Fast Food: Foraging Ecology of an Endangered Cockatoo in a Forestry Landscape

PubMed Central

Stock, William D.; Finn, Hugh; Parker, Jackson; Dods, Ken

2013-01-01

Pine plantations near Perth, Western Australia have provided an important food source for endangered Carnaby’s Cockatoos (Calyptorhynchus latirostris) since the 1940s. Plans to harvest these plantations without re-planting will remove this food source by 2031 or earlier. To assess the impact of pine removal, we studied the ecological association between Carnaby’s Cockatoos and pine using behavioural, nutritional, and phenological data. Pine plantations provided high densities of seed (158 025 seeds ha−1) over a large area (c. 15 000 ha). Carnaby’s Cockatoos fed throughout these plantations and removed almost the entire annual crop of pine cones. Peak cockatoo abundance coincided with pine seed maturation. Pine seed had energy and protein contents equivalent to native food sources and, critically, is available in summer when breeding pairs have young offspring to feed. This strong and enduring ecological association clearly suggests that removing pine will have a significant impact on this endangered species unless restoration strategies, to establish alternative food sources, are implemented. PMID:23593413

Global phenotypic characterisation of human platelet lysate expanded MSCs by high-throughput flow cytometry.

PubMed

Reis, Monica; McDonald, David; Nicholson, Lindsay; Godthardt, Kathrin; Knobel, Sebastian; Dickinson, Anne M; Filby, Andrew; Wang, Xiao-Nong

2018-03-02

Mesenchymal stromal cells (MSCs) are a promising cell source to develop cell therapy for many diseases. Human platelet lysate (PLT) is increasingly used as an alternative to foetal calf serum (FCS) for clinical-scale MSC production. To date, the global surface protein expression of PLT-expended MSCs (MSC-PLT) is not known. To investigate this, paired MSC-PLT and MSC-FCS were analysed in parallel using high-throughput flow cytometry for the expression of 356 cell surface proteins. MSC-PLT showed differential surface protein expression compared to their MSC-FCS counterpart. Higher percentage of positive cells was observed in MSC-PLT for 48 surface proteins, of which 13 were significantly enriched on MSC-PLT. This finding was validated using multiparameter flow cytometry and further confirmed by quantitative staining intensity analysis. The enriched surface proteins are relevant to increased proliferation and migration capacity, as well as enhanced chondrogenic and osteogenic differentiation properties. In silico network analysis revealed that these enriched surface proteins are involved in three distinct networks that are associated with inflammatory responses, carbohydrate metabolism and cellular motility. This is the first study reporting differential cell surface protein expression between MSC-PLT and MSC-FSC. Further studies are required to uncover the impact of those enriched proteins on biological functions of MSC-PLT.

Cytochrome and Alternative Pathway Respiration in Tobacco (Effects of Salicylic Acid).

PubMed

Rhoads, D. M.; McIntosh, L.

1993-11-01

In suspension cultures of NT1 tobacco (Nicotiana tabacum L. cv Bright Yellow) cells the cytochrome pathway capacity increased between d 3 and d 4 following subculturing and reached the highest level observed on d 7. The capacity decreased significantly by d 10 and was at the same level on d 14. Both alternative pathway capacity and the amount of the 35-kD alternative oxidase protein increased significantly between d 5 and d 6, reached the highest point observed on d 7, remained constant until d 10, and decreased by d 14. The highest capacities of the alternative and cytochrome pathways and the highest amount of the 35-kD protein were attained on the day that cell cultures reached a stationary phase of growth. Addition of salicylic acid to cell cultures on d 4 caused a significant increase in alternative pathway capacity and a dramatic accumulation of the 35-kD protein by 12 h. The alternative pathway capacity and the protein level reached the highest level observed by 16 h after salicylic acid addition, and the cytochrome pathway capacity was at about the same level at each time point. The accumulation of the 35-kD alternative oxidase protein was significantly decreased by addition of actinomycin D 1 h before salicylic acid and was blocked by addition of cycloheximide. These results indicate that de novo transcription and translation were necessary for salicylic acid to cause the maximum accumulation of the 35-kD protein.

Cytochrome and Alternative Pathway Respiration in Tobacco (Effects of Salicylic Acid).

PubMed Central

Rhoads, D. M.; McIntosh, L.

1993-01-01

In suspension cultures of NT1 tobacco (Nicotiana tabacum L. cv Bright Yellow) cells the cytochrome pathway capacity increased between d 3 and d 4 following subculturing and reached the highest level observed on d 7. The capacity decreased significantly by d 10 and was at the same level on d 14. Both alternative pathway capacity and the amount of the 35-kD alternative oxidase protein increased significantly between d 5 and d 6, reached the highest point observed on d 7, remained constant until d 10, and decreased by d 14. The highest capacities of the alternative and cytochrome pathways and the highest amount of the 35-kD protein were attained on the day that cell cultures reached a stationary phase of growth. Addition of salicylic acid to cell cultures on d 4 caused a significant increase in alternative pathway capacity and a dramatic accumulation of the 35-kD protein by 12 h. The alternative pathway capacity and the protein level reached the highest level observed by 16 h after salicylic acid addition, and the cytochrome pathway capacity was at about the same level at each time point. The accumulation of the 35-kD alternative oxidase protein was significantly decreased by addition of actinomycin D 1 h before salicylic acid and was blocked by addition of cycloheximide. These results indicate that de novo transcription and translation were necessary for salicylic acid to cause the maximum accumulation of the 35-kD protein. PMID:12231986

The yeast stands alone: the future of protein biologic production.

PubMed

Love, Kerry R; Dalvie, Neil C; Love, J Christopher

2017-12-22

Yeasts are promising alternative hosts for the manufacturing of recombinant protein therapeutics because they simply and efficiently meet needs for both platform and small-market drugs. Fast accumulation of biomass and low-cost media reduce the cost-of-goods when using yeast, which in turn can enable agile, small-volume manufacturing facilities. Small, tractable yeast genomes are amenable to rapid process development, facilitating strain and product quality by design. Specifically, Pichia pastoris is becoming a widely accepted yeast for biopharmaceutical manufacturing in much of the world owing to a clean secreted product and the rapidly expanding understanding of its cell biology as a host organism. We advocate for a near term partnership spanning industry and academia to promote open source, timely development of yeast hosts. Copyright © 2017. Published by Elsevier Ltd.

Effect of feed moisture, extrusion temperature and screw speed on properties of soy white flakes based aquafeed: a response surface analysis.

PubMed

Singh, Sushil K; Muthukumarappan, Kasiviswanathan

2016-04-01

Soy white flakes (SWF) is an intermediate product during soy bean processing. It is an untoasted inexpensive product and contains around 51% of crude protein. It can be a potential source of protein to replace fish meal for developing aquafeed. The extrusion process is versatile and is used for the development of aquafeed. Our objective was to study the effects of inclusion of SWF (up to 50%) and other extrusion processing parameters such as barrel temperature and screw speed on the properties of aquafeed extrudates using a single-screw extruder. Extrudate properties, including pellet durability index, bulk density, water absorption and solubility indices and mass flow rate, were significantly (P < 0.05) affected by the process variables. SWF was the most significant variable with quadratic effects on most of the properties. Increasing temperature and screw speed resulted in increase in durability and mass flow rate of extrudates. Response surface regression models were established to correlate the properties of extrudates to the process variables. SWF was used as an alternative protein source of fish meal. Our study shows that aquafeed with high durability, lower bulk density and lower water absorption and higher solubility indices can be obtained by adding SWF up to 40%. © 2015 Society of Chemical Industry.

Evidence that "brain-specific" FOX-1, FOX-2, and nPTB alternatively spliced isoforms are produced in the lens.

PubMed

Bitel, Claudine L; Nathan, Rachel; Wong, Patrick; Kuppasani, Sunil; Matsushita, Masafumi; Kanazawa, Hrioshi; Frederikse, Peter H

2011-04-01

Alternative RNA splicing is essential in development and more rapid physiological processes that include disease mechanisms. Studies over the last 20 years demonstrated that RNA binding protein families, which mediate the alternative splicing of a large percentage of genes in mammals, contain isoforms with mutually exclusive expression in non-neural and neural progenitor cells vs. post-mitotic neurons, and regulate the comprehensive reprogramming of alternative splicing during neurogenesis. Polypyrimidine tract binding (PTB) proteins and Fox-1 proteins also undergo mutually exclusive alternative splicing in neural and non-neural cells that regulates their tissue-specific expression and splicing activities. Over the past 50 years, striking morphological similarities noted between lens fiber cells and neurons suggested that cell biology processes and gene expression profiles may be shared as well. Here, we examined mouse and rat lenses to determine if alternative splicing of neuronal nPTB and Fox-1/Fox-2 isoforms also occurs in lenses. Immunoblot, immunofluorescence, and RT-PCR were used to examine expression and alternative splicing of transcripts in lens and brain. We demonstrated that exon 10 is predominantly included in nPTB transcripts consistent with nPTB protein in lenses, and that alternatively spliced Fox-1/-2 lens transcripts contain exons that have been considered neuron-specific. We identified a 3' alternative Fox-1 exon in lenses that encodes a nuclear localization signal consistent with its protein distribution detected in fiber cells. Neuronal alternative splicing of kinesin KIF1Bβ2 has been associated with PTB/nPTB and Fox-2, and we found that two 'neuron-specific' exons are also included in lenses. The present study provides evidence that alternative neuronal nPTB and Fox-1/Fox-2 isoforms are also produced in lenses. These findings raise questions regarding the extent these factors contribute to a similar reprogramming of alternative splicing during lens differentiation, and the degree that alternative gene transcripts produced during neurogenesis are also expressed in the lens.

Impact of Glycerol as Carbon Source onto Specific Sugar and Inducer Uptake Rates and Inclusion Body Productivity in E. coli BL21(DE3).

PubMed

Kopp, Julian; Slouka, Christoph; Ulonska, Sophia; Kager, Julian; Fricke, Jens; Spadiut, Oliver; Herwig, Christoph

2017-12-21

The Gram-negative bacterium E. coli is the host of choice for a multitude of used recombinant proteins. Generally, cultivation is easy, media are cheap, and a high product titer can be obtained. However, harsh induction procedures using isopropyl β-d-1 thiogalactopyranoside as inducer are often referred to cause stress reactions, leading to a phenomenon known as "metabolic" or "product burden". These high expressions of recombinant proteins mainly result in decreased growth rates and cell lysis at elevated induction times. Therefore, approaches tend to use "soft" or "tunable" induction with lactose and reduce the stress level of the production host. The usage of glucose as energy source in combination with lactose as induction reagent causes catabolite repression effects on lactose uptake kinetics and as a consequence reduced product titer. Glycerol-as an alternative carbon source-is already known to have positive impact on product formation when coupled with glucose and lactose in auto-induction systems, and has been referred to show no signs of repression when cultivated with lactose concomitantly. In recent research activities, the impact of different products on the lactose uptake using glucose as carbon source was highlighted, and a mechanistic model for glucose-lactose induction systems showed correlations between specific substrate uptake rate for glucose or glycerol (q s,C ) and the maximum specific lactose uptake rate (q s,lac,max ). In this study, we investigated the mechanistic of glycerol uptake when using the inducer lactose. We were able to show that a product-producing strain has significantly higher inducer uptake rates when being compared to a non-producer strain. Additionally, it was shown that glycerol has beneficial effects on viability of cells and on productivity of the recombinant protein compared to glucose.

Intramuscular fatty acid composition of lambs fed diets containing alternative protein sources.

PubMed

Scerra, M; Caparra, P; Foti, F; Cilione, C; Zappia, G; Motta, C; Scerra, V

2011-03-01

Thirty male Merinizzata italiana lambs were divided into three groups after weaning according to live weight. The diet of the three groups differed in the main protein source used in the concentrate, soybean meal for treatment SBM, faba bean for treatment FB and peas for treatment PEA. Lambs were fed ad libitum and slaughtered at about 160 days of age. Meat from the PEA group had higher proportions of the essential fatty acids C18:2 ω-6 and C18:3 ω-3 than from FB and SBM lambs and consequently its derivatives, C20:4 ω-6 and C20:5 ω-3 respectively, were higher in meat from PEA animals, compared to SBM and FB ones. The total n-3 fatty acids were highest in meat from PEA lambs and consequently PEA lambs showed a more favourable n-6/n-3 ratio. In conclusion the use of legume seeds such as peas in lamb diets positively affected intramuscular fatty acid composition. Copyright © 2010 The American Meat Science Association. Published by Elsevier Ltd. All rights reserved.

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics.

PubMed

Levitsky, Lev I; Ivanov, Mark V; Lobas, Anna A; Bubis, Julia A; Tarasova, Irina A; Solovyeva, Elizaveta M; Pridatchenko, Marina L; Gorshkov, Mikhail V

2018-06-18

We present an open-source, extensible search engine for shotgun proteomics. Implemented in Python programming language, IdentiPy shows competitive processing speed and sensitivity compared with the state-of-the-art search engines. It is equipped with a user-friendly web interface, IdentiPy Server, enabling the use of a single server installation accessed from multiple workstations. Using a simplified version of X!Tandem scoring algorithm and its novel "autotune" feature, IdentiPy outperforms the popular alternatives on high-resolution data sets. Autotune adjusts the search parameters for the particular data set, resulting in improved search efficiency and simplifying the user experience. IdentiPy with the autotune feature shows higher sensitivity compared with the evaluated search engines. IdentiPy Server has built-in postprocessing and protein inference procedures and provides graphic visualization of the statistical properties of the data set and the search results. It is open-source and can be freely extended to use third-party scoring functions or processing algorithms and allows customization of the search workflow for specialized applications.

Effect of maggot (Hermetia illucens) flour in commercial feed on protein retention, energy retention, protein content, and fat content in tilapia (Oreochromis niloticus)

NASA Astrophysics Data System (ADS)

Kurniawan, D. R.; Arief, M.; Agustono; Lamid, M.

2018-04-01

Nile tilapia is a fish with a nature of breeding throughout the year and has a high adaptation. Feed is one of the most important factors that will affect the growth and the sustainability of fish. Maggot is one of the alternative feeds which has function as source of protein.The aim of this research is to ascertain the influence of maggot (Hermetia illucens) flour substitution on commercial feed which affect the retention of energy, retention of protein, and also rough fat and protein of Nile tilapia flesh. The treatment was to substitute the commercial feed with different doses of maggot flour. In this study, the amount of maggot flour substituted on commercial feed is as follows: treatment P0 (0 %), P1 (12 %), P2 (14 %), P3 (16 %) and P4 (18 %). The parameter observed in this study is an effect on to protein retention, energy retention, and also rough fat and protein in Nile tilapia flesh. The result showed the highest protein content was gained from the treatment P4 with 17.267 %. The lowest protein content was 16.344 % obtained in the treatment P0. There was an increasing protein content in Nile tilapia along with the increase of the maggot flour addition in each treatment.

Differential HFE Gene Expression Is Regulated by Alternative Splicing in Human Tissues

PubMed Central

Proença, Daniela; Faustino, Paula

2011-01-01

Background The pathophysiology of HFE-derived Hereditary Hemochromatosis and the function of HFE protein in iron homeostasis remain uncertain. Also, the role of alternative splicing in HFE gene expression regulation and the possible function of the corresponding protein isoforms are still unknown. The aim of this study was to gain insights into the physiological significance of these alternative HFE variants. Methodology/Principal Findings Alternatively spliced HFE transcripts in diverse human tissues were identified by RT-PCR, cloning and sequencing. Total HFE transcripts, as well as two alternative splicing transcripts were quantified using a real-time PCR methodology. Intracellular localization, trafficking and protein association of GFP-tagged HFE protein variants were analysed in transiently transfected HepG2 cells by immunoprecipitation and immunofluorescence assays. Alternatively spliced HFE transcripts present both level- and tissue-specificity. Concerning the exon 2 skipping and intron 4 inclusion transcripts, the liver presents the lowest relative level, while duodenum presents one of the highest amounts. The protein resulting from exon 2 skipping transcript is unable to associate with β2M and TfR1 and reveals an ER retention. Conversely, the intron 4 inclusion transcript gives rise to a truncated, soluble protein (sHFE) that is mostly secreted by cells to the medium in association with β2M. Conclusions/Significance HFE gene post-transcriptional regulation is clearly affected by a tissue-dependent alternative splicing mechanism. Among the corresponding proteins, a sHFE isoform stands out, which upon being secreted into the bloodstream, may act in remote tissues. It could be either an agonist or antagonist of the full length HFE, through hepcidin expression regulation in the liver or by controlling dietary iron absorption in the duodenum. PMID:21407826

Differential HFE gene expression is regulated by alternative splicing in human tissues.

PubMed

Martins, Rute; Silva, Bruno; Proença, Daniela; Faustino, Paula

2011-03-03

The pathophysiology of HFE-derived Hereditary Hemochromatosis and the function of HFE protein in iron homeostasis remain uncertain. Also, the role of alternative splicing in HFE gene expression regulation and the possible function of the corresponding protein isoforms are still unknown. The aim of this study was to gain insights into the physiological significance of these alternative HFE variants. Alternatively spliced HFE transcripts in diverse human tissues were identified by RT-PCR, cloning and sequencing. Total HFE transcripts, as well as two alternative splicing transcripts were quantified using a real-time PCR methodology. Intracellular localization, trafficking and protein association of GFP-tagged HFE protein variants were analysed in transiently transfected HepG2 cells by immunoprecipitation and immunofluorescence assays. Alternatively spliced HFE transcripts present both level- and tissue-specificity. Concerning the exon 2 skipping and intron 4 inclusion transcripts, the liver presents the lowest relative level, while duodenum presents one of the highest amounts. The protein resulting from exon 2 skipping transcript is unable to associate with β2M and TfR1 and reveals an ER retention. Conversely, the intron 4 inclusion transcript gives rise to a truncated, soluble protein (sHFE) that is mostly secreted by cells to the medium in association with β2M. HFE gene post-transcriptional regulation is clearly affected by a tissue-dependent alternative splicing mechanism. Among the corresponding proteins, a sHFE isoform stands out, which upon being secreted into the bloodstream, may act in remote tissues. It could be either an agonist or antagonist of the full length HFE, through hepcidin expression regulation in the liver or by controlling dietary iron absorption in the duodenum.

77 FR 41873 - In the Matter of Alternative Energy Sources, Inc., Arlington Hospitality, Inc., Consolidated Oil...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-16

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] In the Matter of Alternative Energy Sources, Inc., Arlington Hospitality, Inc., Consolidated Oil & Gas, Inc., CSMG Technologies, Inc., Dakotah... Alternative Energy Sources, Inc. because it has not filed any periodic reports since the period ended...

Evaluation of growth performance, serum biochemistry and haematological parameters on broiler birds fed with raw and processed samples of Entada scandens, Canavalia gladiata and Canavalia ensiformis seed meal as an alternative protein source.

PubMed

Sasipriya, Gopalakrishnan; Siddhuraju, Perumal

2013-03-01

The experiment was carried out to investigate the inclusion of underutilised legumes, Entada scandens, Canavalia gladiata and Canavalia ensiformis, seed meal in soybean-based diet in broilers. The utilisation of these wild legumes is limited by the presence of antinutrient compounds. Processing methods like soaking followed by autoclaving in sodium bicarbonate solution in E. scandens and C. gladiata and soaking followed by autoclaving in ash solution in C. ensiformis were adopted. The proximate composition of raw and processed samples of E. scandens, C. gladiata and C. ensiformis were determined. The protein content was enhanced in processed sample of E. scandens (46 %) and C. ensiformis (16 %). This processing method had reduced the maximum number of antinutrients such as tannins (10-100 %), trypsin inhibitor activity (99 %), chymotrypsin inhibitor activity (72-100 %), canavanine (60-62 %), amylase inhibitor activity (73-100 %), saponins (78-92 %), phytic acid (19-40 %) and lectins. Hence, the raw samples at 15 % and processed samples at 15 and 30 % were replaced with soybean protein in commercial broiler diet respectively. Birds fed with 30 % processed samples of E. scandens, C. gladiata and C. ensiformis showed significantly similar results of growth performance, carcass characteristics, organ weight, haematological parameters and serum biochemical parameters (cholesterol, protein, bilirubin, albumin, globulin and liver and kidney function parameters) without any adverse effects after 42 days of supplementation. The proper utilisation of these underutilised legumes may act as an alternative protein ingredient in poultry diets.

Studies on chemical constituents and bioactivity of Rosa micrantha: an alternative antioxidants source for food, pharmaceutical, or cosmetic applications.

PubMed

Guimarães, Rafaela; Barros, Lillian; Carvalho, Ana Maria; Ferreira, Isabel C F R

2010-05-26

Rose species have long been used for food and medicinal purposes. Rosa micrantha is one of the rose species that grow feral in the northeastern Portuguese region so-called Nordeste Transmontano. For the first time, chemical composition and bioactivity of their petals, fertilized flowers, unripe, ripening, and overripe hips were evaluated in order to valorize them as sources of important phytochemicals. Chemical characterization included determination of proteins, fats, ash, and carbohydrates, particularly sugars, by HPLC-RI, fatty acids by GC-FID, tocopherols by HPLC-fluorescence, and phenolics, flavonoids, carotenoids, and ascorbic acid by spectrophotometric techniques. Bioactivity was evaluated through screening of antioxidant properties: radical scavenging effects, reducing power, and inhibition of lipid peroxidation. Ripening and overripe hips showed high nutritional value including proteins, carbohydrates, omega-3 and omega-6 fatty acids, energy, sugars, particularly the reducing sugars fructose and glucose, and ascorbic acid (>693 mg/100 g). Fertilized flowers and petals revealed the highest antioxidant activity (EC(50) > 152 microg/mL) and phenolics, flavonoids, and tocopherols contents (>35 mg/100 g). Furthermore, petals, ripening, and overripe hips are important sources of carotenoid pigments (>64 mg/100 g). Because of the diversity and abundance of antioxidants found in this species, some food, cosmetic, and pharmaceutical applications could be explored.

Optical and spectroscopic studies on tannery wastes as a possible source of organic semiconductors

NASA Astrophysics Data System (ADS)

Nashy, El-Shahat H. A.; Al-Ashkar, Emad; Abdel Moez, A.

2012-02-01

Tanning industry produces a large quantity of solid wastes which contain hide proteins in the form of protein shavings containing chromium salts. The chromium wastes are the main concern from an environmental stand point of view, because chrome wastes posses a significant disposal problem. The present work is devoted to investigate the possibility of utilizing these wastes as a source of organic semi-conductors as an alternative method instead of the conventional ones. The chemical characterization of these wastes was determined. In addition, the Horizontal Attenuated Total Reflection (HATR) FT-IR spectroscopic analysis and optical parameters were also carried out for chromated samples. The study showed that the chromated samples had suitable absorbance and transmittance in the wavelength range (500-850 nm). Presence of chromium salt in the collagen samples increases the absorbance which improves the optical properties of the studied samples and leads to decrease the optical energy gap. The obtained optical energy gap gives an impression that the environmentally hazardous chrome shavings wastes can be utilized as a possible source of natural organic semiconductors with direct and indirect energy gap. This work opens the door to use some hazardous wastes in the manufacture of electronic devices such as IR-detectors, solar cells and also as solar cell windows.

Mineral Properties and Dietary Value of Raw and Processed Stinging Nettle (Urtica dioica L.)

PubMed Central

Xu, Yixiang; Ramirez, Elizabeth

2013-01-01

Stinging nettle (Urtica dioica L.) has a long history of usage and is currently receiving attention as a source of fiber and alternative medicine. In many cultures, nettle is also eaten as a leafy vegetable. In this study, we focused on nettle yield (edible portion) and processing effects on nutritive and dietary properties. Actively growing shoots were harvested from field plots and leaves separated from stems. Leaf portions (200 g) were washed and processed by blanching (1 min at 96–98°C) or cooking (7 min at 98-99°C) with or without salt (5 g·L−1). Samples were cooled immediately after cooking and kept in frozen storage before analysis. Proximate composition, mineral, amino acid, and vitamin contents were determined, and nutritive value was estimated based on 100 g serving portions in a 2000 calorie diet. Results show that processed nettle can supply 90%–100% of vitamin A (including vitamin A as β-carotene) and is a good source of dietary calcium, iron, and protein. We recommend fresh or processed nettle as a high-protein, low-calorie source of essential nutrients, minerals, and vitamins particularly in vegetarian, diabetic, or other specialized diets. PMID:26904610

Salicylic Acid Regulation of Respiration in Higher Plants: Alternative Oxidase Expression.

PubMed Central

Rhoads, DM; McIntosh, L

1992-01-01

Alternative respiratory pathway capacity increases during the development of the thermogenic appendix of a voodoo lily inflorescence. The levels of the alternative oxidase proteins increased dramatically between D-4 (4 days prior to the day of anthesis) and D-3 and continued to increase until the day of anthesis (D-day). The level of salicylic acid (SA) in the appendix is very low early on D-1, but increases to a high level in the evening of D-1. Thermogenesis occurs after a few hours of light on D-day. Therefore, the initial accumulation of the alternative oxidase proteins precedes the increase in SA by 3 days, indicating that other regulators may be involved. A 1.6-kb transcript encoding the alternative oxidase precursor protein accumulated to a high level in the appendix tissue by D-1. Application of SA to immature appendix tissue caused an increase in alternative pathway capacity and a dramatic accumulation of the alternative oxidase proteins and the 1.6-kb transcript. Time course experiments showed that the increase in capacity, protein levels, and transcript level corresponded precisely. The response to SA was blocked by cycloheximide or actinomycin D, indicating that de novo transcription and translation are required. However, nuclear, in vitro transcription assays indicated that the accumulation of the 1.6-kb transcript did not result from a simple increase in the rate of transcription of aox1. PMID:12297672

Silkworm (Bombyx mori) hemolymph unable to substitute fetal bovine serum in insect cell culture

NASA Astrophysics Data System (ADS)

Suparto, Irma H.; Khalam, Chandra Nur; Praira, Willy; Sajuthi, Dondin

2014-03-01

Fetal Bovine Serum (FBS) in animal cell culture media is an important source of nutrients for cell growth. However, the harvest and collection of FBS cause bioethical concerns. Efforts to reduce and preferably replace FBS with synthetic or other natural alternatives are continually being explored. Hemolymph silkworm (Bombyx mori) contains many nutrients needed for the process of metamorphosis. Therefore, there is possibility as an alternative nutritional supplement for cell culture to reduce the use of FBS. The objective of this study was to evaluate the macrocomponent of hemolymph and the possibility as medium supplement for Spodoptera fugiperda (Sf9) cell culture. Proximate analyses showed that hemolymph contains 89.76% of water, 2.52 mg/mL carbohydrate, 2.35% fat and 55.61 mg/mL protein. Further protein analysis, it consists of 15 fractions containing molecular weight of 22 - 152 kDa. The use of hemolymph as FBS substitution in Sf9 cell culture with various concentrations was unable to maintain and support cell growth. Further research still needed by prior adaptation of the tissue culture to minimal nutrition media before introduction of the hemolymph as supplement.

Non-avian animal reservoirs present a source of influenza A PB1-F2 proteins with novel virulence-enhancing markers.

PubMed

Alymova, Irina V; York, Ian A; McCullers, Jonathan A

2014-01-01

PB1-F2 protein, expressed from an alternative reading frame of most influenza A virus (IAV) PB1 segments, may possess specific residues associated with enhanced inflammation (L62, R75, R79, and L82) and cytotoxicity (I68, L69, and V70). These residues were shown to increase the pathogenicity of primary viral and secondary bacterial infections in a mouse model. In contrast to human seasonal influenza strains, virulence-associated residues are present in PB1-F2 proteins from pandemic H1N1 1918, H2N2 1957, and H3N2 1968, and highly pathogenic H5N1 strains, suggesting their contribution to viruses' pathogenic phenotypes. Non-human influenza strains may act as donors of virulent PB1-F2 proteins. Previously, avian influenza strains were identified as a potential source of inflammatory, but not cytotoxic, PB1-F2 residues. Here, we analyze the frequency of virulence-associated residues in PB1-F2 sequences from IAVs circulating in mammalian species in close contact with humans: pigs, horses, and dogs. All four inflammatory residues were found in PB1-F2 proteins from these viruses. Among cytotoxic residues, I68 was the most common and was especially prevalent in equine and canine IAVs. Historically, PB1-F2 from equine (about 75%) and canine (about 20%) IAVs were most likely to have combinations of the highest numbers of residues associated with inflammation and cytotoxicity, compared to about 7% of swine IAVs. Our analyses show that, in addition to birds, pigs, horses, and dogs are potentially important sources of pathogenic PB1-F2 variants. There is a need for surveillance of IAVs with genetic markers of virulence that may be emerging from these reservoirs in order to improve pandemic preparedness and response.

Alternative Fuels Data Center: Oklahoma Transportation Data for Alternative

Science.gov Websites

Fuel Consumption Source: State Energy Data System based on beta data converted to gasoline gallon ) 2,573 Source: BioFuels Atlas from the National Renewable Energy Laboratory Case Studies Video thumbnail Source: Average prices per gasoline gallon equivalent (GGE) for the Midwest PADD from the Alternative

Alternative Fuels Data Center: Nevada Transportation Data for Alternative

Science.gov Websites

. Gasoline Diesel Natural Gas Electricity Transportation Fuel Consumption Source: State Energy Data System Renewable Power Plant Capacity (nameplate, MW) 1,684 Source: BioFuels Atlas from the National Renewable Source: Average prices per gasoline gallon equivalent (GGE) for the West Coast PADD from the Alternative

Stabilizing and destabilizing protein surfactant-based foams in the presence of a chemical surfactant: Effect of adsorption kinetics.

PubMed

Li, Huazhen; Le Brun, Anton P; Agyei, Dominic; Shen, Wei; Middelberg, Anton P J; He, Lizhong

2016-01-15

Stimuli-responsive protein surfactants promise alternative foaming materials that can be made from renewable sources. However, the cost of protein surfactants is still higher than their chemical counterparts. In order to reduce the required amount of protein surfactant for foaming, we investigated the foaming and adsorption properties of the protein surfactant, DAMP4, with addition of low concentrations of the chemical surfactant sodium dodecylsulfate (SDS). The results show that the small addition of SDS can enhance foaming functions of DAMP4 at a lowered protein concentration. Dynamic surface tension measurements suggest that there is a synergy between DAMP4 and SDS which enhances adsorption kinetics of DAMP4 at the initial stage of adsorption (first 60s), which in turn stabilizes protein foams. Further interfacial properties were revealed by X-ray reflectometry measurements, showing that there is a re-arrangement of adsorbed protein-surfactant layer over a long period of 1h. Importantly, the foaming switchability of DAMP4 by metal ions is not affected by the presence of SDS, and foams can be switched off by the addition of zinc ions at permissive pH. This work provides fundamental knowledge to guide formulation using a mixture of protein and chemical surfactants towards a high performance of foaming at a low cost. Copyright © 2015 Elsevier Inc. All rights reserved.

ELAV, a Drosophila neuron-specific protein, mediates the generation of an alternatively spliced neural protein isoform.

PubMed

Koushika, S P; Lisbin, M J; White, K

1996-12-01

Tissue-specific alternative pre-mRNA splicing is a widely used mechanism for gene regulation and the generation of different protein isoforms, but relatively little is known about the factors and mechanisms that mediate this process. Tissue-specific RNA-binding proteins could mediate alternative pre-mRNA splicing. In Drosophila melanogaster, the RNA-binding protein encoded by the elav (embryonic lethal abnormal visual system) gene is a candidate for such a role. The ELAV protein is expressed exclusively in neurons, and is important for the formation and maintenance of the nervous system. In this study, photoreceptor neurons genetically depleted of ELAV, and elav-null central nervous system neurons, were analyzed immunocytochemically for the expression of neural proteins. In both situations, the lack of ELAV corresponded with a decrease in the immunohistochemical signal of the neural-specific isoform of Neuroglian, which is generated by alternative splicing. Furthermore, when ELAV was expressed ectopically in cells that normally express only the non-neural isoform of Neuroglian, we observed the generation of the neural isoform of Neuroglian. Drosophila ELAV promotes the generation of the neuron-specific isoform of Neuroglian by the regulation of pre-mRNA splicing. The findings reported in this paper demonstrate that ELAV is necessary, and the ectopic expression of ELAV in imaginal disc cells is sufficient, to mediate neuron-specific alternative splicing.

Pentoses and light intensity increase the growth and carbohydrate production and alter the protein profile of Chlorella minutissima.

PubMed

Freitas, B C B; Cassuriaga, A P A; Morais, M G; Costa, J A V

2017-08-01

High concentrations of carbon, which is considered a necessary element, are required for microalgal growth. Therefore, the identification of alternative carbon sources available in large quantities is increasingly important. This study evaluated the effects of light variation and pentose addition on the carbohydrate content and protein profile of Chlorella minutissima grown in a raceway photobioreactor. The kinetic parameters, carbohydrate content, and protein profile of Chlorella minutissima and its theoretical potential for ethanol production were estimated. The highest cellular concentrations were obtained with a light intensity of 33.75µmol.m -2 .s -1 . Arabinose addition combined with a light intensity of 33.75µmol.m -2 .s -1 increased the carbohydrate content by 53.8% and theoretically produced 39.1mL·100g -1 ethanol. All of the assays showed that a lower light availability altered the protein profile. The luminous intensity affects xylose and arabinose assimilation and augments the carbohydrate content in C. minutissima, making this microalga appropriate for bioethanol production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bioactive Peptides in Animal Food Products.

PubMed

Albenzio, Marzia; Santillo, Antonella; Caroprese, Mariangela; Della Malva, Antonella; Marino, Rosaria

2017-05-09

Proteins of animal origin represent physiologically active components in the human diet; they exert a direct action or constitute a substrate for enzymatic hydrolysis upon food processing and consumption. Bioactive peptides may descend from the hydrolysis by digestive enzymes, enzymes endogenous to raw food materials, and enzymes from microorganisms added during food processing. Milk proteins have different polymorphisms for each dairy species that influence the amount and the biochemical characteristics (e.g., amino acid chain, phosphorylation, and glycosylation) of the protein. Milk from other species alternative to cow has been exploited for their role in children with cow milk allergy and in some infant pathologies, such as epilepsy, by monitoring the immune status. Different mechanisms concur for bioactive peptides generation from meat and meat products, and their functionality and application as functional ingredients have proven effects on consumer health. Animal food proteins are currently the main source of a range of biologically-active peptides which have gained special interest because they may also influence numerous physiological responses in the organism. The addition of probiotics to animal food products represent a strategy for the increase of molecules with health and functional properties.

Biological and Pathological Implications of an Alternative ATP-Powered Proteasomal Assembly With Cdc48 and the 20S Peptidase.

PubMed

Esaki, Masatoshi; Johjima-Murata, Ai; Islam, Md Tanvir; Ogura, Teru

2018-01-01

The ATP-powered protein degradation machinery plays essential roles in maintaining protein homeostasis in all organisms. Robust proteolytic activities are typically sequestered within protein complexes to avoid the fatal removal of essential proteins. Because the openings of proteolytic chambers are narrow, substrate proteins must undergo unfolding. AAA superfamily proteins (ATPases associated with diverse cellular activities) are mostly located at these openings and regulate protein degradation appropriately. The 26S proteasome, comprising 20S peptidase and 19S regulatory particles, is the major ATP-powered protein degradation machinery in eukaryotes. The 19S particles are composed of six AAA proteins and 13 regulatory proteins, and bind to both ends of a barrel-shaped proteolytic chamber formed by the 20S peptidase. Several recent studies have reported that another AAA protein, Cdc48, can replace the 19S particles to form an alternative ATP-powered proteasomal complex, i.e., the Cdc48-20S proteasome. This review focuses on our current knowledge of this alternative proteasome and its possible linkage to amyotrophic lateral sclerosis.

Dietary Protein Intake in Dutch Elderly People: A Focus on Protein Sources.

PubMed

Tieland, Michael; Borgonjen-Van den Berg, Karin J; Van Loon, Luc J C; de Groot, Lisette C P G M

2015-11-25

Sufficient high quality dietary protein intake is required to prevent or treat sarcopenia in elderly people. Therefore, the intake of specific protein sources as well as their timing of intake are important to improve dietary protein intake in elderly people. to assess the consumption of protein sources as well as the distribution of protein sources over the day in community-dwelling, frail and institutionalized elderly people. Habitual dietary intake was evaluated using 2- and 3-day food records collected from various studies involving 739 community-dwelling, 321 frail and 219 institutionalized elderly people. Daily protein intake averaged 71 ± 18 g/day in community-dwelling, 71 ± 20 g/day in frail and 58 ± 16 g/day in institutionalized elderly people and accounted for 16% ± 3%, 16% ± 3% and 17% ± 3% of their energy intake, respectively. Dietary protein intake ranged from 10 to 12 g at breakfast, 15 to 23 g at lunch and 24 to 31 g at dinner contributing together over 80% of daily protein intake. The majority of dietary protein consumed originated from animal sources (≥60%) with meat and dairy as dominant sources. Thus, 40% of the protein intake in community-dwelling, 37% in frail and 29% in institutionalized elderly originated from plant based protein sources with bread as the principle source. Plant based proteins contributed for >50% of protein intake at breakfast and between 34% and 37% at lunch, with bread as the main source. During dinner, >70% of the protein intake originated from animal protein, with meat as the dominant source. Daily protein intake in these older populations is mainly (>80%) provided by the three main meals, with most protein consumed during dinner. More than 60% of daily protein intake consumed is of animal origin, with plant based protein sources representing nearly 40% of total protein consumed. During dinner, >70% of the protein intake originated from animal protein, while during breakfast and lunch a large proportion of protein is derived from plant based protein sources.

