Production of microbial biomass protein by sequential culture fermentation of Arachniotus sp., and Candida utilis

International Nuclear Information System (INIS)

Ahmed, S.; Ahmad, F.; Hashmi, A.S.

2010-01-01

Sequential culture fermentation by Arachniotus sp. at 35 deg. C for 72 h and followed by Candida utilis fermentation at 35 deg. C for 72 h more resulted in higher production of microbial biomass protein. 6% (w/v) corn stover, 0.0075% CaCl/sub 2/.2H/sub 2/O, 0.005% MgSO/sub 4/.7H/sub 2/O, 0.01% KH/sub 2/PO/sub 4/, C:N ratio of 30:1 and 1% molasses gave higher microbial biomass protein production by the sequential culture fermentation of Arachniotus sp., and C. utilis. The mixed microbial biomass protein produced in the 75-L fermentor contained 16.41%, 23.51%, 10.9%, 12.11% and 0.12% true protein, crude protein, crude fiber, ash and RNA content, respectively. The amino acid profile of final mixed microbial biomass protein showed that it was enriched with essential amino acids. Thus, the potential utilization of corn stover can minimize the cost for growth of these microorganisms and enhance microbial biomass protein production by sequential culture fermentation. (author)

Nuclear based technologies for estimating microbial protein supply in ruminant livestock. Proceedings of the second research co-ordination meeting of a co-ordinated research project (phase 1)

International Nuclear Information System (INIS)

1999-06-01

The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture through its Co-ordinated Research Projects (CRPs), has been assisting national agricultural research systems in Member States to develop and apply nuclear and related techniques for improving livestock productivity. The programmes have focused on animal nutrition, animal reproduction and more recently on animal nutrition/reproduction interactions with emphasis on smallholder farming systems. The measurement of microbial protein supply to ruminant livestock has been an important area of research in ruminant nutrition. An estimate of microbial protein contribution to the intestinal protein flow is important for estimating the protein requirement of ruminant animals. Understanding the process of microbial protein synthesis has been difficult however, and due to the lack of simple and accurate methods for measuring microbial protein production in vivo, the methods used are based on complex microbial markers which require surgically prepared animals. As a result of a consultants meeting held in May 1995 to advise the Joint FAO/IAEA Division on the feasibility of using nuclear and related techniques for the development and validation of techniques for measuring microbial protein supply in ruminant animals, an FAO/IAEA Co-ordinated Research Project on Development, Standardization and Validation of Nuclear Based Technologies for Measuring Microbial Protein Supply in Ruminant Livestock for Improving Productivity was initiated in 1996, with a view to validating and adapting this technology for use in developing countries. To assist scientists participating in the CRP, a laboratory manual containing experimental protocols and methodologies for standardization and validation of the urine purine derivative technique and the development of models to suit local conditions, was published as IAEA-TECDOC-945. The present publication contains the final reports from participants in Phase 1 of the project

Nuclear based technologies for estimating microbial protein supply in ruminant livestock. Proceedings of the second research co-ordination meeting of a co-ordinated research project (phase 1)

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-06-01

The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture through its Co-ordinated Research Projects (CRPs), has been assisting national agricultural research systems in Member States to develop and apply nuclear and related techniques for improving livestock productivity. The programmes have focused on animal nutrition, animal reproduction and more recently on animal nutrition/reproduction interactions with emphasis on smallholder farming systems. The measurement of microbial protein supply to ruminant livestock has been an important area of research in ruminant nutrition. An estimate of microbial protein contribution to the intestinal protein flow is important for estimating the protein requirement of ruminant animals. Understanding the process of microbial protein synthesis has been difficult however, and due to the lack of simple and accurate methods for measuring microbial protein production in vivo, the methods used are based on complex microbial markers which require surgically prepared animals. As a result of a consultants meeting held in May 1995 to advise the Joint FAO/IAEA Division on the feasibility of using nuclear and related techniques for the development and validation of techniques for measuring microbial protein supply in ruminant animals, an FAO/IAEA Co-ordinated Research Project on Development, Standardization and Validation of Nuclear Based Technologies for Measuring Microbial Protein Supply in Ruminant Livestock for Improving Productivity was initiated in 1996, with a view to validating and adapting this technology for use in developing countries. To assist scientists participating in the CRP, a laboratory manual containing experimental protocols and methodologies for standardization and validation of the urine purine derivative technique and the development of models to suit local conditions, was published as IAEA-TECDOC-945. The present publication contains the final reports from participants in Phase 1 of the project

Summary of the co-ordinated research project on development, standardization and validation of nuclear based technologies for estimating microbial protein supply in ruminant livestock for improving productivity

International Nuclear Information System (INIS)

Jayasuriya, M.C.N.

1999-01-01

A major constraint to animal production in developing countries is poor nutrition due to inadequate or fluctuating nutrient supply. This results in low rates of reproduction and production as well as increased susceptibility to disease and mortality. Microbial cells formed as a result of rumen degradation of carbohydrates under anaerobic conditions are a major source of protein for ruminants. They provide the majority of the amino acids that the host animal requires for tissue maintenance, growth and production. In roughage-fed ruminants, micro-organisms are virtually the only source of protein. Therefore, a knowledge of the microbial contribution to the nutrition of the host animal is essential to developing feed supplementation strategies for improving ruminant production. While this factor has been recognized for many years, it has been extremely difficult to determine the microbial protein contribution to ruminant nutrition. The methods generally used for determining microbial protein production depend on the use of natural microbial markers such as RNA (ribonucleic acid) and DAPA (diamino-pimelic acid) or of isotopes 35 S, 15 N or 32 P. However, these methods involve surgical intervention such as post-rumen cannulation and complex procedures that require accurate and quantitative information on both digesta and microbial marker flow. A calorimetric technique using enzymatic procedures was developed for measuring purine derivatives (PD) in urine under a Technical Contract. With knowledge of the amount of PD excreted in the urine, the microbial protein supply to the host animal can be estimated. The principle of the method is that nucleic acids leaving the rumen are essentially of microbial origin. The nucleic acids are extensively digested in the small intestine and the resulting purines are absorbed

Ammonia treatment of wheat straw. 2. Efficiency of microbial protein synthesis, rumen microbial protein pool size and turnover, and small intestinal protein digestion in sheep.

NARCIS (Netherlands)

Oosting, S.J.; Viets, T.C.; Lammers-Wienhoven, S.C.W.; Bruchem, van J.

1993-01-01

Ammonia-treated wheat straw (AWS) was compared with untreated wheat straw (UWS) and untreated wheat straw supplemented with urea (SWS) in an experiment with 6 wether sheep. Microbial protein synthesis increased after ammonia treatment due to the higher intake of rumen degradable organic matter (OM).

Microbial alignment in flow changes ocean light climate.

Science.gov (United States)

Marcos; Seymour, Justin R; Luhar, Mitul; Durham, William M; Mitchell, James G; Macke, Andreas; Stocker, Roman

2011-03-08

The growth of microbial cultures in the laboratory often is assessed informally with a quick flick of the wrist: dense suspensions of microorganisms produce translucent "swirls" when agitated. Here, we rationalize the mechanism behind this phenomenon and show that the same process may affect the propagation of light through the upper ocean. Analogous to the shaken test tubes, the ocean can be characterized by intense fluid motion and abundant microorganisms. We demonstrate that the swirl patterns arise when elongated microorganisms align preferentially in the direction of fluid flow and alter light scattering. Using a combination of experiments and mathematical modeling, we find that this phenomenon can be recurrent under typical marine conditions. Moderate shear rates (0.1 s(-1)) can increase optical backscattering of natural microbial assemblages by more than 20%, and even small shear rates (0.001 s(-1)) can increase backscattering from blooms of large phytoplankton by more than 30%. These results imply that fluid flow, currently neglected in models of marine optics, may exert an important control on light propagation, influencing rates of global carbon fixation and how we estimate these rates via remote sensing.

Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation

DEFF Research Database (Denmark)

Martinez Ruiz, José Luis; Liu, Lifang; Petranovic, Dina

2012-01-01

Since the approval of recombinant insulin from Escherichia coli for its clinical use in the early 1980s, the amount of recombinant pharmaceutical proteins obtained by microbial fermentations has significantly increased. The recent advances in genomics together with high throughput analysis...... of recombinant therapeutics using yeast Saccharomyces cerevisiae as a model platform, and discusses the future potential of this platform for production of blood proteins and substitutes....

Effects of grain source, grain processing, and protein degradability on rumen kinetics and microbial protein synthesis in Boer kids.

Science.gov (United States)

Brassard, M-E; Chouinard, P Y; Berthiaume, R; Tremblay, G F; Gervais, R; Martineau, R; Cinq-Mars, D

2015-11-01

Microbial protein synthesis in the rumen would be optimized when dietary carbohydrates and proteins have synchronized rates and extent of degradation. The aim of this study was to evaluate the effect of varying ruminal degradation rate of energy and nitrogen sources on intake, nitrogen balance, microbial protein yield, and kinetics of nutrients in the rumen of growing kids. Eight Boer goats (38.2 ± 3.0 kg) were used. The treatments were arranged in a split-plot Latin square design with grain sources (barley or corn) forming the main plots (squares). Grain processing methods and levels of protein degradability formed the subplots in a 2 × 2 factorial arrangement for a total of 8 dietary treatments. The grain processing method was rolling for barley and cracking for corn. Levels of protein degradability were obtained by feeding untreated soybean meal (SBM) or heat-treated soybean meal (HSBM). Each experimental period lasted 21 d, consisting of a 10-d adaptation period, a 7-d digestibility determination period, and a 4-d rumen evacuation and sampling period. Kids fed with corn had higher purine derivatives (PD) excretion when coupled with SBM compared with HSBM and the opposite occurred with barley-fed kids ( ≤ 0.01). Unprocessed grain offered with SBM led to higher PD excretion than with HSBM whereas protein degradability had no effect when processed grain was fed ( ≤ 0.03). Results of the current experiment with high-concentrate diets showed that microbial N synthesis could be maximized in goat kids by combining slowly fermented grains (corn or unprocessed grains) with a highly degradable protein supplement (SBM). With barley, a more rapidly fermented grain, a greater microbial N synthesis was observed when supplementing a low-degradable protein (HSBM).

In vitro estimation of rumen microbial protein synthesis of water buffaloes using 30S as tracer

International Nuclear Information System (INIS)

Hendratno, C.; Abidin, Z.; Bahaudin, R.; Sastrapradja, D.

1977-01-01

An experiment to study the effect of diet and individual differences of animals on the in vitro estimation of rumen microbial protein synthesis in young female water buffaloes using the technique of inorganic 35 S incorporation, is described. The dietary treatments were four combinations of roughage supplemented with cassava meal. From the value of rate constant for dilution of radioactivity in the sulphide pool and percentage of inorganic 35 S incorporated into microbial protein, it can be concluded that individual differences of animals have no influence on the efficiency of microbial protein synthesis. Feed composition, on the other hand, tends to have some influence on the efficiency of protein synthesis(P3O.15). (author)

The Growth Rate and Efficiency of Rumen Microbial Protein Digestion of Red Clover Silage (Trifolium pratense cv. Sabatron)

International Nuclear Information System (INIS)

Asih Kurniawati

2004-01-01

(Trifolium pratense cv. Sabatron). Red clover silage supplemented with different level of carbohydrates has been examined using the in-vitro gas production technique. Cumulative gas production, hydro.gen sulfite production, and ammonia was followed and used as indicators of microbial growth rate and extent of protein degradation. Microbial nitrogen production, VFA, and efficiency microbial production was used as indicator of nitrogen use efficiency. 15 N was used as a microbial marker to estimate the amount of nitrogen incorporation into microbial protein. Supplementation of Red clover with increasing 5 levels; 0 g; 0.625 g; 0.15 g; 0.225 g and 0.3 g of maize starch led to graded increase in microbial growth and protein degradation. This was reflected in the increasing gas production and the accumulation of hydrogen sulfite. Diurnal change in ammonia production reflected the microbial utilization of ammonia for protein synthesis. Protein microbe (P<0.001) as VFA (P<0.001) increased due to carbohydrate addition as well as utilization of nitrogen (P<0.001). There was also the efficiency of nitrogen utilization which increased significantly. This result suggested that energy supply can increased efficiency of nitrogen use in the rumen and may reduce nitrogen losses into the environment. (author)

Effect of inclusion of different levels of silage on rumen microbial population and microbial protein synthesis in dairy steers fed on rice straw

Directory of Open Access Journals (Sweden)

Thien Truong Giang Nguyen

2017-02-01

Full Text Available Objective Leucaena leucocephala (Leucaena is a perennial tropical legume that can be directly grazed or harvested and offered to ruminants as hay, silage, or fresh. However, Leucaena contain phenolic compounds, which are considered anti-nutritional factors as these may reduce intake, digestibility and thus animal performance. Therefore, the objective of this experiment was to determine effects of Leucaena silage (LS feeding levels on rumen microbial populations, N-balance and microbial protein synthesis in dairy steers. Methods Four, rumen fistulated dairy steers with initial weight of 167±12 kg were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. Treatments were as followings: T1 = untreated rice straw (RS; Control, T2 = 70% RS+30% LS, T3 = 40% RS+60% LS, and T4 = 100% LS. Dairy steers were fed rice straw and LS ad libitum and supplemented with concentrate at 0.2% of body weight/d. Results Results revealed that the rumen microbial population, especially cellulolytic, proteolytic bacteria and fungal zoospores were enhanced in steers that received 60% of LS (p0.05. Protozoal population was linearly decreased with increasing level of LS (p<0.05. Moreover, N-balance and microbial protein synthesis were enhanced by LS feeding (p<0.05 and were the highest in 60% LS group. Conclusion Based on this study, it could be concluded that replacement of RS with 60% LS significantly improved microbial population and microbial protein synthesis in diary steers.

Effects of feeding wheat or corn-wheat dried distillers grains with solubles in low- or high-crude protein diets on ruminal function, omasal nutrient flows, urea-N recycling, and performance in cows.

Science.gov (United States)

Chibisa, G E; Mutsvangwa, T

2013-10-01

A study was conducted to determine the effects of including either wheat-based (W-DDGS) or corn-wheat blend (B-DDGS) dried distillers grains with solubles as the major protein source in low- or high-crude protein (CP) diets fed to dairy cows on ruminal function, microbial protein synthesis, omasal nutrient flows, urea-N recycling, and milk production. Eight lactating Holstein cows (768.5 ± 57.7 kg of body weight; 109.5 ± 40.0 d in milk) were used in a replicated 4 × 4 Latin square design with 28-d periods (18d of dietary adaptation and 10d of measurements) and a 2 × 2 factorial arrangement of dietary treatments. Four cows in one Latin square were ruminally cannulated for the measurement of ruminal fermentation characteristics, microbial protein synthesis, urea-N recycling kinetics, and omasal nutrient flow. The treatment factors were type of distillers co-product (W-DDGS vs. B-DDGS) and dietary CP content [15.2 vs. 17.3%; dry matter (DM) basis]. The B-DDGS was produced from a mixture of 15% wheat and 85% corn grain. All diets were formulated to contain 10% W-DDGS or B-DDGS on a DM basis. No diet effect was observed on DM intake. Yields of milk, fat, protein, and lactose, and plasma urea-N and milk urea-N concentrations were lower in cows fed the low-CP compared with those fed the high-CP diet. Although feeding B-DDGS tended to reduce ruminal ammonia-N (NH3-N) concentration compared with feeding W-DDGS (9.3 vs. 10.5mg/dL), no differences were observed in plasma urea-N and milk urea-N concentrations. Additionally, dietary inclusion of B-DDGS compared with W-DDGS did not affect rumen-degradable protein supply, omasal flows of total N, microbial nonammonia N (NAN), rumen-undegradable protein, and total NAN, or urea-N recycling kinetics and milk production. However, cows fed the low-CP diet had lower N intake, rumen-degradable protein supply, ruminal NH3-N concentration, and omasal flows of N, microbial NAN, and total NAN compared with those fed the high-CP diet

Effect of Plants Containing Secondary Compounds with Palm Oil on Feed Intake, Digestibility, Microbial Protein Synthesis and Microbial Population in Dairy Cows

Directory of Open Access Journals (Sweden)

N. Anantasook

2013-06-01

Full Text Available The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75% lactating dairy cows with an initial body weight (BW of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control, supplementation with rain tree pod meal (RPM at 60 g/kg, supplementation with palm oil (PO at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO, of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05. However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05. In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05 while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows.

Estimation of microbial protein supply in ruminants using urinary purine derivatives

International Nuclear Information System (INIS)

Makkar, H.P.S.; Chen, X.B.

2004-01-01

This publication presents various models, describing the quantitative excretion of purine derivatives in urine, developed for various breeds of cattle and for sheep, goat, camel and buffalo and their use for estimation of microbial protein supply in ruminant livestock. It also describes progress made over the last decade in analytical methods for determining purine derivatives, and a unique approach for estimating microbial protein supply using spot urine samples developed under the FAO/IAEA CRP. This approach of using spot urine samples dispenses with quantitative recovery of urine, enabling its use by field and extension workers for evaluation of the nutritional status of farm animals. Future areas of research are also highlighted in the book. This book is a good source of reference for research workers, students and extension workers alike

Microbial Eco-Physiology of the human intestinal tract: a flow cytometric approach

NARCIS (Netherlands)

Amor, Ben K.

2004-01-01

This thesis describes a multifaceted approach to further enhance our view of the complex human intestinal microbial ecosystem. This approach combines me advantages of flow cyrometry (FCM), a single cell and high-throughput technology, and molecular techniques that have proven themselves to be

Crosslinking of milk proteins by microbial transglutaminase: Utilization in functional yogurt products

DEFF Research Database (Denmark)

Gharibzahedi, Seyed Mohammad Taghi; Chronakis, Ioannis S.

2018-01-01

Key modifying roles of microbial transglutaminase (MTGase) in the development of innovative probiotic and non-probiotic yogurts with improved functional and quality characteristics have been comprehensively reviewed. MTGase crosslinking reactions with milk proteins stabilize the three-dimensional......Key modifying roles of microbial transglutaminase (MTGase) in the development of innovative probiotic and non-probiotic yogurts with improved functional and quality characteristics have been comprehensively reviewed. MTGase crosslinking reactions with milk proteins stabilize the three......-dimensional structure of yogurt. Yogurts treated with MTGase showed decreased syneresis, increased water-holding capacity and viscosity, homogeneous structure, desired texture, and physicochemical high stability during storage time. The utilization of MTGase does not affect negatively the sensory attributes of yogurt...

Effect of monensin on in vitro fermentation of silages and microbial protein synthesis.