Proteins for breaking barriers in lignocellulosic bioethanol production.

PubMed

Ulaganathan, Kandasamy; Goud, Burragoni S; Reddy, Mettu M; Kumar, Vanaparthi P; Balsingh, Jatoth; Radhakrishna, Surabhi

2015-01-01

Reduction in fossil fuel consumption by using alternate sources of energy is a major challenge facing mankind in the coming decades. Bioethanol production using lignocellulosic biomass is the most viable option for addressing this challenge. Industrial bioconversion of lignocellulosic biomass, though possible now, is not economically viable due to presence of barriers that escalate the cost of production. As cellulose and hemicellulose are the major constituents of terrestrial biomass, which is available in massive quantities, hydrolysis of cellulose and hemicellulose by the microorganisms are the most prominent biochemical processes happening in the earth. Microorganisms possess different categories of proteins associated with different stages of bioethanol production and a number of them are already found and characterized. Many more of these proteins need to be identified which suit the specificities needed for the bioethanol production process. Discovery of proteins with novel specificities and application of genetic engineering technologies to harvest the synergies existing between them with the aim to develop consolidated bioprocess is the major direction of research in the future. In this review, we discuss the different categories of proteins used for bioethanol production in the context of breaking the barriers existing for the economically feasible lignocellulosic bioethanol production.

Chemical composition, nutritive value, and toxicological evaluation of Bauhinia cheilantha seeds: a legume from semiarid regions widely used in folk medicine.

PubMed

Teixeira, Daniel Câmara; Farias, Davi Felipe; Carvalho, Ana Fontenele Urano; Arantes, Mariana Reis; Oliveira, José Tadeu Abreu; Sousa, Daniele Oliveira Bezerra; Pereira, Mirella Leite; Oliveira, Hermogenes David; Andrade-Neto, Manoel; Vasconcelos, Ilka Maria

2013-01-01

Among the Bauhinia species, B. cheilantha stands out for its seed protein content. However, there is no record of its nutritional value, being used in a nonsustainable way in the folk medicine and for large-scale extraction of timber. The aim of this study was to investigate the food potential of B. cheilantha seeds with emphasis on its protein quality to provide support for flora conservation and use as raw material or as prototype for the development of bioproducts with high added socioeconomic value. B. cheilantha seeds show high protein content (35.9%), reasonable essential amino acids profile, low levels of antinutritional compounds, and nutritional parameters comparable to those of legumes widely used such as soybean and cowpea. The heat treatment of the seeds as well as the protein extraction process (to obtain the protein concentrate) increased the acceptance of diets by about 100% when compared to that of raw Bc diet. These wild legume seeds can be promising alternative source of food to overcome the malnutrition problem faced by low income people adding socioeconomic value to the species.

Chemical Composition, Nutritive Value, and Toxicological Evaluation of Bauhinia cheilantha Seeds: A Legume from Semiarid Regions Widely Used in Folk Medicine

PubMed Central

Teixeira, Daniel Câmara; Farias, Davi Felipe; Carvalho, Ana Fontenele Urano; Arantes, Mariana Reis; Oliveira, José Tadeu Abreu; Sousa, Daniele Oliveira Bezerra; Pereira, Mirella Leite; Oliveira, Hermogenes David; Andrade-Neto, Manoel; Vasconcelos, Ilka Maria

2013-01-01

Among the Bauhinia species, B. cheilantha stands out for its seed protein content. However, there is no record of its nutritional value, being used in a nonsustainable way in the folk medicine and for large-scale extraction of timber. The aim of this study was to investigate the food potential of B. cheilantha seeds with emphasis on its protein quality to provide support for flora conservation and use as raw material or as prototype for the development of bioproducts with high added socioeconomic value. B. cheilantha seeds show high protein content (35.9%), reasonable essential amino acids profile, low levels of antinutritional compounds, and nutritional parameters comparable to those of legumes widely used such as soybean and cowpea. The heat treatment of the seeds as well as the protein extraction process (to obtain the protein concentrate) increased the acceptance of diets by about 100% when compared to that of raw Bc diet. These wild legume seeds can be promising alternative source of food to overcome the malnutrition problem faced by low income people adding socioeconomic value to the species. PMID:23691507

The Functional Impact of Alternative Splicing in Cancer.

PubMed

Climente-González, Héctor; Porta-Pardo, Eduard; Godzik, Adam; Eyras, Eduardo

2017-08-29

Alternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remain mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein-protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer, and some of them could potentially be considered alternative splicing drivers (AS drivers). Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Coordinate regulation of cytochrome and alternative pathway respiration in tobacco.

PubMed

Vanlerberghe, G C; McIntosh, L

1992-12-01

In suspension cells of NT1 tobacco (Nicotiana tabacum L. cv bright yellow), inhibition of the cytochrome pathway of respiration with antimycin A induced a large increase in the capacity of the alternative pathway over a period of approximately 12 h, as confirmed in both whole cells and isolated mitochondria. The increase in alternative pathway capacity required de novo RNA and protein synthesis and correlated closely with the increase of a 35-kD alternative oxidase protein. When the cytochrome pathway of intact cells was inhibited by antimycin A, respiration proceeded exclusively through the alternative pathway, reached rates significantly higher than before antimycin A addition, and was not stimulated by p-trifluoromethoxycarbonylcyanide (FCCP). When inhibition of the cytochrome pathway was relieved, alternative pathway capacity and the level of the 35-kD alternative oxidase protein declined. Respiration rate also declined and could once again be stimulated by FCCP. These observations show that the capacities of the mitochondrial electron transport pathways can be regulated in a coordinate fashion.

Evaluation of low-protein alternative diets for pond-raised hybrid catfish, Ictalurus puncatus X Ictalurus furcatus

USDA-ARS?s Scientific Manuscript database

A study was conducted to evaluate low-protein traditional or alternative diets for pond-raised hybrid catfish, Ictalurus punctatus × Ictalurus furcatus. Three 24% protein diets containing decreasing levels of soybean meal (30, 20, and 15%) and increasing levels of cottonseed meal and corn germ meal ...

40 CFR 96.212 - Changing CAIR designated representative and alternate CAIR designated representative; changes in...

Code of Federal Regulations, 2010 CFR

2010-07-01

... BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR Designated Representative for CAIR SO2 Sources § 96.212 Changing CAIR designated representative and alternate... CAIR SO2 source and the CAIR SO2 units at the source. (b) Changing alternate CAIR designated...

Alternative Fuels Data Center: Hybrid and Plug-In Electric Vehicle

Science.gov Websites

Emissions Data Sources and Assumptions Hybrid and Plug-In Electric Vehicle Emissions Data Sources and Assumptions to someone by E-mail Share Alternative Fuels Data Center: Hybrid and Plug-In Electric Vehicle Emissions Data Sources and Assumptions on Facebook Tweet about Alternative Fuels Data

Identification of protein features encoded by alternative exons using Exon Ontology.

PubMed

Tranchevent, Léon-Charles; Aubé, Fabien; Dulaurier, Louis; Benoit-Pilven, Clara; Rey, Amandine; Poret, Arnaud; Chautard, Emilie; Mortada, Hussein; Desmet, François-Olivier; Chakrama, Fatima Zahra; Moreno-Garcia, Maira Alejandra; Goillot, Evelyne; Janczarski, Stéphane; Mortreux, Franck; Bourgeois, Cyril F; Auboeuf, Didier

2017-06-01

Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named "Exon Ontology," based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information. © 2017 Tranchevent et al.; Published by Cold Spring Harbor Laboratory Press.

Purification and characterization of recombinant supersweet protein thaumatin II from tomato fruit.

PubMed

Firsov, Aleksey; Shaloiko, Lyubov; Kozlov, Oleg; Vinokurov, Leonid; Vainstein, Alexander; Dolgov, Sergey

2016-07-01

Thaumatin, a supersweet protein from the African plant katemfe (Thaumatococcus daniellii Benth.), is a promising zero-calorie sweetener for use in the food and pharmaceutical industries. Due to limited natural sources of thaumatin, its production using transgenic plants is an advantageous alternative. We report a simple protocol for purification of recombinant thaumatin II from transgenic tomato. Thaumatin was extracted from ripe tomato fruit in a low-salt buffer and purified on an SP-Sephacryl column. Recombinant thaumatin yield averaged 50 mg/kg fresh fruit. MALDI-MS analysis showed correct processing of thaumatin in tomato plants. The recombinant thaumatin was indistinguishable from the native protein in a taste test. The purified tomato-derived thaumatin had an intrinsic sweetness with a threshold value in taste tests of around 50 nM. These results demonstrate the potential of an expression system based on transgenic tomato plants for production of recombinant thaumatin for the food and pharmaceutical industries. Copyright © 2016 Elsevier Inc. All rights reserved.

Recombinant VP1 protein as a potential marker for the diagnosis of acute hepatitis A virus infection.

PubMed

da Silva Junior, Haroldo Cid; da Silva, Edimilson Domingos; Lewis-Ximenez de Souza Rodrigues, Lia Laura; Medeiros, Marco Alberto

2017-07-01

Since hepatitis A virus (HAV) production is time-consuming and expensive, the use of recombinant proteins may represent an alternative source of antigens for diagnostic purposes. The present study aimed to express, purify and evaluate the potential of recombinant VP1 protein (rVP1) as a marker for the diagnosis of acute HAV infection. The rVP1 was expressed and purified successfully from Escherichia coli. The purified rVP1 was used to establish an in-house enzyme-linked immunosorbent assay (ELISA-rVP1) for detection of IgM antibodies in sera from HAV-positive patients. For a cut-off point of 0.351, the sensitivity and specificity of ELISA-rVP1 were 100.0% and 95.0%, respectively. These results indicate that rVP1 may be a useful antigen for detection of IgM antibodies against HAV. Copyright © 2017 Elsevier B.V. All rights reserved.

An alternative easy method for antibody purification and analysis of protein-protein interaction using GST fusion proteins immobilized onto glutathione-agarose.

PubMed

Zalazar, L; Alonso, C A I; De Castro, R E; Cesari, A

2014-01-01

Immobilization of small proteins designed to perform protein-protein assays can be a difficult task. Often, the modification of reactive residues necessary for the interaction between the immobilized protein and the matrix compromises the interaction between the protein and its target. In these cases, glutathione-S-transferase (GST) is a valuable tag providing a long arm that makes the bait protein accessible to the mobile flow phase of the chromatography. In the present report, we used a GST fusion version of the 8-kDa protein serine protease inhibitor Kazal-type 3 (SPINK3) as the bait to purify anti-SPINK3 antibodies from a rabbit crude serum. The protocol for immobilization of GST-SPINK3 to glutathione-agarose beads was modified from previously reported protocols by using an alternative bifunctional cross-linker (dithiobis(succinimidyl propionate)) in a very simple procedure and by using simple buffers under physiological conditions. We concluded that the immobilized protein remained bound to the column after elution with low pH, allowing the reuse of the column for alternative uses, such as screening for other protein-protein interactions using SPINK3 as the bait.

Linking freshwater fishery management to global food security and biodiversity conservation.

PubMed

McIntyre, Peter B; Reidy Liermann, Catherine A; Revenga, Carmen

2016-10-24

Fisheries are an essential ecosystem service, but catches from freshwaters are often overlooked. Hundreds of millions of people around the world benefit from low-cost protein, recreation, and commerce provided by freshwater fisheries, particularly in regions where alternative sources of nutrition and employment are scarce. Here, we derive a gridded global map of riverine fisheries and assess its implications for biodiversity conservation, fishery sustainability, and food security. Catches increase with river discharge and human population density, and 90% of global catch comes from river basins with above-average stress levels. Fish richness and catches are positively but not causally correlated, revealing that fishing pressure is most intense in rivers where potential impacts on biodiversity are highest. Merging our catch analysis with nutritional and socioeconomic data, we find that freshwater fisheries provide the equivalent of all dietary animal protein for 158 million people. Poor and undernourished populations are particularly reliant on inland fisheries compared with marine or aquaculture sources. The spatial coincidence of productive freshwater fisheries and low food security highlights the critical role of rivers and lakes in providing locally sourced, low-cost protein. At the same time, intensive fishing in regions where rivers are already degraded by other stressors may undermine efforts to conserve biodiversity. This syndrome of poverty, nutritional deficiency, fishery dependence, and extrinsic threats to biodiverse river ecosystems underscores the high stakes for improving fishery management. Our enhanced spatial data on estimated catches can facilitate the inclusion of inland fisheries in environmental planning to protect both food security and species diversity.

Linking freshwater fishery management to global food security and biodiversity conservation

PubMed Central

McIntyre, Peter B.; Reidy Liermann, Catherine A.; Revenga, Carmen

2016-01-01

Fisheries are an essential ecosystem service, but catches from freshwaters are often overlooked. Hundreds of millions of people around the world benefit from low-cost protein, recreation, and commerce provided by freshwater fisheries, particularly in regions where alternative sources of nutrition and employment are scarce. Here, we derive a gridded global map of riverine fisheries and assess its implications for biodiversity conservation, fishery sustainability, and food security. Catches increase with river discharge and human population density, and 90% of global catch comes from river basins with above-average stress levels. Fish richness and catches are positively but not causally correlated, revealing that fishing pressure is most intense in rivers where potential impacts on biodiversity are highest. Merging our catch analysis with nutritional and socioeconomic data, we find that freshwater fisheries provide the equivalent of all dietary animal protein for 158 million people. Poor and undernourished populations are particularly reliant on inland fisheries compared with marine or aquaculture sources. The spatial coincidence of productive freshwater fisheries and low food security highlights the critical role of rivers and lakes in providing locally sourced, low-cost protein. At the same time, intensive fishing in regions where rivers are already degraded by other stressors may undermine efforts to conserve biodiversity. This syndrome of poverty, nutritional deficiency, fishery dependence, and extrinsic threats to biodiverse river ecosystems underscores the high stakes for improving fishery management. Our enhanced spatial data on estimated catches can facilitate the inclusion of inland fisheries in environmental planning to protect both food security and species diversity. PMID:27791055

An ambiguity principle for assigning protein structural domains.

PubMed

Postic, Guillaume; Ghouzam, Yassine; Chebrek, Romain; Gelly, Jean-Christophe

2017-01-01

Ambiguity is the quality of being open to several interpretations. For an image, it arises when the contained elements can be delimited in two or more distinct ways, which may cause confusion. We postulate that it also applies to the analysis of protein three-dimensional structure, which consists in dividing the molecule into subunits called domains. Because different definitions of what constitutes a domain can be used to partition a given structure, the same protein may have different but equally valid domain annotations. However, knowledge and experience generally displace our ability to accept more than one way to decompose the structure of an object-in this case, a protein. This human bias in structure analysis is particularly harmful because it leads to ignoring potential avenues of research. We present an automated method capable of producing multiple alternative decompositions of protein structure (web server and source code available at www.dsimb.inserm.fr/sword/). Our innovative algorithm assigns structural domains through the hierarchical merging of protein units, which are evolutionarily preserved substructures that describe protein architecture at an intermediate level, between domain and secondary structure. To validate the use of these protein units for decomposing protein structures into domains, we set up an extensive benchmark made of expert annotations of structural domains and including state-of-the-art domain parsing algorithms. The relevance of our "multipartitioning" approach is shown through numerous examples of applications covering protein function, evolution, folding, and structure prediction. Finally, we introduce a measure for the structural ambiguity of protein molecules.

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.

PubMed

Ghadie, Mohamed Ali; Lambourne, Luke; Vidal, Marc; Xia, Yu

2017-08-01

Alternative splicing is known to remodel protein-protein interaction networks ("interactomes"), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experimentally-determined interactions between reference proteins. Then, we construct the isoform interactome by predicting that an isoform loses an interaction if it loses the domain mediating the interaction. Our prediction framework is of high-quality when assessed by experimental data. The predicted human isoform interactome reveals extensive network remodeling by alternative splicing. Protein pairs interacting with different isoforms of the same gene tend to be more divergent in biological function, tissue expression, and disease phenotype than protein pairs interacting with the same isoforms. Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing.

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing

PubMed Central

Lambourne, Luke; Vidal, Marc

2017-01-01

Alternative splicing is known to remodel protein-protein interaction networks (“interactomes”), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experimentally-determined interactions between reference proteins. Then, we construct the isoform interactome by predicting that an isoform loses an interaction if it loses the domain mediating the interaction. Our prediction framework is of high-quality when assessed by experimental data. The predicted human isoform interactome reveals extensive network remodeling by alternative splicing. Protein pairs interacting with different isoforms of the same gene tend to be more divergent in biological function, tissue expression, and disease phenotype than protein pairs interacting with the same isoforms. Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing. PMID:28846689

Alternative light source (polilight) illumination with digital image analysis does not assist in determining the age of bruises.

PubMed

Hughes, V K; Ellis, P S; Langlois, N E I

2006-05-10

The age of a bruise may be of interest to forensic investigators. Previous research has demonstrated that an alternative light source may assist in the visualisation of faint or non-visible bruises. This project aimed to determine if an alternative light source could be utilised to assist investigators estimate the age of a bruise. Forty braises, sustained from blunt force trauma, were examined from 30 healthy subjects. The age of the bruises ranged from 2 to 231 h (mean = 74.6, median = 69.0). Alternative light source (polilight) illumination at 415 and 450 nm was used. The black and white photographs obtained were assessed using densitometry. A statistical analysis indicated that there was no correlation between time and the mean densitometry values. The alternative light source used in this study was unable to assist in determining the age of a bruise.

Artificial Affinity Proteins as Ligands of Immunoglobulins

PubMed Central

Mouratou, Barbara; Béhar, Ghislaine; Pecorari, Frédéric

2015-01-01

A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized. PMID:25647098

In vitro protein expression: an emerging alternative to cell-based approaches.

PubMed

He, Mingyue

2011-04-30

Protein expression remains a bottleneck in the production of proteins. Owing to several advantages, cell-free translation is emerging as an alternative to cell-based methods for the generation of proteins. Recent advances have led to many novel applications of cell-free systems in biotechnology, proteomics and fundamental biological research. This special issue of New Biotechnology describes recent advances in cell-free protein expression systems and their applications. Copyright © 2010 Elsevier B.V. All rights reserved.

Microseed matrix screening for optimization in protein crystallization: what have we learned?

PubMed

D'Arcy, Allan; Bergfors, Terese; Cowan-Jacob, Sandra W; Marsh, May

2014-09-01

Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems.

Microseed matrix screening for optimization in protein crystallization: what have we learned?

PubMed Central

D’Arcy, Allan; Bergfors, Terese; Cowan-Jacob, Sandra W.; Marsh, May

2014-01-01

Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems. PMID:25195878

Fault current limiter and alternating current circuit breaker

DOEpatents

Boenig, Heinrich J.

1998-01-01

A solid-state circuit breaker and current limiter for a load served by an alternating current source having a source impedance, the solid-state circuit breaker and current limiter comprising a thyristor bridge interposed between the alternating current source and the load, the thyristor bridge having four thyristor legs and four nodes, with a first node connected to the alternating current source, and a second node connected to the load. A coil is connected from a third node to a fourth node, the coil having an impedance of a value calculated to limit the current flowing therethrough to a predetermined value. Control means are connected to the thyristor legs for limiting the alternating current flow to the load under fault conditions to a predetermined level, and for gating the thyristor bridge under fault conditions to quickly reduce alternating current flowing therethrough to zero and thereafter to maintain the thyristor bridge in an electrically open condition preventing the alternating current from flowing therethrough for a predetermined period of time.

Fault current limiter and alternating current circuit breaker

DOEpatents

Boenig, H.J.

1998-03-10

A solid-state circuit breaker and current limiter are disclosed for a load served by an alternating current source having a source impedance, the solid-state circuit breaker and current limiter comprising a thyristor bridge interposed between the alternating current source and the load, the thyristor bridge having four thyristor legs and four nodes, with a first node connected to the alternating current source, and a second node connected to the load. A coil is connected from a third node to a fourth node, the coil having an impedance of a value calculated to limit the current flowing therethrough to a predetermined value. Control means are connected to the thyristor legs for limiting the alternating current flow to the load under fault conditions to a predetermined level, and for gating the thyristor bridge under fault conditions to quickly reduce alternating current flowing therethrough to zero and thereafter to maintain the thyristor bridge in an electrically open condition preventing the alternating current from flowing therethrough for a predetermined period of time. 9 figs.

Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation.

PubMed

Setzer, Mary Snow; Byler, Kendall G; Ogungbe, Ifedayo Victor; Setzer, William N

2017-01-27

Trichomoniasis, caused by the parasitic protozoan Trichomonas vaginalis, is the most common non-viral sexually-transmitted disease, and there can be severe complications from trichomoniasis. Antibiotic resistance in T. vaginalis is increasing, but there are currently no alternatives treatment options. There is a need to discover and develop new chemotherapeutic alternatives. Plant-derived natural products have long served as sources for new medicinal agents, as well as new leads for drug discovery and development. In this work, we have carried out an in silico screening of 952 antiprotozoal phytochemicals with specific protein drug targets of T. vaginalis. A total of 42 compounds showed remarkable docking properties to T. vaginalis methionine gamma-lyase (TvMGL) and to T. vaginalis purine nucleoside phosphorylase (TvPNP). The most promising ligands were polyphenolic compounds, and several of these showed docking properties superior to either co-crystallized ligands or synthetic enzyme inhibitors.

COMMUNICATION: Alternative splicing and genomic stability

NASA Astrophysics Data System (ADS)

Cahill, Kevin

2004-06-01

Alternative splicing allows an organism to make different proteins in different cells at different times, all from the same gene. In a cell that uses alternative splicing, the total length of all the exons is much shorter than in a cell that encodes the same set of proteins without alternative splicing. This economical use of exons makes genes more stable during reproduction and development because a genome with a shorter exon length is more resistant to harmful mutations. Genomic stability may be the reason why higher vertebrates splice alternatively. For a broad class of alternatively spliced genes, a formula is given for the increase in their stability.

DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation.

PubMed

You, Ronghui; Huang, Xiaodi; Zhu, Shanfeng

2018-06-06

As of April 2018, UniProtKB has collected more than 115 million protein sequences. Less than 0.15% of these proteins, however, have been associated with experimental GO annotations. As such, the use of automatic protein function prediction (AFP) to reduce this huge gap becomes increasingly important. The previous studies conclude that sequence homology based methods are highly effective in AFP. In addition, mining motif, domain, and functional information from protein sequences has been found very helpful for AFP. Other than sequences, alternative information sources such as text, however, may be useful for AFP as well. Instead of using BOW (bag of words) representation in traditional text-based AFP, we propose a new method called DeepText2GO that relies on deep semantic text representation, together with different kinds of available protein information such as sequence homology, families, domains, and motifs, to improve large-scale AFP. Furthermore, DeepText2GO integrates text-based methods with sequence-based ones by means of a consensus approach. Extensive experiments on the benchmark dataset extracted from UniProt/SwissProt have demonstrated that DeepText2GO significantly outperformed both text-based and sequence-based methods, validating its superiority. Copyright © 2018 Elsevier Inc. All rights reserved.

A Green Fluorescent Protein with Photoswitchable Emission from the Deep Sea

PubMed Central

Vogt, Alexander; D'Angelo, Cecilia; Oswald, Franz; Denzel, Andrea; Mazel, Charles H.; Matz, Mikhail V.; Ivanchenko, Sergey; Nienhaus, G. Ulrich; Wiedenmann, Jörg

2008-01-01

A colorful variety of fluorescent proteins (FPs) from marine invertebrates are utilized as genetically encoded markers for live cell imaging. The increased demand for advanced imaging techniques drives a continuous search for FPs with new and improved properties. Many useful FPs have been isolated from species adapted to sun-flooded habitats such as tropical coral reefs. It has yet remained unknown if species expressing green fluorescent protein (GFP)-like proteins also exist in the darkness of the deep sea. Using a submarine-based and -operated fluorescence detection system in the Gulf of Mexico, we discovered ceriantharians emitting bright green fluorescence in depths between 500 and 600 m and identified a GFP, named cerFP505, with bright fluorescence emission peaking at 505 nm. Spectroscopic studies showed that ∼15% of the protein bulk feature reversible ON/OFF photoswitching that can be induced by alternating irradiation with blue und near-UV light. Despite being derived from an animal adapted to essentially complete darkness and low temperatures, cerFP505 maturation in living mammalian cells at 37°C, its brightness and photostability are comparable to those of EGFP and cmFP512 from shallow water species. Therefore, our findings disclose the deep sea as a potential source of GFP-like molecular marker proteins. PMID:19018285

7 CFR Appendix A to Part 210 - Alternate Foods for Meals

Code of Federal Regulations, 2010 CFR

2010-01-01

...—Alternate Foods for Meals I. Enriched Macaroni Products with Fortified Protein 1. Schools may utilize the enriched macaroni products with fortified protein defined in paragraph 3 as a food item in meeting the meal... enriched macaroni product with fortified protein may be used to meet not more than one-half of the meat or...

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level

PubMed Central

Abascal, Federico; Ezkurdia, Iakes; Rodriguez-Rivas, Juan; Rodriguez, Jose Manuel; del Pozo, Angela; Vázquez, Jesús; Valencia, Alfonso; Tress, Michael L.

2015-01-01

Alternative splicing of messenger RNA can generate a wide variety of mature RNA transcripts, and these transcripts may produce protein isoforms with diverse cellular functions. While there is much supporting evidence for the expression of alternative transcripts, the same is not true for the alternatively spliced protein products. Large-scale mass spectroscopy experiments have identified evidence of alternative splicing at the protein level, but with conflicting results. Here we carried out a rigorous analysis of the peptide evidence from eight large-scale proteomics experiments to assess the scale of alternative splicing that is detectable by high-resolution mass spectroscopy. We find fewer splice events than would be expected: we identified peptides for almost 64% of human protein coding genes, but detected just 282 splice events. This data suggests that most genes have a single dominant isoform at the protein level. Many of the alternative isoforms that we could identify were only subtly different from the main splice isoform. Very few of the splice events identified at the protein level disrupted functional domains, in stark contrast to the two thirds of splice events annotated in the human genome that would lead to the loss or damage of functional domains. The most striking result was that more than 20% of the splice isoforms we identified were generated by substituting one homologous exon for another. This is significantly more than would be expected from the frequency of these events in the genome. These homologous exon substitution events were remarkably conserved—all the homologous exons we identified evolved over 460 million years ago—and eight of the fourteen tissue-specific splice isoforms we identified were generated from homologous exons. The combination of proteomics evidence, ancient origin and tissue-specific splicing indicates that isoforms generated from homologous exons may have important cellular roles. PMID:26061177

Time, space, and disorder in the expanding proteome universe.

PubMed

Minde, David-Paul; Dunker, A Keith; Lilley, Kathryn S

2017-04-01

Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms. © 2017 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

DOE PAGES

Brooks, Angela N.; Duff, Michael O.; May, Gemma; ...

2015-08-20

Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA sequence elements and activate or repress adjacent exons. Here, we used RNA interference and RNA-seq to identify splicing events regulated by 56 Drosophila proteins, some previously unknown to regulate splicing. Nearly all proteins affected alternative first exons, suggesting that RBPs play important roles in first exon choice. Half of the splicing events were regulated by multiple proteins, demonstrating extensive combinatorial regulation. We observed that SR and hnRNP proteins tend to act coordinately with each other, not antagonistically. We also identified a cross-regulatory network where splicing regulators affected themore » splicing of pre-mRNAs encoding other splicing regulators. In conclusion, this large-scale study substantially enhances our understanding of recent models of splicing regulation and provides a resource of thousands of exons that are regulated by 56 diverse RBPs.« less

Assessment of source-based nitrogen removal alternatives in leather tanning industry wastewater.

PubMed

Zengin, G; Olmez, T; Doğruel, S; Kabdaşli, I; Tünay, O

2002-01-01

Nitrogen is an important parameter of leather tanning wastewaters. Magnesium ammonium phosphate (MAP) precipitation is a chemical treatment alternative for ammonia removal. In this study, a detailed source-based wastewater characterisation of a bovine leather tannery was made and nitrogen speciation as well as other basic pollutant parameter values was evaluated. This evaluation has led to definition of alternatives for source-based MAP treatment. MAP precipitation experiments conducted on these alternatives have yielded over 90% ammonia removal at pH 9.5 and using stoichiometric doses. Among the alternatives tested liming-deliming and bating-washing was found to be the most advantageous providing 71% ammonia removal.

Fusion proteins as alternate crystallization paths to difficult structure problems

NASA Technical Reports Server (NTRS)

Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

1994-01-01

The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

Approaches to achieve high-level heterologous protein production in plants.

PubMed

Streatfield, Stephen J

2007-01-01

Plants offer an alternative to microbial fermentation and animal cell cultures for the production of recombinant proteins. For protein pharmaceuticals, plant systems are inherently safer than native and even recombinant animal sources. In addition, post-translational modifications, such as glycosylation, which cannot be achieved with bacterial fermentation, can be accomplished using plants. The main advantage foreseen for plant systems is reduced production costs. Plants should have a particular advantage for proteins produced in bulk, such as industrial enzymes, for which product pricing is low. In addition, edible plant tissues are well suited to the expression of vaccine antigens and pharmaceuticals for oral delivery. Three approaches have been followed to express recombinant proteins in plants: expression from the plant nuclear genome; expression from the plastid genome; and expression from plant tissues carrying recombinant plant viral sequences. The most important factor in moving plant-produced heterologous proteins from developmental research to commercial products is to ensure competitive production costs, and the best way to achieve this is to boost expression. Thus, considerable research effort has been made to increase the amount of recombinant protein produced in plants. This research includes molecular technologies to increase replication, to boost transcription, to direct transcription in tissues suited for protein accumulation, to stabilize transcripts, to optimize translation, to target proteins to subcellular locations optimal for their accumulation, and to engineer proteins to stabilize them. Other methods include plant breeding to increase transgene copy number and to utilize germplasm suited to protein accumulation. Large-scale commercialization of plant-produced recombinant proteins will require a combination of these technologies.

Optical and spectroscopic studies on tannery wastes as a possible source of organic semiconductors.

PubMed

Nashy, El-Shahat H A; Al-Ashkar, Emad; Moez, A Abdel

2012-02-01

Tanning industry produces a large quantity of solid wastes which contain hide proteins in the form of protein shavings containing chromium salts. The chromium wastes are the main concern from an environmental stand point of view, because chrome wastes posses a significant disposal problem. The present work is devoted to investigate the possibility of utilizing these wastes as a source of organic semi-conductors as an alternative method instead of the conventional ones. The chemical characterization of these wastes was determined. In addition, the Horizontal Attenuated Total Reflection (HATR) FT-IR spectroscopic analysis and optical parameters were also carried out for chromated samples. The study showed that the chromated samples had suitable absorbance and transmittance in the wavelength range (500-850 nm). Presence of chromium salt in the collagen samples increases the absorbance which improves the optical properties of the studied samples and leads to decrease the optical energy gap. The obtained optical energy gap gives an impression that the environmentally hazardous chrome shavings wastes can be utilized as a possible source of natural organic semiconductors with direct and indirect energy gap. This work opens the door to use some hazardous wastes in the manufacture of electronic devices such as IR-detectors, solar cells and also as solar cell windows. Copyright © 2011 Elsevier B.V. All rights reserved.

Improved feed protein fractionation schemes for formulating rations with the cornell net carbohydrate and protein system.

PubMed

Lanzas, C; Broderick, G A; Fox, D G

2008-12-01

Adequate predictions of rumen-degradable protein (RDP) and rumen-undegradable protein (RUP) supplies are necessary to optimize performance while minimizing losses of excess nitrogen (N). The objectives of this study were to evaluate the original Cornell Net Carbohydrate Protein System (CNCPS) protein fractionation scheme and to develop and evaluate alternatives designed to improve its adequacy in predicting RDP and RUP. The CNCPS version 5 fractionates CP into 5 fractions based on solubility in protein precipitant agents, buffers, and detergent solutions: A represents the soluble nonprotein N, B1 is the soluble true protein, B2 represents protein with intermediate rates of degradation, B3 is the CP insoluble in neutral detergent solution but soluble in acid detergent solution, and C is the unavailable N. Model predictions were evaluated with studies that measured N flow data at the omasum. The N fractionation scheme in version 5 of the CNCPS explained 78% of the variation in RDP with a root mean square prediction error (RMSPE) of 275 g/d, and 51% of the RUP variation with RMSPE of 248 g/d. Neutral detergent insoluble CP flows were overpredicted with a mean bias of 128 g/d (40% of the observed mean). The greatest improvements in the accuracy of RDP and RUP predictions were obtained with the following 2 alternative schemes. Alternative 1 used the inhibitory in vitro system to measure the fractional rate of degradation for the insoluble protein fraction in which A = nonprotein N, B1 = true soluble protein, B2 = insoluble protein, C = unavailable protein (RDP: R(2) = 0.84 and RMSPE = 167 g/d; RUP: R(2) = 0.61 and RMSPE = 209 g/d), whereas alternative 2 redefined A and B1 fractions as the non-amino-N and amino-N in the soluble fraction respectively (RDP: R(2) = 0.79 with RMSPE = 195 g/d and RUP: R(2) = 0.54 with RMSPE = 225 g/d). We concluded that implementing alternative 1 or 2 will improve the accuracy of predicting RDP and RUP within the CNCPS framework.

Potential Use of Food Protein-Derived Peptides in the Treatment of Inflammatory Diseases.

PubMed

Santiago-Lopez, Lourdes; Gonzalez-Cordova, Aaron F; Hernandez-Mendoza, Adrian; Vallejo-Cordoba, Belinda

2017-01-01

In recent years, major developments in the field of inflammatory pathophysiology have clearly shown that arthritis, diabetes, intestinal bowel diseases, and obesity, which affect many people around the world, are essentially inflammatory in nature. Different anti-inflammatory drugs have been used to treat these conditions. Some people are able to take these drugs without difficulty, yet others experience negative side effects. Hence, the search for new, natural anti-inflammatory alternatives has rapidly increased in recent years. Evidence has shown that food protein-derived peptides may be one alternative for treating inflammatory diseases. Peptides are encrypted in food proteins, can be released under hydrolysis conditions, and do not cause adverse effects. Despite limited information on the mechanism of action of peptides, in vitro and animal model studies have demonstrated their potential anti-inflammatory activity. Several in vitro studies have demonstrated that peptides can inhibit different pathways of inflammation processes such as that of the nuclear factor kappalight- chain of activated B cells (NF-κB). They can also induce the production of nitric oxide synthase (iNOs) and c-Jun N-terminal kinases (JNK) as well as influence PepT1 and CaRS, the transporters of peptides to the gastrointestinal tract that are responsible for the absorption of dietary peptides in the intestine. However, contradictory evidence has been reported in clinical assays. Hence, in this review, we present the latest research on the anti-inflammatory activity of food protein-derived peptides and provide future perspectives on the use of peptides as potential natural sources of therapeutic treatments. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Expanded subgenomic mRNA transcriptome and coding capacity of a nidovirus

PubMed Central

Di, Han; Madden, Joseph C.; Morantz, Esther K.; Tang, Hsin-Yao; Graham, Rachel L.; Baric, Ralph S.

2017-01-01

Members of the order Nidovirales express their structural protein ORFs from a nested set of 3′ subgenomic mRNAs (sg mRNAs), and for most of these ORFs, a single genomic transcription regulatory sequence (TRS) was identified. Nine TRSs were previously reported for the arterivirus Simian hemorrhagic fever virus (SHFV). In the present study, which was facilitated by next-generation sequencing, 96 SHFV body TRSs were identified that were functional in both infected MA104 cells and macaque macrophages. The abundance of sg mRNAs produced from individual TRSs was consistent over time in the two different cell types. Most of the TRSs are located in the genomic 3′ region, but some are in the 5′ ORF1a/1b region and provide alternative sources of nonstructural proteins. Multiple functional TRSs were identified for the majority of the SHFV 3′ ORFs, and four previously identified TRSs were found not to be the predominant ones used. A third of the TRSs generated sg mRNAs with variant leader–body junction sequences. Sg mRNAs encoding E′, GP2, or ORF5a as their 5′ ORF as well as sg mRNAs encoding six previously unreported alternative frame ORFs or 14 previously unreported C-terminal ORFs of known proteins were also identified. Mutation of the start codon of two C-terminal ORFs in an infectious clone reduced virus yield. Mass spectrometry detected one previously unreported protein and suggested translation of some of the C-terminal ORFs. The results reveal the complexity of the transcriptional regulatory mechanism and expanded coding capacity for SHFV, which may also be characteristic of other nidoviruses. PMID:29073030

48 CFR 715.370 - Alternative source selection procedures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... selection procedures. 715.370 Section 715.370 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Source Selection 715.370 Alternative source selection procedures. The following selection procedures may be used, when...

TGFβ1-mediated PI3K/Akt and p38 MAP kinase dependent alternative splicing of fibronectin extra domain A in human podocyte culture.

PubMed

Madne, Tarunkumar Hemraj; Dockrell, Mark Edward Carl

2018-04-30

Alternative splicing is an important gene regulation process to distribute proteins in health and diseases. Extra Domain A+ Fibronectin (EDA+Fn) is an alternatively spliced form of fibronectin (Fn) protein, present in the extra cellular matrix (ECM) and a recognised marker of various pathologies. TGFβ1 has been shown to induce alternative splicing of EDA+Fn in many cell types. Podocytes are spectacular cell type and play a key role in filtration and synthesise ECM proteins in renal physiology and pathology. In our previous study we have demonstrated expression and alternative splicing of EDA+Fn in basal condition in human podocytes culture. TGFβ1 further induced the basal expression and alternative splicing of EDA+Fn through Alk5 receptor and SR proteins. In this study, we have investigated TGFβ1 mediated signalling involved in alternative splicing of EDA+Fn in human podocytes. We have performed western blotting to characterise the expression of the EDA+Fn protein and other signalling proteins and RT-PCR to look for signalling pathways involved in regulation of alternative splicing of EDA+Fn in conditionally immortalised human podocytes culture.We have used TGFβ1 as a stimulator and SB431542, SB202190 and LY294002 for inhibitory studies. In this work, we have demonstrated in human podocytes culture TGFβ1 2.5ng/ml induced phosphorylation of Smad1/5/8, Smad2 and Smad3 via the ALK5 receptor. TGFβ1 significantly induced the PI3K/Akt pathway and the PI3K/Akt pathway inhibitor LY294002 significantly downregulated basal as well as TGFβ1 induced alternative splicing of EDA+Fn in human podocytes. In addition to this, TGFβ1 significantly induced the p38 MAP kinase signalling pathway and p38 MAP kinase signalling pathway inhibitor SB202190 downregulated the TGFβ1-mediated alternative splicing of EDA+Fn in human podocytes. The results with PI3K and p38 MAP kinase signalling pathway suggest that inhibiting PI3K signalling pathway downregulated the basal alternative splicing of EDA+Fn in human podocytes and its the inhibition of p38 Map Kinase signalling pathway which had specifically downregulated the TGFβ1 mediated alternative splicing of EDA+Fn in human podocytes culture. Activation of TGFβ1-mediated Smad1/5/8 via Alk5 receptor suggests that TGFβ1 signalling pathway involved Alk5/Alk1 receptor axis signalling in human podocytes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiser, C.; McIntosh, L.

Mitochondria from 24-hour-aged potato slices possess an alternative path capacity and a 36kD protein not present in fresh potato mitochondria. This 36kD protein was identified by a monoclonal antibody against the Sauromatum guttatum alternative oxidase. These results suggest de novo synthesis of the 36kD protein during the aging process. To investigate this phenomenon, a clone containing a potato alternative oxidase gene was isolated from a cDNA library using the S. guttatum gene as a probe. This clone shows areas of high homology to the S. guttatum gene. Norther blots of RNA from fresh and 24-hour-aged potato slices are being probedmore » with the potato gene to examine its expression in relation to the appearance of the 36kD protein.« less

Good response of low-fat/high-protein diet in a patient with chyluria.

PubMed

Triffoni-Melo, Andresa T; Diez-Garcia, Rosa Wanda; Barros Silva, Gyl Eanes; Garcia Caldas, Fernando de Freitas; Wichert-Ana, Lauro; Corte Denardi, Rafaela; Kato, Mery; Júnior Lucca, Leandro; Dantas, Márcio

2014-04-01

Chyluria is an inappropriate urinary excretion of chyle that turns the urine milky. A nutritional approach based on low-fat/high-protein content diet associated or not with medium-chain triglyceride (MCT) showed to be an efficient conservative treatment to improve the milky urine appearance in a patient with chyluria. A 30-year-old female patient was admitted with chyluria of unknown etiology. An ureteropyeloscopy revealed a single lesion in each kidney, both with linear aspect and measuring 5 mm in extension. These lesions were located close to the renal papillae and were leaking a cloudy and milky fluid. Both lesions were laser cauterized followed by improvement of the milky urine. However, the chyluria relapsed after few months and a low-fat/high-protein content diet with 10 g of soybean oil to meet the requirements essential fatty acids (EFA) and with MCT from coconut oil as alternative to prepare foods was started. Few weeks later the patient returned reporting consistent improvement of the milky urine appearance related with the use of the diet. However since the diet was tasteless and time consuming to prepare, she reported low compliance to diet with MCT and the milky urine relapsed. The MCT was discontinued and the diet with EFA source was maintained with better compliance. Since then the chyluria remains in remission. In conclusion, the dramatic improvement of the milky urine with low-fat/high-protein diet with EFA source observed in our patient demonstrates that this nutritional approach is efficient with fast results to treat chyluria during long term.

Protein - Which is Best?

PubMed

Hoffman, Jay R; Falvo, Michael J

2004-09-01

Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids), whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function) are also reviewed. Key PointsHigher protein needs are seen in athletic populations.Animal proteins is an important source of protein, however potential health concerns do exist from a diet of protein consumed from primarily animal sources.With a proper combination of sources, vegetable proteins may provide similar benefits as protein from animal sources.Casein protein supplementation may provide the greatest benefit for increases in protein synthesis for a prolonged duration.

Protein – Which is Best?

PubMed Central

Hoffman, Jay R.; Falvo, Michael J.

2004-01-01

Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids), whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function) are also reviewed. Key Points Higher protein needs are seen in athletic populations. Animal proteins is an important source of protein, however potential health concerns do exist from a diet of protein consumed from primarily animal sources. With a proper combination of sources, vegetable proteins may provide similar benefits as protein from animal sources. Casein protein supplementation may provide the greatest benefit for increases in protein synthesis for a prolonged duration. PMID:24482589

40 CFR 142.14 - Records kept by States.

Code of Federal Regulations, 2012 CFR

2012-07-01

... disinfectant concentration at alternate locations if it also has ground water source(s); (5) Section 141.74(c... residual concentration at alternate locations if it also has ground water source(s); (7) Section 141.75(a... provided to the system. (3) Section 141.71(b)(2)—Any decision that a public water system's watershed...

Assessment of alternative power sources for mobile mining machinery

NASA Technical Reports Server (NTRS)

Cairelli, J. E.; Tomazic, W. A.; Evans, D. G.; Klann, J. L.

1981-01-01

Alternative mobile power sources for mining applications were assessed. A wide variety of heat engines and energy systems was examined as potential alternatives to presently used power systems. The present mobile power systems are electrical trailing cable, electrical battery, and diesel - with diesel being largely limited in the United States to noncoal mines. Each candidate power source was evaluated for the following requirements: (1) ability to achieve the duty cycle; (2) ability to meet Government regulations; (3) availability (production readiness); (4) market availability; and (5) packaging capability. Screening reduced the list of candidates to the following power sources: diesel, stirling, gas turbine, rankine (steam), advanced electric (batteries), mechanical energy storage (flywheel), and use of hydrogen evolved from metal hydrides. This list of candidates is divided into two classes of alternative power sources for mining applications, heat engines and energy storage systems.

Assessment of alternative power sources for mobile mining machinery

NASA Astrophysics Data System (ADS)

Cairelli, J. E.; Tomazic, W. A.; Evans, D. G.; Klann, J. L.

1981-12-01

Alternative mobile power sources for mining applications were assessed. A wide variety of heat engines and energy systems was examined as potential alternatives to presently used power systems. The present mobile power systems are electrical trailing cable, electrical battery, and diesel - with diesel being largely limited in the United States to noncoal mines. Each candidate power source was evaluated for the following requirements: (1) ability to achieve the duty cycle; (2) ability to meet Government regulations; (3) availability (production readiness); (4) market availability; and (5) packaging capability. Screening reduced the list of candidates to the following power sources: diesel, stirling, gas turbine, rankine (steam), advanced electric (batteries), mechanical energy storage (flywheel), and use of hydrogen evolved from metal hydrides. This list of candidates is divided into two classes of alternative power sources for mining applications, heat engines and energy storage systems.

48 CFR 715.370 - Alternative source selection procedures.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false Alternative source selection procedures. 715.370 Section 715.370 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Source Selection 715...

Physical Principles of Discrete Hierarchies Formation in Protein Macromolecules

NASA Astrophysics Data System (ADS)

Malyshko, E. V.; Tverdislov, V. A.

2017-11-01

A model for chiral periodicity with alternating chiral sense in hierarchies of protein and nucleic acid structures is proposed and substantiated. Regular alternation of the chirality sense is revealed in transitions from the lowest to higher levels of structural-functional organization in proteins where it is L-D-L-D. The stratification principle combines the ideas of biomacromolecules folding and molecular biological machines.

An ambiguity principle for assigning protein structural domains

PubMed Central

Postic, Guillaume; Ghouzam, Yassine; Chebrek, Romain; Gelly, Jean-Christophe

2017-01-01

Ambiguity is the quality of being open to several interpretations. For an image, it arises when the contained elements can be delimited in two or more distinct ways, which may cause confusion. We postulate that it also applies to the analysis of protein three-dimensional structure, which consists in dividing the molecule into subunits called domains. Because different definitions of what constitutes a domain can be used to partition a given structure, the same protein may have different but equally valid domain annotations. However, knowledge and experience generally displace our ability to accept more than one way to decompose the structure of an object—in this case, a protein. This human bias in structure analysis is particularly harmful because it leads to ignoring potential avenues of research. We present an automated method capable of producing multiple alternative decompositions of protein structure (web server and source code available at www.dsimb.inserm.fr/sword/). Our innovative algorithm assigns structural domains through the hierarchical merging of protein units, which are evolutionarily preserved substructures that describe protein architecture at an intermediate level, between domain and secondary structure. To validate the use of these protein units for decomposing protein structures into domains, we set up an extensive benchmark made of expert annotations of structural domains and including state-of-the-art domain parsing algorithms. The relevance of our “multipartitioning” approach is shown through numerous examples of applications covering protein function, evolution, folding, and structure prediction. Finally, we introduce a measure for the structural ambiguity of protein molecules. PMID:28097215

How Much and What Type of Protein Should a Critically Ill Patient Receive?

PubMed

Ochoa Gautier, Juan B; Martindale, Robert G; Rugeles, Saúl J; Hurt, Ryan T; Taylor, Beth; Heyland, Daren K; McClave, Stephen A

2017-04-01

Protein loss, manifested as loss of muscle mass, is observed universally in all critically ill patients. Depletion of muscle mass is associated with impaired function and poor outcomes. In extreme cases, protein malnutrition is manifested by respiratory failure, lack of wound healing, and immune dysfunction. Protecting muscle loss focused initially on meeting energy requirements. The assumption was that protein was being used (through oxidation) as an energy source. In healthy individuals, small amounts of glucose (approximately 400 calories) protect muscle loss and decrease amino acid oxidation (protein-sparing effect of glucose). Despite expectations of the benefits, the high provision of energy (above basal energy requirements) through the delivery of nonprotein calories has failed to demonstrate a clear benefit at curtailing protein loss. The protein-sparing effect of glucose is not clearly observed during illness. Increasing protein delivery beyond the normal nutrition requirements (0.8 g/k/d) has been investigated as an alternative solution. Over a dozen observational studies in critically ill patients suggest that higher protein delivery is beneficial at protecting muscle mass and associated with improved outcomes (decrease in mortality). Not surprisingly, new Society of Critical Care Medicine/American Society for Parenteral and Enteral Nutrition guidelines and expert recommendations suggest higher protein delivery (>1.2 g/kg/d) for critically ill patients. This article provides an introduction to the concepts that delineate the basic principles of modern medical nutrition therapy as it relates to the goal of achieving an optimal management of protein metabolism during critical care illness, highlighting successes achieved so far but also placing significant challenges limiting our success in perspective.

Pachyrhizus ahipa (Wedd.) Parodi roots and flour: Biochemical and functional characteristics.

PubMed

Doporto, María C; Mugridge, Alicia; García, María A; Viña, Sonia Z

2011-06-15

Ahipa roots' chemical composition and physiological parameters were characterised; ahipa flour preparation procedures were selected and the chemical composition and functional properties of these products were studied. Ahipa roots and flour can be considered alternative food sources of gluten-free starch, with a considerable contribution of protein, fibre and minerals, such as potassium, calcium and iron. The grating process for ahipa flour production required a pressing step (AFGP) and the recovery of the starch leached. The slicing procedure (AFS) was simpler and the resulting product showed higher contents of potassium, magnesium, calcium and protein than did AFGP, which showed lower sodium and higher acid detergent fibre contents, together with lower gelatinisation temperature. Both flours differed in terms of α-amylase activity and swelling power, characteristics that may condition their specific applications, such as the incorporation of these flours as gluten-free functional food ingredients. Copyright © 2010 Elsevier Ltd. All rights reserved.

Light-driven solute transport in Halobacterium halobium

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1979-01-01

The cell membrane of Halobacterium halobium exhibits differential regions which contain crystalline arrays of a single kind of protein, termed bacteriorhodopsin. This bacterial retinal-protein complex resembles the visual pigment and, after the absorption of protons, translocates H(+) across the cell membrane, leading to an electrochemical gradient for protons between the inside and the outside of the cell. Thus, light is an alternate source of energy in these bacteria, in addition to terminal oxidation. The paper deals with work on light-driven transport in H. halobium with cell envelope vesicles. The discussion covers light-driven movements of H(+), Na(+), and K(+); light-driven amino acid transport; and apparent allosteric control of amino acid transport. The scheme of energy coupling in H. halobium vesicles appears simple, its quantitative details are quite complex and reveal regulatory phenomena. More knowledge is required of the way the coupling components are regulated by the ion gradients present.

ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes.

PubMed

Engqvist, Martin K M; Nielsen, Jens

2015-08-21

The Ambiguous Nucleotide Tool (ANT) is a desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms. The Python source code for ANT is freely distributed so that it may be used without restriction, modified, and incorporated in other software or custom data pipelines.

The Potential for Microalgae as Bioreactors to Produce Pharmaceuticals

PubMed Central

Yan, Na; Fan, Chengming; Chen, Yuhong; Hu, Zanmin

2016-01-01

As photosynthetic organisms, microalgae can efficiently convert solar energy into biomass. Microalgae are currently used as an important source of valuable natural biologically active molecules, such as carotenoids, chlorophyll, long-chain polyunsaturated fatty acids, phycobiliproteins, carotenoids and enzymes. Significant advances have been achieved in microalgae biotechnology over the last decade, and the use of microalgae as bioreactors for expressing recombinant proteins is receiving increased interest. Compared with the bioreactor systems that are currently in use, microalgae may be an attractive alternative for the production of pharmaceuticals, recombinant proteins and other valuable products. Products synthesized via the genetic engineering of microalgae include vaccines, antibodies, enzymes, blood-clotting factors, immune regulators, growth factors, hormones, and other valuable products, such as the anticancer agent Taxol. In this paper, we briefly compare the currently used bioreactor systems, summarize the progress in genetic engineering of microalgae, and discuss the potential for microalgae as bioreactors to produce pharmaceuticals. PMID:27322258

Mechanisms of Bone Mineralization and Effects of Mechanical Loading

NASA Technical Reports Server (NTRS)

Babich, Michael

1996-01-01

The data suggest that PTH and PKC inhibit nodule formation, and that alternative energy sources are utilized by osteoblasts in the process of mineralization. The conditions and techniques to grow, fix, photograph, and measure bone mineralization in vitro were defined. The results are presently in preliminary form and require further assessment as follows; quantitate the surface area of nodules + treatments via computer-aided image analysis; use PTH + inhibitors of signaling pathways to determine the mechanism of nodule formation; determine how protein kinase C is involved as a promotor of nodule formation; cell proliferation vs. cell death affected by modulation of signal transduction (i.e., PTH, enzyme inhibitors and activators); identify mRNA induced or decreased in response to PTH and signaling modulators that encode proteins that regulate cell morphology, proliferation, and nodule formation. Therefore, several follow-up studies between the laboratories at NASA-Ames Research Center and my laboratory at the University of Illinois have been initiated.

Biology and Industrial Applications of Chlorella: Advances and Prospects.

PubMed

Liu, Jin; Chen, Feng

2016-01-01

Chlorella represents a group of eukaryotic green microalgae that has been receiving increasing scientific and commercial interest. It possesses high photosynthetic ability and is capable of growing robustly under mixotrophic and heterotrophic conditions as well. Chlorella has long been considered as a source of protein and is now industrially produced for human food and animal feed. Chlorella is also rich in oil, an ideal feedstock for biofuels. The exploration of biofuel production by Chlorella is underway. Chlorella has the ability to fix carbon dioxide efficiently and to remove nutrients of nitrogen and phosphorous, making it a good candidate for greenhouse gas biomitigation and wastewater bioremediation. In addition, Chlorella shows potential as an alternative expression host for recombinant protein production, though challenges remain to be addressed. Currently, omics analyses of certain Chlorella strains are being performed, which will help to unravel the biological implications of Chlorella and facilitate the future exploration of industrial applications.

Quinoa (Chenopodium quinoa Willd.): composition, chemistry, nutritional, and functional properties.

PubMed

Abugoch James, Lilian E

2009-01-01

Quinoa (Chenopodium quinoa Willd.), which is considered a pseudocereal or pseudograin, has been recognized as a complete food due to its protein quality. It has remarkable nutritional properties; not only from its protein content (15%) but also from its great amino acid balance. It is an important source of minerals and vitamins, and has also been found to contain compounds like polyphenols, phytosterols, and flavonoids with possible nutraceutical benefits. It has some functional (technological) properties like solubility, water-holding capacity (WHC), gelation, emulsifying, and foaming that allow diversified uses. Besides, it has been considered an oil crop, with an interesting proportion of omega-6 and a notable vitamin E content. Quinoa starch has physicochemical properties (such as viscosity, freeze stability) which give it functional properties with novel uses. Quinoa has a high nutritional value and has recently been used as a novel functional food because of all these properties; it is a promising alternative cultivar.

Impact of alternative energy forms on public utilities

NASA Technical Reports Server (NTRS)

Keith, F. W., Jr.

1977-01-01

The investigation of alternative energy sources by the electric utility industry is discussed. Research projects are reviewed in each of the following areas; solar energy, wind energy conversion, photosynthesis of biomass, ocean thermal energy conversion, geothermal energy, fusion, and the environmental impact of alternative energy sources.

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

PubMed Central

Briese, Michael; Zarnack, Kathi; Luscombe, Nicholas M.; Rot, Gregor; Zupan, Blaž; Curk, Tomaž; Ule, Jernej

2010-01-01

The regulation of alternative splicing involves interactions between RNA-binding proteins and pre-mRNA positions close to the splice sites. T-cell intracellular antigen 1 (TIA1) and TIA1-like 1 (TIAL1) locally enhance exon inclusion by recruiting U1 snRNP to 5′ splice sites. However, effects of TIA proteins on splicing of distal exons have not yet been explored. We used UV-crosslinking and immunoprecipitation (iCLIP) to find that TIA1 and TIAL1 bind at the same positions on human RNAs. Binding downstream of 5′ splice sites was used to predict the effects of TIA proteins in enhancing inclusion of proximal exons and silencing inclusion of distal exons. The predictions were validated in an unbiased manner using splice-junction microarrays, RT-PCR, and minigene constructs, which showed that TIA proteins maintain splicing fidelity and regulate alternative splicing by binding exclusively downstream of 5′ splice sites. Surprisingly, TIA binding at 5′ splice sites silenced distal cassette and variable-length exons without binding in proximity to the regulated alternative 3′ splice sites. Using transcriptome-wide high-resolution mapping of TIA-RNA interactions we evaluated the distal splicing effects of TIA proteins. These data are consistent with a model where TIA proteins shorten the time available for definition of an alternative exon by enhancing recognition of the preceding 5′ splice site. Thus, our findings indicate that changes in splicing kinetics could mediate the distal regulation of alternative splicing. PMID:21048981

A Kernel for Open Source Drug Discovery in Tropical Diseases

PubMed Central

Ortí, Leticia; Carbajo, Rodrigo J.; Pieper, Ursula; Eswar, Narayanan; Maurer, Stephen M.; Rai, Arti K.; Taylor, Ginger; Todd, Matthew H.; Pineda-Lucena, Antonio; Sali, Andrej; Marti-Renom, Marc A.

2009-01-01

Background Conventional patent-based drug development incentives work badly for the developing world, where commercial markets are usually small to non-existent. For this reason, the past decade has seen extensive experimentation with alternative R&D institutions ranging from private–public partnerships to development prizes. Despite extensive discussion, however, one of the most promising avenues—open source drug discovery—has remained elusive. We argue that the stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. Historically, open source software collaborations have almost never succeeded without such “kernels”. Methodology/Principal Findings Here, we use a computational pipeline for: (i) comparative structure modeling of target proteins, (ii) predicting the localization of ligand binding sites on their surfaces, and (iii) assessing the similarity of the predicted ligands to known drugs. Our kernel currently contains 143 and 297 protein targets from ten pathogen genomes that are predicted to bind a known drug or a molecule similar to a known drug, respectively. The kernel provides a source of potential drug targets and drug candidates around which an online open source community can nucleate. Using NMR spectroscopy, we have experimentally tested our predictions for two of these targets, confirming one and invalidating the other. Conclusions/Significance The TDI kernel, which is being offered under the Creative Commons attribution share-alike license for free and unrestricted use, can be accessed on the World Wide Web at http://www.tropicaldisease.org. We hope that the kernel will facilitate collaborative efforts towards the discovery of new drugs against parasites that cause tropical diseases. PMID:19381286

Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations”

PubMed Central

Ollikainen, Noah; Smith, Colin A.; Fraser, James S.; Kortemme, Tanja

2013-01-01

Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remains experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side chain conformations, native side chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid co-variation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. PMID:23422426

Pre-mRNA mis-splicing of sarcomeric genes in heart failure.

PubMed

Zhu, Chaoqun; Chen, Zhilong; Guo, Wei

2017-08-01

Pre-mRNA splicing is an important biological process that allows production of multiple proteins from a single gene in the genome, and mainly contributes to protein diversity in eukaryotic organisms. Alternative splicing is commonly governed by RNA binding proteins to meet the ever-changing demands of the cell. However, the mis-splicing may lead to human diseases. In the heart of human, mis-regulation of alternative splicing has been associated with heart failure. In this short review, we focus on alternative splicing of sarcomeric genes and review mis-splicing related heart failure with relatively well studied Sarcomeric genes and splicing mechanisms with identified regulatory factors. The perspective of alternative splicing based therapeutic strategies in heart failure has also been discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Deciphering how LIP2 and POX2 promoters can optimally regulate recombinant protein production in the yeast Yarrowia lipolytica.

PubMed

Sassi, Hosni; Delvigne, Frank; Kar, Tambi; Nicaud, Jean-Marc; Coq, Anne-Marie Crutz-Le; Steels, Sebastien; Fickers, Patrick

2016-09-20

In recent years, the non-conventional model yeast species Yarrowia lipolytica has received much attention because it is a useful cell factory for producing recombinant proteins. In this species, expression vectors involving LIP2 and POX2 promoters have been developed and used successfully for protein production at yields similar to or even higher than those of other cell factories, such as Pichia pastoris. However, production processes involving these promoters can be difficult to manage, especially if carried out at large scales in fed-batch bioreactors, because they require hydrophobic inducers, such as oleic acid or methyl oleate. Thus, the challenge has become to reduce loads of hydrophobic substrates while simultaneously promoting recombinant protein production. One possible solution is to replace a portion of the inducer with a co-substrate that can serve as an alternative energy source. However, implementing such an approach would require detailed knowledge of how carbon sources impact promoter regulation, which is surprisingly still lacking for the LIP2 and POX2 promoters. This study's aim was thus to better characterize promoter regulation and cell metabolism in Y. lipolytica cultures grown in media supplemented with different carbon sources. pPOX2 induction could be detected when glucose or glycerol was used as sole carbon source, which meant these carbon source could not prevent promoter induction. In addition, when a mixture of glucose and oleic acid was used in complex medium, pPOX2 induction level was lower that that of pLIP2. In contrast, pLIP2 induction was absent when glucose was present in the culture medium, which meant that cell growth could occur without any recombinant gene expression. When a 40/60 mixture of glucose and oleic acid (w/w) was used, a tenfold increase in promoter induction, as compared to when an oleic-acid-only medium was observed. It was also clear that individual cells were adapting metabolically to use both glucose and oleic acid. Indeed, no distinct subpopulations that specialized on glucose versus oleic acid were observed; such an outcome would have led to producer and non-producer phenotypes. In medium containing both glucose and oleic acid, cells tended to directly metabolize oleic acid instead of storing it in lipid bodies. This study found that pLIP2 is a promoter of choice as compared to pPOX2 to drive gene expression for recombinant protein production by Y. lipolytica used as cell factory.

Climatic variability and plant food distribution in Pleistocene Europe: Implications for Neanderthal diet and subsistence

NASA Astrophysics Data System (ADS)

Hardy, Bruce L.

2010-03-01

Contrary to their cold-adapted image, Neanderthals inhabited Pleistocene Europe during a time of great climatic fluctuation with temperatures ranging from as warm as present-day during the last interglacial to as cold as those of the last glacial maximum. Cold-adapted Neanderthals are similarly most often associated with the exploitation of large mammals who are themselves cold-adapted (mammoth, bison, reindeer, etc.). Cold, high-latitude environments are typically seen as lacking in plants generally and in plant foods in particular. Plant foods are therefore usually ignored and Neanderthals are increasingly being viewed as top carnivores who derived the vast majority of their diet from meat. Support for this hypothesis comes largely from stable isotope analysis which tracks only the protein portion of the diet. Diets high in lean meat largely fulfill micronutrient needs but can pose a problem at the macronutrient level. Lean meat can compose no more than 35% of dietary energy before a protein ceiling is reached. Exceeding the protein ceiling can have detrimental physiological effects on the individual. Neanderthals would have needed energy from alternative sources, particularly when animals are fat-depleted and lean meat intake is high. Underground storage organs (USOs) of plants offer one such source, concentrating carbohydrates and energy. USOs could also provide an important seasonal energy source since they are at their maximum energy storage in late fall/winter. Although Paleolithic sites are increasingly yielding plant remains, their presence is rare and they are often given only passing mention in Neanderthal dietary reconstructions. The complexity and number of potential wild plant foods, however, defies easy discussion. Native European wild edible plants with starchy USOs would have been potentially available throughout the Neanderthal range, even during the coldest periods of the Late Pleistocene.

Seed Dormancy in Arabidopsis Requires Self-Binding Ability of DOG1 Protein and the Presence of Multiple Isoforms Generated by Alternative Splicing.

PubMed

Nakabayashi, Kazumi; Bartsch, Melanie; Ding, Jia; Soppe, Wim J J

2015-12-01

The Arabidopsis protein DELAY OF GERMINATION 1 (DOG1) is a key regulator of seed dormancy, which is a life history trait that determines the timing of seedling emergence. The amount of DOG1 protein in freshly harvested seeds determines their dormancy level. DOG1 has been identified as a major dormancy QTL and variation in DOG1 transcript levels between accessions contributes to natural variation for seed dormancy. The DOG1 gene is alternatively spliced. Alternative splicing increases the transcriptome and proteome diversity in higher eukaryotes by producing transcripts that encode for proteins with altered or lost function. It can also generate tissue specific transcripts or affect mRNA stability. Here we suggest a different role for alternative splicing of the DOG1 gene. DOG1 produces five transcript variants encoding three protein isoforms. Transgenic dog1 mutant seeds expressing single DOG1 transcript variants from the endogenous DOG1 promoter did not complement because they were non-dormant and lacked DOG1 protein. However, transgenic plants overexpressing single DOG1 variants from the 35S promoter could accumulate protein and showed complementation. Simultaneous expression of two or more DOG1 transcript variants from the endogenous DOG1 promoter also led to increased dormancy levels and accumulation of DOG1 protein. This suggests that single isoforms are functional, but require the presence of additional isoforms to prevent protein degradation. Subsequently, we found that the DOG1 protein can bind to itself and that this binding is required for DOG1 function but not for protein accumulation. Natural variation for DOG1 binding efficiency was observed among Arabidopsis accessions and contributes to variation in seed dormancy.

A role for SR proteins in plant stress responses.

PubMed

Duque, Paula

2011-01-01

Members of the SR (serine/arginine-rich) protein gene family are key players in the regulation of alternative splicing, an important means of generating proteome diversity and regulating gene expression. In plants, marked changes in alternative splicing are induced by a wide variety of abiotic stresses, suggesting a role for this highly versatile gene regulation mechanism in the response to environmental cues. In support of this notion, the expression of plant SR proteins is stress-regulated at multiple levels, with environmental signals controlling their own alternative splicing patterns, phosphorylation status and subcellular distribution. Most importantly, functional links between these RNA-binding proteins and plant stress tolerance are beginning to emerge, including a role in the regulation of abscisic acid (ABA) signaling. Future identification of the physiological mRNA targets of plant SR proteins holds much promise for the elucidation of the molecular mechanisms underlying their role in the response to abiotic stress.

A role for SR proteins in plant stress responses

PubMed Central

2011-01-01

Members of the SR (serine/arginine-rich) protein gene family are key players in the regulation of alternative splicing, an important means of generating proteome diversity and regulating gene expression. In plants, marked changes in alternative splicing are induced by a wide variety of abiotic stresses, suggesting a role for this highly versatile gene regulation mechanism in the response to environmental cues. In support of this notion, the expression of plant SR proteins is stress-regulated at multiple levels, with environmental signals controlling their own alternative splicing patterns, phosphorylation status and subcellular distribution. Most importantly, functional links between these RNA-binding proteins and plant stress tolerance are beginning to emerge, including a role in the regulation of abscisic acid (ABA) signaling. Future identification of the physiological mRNA targets of plant SR proteins holds much promise for the elucidation of the molecular mechanisms underlying their role in the response to abiotic stress. PMID:21258207

Autophagic pathways and metabolic stress

PubMed Central

Kaushik, S.; Singh, R.; Cuervo, A. M.

2014-01-01

Autophagy is an essential intracellular process that mediates degradation of intracellular proteins and organelles in lysosomes. Autophagy was initially identified for its role as alternative source of energy when nutrients are scarce but, in recent years, a previously unknown role for this degradative pathway in the cellular response to stress has gained considerable attention. In this review, we focus on the novel findings linking autophagic function with metabolic stress resulting either from proteins or lipids. Proper autophagic activity is required in the cellular defense against proteotoxicity arising in the cytosol and also in the endoplasmic reticulum, where a vast amount of proteins are synthesized and folded. In addition, autophagy contributes to mobilization of intracellular lipid stores and may be central to lipid metabolism in certain cellular conditions. In this review, we focus on the interrelation between autophagy and different types of metabolic stress, specifically the stress resulting from the presence of misbehaving proteins within the cytosol or in the endoplasmic reticulum and the stress following a lipogenic challenge. We also comment on the consequences that chronic exposure to these metabolic stressors could have on autophagic function and on how this effect may underlie the basis of some common metabolic disorders. PMID:21029294

Autophagic pathways and metabolic stress.

PubMed

Kaushik, S; Singh, R; Cuervo, A M

2010-10-01

Autophagy is an essential intracellular process that mediates degradation of intracellular proteins and organelles in lysosomes. Autophagy was initially identified for its role as alternative source of energy when nutrients are scarce but, in recent years, a previously unknown role for this degradative pathway in the cellular response to stress has gained considerable attention. In this review, we focus on the novel findings linking autophagic function with metabolic stress resulting either from proteins or lipids. Proper autophagic activity is required in the cellular defense against proteotoxicity arising in the cytosol and also in the endoplasmic reticulum, where a vast amount of proteins are synthesized and folded. In addition, autophagy contributes to mobilization of intracellular lipid stores and may be central to lipid metabolism in certain cellular conditions. In this review, we focus on the interrelation between autophagy and different types of metabolic stress, specifically the stress resulting from the presence of misbehaving proteins within the cytosol or in the endoplasmic reticulum and the stress following a lipogenic challenge. We also comment on the consequences that chronic exposure to these metabolic stressors could have on autophagic function and on how this effect may underlie the basis of some common metabolic disorders. © 2010 Blackwell Publishing Ltd.

Palaeoproteomics for human evolution studies

NASA Astrophysics Data System (ADS)

Welker, Frido

2018-06-01

The commonplace sequencing of Neanderthal, Denisovan and ancient modern human DNA continues to revolutionize our understanding of hominin phylogeny and interaction(s). The challenge with older fossils is that the progressive fragmentation of DNA even under optimal conditions, a function of time and temperature, results in ever shorter fragments of DNA. This process continues until no DNA can be sequenced or reliably aligned. Ancient proteins ultimately suffer a similar fate, but are a potential alternative source of biomolecular sequence data to investigate hominin phylogeny given their slower rate of fragmentation. In addition, ancient proteins have been proposed to potentially provide insights into in vivo biological processes and can be used to provide additional ecological information through large scale ZooMS (Zooarchaeology by Mass Spectrometry) screening of unidentifiable bone fragments. However, as initially with ancient DNA, most ancient protein research has focused on Late Pleistocene or Holocene samples from Europe. In addition, only a limited number of studies on hominin remains have been published. Here, an updated review on ancient protein analysis in human evolutionary contexts is given, including the identification of specific knowledge gaps and existing analytical limits, as well as potential avenues to overcome these.

The design features cells use to build their transmembrane proton gradient

NASA Astrophysics Data System (ADS)

Gunner, M. R.; Koder, Ronald

2017-02-01

Organisms store energy from food and sunlight as an electrochemical gradient across the membranes of mitochondria, chloroplasts and bacteria. The gradient arises from differences in the concentration of protons and ions on the negative (N) and positive (P) sides of these membranes. This perspective describes how the proton gradient is formed. One strategy is the movement of electrons but not protons across a membrane-embedded protein from a site of proton-releasing oxidative chemistry on the P-side of the protein to a site of proton-binding reductive chemistry on the N-side. Alternately, protons are directly pumped across membrane-embedded proteins, which have gated proton transfer pathways that are opened and closed, as well as internal sites where the proton affinity varies as the protein goes through the reaction cycle. The molecules that carry out these roles are complex, utilizing non-amino acid cofactors and earth-abundant metals. However, these are also potential sources of high-energy toxic byproducts. Understanding these reactions can open the door to their rational redesign, with possible beneficial effects as far-reaching as improving the global food supply, preventing neurodegenerative diseases, and better understanding the role of metabolism in aging.

The design features cells use to build their transmembrane proton gradient.

PubMed

Gunner, M R; Koder, Ronald

2017-02-07

Organisms store energy from food and sunlight as an electrochemical gradient across the membranes of mitochondria, chloroplasts and bacteria. The gradient arises from differences in the concentration of protons and ions on the negative (N) and positive (P) sides of these membranes. This perspective describes how the proton gradient is formed. One strategy is the movement of electrons but not protons across a membrane-embedded protein from a site of proton-releasing oxidative chemistry on the P-side of the protein to a site of proton-binding reductive chemistry on the N-side. Alternately, protons are directly pumped across membrane-embedded proteins, which have gated proton transfer pathways that are opened and closed, as well as internal sites where the proton affinity varies as the protein goes through the reaction cycle. The molecules that carry out these roles are complex, utilizing non-amino acid cofactors and earth-abundant metals. However, these are also potential sources of high-energy toxic byproducts. Understanding these reactions can open the door to their rational redesign, with possible beneficial effects as far-reaching as improving the global food supply, preventing neurodegenerative diseases, and better understanding the role of metabolism in aging.

Conserved developmental alternative splicing of muscleblind-like (MBNL) transcripts regulates MBNL localization and activity.

PubMed

Terenzi, Fulvia; Ladd, Andrea N

2010-01-01

Muscleblind-like (MBNL) proteins have been shown to regulate pre-mRNA alternative splicing, and MBNL1 has been implicated in regulating fetal-to-adult transitions in alternative splicing in the heart. MBNL1 is highly conserved, exhibiting more than 95% identity at the amino acid level between birds and mammals. To investigate MBNL1 expression during embryonic heart development, we examined MBNL1 transcript and protein expression in the embryonic chicken heart from the formation of the primitive heart tube through cardiac morphogenesis (embryonic days 1.5 through 8). MBNL1 transcript levels remained steady throughout these stages, whereas MBNL1 protein levels increased and exhibited a shift in isoforms. MBNL1 has several alternatively spliced exons. Using RT-PCR, we determined that the inclusion of one of these, exon 5, decreases dramatically during cardiac morphogenesis. This developmental transition is conserved in mice. Functional analyses of MBNL1 isoforms containing or lacking exon 5-encoded sequences revealed that exon 5 is important for the regulation of the subcellular localization, RNA binding affinity, and alternative splicing activity of MBNL1 proteins. A second MBNL protein, MBNL2, is also expressed in the embryonic heart. We found that MBNL2 exon 5, which is paralogous to MBNL1 exon 5, is similarly regulated during embryonic heart development. Analysis of MBNL1 and MBNL2 transcripts in several embryonic tissues in chicken and mouse indicate that exon 5 alternative splicing is highly conserved and tissue-specific. Thus, we propose that conserved developmental stage- and tissue-specific alternative splicing of MBNL transcripts is an important mechanism by which MBNL activity is regulated during embryonic development.

Using Value-Focused Thinking as an Alternative Means of Opportunity Assessment for Strategic Sourcing Applications

DTIC Science & Technology

2013-03-01

comparison between two objectives at a time. The decision maker develops a micro - version of the value equation using only the two objectives that...variety of different functional areas. Table 10. New Alternatives Identified Alternative Source Base Recycling Services AFCEC Airfield Pavement Repair

qPMS9: An Efficient Algorithm for Quorum Planted Motif Search

NASA Astrophysics Data System (ADS)

Nicolae, Marius; Rajasekaran, Sanguthevar

2015-01-01

Discovering patterns in biological sequences is a crucial problem. For example, the identification of patterns in DNA sequences has resulted in the determination of open reading frames, identification of gene promoter elements, intron/exon splicing sites, and SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have led to domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, discovery of short functional motifs, etc. In this paper we focus on the identification of an important class of patterns, namely, motifs. We study the (l, d) motif search problem or Planted Motif Search (PMS). PMS receives as input n strings and two integers l and d. It returns all sequences M of length l that occur in each input string, where each occurrence differs from M in at most d positions. Another formulation is quorum PMS (qPMS), where the motif appears in at least q% of the strings. We introduce qPMS9, a parallel exact qPMS algorithm that offers significant runtime improvements on DNA and protein datasets. qPMS9 solves the challenging DNA (l, d)-instances (28, 12) and (30, 13). The source code is available at https://code.google.com/p/qpms9/.