Science.gov (United States)

Wischer, Gerald; Boguhn, Jeannette; Steingaß, Herbert; Schollenberger, Margit; Hartung, Karin; Rodehutscord, Markus

2013-06-01

The objective of the study was to investigate the effects of monensin on silage fermentation and microbial net protein synthesis. In Experiment 1, monensin (0.5, 1, 2, 4, 6, or 10 µg) was added to syringes that contained 120 mg of grass silage (GS), grass silage and concentrate (GS + C), or maize silage (MS), resulting in concentrations of 4.2, 8.3, 16.7, 33.3, 50.0 and 83.3 mg monensin/kg feed. Samples were incubated for 24 h to determine the monensin concentration that resulted in the maximum reduction in methane production without effects on the total gas production. In Experiment 2, GS and GS + C were incubated in a rumen simulation technique (Rusitec) to assess the monensin effects (133 and 266 mg/kg feed) on the production of total gas, methane and volatile fatty acids (VFA), degradation of nutrients and microbial net protein synthesis. In Experiment 1, methane production was reduced without significant effects on the total gas production; the reductions were 17% (GS), 10% (GS + C) and 13% (MS) with 16.7 (GS), 50.0 (GS + C) and 33.3 (MS) mg monensin/kg feed. Monensin reduced the total gas and methane production in GS and GS + C in Experiment 2. Propionate production was enhanced by monensin, accompanied by a decrease in acetate production. Along with a reduction in crude protein (CP) degradation, monensin reduced the ammonia nitrogen concentration in the effluent of both treatments. While the protein produced by liquid-associated microbes increased with monensin, protein production by solid-associated microbes was reduced. Total microbial net protein synthesis increased in the presence of monensin. Monensin influenced the production of total gas, methane and VFA from the silages without an effect on the degradation of organic matter (OM). Different microbial fractions were affected differently by monensin supplementation. If monensin is used as a tool to reduce methane emission, the supplementation level must be carefully chosen to avoid negative effects on

Circulating microbial products and acute phase proteins as markers of pathogenesis in lymphatic filarial disease.

Directory of Open Access Journals (Sweden)

R Anuradha

Full Text Available Lymphatic filariasis can be associated with development of serious pathology in the form of lymphedema, hydrocele, and elephantiasis in a subset of infected patients. Dysregulated host inflammatory responses leading to systemic immune activation are thought to play a central role in filarial disease pathogenesis. We measured the plasma levels of microbial translocation markers, acute phase proteins, and inflammatory cytokines in individuals with chronic filarial pathology with (CP Ag+ or without (CP Ag- active infection; with clinically asymptomatic infections (INF; and in those without infection (endemic normal [EN]. Comparisons between the two actively infected groups (CP Ag+ compared to INF and those without active infection (CP Ag- compared to EN were used preliminarily to identify markers of pathogenesis. Thereafter, we tested for group effects among all the four groups using linear models on the log transformed responses of the markers. Our data suggest that circulating levels of microbial translocation products (lipopolysaccharide and LPS-binding protein, acute phase proteins (haptoglobin and serum amyloid protein-A, and inflammatory cytokines (IL-1β, IL-12, and TNF-α are associated with pathogenesis of disease in lymphatic filarial infection and implicate an important role for circulating microbial products and acute phase proteins.

Digestion and microbial protein synthesis in sheep as affected by ...

African Journals Online (AJOL)

Useni , Alain

enzyme (EFE) on the in vitro gas production (GP) and ANKOM digestion systems on the mixture of milled ... determine the EFE effect on the DM, CP and NDF digestion of a mixture of lucerne hay and wheat straw .... and the microbial protein synthesis (MPS) measured as purine derivates (RNA equivalent in µg/DM g) on.

Phosphatase Activity of Microbial Populations in Different Milk Samples in Relation to Protein and Carbohydrate Content

Directory of Open Access Journals (Sweden)

Sosanka Protim SANDILYA

2014-12-01

Full Text Available Cattle milk is a rich source of protein, carbohydrate, vitamins, minerals and all other major and micro nutrients. At a moderate pH, milk is an excellent media for the growth of microbes and thus, intake of raw milk is precarious. In this study, attempt was made for a qualitative study of eight raw milk samples of different varieties of cow and goat milk, collected from Jorhat district of Assam, India, on the basis of nutritional value and microbial population. The highest microbial population was found in the milk collected from cross hybrid variety of cow, whereas microbial contamination was the least in Jersey cow milk. Samples of C1 (Jersey cow variety showed presence of the highest amount of protein and carbohydrate content as compared to the others. Almost all the milk samples showed positive acid and alkaline phosphatase activity. Maximum acid phosphatase activity was observed in cross hybrid cow milk, whereas local cow milk exhibited the highest alkaline phosphatase activity. Phosphatase activity did not show any co-relationship with microbial population of the milk samples. Similarly, the protein and carbohydrate content of the samples did not have any significant impact on both acid and alkaline phosphatase activity.

PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

Science.gov (United States)

Paul, Sandip; Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V; Chattopadhyay, Sujay

2015-12-01

A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. Copyright © 2015 Elsevier Inc. All rights reserved.

Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes

Energy Technology Data Exchange (ETDEWEB)

Kent, Stephen [University of Chicago

2012-07-20

The objective of this research program was to prototype methods for the chemical synthesis of predicted protein molecules in annotated microbial genomes. High throughput chemical methods were to be used to make large numbers of predicted proteins and protein domains, based on microbial genome sequences. Microscale chemical synthesis methods for the parallel preparation of peptide-thioester building blocks were developed; these peptide segments are used for the parallel chemical synthesis of proteins and protein domains. Ultimately, it is envisaged that these synthetic molecules would be ‘printed’ in spatially addressable arrays. The unique ability of total synthesis to precision label protein molecules with dyes and with chemical or biochemical ‘tags’ can be used to facilitate novel assay technologies adapted from state-of-the art single molecule fluorescence detection techniques. In the future, in conjunction with modern laboratory automation this integrated set of techniques will enable high throughput experimental validation of the functional annotation of microbial genomes.

The influence of nitrogen supplementation on microbial protein synthesis on water-buffaloes

International Nuclear Information System (INIS)

Abidin, Zainal; Hendratno, C.; Suharjono; Rustam, B.

1982-01-01

This work was carried out to observe the effects of nitrogen supplementation from urea and soybean meal on microbial protein synthesis, and other parameters of rumen functions of the waterbuffalo. Four rations were given to four water-buffaloes assigned in 4x4 latin square design. Ration A consisted of local grass+0% urea, ration B local grass+0.7% urea, ration C local grass+1.4% urea and ration D local grass+8.5% soybean meal. The result indicated that microbial protein synthesis was significantly affected (P/0.05) by the supplementation of urea, and the utilization of N in ration B was more efficient compared to the other rations. The ammonia concentration in the rumen fluid also increased (P/0.05) as a result of urea supplementation. However, no changes were found in the total volatile fatty acids production and total protozoal counts. An increased (P/0.05) of pH in the rumen fluid was also observed in the rations B and C. (author)

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

Directory of Open Access Journals (Sweden)

Li Weizhong

2008-04-01

Full Text Available Abstract Background The identification and study of proteins from metagenomic datasets can shed light on the roles and interactions of the source organisms in their communities. However, metagenomic datasets are characterized by the presence of organisms with varying GC composition, codon usage biases etc., and consequently gene identification is challenging. The vast amount of sequence data also requires faster protein family classification tools. Results We present a computational improvement to a sequence clustering approach that we developed previously to identify and classify protein coding genes in large microbial metagenomic datasets. The clustering approach can be used to identify protein coding genes in prokaryotes, viruses, and intron-less eukaryotes. The computational improvement is based on an incremental clustering method that does not require the expensive all-against-all compute that was required by the original approach, while still preserving the remote homology detection capabilities. We present evaluations of the clustering approach in protein-coding gene identification and classification, and also present the results of updating the protein clusters from our previous work with recent genomic and metagenomic sequences. The clustering results are available via CAMERA, (http://camera.calit2.net. Conclusion The clustering paradigm is shown to be a very useful tool in the analysis of microbial metagenomic data. The incremental clustering method is shown to be much faster than the original approach in identifying genes, grouping sequences into existing protein families, and also identifying novel families that have multiple members in a metagenomic dataset. These clusters provide a basis for further studies of protein families.

Effects of feeding canola meal or wheat dried distillers grains with solubles as a major protein source in low- or high-crude protein diets on ruminal fermentation, omasal flow, and production in cows.

Science.gov (United States)

Mutsvangwa, T; Kiran, D; Abeysekara, S

2016-02-01

The objective of this study was to determine the effects of feeding canola meal (CM) or wheat dried distillers grains with solubles (W-DDGS) as the major source of protein in diets varying in crude protein (CP) content on ruminal fermentation, microbial protein production, omasal nutrient flow, and production performance in lactating dairy cows. Eight lactating dairy cows were used in a replicated 4×4 Latin square design with 29-d periods (21 d of dietary adaptation and 8 d of measurements) and a 2×2 factorial arrangement of dietary treatments. Four cows in 1 Latin square were ruminally cannulated to allow ruminal and omasal sampling. The treatment factors were (1) source of supplemental protein (CM vs. W-DDGS) and (2) dietary CP content (15 vs. 17%; DM basis). Diets contained 50% forage and 50% concentrate, and were fed twice daily at 0900 and 1600 h as total mixed rations for ad libitum intake. Dry matter intake and milk yield were unaffected by dietary treatments; however, milk yield in cows that were fed CM was numerically greater (+1.1 kg/d) when compared with cows fed W-DDGS. Feeding CM increased milk lactose content compared with feeding W-DDGS. Milk urea nitrogen and ruminal NH3-N concentrations were greater in cows fed the high-CP compared with those fed the low-CP diet. The rumen-degradable protein supply was greater in cows fed the high-CP when compared with those fed the low-CP diet when diets contained CM, whereas rumen-degradable protein supply was lower in cows fed the high-CP when compared with those fed the low-CP diet when diets contained W-DDGS. Total N flow at the omasal canal was not affected by diet; however, omasal flow of NH3-N was greater in cows fed CM when compared with those fed W-DDGS. The rumen-undegradable protein supply was greater in cows fed the low-CP when compared with those fed the high-CP diet when diets contained CM, whereas rumen-undegradable protein supply was lower in cows fed the low-CP when compared with those fed the

Nitrogen balance, microbial protein synthesis and blood metabolites in fattening of male Bali cattle fed ration with different protein levels in smallholder farms

Directory of Open Access Journals (Sweden)

P. K. Tahuk

2018-03-01

Full Text Available Research was aimed to determine nitrogen balance, microbial protein synthesis, and blood metabolites of male Bali cattle fattening fed ration with different protein level in smallholder farms North Central Timor, Province of East Timor Tenggara, Indonesia. The cattle used were 18 heads aged 2 to 2.5 years with initial body weight of 229.86±12.46 kg. The cattle were randomly divided into three treatment groups. The T0 group was given feed the same as traditional fattening cattle practices by farmers,T1 group fed ration containing 12% crude protein (CP and 72% total digestible nutrients (TDN, andT2 group fedration containing 15% CP and 72%TDN. Cattle were fed individually for 90 days and drinkingwater ad libitum. The data were analyzedby analysis of variance.Results of research indicated the nitrogen balance, and blood urea nitrogen between T1 and T2 were relatively similar, but those were higher (P<0.05 than T0 . In contrast, microbial proteins synthesis, and blood glucose at 0, 4, and 6 hours before and after feeding were relatively similar between the groups. Blood glucose of T2 at 2 hours after intake were higher (P <0.05 than T0, but was not different with T1 . It can be concluded, that the fattening maleBali cattle fed ration containing 12% CP and 72% TDNimprovedthe nitrogen balance and blood metabolites, butit was no positive effect on the microbial proteins and N synthesis.

Prediction of rumen microbial outflow based on urinary excretion of purine derivatives

International Nuclear Information System (INIS)

Nolan, J.V.

1999-01-01

The method for predicting microbial protein outflow from the rumen based on the excretion of purine derivatives (PD) in the urine is being increasingly used by nutritionists. In contrast to methods that depend on estimates of digesta flow, the PD method does not require animals to be fitted surgically with cannulae into the gut, and studies can be performed with minimal disturbance to the experimental animals. Methods of analysis of PD have been improved and standardized. Certain assumptions, however, are required that could lead to errors when this method is used to predict microbial protein outflow from the rumen. The need for further investigation of these assumptions by means of isotopic tracers and other techniques is examined. (author)

Ability of commercially available dairy ration programs to predict duodenal flows of protein and essential amino acids in dairy cows.

Science.gov (United States)

Pacheco, D; Patton, R A; Parys, C; Lapierre, H

2012-02-01

The objective of this analysis was to compare the rumen submodel predictions of 4 commonly used dairy ration programs to observed values of duodenal flows of crude protein (CP), protein fractions, and essential AA (EAA). The literature was searched and 40 studies, including 154 diets, were used to compare observed values with those predicted by AminoCow (AC), Agricultural Modeling and Training Systems (AMTS), Cornell-Penn-Miner (CPM), and National Research Council 2001 (NRC) models. The models were evaluated based on their ability to predict the mean, their root mean square prediction error (RMSPE), error bias, and adequacy of regression equations for each protein fraction. The models predicted the mean duodenal CP flow within 5%, with more than 90% of the variation due to random disturbance. The models also predicted within 5% the mean microbial CP flow except CPM, which overestimated it by 27%. Only NRC, however, predicted mean rumen-undegraded protein (RUP) flows within 5%, whereas AC and AMTS underpredicted it by 8 to 9% and CPM by 24%. Regarding duodenal flows of individual AA, across all diets, CPM predicted substantially greater (>10%) mean flows of Arg, His, Ile, Met, and Lys; AMTS predicted greater flow for Arg and Met, whereas AC and NRC estimations were, on average, within 10% of observed values. Overpredictions by the CPM model were mainly related to mean bias, whereas the NRC model had the highest proportion of bias in random disturbance for flows of EAA. Models tended to predict mean flows of EAA more accurately on corn silage and alfalfa diets than on grass-based diets, more accurately on corn grain-based diets than on non-corn-based diets, and finally more accurately in the mid range of diet types. The 4 models were accurate at predicting mean dry matter intake. The AC, AMTS, and NRC models were all sufficiently accurate to be used for balancing EAA in dairy rations under field conditions. Copyright © 2012 American Dairy Science Association

Elevated temperature alters carbon cycling in a model microbial community

Science.gov (United States)

Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

2013-12-01

Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

Effects of degradable protein and non-fibre carbohydrates on microbial growth and fermentation in the rumen simulating fermenter (Rusitec

Directory of Open Access Journals (Sweden)

Xiang H. Zhao

2015-05-01

Full Text Available A rumen simulation technique (Rusitec apparatus with eight 800 ml fermentation vessels was used to investigate the effects of rumen degradable protein (RDP level and non-fibre carbohydrate (NFC type on ruminal fermentation, microbial growth, and populations of ruminal cellulolytic bacteria. Treatments consisted of two NFC types (starch and pectin supplemented with 0 g/d (low RDP or 1.56 g/d (high RDP sodium caseinate. Apparent disappearance of dry matter and organic matter was greater for pectin than for starch treatment (P<0.01 with low or high RDP. A NFC × RDP interaction was observed for neutral detergent fibre disappearance (P=0.01, which was lower for pectin than for starch only under low RDP conditions. Compared with starch, pectin treatment increased the copy numbers of Ruminococcus albus (P≤0.01 and Ruminococcus flavefaciens (P≤0.09, the molar proportion of acetate (P<0.01, the acetate:propionate ratio (P<0.01, and methane production (P<0.01, but reduced the propionate proportion (P<0.01. Increasing dietary RDP increased the production of total VFA (P=0.01, methane (P<0.01, ammonia N (P<0.01, and microbial N (P<0.01. Significant NFC × RDP interaction and interaction tendency were observed for ammonia N production (P=0.01 and daily N flow of total microorganisms (P=0.07, which did not differ under low RDP conditions, but pectin produced greater microbial N and less ammonia N than starch with increased RDP. Results showed NFC type, RDP level, and their interaction affected ruminal fermentation and microbial growth, and under sufficient ruminal degradable N pectin had greater advantage in microbial N synthesis than starch in vitro.

PanCoreGen – profiling, detecting, annotating protein-coding genes in microbial genomes

Science.gov (United States)

Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V.

2015-01-01

A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen – a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars – Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. PMID:26456591

Effect of Fixed Orthodontic Treatment on Salivary Flow, pH and Microbial Count

Directory of Open Access Journals (Sweden)

Sepideh Arab

2016-08-01

Full Text Available Objectives: The present study was designed to evaluate the changes in saliva properties and oral microbial flora in patients undergoing fixed orthodontic treatment.Materials and Methods: Two important saliva properties namely the salivary flow rate and pH as well as oral microbial flora were assessed in 30 orthodontic patients before starting fixed orthodontic treatment and after six, 12 and 18 weeks of treatment. Selective media, Sabouraud dextrose agar, Mitis salivarius agar and Rogosa agar were used for isolation of Candida albicans, Streptococcus mutans and Lactobacillus acidophilus, respectively. Statistical analysis was performed using Friedman and Dunn’s tests. P< 0.05 was considered statistically significant.Results: After six, 12 and 18 weeks of commencing fixed orthodontic treatment, the total colony counts of Candida albicans, Streptococcus mutans and Lactobacillus acidophilus showed a significant increase. The saliva pH decreased during the orthodontic treatment (P< 0.05 while the salivary flow did not change significantly. Conclusions: Fixed orthodontic treatment causes major changes in the saliva properties. The changes in oral microflora and saliva properties show the importance of caries preventive measures during orthodontic treatment.

Complete all-atom hydrodynamics of protein unfolding in uniform flow

International Nuclear Information System (INIS)

Wang, Guan M; Sandberg, William C

2010-01-01

The unfolding dynamics of a protein, ubiquitin, pinned in several uniform flows, was studied at low and high flow rates in an all-atom style through a non-equilibrium molecular dynamics approach with explicit water molecules included. Atomic hydrodynamic force components on individual amino acids, as a function of time, due to the collisional interactions with the flowing water molecules were calculated explicitly. The protein conformational change in response to those time-varying forces was computed completely at the high flow rate up to nanosecond until the fully stretched state was reached. The end-to-end length of the single ubiquitin protein molecule at high flow rate is smoothly increasing. The step-like jumps between metastable states that describe the μm ms -1 scale force pulling experiments conducted on polyubiquitins at low flow rates, are not seen at the high flow speeds necessary to computationally probe the ns nm -1 scale regime. No unfolding was observed in the low flow rate atomic computations at nanosecond scale while partial and complete unfolding was observed in the coarse-grained low flow rate computations at microsecond scale. Examination of the all-atom computation of the time variation of the hydrodynamic forces on, and the velocity components of, the protein molecule unveiled to some extent the details of the complexity of the hydrodynamic friction variation in the nm ns -1 regime of high rate flow-driven protein unfolding. This demonstrates quantitatively that all-atom computations are more suitable than the Langevin equation or Brownian dynamics methods for probing the interaction dynamics and resulting conformational dynamics of protein unfolding in strong flows on nm ns -1 time/length scales while the reverse is true for investigation of slow, diffusively driven systems.

Microbial community composition of a down-flow hanging sponge (DHS) reactor combined with an up-flow anaerobic sludge blanket (UASB) reactor for the treatment of municipal sewage.

Science.gov (United States)

Kubota, Kengo; Hayashi, Mikio; Matsunaga, Kengo; Iguchi, Akinori; Ohashi, Akiyoshi; Li, Yu-You; Yamaguchi, Takashi; Harada, Hideki

2014-01-01

The microbial community composition of a down-flow hanging sponge (DHS) reactor in an up-flow anaerobic sludge blanket (UASB)-DHS system used for the treatment of municipal sewage was investigated. The clone libraries showed marked differences in microbial community composition at different reactor heights and in different seasons. The dominant phylotypes residing in the upper part of the reactor were likely responsible for removing organic matters because a significant reduction in organic matter in the upper part was observed. Quantification of the amoA genes revealed that the proportions of ammonia oxidizing bacteria (AOB) varied along the vertical length of the reactor, with more AOB colonizing the middle and lower parts of the reactor than the top of the reactor. The findings indicated that sewage treatment was achieved by a separation of microbial habitats responsible for organic matter removal and nitrification in the DHS reactor. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dietary protein reduction on microbial protein, amino acids digestibility, and body retention in beef cattle. I. Digestibility sites and ruminal synthesis estimated by purine bases and 15N as markers.