Optimization strategies for a fluorescent dye with bimodal excitation spectra: application to semiautomated proteomics

NASA Astrophysics Data System (ADS)

Patton, Wayne F.; Berggren, Kiera N.; Lopez, Mary F.

2001-04-01

Facilities engaged in proteome analysis differ significantly in the degree that they implement automated systems for high-throughput protein characterization. Though automated workstation environments are becoming more routine in the biotechnology and pharmaceutical sectors of industry, university-based laboratories often perform these tasks manually, submitting protein spots excised from polyacrylamide gels to institutional core facilities for identification. For broad compatibility with imaging platforms, an optimized fluorescent dye developed for proteomics applications should be designed taking into account that laser scanners use visible light excitation and that charge-coupled device camera systems and gas discharge transilluminators rely upon UV excitation. The luminescent ruthenium metal complex, SYPRO Ruby protein gel stain, is compatible with a variety of excitation sources since it displays intense UV (280 nm) and visible (470 nm) absorption maxima. Localization is achieved by noncovalent, electrostatic and hydrophobic binding of dye to proteins, with signal being detected at 610 nm. Since proteins are not covalently modified by the dye, compatibility with downstream microchemical characterization techniques such as matrix-assisted laser desorption/ionization-mass spectrometry is assured. Protocols have been devised for optimizing fluorophore intensity. SYPRO Ruby dye outperforms alternatives such as silver staining in terms of quantitative capabilities, compatibility with mass spectrometry and ease of integration into automated work environments.

Stem cells as a good tool to investigate dysregulated biological systems in autism spectrum disorders.

PubMed

Griesi-Oliveira, Karina; Sunaga, Daniele Yumi; Alvizi, Lucas; Vadasz, Estevão; Passos-Bueno, Maria Rita

2013-10-01

Identification of the causes of autism spectrum disorders (ASDs) is hampered by their genetic heterogeneity; however, the different genetic alterations leading to ASD seem to be implicated in the disturbance of common molecular pathways or biological processes. In this scenario, the search for differentially expressed genes (DEGs) between ASD patients and controls is a good alternative to identify the molecular etiology of such disorders. Here, we employed genome-wide expression analysis to compare the transcriptome of stem cells of human exfoliated deciduous teeth (SHEDs) of idiopathic autistic patients (n = 7) and control samples (n = 6). Nearly half of the 683 identified DEGs are expressed in the brain (P = 0.003), and a significant number of them are involved in mechanisms previously associated with ASD such as protein synthesis, cytoskeleton regulation, cellular adhesion and alternative splicing, which validate the use of SHEDs to disentangle the causes of autism. Autistic patients also presented overexpression of genes regulated by androgen receptor (AR), and AR itself, which in turn interacts with CHD8 (chromodomain helicase DNA binding protein 8), a gene recently shown to be associated with the cause of autism and found to be upregulated in some patients tested here. These data provide a rationale for the mechanisms through which CHD8 leads to these diseases. In summary, our results suggest that ASD share deregulated pathways and revealed that SHEDs represent an alternative cell source to be used in the understanding of the biological mechanisms involved in the etiology of ASD. © 2013 International Society for Autism Research, Wiley Periodicals, Inc.

Use of Vendedores (Mobile Food Vendors), Pulgas (Flea Markets), and Vecinos o Amigos (Neighbors or Friends) as Alternative Sources of Food for Purchase among Mexican-origin Households in Texas Border Colonias

PubMed Central

Sharkey, Joseph R.; Dean, Wesley R.; Johnson, Cassandra M.

2012-01-01

There is a paucity of studies acknowledging the existence of alternative food sources, and factors associated with food purchasing from three common alternative sources: vendedores (mobile food vendors), pulgas (flea markets), and vecinos/amigos (neighbors/friends). This analysis aims to examine the use of alternative food sources by Mexican-origin women from Texas-border colonias and determine factors associated with their use. The design was cross-sectional. Promotora-researchers (promotoras de salud trained in research methods) recruited 610 Mexican-origin women from 44 colonias and conducted in-person surveys. Surveys included participant characteristics and measures of food environment use and household food security. Statistical analyses included separate logistic regressions, modeled for food purchase from mobile food vendors, pulgas, or neighbors/friends (NFs). Child food insecurity was associated with purchasing food from mobile food vendors, while household food security was associated with using pulgas or NFs. School nutrition program participants were more likely to live in households that depend on alternative food sources. Efforts to increase healthful food consumption such as fruits and vegetables should acknowledge all potential food sources (traditional, convenience, non-traditional, and alternative), especially those preferred by colonia residents. Current findings support the conceptual broadening of the retail food environment, and the importance of linking use with spatial access (proximity) to more accurately depict access to food sources. PMID:22709775

40 CFR 63.5987 - What are my alternatives for meeting the emission limits for tire cord production affected sources?

Code of Federal Regulations, 2010 CFR

2010-07-01

... the emission limits for tire cord production affected sources? 63.5987 Section 63.5987 Protection of... Pollutants: Rubber Tire Manufacturing Emission Limits for Tire Cord Production Affected Sources § 63.5987 What are my alternatives for meeting the emission limits for tire cord production affected sources? You...

40 CFR Table 6 to Subpart Xxxx of... - Initial Compliance With the Emission Limits for Tire Production Affected Sources

Code of Federal Regulations, 2011 CFR

2011-07-01

... if . . . 1. Sources complying with the purchase compliance alternative in § 63.5985(a) The HAP... cements and solvents were purchased and used at the affected source containing HAP in amounts above the...) and (b)(1). 2. Sources complying with the monthly average compliance alternative without using a...

40 CFR Table 6 to Subpart Xxxx of... - Initial Compliance With the Emission Limits for Tire Production Affected Sources

Code of Federal Regulations, 2010 CFR

2010-07-01

... if . . . 1. Sources complying with the purchase compliance alternative in § 63.5985(a) The HAP... cements and solvents were purchased and used at the affected source containing HAP in amounts above the...) and (b)(1). 2. Sources complying with the monthly average compliance alternative without using a...

48 CFR 32.304-2 - Certificate of eligibility.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) There is no practicable alternate source for the acquisition without prejudice to the national defense... contracting officer shall consider the following factors in determining if a practicable alternate source exists: (1) Prejudice to the national defense, because reletting of a contract with another source would...

Consequences of the ban of by-products from terrestrial animals in livestock feeding in Germany and the European Union: alternatives, nutrient and energy cycles, plant production, and economic aspects.

PubMed

Rodehutscord, M; Abel, H J; Friedt, W; Wenk, C; Flachowsky, G; Ahlgrimm, H J; Johnke, B; Kühl, R; Breves, G

2002-04-01

Consequences of the ban of meat and bone meal (MBM) and animal fat with regard to livestock feeding, cropping, ecology and economy where investigated with an inter-disciplinary approach for Germany and the European Union. Calculations were made for different production systems with pigs and poultry on the basis of statistical data for the production and for the feed markets as well as from requirement data for the respective species and production system. (1.) The ban of MBM from feeding caused a need for alternative protein sources. If all the amount of protein from MBM is to be replaced by soybean meal, in Germany and the EU about 0.30 and 2.30 x 10(6) t would be needed each year (supplementary amino acids not considered). Alternatively, doubling the grain legume acreage in Germany to about 420,000 ha would supply a similar amount of protein. A wider application of phase feeding with adjusted dietary amino acid concentrations, however, would allow for saving protein to an extent which is similar to the amount of protein that was contributed by MBM in recent years. Thus, the ban is a minor problem in terms of ensuring amino acid supply. (2.) However, alternative plant ingredients cannot compensate for the gap in P supply that is caused by the ban. An additional demand for inorganic feed phosphates of about 14,000 and 110,000 t per year is given in Germany and the EU, respectively. So far, this gap is filled almost completely by increased mining of rock phosphates. Alternatively, a general application of microbial phytase to all diets would largely fill this gap. Until the ban, MBM contributed to 57% of the supplementation of P that was needed for pigs and poultry. The ban of MBM makes large amounts of P irreversibly disappearing from the food chain. (3.) Energy from slaughter offal and cadavers can be utilized in different technologies, in the course of which the efficiency of energy utilisation depends on the technology applied. It is efficient in the cement work or rotation furnace if heat is the main energy required. In contrast, the energetic efficiency of fermentation is low. (4.) Incineration or co-incineration of MBM and other by-products causes pollution gas emissions amounting to about 1.4 kg CO2 and 0.2 kg NOx per kg. The CO2 production as such is hardly disadvantageous, because heat and electrical energy can be generated by the combustion process. The prevention of dangerous gaseous emissions from MBM burning is current standard in the incineration plants in Germany and does not affect the environment inadmissibly. (5.) The effects of the MBM ban on the price for compound feed is not very significant. Obviously, substitution possibilities between different feed ingredients helped to exchange MBM without large price distortions. However, with each kg MBM not used in pig and poultry feeding economic losses of about 0.14 [symbol: see text] have to considered. In conclusion, the by far highest proportion of raw materials for MBM comes as by-products from the slaughter process. Coming this way, and assuring that further treatment is safe from the hygienic point of view, MBM and animal fat can be regarded as valuable sources of amino acids, minerals and energy in feeding pigs and poultry. Using them as feedstuffs could considerably contribute to the goal of keeping limited nutrients, phosphorus in particular, within the nutrient cycle and dealing responsible with limited resources.

Alternative Affinity Ligands for Immunoglobulins.

PubMed

Kruljec, Nika; Bratkovič, Tomaž

2017-08-16

The demand for recombinant therapeutic antibodies and Fc-fusion proteins is expected to increase in the years to come. Hence, extensive efforts are concentrated on improving the downstream processing. In particular, the development of better-affinity chromatography matrices, supporting robust time- and cost-effective antibody purification, is warranted. With the advances in molecular design and high-throughput screening approaches from chemical and biological combinatorial libraries, novel affinity ligands representing alternatives to bacterial immunoglobulin (Ig)-binding proteins have entered the scene. Here, we review the design, development, and properties of diverse classes of alternative antibody-binding ligands, ranging from engineered versions of Ig-binding proteins, to artificial binding proteins, peptides, aptamers, and synthetic small-molecular-weight compounds. We also provide examples of applications for the novel affinity matrices in chromatography and beyond.

The Skeletal Muscle Anabolic Response to Plant- versus Animal-Based Protein Consumption.

PubMed

van Vliet, Stephan; Burd, Nicholas A; van Loon, Luc J C

2015-09-01

Clinical and consumer market interest is increasingly directed toward the use of plant-based proteins as dietary components aimed at preserving or increasing skeletal muscle mass. However, recent evidence suggests that the ingestion of the plant-based proteins in soy and wheat results in a lower muscle protein synthetic response when compared with several animal-based proteins. The possible lower anabolic properties of plant-based protein sources may be attributed to the lower digestibility of plant-based sources, in addition to greater splanchnic extraction and subsequent urea synthesis of plant protein-derived amino acids compared with animal-based proteins. The latter may be related to the relative lack of specific essential amino acids in plant- as opposed to animal-based proteins. Furthermore, most plant proteins have a relatively low leucine content, which may further reduce their anabolic properties when compared with animal proteins. However, few studies have actually assessed the postprandial muscle protein synthetic response to the ingestion of plant proteins, with soy and wheat protein being the primary sources studied. Despite the proposed lower anabolic properties of plant vs. animal proteins, various strategies may be applied to augment the anabolic properties of plant proteins. These may include the following: 1) fortification of plant-based protein sources with the amino acids methionine, lysine, and/or leucine; 2) selective breeding of plant sources to improve amino acid profiles; 3) consumption of greater amounts of plant-based protein sources; or 4) ingesting multiple protein sources to provide a more balanced amino acid profile. However, the efficacy of such dietary strategies on postprandial muscle protein synthesis remains to be studied. Future research comparing the anabolic properties of a variety of plant-based proteins should define the preferred protein sources to be used in nutritional interventions to support skeletal muscle mass gain or maintenance in both healthy and clinical populations. © 2015 American Society for Nutrition.

Aerobic nonaseptic growth of Verticillium on coffee waste waters and cane blackstrap molasses at a pilot plant scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Espinosa, R.; Maldonado, O.; Menchu, J.F.

1977-01-01

An evaluation is made of the pilot plant studies on the biosynthesis of Verticillium sp. both on coffee waste waters and blackstrap molasses. The purpose of the study was two-fold: the first to produce a filamentous fungi as a source of protein and the second to alleviate the serious water pollution resulting from the processing of coffee berries. The molasses was studied as an alternative medium to enable year-round operation of the plant since coffee is a seasonal crop. The results indicated that the growth of Verticillium is technically feasible in a batch operation. (JSR)

Bladder Smooth Muscle Cells Differentiation from Dental Pulp Stem Cells: Future Potential for Bladder Tissue Engineering

PubMed Central

Song, Bing; Jiang, Wenkai; Alraies, Amr; Liu, Qian; Gudla, Vijay; Oni, Julia; Wei, Xiaoqing; Sloan, Alastair; Ni, Longxing; Agarwal, Meena

2016-01-01

Dental pulp stem cells (DPSCs) are multipotent cells capable of differentiating into multiple cell lines, thus providing an alternative source of cell for tissue engineering. Smooth muscle cell (SMC) regeneration is a crucial step in tissue engineering of the urinary bladder. It is known that DPSCs have the potential to differentiate into a smooth muscle phenotype in vitro with differentiation agents. However, most of these studies are focused on the vascular SMCs. The optimal approaches to induce human DPSCs to differentiate into bladder SMCs are still under investigation. We demonstrate in this study the ability of human DPSCs to differentiate into bladder SMCs in a growth environment containing bladder SMCs-conditioned medium with the addition of the transforming growth factor beta 1 (TGF-β1). After 14 days of exposure to this medium, the gene and protein expression of SMC-specific marker (α-SMA, desmin, and calponin) increased over time. In particular, myosin was present in differentiated cells after 11 days of induction, which indicated that the cells differentiated into the mature SMCs. These data suggested that human DPSCs could be used as an alternative and less invasive source of stem cells for smooth muscle regeneration, a technology that has applications for bladder tissue engineering. PMID:26880982

Adverse food reactions: Pathogenesis, clinical signs, diagnosis and alternatives to elimination diets.

PubMed

Mueller, R S; Unterer, S

2018-06-01

This review summarises available information about adverse food reactions in dogs and cats. Much of the published information on the pathogenesis of adverse food reactions in these species is transferred from what is known in mice and human beings. Clinical signs affect mostly the integument and gastrointestinal system. Pruritus of the distal limbs, face, ears and ventrum is the most common cutaneous presentation in dogs, although urticaria has also been reported. In cats, all so-called 'cutaneous reaction patterns' may be due to adverse food reactions. The most common gastrointestinal signs in both species are diarrhoea and vomiting. An elimination diet over several weeks using a protein source and a carbohydrate source previously not fed is still the diagnostic tool of choice. Improvement on such a diet, deterioration on re-challenge with the old food and improvement again on the elimination diet confirms the diagnosis of adverse food reaction, whereas alternative tests of blood, serum, saliva and hair have been found to be unsatisfactory. Patch testing with food antigens has been recommended as an aid to choose the elimination diet ingredients, since it has a reasonable negative predictability and likelihood ratio, but is laborious and costly. Copyright © 2018 Elsevier Ltd. All rights reserved.

Immortalized N/TERT keratinocytes as an alternative cell source in 3D human epidermal models.

PubMed

Smits, Jos P H; Niehues, Hanna; Rikken, Gijs; van Vlijmen-Willems, Ivonne M J J; van de Zande, Guillaume W H J F; Zeeuwen, Patrick L J M; Schalkwijk, Joost; van den Bogaard, Ellen H

2017-09-19

The strong societal urge to reduce the use of experimental animals, and the biological differences between rodent and human skin, have led to the development of alternative models for healthy and diseased human skin. However, the limited availability of primary keratinocytes to generate such models hampers large-scale implementation of skin models in biomedical, toxicological, and pharmaceutical research. Immortalized cell lines may overcome these issues, however, few immortalized human keratinocyte cell lines are available and most do not form a fully stratified epithelium. In this study we compared two immortalized keratinocyte cell lines (N/TERT1, N/TERT2G) to human primary keratinocytes based on epidermal differentiation, response to inflammatory mediators, and the development of normal and inflammatory human epidermal equivalents (HEEs). Stratum corneum permeability, epidermal morphology, and expression of epidermal differentiation and host defence genes and proteins in N/TERT-HEE cultures was similar to that of primary human keratinocytes. We successfully generated N/TERT-HEEs with psoriasis or atopic dermatitis features and validated these models for drug-screening purposes. We conclude that the N/TERT keratinocyte cell lines are useful substitutes for primary human keratinocytes thereby providing a biologically relevant, unlimited cell source for in vitro studies on epidermal biology, inflammatory skin disease pathogenesis and therapeutics.

Alternative energy resources for MoDOT

DOT National Transportation Integrated Search

2011-02-01

This research investigates environmentally friendly alternative energy sources that could be used by MoDOT in various areas, and develops applicable and sustainable strategies to implement those energy sources.

Biosolar energy generation and harvesting from biomolecule-copolymer hybrid systems

NASA Astrophysics Data System (ADS)

Chu, Bong-Chieh Benjamin

Alternative energy sources have become an increasingly important topic as energy needs outpace supply. Furthermore, as the world moves into the digital age of portable electronics, highly efficient and lightweight energy sources will need to be developed. Current technology, such as lithium ion batteries, provide enough power to run portable electronics for hours or days, but can still allow for improvement in their power density (W/kg). Utilizing energy-transducing membrane proteins, which are by nature highly efficient, it is possible to engineer biological-based energy sources with energy densities far greater than any solid-state systems. Furthermore, solar powered membrane proteins have the added benefit of a virtually unlimited supply of energy. This work has developed protein-polymer hybrid films and nanoscale vesicles for a variety of applications from fuel-cell technology to biological-based photovoltaics. Bacteriorhodopsin (BR), a light-activated proton pump, and Cytochrome C Oxidase (COX), a protein involved in the electron transport chain in mitochondria, were reconstituted into biomimetic triblock copolymer membranes. Block copolymer membranes mimic the amphiphilic nature of a natural lipid bilayer but exhibit greater mechanical stability due to UV-polymerizable endgroups. In BR/COX functionalized nanovesicles, proton gradients generated by the light-activated proton pumping of BR are used to drive COX in reverse to generate electrons, providing a hybrid biologically-active polymer to convert solar energy to chemical energy, and finally to electrical energy. This work has found protein activity in planar membranes through the photoelectric current generation by BR and the proton pumping activity of BR-functionalized polymer membranes deposited onto proton exchange membranes, as well as the coupled functionality of BR and COX through current generation in cyclic voltammetry and direct current measurements. Current switching between light and dark environments of composite BR/COX polymer vesicles show a light-dependent current generation with current changes as high as 10muA. Furthermore, electrode modifications were made using polymer and polymer/carbon nanotube (CNT) coatings as anti-absorbent and conductive anti-absorbent layers for the purpose of a more robust electrode. These findings have shown that biological functionality can be engineered into synthetic polymers to make hybrid devices.

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME

PubMed Central

Berthold, Michael R.; Hedrick, Michael P.; Gilson, Michael K.

2015-01-01

Today’s large, public databases of protein–small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to custom scripting for informatics and data analysis. Here, we illustrate how the large protein-ligand database BindingDB may be incorporated into KNIME workflows as a step toward the integration of pharmacological data with broader biomolecular analyses. Thus, we describe a collection of KNIME workflows that access BindingDB data via RESTful webservices and, for more intensive queries, via a local distillation of the full BindingDB dataset. We focus in particular on the KNIME implementation of knowledge-based tools to generate informed hypotheses regarding protein targets of bioactive compounds, based on notions of chemical similarity. A number of variants of this basic approach are tested for seven existing drugs with relatively ill-defined therapeutic targets, leading to replication of some previously confirmed results and discovery of new, high-quality hits. Implications for future development are discussed. Database URL: www.bindingdb.org PMID:26384374

Molecular mechanism for the operation of nitrogen control in cyanobacteria.

PubMed Central

Luque, I; Flores, E; Herrero, A

1994-01-01

In cyanobacteria, ammonium exerts a negative regulation of the expression of proteins involved in the assimilation of nitrogen sources alternative to ammonium. In Synechococcus, mRNA levels of genes encoding proteins for nitrate and ammonium assimilation were observed to be negatively regulated by ammonium, and ammonium-regulated transcription start points were identified for those genes. The NtcA protein is a positive regulator of genes subjected to nitrogen control by ammonium. Mutants lacking NtcA exhibited only basal mRNA levels of the regulated genes, even in the absence of ammonium, indicating that NtcA exerts its regulatory action by positively influencing mRNA levels of the nitrogen-regulated genes. NtcA was observed to bind directly to the promoters of nitrogen-regulated genes, and the palindromic DNA sequence GTAN8TAC was identified as a sequence signature for NtcA-target sites. The structure of the nitrogen-, NtcA-regulated promoters of Synechococcus was determined to be constituted by a -10, Pribnow-like box in the form TAN3T, and an NtcA-binding site that substituted for the canonical -35 box. Images PMID:8026471

JMJD6 and U2AF65 co-regulate alternative splicing in both JMJD6 enzymatic activity dependent and independent manner

PubMed Central

Yi, Jia; Shen, Hai-Feng; Qiu, Jin-Song; Huang, Ming-Feng; Zhang, Wen-Juan; Ding, Jian-Cheng; Zhu, Xiao-Yan; Zhou, Yu

2017-01-01

Abstract JMJD6, a jumonji C (Jmj C) domain-containing protein demethylase and hydroxylase, has been implicated in an array of biological processes. It has been shown that JMJD6 interacts with and hydroxylates multiple serine/arginine-rich (SR) proteins and SR related proteins, including U2AF65, all of which are known to function in alternative splicing regulation. However, whether JMJD6 is widely involved in alternative splicing and the molecular mechanism underlying JMJD6-regulated alternative splicing have remained incompletely understood. Here, by using RASL-Seq, we investigated the functional impact of RNA-dependent interaction between JMJD6 and U2AF65, revealing that JMJD6 and U2AF65 co-regulated a large number of alternative splicing events. We further demonstrated the JMJD6 function in alternative splicing in jmjd6 knockout mice. Mechanistically, we showed that the enzymatic activity of JMJD6 was required for a subset of JMJD6-regulated splicing, and JMJD6-mediated lysine hydroxylation of U2AF65 could account for, at least partially, their co-regulated alternative splicing events, suggesting both JMJD6 enzymatic activity-dependent and independent control of alternative splicing. These findings reveal an intimate link between JMJD6 and U2AF65 in alternative splicing regulation, which has important implications in development and disease processes. PMID:27899633

A serine–arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii

PubMed Central

Yeoh, Lee M.; Goodman, Christopher D.; Hall, Nathan E.; van Dooren, Giel G.; McFadden, Geoffrey I.; Ralph, Stuart A.

2015-01-01

Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoured in this phylum. We investigated the mechanism of alternative splicing in Toxoplasma gondii, and have identified and localized TgSR3, a homologue of ASF/SF2 (alternative-splicing factor/splicing factor 2, a serine-arginine–rich, or SR protein) to a subnuclear compartment. In addition, we conditionally overexpressed this protein, which was deleterious to growth. qRT-PCR was used to confirm perturbation of splicing in a known alternatively-spliced gene. We performed high-throughput RNA-seq to determine the extent of splicing modulated by this protein. Current RNA-seq algorithms are poorly suited to compact parasite genomes, and hence we complemented existing tools by writing a new program, GeneGuillotine, that addresses this deficiency by segregating overlapping reads into distinct genes. In order to identify the extent of alternative splicing, we released another program, JunctionJuror, that detects changes in intron junctions. Using this program, we identified about 2000 genes that were constitutively alternatively spliced in T. gondii. Overexpressing the splice regulator TgSR3 perturbed alternative splicing in over 1000 genes. PMID:25870410

10 CFR 504.6 - Prohibitions by order (case-by-case).

Code of Federal Regulations, 2013 CFR

2013-01-01

... had, the technical capability to use an alternate fuel as a primary energy source; (2) The unit has... (3) It is financially feasible for the unit to use an alternate fuel as its primary energy source. (b... Energy DEPARTMENT OF ENERGY (CONTINUED) ALTERNATE FUELS EXISTING POWERPLANTS § 504.6 Prohibitions by...

10 CFR 504.6 - Prohibitions by order (case-by-case).

Code of Federal Regulations, 2014 CFR

2014-01-01

... had, the technical capability to use an alternate fuel as a primary energy source; (2) The unit has... (3) It is financially feasible for the unit to use an alternate fuel as its primary energy source. (b... Energy DEPARTMENT OF ENERGY (CONTINUED) ALTERNATE FUELS EXISTING POWERPLANTS § 504.6 Prohibitions by...

10 CFR 504.6 - Prohibitions by order (case-by-case).

Code of Federal Regulations, 2012 CFR

2012-01-01

... had, the technical capability to use an alternate fuel as a primary energy source; (2) The unit has... (3) It is financially feasible for the unit to use an alternate fuel as its primary energy source. (b... Energy DEPARTMENT OF ENERGY (CONTINUED) ALTERNATE FUELS EXISTING POWERPLANTS § 504.6 Prohibitions by...

10 CFR 504.6 - Prohibitions by order (case-by-case).

Code of Federal Regulations, 2011 CFR

2011-01-01

... had, the technical capability to use an alternate fuel as a primary energy source; (2) The unit has... (3) It is financially feasible for the unit to use an alternate fuel as its primary energy source. (b... Energy DEPARTMENT OF ENERGY (CONTINUED) ALTERNATE FUELS EXISTING POWERPLANTS § 504.6 Prohibitions by...

Evolution of the alternative AQP2 gene: Acquisition of a novel protein-coding sequence in dolphins.

PubMed

Kishida, Takushi; Suzuki, Miwa; Takayama, Asuka

2018-01-01

Taxon-specific de novo protein-coding sequences are thought to be important for taxon-specific environmental adaptation. A recent study revealed that bottlenose dolphins acquired a novel isoform of aquaporin 2 generated by alternative splicing (alternative AQP2), which helps dolphins to live in hyperosmotic seawater. The AQP2 gene consists of four exons, but the alternative AQP2 gene lacks the fourth exon and instead has a longer third exon that includes the original third exon and a part of the original third intron. Here, we show that the latter half of the third exon of the alternative AQP2 arose from a non-protein-coding sequence. Intact ORF of this de novo sequence is shared not by all cetaceans, but only by delphinoids. However, this sequence is conservative in all modern cetaceans, implying that this de novo sequence potentially plays important roles for marine adaptation in cetaceans. Copyright © 2017 Elsevier Inc. All rights reserved.

THE GRK4 SUBFAMILY OF G PROTEIN-COUPLED RECEPTOR KINASES: ALTERNATIVE SPLICING, GENE ORGANIZATION, AND SEQUENCE CONSERVATION

EPA Science Inventory

The GRK4 subfamily of G protein-coupled receptor kinases. Alternative splicing, gene organization, and sequence conservation.

Premont RT, Macrae AD, Aparicio SA, Kendall HE, Welch JE, Lefkowitz RJ.

Department of Medicine, Howard Hughes Medical Institute, Duke Univer...

Origins of Protein Functions in Cells

NASA Technical Reports Server (NTRS)

Seelig, Burchard; Pohorille, Andrzej

2011-01-01

In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis and in vitro evolution of very large libraries of random amino acid sequences. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions yet, important clues have been uncovered. In one example (Keefe and Szostak, 2001), novel ATP binding proteins were identified that appear to be unrelated in both sequence and structure to any known ATP binding proteins. One of these proteins was subsequently redesigned computationally to bind GTP through introducing several mutations that introduce targeted structural changes to the protein, improve its binding to guanine and prevent water from accessing the active center. This study facilitates further investigations of individual evolutionary steps that lead to a change of function in primordial proteins. In a second study (Seelig and Szostak, 2007), novel enzymes were generated that can join two pieces of RNA in a reaction for which no natural enzymes are known. Recently it was found that, as in the previous case, the proteins have a structure unknown among modern enzymes. In this case, in vitro evolution started from a small, non-enzymatic protein. A similar selection process initiated from a library of random polypeptides is in progress. These results not only allow for estimating the occurrence of function in random protein assemblies but also provide evidence for the possibility of alternative protein worlds. Extant proteins might simply represent a frozen accident in the world of possible proteins. Alternative collections of proteins, even with similar functions, could originate alternative evolutionary paths.

Alternative Fuels Data Center: Delaware Transportation Data for Alternative

Science.gov Websites

local stakeholders. Gasoline Diesel Natural Gas Transportation Fuel Consumption Source: State Energy Plants 1 Renewable Power Plant Capacity (nameplate, MW) 2 Source: BioFuels Atlas from the National /gallon $2.66/GGE Source: Average prices per gasoline gallon equivalent (GGE) for the Central Atlantic

Alternative Energy Sources. Experiments You Can Do...from Edison.

ERIC Educational Resources Information Center

Benrey, Ronald M.; Schultz, Robert F.

Eight experiments dealing with alternative energy sources are presented. Each experiment includes an introductory section which provides background information and discusses the promises and problems of the particular energy source, a list of materials needed to complete the experiment, and the procedures to be used. The experiments involve:…

Evaluation of the nutritive value of muiumba (Baikiaea plurijuga) seeds: chemical composition, in vitro organic matter digestibility and in vitro gas production.

PubMed

Rodrigues, Miguel A M; Lourenço, Ana L; Cone, John W; Nunes, Fernando M; Santos, Ana S; Cordeiro, José M M; Guedes, Cristina M V; Ferreira, Luis M M

2014-01-01

One of the main constraints hindering the increase of animal production in semi-arid regions of Africa is the inadequate supply of nutrients during the dry season. Incorporation of alternative feed resources in ruminant diets during this period could be a viable approach to overcome these limitations. The objective of this study was to evaluate the nutritive value of muiumba (Baikiaea plurijuga) tree seeds as an alternative nutrient source for ruminants. Muiumba seeds were compared to other eight feedstuffs including two cereal grains (corn and oat), two wheat by-products (wheat bran and distilled wheat) and four protein meals (coconut meal, sunflower meal, soybean meal and rapeseed meal) as to its chemical composition, in vitro organic matter digestibility (IVOMD) and in vitro gas production. The moderate crude protein concentrations (145 g/kg DM) of muiumba seeds indicate that this feedstuff could not be used as a protein supplement, contrarily to the majority of multipurpose tree seeds. Although the starch content was scarce (15 g/kg DM), the low neutral detergent fibre (235 g/kg DM), low molecular weight sugar (76.1 g/kg DM) and non-starch polysaccharide (510.5 g/kg DM) contents indicate that this feedstuff has potential feeding value. This was confirmed by the IVOMD (0.770) and by the data provided by the in vitro gas production showing that muiumba seeds had high (P < 0.05) maximum gas production and fractional fermentation rates, suggesting that these seeds are characterized by a highly fermentable fraction.

Survey of the Effectiveness of Internet Information on Patient Education for Bone Morphogenetic Protein.

PubMed

Huang, Meng; Briceño, Valentina; Lam, Sandi K; Luerssen, Thomas G; Jea, Andrew

2016-03-01

In light of recent reports of potential short- and long-term complications of bone morphogenetic protein (BMP) and increasing "off-label" use among spine surgeons, we wished to analyze online information on BMP and its controversial uses, as patients frequently search the Internet for medical information, even though the quality and accuracy of available information are highly variable. Between December 2014 and January 2015, we conducted a Google search to identify the 50 most accessed websites providing BMP information using the search phrase "bone morphogenetic protein." Websites were classified based on authorship. Each website was examined for the provision of appropriate patient inclusion and exclusion criteria, surgical and nonsurgical treatment alternatives, purported benefits, disclosure of common and potential complications, peer-reviewed literature citations, and discussion of off-label use. Two percent of websites were authored by private medical groups, 2% by academic medical groups, 10% by insurance companies, 16% by biomedical industries, 4% by news sources, 0% by lawyers, and 66% by others. Sixty-two percent referenced peer-reviewed literature. Benefits and complications were reported in 44% and 26% of websites, respectively. Surgical and nonsurgical treatment alternatives were mentioned in 16% and 4% of websites, respectively. Discussion of off-label BMP use occurred in 18% of websites. Our study showed the ineffectiveness of the Internet in reporting quality information on BMP use. We found that websites authored by insurance companies provide an acceptable foundation for patient education. This, however, cannot replace the need for a thorough dialogue between doctor and patient about risks, benefits, and indications. Copyright © 2016. Published by Elsevier Inc.

Alternative energy resources for the Missouri Department of Transportation.

DOT National Transportation Integrated Search

2011-01-01

This research investigates environmentally friendly alternative energy sources that could be used by MoDOT in various areas, and develops applicable and sustainable strategies to implement those energy sources.

Use of vendedores (mobile food vendors), pulgas (flea markets), and vecinos o amigos (neighbors or friends) as alternative sources of food for purchase among Mexican-origin households in Texas border colonias.

PubMed

Sharkey, Joseph R; Dean, Wesley R; Johnson, Cassandra M

2012-05-01

There is a paucity of studies acknowledging the existence of alternative food sources, and factors associated with food purchasing from three common alternative sources: vendedores (mobile food vendors), pulgas (flea markets), and vecinos/amigos (neighbors/friends). This analysis aims to examine the use of alternative food sources by Mexican-origin women from Texas-border colonias and determine factors associated with their use. The design was cross-sectional. Promotora-researchers (promotoras de salud trained in research methods) recruited 610 Mexican-origin women from 44 colonias and conducted in-person surveys. Surveys included participant characteristics and measures of food environment use and household food security. Statistical analyses included separate logistic regressions, modeled for food purchase from mobile food vendors, pulgas, or neighbors/friends. Child food insecurity was associated with purchasing food from mobile food vendors, while household food security was associated with using pulgas or neighbors/friends. School nutrition program participants were more likely to live in households that depend on alternative food sources. Efforts to increase healthful food consumption such as fruits and vegetables should acknowledge all potential food sources (traditional, convenience, nontraditional, and alternative), especially those preferred by colonia residents. Current findings support the conceptual broadening of the retail food environment, and the importance of linking use with spatial access (proximity) to more accurately depict access to food sources. Copyright © 2012 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants.

PubMed

Barta, Andrea; Kalyna, Maria; Reddy, Anireddy S N

2010-09-01

Growing interest in alternative splicing in plants and the extensive sequencing of new plant genomes necessitate more precise definition and classification of genes coding for splicing factors. SR proteins are a family of RNA binding proteins, which function as essential factors for constitutive and alternative splicing. We propose a unified nomenclature for plant SR proteins, taking into account the newly revised nomenclature of the mammalian SR proteins and a number of plant-specific properties of the plant proteins. We identify six subfamilies of SR proteins in Arabidopsis thaliana and rice (Oryza sativa), three of which are plant specific. The proposed subdivision of plant SR proteins into different subfamilies will allow grouping of paralogous proteins and simple assignment of newly discovered SR orthologs from other plant species and will promote functional comparisons in diverse plant species.

Modeling water demand when households have multiple sources of water

NASA Astrophysics Data System (ADS)

Coulibaly, Lassina; Jakus, Paul M.; Keith, John E.

2014-07-01

A significant portion of the world's population lives in areas where public water delivery systems are unreliable and/or deliver poor quality water. In response, people have developed important alternatives to publicly supplied water. To date, most water demand research has been based on single-equation models for a single source of water, with very few studies that have examined water demand from two sources of water (where all nonpublic system water sources have been aggregated into a single demand). This modeling approach leads to two outcomes. First, the demand models do not capture the full range of alternatives, so the true economic relationship among the alternatives is obscured. Second, and more seriously, economic theory predicts that demand for a good becomes more price-elastic as the number of close substitutes increases. If researchers artificially limit the number of alternatives studied to something less than the true number, the price elasticity estimate may be biased downward. This paper examines water demand in a region with near universal access to piped water, but where system reliability and quality is such that many alternative sources of water exist. In extending the demand analysis to four sources of water, we are able to (i) demonstrate why households choose the water sources they do, (ii) provide a richer description of the demand relationships among sources, and (iii) calculate own-price elasticity estimates that are more elastic than those generally found in the literature.

Role of Alternative Donor Allogeneic Transplants in the Therapy of Acute Myeloid Leukemia.

PubMed

Elmariah, Hany; Pratz, Keith W

2017-07-01

Adult acute myeloid leukemia (AML) is often associated with a poor prognosis, with allogeneic transplantation representing the greatest chance of cure for eligible patients. Historically, the preferred donor source is a human leukocyte antigen-matched blood relative, although only approximately 30% of patients have access to such a donor. Alternative donor sources, including matched unrelated donors, umbilical cord blood, and haploidentical related donors, are available for almost every patient and are increasingly being used for patients without a matched related donor. Survival outcomes with these alternative donor sources now approximate those of matched related donor transplants. Given the safety and success of alternative donor transplants, comparative trials are needed to reassess the optimal donor source for patients with AML. This review summarizes the available data on these alternative donor transplants. Further investigation is needed to contemporize donor selection algorithms, but, in the current era, donor availability should no longer preclude a patient's eligibility for an allogeneic blood or marrow transplant. Copyright © 2017 by the National Comprehensive Cancer Network.

Peptide reranking with protein-peptide correspondence and precursor peak intensity information.

PubMed

Yang, Chao; He, Zengyou; Yang, Can; Yu, Weichuan

2012-01-01

Searching tandem mass spectra against a protein database has been a mainstream method for peptide identification. Improving peptide identification results by ranking true Peptide-Spectrum Matches (PSMs) over their false counterparts leads to the development of various reranking algorithms. In peptide reranking, discriminative information is essential to distinguish true PSMs from false PSMs. Generally, most peptide reranking methods obtain discriminative information directly from database search scores or by training machine learning models. Information in the protein database and MS1 spectra (i.e., single stage MS spectra) is ignored. In this paper, we propose to use information in the protein database and MS1 spectra to rerank peptide identification results. To quantitatively analyze their effects to peptide reranking results, three peptide reranking methods are proposed: PPMRanker, PPIRanker, and MIRanker. PPMRanker only uses Protein-Peptide Map (PPM) information from the protein database, PPIRanker only uses Precursor Peak Intensity (PPI) information, and MIRanker employs both PPM information and PPI information. According to our experiments on a standard protein mixture data set, a human data set and a mouse data set, PPMRanker and MIRanker achieve better peptide reranking results than PetideProphet, PeptideProphet+NSP (number of sibling peptides) and a score regularization method SRPI. The source codes of PPMRanker, PPIRanker, and MIRanker, and all supplementary documents are available at our website: http://bioinformatics.ust.hk/pepreranking/. Alternatively, these documents can also be downloaded from: http://sourceforge.net/projects/pepreranking/.

Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing.

PubMed

Floris, Matteo; Orsini, Massimiliano; Thanaraj, Thangavel Alphonse

2008-10-02

It is often the case that mammalian genes are alternatively spliced; the resulting alternate transcripts often encode protein isoforms that differ in amino acid sequences. Changes among the protein isoforms can alter the cellular properties of proteins. The effect can range from a subtle modulation to a complete loss of function. (i) We examined human splice-mediated protein isoforms (as extracted from a manually curated data set, and from a computationally predicted data set) for differences in the annotation for protein signatures (Pfam domains and PRINTS fingerprints) and we characterized the differences & their effects on protein functionalities. An important question addressed relates to the extent of protein isoforms that may lack any known function in the cell. (ii) We present a database that reports differences in protein signatures among human splice-mediated protein isoform sequences. (i) Characterization: The work points to distinct sets of alternatively spliced genes with varying degrees of annotation for the splice-mediated protein isoforms. Protein molecular functions seen to be often affected are those that relate to: binding, catalytic, transcription regulation, structural molecule, transporter, motor, and antioxidant; and the processes that are often affected are nucleic acid binding, signal transduction, and protein-protein interactions. Signatures are often included/excluded and truncated in length among protein isoforms; truncation is seen as the predominant type of change. Analysis points to the following novel aspects: (a) Analysis using data from the manually curated Vega indicates that one in 8.9 genes can lead to a protein isoform of no "known" function; and one in 18 expressed protein isoforms can be such an "orphan" isoform; the corresponding numbers as seen with computationally predicted ASD data set are: one in 4.9 genes and one in 9.8 isoforms. (b) When swapping of signatures occurs, it is often between those of same functional classifications. (c) Pfam domains can occur in varying lengths, and PRINTS fingerprints can occur with varying number of constituent motifs among isoforms - since such a variation is seen in large number of genes, it could be a general mechanism to modulate protein function. (ii) The reported resource (at http://www.bioinformatica.crs4.org/tools/dbs/splivap/) provides the community ability to access data on splice-mediated protein isoforms (with value-added annotation such as association with diseases) through changes in protein signatures.

An alternatively spliced heat shock transcription factor, OsHSFA2dI, functions in the heat stress-induced unfolded protein response in rice.

PubMed

Cheng, Q; Zhou, Y; Liu, Z; Zhang, L; Song, G; Guo, Z; Wang, W; Qu, X; Zhu, Y; Yang, D

2015-03-01

As sessile organisms, plants have evolved a wide range of defence pathways to cope with environmental stress such as heat shock. However, the molecular mechanism of these defence pathways remains unclear in rice. In this study, we found that OsHSFA2d, a heat shock transcriptional factor, encodes two main splice variant proteins, OsHSFA2dI and OsHSFA2dII in rice. Under normal conditions, OsHSFA2dII is the dominant but transcriptionally inactive spliced form. However, when the plant suffers heat stress, OsHSFA2d is alternatively spliced into a transcriptionally active form, OsHSFA2dI, which participates in the heat stress response (HSR). Further study found that this alternative splicing was induced by heat shock rather than photoperiod. We found that OsHSFA2dI is localised to the nucleus, whereas OsHSFA2dII is localised to the nucleus and cytoplasm. Moreover, expression of the unfolded protein response (UNFOLDED PROTEIN RESPONSE) sensors, OsIRE1, OsbZIP39/OsbZIP60 and the UNFOLDED PROTEIN RESPONSE marker OsBiP1, was up-regulated. Interestingly, OsbZIP50 was also alternatively spliced under heat stress, indicating that UNFOLDED PROTEIN RESPONSE signalling pathways were activated by heat stress to re-establish cellular protein homeostasis. We further demonstrated that OsHSFA2dI participated in the unfolded protein response by regulating expression of OsBiP1. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Fluorescent Protein-Based Quantification of Alternative Splicing of a Target Cassette Exon in Mammalian Cells.

PubMed

Gurskaya, N G; Staroverov, D B; Lukyanov, K A

2016-01-01

Alternative splicing is an important mechanism of regulation of gene expression and expansion of proteome complexity. Recently we developed a new fluorescence reporter for quantitative analysis of alternative splicing of a target cassette exon in live cells (Gurskaya et al., 2012). It consists of a specially designed minigene encoding red and green fluorescent proteins (Katushka and TagGFP2) and a fragment of the target gene between them. Skipping or inclusion of the alternative exon induces a frameshift; ie, alternative exon length must not be a multiple of 3. Finally, red and green fluorescence intensities of cells expressing this reporter are used to estimate the percentage of alternative (exon-skipped) and normal (exon-retained) transcripts. Here, we provide a detailed description of design and application of the fluorescence reporter of a target alternative exon splicing in mammalian cell lines. © 2016 Elsevier Inc. All rights reserved.

Drinking water from alternative water sources: differences in beliefs, social norms and factors of perceived behavioural control across eight Australian locations.

PubMed

Dolnicar, S; Hurlimann, A

2009-01-01

Australia is facing serious challenges in the management of water in various urban and regional locations. Two popular responses to these challenges are increasing supply through alternative water sources such as recycled and desalinated water. However, significant gaps exist in our knowledge of community attitudes to these alternative sources of water, particularly for potable use. This paper reports results from an Australian study of community attitudes to alternative water sources. Sixty six qualitative interviews were held at eight locations with distinctly different water situations. This paper explores all three antecedents to the behaviour of drinking recycled water and desalinated water as postulated by the Theory of Planned Behaviour: attitudes, social norms and factors of perceived behavioural control. Key results indicate that while people hold both positive and negative beliefs (mostly cost, health and environmental concerns) about water from alternative sources, nearly all of them are willing to drink it if the water crisis were to deteriorate further. People also feel they lack knowledge and state that information from scientists would influence their decision to drink recycled and desalinated water most. Friends and relatives are most influential in preventing people from drinking recycled water. The findings reported in this paper have major implications for water policy, and will be of particular interest to water engineers. The paper raises a provocative question: Is it better to avoid public consultation in introducing water from alternative sources?

Techno-economic evaluation of an inclusion body solubilization and recombinant protein refolding process.

PubMed

Freydell, Esteban J; van der Wielen, Luuk A M; Eppink, Michel H M; Ottens, Marcel

2011-01-01

Expression of recombinant proteins in Escherichia coli is normally accompanied by the formation of inclusion bodies (IBs). To obtain the protein product in an active (native) soluble form, the IBs must be first solubilized, and thereafter, the soluble, often denatured and reduced protein must be refolded. Several technically feasible alternatives to conduct IBs solubilization and on-column refolding have been proposed in recent years. However, rarely these on-column refolding alternatives have been evaluated from an economical point of view, questioning the feasibility of their implementation at a preparative scale. The presented study assesses the economic performance of four distinct process alternatives that include pH induced IBs solubilization and protein refolding (pH_IndSR); IBs solubilization using urea, dithiothreitol (DTT), and alkaline pH followed by batch size-exclusion protein refolding; inclusion bodies (IBs) solubilization using urea, DTT, and alkaline pH followed by simulated moving bed (SMB) size-exclusion protein refolding, and IBs solubilization using urea, DTT and alkaline pH followed by batch dilution protein refolding. The economic performance was judged on the basis of the direct fixed capital, and the production cost per unit of product (P(C)). This work shows that (1) pH_IndSR system is a relatively economical process, because of the low IBs solubilization cost; (2) substituting β-mercaptoethanol for dithiothreithol is an attractive alternative, as it significantly decreases the product cost contribution from the IBs solubilization; and (3) protein refolding by size-exclusion chromatography becomes economically attractive by changing the mode of operation of the chromatographic reactor from batch to continuous using SMB technology. Copyright © 2011 American Institute of Chemical Engineers (AIChE).

Characterising the muscle anabolic potential of dairy, meat and plant-based protein sources in older adults.

PubMed

Gorissen, Stefan H M; Witard, Oliver C

2018-02-01

The age-related loss of skeletal muscle mass and function is caused, at least in part, by a reduced muscle protein synthetic response to protein ingestion. The magnitude and duration of the postprandial muscle protein synthetic response to ingested protein is dependent on the quantity and quality of the protein consumed. This review characterises the anabolic properties of animal-derived and plant-based dietary protein sources in older adults. While approximately 60 % of dietary protein consumed worldwide is derived from plant sources, plant-based proteins generally exhibit lower digestibility, lower leucine content and deficiencies in certain essential amino acids such as lysine and methionine, which compromise the availability of a complete amino acid profile required for muscle protein synthesis. Based on currently available scientific evidence, animal-derived proteins may be considered more anabolic than plant-based protein sources. However, the production and consumption of animal-derived protein sources is associated with higher greenhouse gas emissions, while plant-based protein sources may be considered more environmentally sustainable. Theoretically, the lower anabolic capacity of plant-based proteins can be compensated for by ingesting a greater dose of protein or by combining various plant-based proteins to provide a more favourable amino acid profile. In addition, leucine co-ingestion can further augment the postprandial muscle protein synthetic response. Finally, prior exercise or n-3 fatty acid supplementation have been shown to sensitise skeletal muscle to the anabolic properties of dietary protein. Applying one or more of these strategies may support the maintenance of muscle mass with ageing when diets rich in plant-based protein are consumed.

Research advances on the multiple uses of Moringa oleifera: A sustainable alternative for socially neglected population.

PubMed

Brilhante, Raimunda Sâmia Nogueira; Sales, Jamille Alencar; Pereira, Vandbergue Santos; Castelo-Branco, Débora de Souza Collares Maia; Cordeiro, Rossana de Aguiar; de Souza Sampaio, Célia Maria; de Araújo Neto Paiva, Manoel; Santos, João Bosco Feitosa Dos; Sidrim, José Júlio Costa; Rocha, Marcos Fábio Gadelha

2017-07-01

Moringa oleifera Lam (Moringaceae) is a plant with high nutritional and medicinal value. Native to India, it is now widely distributed throughout tropical and subtropical regions of the world. Its different parts are sources of proteins, vitamins and minerals and present different pharmacological and biotechnological potential. Moreover, M. oleifera seeds are widely used in water and effluent treatment, for their coagulation, flocculation and sedimentation properties, their ability of improving water quality, by reducing organic matter and microbial load, with special applicability in intensive animal production systems, such as aquaculture. In addition, due to its high nutritional value and several medicinal properties, this tree may act as a nutritional and medical alternative for socially neglected populations. In this context, this review gathers information on M. oleifera, emphasizing its chemical constituents, nutritional, pharmacological and antimicrobial properties, applications in the treatment of water effluents, and ecological and social aspects. Copyright © 2017 Hainan Medical University. Production and hosting by Elsevier B.V. All rights reserved.

SRSF3 represses the expression of PDCD4 protein by coordinated regulation of alternative splicing, export and translation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Seung Kuk; Jeong, Sunjoo, E-mail: sjsj@dankook.ac.kr

2016-02-05

Gene expression is regulated at multiple steps, such as transcription, splicing, export, degradation and translation. Considering diverse roles of SR proteins, we determined whether the tumor-related splicing factor SRSF3 regulates the expression of the tumor-suppressor protein, PDCD4, at multiple steps. As we have reported previously, knockdown of SRSF3 increased the PDCD4 protein level in SW480 colon cancer cells. More interestingly, here we showed that the alternative splicing and the nuclear export of minor isoforms of pdcd4 mRNA were repressed by SRSF3, but the translation step was unaffected. In contrast, only the translation step of the major isoform of pdcd4 mRNAmore » was repressed by SRSF3. Therefore, overexpression of SRSF3 might be relevant to the repression of all isoforms of PDCD4 protein levels in most types of cancer cell. We propose that SRSF3 could act as a coordinator of the expression of PDCD4 protein via two mechanisms on two alternatively spliced mRNA isoforms.« less

The neurogenetics of alternative splicing

PubMed Central

Vuong, Celine K.; Black, Douglas L.; Zheng, Sika

2016-01-01

Alternative precursor-mRNA splicing is a key mechanism for regulating gene expression in mammals and is controlled by specialized RNA-binding proteins. The misregulation of splicing is implicated in multiple neurological disorders. We describe recent mouse genetic studies of alternative splicing that reveal its critical role in both neuronal development and the function of mature neurons. We discuss the challenges in understanding the extensive genetic programmes controlled by proteins that regulate splicing, both during development and in the adult brain. PMID:27094079

Assessment of Nanobiotechnology-Targeted siRNA Designed to inhibit NF-kappaB Classical and Alternative Signaling in Breast Tumor Macrophages

DTIC Science & Technology

2013-07-01

expression of key proteins within each pathway to examine their individual and combined roles with respect to potential breast cancer immunotherapy. We...selected as our initial targets the IKKβ activator (canonical) or p52 (alternative) proteins . In order to harness inhibition of these pathways to...intended to knockdown protein expression of NF-κB modulators with exceptional specificity for TAMs. TAM-specific nanoparticle targeting offers an

Parental vaccine concerns, information source, and choice of alternative immunization schedules.

PubMed

Wheeler, Marissa; Buttenheim, Alison M

2013-08-01

Alternative immunization schedules increase the time a child is unvaccinated and require greater resources from providers. Understanding what drives interest in alternative immunization schedules can potentially inform the design of effective, targeted messages that help to reduce time spent counseling and decrease requests for alternative immunization schedules. This study used the Theory of Planned Behavior to explore associations between sources of vaccine information, parental vaccine concerns, peer norms for vaccine behavior and intentions to follow an alternative immunization schedule. We performed logistic regression using medical record data from a private pediatric practice in a large northeastern city. Routine data were recorded in the EMR by the pediatrician during an initial vaccine counseling conversation with the parent(s). Parents who received vaccine information from doctors were less likely to have immunization concerns while parents who got vaccine information from friends and family or from books were more likely to report specific vaccine concerns. Our multivariate analysis shows that number of reported vaccine concerns and concerns about the utility or necessity of vaccines are strongly associated with alternative immunization intentions. We also find a direct relationship between sources of information about vaccines and alternative immunization intentions. Our results suggest that vaccine concerns and non-physician information sources play an important role in alternative immunization intentions while communication from physicians may play an important role in addressing vaccine concerns and promoting adherence to the ACIP immunization schedule.

Choice feeding of protein concentrate and grain to organic meat chickens

USDA-ARS?s Scientific Manuscript database

In alternative poultry production, such as free-range and organic, alternative feeding methods may be useful. Instead of a fully formulated diet, a “choice” method offers two feeds, a protein concentrate and a grain, between which birds self-select. This method was common in the past and may allo...

Alternative ground states enable pathway switching in biological electron transfer

DOE PAGES

Abriata, Luciano A.; Alvarez-Paggi, Damian; Ledesma, Gabirela N.; ...

2012-10-10

Electron transfer is the simplest chemical reaction and constitutes the basis of a large variety of biological processes, such as photosynthesis and cellular respiration. Nature has evolved specific proteins and cofactors for these functions. The mechanisms optimizing biological electron transfer have been matter of intense debate, such as the role of the protein milieu between donor and acceptor sites. Here we propose a mechanism regulating long-range electron transfer in proteins. Specifically, we report a spectroscopic, electrochemical, and theoretical study on WT and single-mutant CuA redox centers from Thermus thermophilus, which shows that thermal fluctuations may populate two alternative ground-state electronicmore » wave functions optimized for electron entry and exit, respectively, through two different and nearly perpendicular pathways. In conclusion, these findings suggest a unique role for alternative or “invisible” electronic ground states in directional electron transfer. Moreover, it is shown that this energy gap and, therefore, the equilibrium between ground states can be fine-tuned by minor perturbations, suggesting alternative ways through which protein–protein interactions and membrane potential may optimize and regulate electron–proton energy transduction.« less

Alternative Fuels Data Center: Maine Transportation Data for Alternative

Science.gov Websites

connect with other local stakeholders. Gasoline Diesel Natural Gas Transportation Fuel Consumption Source Renewable Power Plants 58 Renewable Power Plant Capacity (nameplate, MW) 984 Source: BioFuels Atlas from the $2.96/gallon $2.66/GGE Source: Average prices per gasoline gallon equivalent (GGE) for the New England

Alternative Fuels Data Center: Hawaii Transportation Data for Alternative

Science.gov Websites

Diesel Natural Gas Transportation Fuel Consumption Source: State Energy Data System based on beta data Plant Capacity (nameplate, MW) 145 Source: BioFuels Atlas from the National Renewable Energy Laboratory $2.96/gallon $2.66/GGE Source: Average prices per gasoline gallon equivalent (GGE) for the West Coast

Alternative Fuels Data Center: Montana Transportation Data for Alternative

Science.gov Websites

. Gasoline Diesel Natural Gas Transportation Fuel Consumption Source: State Energy Data System based on beta Renewable Power Plant Capacity (nameplate, MW) 2,955 Source: BioFuels Atlas from the National Renewable /gallon $2.66/GGE Source: Average prices per gasoline gallon equivalent (GGE) for the Rocky Mountain PADD

hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function.

PubMed

Ye, Junqiang; Beetz, Nadine; O'Keeffe, Sean; Tapia, Juan Carlos; Macpherson, Lindsey; Chen, Weisheng V; Bassel-Duby, Rhonda; Olson, Eric N; Maniatis, Tom

2015-06-09

We report that mice lacking the heterogeneous nuclear ribonucleoprotein U (hnRNP U) in the heart develop lethal dilated cardiomyopathy and display numerous defects in cardiac pre-mRNA splicing. Mutant hearts have disorganized cardiomyocytes, impaired contractility, and abnormal excitation-contraction coupling activities. RNA-seq analyses of Hnrnpu mutant hearts revealed extensive defects in alternative splicing of pre-mRNAs encoding proteins known to be critical for normal heart development and function, including Titin and calcium/calmodulin-dependent protein kinase II delta (Camk2d). Loss of hnRNP U expression in cardiomyocytes also leads to aberrant splicing of the pre-mRNA encoding the excitation-contraction coupling component Junctin. We found that the protein product of an alternatively spliced Junctin isoform is N-glycosylated at a specific asparagine site that is required for interactions with specific protein partners. Our findings provide conclusive evidence for the essential role of hnRNP U in heart development and function and in the regulation of alternative splicing.

Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes.

PubMed

Xia, Jun Hong; Li, Hong Lian; Zhang, Yong; Meng, Zi Ning; Lin, Hao Ran

2018-05-01

Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.

Genomic Analysis of Attenuation in Pandemic Vibrio parahaemolyticus

NASA Astrophysics Data System (ADS)

Pinnell, L. J.; Tallman, J. J., III; Turner, J.

2016-02-01

A critical problem in the prevention and treatment of infectious disease is the ability to differentiate virulent from avirulent bacterial strains. The distinction is commonly based on the presence or absence of specific virulence-associated genes. Alternately, serotypic or phylogenetic typing can accurately differentiate virulent from avirulent strains. When these approaches fail, more discriminatory analysis is needed. Pandemic Vibiro parahaemolyticus, distinguishable by genotyping (thermostable direct hemolysin or tdh), serotyping (O3:K6) and multilocus sequence typing (ST3), is regarded as a highly virulent clonal complex. We have previously shown, through population genetics and cytotoxicity testing, that some pandemic strains isolated from environmental sources are avirulent. To investigate the basis for attenuation, we sequenced the draft genomes of 10 pandemic V. parahaemolyticus isolates originating from environmental (N = 7) and clinical sources (N = 3). Genomic comparison of these 10 draft genomes, and the pandemic type strain (RIMD2210633), revealed a large core genome (5,158,719 bp) and a much smaller accessory genome (141,403 bp). The accessory genome was largely comprised of hypothetical proteins; however, several genes encoded phage-related proteins. Phylogenetic analysis, based on 2,902 single nucleotide polymorphisms in the core genome, did not reveal a discernable pattern. Current efforts are focused on the identification of insertions, deletions and point mutations that may alter protein expression or protein function. Preliminary results show that attenuated strains lack the virulence-associated vacB gene (VP1890). This gene encodes a 741 amino acid exoribonuclease homologous to exoribonucleases known to modulate virulence in Salmonella enterica and Helicobacter pylori. The correlation between attenuation and the absence of this gene, suggests that VP1890 plays an important role in human pathogenesis.

Alternative prediction methods of protein and energy evaluation of pig feeds.

PubMed

Święch, Ewa

2017-01-01

Precise knowledge of the actual nutritional value of individual feedstuffs and complete diets for pigs is important for efficient livestock production. Methods of assessment of protein and energy values in pig feeds have been briefly described. In vivo determination of protein and energy values of feeds in pigs are time-consuming, expensive and very often require the use of surgically-modified animals. There is a need for more simple, rapid, inexpensive and reproducible methods for routine feed evaluation. Protein and energy values of pig feeds can be estimated using the following alternative methods: 1) prediction equations based on chemical composition; 2) animal models as rats, cockerels and growing pigs for adult animals; 3) rapid methods, such as the mobile nylon bag technique and in vitro methods. Alternative methods developed for predicting the total tract and ileal digestibility of nutrients including amino acids in feedstuffs and diets for pigs have been reviewed. This article focuses on two in vitro methods that can be used for the routine evaluation of amino acid ileal digestibility and energy value of pig feeds and on factors affecting digestibility determined in vivo in pigs and by alternative methods. Validation of alternative methods has been carried out by comparing the results obtained using these methods with those acquired in vivo in pigs. In conclusion, energy and protein values of pig feeds may be estimated with satisfactory precision in rats and by the two- or three-step in vitro methods providing equations for the calculation of standardized ileal digestibility of amino acids and metabolizable energy content. The use of alternative methods of feed evaluation is an important way for reduction of stressful animal experiments.

Implications of alternate revenue sources for transportation planning.

DOT National Transportation Integrated Search

2011-12-01

This report focuses on selected issues associated with alternative sources of : transportation funding. In particular, this report: presents a list of funding options, : discusses the advantages and disadvantages of each option, explores public attit...

Regulatory nemesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hinkle, K.D.

1980-01-01

It is the purpose of this paper to discuss the impacts of regulations on current and alternate energy sources. It will examine the effect of the maze on the alternate energy sources of solar, oil shale and geothermal. 46 refs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiser, C.; Herdies, L.; McIntosh, L.

Higher plant mitochondria posses a cyanide-resistant, hydroxamate-sensitive alternative pathway of electron transport that does not conserve energy. Aging of potato tuber slices for 24 hours leads to the development of an alternative pathway capacity. We have shown that a monoclonal antibody raised against the alternative pathway terminal oxidase of Sauromatum guttatum crossreacts with a protein of similar size in aged potato slice mitochondria. This protein was partially purified and characterized by two-dimensional gel electrophoresis, and its relative levels parallel the rise in cyanide-resistant respiration. We are using a putative clone of the S. guttatum alternative oxidase gene to isolate themore » equivalent gene from potato and to examine its expression.« less

JMJD6 and U2AF65 co-regulate alternative splicing in both JMJD6 enzymatic activity dependent and independent manner.

PubMed

Yi, Jia; Shen, Hai-Feng; Qiu, Jin-Song; Huang, Ming-Feng; Zhang, Wen-Juan; Ding, Jian-Cheng; Zhu, Xiao-Yan; Zhou, Yu; Fu, Xiang-Dong; Liu, Wen

2017-04-07

JMJD6, a jumonji C (Jmj C) domain-containing protein demethylase and hydroxylase, has been implicated in an array of biological processes. It has been shown that JMJD6 interacts with and hydroxylates multiple serine/arginine-rich (SR) proteins and SR related proteins, including U2AF65, all of which are known to function in alternative splicing regulation. However, whether JMJD6 is widely involved in alternative splicing and the molecular mechanism underlying JMJD6-regulated alternative splicing have remained incompletely understood. Here, by using RASL-Seq, we investigated the functional impact of RNA-dependent interaction between JMJD6 and U2AF65, revealing that JMJD6 and U2AF65 co-regulated a large number of alternative splicing events. We further demonstrated the JMJD6 function in alternative splicing in jmjd6 knockout mice. Mechanistically, we showed that the enzymatic activity of JMJD6 was required for a subset of JMJD6-regulated splicing, and JMJD6-mediated lysine hydroxylation of U2AF65 could account for, at least partially, their co-regulated alternative splicing events, suggesting both JMJD6 enzymatic activity-dependent and independent control of alternative splicing. These findings reveal an intimate link between JMJD6 and U2AF65 in alternative splicing regulation, which has important implications in development and disease processes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Process Design and Economics of On-Site Cellulase Production on Various Carbon Sources in a Softwood-Based Ethanol Plant

PubMed Central

Barta, Zsolt; Kovacs, Krisztina; Reczey, Kati; Zacchi, Guido

2010-01-01

On-site cellulase enzyme fermentation in a softwood-to-ethanol process, based on SO2-catalysed steam pretreatment followed by simultaneous saccharification and fermentation, was investigated from a techno-economic aspect using Aspen Plus© and Aspen Icarus Process Evaluator© softwares. The effect of varying the carbon source of enzyme fermentation, at constant protein and mycelium yields, was monitored through the whole process. Enzyme production step decreased the overall ethanol yield (270 L/dry tonne of raw material in the case of purchased enzymes) by 5–16 L/tonne. Capital cost was found to be the main cost contributor to enzyme fermentation, constituting to 60–78% of the enzyme production cost, which was in the range of 0.42–0.53 SEK/L ethanol. The lowest minimum ethanol selling prices (4.71 and 4.82 SEK/L) were obtained in those scenarios, where pretreated liquid fraction supplemented with molasses was used as carbon source. In some scenarios, on-site enzyme fermentation was found to be a feasible alternative. PMID:21048869

Process design and economics of on-site cellulase production on various carbon sources in a softwood-based ethanol plant.

PubMed

Barta, Zsolt; Kovacs, Krisztina; Reczey, Kati; Zacchi, Guido

2010-06-28

On-site cellulase enzyme fermentation in a softwood-to-ethanol process, based on SO(2)-catalysed steam pretreatment followed by simultaneous saccharification and fermentation, was investigated from a techno-economic aspect using Aspen Plus© and Aspen Icarus Process Evaluator© softwares. The effect of varying the carbon source of enzyme fermentation, at constant protein and mycelium yields, was monitored through the whole process. Enzyme production step decreased the overall ethanol yield (270 L/dry tonne of raw material in the case of purchased enzymes) by 5-16 L/tonne. Capital cost was found to be the main cost contributor to enzyme fermentation, constituting to 60-78% of the enzyme production cost, which was in the range of 0.42-0.53 SEK/L ethanol. The lowest minimum ethanol selling prices (4.71 and 4.82 SEK/L) were obtained in those scenarios, where pretreated liquid fraction supplemented with molasses was used as carbon source. In some scenarios, on-site enzyme fermentation was found to be a feasible alternative.

Carbon catabolite regulation in Streptomyces: new insights and lessons learned.

PubMed

Romero-Rodríguez, Alba; Rocha, Diana; Ruiz-Villafán, Beatriz; Guzmán-Trampe, Silvia; Maldonado-Carmona, Nidia; Vázquez-Hernández, Melissa; Zelarayán, Augusto; Rodríguez-Sanoja, Romina; Sánchez, Sergio

2017-09-01

One of the most significant control mechanisms of the physiological processes in the genus Streptomyces is carbon catabolite repression (CCR). This mechanism controls the expression of genes involved in the uptake and utilization of alternative carbon sources in Streptomyces and is mostly independent of the phosphoenolpyruvate phosphotransferase system (PTS). CCR also affects morphological differentiation and the synthesis of secondary metabolites, although not all secondary metabolite genes are equally sensitive to the control by the carbon source. Even when the outcome effect of CCR in bacteria is the same, their essential mechanisms can be rather different. Although usually, glucose elicits this phenomenon, other rapidly metabolized carbon sources can also cause CCR. Multiple efforts have been put through to the understanding of the mechanism of CCR in this genus. However, a reasonable mechanism to explain the nature of this process in Streptomyces does not yet exist. Several examples of primary and secondary metabolites subject to CCR will be examined in this review. Additionally, recent advances in the metabolites and protein factors involved in the Streptomyces CCR, as well as their mechanisms will be described and discussed in this review.

Large protein as a potential target for use in rabies diagnostics.

PubMed

Santos Katz, I S; Dias, M H; Lima, I F; Chaves, L B; Ribeiro, O G; Scheffer, K C; Iwai, L K

Rabies is a zoonotic viral disease that remains a serious threat to public health worldwide. The rabies lyssavirus (RABV) genome encodes five structural proteins, multifunctional and significant for pathogenicity. The large protein (L) presents well-conserved genomic regions, which may be a good alternative to generate informative datasets for development of new methods for rabies diagnosis. This paper describes the development of a technique for the identification of L protein in several RABV strains from different hosts, demonstrating that MS-based proteomics is a potential method for antigen identification and a good alternative for rabies diagnosis.

Open Genetic Code: on open source in the life sciences.

PubMed

Deibel, Eric

2014-01-01

The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.

First full dynamic range calibration of the JUNGFRAU photon detector

NASA Astrophysics Data System (ADS)

Redford, S.; Andrä, M.; Barten, R.; Bergamaschi, A.; Brückner, M.; Dinapoli, R.; Fröjdh, E.; Greiffenberg, D.; Lopez-Cuenca, C.; Mezza, D.; Mozzanica, A.; Ramilli, M.; Ruat, M.; Ruder, C.; Schmitt, B.; Shi, X.; Thattil, D.; Tinti, G.; Vetter, S.; Zhang, J.

2018-01-01

The JUNGFRAU detector is a charge integrating hybrid silicon pixel detector developed at the Paul Scherrer Institut for photon science applications, in particular for the upcoming free electron laser SwissFEL. With a high dynamic range, analogue readout, low noise and three automatically switching gains, JUNGFRAU promises excellent performance not only at XFELs but also at synchrotrons in areas such as protein crystallography, ptychography, pump-probe and time resolved measurements. To achieve its full potential, the detector must be calibrated on a pixel-by-pixel basis. This contribution presents the current status of the JUNGFRAU calibration project, in which a variety of input charge sources are used to parametrise the energy response of the detector across four orders of magnitude of dynamic range. Building on preliminary studies, the first full calibration procedure of a JUNGFRAU 0.5 Mpixel module is described. The calibration is validated using alternative sources of charge deposition, including laboratory experiments and measurements at ESRF and LCLS. The findings from these measurements are presented. Calibrated modules have already been used in proof-of-principle style protein crystallography experiments at the SLS. A first look at selected results is shown. Aspects such as the conversion of charge to number of photons, treatment of multi-size pixels and the origin of non-linear response are also discussed.

Spider-Venom Peptides as Bioinsecticides

PubMed Central

Windley, Monique J.; Herzig, Volker; Dziemborowicz, Sławomir A.; Hardy, Margaret C.; King, Glenn F.; Nicholson, Graham M.

2012-01-01

Over 10,000 arthropod species are currently considered to be pest organisms. They are estimated to contribute to the destruction of ~14% of the world’s annual crop production and transmit many pathogens. Presently, arthropod pests of agricultural and health significance are controlled predominantly through the use of chemical insecticides. Unfortunately, the widespread use of these agrochemicals has resulted in genetic selection pressure that has led to the development of insecticide-resistant arthropods, as well as concerns over human health and the environment. Bioinsecticides represent a new generation of insecticides that utilise organisms or their derivatives (e.g., transgenic plants, recombinant baculoviruses, toxin-fusion proteins and peptidomimetics) and show promise as environmentally-friendly alternatives to conventional agrochemicals. Spider-venom peptides are now being investigated as potential sources of bioinsecticides. With an estimated 100,000 species, spiders are one of the most successful arthropod predators. Their venom has proven to be a rich source of hyperstable insecticidal mini-proteins that cause insect paralysis or lethality through the modulation of ion channels, receptors and enzymes. Many newly characterized insecticidal spider toxins target novel sites in insects. Here we review the structure and pharmacology of these toxins and discuss the potential of this vast peptide library for the discovery of novel bioinsecticides. PMID:22741062

Nanostructured biosensor using bioluminescence quenching technique for glucose detection.

PubMed

Chen, Longyan; Chen, Longyi; Dotzert, Michelle; Melling, C W James; Zhang, Jin

2017-08-22

Most methods for monitoring glucose level require an external energy source which may limit their application, particularly in vivo test. Bioluminescence technique offers an alternative way to provide emission light without external energy source by using bioluminescent proteins found from firefly or marine vertebrates and invertebrates. For quick and non-invasive detection of glucose, we herein developed a nanostructured biosensor by applying the bioluminescence technique. Luciferase bioluminescence protein (Rluc) is conjugated with β-cyclodextrin (β-CD). The bioluminescence intensity of Rluc can be quenched by 8 ± 3 nm gold nanoparticles (Au NPs) when Au NPs covalently bind to β-CD. In the presence of glucose, Au NPs are replaced and leave far from Rluc through a competitive reaction, which results in the restored bioluminescence intensity of Rluc. A linear relationship is observed between the restored bioluminescence intensity and the logarithmic glucose concentration in the range of 1-100 µM. In addition, the selectivity of this designed sensor has been evaluated. The performance of the senor for determination of the concentration of glucose in the blood of diabetic rats is studied for comparison with that of the concentration of glucose in aqueous. This study demonstrates the design of a bioluminescence sensor for quickly detecting the concentration of glucose sensitively.

Dynamic Balancing of Isoprene Carbon Sources Reflects Photosynthetic and Photorespiratory Responses to Temperature Stress1[W][OPEN

PubMed Central

Chambers, Jeffrey; Alves, Eliane G.; Teixeira, Andrea; Garcia, Sabrina; Holm, Jennifer; Higuchi, Niro; Manzi, Antonio; Abrell, Leif; Fuentes, Jose D.; Nielsen, Lars K.; Torn, Margaret S.; Vickers, Claudia E.

2014-01-01

The volatile gas isoprene is emitted in teragrams per annum quantities from the terrestrial biosphere and exerts a large effect on atmospheric chemistry. Isoprene is made primarily from recently fixed photosynthate; however, alternate carbon sources play an important role, particularly when photosynthate is limiting. We examined the relative contribution of these alternate carbon sources under changes in light and temperature, the two environmental conditions that have the strongest influence over isoprene emission. Using a novel real-time analytical approach that allowed us to examine dynamic changes in carbon sources, we observed that relative contributions do not change as a function of light intensity. We found that the classical uncoupling of isoprene emission from net photosynthesis at elevated leaf temperatures is associated with an increased contribution of alternate carbon. We also observed a rapid compensatory response where alternate carbon sources compensated for transient decreases in recently fixed carbon during thermal ramping, thereby maintaining overall increases in isoprene production rates at high temperatures. Photorespiration is known to contribute to the decline in net photosynthesis at high leaf temperatures. A reduction in the temperature at which the contribution of alternate carbon sources increased was observed under photorespiratory conditions, while photosynthetic conditions increased this temperature. Feeding [2-13C]glycine (a photorespiratory intermediate) stimulated emissions of [13C1–5]isoprene and 13CO2, supporting the possibility that photorespiration can provide an alternate source of carbon for isoprene synthesis. Our observations have important implications for establishing improved mechanistic predictions of isoprene emissions and primary carbon metabolism, particularly under the predicted increases in future global temperatures. PMID:25318937

Dynamic balancing of isoprene carbon sources reflects photosynthetic and photorespiratory responses to temperature stress.

PubMed

Jardine, Kolby; Chambers, Jeffrey; Alves, Eliane G; Teixeira, Andrea; Garcia, Sabrina; Holm, Jennifer; Higuchi, Niro; Manzi, Antonio; Abrell, Leif; Fuentes, Jose D; Nielsen, Lars K; Torn, Margaret S; Vickers, Claudia E

2014-12-01

The volatile gas isoprene is emitted in teragrams per annum quantities from the terrestrial biosphere and exerts a large effect on atmospheric chemistry. Isoprene is made primarily from recently fixed photosynthate; however, alternate carbon sources play an important role, particularly when photosynthate is limiting. We examined the relative contribution of these alternate carbon sources under changes in light and temperature, the two environmental conditions that have the strongest influence over isoprene emission. Using a novel real-time analytical approach that allowed us to examine dynamic changes in carbon sources, we observed that relative contributions do not change as a function of light intensity. We found that the classical uncoupling of isoprene emission from net photosynthesis at elevated leaf temperatures is associated with an increased contribution of alternate carbon. We also observed a rapid compensatory response where alternate carbon sources compensated for transient decreases in recently fixed carbon during thermal ramping, thereby maintaining overall increases in isoprene production rates at high temperatures. Photorespiration is known to contribute to the decline in net photosynthesis at high leaf temperatures. A reduction in the temperature at which the contribution of alternate carbon sources increased was observed under photorespiratory conditions, while photosynthetic conditions increased this temperature. Feeding [2-(13)C]glycine (a photorespiratory intermediate) stimulated emissions of [(13)C1-5]isoprene and (13)CO2, supporting the possibility that photorespiration can provide an alternate source of carbon for isoprene synthesis. Our observations have important implications for establishing improved mechanistic predictions of isoprene emissions and primary carbon metabolism, particularly under the predicted increases in future global temperatures. © 2014 American Society of Plant Biologists. All Rights Reserved.