Science.gov (United States)

Mariz, Lays Débora Silva; Amaral, Paloma de Melo; Valadares Filho, Sebastião de Campos; Santos, Stefanie Alvarenga; Marcondes, Marcos Inácio; Prados, Laura Franco; Carneiro Pacheco, Marcos Vinícius; Zanetti, Diego; de Castro Menezes, Gustavo Chamon; Faciola, Antonio P

2018-06-04

The objectives of this study were to evaluate the effect of reducing dietary CP contents on 1) total and partial nutrient digestion and nitrogen balance and 2) on microbial crude protein (MCP) synthesis and true MCP digestibility in the small intestine obtained with 15N and purine bases (PB) in beef cattle. Eight bulls (4 Nellore and 4 Crossbred Angus × Nellore) cannulated in the rumen and ileum were distributed in duplicated 4 × 4 Latin squares. The diets consisted of increasing CP contents: 100, 120, or 140 g CP/kg DM offered ad libitum, and restricted intake (RI) diet with 120 g CP/kg DM. The experiment lasted four 17-d periods, with 10 d for adaptation to diets and another 7 for data collection. Omasal digesta flow was obtained using Co-EDTA and indigestible NDF (iNDF) as markers, and to estimate ileal digesta flow only iNDF was used. From days 11 to 17 of each experimental period, ruminal infusions of Co-EDTA (5.0 g/d) and 15N (7.03 g of ammonium sulfate enriched with 10% of 15N atoms) were performed. There was no effect of CP contents (linear effect, P = 0.55 and quadratic effect, P = 0.11) on ruminal OM digestibility. Intake of CP linearly increased (P content (P ruminally degradable OM and true ruminally degradable OM) had a quadratic tendency (P = 0.07 and P = 0.08, respectively) to CP increasing and was numerically greatest at 120 g CP/kg DM. The adjusted equations for estimating true intestinal digestibility of MCP (Y1) and total CP (Y2) were, respectively, as follows: Y1 =--16.724(SEM = 40.06) + 0.86X(SEM = 0.05) and Y2 = -43.81(SEM = 49.19) + 0.75X(SEM = 0.05). It was concluded that diets with 120 g/kg of CP optimize the microbial synthesis and efficiency and ruminal ash and protein NDF digestibility, resulting in a better use of N compounds in the rumen. The PB technique can be used as an alternative to the 15N to estimate microbial synthesis.

Influence of energy concentration and source on the utilization of feed protein and NPN in lambs. 3. Allantoin excretion and microbial protein synthesis

Energy Technology Data Exchange (ETDEWEB)

Ulbrich, M; Geissler, C; Bassuny, S M; Borowiec, F; Hoffmann, M

1989-06-01

In an N balance experiment with male crossbreeding lambs at an age of 3-4 months four different rations were given differing in energy concentration (high > 700 EFU/sub cattle//kg DM and low < 650 EFU/sub cattle//kg DM) and in the energy source (sugar, starch or crude fibre) with crude protein intake being almost equal. The rations contained 2% urea. Microbial protein synthesis in the rumen was assessed according to Roth and Kichgessner (1978) (1), Rys et al. (1975) (2) and Bickel-Baumann and Landis (1986) (3) on the basis of allantoin excretion in urine. The highest ruminal protein synthesis quotas were 868-921 mg protein N per kg LW/sup 0.75/ in (2). In (3) 723-766 mg protein N/kg LW /sup 0.75/ were synthesized. From the /sup 15/N labelling of the supplemented urea and the excreted allantoin it could be calculated that 26-40% of the microbial protein resulted from the urea-N of the ration. Despite a high crude protein content of the ration of between 16 and 17% in the DM and a relation of NPN: pure protein of 0.95 the utilization of the NPN in the ration was relatively high but slightly lower than the utilization of pure protein. The variants with higher energy concentration showed as a tendency higher allantoin excretion in spite of slightly lower dry matter intake and a slightly higher NPN utilization than the variants with lower energy concentration. (author).

Expanded microbial genome coverage and improved protein family annotation in the COG database.

Science.gov (United States)

Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2015-01-01

Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the

Microbial Physiology of the Conversion of Residual Oil to Methane: A Protein Prospective

Science.gov (United States)

Morris, Brandon E. L.; Bastida-Lopez, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Suflita, Joseph M.

2010-05-01

Traditional petroleum recovery techniques are unable to extract the majority of oil in most petroliferous deposits. The recovery of even a fraction of residual hydrocarbon in conventional reserves could represent a substantive energy supply. To this end, the microbial conversion of residual oil to methane has gained increasing relevance in recent years [1,2]. Worldwide demand for methane is expected to increase through 2030 [3], as it is a cleaner-burning alternative to traditional fuels [4]. To investigate the microbial physiology of hydrocarbon-decomposition and ultimate methanogenesis, we initiated a two-pronged approach. First, a model alkane-degrading sulfate-reducing bacterium, Desulfoglaeba alkanexedens, was used to interrogate the predominant metabolic pathway(s) differentially expressed during growth on either n-decane or butyrate. A total of 81 proteins were differentially expressed during bacterial growth on butyrate, while 100 proteins were unique to the alkane-grown condition. Proteins related to alkylsuccinate synthase, or the homologous 1-methyl alkylsuccinate synthase, were identified only in the presence of the hydrocarbon. Secondly, we used a newly developed stable isotope probing technique [5] targeted towards proteins to monitor the flux of carbon through a residual oil-degrading bacterial consortium enriched from a gas-condensate contaminated aquifer [1]. Combined carbon and hydrogen stable isotope fractionation identified acetoclastic methanogenesis as the dominant process in this system. Such findings agree with the previous clone library characterization of the consortium. Furthermore, hydrocarbon activation was determined to be the rate-limiting process during the net conversion of residual oil to methane. References 1. Gieg, L.M., K.E. Duncan, and J.M. Suflita, Bioenegy production via microbial conversion of residual oil to natural gas. Appl Environ Micro, 2008. 74(10): p. 3022-3029. 2. Jones, D.M., et al., Crude-oil biodegradation via

Influence of shear on microbial adhesion to PEO-brushes and glass by convective-diffusion and sedimentation in a parallel plate flow chamber

NARCIS (Netherlands)

Roosjen, A; Boks, NP; van der Mei, HC; Busscher, HJ; Norde, W

2005-01-01

Microbial adhesion to surfaces often occurs despite high wall shear rates acting on the adhering microorganisms. In this paper, we compare the wall shear rates needed to prevent microbial adhesion to bare glass and poly(ethylene oxide) (PEO)-brush coated glass in a parallel plate flow chamber.

PATtyFams: Protein families for the microbial genomes in the PATRIC database

Directory of Open Access Journals (Sweden)

James J Davis

2016-02-01

Full Text Available The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based function assignments available through RAST (Rapid Annotation using Subsystem Technology to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL. This new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.

Estimation of microbial protein supply of lactating dairy cows under smallholder farms in north-east Thailand using urinary purine derivative technique

International Nuclear Information System (INIS)

Pimpa, O.; Liang, J.B.

2004-01-01

Two experiments were conducted to examine the potential of urinary purine derivative (PD) as a predictive index of microbial protein supply in ruminant livestock under farm conditions. Results of Experiment 1 indicated that diurnal variation in the PDC index ( [mmol/L PD]/[mmol/L creatinine] kgW 0.75 ) in spot urine samples of zebu cattle was small and highly correlated with the daily PD output, suggesting that spot urine samples could be used to derive an index for estimating microbial protein supply of cattle under farm conditions. However, the PDC index for buffaloes was poorly correlated to daily urinary PD output, therefore the use of spot urine samples appeared to be unsuitable for buffaloes. Based on the above results, spot urine samples were used to estimate the microbial protein supply of lactating dairy cows under farm conditions in a follow-up experiment. The study was conducted using 24 lactating cows in 6 smallholder dairy farms situated in Khon Kaen province of Northeast Thailand. The study was conducted over two climatic seasons (raining and dry), where the animals were fed 5 kg of farm-mixed concentrate feed supplemented either with green grass (cut or grazing) or rice straw as roughage source during the raining and dry seasons, respectively. The results indicated that microbial protein supply was not significantly different and therefore, the nutritional status of the lactating cows was not significantly different between the two seasons. The absence of differences in milk yield between seasons seems to support our findings. We conclude that urinary PD technique could be used to estimate rumen microbial protein production for dairy cattle under farm conditions. (author)

Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells

DEFF Research Database (Denmark)

Weiss Nielsen, Martin; Sternberg, Claus; Molin, Søren

2011-01-01

or proteins compatible with CLSM analysis. This enables online visualization and allows investigation of niches in the developing biofilm. Microbial interrelationship, investigation of antimicrobial agents or the expression of specific genes, are of the many experimental setups that can be investigated......). Using a transparent substratum it is possible to device a system where simple biofilms can be examined in a non-destructive way in real-time: here we demonstrate the assembly and operation of a flow cell model system, for in vitro 3D studies of microbial biofilms generating high reproducibility under...... well-defined conditions(2,3). The system consists of a flow cell that serves as growth chamber for the biofilm. The flow cell is supplied with nutrients and oxygen from a medium flask via a peristaltic pump and spent medium is collected in a waste container. This construction of the flow system allows...

The Concentrations of Rumen Fluid Volatile Fatty Acids and Ammonia, and Rumen Microbial Protein Production in Sheep Given Feed During the Day and Night Time

Science.gov (United States)

Gumilar, D. A. K. W.; Rianto, E.; Arifin, M.

2018-02-01

An experimental study was carried out to investigate the concentrations of volatile (VFA), ammonia and microbial protein production of rumen fluid in sheep given fedd during the day and at night. This study used 12 fat-tailed rams aged 12-18 months and weighed 24,12 ± 25 kg (CV = 10,51%). The rams were fed a complete feed containing 16.64% protein and 68,33% total digestible nutrients (TDN). The rams were allocated into a completely randomised design with 3 treatments and 4 replications. The treatments applied were: T1: day time feeding (6.00 hrs - 18.00 hrs); T2: night time feeding (18.00 hrs - 6.00 hrs); and T3: day and night time feedings (6.00 hrs - 6.00 hrs). The parameters observed were dry matter intake (DMI), rumen VFA concentration, rumen ammonia concentration, rumen rmicrobial protein production and the efficiency of rumen microbial protein production. The results showed that feeding time did not significantly affect (P>0.05) all the parameters observed. Dry matter intake, VFA concentration, ammonia concentration, the microbial protein production of rumen fluid and the efficiency of microbial protein production were 1,073g/d, 49.69 mmol; 4.77 mg N/100 ml, 12,111 g/d and 19.96 g per kg digestible organic matter intake (DOMI), respectively. It is concluded that feeding time did not affect DMI, condition of rumen fluid and rumen microbial protein production in sheep.

Effect of Fixed Orthodontic Treatment on Salivary Flow, pH and Microbial Count.

Science.gov (United States)

Arab, Sepideh; Nouhzadeh Malekshah, Sepideh; Abouei Mehrizi, Ehsan; Ebrahimi Khanghah, Anita; Naseh, Roya; Imani, Mohammad Moslem

2016-01-01

The present study was designed to evaluate the changes in saliva properties and oral microbial flora in patients undergoing fixed orthodontic treatment. Two important saliva properties namely the salivary flow rate and pH as well as oral microbial flora were assessed in 30 orthodontic patients before starting fixed orthodontic treatment and after six, 12 and 18 weeks of treatment. Selective media, Sabouraud dextrose agar, Mitis salivarius agar and Rogosa agar were used for isolation of Candida albicans, Streptococcus mutans and Lactobacillus acidophilus, respectively. Statistical analysis was performed using Friedman and Dunn's tests. Porthodontic treatment, the total colony counts of Candida albicans, Streptococcus mutans and Lactobacillus acidophilus showed a significant increase. The saliva pH decreased during the orthodontic treatment (Porthodontic treatment causes major changes in the saliva properties. The changes in oral microflora and saliva properties show the importance of caries preventive measures during orthodontic treatment.

Microbial protein synthesis, digestion and lactation responses of cows to grass or grass-red clover silage diet supplemented with barley or oats

Directory of Open Access Journals (Sweden)

A. VANHATALO

2008-12-01

Full Text Available The study was conducted to evaluate effects of silage type (grass-red clover vs. pure grass and grain supplement (oats vs. barley on rumen fermentation, post-ruminal nutrient flows, diet digestion and milk production. Four primiparous Finnish Ayrshire cows fitted with cannulae in the rumen and duodenum were used in a 4 × 4 Latin square experiment with four 28-d experimental periods and 2 × 2 factorial arrangements of treatments. Using red clover-containing (40% silage rather than pure grass silage had minor effects on rumen fermentation or diet digestion but increased non-ammonia nitrogen (N flow in terms of increased flows of microbial and dietary N entering to the small intestine. This was reflected as a reduced ruminal N degradability on grass-red clover diets. Furthermore, grass-red clover diets in comparison to grass silage diets increased milk lactose concentration and yields of milk, protein and lactose. Feeding oats in replacement for barley had minor effects on rumen fermentation or post-ruminal non-ammonia N flows but reduced digestibility of organic matter and neutral detergent fibre in the diet. Using oats rather than barley increased yields of milk and lactose but reduced milk protein concentration. Oats also increased proportions of C18:0 and C18:1 in milk fat and reduced those of C10:0 to C16:0. It is concluded that inclusion of red clover and replacement of barley with oats in grass silage based diets have beneficial effects in dairy cow production.;

Flow cytometric analysis of microbial contamination in food industry technological lines – initial study

OpenAIRE

Katarzyna Czaczyk; Wojciech Juzwa

2012-01-01

Background. Flow cytometry constitutes an alternative for traditional methods of microorganisms identifi cation and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer) may be analysed directly. This leads to a signifi cant reduction of time required for analysis allowing monitoring of production process...

Modelling of microbial polyhydroxyalkanoate surface binding protein PhaP for rational mutagenesis.

Science.gov (United States)

Zhao, Hongyu; Yao, Zhenyu; Chen, Xiangbin; Wang, Xinquan; Chen, Guo-Qiang

2017-11-01

Phasins are unusual amphiphilic proteins that bind to microbial polyhydroxyalkanoate (PHA) granules in nature and show great potential for various applications in biotechnology and medicine. Despite their remarkable diversity, only the crystal structure of PhaP A h from Aeromonas hydrophila has been solved to date. Based on the structure of PhaP A h , homology models of PhaP A z from Azotobacter sp. FA-8 and PhaP TD from Halomonas bluephagenesis TD were successfully established, allowing rational mutagenesis to be conducted to enhance the stability and surfactant properties of these proteins. PhaP A z mutants, including PhaP A z Q38L and PhaP A z Q78L, as well as PhaP TD mutants, including PhaP TD Q38M and PhaP TD Q72M, showed better emulsification properties and improved thermostability (6-10°C higher melting temperatures) compared with their wild-type homologues under the same conditions. Importantly, the established PhaP homology-modelling approach, based on the high-resolution structure of PhaP A h , can be generalized to facilitate the study of other PhaP members. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Metabolisable protein supply to lactating dairy cows increased with increasing dry matter concentration in grass-clover silage

DEFF Research Database (Denmark)

Johansen, Marianne; Hellwing, Anne Louise Frydendahl; Lund, Peter

2017-01-01

The aim of this experiment was to study the effect of increased dry matter (DM) concentration in grass-clover silage, obtained by extending the pre-wilting period before ensiling, on the amount of metabolisable protein (MP) supplied to lactating dairy cows. Spring growth and first regrowth of grass...... and faeces, respectively, were collected over 94 h to cover the diurnal variation, pooled, and subsequently analysed. Rumen fluid was collected in same sampling procedure. To estimate the duodenal flow of microbial protein, microbes were isolated from the rumen and analysed for amino acids (AA) and purines...... flow of AA. The higher duodenal flow of AA derived from a lower rumen degradation of feed protein and a tendency towards a higher microbial synthesis in the rumen. Fibre digestibility and CH4 production were not affected by silage DM concentration. In conclusion, MP concentration in grass-clover silage...

Ruminal, Intestinal, and Total Digestibilities of Nutrients in Cows Fed Diets High in Fat and Undegradable Protein

DEFF Research Database (Denmark)

Palmquist, D.L.; Weisbjerg, Martin Riis; Hvelplund, Torben

1993-01-01

To study relationships of high undegradable intake protein and dietary fat on intestinal AA supply, the ruminal, intestinal, and total digestibilities of diets with or without added fat (5% of DM) and animal protein (blood meal: hydrolyzed feather meal, 1:1; 8% of DM) were examined with four cows...... with cows cannulated 100-cm distal to the pylorus, but only when cows were fed protein-supplemented diets; the estimates from those diets caused calculated microbial protein efficiency to exceed theoretical values. We postulated that blood meal and feather meal segregated near the pylorus, yielding high...... estimates of duodenal AA N flow. Removal of data for protein-supplemented diets obtained from cows cannulated at the pylorus yielded estimates of microbial protein synthetic efficiency consistent with literature values. Microbial synthesis of AA N was related linearly to ruminal digestion of carbohydrate...

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems.

Science.gov (United States)

Babatunde, A O; Miranda-CasoLuengo, Raul; Imtiaz, Mehreen; Zhao, Y Q; Meijer, Wim G

2016-08-01

This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance. Copyright © 2016. Published by Elsevier B.V.

Effects of the dietary ratio of ruminal degraded to undegraded protein and feed intake on intestinal flows of endogenous nitrogen and amino acids in goats.

Science.gov (United States)

Zhou, Chuanshe; Chen, Liang; Tan, Zhiliang; Tang, Shaoxun; Han, Xuefeng; Wang, Min; Kang, Jinhe; Yan, Qiongxian

2015-01-01

This study was conducted to evaluate the effects of the dietary ratio of ruminal degraded protein (RDP) to ruminal undegraded protein (RUP) and the dry matter intake (DMI) on the intestinal flows of endogenous nitrogen (N) and amino acids (AA) in goats. The experiment was designed as a 4×4 Latin square using four ruminally, duodenally and ileally cannulated goats. The treatments were arranged in a 2×2 factorial design; two ratios of RDP to RUP (65:35 and 45:55, RDP1 and RDP2, respectively) and two levels at 95% and 75% of voluntary feed intake (DMI1 and DMI2, respectively) were fed to the goats. There were no significant differences in the N intake, duodenal flow of total N, undegraded feed N, microbial N, endogenous N or ileal flow of endogenous N, but the duodenal and ileal flow of endogenous N numerically decreased by approximately 22% and 9%, respectively, when the feed intake changed from DMI1 (0.63 kg/d) to DMI2 (0.50 kg/d). The dietary ratio of RDP to RUP had significant effects (pRUP ratio and DMI decreased, and the flow of endogenous AA at the ileum also decreased when the DMI decreased but increased with decreasing RDP to RUP ratios.