Effects of Dietary Protein Source and Quantity during Weight Loss on Appetite, Energy Expenditure, and Cardio-Metabolic Responses.

PubMed

Li, Jia; Armstrong, Cheryl L H; Campbell, Wayne W

2016-01-26

Higher protein meals increase satiety and the thermic effect of feeding (TEF) in acute settings, but it is unclear whether these effects remain after a person becomes acclimated to energy restriction or a given protein intake. This study assessed the effects of predominant protein source (omnivorous, beef/pork vs. lacto-ovo vegetarian, soy/legume) and quantity (10%, 20%, or 30% of energy from protein) on appetite, energy expenditure, and cardio-metabolic indices during energy restriction (ER) in overweight and obese adults. Subjects were randomly assigned to one protein source and then consumed diets with different quantities of protein (4 weeks each) in a randomized crossover manner. Perceived appetite ratings (free-living and in-lab), TEF, and fasting cardio-metabolic indices were assessed at the end of each 4-week period. Protein source and quantity did not affect TEF, hunger, or desire to eat, other than a modestly higher daily composite fullness rating with 30% vs. 10% protein diet (p = 0.03). While the 20% and 30% protein diets reduced cholesterol, triacylglycerol, and APO-B vs. 10% protein (p < 0.05), protein source did not affect cardio-metabolic indices. In conclusion, diets varying in protein quantity with either beef/pork or soy/legume as the predominant source have minimal effects on appetite control, energy expenditure and cardio-metabolic risk factors during ER-induced weight loss.

A kinetic study on sesame cake protein hydrolysis by Alcalase.

PubMed

Demirhan, Elçin; Apar, Dilek Kılıç; Özbek, Belma

2011-01-01

In the present study, the hydrolysis of sesame cake protein was performed by Alcalase, a bacterial protease produced by Bacillus licheniformis, to investigate the reaction kinetics of sesame cake hydrolysis and to determine decay and product inhibition effects for Alcalase. The reactions were carried out for 10 min in 0.1 L of aqueous solutions containing 10, 15, 20, 25, and 30 g protein/L at various temperature and pH values. To determine decay and product inhibition effects for Alcalase, a series of inhibition experiments were conducted with the addition of various amounts of hydrolysate. The reaction kinetics was investigated by initial rate approach. The initial reaction rates were determined from the slopes of the linear models that fitted to the experimental data. The kinetic parameters, K(m) and V(max), were estimated as 41.17 g/L and 9.24 meqv/L x min. The Lineweaver-Burk plots showed that the type of inhibition for Alcalase determined as uncompetitive, and the inhibition constant, K(i), was estimated as 38.24% (hydrolysate/substrate mixture). Practical Application: Plant proteins are increasingly being used as an alternative to proteins from animal sources to perform functional roles in food formulation. Knowledge of the kinetics of the hydrolysis reaction is essential for the optimization of enzymatic protein hydrolysis and for increasing the utilization of plant proteins in food products. Therefore, in the present study, the hydrolysis of sesame cake protein was performed by Alcalase, a bacterial protease produced by B. licheniformis, to investigate the reaction kinetics of sesame cake hydrolysis and to determine decay and product inhibition effects for Alcalase.

Origins of Genes: "Big Bang" or Continuous Creation?

NASA Astrophysics Data System (ADS)

Kesse, Paul K.; Gibbs, Adrian

1992-10-01

Many protein families are common to all cellular organisms, indicating that many genes have ancient origins. Genetic variation is mostly attributed to processes such as mutation, duplication, and rearrangement of ancient modules. Thus it is widely assumed that much of present-day genetic diversity can be traced by common ancestry to a molecular "big bang." A rarely considered alternative is that proteins may arise continuously de novo. One mechanism of generating different coding sequences is by "overprinting," in which an existing nucleotide sequence is translated de novo in a different reading frame or from noncoding open reading frames. The clearest evidence for overprinting is provided when the original gene function is retained, as in overlapping genes. Analysis of their phylogenies indicates which are the original genes and which are their informationally novel partners. We report here the phylogenetic relationships of overlapping coding sequences from steroid-related receptor genes and from tymovirus, luteovirus, and lentivirus genomes. For each pair of overlapping coding sequences, one is confined to a single lineage, whereas the other is more widespread. This suggests that the phylogenetically restricted coding sequence arose only in the progenitor of that lineage by translating an out-of-frame sequence to yield the new polypeptide. The production of novel exons by alternative splicing in thyroid receptor and lentivirus genes suggests that introns can be a valuable evolutionary source for overprinting. New genes and their products may drive major evolutionary changes.

Power from Ocean Waves.

ERIC Educational Resources Information Center

Newman, J. N.

1979-01-01

Discussed is the utilization of surface ocean waves as a potential source of power. Simple and large-scale wave power devices and conversion systems are described. Alternative utilizations, environmental impacts, and future prospects of this alternative energy source are detailed. (BT)

Alternative Sources of Funding Early Childhood Education for School Effectiveness in Nigeria

ERIC Educational Resources Information Center

Olubor, Roseline O.; Inua, Ofe I.

2015-01-01

The authors examined the sources of funding early childhood education in existence in Nigeria with a view towards suggesting alternative sources to boost the revenue base for school effectiveness. The diminishing culture of the extended family system and the need for both parents to be in employment coupled with the need to provide access and…

Alternative Fuels Data Center: Iowa Transportation Data for Alternative

Science.gov Websites

Consumption Source: State Energy Data System based on beta data converted to gasoline gallon equivalents of (bbl/day) 0 Renewable Power Plants 41 Renewable Power Plant Capacity (nameplate, MW) 3,807 Source /gallon $2.60/GGE $2.96/gallon $2.66/GGE Source: Average prices per gasoline gallon equivalent (GGE) for

Phenylbutyrate improves nitrogen disposal via alternative pathway without eliciting an increase in protein breakdown and catabolism in control and ornithine transcarbamylace-deficient patients

USDA-ARS?s Scientific Manuscript database

Phenylbutyrate (PB) is a drug used in urea cycle disorder patients to elicit alternative pathways for nitrogen disposal. However, PB decreases plasma branched chain amino acid (BCAA) concentrations and prior research suggests that PB may increase leucine oxidation, indicating increased protein degra...

Rumen-degradable protein in roll conditioned or macerated legume hays and silages estimated by in situ kinetics vs. alternative methods

USDA-ARS?s Scientific Manuscript database

Alternatives to the in situ method for estimating rumen-degradable protein (RDP) in diverse forage legumes should be validated. In this study, RDP in roll conditioned or macerated silages and hays of Medicago, Lotus, and Trifolium species with differing polyphenol compositions were estimated from in...

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

PubMed

Mo, Fan; Hong, Xu; Gao, Feng; Du, Lin; Wang, Jun; Omenn, Gilbert S; Lin, Biaoyang

2008-12-16

Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.

Interplay between intrinsic noise and the stochasticity of the cell cycle in bacterial colonies.

PubMed

Canela-Xandri, Oriol; Sagués, Francesc; Buceta, Javier

2010-06-02

Herein we report on the effects that different stochastic contributions induce in bacterial colonies in terms of protein concentration and production. In particular, we consider for what we believe to be the first time cell-to-cell diversity due to the unavoidable randomness of the cell-cycle duration and its interplay with other noise sources. To that end, we model a recent experimental setup that implements a protein dilution protocol by means of division events to characterize the gene regulatory function at the single cell level. This approach allows us to investigate the effect of different stochastic terms upon the total randomness experimentally reported for the gene regulatory function. In addition, we show that the interplay between intrinsic fluctuations and the stochasticity of the cell-cycle duration leads to different constructive roles. On the one hand, we show that there is an optimal value of protein concentration (alternatively an optimal value of the cell cycle phase) such that the noise in protein concentration attains a minimum. On the other hand, we reveal that there is an optimal value of the stochasticity of the cell cycle duration such that the coherence of the protein production with respect to the colony average production is maximized. The latter can be considered as a novel example of the recently reported phenomenon of diversity induced resonance. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Protein Expression Modifications in Phage-Resistant Mutants of Aeromonas salmonicida after AS-A Phage Treatment

PubMed Central

Osório, Nádia; Pereira, Carla; Simões, Sara; Delgadillo, Ivonne

2018-01-01

The occurrence of infections by pathogenic bacteria is one of the main sources of financial loss for the aquaculture industry. This problem often cannot be solved with antibiotic treatment or vaccination. Phage therapy seems to be an alternative environmentally-friendly strategy to control infections. Recognizing the cellular modifications that bacteriophage therapy may cause to the host is essential in order to confirm microbial inactivation, while understanding the mechanisms that drive the development of phage-resistant strains. The aim of this work was to detect cellular modifications that occur after phage AS-A treatment in A. salmonicida, an important fish pathogen. Phage-resistant and susceptible cells were subjected to five successive streak-plating steps and analysed with infrared spectroscopy, a fast and powerful tool for cell study. The spectral differences of both populations were investigated and compared with a phage sensitivity profile, obtained through the spot test and efficiency of plating. Changes in protein associated peaks were found, and these results were corroborated by 1-D electrophoresis of intracellular proteins analysis and by phage sensitivity profiles. Phage AS-A treatment before the first streaking-plate step clearly affected the intracellular proteins expression levels of phage-resistant clones, altering the expression of distinct proteins during the subsequent five successive streak-plating steps, making these clones recover and be phenotypically more similar to the sensitive cells. PMID:29518018

Sustainable production of housefly (Musca domestica) larvae as a protein-rich feed ingredient by utilizing cattle manure.

PubMed

Hussein, Mahmoud; Pillai, Viju V; Goddard, Joshua M; Park, Hui G; Kothapalli, Kumar S; Ross, Deborah A; Ketterings, Quirine M; Brenna, J Thomas; Milstein, Mark B; Marquis, Helene; Johnson, Patricia A; Nyrop, Jan P; Selvaraj, Vimal

2017-01-01

The common housefly, Musca domestica, is a considerable component of nutrient recycling in the environment. Use of housefly larvae to biodegrade manure presents an opportunity to reduce waste disposal while the rapidly assimilated insect biomass can also be used as a protein rich animal feed. In this study, we examine the biodegradation of dairy cattle manure using housefly larvae, and the nutritional value of the resulting larva meal as a feed ingredient. Our results demonstrated that dairy cattle manure presents a balanced substrate for larval growth, and the spent manure showed reductions in concentration of total nitrogen (24.9%) and phosphorus (6.2%) with an overall reduction in mass. Larva yield at an optimum density was approximately 2% of manure weight. Nutritional analysis of M. domestica larva meal showed values comparable to most high protein feed ingredients. Larva meal was 60% protein with a well-balanced amino acid profile, and 20% fat with 57% monounsaturated fatty acids, and 39% saturated fatty acids. Larva meal lacked any significant amount of omega-3 fatty acids. Evaluation of micronutrients in larva meal suggested that it is a good source of calcium and phosphorus (0.5% and 1.1% respectively). The nutritional value of larva meal closely matches that of fishmeal, making it a potentially attractive alternative for use as a protein-rich feed ingredient for livestock and aquaculture operations.

Sustainable production of housefly (Musca domestica) larvae as a protein-rich feed ingredient by utilizing cattle manure

PubMed Central

Hussein, Mahmoud; Pillai, Viju V.; Goddard, Joshua M.; Park, Hui G.; Kothapalli, Kumar S.; Ross, Deborah A.; Ketterings, Quirine M.; Brenna, J. Thomas; Milstein, Mark B.; Marquis, Helene; Johnson, Patricia A.; Nyrop, Jan P.

2017-01-01

The common housefly, Musca domestica, is a considerable component of nutrient recycling in the environment. Use of housefly larvae to biodegrade manure presents an opportunity to reduce waste disposal while the rapidly assimilated insect biomass can also be used as a protein rich animal feed. In this study, we examine the biodegradation of dairy cattle manure using housefly larvae, and the nutritional value of the resulting larva meal as a feed ingredient. Our results demonstrated that dairy cattle manure presents a balanced substrate for larval growth, and the spent manure showed reductions in concentration of total nitrogen (24.9%) and phosphorus (6.2%) with an overall reduction in mass. Larva yield at an optimum density was approximately 2% of manure weight. Nutritional analysis of M. domestica larva meal showed values comparable to most high protein feed ingredients. Larva meal was 60% protein with a well-balanced amino acid profile, and 20% fat with 57% monounsaturated fatty acids, and 39% saturated fatty acids. Larva meal lacked any significant amount of omega-3 fatty acids. Evaluation of micronutrients in larva meal suggested that it is a good source of calcium and phosphorus (0.5% and 1.1% respectively). The nutritional value of larva meal closely matches that of fishmeal, making it a potentially attractive alternative for use as a protein-rich feed ingredient for livestock and aquaculture operations. PMID:28170420

Characterization of two distinct dual specificity phosphatases encoded in alternative open reading frames of a single gene located on human chromosome 10q22.2.

PubMed

Chen, Hsu-Hsin; Luche, Ralf; Wei, Bo; Tonks, Nicholas K

2004-10-01

Dual specificity phosphatases (DSPs) are members of the protein-tyrosine phosphatase superfamily that dephosphorylate both phosphotyrosine and phosphoserine/threonine residues in vitro. Many DSPs have been found to play important roles in various aspects of cellular function and to be involved in human disease. We have identified a gene located on human chromosome 10q22.2, which utilizes alternative open reading frames (ORFs) to encode the following two distinct DSPs: the previously described testis and skeletal muscle-specific dual specificity phosphatase (TMDP) and a novel DSP, muscle-restricted dual specificity phosphatase (MDSP). Use of alternative ORFs encoding distinct proteins from a single gene is extremely rare in eukaryotes, and in all previously reported cases the two proteins produced from one gene are unrelated. To our knowledge this is the first example of a gene from which two distinct proteins of the same family are expressed using alternative ORFs. Here we provide evidence that both MDSP and TMDP proteins are expressed in vivo and are restricted to specific tissues, skeletal muscle and testis, respectively. Most interestingly, the protein expression profiles of both MDSP and TMDP during mouse postnatal development are strikingly similar. MDSP is expressed at very low levels in myotubes and early postnatal muscle. TMDP is not detectable in testis lysate in the first 3 weeks of life. The expression of both MDSP and TMDP proteins was markedly increased at approximately the 3rd week after birth and continued to increase gradually into adulthood, implying that the physiological functions of both DSPs are specific to the mature/late-developing organs. The conserved gene structure and the similarity in postnatal expression profile of these two proteins suggest biological significance of the unusual gene arrangement.

[Research progress in fusion expression of antimicrobial peptides].

PubMed

Ma, Qingshan; Yu, Zhanqiao; Han, Bing; Zhang, Rijun

2011-10-01

Antimicrobial peptides (AMPs) are of great significance in the field of food, feed and medicine due to their wide spectrum of antimicrobial activity and new mechanism of action different from conventional antibiotics. AMPs production from natural sources is usually limited, and chemical synthesis is not economically practical, especially for the production of long peptides. Therefore, heterologous expression of AMPs has been widely studied as an alternative, and fusion expression plays an important role in increasing production. The present review mainly focuses on the types and bioactivities of AMPs. In addition, the recent strategies to the most commonly used carrier proteins for fusion expression of AMPs and prospects for future research were also discussed.

Generation of Hepatocytes from Pluripotent Stem Cells for Drug Screening and Developmental Modeling.

PubMed

Gieseck, Richard L; Vallier, Ludovic; Hannan, Nicholas R F

2015-01-01

Hepatocytes produced from the differentiation of human pluripotent stem cells can be used to study human development and liver disease, to investigate the toxicological response of novel drug candidates, and as an alternative source of primary cells for transplantation therapies. Here, we describe a method to produce hepatocytes by differentiating human pluripotent stem cells into definitive endoderm, patterning definitive endoderm into anterior definitive endoderm, specifying anterior definitive endoderm into hepatic endoderm, and differentiating hepatic endoderm into immature hepatocytes. These cells are further matured in either two-dimensional or three-dimensional culture conditions to produce cells capable of metabolizing xenobiotics and generating liver-specific proteins, such as albumin and alpha 1 antitrypsin.

Inland capture fishery contributions to global food security and threats to their future

USGS Publications Warehouse

Youn, So-Jung; Taylor, William W.; Lynch, Abigail J.; Cowx, Ian G.; Beard, T. Douglas; Bartley, Devin; Wu, Felicia

2014-01-01

Inland fish and fisheries play important roles in ensuring global food security. They provide a crucial source of animal protein and essential micronutrients for local communities, especially in the developing world. Data concerning fisheries production and consumption of freshwater fish are generally inadequately assessed, often leading decision makers to undervalue their importance. Modification of inland waterways for alternative uses of freshwater (particularly dams for hydropower and water diversions for human use) negatively impacts the productivity of inland fisheries for food security at local and regional levels. This paper highlights the importance of inland fisheries to global food security, the challenges they face due to competing demands for freshwater, and possible solutions.

Immortalized Human Hepatic Cell Lines for In Vitro Testing and Research Purposes.

PubMed

Ramboer, Eva; Vanhaecke, Tamara; Rogiers, Vera; Vinken, Mathieu

2015-01-01

The ubiquitous shortage of primary human hepatocytes has urged the scientific community to search for alternative cell sources, such as immortalized hepatic cell lines. Over the years, several human hepatic cell lines have been produced, whether or not using a combination of viral oncogenes and human telomerase reverse transcriptase protein. Conditional approaches for hepatocyte immortalization have also been established and allow generation of growth-controlled cell lines. A variety of immortalized human hepatocytes have already proven useful as tools for liver-based in vitro testing and fundamental research purposes. The present chapter describes currently applied immortalization strategies and provides an overview of the actually available immortalized human hepatic cell lines and their in vitro applications.

Links between Dietary Protein Sources, the Gut Microbiota, and Obesity.

PubMed

Madsen, Lise; Myrmel, Lene S; Fjære, Even; Liaset, Bjørn; Kristiansen, Karsten

2017-01-01

The association between the gut microbiota and obesity is well documented in both humans and in animal models. It is also demonstrated that dietary factors can change the gut microbiota composition and obesity development. However, knowledge of how diet, metabolism and gut microbiota mutually interact and modulate energy metabolism and obesity development is still limited. Epidemiological studies indicate an association between intake of certain dietary protein sources and obesity. Animal studies confirm that different protein sources vary in their ability to either prevent or induce obesity. Different sources of protein such as beans, vegetables, dairy, seafood, and meat differ in amino acid composition. Further, the type and level of other factors, such as fatty acids and persistent organic pollutants (POPs) vary between dietary protein sources. All these factors can modulate the composition of the gut microbiota and may thereby influence their obesogenic properties. This review summarizes evidence of how different protein sources affect energy efficiency, obesity development, and the gut microbiota, linking protein-dependent changes in the gut microbiota with obesity.

Links between Dietary Protein Sources, the Gut Microbiota, and Obesity

PubMed Central

Madsen, Lise; Myrmel, Lene S.; Fjære, Even; Liaset, Bjørn; Kristiansen, Karsten

2017-01-01

The association between the gut microbiota and obesity is well documented in both humans and in animal models. It is also demonstrated that dietary factors can change the gut microbiota composition and obesity development. However, knowledge of how diet, metabolism and gut microbiota mutually interact and modulate energy metabolism and obesity development is still limited. Epidemiological studies indicate an association between intake of certain dietary protein sources and obesity. Animal studies confirm that different protein sources vary in their ability to either prevent or induce obesity. Different sources of protein such as beans, vegetables, dairy, seafood, and meat differ in amino acid composition. Further, the type and level of other factors, such as fatty acids and persistent organic pollutants (POPs) vary between dietary protein sources. All these factors can modulate the composition of the gut microbiota and may thereby influence their obesogenic properties. This review summarizes evidence of how different protein sources affect energy efficiency, obesity development, and the gut microbiota, linking protein-dependent changes in the gut microbiota with obesity. PMID:29311977

Regulation of Aspergillus nidulans CreA-Mediated Catabolite Repression by the F-Box Proteins Fbx23 and Fbx47.

PubMed

de Assis, Leandro José; Ulas, Mevlut; Ries, Laure Nicolas Annick; El Ramli, Nadia Ali Mohamed; Sarikaya-Bayram, Ozlem; Braus, Gerhard H; Bayram, Ozgur; Goldman, Gustavo Henrique

2018-06-19

The attachment of one or more ubiquitin molecules by SCF ( S kp- C ullin- F -box) complexes to protein substrates targets them for subsequent degradation by the 26S proteasome, allowing the control of numerous cellular processes. Glucose-mediated signaling and subsequent carbon catabolite repression (CCR) are processes relying on the functional regulation of target proteins, ultimately controlling the utilization of this carbon source. In the filamentous fungus Aspergillus nidulans , CCR is mediated by the transcription factor CreA, which modulates the expression of genes encoding biotechnologically relevant enzymes. Although CreA-mediated repression of target genes has been extensively studied, less is known about the regulatory pathways governing CCR and this work aimed at further unravelling these events. The Fbx23 F-box protein was identified as being involved in CCR and the Δ fbx23 mutant presented impaired xylanase production under repressing (glucose) and derepressing (xylan) conditions. Mass spectrometry showed that Fbx23 is part of an SCF ubiquitin ligase complex that is bridged via the GskA protein kinase to the CreA-SsnF-RcoA repressor complex, resulting in the degradation of the latter under derepressing conditions. Upon the addition of glucose, CreA dissociates from the ubiquitin ligase complex and is transported into the nucleus. Furthermore, casein kinase is important for CreA function during glucose signaling, although the exact role of phosphorylation in CCR remains to be determined. In summary, this study unraveled novel mechanistic details underlying CreA-mediated CCR and provided a solid basis for studying additional factors involved in carbon source utilization which could prove useful for biotechnological applications. IMPORTANCE The production of biofuels from plant biomass has gained interest in recent years as an environmentally friendly alternative to production from petroleum-based energy sources. Filamentous fungi, which naturally thrive on decaying plant matter, are of particular interest for this process due to their ability to secrete enzymes required for the deconstruction of lignocellulosic material. A major drawback in fungal hydrolytic enzyme production is the repression of the corresponding genes in the presence of glucose, a process known as carbon catabolite repression (CCR). This report provides previously unknown mechanistic insights into CCR through elucidating part of the protein-protein interaction regulatory system that governs the CreA transcriptional regulator in the reference organism Aspergillus nidulans in the presence of glucose and the biotechnologically relevant plant polysaccharide xylan. Copyright © 2018 de Assis et al.

The stress-induced heat shock protein 70.3 expression is regulated by a dual-component mechanism involving alternative polyadenylation and HuR.

PubMed

Kraynik, Stephen M; Gabanic, Andrew; Anthony, Sarah R; Kelley, Melissa; Paulding, Waltke R; Roessler, Anne; McGuinness, Michael; Tranter, Michael

2015-06-01

Heat shock protein 70.3 (Hsp70.3) expression increases in response to cellular stress and plays a cytoprotective role. We have previously shown that Hsp70.3 expression is controlled through coordinated post-transcriptional regulation by miRNAs and alternative polyadenylation (APA), and APA-mediated shortening of the Hsp70.3 3'-UTR facilitates increased protein expression. A stress-induced increase in Hsp70.3 mRNA and protein expression is accompanied by alternative polyadenylation (APA)-mediated truncation of the 3'UTR of the Hsp70.3 mRNA transcript. However, the role that APA plays in stress-induced expression of Hsp70.3 remains unclear. Our results show that APA-mediated truncation of the Hsp70.3 3'UTR increases protein expression through enhanced polyribosome loading. Additionally, we demonstrate that the RNA binding protein HuR, which has been previously shown to play a role in mediating APA, is necessary for heat shock mediated increase in Hsp70.3 mRNA and protein. However, it is somewhat surprising to note that HuR does not play a role in APA of the Hsp70.3 mRNA, and these two regulatory events appear to be mutually exclusive regulators of Hsp70.3 expression. These results not only provide important insight to the regulation of stress response genes following heat shock, but also contribute an enhanced understanding of how alternative polyadenylation contributes to gene regulation. Copyright © 2015 Elsevier B.V. All rights reserved.

Smart polyhydroxyalkanoate nanobeads by protein based functionalization.

PubMed

Dinjaski, Nina; Prieto, M Auxiliadora

2015-05-01

The development of innovative medicines and personalized biomedical approaches calls for new generation easily tunable biomaterials that can be manufactured applying straightforward and low-priced technologies. Production of functionalized bacterial polyhydroxyalkanoate (PHA) nanobeads by harnessing their natural carbon-storage granule production system is a thrilling recent development. This branch of nanobiotechnology employs proteins intrinsically binding the PHA granules as tags to immobilize recombinant proteins of interest and design functional nanocarriers for wide range of applications. Additionally, the implementation of new methodological platforms regarding production of endotoxin free PHA nanobeads using Gram-positive bacteria opened new avenues for biomedical applications. This prompts serious considerations of possible exploitation of bacterial cell factories as alternatives to traditional chemical synthesis and sources of novel bioproducts that could dramatically expand possible applications of biopolymers. In the 21st century, we are coming into the age of personalized medicine. There is a growing use of biomaterials in the clinical setting. In this review article, the authors describe the use of natural polyhydroxyalkanoate (PHA) nanoparticulates, which are formed within bacterial cells and can be easily functionalized. The potential uses would include high-affinity bioseparation, enzyme immobilization, protein delivery, diagnostics etc. The challenges of this approach remain the possible toxicity from endotoxin and the high cost of production. Copyright © 2015 Elsevier Inc. All rights reserved.

Evidence for symbiont-induced alteration of a host's gene expression: irreversible loss of SAM synthetase from Amoeba proteus.

PubMed

Choi, J Y; Lee, T W; Jeon, K W; Ahn, T I

1997-01-01

Symbiont-bearing xD amoebae no longer produce a 45-kDa cytoplasmic protein that functions as S-adenosylmethionine synthetase in symbiont-free D amoebae. The absence of the protein in xD amoebae is attributable to xD amoeba's failure to transcribe the corresponding gene as a result of harboring bacterial symbionts. However, xD amoebae have about half the level of enzyme activity found in D amoebae, indicating that they use an alternative source for the enzyme. xD amoebae originated from D amoebae by bacterial infection and now depend on their symbionts for survival. xD amoebae exhibit irreversible nucleolar abnormalities when their symbionts are removed, suggesting that X-bacteria supply the needed enzyme. A monoclonal antibody against the 45-kDa protein was produced and used as a probe in cloning its corresponding cDNA. The product of the cDNA was found to have S-adenosylmethionine synthetase activity. These results show how symbiotic X-bacteria may become essential cellular components of amoeba by supplementing a genetic defect for an amoeba's house-keeping gene that is brought about by an action of X-bacteria themselves. This is the first reported example in which symbionts alter the host's gene expression to block the production of an essential protein.

Fuel-conservative engine technology

NASA Technical Reports Server (NTRS)

Dugan, J. F., Jr.; Mcaulay, J. E.; Reynolds, T. W.; Strack, W. C.

1975-01-01

Aircraft fuel consumption is discussed in terms of its efficient use, and the conversion of energy from sources other than petroleum. Topics discussed include: fuel from coal and oil shale, hydrogen deficiency of alternate sources, alternate fuels evaluation program, and future engines.

ALTERNATIVE ENERGY SOURCES FOR WASTEWATER TREATMENT PLANTS

EPA Science Inventory

The technology assessment provides an introduction to the use of several alternative energy sources at wastewater treatment plants. The report contains fact sheets (technical descriptions) and data sheets (cost and design information) for the technologies. Cost figures and schema...

Human periapical cyst-mesenchymal stem cells differentiate into neuronal cells.

PubMed

Marrelli, M; Paduano, F; Tatullo, M

2015-06-01

It was recently reported that human periapical cysts (hPCys), a commonly occurring odontogenic cystic lesion of inflammatory origin, contain mesenchymal stem cells (MSCs) with the capacity for self-renewal and multilineage differentiation. In this study, periapical inflammatory cysts were compared with dental pulp to determine whether this tissue may be an alternative accessible tissue source of MSCs that retain the potential for neurogenic differentiation. Flow cytometry and immunofluorescence analysis indicated that hPCy-MSCs and dental pulp stem cells spontaneously expressed the neuron-specific protein β-III tubulin and the neural stem-/astrocyte-specific protein glial fibrillary acidic protein (GFAP) in their basal state before differentiation occurs. Furthermore, undifferentiated hPCy-MSCs showed a higher expression of transcripts for neuronal markers (β-III tubulin, NF-M, MAP2) and neural-related transcription factors (MSX-1, Foxa2, En-1) as compared with dental pulp stem cells. After exposure to neurogenic differentiation conditions (neural media containing epidermal growth factor [EGF], basic fibroblast growth factor [bFGF], and retinoic acid), the hPCy-MSCs showed enhanced expression of β-III tubulin and GFAP proteins, as well as increased expression of neurofilaments medium, neurofilaments heavy, and neuron-specific enolase at the transcript level. In addition, neurally differentiated hPCy-MSCs showed upregulated expression of the neural transcription factors Pitx3, Foxa2, Nurr1, and the dopamine-related genes tyrosine hydroxylase and dopamine transporter. The present study demonstrated for the first time that hPCy-MSCs have a predisposition toward the neural phenotype that is increased when exposed to neural differentiation cues, based on upregulation of a comprehensive set of proteins and genes that define neuronal cells. In conclusion, these results provide evidence that hPCy-MSCs might be another optimal source of neural/glial cells for cell-based therapies to treat neurologic diseases. © International & American Associations for Dental Research 2015.

Investigation of the effects of dietary protein source on copper and zinc bioavailability in rainbow trout

USDA-ARS?s Scientific Manuscript database

Limited research has examined the effects that dietary protein sources have on copper (Cu) and Zinc (Zn) absorption, interactions and utilization in rainbow trout. Therefore, the objective of the first trial was to determine what effect protein source (plant vs. animal based), Cu source (complex vs....

Evaluation of formalin-fixed paraffin-embedded tissues in the proteomic analysis of parathyroid glands

PubMed Central

2011-01-01

Background Proteomic research in the field of parathyroid tissues is limited by the very small dimension of the glands and by the low incidence of cancer lesions (1%). Formalin-fixed paraffin-embedded (FFPE) tissue specimens are a potentially valuable resource for discovering protein cancer biomarkers. In this study we have verified the applicability of a heat induced protein extraction from FFPE parathyroid adenoma tissues followed by a gel-based or gel-free proteomic approach in order to achieve protein separation and identification. Results The best results for high quality MS spectra and parameters, were obtained by using a gel-free approach, and up to 163 unique proteins were identified. Similar results were obtained by applying both SDS-out and SDS-out + TCA/Acetone techniques during the gel-free method. Western blot analysis carried out with specific antibodies suggested that the antigenicity was not always preserved, while specific immunoreactions were detected for calmodulin, B box and SPRY domain-containing protein (BSPRY), peroxiredoxin 6 (PRDX 6) and parvalbumin. Conclusions In spite of some limitations mainly due to the extensive formalin-induced covalent cross-linking, our results essentially suggest the applicability of a proteomic approach to FFPE parathyroid specimens. From our point of view, FFPE extracts might be an alternative source, especially in the validation phase of protein biomarkers when a large cohort of samples is required and the low availability of frozen tissues might be constraining. PMID:21651755

In vivo digestomics of milk proteins in human milk and infant formula using a suckling rat pup model.

PubMed

Wada, Yasuaki; Phinney, Brett S; Weber, Darren; Lönnerdal, Bo

2017-02-01

Human milk is the optimal mode of infant feeding for the first several months of life, and infant formulas serve as an alternative when breast-feeding is not possible. Milk proteins have a balanced amino acid composition and some of them provide beneficial bioactivities in their intact forms. They also encrypt a variety of bioactive peptides, possibly contributing to infant health and growth. However, there is limited knowledge of how milk proteins are digested in the gastrointestinal tract and bioactive peptides are released in infants. A peptidomic analysis was conducted to identify peptides released from milk proteins in human milk and infant formula, using a suckling rat pup model. Among the major milk proteins targeted, α-lactalbumin and β-casein in human milk, and β-lactoglobulin and β-casein in infant formula were the main sources of peptides, and these peptides covered large parts of the parental proteins' sequences. Release of peptides was concentrated to specific regions, such as residues 70-92 of β-casein in human milk, residues 39-55 of β-lactoglobulin in infant formula, and residues 57-96 and 145-161 of β-CN in infant formula, where resistance to gastrointestinal digestion was suggested. In the context of bioactive peptides, release of fragments containing known bioactive peptides was confirmed, such as β-CN-derived opioid and antihypertensive peptides. It is therefore likely that these fragments are of biological significance in neonatal health and development. Copyright © 2016 Elsevier Inc. All rights reserved.

Understanding the Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 1 (MMDS1)-Impact of a Disease-Causing Gly208Cys Substitution on Structure and Activity of NFU1 in the Fe/S Cluster Biosynthetic Pathway.

PubMed

Wachnowsky, Christine; Wesley, Nathaniel A; Fidai, Insiya; Cowan, J A

2017-03-24

Iron-sulfur (Fe/S)-cluster-containing proteins constitute one of the largest protein classes, with varied functions that include electron transport, regulation of gene expression, substrate binding and activation, and radical generation. Consequently, the biosynthetic machinery for Fe/S clusters is evolutionarily conserved, and mutations in a variety of putative intermediate Fe/S cluster scaffold proteins can cause disease states, including multiple mitochondrial dysfunctions syndrome (MMDS), sideroblastic anemia, and mitochondrial encephalomyopathy. Herein, we have characterized the impact of defects occurring in the MMDS1 disease state that result from a point mutation (Gly208Cys) near the active site of NFU1, an Fe/S scaffold protein, via an in vitro investigation into the structural and functional consequences. Analysis of protein stability and oligomeric state demonstrates that the mutant increases the propensity to dimerize and perturbs the secondary structure composition. These changes appear to underlie the severely decreased ability of mutant NFU1 to accept an Fe/S cluster from physiologically relevant sources. Therefore, the point mutation on NFU1 impairs downstream cluster trafficking and results in the disease phenotype, because there does not appear to be an alternative in vivo reconstitution path, most likely due to greater protein oligomerization from a minor structural change. Copyright © 2017 Elsevier Ltd. All rights reserved.

Alternative Fuels Data Center: Arkansas Transportation Data for Alternative

Science.gov Websites

Diesel Natural Gas Electricity Transportation Fuel Consumption Source: State Energy Data System based on Renewable Power Plant Capacity (nameplate, MW) 1,349 Source: BioFuels Atlas from the National Renewable $2.50/gallon $2.50/GGE Diesel $2.61/gallon $2.35/GGE $2.96/gallon $2.66/GGE Source: Average prices per

Alternative Fuels Data Center: Nebraska Transportation Data for Alternative

Science.gov Websites

Diesel Natural Gas Transportation Fuel Consumption Source: State Energy Data System based on beta data Capacity (nameplate, MW) 546 Source: BioFuels Atlas from the National Renewable Energy Laboratory Videos $2.50/gallon $2.50/GGE Diesel $2.89/gallon $2.60/GGE $2.96/gallon $2.66/GGE Source: Average prices per

Alternative Fuels Data Center: Utah Transportation Data for Alternative

Science.gov Websites

Transportation Fuel Consumption Source: State Energy Data System based on beta data converted to gasoline gallon Source: BioFuels Atlas from the National Renewable Energy Laboratory Case Studies Video thumbnail for /gallon $2.42/GGE $2.50/gallon $2.50/GGE Diesel $2.82/gallon $2.54/GGE $2.96/gallon $2.66/GGE Source

40 CFR 97.212 - Changing CAIR designated representative and alternate CAIR designated representative; changes in...

Code of Federal Regulations, 2010 CFR

2010-07-01

...) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS CAIR Designated Representative for CAIR SO2 Sources § 97.212 Changing CAIR designated representative and alternate CAIR designated... representative and the owners and operators of the CAIR SO2 source and the CAIR SO2 units at the source. (b...

Accumulation of Dissolved DMSP by Marine Bacteria and its Degradation Via Bacterivory

NASA Technical Reports Server (NTRS)

Wolfe, Gordon V.

1996-01-01

Several bacterial isolates enriched from seawater using complex media were able to accumulate dimethylsulfoniopropionate (DMSP) from media into cells over several hours without degrading it. Uptake only occurred in metabolically active cells, and was repressed in some strains by the presence of additional carbon sources. Accumulation was also more rapid in osmotically-stressed cells, suggesting DMSP is used as an osmotic solute. Uptake could be blocked by inhibitors of active transport systems (2,4-dinitrophenol, azide, arsenate) and of protein synthesis (chloramphenicol). Some structural analogs such as glycine betaine and S-methyl methionine also blocked DMSP uptake, suggesting that the availability of alternate organic osmolytes may influence DMSP uptake. Stresses such as freezing, heating, or osmotic down shock resulted in partial release of DMSP back to the medium. One strain which contained a DMSP-lyase was also able to accumulate DMSP, and DMS was only produced in the absence of alternate carbon sources. Bacteria containing DMSP were prepared as prey for bacterivorous ciliates and flagellates, to examine the fate of the DMSP during grazing. In all cases, predators metabolized the DMSP in bacteria. In some cases, DMS was produced, but it is not clear if this was due to the predators or to associated bacteria in the non-axenic grazer cultures. Bacterivores may influence DMSP cycling by either modulating populations of DMSP-metabolizing bacteria, or by metabolizing DMSP accumulated by bacterial prey.

Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings.

PubMed

Zhu, Fu-Yuan; Chen, Mo-Xian; Ye, Neng-Hui; Shi, Lu; Ma, Kai-Long; Yang, Jing-Fang; Cao, Yun-Ying; Zhang, Youjun; Yoshida, Takuya; Fernie, Alisdair R; Fan, Guang-Yi; Wen, Bo; Zhou, Ruo; Liu, Tie-Yuan; Fan, Tao; Gao, Bei; Zhang, Di; Hao, Ge-Fei; Xiao, Shi; Liu, Ying-Gao; Zhang, Jianhua

2017-08-01

In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters

DOE PAGES

Seppala, Susanna; Solomon, Kevin V.; Gilmore, Sean P.; ...

2016-12-20

Here, engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. Although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. Anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of these non-conventional organisms. Here, we mined the transcriptome of three recently isolated strains of anaerobic fungi to identify membrane proteins responsible for sensing and transporting biomass hydrolysates within a competitive andmore » rather extreme environment. Using sequence analyses and homology, we identified membrane protein-coding sequences from assembled transcriptomes from three strains of anaerobic gut fungi: Neocallimastix californiae, Anaeromyces robustus, and Piromyces finnis. We identified nearly 2000 transporter components: about half of these are involved in the general secretory pathway and intracellular sorting of proteins; the rest are predicted to be small-solute transporters. Unexpectedly, we found a number of putative sugar binding proteins that are associated with prokaryotic uptake systems; and approximately 100 class C G-protein coupled receptors (GPCRs) with non-canonical putative sugar binding domains. In conclusion, we report the first comprehensive characterization of the membrane protein machinery of biotechnologically relevant anaerobic gut fungi. Apart from identifying conserved machinery for protein sorting and secretion, we identify a large number of putative solute transporters that are of interest for biotechnological applications. Notably, our data suggests that the fungi display a plethora of carbohydrate binding domains at their surface, perhaps as a means to sense and sequester some of the sugars that their biomass degrading, extracellular enzymes produce.« less

Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters.

PubMed

Seppälä, Susanna; Solomon, Kevin V; Gilmore, Sean P; Henske, John K; O'Malley, Michelle A

2016-12-20

Engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. Although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. Anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of these non-conventional organisms. Here, we mined the transcriptome of three recently isolated strains of anaerobic fungi to identify membrane proteins responsible for sensing and transporting biomass hydrolysates within a competitive and rather extreme environment. Using sequence analyses and homology, we identified membrane protein-coding sequences from assembled transcriptomes from three strains of anaerobic gut fungi: Neocallimastix californiae, Anaeromyces robustus, and Piromyces finnis. We identified nearly 2000 transporter components: about half of these are involved in the general secretory pathway and intracellular sorting of proteins; the rest are predicted to be small-solute transporters. Unexpectedly, we found a number of putative sugar binding proteins that are associated with prokaryotic uptake systems; and approximately 100 class C G-protein coupled receptors (GPCRs) with non-canonical putative sugar binding domains. We report the first comprehensive characterization of the membrane protein machinery of biotechnologically relevant anaerobic gut fungi. Apart from identifying conserved machinery for protein sorting and secretion, we identify a large number of putative solute transporters that are of interest for biotechnological applications. Notably, our data suggests that the fungi display a plethora of carbohydrate binding domains at their surface, perhaps as a means to sense and sequester some of the sugars that their biomass degrading, extracellular enzymes produce.

Effect of mineral phosphates on growth and nitrogen fixation of diazotrophic cyanobacteria Anabaena variabilis and Westiellopsis prolifica.

PubMed

Yandigeri, Mahesh S; Yadav, Arvind K; Meena, Kamlesh Kumar; Pabbi, Sunil

2010-03-01

The nitrogen fixing cyanobacterial strains namely Anabaena variabilis (Nostocales, Nostocaceae) and Westiellopsis prolifica (Nostocales, Hapalosiphonaceae) were evaluated for their nitrogen fixation and growth potential in response to different concentrations (10, 20 and 30 mg P) of the alternate insoluble P-sources Mussorie Rock Phosphate and Tricalcium Phosphate. Distinct and significant intergeneric differences were observed with respect to nitrogen fixation measured as Acetylene Reduction Activity (ARA) and growth potential as soluble proteins, total carbohydrate content, dry weight and total chlorophyll content in response to different concentrations of Mussorie Rock Phosphate and Tricalcium Phosphate. Both the strains showed higher soluble protein content at 20 mg P (Mussorie Rock Phosphate) that increased with time of incubation in A. variabilis. Both cyanobacteria recorded maximum Acetylene Reduction Activity at 20 mg P (Tricalcium Phosphate) followed by activity in presence of soluble phosphate (K2HPO4). The mean activity at all concentrations of insoluble phosphate (Mussorie Rock Phosphate and Tricalcium Phosphate) was more than in the presence of soluble phosphate.

Effect of increased CRM₁₉₇ carrier protein dose on meningococcal C bactericidal antibody response.

PubMed

Lee, Lucia H; Blake, Milan S

2012-04-01

New multivalent CRM(197)-based conjugate vaccines are available for childhood immunization. Clinical studies were reviewed to assess meningococcal group C (MenC) antibody responses following MenC-CRM(197) coadministration with CRM(197)-based pneumococcal or Haemophilus influenzae type b conjugate vaccines. Infants receiving a total CRM(197) carrier protein dose of ∼50 μg and concomitant diphtheria-tetanus-acellular pertussis (DTaP)-containing vaccine tended to have lower MenC geometric mean antibody titers and continued to have low titers after the toddler dose. Nevertheless, at least 95% of children in the reported studies achieved a MenC serum bactericidal antibody (SBA) titer of ≥ 1:8 after the last infant or toddler dose. SBA was measured using an assay with a baby rabbit or human complement source. Additional studies are needed to assess long-term antibody persistence and MenC CRM(197) conjugate vaccine immunogenicity using alternative dosing schedules.

A Comprehensive Approach to Assess Feathermeal as an Alternative Protein Source in Aquafeed.

PubMed

Jasour, Mohammad Sedigh; Wagner, Liane; Sundekilde, Ulrik K; Larsen, Bodil K; Greco, Ines; Orlien, Vibeke; Olsen, Karsten; Rasmussen, Hanne T; Hjermitslev, Niels H; Hammershøj, Marianne; Dalsgaard, Anne J T; Dalsgaard, Trine K

2017-12-06

The effect of partially replacing fishmeal in aquafeed with feathermeal (FTH) at three levels (0%: FTH0, 8%: FTH8, 24%: FTH24) and two extrusion temperatures (100 and 130 °C) was evaluated in rainbow trout (Oncorhynchus mykiss) with respect to growth performance, metabolism response, and oxidative status of the feed proteins. Multivariate data analyses revealed that FTH24 correlated positively with high levels of oxidation products, amino acids (AA) racemization, glucogenic AAs level in liver, feed intake (FI), specific growth rate (SGR), and feed conversion ratio (FCR); and low AAs digestibility. Both FI and SGR were significantly increased when 8 and 24% feathermeal was included in the feed extruded at 100 °C, while there was a negative effect on FCR in fish fed FTH24. In conclusion, higher oxidation levels in FTH24 may give rise to metabolic alterations while lower levels of FTH may be considered as fishmeal substitute in aquafeed for rainbow trout.

Modulation of Glucose Transporter Protein by Dietary Flavonoids in Type 2 Diabetes Mellitus

PubMed Central

Hajiaghaalipour, Fatemeh; Khalilpourfarshbafi, Manizheh; Arya, Aditya

2015-01-01

Diabetes mellitus (DM) is a metabolic diseases characterized by hyperglycemia due to insufficient or inefficient insulin secretory response. This chronic disease is a global problem and there is a need for greater emphasis on therapeutic strategies in the health system. Phytochemicals such as flavonoids have recently attracted attention as source materials for the development of new antidiabetic drugs or alternative therapy for the management of diabetes and its related complications. The antidiabetic potential of flavonoids are mainly through their modulatory effects on glucose transporter by enhancing GLUT-2 expression in pancreatic β cells and increasing expression and promoting translocation of GLUT-4 via PI3K/AKT, CAP/Cb1/TC10 and AMPK pathways. This review highlights the recent findings on beneficial effects of flavonoids in the management of diabetes with particular emphasis on the investigations that explore the role of these compounds in modulating glucose transporter proteins at cellular and molecular level. PMID:25892959

Hematopoietic stem cell transplantation donor sources in the 21st century: choosing the ideal donor when a perfect match does not exist.

PubMed

Kekre, Natasha; Antin, Joseph H

2014-07-17

Most patients who require allogeneic stem cell transplantation do not have a matched sibling donor, and many patients do not have a matched unrelated donor. In an effort to increase the applicability of transplantation, alternative donors such as mismatched adult unrelated donors, haploidentical related donors, and umbilical cord blood stem cell products are frequently used when a well matched donor is unavailable. We do not yet have the benefit of randomized trials comparing alternative donor stem cell sources to inform the choice of donor; however, the existing data allow some inferences to be made on the basis of existing observational and phase 2 studies. All 3 alternative donor sources can provide effective lymphohematopoietic reconstitution, but time to engraftment, graft failure rate, graft-versus-host disease, transplant-related mortality, and relapse risk vary by donor source. These factors all contribute to survival outcomes and an understanding of them should help guide clinicians when choosing among alternative donor sources when a matched related or matched unrelated donor is not available. © 2014 by The American Society of Hematology.

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. Daniel Arthur

In recent years, rising populations and regional droughts have caused coal-fired power plants to temporarily curtail or cease production due to a lack of available water for cooling. In addition, concerns about the availability of adequate supplies of cooling water have resulted in cancellation of plans to build much-needed new power plants. These issues, coupled with concern over the possible impacts of global climate change, have caused industry and community planners to seek alternate sources of water to supplement or replace existing supplies. The Department of Energy, through the National Energy Technology Laboratory (NETL) is researching ways to reduce themore » water demands of coal-fired power plants. As part of the NETL Program, ALL Consulting developed an internet-based Catalog of potential alternative sources of cooling water. The Catalog identifies alternative sources of water, such as mine discharge water, oil and gas produced water, saline aquifers, and publicly owned treatment works (POTWs), which could be used to supplement or replace existing surface water sources. This report provides an overview of the Catalog, and examines the benefits and challenges of using these alternative water sources for cooling water.« less

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity

PubMed Central

Milanesi, Luciano; Petrillo, Mauro; Sepe, Leandra; Boccia, Angelo; D'Agostino, Nunzio; Passamano, Myriam; Di Nardo, Salvatore; Tasco, Gianluca; Casadio, Rita; Paolella, Giovanni

2005-01-01

Background Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular processes, such as proliferation, maintenance of cell shape, apoptosys. In many members of the family, additional non-kinase domains contribute further specialization, resulting in subcellular localization, protein binding and regulation of activity, among others. About 500 genes encode members of the kinase family in the human genome, and although many of them represent well known genes, a larger number of genes code for proteins of more recent identification, or for unknown proteins identified as kinase only after computational studies. Results A systematic in silico study performed on the human genome, led to the identification of 5 genes, on chromosome 1, 11, 13, 15 and 16 respectively, and 1 pseudogene on chromosome X; some of these genes are reported as kinases from NCBI but are absent in other databases, such as KinBase. Comparative analysis of 483 gene regions and subsequent computational analysis, aimed at identifying unannotated exons, indicates that a large number of kinase may code for alternately spliced forms or be incorrectly annotated. An InterProScan automated analysis was perfomed to study domain distribution and combination in the various families. At the same time, other structural features were also added to the annotation process, including the putative presence of transmembrane alpha helices, and the cystein propensity to participate into a disulfide bridge. Conclusion The predicted human kinome was extended by identifiying both additional genes and potential splice variants, resulting in a varied panorama where functionality may be searched at the gene and protein level. Structural analysis of kinase proteins domains as defined in multiple sources together with transmembrane alpha helices and signal peptide prediction provides hints to function assignment. The results of the human kinome analysis are collected in the KinWeb database, available for browsing and searching over the internet, where all results from the comparative analysis and the gene structure annotation are made available, alongside the domain information. Kinases may be searched by domain combinations and the relative genes may be viewed in a graphic browser at various level of magnification up to gene organization on the full chromosome set. PMID:16351747

Global regulation of alternative RNA splicing by the SR-rich protein RBM39.

PubMed

Mai, Sanyue; Qu, Xiuhua; Li, Ping; Ma, Qingjun; Cao, Cheng; Liu, Xuan

2016-08-01

RBM39 is a serine/arginine-rich RNA-binding protein that is highly homologous to the splicing factor U2AF65. However, the role of RBM39 in alternative splicing is poorly understood. In this study, RBM39-mediated global alternative splicing was investigated using RNA-Seq and genome-wide RBM39-RNA interactions were mapped via cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq) in wild-type and RBM39-knockdown MCF-7 cells. RBM39 was involved in the up- or down-regulation of the transcript levels of various genes. Hundreds of alternative splicing events regulated by endogenous RBM39 were identified. The majority of these events were cassette exons. Genes containing RBM39-regulated alternative exons were found to be linked to G2/M transition, cellular response to DNA damage, adherens junctions and endocytosis. CLIP-Seq analysis showed that the binding site of RBM39 was mainly in proximity to 5' and 3' splicing sites. Considerable RBM39 binding to mRNAs encoding proteins involved in translation was observed. Of particular importance, ~20% of the alternative splicing events that were significantly regulated by RBM39 were similarly regulated by U2AF65. RBM39 is extensively involved in alternative splicing of RNA and helps regulate transcript levels. RBM39 may modulate alternative splicing similarly to U2AF65 by either directly binding to RNA or recruiting other splicing factors, such as U2AF65. The current study offers a genome-wide view of RBM39's regulatory function in alternative splicing. RBM39 may play important roles in multiple cellular processes by regulating both alternative splicing of RNA molecules and transcript levels. Copyright © 2016 Elsevier B.V. All rights reserved.

Splicing regulatory factors, ageing and age-related disease.

PubMed

Latorre, Eva; Harries, Lorna W

2017-07-01

Alternative splicing is a co-transcriptional process, which allows for the production of multiple transcripts from a single gene and is emerging as an important control point for gene expression. Alternatively expressed isoforms often have antagonistic function and differential temporal or spatial expression patterns, yielding enormous plasticity and adaptability to cells and increasing their ability to respond to environmental challenge. The regulation of alternative splicing is critical for numerous cellular functions in both pathological and physiological conditions, and deregulated alternative splicing is a key feature of common chronic diseases. Isoform choice is controlled by a battery of splicing regulatory proteins, which include the serine arginine rich (SRSF) proteins and the heterogeneous ribonucleoprotein (hnRNP) classes of genes. These important splicing regulators have been implicated in age-related disease, and in the ageing process itself. This review will outline the important contribution of splicing regulator proteins to ageing and age-related disease. Copyright © 2017 Elsevier B.V. All rights reserved.

Autophagy is activated in colorectal cancer cells and contributes to the tolerance to nutrient deprivation.

PubMed

Sato, Kazunori; Tsuchihara, Katsuya; Fujii, Satoshi; Sugiyama, Masanori; Goya, Tomoyuki; Atomi, Yutaka; Ueno, Takashi; Ochiai, Atsushi; Esumi, Hiroyasu

2007-10-15

Several types of cancer cells, including colorectal cancer-derived cell lines, show austerity, the resistance to nutrient starvation, but exactly how cancer cells obtain energy sources under conditions in which their external nutrient supply is extremely limited remains to be clarified. Because autophagy is a catabolic process by which cells supply amino acids from self-digested organelles, cancer cells are likely to use autophagy to obtain amino acids as alternative energy sources. Amino acid deprivation-induced autophagy was assessed in DLD-1 and other colorectal cancer-derived cell lines. The autophagosome-incorporated LC3-II protein level increased after treatment with a combination of autolysosome inhibitors, which interferes with the consumption of autophagosomes. Autophagosome formation was also morphologically confirmed using ectopically expressed green fluorescent protein-LC3 fusion proteins in DLD-1 and SW480 cells. These data suggest that autophagosomes were actively produced and promptly consumed in colorectal cancer cells under nutrient starvation. Autolysosome inhibitors and 3-methyl adenine, which suppresses autophagosome formation, remarkably enhanced apoptosis under amino acid-deprived and glucose-deprived condition. Similar results were obtained in the cells with decreased ATG7 level by the RNA interference. These data suggest that autophagy is pivotal for the survival of colorectal cancer cells that have acquired austerity. Furthermore, autophagosome formation was seen only in the tumor cells but not in the adjacent noncancerous epithelial cells of colorectal cancer specimens. Taken together, autophagy is activated in colorectal cancers in vitro and in vivo, and autophagy may contribute to the survival of the cancer cells in their microenvironment.

Our Town

ERIC Educational Resources Information Center

Robinson, Amanda

2015-01-01

This article outlines an issue-based lesson for a physical science course in which students investigate potential alternative energy sources for Alternatown, a fictitious city. Students are randomly selected to serve as town council members or as representatives of different alternative energy source options put before the council. The…

48 CFR 932.7004-2 - Criteria.

Code of Federal Regulations, 2012 CFR

2012-10-01

... services cannot as a practical matter be obtained from alternate sources without delay or impeding the... Section 932.7004-2 Federal Acquisition Regulations System DEPARTMENT OF ENERGY GENERAL CONTRACTING... such guarantee by reason of alternative sources of supply. (c) The contractor has demonstrated its...

48 CFR 932.7004-2 - Criteria.

Code of Federal Regulations, 2014 CFR

2014-10-01

... services cannot as a practical matter be obtained from alternate sources without delay or impeding the... Section 932.7004-2 Federal Acquisition Regulations System DEPARTMENT OF ENERGY GENERAL CONTRACTING... such guarantee by reason of alternative sources of supply. (c) The contractor has demonstrated its...

48 CFR 932.7004-2 - Criteria.

Code of Federal Regulations, 2013 CFR

2013-10-01

... services cannot as a practical matter be obtained from alternate sources without delay or impeding the... Section 932.7004-2 Federal Acquisition Regulations System DEPARTMENT OF ENERGY GENERAL CONTRACTING... such guarantee by reason of alternative sources of supply. (c) The contractor has demonstrated its...

Supplementing Conservation Practices with Alternative Energy Sources.

ERIC Educational Resources Information Center

Kraetsch, Gayla A.

1981-01-01

Universities and colleges have two major roles: to reduce their own energy consumption and costs, and to develop and test new energy options. Alternative energy sources considered include solar energy, wind power, biomass, hydropower, ocean energy, geothermal heat, coal, and nuclear energy. (MLW)

Complementarity of SOMAscan to LC-MS/MS and RNA-seq for quantitative profiling of human embryonic and mesenchymal stem cells.

PubMed

Billing, Anja M; Ben Hamidane, Hisham; Bhagwat, Aditya M; Cotton, Richard J; Dib, Shaima S; Kumar, Pankaj; Hayat, Shahina; Goswami, Neha; Suhre, Karsten; Rafii, Arash; Graumann, Johannes

2017-01-06

Dynamic range limitations are challenging to proteomics, particularly in clinical samples. Affinity proteomics partially overcomes this, yet suffers from dependence on reagent quality. SOMAscan, an aptamer-based platform for over 1000 proteins, avoids that issue using nucleic acid binders. Targets include low expressed proteins not easily accessible by other approaches. Here we report on the potential of SOMAscan for the study of differently sourced mesenchymal stem cells (MSC) in comparison to LC-MS/MS and RNA sequencing. While targeting fewer analytes, SOMAscan displays high precision and dynamic range coverage, allowing quantification of proteins not measured by the other platforms. Expression between cell types (ESC and MSC) was compared across techniques and uncovered the expected large differences. Sourcing was investigated by comparing subtypes: bone marrow-derived, standard in clinical studies, and ESC-derived MSC, thought to hold similar potential but devoid of inter-donor variability and proliferating faster in vitro. We confirmed subtype-equivalency, as well as vesicle and extracellular matrix related processes in MSC. In contrast, the proliferative nature of ESC was captured less by SOMAscan, where nuclear proteins are underrepresented. The complementary of SOMAscan allowed the comprehensive exploration of CD markers and signaling molecules, not readily accessible otherwise and offering unprecedented potential in subtype characterization. Mesenchymal stem cells (MSC) represent promising stem cell-derived therapeutics as indicated by their application in >500 clinical trials currently registered with the NIH. Tissue-derived MSC require invasive harvesting and imply donor-to-donor differences, to which embryonic stem cell (ESC)-derived MSC may provide an alternative and thus warrant thorough characterization. In continuation of our previous study where we compared in depth embryonic stem cells (ESC) and MSC from two sources (bone marrow and ESC-derived), we included the aptamer-based SOMAscan assay, complementing LC-MS/MS and RNA-seq data. Furthermore, SOMAscan, a targeted proteomics platform developed for analyzing clinical samples, has been benchmarked against established analytical platforms (LC-MS/MS and RNA-seq) using stem cell comparisons as a model. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Alternate-Day High-Fat Diet Induces an Increase in Mitochondrial Enzyme Activities and Protein Content in Rat Skeletal Muscle.

PubMed

Li, Xi; Higashida, Kazuhiko; Kawamura, Takuji; Higuchi, Mitsuru

2016-04-06

Long-term high-fat diet increases muscle mitochondrial enzyme activity and endurance performance. However, excessive calorie intake causes intra-abdominal fat accumulation and metabolic syndrome. The purpose of this study was to investigate the effect of an alternating day high-fat diet on muscle mitochondrial enzyme activities, protein content, and intra-abdominal fat mass in rats. Male Wistar rats were given a standard chow diet (CON), high-fat diet (HFD), or alternate-day high-fat diet (ALT) for 4 weeks. Rats in the ALT group were fed a high-fat diet and standard chow every other day for 4 weeks. After the dietary intervention, mitochondrial enzyme activities and protein content in skeletal muscle were measured. Although body weight did not differ among groups, the epididymal fat mass in the HFD group was higher than those of the CON and ALT groups. Citrate synthase and beta-hydroxyacyl CoA dehydrogenase activities in the plantaris muscle of rats in HFD and ALT were significantly higher than that in CON rats, whereas there was no difference between HFD and ALT groups. No significant difference was observed in muscle glycogen concentration or glucose transporter-4 protein content among the three groups. These results suggest that an alternate-day high-fat diet induces increases in mitochondrial enzyme activities and protein content in rat skeletal muscle without intra-abdominal fat accumulation.

Move over protein kinase C, you've got company: alternative cellular effectors of diacylglycerol and phorbol esters.

PubMed

Brose, Nils; Rosenmund, Christian

2002-12-01

Diacylglycerol is an essential second messenger in mammalian cells. The most prominent intracellular targets of diacylglycerol and of the functionally analogous phorbol esters belong to the protein kinase C (PKC) family. However, at least five alternative types of high-affinity diacylglycerol/phorbol-ester receptor are known: chimaerins, protein kinase D, RasGRPs, Munc13s and DAG kinase gamma. Recent evidence indicates that these have functional roles in diacylglycerol second messenger signalling in vivo and that several cellular processes depend on these targets rather than protein kinase C isozymes. These findings contradict the still prevalent view according to which all diacylglycerol/phorbol-ester effects are caused by the activation of protein kinase C isozymes. RasGRP1 (in Ras/Raf/MEK/ERK signalling) and Munc13-1 (in neurotransmitter secretion) are examples of non-PKC diacylglycerol/phorbol-ester receptors that mediate diacylglycerol and phorbol-ester effects originally thought to be caused by PKC isozymes. In the future, pharmacological studies on PKC must be complemented with alternative experimental approaches to allow the separation of PKC-mediated effects from those caused by alternative targets of the diacylglycerol second messenger pathway. The examples of RasGRP1 and Munc13-1 show that detailed genetic analyses of C(1)-domain-containing non-PKC diacylglycerol/phorbol-ester receptors in mammals are ideally suited to achieve this goal.

Alternative splice variants of AID are not stoichiometrically present at the protein level in chronic lymphocytic leukemia

PubMed Central

Rebhandl, Stefan; Huemer, Michael; Zaborsky, Nadja; Gassner, Franz Josef; Catakovic, Kemal; Felder, Thomas Klaus; Greil, Richard; Geisberger, Roland

2014-01-01

Activation-induced deaminase (AID) is a DNA-mutating enzyme that mediates class-switch recombination as well as somatic hypermutation of antibody genes in B cells. Due to off-target activity, AID is implicated in lymphoma development by introducing genome-wide DNA damage and initiating chromosomal translocations such as c-myc/IgH. Several alternative splice transcripts of AID have been reported in activated B cells as well as malignant B cells such as chronic lymphocytic leukemia (CLL). As most commercially available antibodies fail to recognize alternative splice variants, their abundance in vivo, and hence their biological significance, has not been determined. In this study, we assessed the protein levels of AID splice isoforms by introducing an AID splice reporter construct into cell lines and primary CLL cells from patients as well as from WT and TCL1tg C57BL/6 mice (where TCL1 is T-cell leukemia/lymphoma 1). The splice construct is 5′-fused to a GFP-tag, which is preserved in all splice isoforms and allows detection of translated protein. Summarizing, we show a thorough quantification of alternatively spliced AID transcripts and demonstrate that the corresponding protein abundances, especially those of splice variants AID-ivs3 and AID-ΔE4, are not stoichiometrically equivalent. Our data suggest that enhanced proteasomal degradation of low-abundance proteins might be causative for this discrepancy. PMID:24668151

Application of “omics” to Prion Biomarker Discovery

PubMed Central

Huzarewich, Rhiannon L. C. H.; Siemens, Christine G.; Booth, Stephanie A.

2010-01-01

The advent of genomics and proteomics has been a catalyst for the discovery of biomarkers able to discriminate biological processes such as the pathogenesis of complex diseases. Prompt detection of prion diseases is particularly desirable given their transmissibility, which is responsible for a number of human health risks stemming from exogenous sources of prion protein. Diagnosis relies on the ability to detect the biomarker PrPSc, a pathological isoform of the host protein PrPC, which is an essential component of the infectious prion. Immunochemical detection of PrPSc is specific and sensitive enough for antemortem testing of brain tissue, however, this is not the case in accessible biological fluids or for the detection of recently identified novel prions with unique biochemical properties. A complementary approach to the detection of PrPSc itself is to identify alternative, “surrogate” gene or protein biomarkers indicative of disease. Biomarkers are also useful to track the progress of disease, especially important in the assessment of therapies, or to identify individuals “at risk”. In this review we provide perspective on current progress and pitfalls in the use of “omics” technologies to screen body fluids and tissues for biomarker discovery in prion diseases. PMID:20224650

Optimization studies on production of a salt-tolerant protease from Pseudomonas aeruginosa strain BC1 and its application on tannery saline wastewater treatment

PubMed Central

Sivaprakasam, Senthilkumar; Dhandapani, Balaji; Mahadevan, Surianarayanan

2011-01-01

Treatment and safe disposal of tannery saline wastewater, a primary effluent stream that is generated by soaking salt-laden hides and skin is one of the major problems faced by the leather manufacturing industries. Conventional treatment methods like solar evaporation ponds and land composting are not eco-friendly as they deteriorate the ground water quality. Though, this waste stream is comprised of high concentration of dissolved proteins the presence of high salinity (1–6 % NaCl by wt) makes it non-biodegradable. Enzymatic treatment is one of the positive alternatives for management of such kind of waste streams. A novel salt-tolerant alkaline protease obtained from P.aeruginosa (isolated from tannery saline wastewater) was used for enzymatic degradation studies. The effect of various physical factors including pH, temperature, incubation time, protein source and salinity on the activity of identified protease were investigated. Kinetic parameters (Km , Vmax) were calculated for the identified alkaline protease at varying substrate concentrations. Tannery saline wastewater treated with identified salt tolerant protease showed 75 % protein removal at 6 h duration and 2 % (v/v) protease addition was found to be the optimum dosage value. PMID:24031785

Genome and metabolic engineering in non-conventional yeasts: Current advances and applications.

PubMed

Löbs, Ann-Kathrin; Schwartz, Cory; Wheeldon, Ian

2017-09-01

Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisia e is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.

Fibrinogen inhibits fibroblast-mediated contraction of collagen

PubMed Central

Nien, Yih-Dar; Han, Yuan-Ping; Tawil, Bill; Chan, Linda S.; Tuan, Tai-Lan; Garner, Warren L.

2008-01-01

Extracellular matrix changes in composition and organization as it transitions from the provisional matrix of the fibrin/platelet plug to collagen scar in healed wounds. The manner in which individual matrix proteins affect these activities is not well established. In this article we describe the interactions of two important extracellular matrix components, fibrin and collagen, using an in vitro model of wound contraction, the fibroblast-populated collagen lattice. We utilized different fibrinogen sources and measured tissue reorganization in floating and tensioned collagen lattices. Our results showed that both fibrin and fibrinogen decreased the contraction of fibroblast populated collagen lattices in a dose-dependent manner. Polymerization of fibrinogen to fibrin using thrombin had no effect on this inhibition. Further, there was no effect due to changes in protein concentration, alternate components of the fibrin sealant, or the enzymatic action of thrombin. These results suggest that the initial stability of the fibrin provisional matrix is due to the fibrin, because this protein appears to inhibit contraction of the matrix. This may be important in the early phases of wound healing when clot stability is vital for hemostasis. Later, as fibrin is replaced by collagen, wound contraction can occur. PMID:12950643

Impact of water control projects on fisheries resources in Bangladesh

NASA Astrophysics Data System (ADS)

Mirza, Monirul Qader; Ericksen, Neil J.

1996-07-01

Bangladesh is a very flat delta built up by the Ganges—Brahmaputra—Meghna/Barak river systems. Because of its geographical location, floods cause huge destruction of lives and properties almost every year. Water control programs have been undertaken to enhance development through mitigating the threat of disasters. This structural approach to flood hazard has severely affected floodplain fisheries that supply the major share of protein to rural Bangladesh, as exemplified by the Chandpur Irrigation Project. Although the regulated environment of the Chandpur project has become favorable for closed-water cultured fish farming, the natural open-water fishery loss has been substantial. Results from research show that fish yields were better under preproject conditions. Under project conditions per capita fish consumption has dropped significantly, and the price of fish has risen beyond the means of the poor people, so that fish protein in the diet of poor people is gradually declining. Bangladesh is planning to expand water control facilities to the remaining flood-prone areas in the next 15 20 years. This will cause further loss of floodplain fisheries. If prices for closed-water fish remain beyond the buying power of the poor, alternative sources of cheap protein will be required.

Development of real-time PCR tests for the detection of Tenebrio molitor in food and feed.

PubMed

Debode, Frédéric; Marien, Aline; Gérard, Amaury; Francis, Frédéric; Fumière, Olivier; Berben, Gilbert

2017-08-01

Insects are rich in proteins and could be an alternative source of proteins to feed animals and humans. Numerous companies have started the production of insects for feed purposes. In Europe, these processed animal proteins are not yet authorised by legislation as many questions still need to be answered concerning this 'novel food'. Authorisations will be possible when methods of authentication of the products are available. In this study we propose real-time PCR methods for the specific detection of the mealworm (Tenebriomolitor), one of the most widely used insects for food and feed production. Two PCR assays are proposed: the first based on the wingless gene and the second based on the cadherin gene. The PCR tests amplify fragments of 87 bp. These qualitative methods were tested according to several performance criteria. The specificity was tested on 34 insect species' DNA, but also on non-insect species including crustacean, mammals, birds and plants. The limit of detection was determined and was below 20 copies for the two PCR tests. The applicability of the tests was demonstrated by the analysis of real-life processed samples containing T. molitor.

Helios Dynamics A Potential Future Power Source for the Greek Islands

DTIC Science & Technology

2007-06-01

offer an apparent understanding of the capabilities of the emerging Photovoltaic Power Converter (PVPC) technology used in panels for electricity... powering method that uses fueled generators and the alternative option is photovoltaic panels with the Atira technology embedded. This analysis is... POWER SOURCE FOR THE GREEK ISLANDS ABSTRACT The use of Alternative Renewable Energy Sources is becoming an increasing possibility to

Preliminary Feasibility Report Stage II, Lorain Small-Boat Harbor, Lorain, Ohio. Revision.

DTIC Science & Technology

1982-03-01

effects of each alternative plan. Activities consist of analyzing each measure to deter- mine potential sources , the incidence, and the magni- tude...using existing reports, available data sources , visual inspections, onsite interviews, and workshop discussions. Alternative small-boat harbor designs...were developed to a consistent level of detail. Prior reports were used as data sources for preliminary design of break- waters, including length

40 CFR Table 9 to Subpart Xxxx of... - Minimum Data for Continuous Compliance With the Emission Limits for Tire Production Affected Sources

Code of Federal Regulations, 2010 CFR

2010-07-01

... cement and solvent as purchased. 2. Sources complying with the monthly average compliance alternative... maintain . . . 1. Sources complying with purchase compliance alternative in § 63.5985(a) that are meeting the HAP constituent emission limit (option 1) in Table 1 to this subpart a. A list of each cement and...

Alternate method of source preparation for alpha spectrometry: No electrodeposition, no hydrofluoric acid

DOE PAGES

Kurosaki, Hiromu; Mueller, Rebecca J.; Lambert, Susan B.; ...

2016-07-15

An alternate method of preparing actinide alpha counting sources was developed in place of electrodeposition or lanthanide fluoride micro-precipitation. The method uses lanthanide hydroxide micro-precipitation to avoid the use of hazardous hydrofluoric acid. Lastly, it provides a quicker, simpler, and safer way of preparing actinide alpha counting sources in routine, production-type laboratories that process many samples daily.

In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh.

PubMed

Sheikh, Alaullah; Charles, Richelle C; Sharmeen, Nusrat; Rollins, Sean M; Harris, Jason B; Bhuiyan, Md Saruar; Arifuzzaman, Mohammad; Khanam, Farhana; Bukka, Archana; Kalsy, Anuj; Porwollik, Steffen; Leung, Daniel T; Brooks, W Abdullah; LaRocque, Regina C; Hohmann, Elizabeth L; Cravioto, Alejandro; Logvinenko, Tanya; Calderwood, Stephen B; McClelland, Michael; Graham, James E; Qadri, Firdausi; Ryan, Edward T

2011-12-01

Salmonella enterica serotype Typhi is the cause of typhoid fever. It is a human-restricted pathogen, and few data exist on S. Typhi gene expression in humans. We applied an RNA capture and amplification technique, Selective Capture of Transcribed Sequences (SCOTS), and microarray hybridization to identify S. Typhi transcripts expressed in the blood of five humans infected with S. Typhi in Bangladesh. In total, we detected the expression of mRNAs for 2,046 S. Typhi genes (44% of the S. Typhi genome) in human blood; expression of 912 genes was detected in all 5 patients, and expression of 1,100 genes was detected in 4 or more patients. Identified transcripts were associated with the virulence-associated PhoP regulon, Salmonella pathogenicity islands, the use of alternative carbon and energy sources, synthesis and transport of iron, thiamine, and biotin, and resistance to antimicrobial peptides and oxidative stress. The most highly represented group were genes currently annotated as encoding proteins designated as hypothetical, unknown, or unclassified. Of the 2,046 detected transcripts, 1,320 (29% of the S. Typhi genome) had significantly different levels of detection in human blood compared to in vitro cultures; detection of 141 transcripts was significantly different in all 5 patients, and detection of 331 transcripts varied in at least 4 patients. These mRNAs encode proteins of unknown function, those involved in energy metabolism, transport and binding, cell envelope, cellular processes, and pathogenesis. We confirmed increased expression of a subset of identified mRNAs by quantitative-PCR. We report the first characterization of bacterial transcriptional profiles in the blood of patients with typhoid fever. S. Typhi is an important global pathogen whose restricted host range has greatly inhibited laboratory studies. Our results suggest that S. Typhi uses a largely uncharacterized genetic repertoire to survive within cells and utilize alternate energy sources during infection.

Context-dependent control of alternative splicing by RNA-binding proteins

PubMed Central

Fu, Xiang-Dong; Ares, Manuel

2015-01-01

Sequence-specific RNA-binding proteins (RBPs) bind to pre-mRNA to control alternative splicing, but it is not yet possible to read the ‘splicing code’ that dictates splicing regulation on the basis of genome sequence. Each alternative splicing event is controlled by multiple RBPs, the combined action of which creates a distribution of alternatively spliced products in a given cell type. As each cell type expresses a distinct array of RBPs, the interpretation of regulatory information on a given RNA target is exceedingly dependent on the cell type. RBPs also control each other’s functions at many levels, including by mutual modulation of their binding activities on specific regulatory RNA elements. In this Review, we describe some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation. PMID:25112293

Composition and Potency Characterization of Mycobacterium avium subsp. paratuberculosis Purified Protein Derivatives

PubMed Central

Capsel, Randal T.; Thoen, Charles O.; Reinhardt, Timothy A.; Lippolis, John D.; Olsen, Renee; Stabel, Judith R.; Bannantine, John P.

2016-01-01

Mycobacterium avium subsp. paratuberculosis (MAP) purified protein derivatives (PPDs) are immunologic reagents prepared from cultured filtrates of the type strain. Traditional production consists of floating culture incubation at 37°C, organism inactivation by autoclaving, coarse filtration, and protein precipitation. Three traditional production PPDs were used in this study including lot 9801, which served as a reference and has been used in the field for decades. Alternative production PPDs (0902A and 0902B), in which the autoclaving step was removed, were also analyzed in this study. SDS-PAGE analysis revealed protein smearing in traditional PPDs, but distinct bands were observed in the alternative PPD preparations. Antibody bound distinct protein bands in the alternative PPDs by immunoblot analysis, whereas an immunoreactive smear was observed with the traditional PPDs. Mass spectrometry identified 194 proteins among three PPD lots representing the two different production methods, ten of which were present in all PPDs examined. Selected proteins identified by mass spectrometry were recombinantly expressed and purified from E. coli and evaluated by the guinea pig potency test. Seven recombinant proteins showed greater erythema as compared to the reference PPD lot 9801 in paired guinea pigs and were able to stimulate interferon-gamma production in blood from Johne’s positive animals. These results suggest that autoclaving culture suspensions is not a necessary step in PPD production and specific proteins could supplant the PPD antigen for intradermal skin testing procedures and for use as in-vitro assay reagents. PMID:27136199

Personalizing Protein Nourishment

PubMed Central

DALLAS, DAVID C.; SANCTUARY, MEGAN R.; QU, YUNYAO; KHAJAVI, SHABNAM HAGHIGHAT; VAN ZANDT, ALEXANDRIA E.; DYANDRA, MELISSA; FRESE, STEVEN A.; BARILE, DANIELA; GERMAN, J. BRUCE

2016-01-01

Proteins are not equally digestible—their proteolytic susceptibility varies by their source and processing method. Incomplete digestion increases colonic microbial protein fermentation (putrefaction), which produces toxic metabolites that can induce inflammation in vitro and have been associated with inflammation in vivo. Individual humans differ in protein digestive capacity based on phenotypes, particularly disease states. To avoid putrefaction-induced intestinal inflammation, protein sources and processing methods must be tailored to the consumer’s digestive capacity. This review explores how food processing techniques alter protein digestibility and examines how physiological conditions alter digestive capacity. Possible solutions to improving digestive function or matching low digestive capacity with more digestible protein sources are explored. Beyond the ileal digestibility measurements of protein digestibility, less invasive, quicker and cheaper techniques for monitoring the extent of protein digestion and fermentation are needed to personalize protein nourishment. Biomarkers of protein digestive capacity and efficiency can be identified with the toolsets of peptidomics, metabolomics, microbial sequencing and multiplexed protein analysis of fecal and urine samples. By monitoring individual protein digestive function, the protein component of diets can be tailored via protein source and processing selection to match individual needs to minimize colonic putrefaction and, thus, optimize gut health. PMID:26713355

Soy and cottonseed protein blends as wood adhesives

USDA-ARS?s Scientific Manuscript database

As an environmentally friendlier alternative to adhesives from petroleum feedstock, soy proteins are currently being formulated as wood adhesives. Cottonseed proteins have also been found to provide good adhesive properties. In at least some cases, cottonseed proteins appear to form greater shear ...

Complement proteins bind to nanoparticle protein corona and undergo dynamic exchange in vivo

NASA Astrophysics Data System (ADS)

Chen, Fangfang; Wang, Guankui; Griffin, James I.; Brenneman, Barbara; Banda, Nirmal K.; Holers, V. Michael; Backos, Donald S.; Wu, Linping; Moghimi, Seyed Moein; Simberg, Dmitri

2017-05-01

When nanoparticles are intravenously injected into the body, complement proteins deposit on the surface of nanoparticles in a process called opsonization. These proteins prime the particle for removal by immune cells and may contribute toward infusion-related adverse effects such as allergic responses. The ways complement proteins assemble on nanoparticles have remained unclear. Here, we show that dextran-coated superparamagnetic iron oxide core-shell nanoworms incubated in human serum and plasma are rapidly opsonized with the third complement component (C3) via the alternative pathway. Serum and plasma proteins bound to the nanoworms are mostly intercalated into the nanoworm shell. We show that C3 covalently binds to these absorbed proteins rather than the dextran shell and the protein-bound C3 undergoes dynamic exchange in vitro. Surface-bound proteins accelerate the assembly of the complement components of the alternative pathway on the nanoworm surface. When nanoworms pre-coated with human plasma were injected into mice, C3 and other adsorbed proteins undergo rapid loss. Our results provide important insight into dynamics of protein adsorption and complement opsonization of nanomedicines.

Manufacturing Economics of Plant-Made Biologics: Case Studies in Therapeutic and Industrial Enzymes

PubMed Central

Tusé, Daniel; McDonald, Karen A.

2014-01-01

Production of recombinant biologics in plants has received considerable attention as an alternative platform to traditional microbial and animal cell culture. Industrially relevant features of plant systems include proper eukaryotic protein processing, inherent safety due to lack of adventitious agents, more facile scalability, faster production (transient systems), and potentially lower costs. Lower manufacturing cost has been widely claimed as an intuitive feature of the platform by the plant-made biologics community, even though cost information resides within a few private companies and studies accurately documenting such an advantage have been lacking. We present two technoeconomic case studies representing plant-made enzymes for diverse applications: human butyrylcholinesterase produced indoors for use as a medical countermeasure and cellulases produced in the field for the conversion of cellulosic biomass into ethanol as a fuel extender. Production economics were modeled based on results reported with the latest-generation expression technologies on Nicotiana host plants. We evaluated process unit operations and calculated bulk active and per-dose or per-unit costs using SuperPro Designer modeling software. Our analyses indicate that substantial cost advantages over alternative platforms can be achieved with plant systems, but these advantages are molecule/product-specific and depend on the relative cost-efficiencies of alternative sources of the same product. PMID:24977145

Manufacturing economics of plant-made biologics: case studies in therapeutic and industrial enzymes.

PubMed

Tusé, Daniel; Tu, Tiffany; McDonald, Karen A

2014-01-01

Production of recombinant biologics in plants has received considerable attention as an alternative platform to traditional microbial and animal cell culture. Industrially relevant features of plant systems include proper eukaryotic protein processing, inherent safety due to lack of adventitious agents, more facile scalability, faster production (transient systems), and potentially lower costs. Lower manufacturing cost has been widely claimed as an intuitive feature of the platform by the plant-made biologics community, even though cost information resides within a few private companies and studies accurately documenting such an advantage have been lacking. We present two technoeconomic case studies representing plant-made enzymes for diverse applications: human butyrylcholinesterase produced indoors for use as a medical countermeasure and cellulases produced in the field for the conversion of cellulosic biomass into ethanol as a fuel extender. Production economics were modeled based on results reported with the latest-generation expression technologies on Nicotiana host plants. We evaluated process unit operations and calculated bulk active and per-dose or per-unit costs using SuperPro Designer modeling software. Our analyses indicate that substantial cost advantages over alternative platforms can be achieved with plant systems, but these advantages are molecule/product-specific and depend on the relative cost-efficiencies of alternative sources of the same product.

Test Operations Procedure (TOP) 01-2-624 High Power Microwave (HPM) Testing

DTIC Science & Technology

2015-07-06

Requests _____ The proposed frequency list for the HPM facility is listed below. Source Primary Frequencies (MHz) Alternate Frequencies (MHz) NBTS...during testing. The proposed frequency list for the HPM facility is listed below. Source Primary Frequencies (MHz) Alternate Frequencies (MHz

Aberrant alternative splicing is another hallmark of cancer.

PubMed

Ladomery, Michael

2013-01-01

The vast majority of human genes are alternatively spliced. Not surprisingly, aberrant alternative splicing is increasingly linked to cancer. Splice isoforms often encode proteins that have distinct and even antagonistic properties. The abnormal expression of splice factors and splice factor kinases in cancer changes the alternative splicing of critically important pre-mRNAs. Aberrant alternative splicing should be added to the growing list of cancer hallmarks.

A Plant 5S Ribosomal RNA Mimic Regulates Alternative Splicing of Transcription Factor IIIA Pre-mRNAs

PubMed Central

Hammond, Ming C.; Wachter, Andreas; Breaker, Ronald R.

2009-01-01

Transcription factor IIIA (TFIIIA) is required for eukaryotic synthesis of 5S ribosomal RNA by RNA polymerase III. Here we report the discovery of a structured RNA element with striking resemblance to 5S rRNA that is conserved within TFIIIA precursor mRNAs (pre-mRNAs) from diverse plant lineages. TFIIIA protein expression is controlled by alternative splicing of the exon containing the plant 5S rRNA mimic (P5SM). P5SM triggers exon skipping upon binding of ribosomal protein L5, a natural partner of 5S rRNA, which demonstrates the functional adaptation of its structural mimicry. Since the exon-skipped splice product encodes full-length TFIIIA protein, these results reveal a ribosomal protein-mRNA interaction that is involved in 5S rRNA synthesis and has implications for cross-coordination of ribosomal components. This study also provides insight into the origin and function of a newfound class of structured RNA that regulates alternative splicing. PMID:19377483

A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.

PubMed

Hammond, Ming C; Wachter, Andreas; Breaker, Ronald R

2009-05-01

Transcription factor IIIA (TFIIIA) is required for eukaryotic synthesis of 5S ribosomal RNA by RNA polymerase III. Here we report the discovery of a structured RNA element with clear resemblance to 5S rRNA that is conserved within TFIIIA precursor mRNAs from diverse plant lineages. TFIIIA protein expression is controlled by alternative splicing of the exon containing the plant 5S rRNA mimic (P5SM). P5SM triggers exon skipping upon binding of ribosomal protein L5, a natural partner of 5S rRNA, which demonstrates the functional adaptation of its structural mimicry. As the exon-skipped splice product encodes full-length TFIIIA protein, these results reveal a ribosomal protein-mRNA interaction that is involved in 5S rRNA synthesis and has implications for cross-coordination of ribosomal components. This study also provides insight into the origin and function of a newfound class of structured RNA that regulates alternative splicing.

The role of red meat in the diet: nutrition and health benefits.

PubMed

Wyness, Laura

2016-08-01

Red meat has been an important part of the human diet throughout human evolution. When included as part of a healthy, varied diet, red meat provides a rich source of high biological value protein and essential nutrients, some of which are more bioavailable than in alternative food sources. Particular nutrients in red meat have been identified as being in short supply in the diets of some groups of the population. The present paper discusses the role of red meat in the diets of young infants, adolescents, women of childbearing age and older adults and highlights key nutrients red meat can provide for these groups. The role of red meat in relation to satiety and weight control is discussed as the inclusion of lean red meat in a healthy, varied diet may help weight loss as part of an energy-reduced diet. A summary of the UK advice on the amount of red meat that can be consumed as part of a healthy, varied diet is also provided.

Iron translocation in Pleurotus ostreatus basidiocarps: production, bioavailability, and antioxidant activity.

PubMed

Yokota, M E; Frison, P S; Marcante, R C; Jorge, L F; Valle, J S; Dragunski, D C; Colauto, N B; Linde, G A

2016-02-22

Translocation of minerals from substrate to mushrooms can change the medicinal characteristics, commercial value, and biological efficiency of mushroom. In the present study, we demonstrated that addition of iron to the substrate reduces the yield of Pleurotus ostreatus mushroom. The biological efficiency of the mushroom varied from 36.53% on the unsupplemented substrate to 2.08% for the substrate with 500 mg/kg iron added. The maximum iron concentration obtained for mushroom was 478.66 mg/kg (dry basis) and the maximum solubility in vitro was 293.70 mg/kg (dry basis). Iron translocation increased the ash and protein content, reduced antioxidant activity, and enhanced the aroma and flavor characteristics of the mushroom. However mushroom has higher amounts of iron than vegetables like collard greens, it is not feasible to use mushrooms as the only dietary source of iron. The study also indicated that because of more bioaccumulation of iron in mycelium than in the mushroom, mycelium and not mushroom, could be a better alternative as a non-animal iron source.

Influence of processing and in vitro digestion on the allergic cross-reactivity of three mealworm species.

PubMed

van Broekhoven, Sarah; Bastiaan-Net, Shanna; de Jong, Nicolette W; Wichers, Harry J

2016-04-01

Edible insects are currently being evaluated as an alternative and more sustainable protein source for humans. The introduction of new food sources can lead to development of novel allergies. Because in the Western world, insects are unlikely to be consumed raw, it is important to know how processing and in vitro digestion might influence their allergenicity. Three edible mealworm species (Tenebrio molitor, Zophobas atratus and Alphitobius diaperinus) subjected to processing and in vitro digestion were analysed for IgE cross-reactivity. Immunoblot and MALDI-MS/MS analyses revealed that IgE from crustaceans or House dust mite (HDM) allergic patients showed cross-reactivity to mealworm tropomyosin or α-amylase, hexamerin 1B precursor and muscle myosin, respectively. Heat processing as well as in vitro digestion did diminish, but not eliminate, HDM or tropomyosin IgE cross-reactivity. Results show that individuals allergic to HDM or crustaceans might be at risk when consuming mealworms, even after heat processing. Copyright © 2015 Elsevier Ltd. All rights reserved.

Promising perspectives for ruminal protection of polyunsaturated fatty acids through polyphenol-oxidase-mediated crosslinking of interfacial protein in emulsions.

PubMed

De Neve, N; Vlaeminck, B; Gadeyne, F; Claeys, E; Van der Meeren, P; Fievez, V

2018-03-16

Previously, polyunsaturated fatty acids (PUFA) from linseed oil were effectively protected (>80%) against biohydrogenation through polyphenol-oxidase-mediated protein crosslinking of an emulsion, prepared with polyphenol oxidase (PPO) extract from potato tuber peelings. However, until now, emulsions of only 2 wt% oil have been successfully protected, which implies serious limitations both from a research perspective (e.g. in vivo trials) as well as for further upscaling toward practical applications. Therefore, the aim of this study was to increase the oil/PPO ratio. In the original protocol, the PPO extract served both an emulsifying function as well as a crosslinking function. Here, it was first evaluated whether alternative protein sources could replace the emulsifying function of the PPO extract, with addition of PPO extract and 4-methylcatechol (4MC) to induce crosslinking after emulsion preparation. This approach was then further used to evaluate protection of emulsions with higher oil content. Five candidate emulsifiers (soy glycinin, gelatin, whey protein isolate (WPI), bovine serum albumin and sodium caseinate) were used to prepare 10 wt% oil emulsions, which were diluted five times (w/w) with PPO extract (experiment 1). As a positive control, 2 wt% oil emulsions were prepared directly with PPO extract according to the original protocol. Further, emulsions of 2, 4, 6, 8 and 10 wt% oil were prepared, with 80 wt% PPO extract (experiment 2), or with 90, 80, 70, 60 and 50 wt% PPO extract, respectively (experiment 3) starting from WPI-stabilized emulsions. Enzymatic crosslinking was induced by 24-h incubation with 4MC. Ruminal protection efficiency was evaluated by 24-h in vitro batch simulation of the rumen metabolism. In experiment 1, protection efficiencies were equal or higher than the control (85.5% to 92.5% v. 81.3%). In both experiments 2 and 3, high protection efficiencies (>80%) were achieved, except for emulsions containing 10 wt% oil emulsions (<50% protection), which showed oiling-off after enzymatic crosslinking. This study demonstrated that alternative emulsifier proteins can be used in combination with PPO extract to protect emulsified PUFA-rich oils against ruminal biohydrogenation. By applying the new protocol, 6.5 times less PPO extract was required.

Use of food waste-recycling wastewater as an alternative carbon source for denitrification process: A full-scale study.

PubMed

Kim, Eunji; Shin, Seung Gu; Jannat, Md Abu Hanifa; Tongco, Jovale Vincent; Hwang, Seokhwan

2017-12-01

Using organic wastes as an alternative to commercial carbon sources could be beneficial by reducing costs and environmental impacts. In this study, food waste-recycling wastewater (FRW) was evaluated as an alternative carbon source for biological denitrification over a period of seven months in a full-scale sewage wastewater treatment plant. The denitrification performance was stable with a mean nitrate removal efficiency of 97.2%. Propionate was initially the most persistent volatile fatty acid, but was completely utilized after 19days. Eubacteriacea, Saprospiraceae, Rhodocyclaceae and Comamonadaceae were the major bacterial families during FRW treatment and were regarded as responsible for hydrolysis (former two) and nitrate removal (latter two) of FRW. These results demonstrate that FRW can be an effective external carbon source; process stabilization was linked to the acclimation and function of bacterial populations to the change of carbon source. Copyright © 2017 Elsevier Ltd. All rights reserved.

A saga of cancer epigenetics: linking epigenetics to alternative splicing.

PubMed

Narayanan, Sathiya Pandi; Singh, Smriti; Shukla, Sanjeev

2017-03-07

The discovery of an increasing number of alternative splicing events in the human genome highlighted that ∼94% of genes generate alternatively spliced transcripts that may produce different protein isoforms with diverse functions. It is now well known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by ' cis ' RNA-binding sites and ' trans' RNA-binding proteins, recent literature provides enormous evidence for epigenetic regulation of alternative splicing. The epigenetic modifications may regulate alternative splicing by either influencing the transcription elongation rate of RNA polymerase II or by recruiting a specific splicing regulator via different chromatin adaptors. The epigenetic alterations and aberrant alternative splicing are known to be associated with various diseases individually, but this review discusses/highlights the latest literature on the role of epigenetic alterations in the regulation of alternative splicing and thereby cancer progression. This review also points out the need for further studies to understand the interplay between epigenetic modifications and aberrant alternative splicing in cancer progression. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Short term effects on bone quality associated with consumption of soy protein isolate and other dietary protein sources in rapidly growing female rats

USDA-ARS?s Scientific Manuscript database

Beneficial effects of soy protein consumption on bone quality have been reported. The effects of other dietary protein sources such as whey protein hydrolysate (WPH) and rice protein isolate (RPI) on bone growth has been less well examined. The current study compared effects of feeding soy protein i...

Nutritional status in patients with phenylketonuria using glycomacropeptide as their major protein source.

PubMed

Pinto, A; Almeida, M F; Ramos, P C; Rocha, S; Guimas, A; Ribeiro, R; Martins, E; Bandeira, A; MacDonald, A; Rocha, J C

2017-10-01

Low phenylalanine (PHE), glycomacropeptide-based protein substitute (GMP) is an alternative to traditional L-amino acid supplements (AA) used in the dietary management of phenylketonuria (PKU). In a retrospective, longitudinal study, we report the nutritional status of PKU patients taking AA and GMP. Eleven PKU patients aged 27±10 years (1 HPA, 4 mild and 6 classical PKU) on dietary treatment were evaluated (anthropometry, body composition, blood pressure measurements, biochemical markers including vitamin, mineral, lipids, carbohydrates and protein status/metabolism, and nutritional intake assessment) at two different annual reviews. The mean time taking AA was 13±5 months and GMP 13±7 months. Blood phenylalanine (PHE) and tyrosine (TYR) were analysed before and after GMP introduction. Both GMP and AA protein substitutes provided similar protein equivalent intake (0.85 vs 0.75 g/kg/day, P=0.182). In the GMP group, it contributed 57% (27-100%) of the protein substitute intake (with AA delivering the rest of protein substitute intake), providing an additional 34±12 mg/day PHE. Nutritional intake, anthropometry and body composition measurements were similar in both the groups. Median blood PHE did not change (P=0.594), although values within target range improved (36 vs 46%), but this was not statistically significant. Mean blood TYR increased (52.0±19.2 vs 63.2±25.6 μmol/l, P=0.033), and all biochemical markers remained stable, except for a lower A1C haemoglobin (P=0.011). Partial GMP contribution to total protein substitute intake did not affect nutritional status in patients with PKU. Blood PHE control was not adversely affected. The increased blood TYR after GMP introduction necessitates further study.

[Establishment of optimun conditions in order to obtain a protein isolate from Chilean Hazelnut].

PubMed

Villarroel, Mario; Zapata, Constanza; Pino, Leonardo; Rubilar, Mónica

2012-03-01

An alternative to solve the problem of the overall deficit of proteins has been the use ofdefatted cakes generated by the extraction of oil from vegetable sources such as rapeseed, soybean, lupin, etc. This process at the same time increases the protein content, making this feasible to be used to enrich some types of food. This is the case of the chilean hazelnut (Gevuina avellana, Mol), monotypic species characterized by their high percentage of oil (50%) and whose defatted cake isolated protein could be used to obtain an isolated protein. For this purpose optimized conditions of extraction of protein were carried out using the surface response methodology (SRM) and a central composite design with three independent variables: time of contact of the cake with the solvent, sample/solvent ratio and pH was used. All variables were controlled at five different levels. The data were subjected to an analysis of regression and ANOVA, the first to determine the polynomial equation and the second to select the control factors with significant effect on the extraction of the protein. The best combination of factors turned out to be: time between 30 and 40 minutes, pH between 9 and 9.5 and a relationship sample/solvent between 1/15 to 1/16 with a final yield of 76%. The physical characteristics were: density 0,504 g/cm3, compaction 43, 34% apparent and pale yellow. Proximal analysis showed a concentration of protein of 76%, 13%, raw fiber carbohydrate 0.68% and oil 1.29%. With regard to the functional properties emphasized water absorption (320 g/100 g), absorption of oil (410 g/100 g) and foaming capacity (221%).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seppala, Susanna; Solomon, Kevin V.; Gilmore, Sean P.

Here, engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. Although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. Anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of these non-conventional organisms. Here, we mined the transcriptome of three recently isolated strains of anaerobic fungi to identify membrane proteins responsible for sensing and transporting biomass hydrolysates within a competitive andmore » rather extreme environment. Using sequence analyses and homology, we identified membrane protein-coding sequences from assembled transcriptomes from three strains of anaerobic gut fungi: Neocallimastix californiae, Anaeromyces robustus, and Piromyces finnis. We identified nearly 2000 transporter components: about half of these are involved in the general secretory pathway and intracellular sorting of proteins; the rest are predicted to be small-solute transporters. Unexpectedly, we found a number of putative sugar binding proteins that are associated with prokaryotic uptake systems; and approximately 100 class C G-protein coupled receptors (GPCRs) with non-canonical putative sugar binding domains. In conclusion, we report the first comprehensive characterization of the membrane protein machinery of biotechnologically relevant anaerobic gut fungi. Apart from identifying conserved machinery for protein sorting and secretion, we identify a large number of putative solute transporters that are of interest for biotechnological applications. Notably, our data suggests that the fungi display a plethora of carbohydrate binding domains at their surface, perhaps as a means to sense and sequester some of the sugars that their biomass degrading, extracellular enzymes produce.« less

Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance

PubMed Central

Bertaux, François; Stoma, Szymon; Drasdo, Dirk; Batt, Gregory

2014-01-01

Isogenic cells sensing identical external signals can take markedly different decisions. Such decisions often correlate with pre-existing cell-to-cell differences in protein levels. When not neglected in signal transduction models, these differences are accounted for in a static manner, by assuming randomly distributed initial protein levels. However, this approach ignores the a priori non-trivial interplay between signal transduction and the source of this cell-to-cell variability: temporal fluctuations of protein levels in individual cells, driven by noisy synthesis and degradation. Thus, modeling protein fluctuations, rather than their consequences on the initial population heterogeneity, would set the quantitative analysis of signal transduction on firmer grounds. Adopting this dynamical view on cell-to-cell differences amounts to recast extrinsic variability into intrinsic noise. Here, we propose a generic approach to merge, in a systematic and principled manner, signal transduction models with stochastic protein turnover models. When applied to an established kinetic model of TRAIL-induced apoptosis, our approach markedly increased model prediction capabilities. One obtains a mechanistic explanation of yet-unexplained observations on fractional killing and non-trivial robust predictions of the temporal evolution of cell resistance to TRAIL in HeLa cells. Our results provide an alternative explanation to survival via induction of survival pathways since no TRAIL-induced regulations are needed and suggest that short-lived anti-apoptotic protein Mcl1 exhibit large and rare fluctuations. More generally, our results highlight the importance of accounting for stochastic protein turnover to quantitatively understand signal transduction over extended durations, and imply that fluctuations of short-lived proteins deserve particular attention. PMID:25340343

The plant energy-dissipating mitochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots.

PubMed

Borecky, Jirí; Nogueira, Fábio T S; de Oliveira, Kívia A P; Maia, Ivan G; Vercesi, Aníbal E; Arruda, Paulo

2006-01-01

The simultaneous existence of alternative oxidases and uncoupling proteins in plants has raised the question as to why plants need two energy-dissipating systems with apparently similar physiological functions. A probably complete plant uncoupling protein gene family is described and the expression profiles of this family compared with the multigene family of alternative oxidases in Arabidopsis thaliana and sugarcane (Saccharum sp.) employed as dicot and monocot models, respectively. In total, six uncoupling protein genes, AtPUMP1-6, were recognized within the Arabidopsis genome and five (SsPUMP1-5) in a sugarcane EST database. The recombinant AtPUMP5 protein displayed similar biochemical properties as AtPUMP1. Sugarcane possessed four Arabidopsis AOx1-type orthologues (SsAOx1a-1d); no sugarcane orthologue corresponding to Arabidopsis AOx2-type genes was identified. Phylogenetic and expression analyses suggested that AtAOx1d does not belong to the AOx1-type family but forms a new (AOx3-type) family. Tissue-enriched expression profiling revealed that uncoupling protein genes were expressed more ubiquitously than the alternative oxidase genes. Distinct expression patterns among gene family members were observed between monocots and dicots and during chilling stress. These findings suggest that the members of each energy-dissipating system are subject to different cell or tissue/organ transcriptional regulation. As a result, plants may respond more flexibly to adverse biotic and abiotic conditions, in which oxidative stress is involved.

Relationships between morphometrical properties and the texture of an extrusion-expanded snack made from squid mantle (Dosidicus gigas).

PubMed

Valenzuela-Lagarda, José Luis; García-Armenta, Evangelina; Pacheco-Aguilar, Ramón; Gutiérrez-Dorado, Roberto; Mazorra-Manzano, Miguel Ángel; Lugo-Sánchez, María Elena; Muy-Rangel, María Dolores

2018-01-24

The giant squid (Dosidicus gigas) is a species of commercial interest as a source of protein, and it can be developed into ready-to-eat food products, including expanded extrusion snacks (EES). EES are prepared primarily from starch; however, adding animal protein increases the nutritional contents. The objective of this study was to evaluate the effect of the protein-carbohydrate interactions on the physical and morphological characteristics of an EES made of squid mantle and potato-corn flour. The independent variable was the squid mantle content (40, 60, 80, and 100%) and two controls (0 1  = 100% potato, 0 2  = 100% corn). The expansion rate (ER) of the sample is significantly minor (p < .5) when the squid mantle content increases ER = 2.0, 1.8 1.4 to 40, 60, and 80%, respectively. In samples with more protein, crispness and crunchiness were reduced, whereas the hardness increased. Digital imaging analysis indicated that the interaction between protein and starch causes significant morphometric changes to the fractal dimension (2.665-2.739) and lacunarity (0.61-1.29). The results showed that it is possible to incorporate up to 60% squid mantle to prepare EES that possess texture and morphometric characteristics competitive in reported studies with snacks usually incorporating flours, corn, and wheat in the formulations. The giant squid is a very attractive species because its meat has low caloric intake, high protein content, and is an important source of omega 3 fatty acids. Despite the desirable qualities of the squid meat its consumption is very low due to the low diffusion of the properties of its meat, acid, and ammoniacal flavor, rigid texture that requires prolonged cooking times and lack of alternatives of consumption. In Mexico, this type of squid is mainly destined for export as frozen mantle and products with little added value, which generates little economic benefit. Therefore, the results of this research may be of interest to the squid processing industry, which demands new forms of consumption of this marine species to increase their commercialization and added value. © 2018 Wiley Periodicals, Inc.

Targeted mass spectrometric analysis of N-terminally truncated isoforms generated via alternative translation initiation.

PubMed

Kobayashi, Ryuji; Patenia, Rebecca; Ashizawa, Satoshi; Vykoukal, Jody

2009-07-21

Alternative translation initiation is a mechanism whereby functionally altered proteins are produced from a single mRNA. Internal initiation of translation generates N-terminally truncated protein isoforms, but such isoforms observed in immunoblot analysis are often overlooked or dismissed as degradation products. We identified an N-terminally truncated isoform of human Dok-1 with N-terminal acetylation as seen in the wild-type. This Dok-1 isoform exhibited distinct perinuclear localization whereas the wild-type protein was distributed throughout the cytoplasm. Targeted analysis of blocked N-terminal peptides provides rapid identification of protein isoforms and could be widely applied for the general evaluation of perplexing immunoblot bands.

Alternative mitochondrial respiratory chains from two crustaceans: Artemia franciscana nauplii and the white shrimp, Litopenaeus vannamei.

PubMed

Rodriguez-Armenta, Chrystian; Uribe-Carvajal, Salvador; Rosas-Lemus, Monica; Chiquete-Felix, Natalia; Huerta-Ocampo, Jose Angel; Muhlia-Almazan, Adriana

2018-04-01

Mitochondrial ATP is synthesized by coupling between the electron transport chain and complex V. In contrast, physiological uncoupling of these processes allows mitochondria to consume oxygen at high rates without ATP synthesis. Such uncoupling mechanisms prevent reactive oxygen species overproduction. One of these mechanisms are the alternative redox enzymes from the mitochondrial respiratory chain, which may help cells to maintain homeostasis under stress independently of ATP synthesis. To date, no reports have been published on alternative redox enzymes in crustaceans mitochondria. Specific inhibitors were used to identify alternative redox enzymes in mitochondria isolated from Artemia franciscana nauplii, and the white shrimp, Litopenaeus vannamei. We report the presence of two alternative redox enzymes in the respiratory chain of A. franciscana nauplii, whose isolated mitochondria used glycerol-3-phosphate as a substrate, suggesting the existence of a glycerol-3-phosphate dehydrogenase. In addition, cyanide and octyl-gallate were necessary to fully inhibit this species' mitochondrial oxygen consumption, suggesting an alternative oxidase is present. The in-gel activity analysis confirmed that additional mitochondrial redox proteins exist in A. franciscana. A mitochondrial glycerol-3-phosphate dehydrogenase oxidase was identified by protein sequencing as part of a branched respiratory chain, and an alternative oxidase was also identified in this species by western blot. These results indicate different adaptive mechanisms from artemia to face environmental challenges related to the changing levels of oxygen concentration in seawater through their life cycles. No alternative redox enzymes were found in shrimp mitochondria, further efforts will determine the existence of an uncoupling mechanism such as uncoupling proteins.

Functional expression of the taste-modifying protein, miraculin, in transgenic lettuce.

PubMed

Sun, Hyeon-Jin; Cui, Min-Long; Ma, Biao; Ezura, Hiroshi

2006-01-23

Taste-modifying proteins are a natural alternative to artificial sweeteners and flavor enhancers and have been used in some cultures for centuries. The taste-modifying protein, miraculin, has the unusual property of being able to modify a sour taste into a sweet taste. Here, we report the use of a plant expression system for the production of miraculin. A synthetic gene encoding miraculin was placed under the control of constitutive promoters and transferred to lettuce. Expression of this gene in transgenic lettuce resulted in the accumulation of significant amounts of miraculin protein in the leaves. The miraculin expressed in transgenic lettuce possessed sweetness-inducing activity. These results demonstrate that the production of miraculin in edible plants can be a good alternative strategy to enhance the availability of this protein.

Bulawayo water supplies: Sustainable alternatives for the next decade

NASA Astrophysics Data System (ADS)

Mkandla, Noel; Van der Zaag, Pieter; Sibanda, Peter

Bulawayo is the second largest city in Zimbabwe with a population of nearly one million people. It is located on the watershed of Umzingwane and Gwayi catchments. The former is part of the Limpopo basin, while the latter drains into the Zambezi basin. Bulawayo has a good potential of economic development but has been stymied by lack of sufficient water. The city currently relies on five surface sources in the Umzingwane catchment where it has to compete with evaporation. The well field from the Nyamandlovu aquifer in the Gwayi catchment, which was constructed as an emergency measure during the 1992 drought, is currently not operational. Alternative water supply sources are far and expensive. A multilinear regression model was developed to analyse and quantify the factors affecting water consumption. It was found that per capita water consumption is very low, indicating suppressed demand. Water rationing, tariffs, rainfall, population growth and gross domestic product are the main factors influencing water consumption in Bulawayo. Assuming that these factors will continue to be influential, future water consumption was projected for intensive, regular and slack water demand management. Future water consumption was then compared with the current water supply capacity in order to determine the date by which the next water supply source is required. With slack demand management, the Nyamandlovu well field should have been operational by 2003, while by the year 2007 an additional source of water is required. With intensive demand management and assuming low population growth, current capacities may suffice to satisfy the suppressed demand until the year 2015, by which time Nyamandlovu wells should be operational again. The additional water supply sources that are currently being considered for Bulawayo (namely the Zambezi water pipeline; Gwayi Shangani dam; Mtshabezi dam; Lower Tuli dam; and Glass block dam) were then compared with an alternative water source not yet contemplated, namely drawing groundwater from Umguza, part of the Nyamandlovu aquifer. The paper then provides details of the Umguza alternative, which was designed at pre-feasibility level by Mkandla [Mkandla, N., 2003. Bulawayo water supplies: Umguza well field as a sustainable alternative for the next decade. Unpublished M.Sc. WREM dissertation. University of Zimbabwe, Harare]. All alternative additional water supply sources were compared in terms of their Net Present Values. It was found that Umguza well field is the least-cost alternative to meet additional water demand. The Umguza alternative will be able to satisfy water demand for a period of six to ten years. Thereafter, the second least-cost alternative, namely Gwayi Shangani dam, must be on stream.

An Efficient Variable Length Coding Scheme for an IID Source

NASA Technical Reports Server (NTRS)

Cheung, K. -M.

1995-01-01

A scheme is examined for using two alternating Huffman codes to encode a discrete independent and identically distributed source with a dominant symbol. This combined strategy, or alternating runlength Huffman (ARH) coding, was found to be more efficient than ordinary coding in certain circumstances.

What Is the Reference? An Examination of Alternatives to the Reference Sources Used in IES TM-30-15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Royer, Michael P.

A study was undertaken to document the role of the reference illuminant in the IES TM-30-15 method for evaluating color rendition. TM-30-15 relies on a relative reference scheme; that is, the reference illuminant and test source always have the same correlated color temperature (CCT). The reference illuminant is a Planckian radiator, model of daylight, or combination of those two, depending on the exact CCT of the test source. Three alternative reference schemes were considered: 1) either using all Planckian radiators or all daylight models; 2) using only one of ten possible illuminants (Planckian, daylight, or equal energy), regardless of themore » CCT of the test source; 3) using an off-Planckian reference illuminant (i.e., a source with a negative Duv). No reference scheme is inherently superior to another, with differences in metric values largely a result of small differences in gamut shape of the reference alternatives. While using any of the alternative schemes is more reasonable in the TM-30-15 evaluation framework than it was with the CIE CRI framework, the differences still ultimately manifest only as changes in interpretation of the results. References are employed in color rendering measures to provide a familiar point of comparison, not to establish an ideal source.« less

Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.

PubMed

Roche, Daniel Barry; Brackenridge, Danielle Allison; McGuffin, Liam James

2015-12-15

Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein-ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein-ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein-ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.

The impact of carbohydrate and protein level and sources on swine manure foaming properties

USDA-ARS?s Scientific Manuscript database

This study explored the impact of swine diet on the composition, methane production potential, and foaming properties of manure. Samples of swine manure were collected from controlled feeding trials with diets varying in protein and carbohydrate levels and sources. Protein sources consisted of corn ...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Litchfield, J.H.; Inglett, G.E.; Weber, C.W.

Unconventional protein sources from cereals; citrulis, apodanthera, cucurbita, and hibiscus seeds; nonconventional legume grains; and leaves are explored. Single-celled proteins and expanded uses for fish protein from underutilized species are examined. Economic considerations of the protein sources and the need for future research are assessed. Present dwindling supplies of protein dictate the need for future research.

Alternatively activated macrophages do not synthesize catecholamines or contribute to adipose tissue adaptive thermogenesis

PubMed Central

Fischer, Katrin; Ruiz, Henry H.; Jhun, Kevin; Finan, Brian; Oberlin, Douglas J.; van der Heide, Verena; Kalinovich, Anastasia V.; Petrovic, Natasa; Wolf, Yochai; Clemmensen, Christoffer; Shin, Andrew C.; Divanovic, Senad; Brombacher, Frank; Glasmacher, Elke; Keipert, Susanne; Jastroch, Martin; Nagler, Joachim; Schramm, Karl-Werner; Medrikova, Dasa; Collden, Gustav; Woods, Stephen C.; Herzig, Stephan; Homann, Dirk; Jung, Steffen; Nedergaard, Jan; Cannon, Barbara; Tschöp, Matthias H.

2017-01-01

Adaptive thermogenesis is the process of heat generation in response to cold stimulation and is under the control of the sympathetic nervous system whose chief effector is the catecholamine norepinephrine (NE). NE enhances thermogenesis through beta3 adrenergic receptors to activate brown adipose tissue and by “browning” white adipose tissue. Recent studies reported that the alternative activation of macrophages in response to IL-4 stimulation induces the expression of tyrosine hydroxylase (TH), a key enzyme in the catecholamine synthesis pathway, and to provide an alternative source of locally produced catecholamines during the thermogenic process. We here report that the deletion of Th in hematopoetic cells of adult mice neither alters energy expenditure upon cold exposure nor reduces browning in inguinal adipose tissue. Bone marrow-derived macrophages did not release NE in response to stimulation with Interleukin-4 (IL-4), and conditioned media from IL-4 stimulated macrophages failed to induce expression of thermogenic genes, such as the one for uncoupling protein 1 (Ucp1) in adipocytes cultured with the conditioned media. Further, chronic IL-4 treatment failed to increase energy expenditure in WT, Ucp1-/- and Il4ra-/- mice. Consistent with these findings, adipose tissue-resident macrophages did not express TH. Thus, we conclude that alternatively activated macrophages do not synthesize relevant amounts of catecholamines and hence are not likely to play a direct role in adipocyte metabolism or adaptive thermogenesis. PMID:28414329