Microbial electrosynthesis of hydrogen peroxide in microbial reverse-electrodialysis electrolysis cell

DEFF Research Database (Denmark)

Li, Xiaohu; Angelidaki, Irini; Zhang, Yifeng

2016-01-01

Microbial reverse-electrodialysis electrolysis cell (MREC) as a novel type of microbial electrochemical technologies has been proposed to produce H2 and CH4. In this study, we developed MREC to produce the strong oxidant H2O2. In the MREC, electrical potential generated by the exoelectrogens...... and the salinity-gradient between sea water and river water were utilized to drive the high-rate H2O2 production without external power supply. Operational parameters such as air flow rate, pH, cathodic potential, flow rate of high and low concentration solution were investigated. The optimal H2O2 production were...

Multiple paths of electron flow to current in microbial electrolysis cells fed with low and high concentrations of propionate

KAUST Repository

Rao, Hari Ananda; Katuri, Krishna; Gorron, Eduardo; Logan, Bruce E.; Saikaly, Pascal

2016-01-01

Microbial electrolysis cells (MECs) provide a viable approach for bioenergy generation from fermentable substrates such as propionate. However, the paths of electron flow during propionate oxidation in the anode of MECs are unknown. Here, the paths

Coupled modeling of groundwater flow solute transport, chemical reactions and microbial processes in the 'SP' island

Energy Technology Data Exchange (ETDEWEB)

Samper, Javier; Molinero, Jorg; Changbing, Yang; Zhang, Guoxiang

2003-12-01

The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behavior and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by /Banwart et al, 1995/. Later, /Banwart et al, 1999/ presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by /Molinero, 2000/ who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulfate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of /Molinero, 2000/ and extends the preliminary microbial model of /Zhang, 2001/ by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfate concentration, thus

Salt removal using multiple microbial desalination cells under continuous flow conditions

KAUST Repository

Qu, Youpeng

2013-05-01

Four microbial desalination cells (MDCs) were hydraulically connected and operated under continuous flow conditions. The anode solution from the first MDC flowed into the cathode, and then on to the anode of the next reactor, which avoided pH imbalances that inhibit bacterial metabolism. The salt solution also moved through each desalination chamber in series. Increasing the hydraulic retention times (HRTs) of the salt solution from 1 to 2. days increased total NaCl removal from 76 ± 1% to 97 ± 1%, but coulombic efficiencies decreased from 49 ± 4% to 35 ± 1%. Total COD removals were similar at both HRTs (60 ± 2%, 2. days; 59 ± 2%, 1. day). Community analysis of the anode biofilms showed that bacteria most similar to the xylose fermenting bacterium Klebsiella ornithinolytica predominated in the anode communities, and sequences most similar to Geobacter metallireducens were identified in all MDCs except the first one. These results demonstrated successful operation of a series of hydraulically connected MDCs and good desalination rates. © 2013 Elsevier B.V..

Microbial activities in a vertical-flow wetland system treating sewage sludge with high organic loads

Energy Technology Data Exchange (ETDEWEB)

Wang, R. Y.; Perissol, C.; Baldy, V.; Bonin, G.; Korboulewsky, N.

2009-07-01

The rhizosphere is the most active zone in treatment wetlands where take place physicochemical and biological processes between the substrate, plants, microorganisms, and contaminants. Microorganisms play the key role in the mineralisation of organic matter. substrate respiration and phosphatase activities (acid and alkaline) were chosen as indicators of microbial activities, and studied in a vertical-flow wetland system receiving sewage sludge with high organic loads under the Mediterranean climate. (Author)

Microbial ecology of phototrophic biofilms

NARCIS (Netherlands)

Roeselers, G.

2007-01-01

Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

The effect of starch, inulin, and degradable protein on ruminal fermentation and microbial growth in rumen simulation technique

Directory of Open Access Journals (Sweden)

Xiang H. Zhao

2014-03-01

Full Text Available A rumen simulation technique apparatus with eight 800 mL fermentation vessels was used to investigate the effects of rumen degradable protein (RDP level and non-fibre carbohydrate (NFC type on ruminal fermentation, microbial growth, and populations of ruminal cellulolytic bacteria. Treatments consisted of two NFC types (starch and inulin supplemented with 0 g/d (low RDP or 1.56 g/d (high RDP sodium caseinate. No significant differences existed among dietary treatments in the apparent disappearance of dietary nutrients except for dietary N, which increased with increased dietary RDP (P<0.001. Compared with starch, inulin treatments reduced the molar proportion of acetate (P<0.001, the acetate:propionate ratio (P<0.001, and methane production (P=0.006, but increased the butyrate proportion (P<0.001. Increased dietary RDP led to increases in production of total volatile fatty acid (P=0.014 and methane (P=0.050, various measures of N (P≤0.046, and 16s rDNA copy numbers of Ruminococcus flavefaciens (P≤0.010. Non-fibre carbohydrate source did not affect daily microbial N flow regardless of dietary RDP, but ammonia N production was lower for inulin than for starch treatments under high RDP conditions (P<0.001. Compared with starch treatments, inulin depressed the copy numbers of Fibrobacter succinogenes in solid fraction (P=0.023 and R. flavefaciens in liquid (P=0.017 and solid fractions (P=0.007, but it increased the carboxymethylcellulase activity in solid fraction (P=0.045. Current results suggest that starch and inulin differ in ruminal volatile fatty acid fermentation but have similar effects on ruminal digestion and microbial synthesis in vitro, although inulin suppressed the growth of partial ruminal cellulolytic bacteria.

Computational investigation of the flow field contribution to improve electricity generation in granular activated carbon-assisted microbial fuel cells

Science.gov (United States)

Zhao, Lei; Li, Jian; Battaglia, Francine; He, Zhen

2016-11-01

Microbial fuel cells (MFCs) offer an alternative approach to treat wastewater with less energy input and direct electricity generation. To optimize MFC anodic performance, adding granular activated carbon (GAC) has been proved to be an effective way, most likely due to the enlarged electrode surface for biomass attachment and improved mixing of the flow field. The impact of a flow field on the current enhancement within a porous anode medium (e.g., GAC) has not been well understood before, and thus is investigated in this study by using mathematical modeling of the multi-order Butler-Volmer equation with computational fluid dynamics (CFD) techniques. By comparing three different CFD cases (without GAC, with GAC as a nonreactive porous medium, and with GAC as a reactive porous medium), it is demonstrated that adding GAC contributes to a uniform flow field and a total current enhancement of 17%, a factor that cannot be neglected in MFC design. However, in an actual MFC operation, this percentage could be even higher because of the microbial competition and energy loss issues within a porous medium. The results of the present study are expected to help with formulating strategies to optimize MFC with a better flow pattern design.

Microbial protein synthesis and nitrogen metabolism in cows bred on tropical pasture and fed on cassava root and corn

Directory of Open Access Journals (Sweden)

Ádler Carvalho da Silva

2014-05-01

Full Text Available Current experiment evaluated the effect of replacement of full corn meal by dehydrated ground cassava roots at levels 0%, 25%, 50%, 75% and 100% in experimental supplements for lactating cows grazing on irrigated and fertilized tropical pastures. Ten Holstein cows were divided into two 5 x 5 Latin squares, with average initial 150 days of lactation, milk production 22±3.30 kg day-1 at the beginning of experiment and initial body weight of 603±65 kg. Cows were maintained on pasture consisting of elephant grass (Pennisetum purpureum, Schum cultivar Pioneiro, intercropped with Tifton 85 (Cynodon nlemfuensis, fertilized with 600 kg nitrogen per hectare year-1. There was no significant difference (p > 0.05 between the substitution levels of corn meal by ground and dehydrated cassava root in the concentrate on the synthesis of microbial protein with an estimated average of 1,288.49 g day-1 and efficiency in the synthesis of microbial protein per kilogram of TDN with estimated average of 91.30 g kg-1 TDN. Nitrogen equilibrium showed an estimated average of 218.79 g day-1 of retained nitrogen. The microbial protein synthesis and nitrogen balance were not affected by treatments.

Medium-Throughput Screen of Microbially Produced Serotonin via a G-Protein-Coupled Receptor-Based Sensor.

Science.gov (United States)

Ehrenworth, Amy M; Claiborne, Tauris; Peralta-Yahya, Pamela

2017-10-17

Chemical biosensors, for which chemical detection triggers a fluorescent signal, have the potential to accelerate the screening of noncolorimetric chemicals produced by microbes, enabling the high-throughput engineering of enzymes and metabolic pathways. Here, we engineer a G-protein-coupled receptor (GPCR)-based sensor to detect serotonin produced by a producer microbe in the producer microbe's supernatant. Detecting a chemical in the producer microbe's supernatant is nontrivial because of the number of other metabolites and proteins present that could interfere with sensor performance. We validate the two-cell screening system for medium-throughput applications, opening the door to the rapid engineering of microbes for the increased production of serotonin. We focus on serotonin detection as serotonin levels limit the microbial production of hydroxystrictosidine, a modified alkaloid that could accelerate the semisynthesis of camptothecin-derived anticancer pharmaceuticals. This work shows the ease of generating GPCR-based chemical sensors and their ability to detect specific chemicals in complex aqueous solutions, such as microbial spent medium. In addition, this work sets the stage for the rapid engineering of serotonin-producing microbes.

Disruption of microbial biofilms by an extracellular protein isolated from epibiotic tropical marine strain of Bacillus licheniformis.

Directory of Open Access Journals (Sweden)

Devendra H Dusane

Full Text Available BACKGROUND: Marine epibiotic bacteria produce bioactive compounds effective against microbial biofilms. The study examines antibiofilm ability of a protein obtained from a tropical marine strain of Bacillus licheniformis D1. METHODOLOGY/PRINCIPAL FINDINGS: B. licheniformis strain D1 isolated from the surface of green mussel, Perna viridis showed antimicrobial activity against pathogenic Candida albicans BH, Pseudomonas aeruginosa PAO1 and biofouling Bacillus pumilus TiO1 cultures. The antimicrobial activity was lost after treatment with trypsin and proteinase K. The protein was purified by ultrafiltration and size-exclusion chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF analysis revealed the antimicrobial agent to be a 14 kDa protein designated as BL-DZ1. The protein was stable at 75°C for 30 min and over a pH range of 3.0 to 11.0. The sequence alignment of the MALDI-fingerprint showed homology with the NCBI entry for a hypothetical protein (BL00275 derived from B. licheniformis ATCC 14580 with the accession number gi52082584. The protein showed minimum inhibitory concentration (MIC value of 1.6 µg/ml against C. albicans. Against both P. aeruginosa and B. pumilus the MIC was 3.12 µg/ml. The protein inhibited microbial growth, decreased biofilm formation and dispersed pre-formed biofilms of the representative cultures in polystyrene microtiter plates and on glass surfaces. CONCLUSION/SIGNIFICANCE: We isolated a protein from a tropical marine strain of B. licheniformis, assigned a function to the hypothetical protein entry in the NCBI database and described its application as a potential antibiofilm agent.

Disruption of Microbial Biofilms by an Extracellular Protein Isolated from Epibiotic Tropical Marine Strain of Bacillus licheniformis

Science.gov (United States)

Dusane, Devendra H.; Damare, Samir R.; Nancharaiah, Yarlagadda V.; Ramaiah, N.; Venugopalan, Vayalam P.; Kumar, Ameeta Ravi; Zinjarde, Smita S.

2013-01-01

Background Marine epibiotic bacteria produce bioactive compounds effective against microbial biofilms. The study examines antibiofilm ability of a protein obtained from a tropical marine strain of Bacillus licheniformis D1. Methodology/Principal Findings B. licheniformis strain D1 isolated from the surface of green mussel, Perna viridis showed antimicrobial activity against pathogenic Candida albicans BH, Pseudomonas aeruginosa PAO1 and biofouling Bacillus pumilus TiO1 cultures. The antimicrobial activity was lost after treatment with trypsin and proteinase K. The protein was purified by ultrafiltration and size-exclusion chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis revealed the antimicrobial agent to be a 14 kDa protein designated as BL-DZ1. The protein was stable at 75°C for 30 min and over a pH range of 3.0 to 11.0. The sequence alignment of the MALDI-fingerprint showed homology with the NCBI entry for a hypothetical protein (BL00275) derived from B. licheniformis ATCC 14580 with the accession number gi52082584. The protein showed minimum inhibitory concentration (MIC) value of 1.6 µg/ml against C. albicans. Against both P. aeruginosa and B. pumilus the MIC was 3.12 µg/ml. The protein inhibited microbial growth, decreased biofilm formation and dispersed pre-formed biofilms of the representative cultures in polystyrene microtiter plates and on glass surfaces. Conclusion/Significance We isolated a protein from a tropical marine strain of B. licheniformis, assigned a function to the hypothetical protein entry in the NCBI database and described its application as a potential antibiofilm agent. PMID:23691235

Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

International Nuclear Information System (INIS)

Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang

2003-12-01

The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

Energy Technology Data Exchange (ETDEWEB)

Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang [Univ. Da Coruna (Spain)

2003-12-01

The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

Determination of microbial protein in perennial ryegrass silage

NARCIS (Netherlands)

Driehuis, F.; Wikselaar, van P.G.

2001-01-01

The microbial matter fraction was determined in perennial ryegrass silages of different dry-matter (DM) contents, ensiled with or without Lactobacillus plantarum. 15N-Leucine and the bacterial cell wall constituent diaminopimelic acid (DAPA) were used as markers for microbial-N. Perennial ryegrass

Microbial Protein Production from Candida tropicalis ATCC13803 in a Submerged Batch Fermentation Process

Directory of Open Access Journals (Sweden)

Sahar Golaghaiee

2017-01-01

Full Text Available Background and Objective: Microbial protein production can resolve one of the major world challenges, i.e. lack of protein sources. Candida tropicalis growth was investigated to specify a medium to reach the highest cell proliferation and protein production.Material and Methods: Fractional factorial design and the index of signal to noise ratio were applied for optimization of microbial protein production. Optimization process was conducted based on the experimental results of Taguchi approach designs. Fermentationwas performed at 25oC and the agitation speed of 300 rpm for 70 h. Ammonium sulfate, iron sulfate, glycine and glucose concentrations were considered as process variables. Optimization of the culture medium composition was conducted in order to obtain the highest cell biomass concentration and protein content. Experiment design was performed based on the Taguchi approach and L-16 orthogonal arrays using Qualitek-4 software.Results and Conclusion: Maximum biomass of 8.72 log (CFU ml-1 was obtained using the optimized medium with 0.3, 0.15, 2 and 80 g l-1 of ammonium sulfate, iron sulfate, glycine and glucose, respectively. Iron sulfate and ammonium sulfate with 41.76% (w w-1 and 35.27% (w w-1 contributions, respectively, were recognized as the main components for cell growth. Glucose and glycine with 17.12% and 5.86% (w w-1 contributions,respectively, also affected cell production. The highest interaction severity index of +54.16% was observed between glycine and glucose while the least one of +0.43% was recorded for ammonium sulfate and glycine. A deviation of 7% between the highestpredicted cell numbers and the experimented count confirms the suitability of the applied statistical method. High protein content of 52.16% (w w-1 as well as low fat and nucleic acids content suggest that Candida tropicalis is a suitable case for commercial processes.Conflict of interest: The authors declare that there is no conflict of interest.

Semi-continuous protein fractionating using affinity cross-flow filtration

NARCIS (Netherlands)

Borneman, Zandrie; Zhang, W.; van den Boomgaard, Anthonie; Smolders, C.A.

2002-01-01

Protein purification by means of downstream processing is increasingly important. At the University of Twente a semi-continuous process is developed for the isolation of BSA out of crude protein mixtures. For this purpose an automated Affinity Cross-Flow Filtration, ACFF, process is developed. This

A 100-Year Review: Protein and amino acid nutrition in dairy cows.

Science.gov (United States)

Schwab, Charles G; Broderick, Glen A

2017-12-01

Considerable progress has been made in understanding the protein and amino acid (AA) nutrition of dairy cows. The chemistry of feed crude protein (CP) appears to be well understood, as is the mechanism of ruminal protein degradation by rumen bacteria and protozoa. It has been shown that ammonia released from AA degradation in the rumen is used for bacterial protein formation and that urea can be a useful N supplement when lower protein diets are fed. It is now well documented that adequate rumen ammonia levels must be maintained for maximal synthesis of microbial protein and that a deficiency of rumen-degradable protein can decrease microbial protein synthesis, fiber digestibility, and feed intake. Rumen-synthesized microbial protein accounts for most of the CP flowing to the small intestine and is considered a high-quality protein for dairy cows because of apparent high digestibility and good AA composition. Much attention has been given to evaluating different methods to quantify ruminal protein degradation and escape and for measuring ruminal outflows of microbial protein and rumen-undegraded feed protein. The methods and accompanying results are used to determine the nutritional value of protein supplements and to develop nutritional models and evaluate their predictive ability. Lysine, methionine, and histidine have been identified most often as the most-limiting amino acids, with rumen-protected forms of lysine and methionine available for ration supplementation. Guidelines for protein feeding have evolved from simple feeding standards for dietary CP to more complex nutrition models that are designed to predict supplies and requirements for rumen ammonia and peptides and intestinally absorbable AA. The industry awaits more robust and mechanistic models for predicting supplies and requirements of rumen-available N and absorbed AA. Such models will be useful in allowing for feeding lower protein diets and increased efficiency of microbial protein synthesis

Urinary excretion of purine derivatives as an index of microbial protein synthesis in the camel (Camelus dromedarius).

Science.gov (United States)

Guerouali, Abdelhai; El Gass, Youssef; Balcells, Joaquim; Belenguer, Alvaro; Nolan, John

2004-08-01

Five experiments were carried out to extend knowledge of purine metabolism in the camel (Camelus dromedarius) and to establish a model to enable microbial protein outflow from the forestomachs to be estimated from the urinary excretion of purine derivatives (PD; i.e. xanthine, hypoxanthine, uric acid, allantoin). In experiment 1, four camels were fasted for five consecutive days to enable endogenous PD excretion in urine to be determined. Total PD excretion decreased during the fasting period to 267 (SE 41.5) micromol/kg body weight (W)0.75 per d. Allantoin and xanthine + hypoxanthine were consistently 86 and 6.1 % of total urinary PD during this period but uric acid increased from 3.6 % to 7.4 %. Xanthine oxidase activity in tissues (experiment 2) was (micromol/min per g fresh tissue) 0.038 in liver and 0.005 in gut mucosa but was not detected in plasma. In experiment 3, the duodenal supply of yeast containing exogenous purines produced a linear increase in urinary PD excretion rate with the slope indicating that 0.63 was excreted in urine. After taking account of endogenous PD excretion, the relationship can be used to predict purine outflow from the rumen. From the latter prediction, and also the purine:protein ratio in bacteria determined in experiment 5, we predicted the net microbial outflow from the rumen. In experiment 4, with increasing food intake, the rate of PD excretion in the urine increased linearly by about 11.1 mmol PD/kg digestible organic matter intake (DOMI), equivalent to 95 g microbial protein/kg DOMI.

Analysis of electrode microbial communities in an up-flow bioelectrochemical system treating azo dye wastewater

International Nuclear Information System (INIS)

Cui, Min-Hua; Cui, Dan; Gao, Lei; Cheng, Hao-Yi; Wang, Ai-Jie

2016-01-01

Bioelectrochemical system (BES) is a rapidly developing technology covering contamination remediation, resource recovery and power generation. Electrode biofilms play a key role in BES operation. In this work, a single chamber up-flow bioelectrochemical system (UBES) was assembled with two preinoculated anodes and two raw cathodes for azo dye wastewater treatment. Microbial community structures of these electrodes after long-term operation (more than 200 days) were carried out by high-throughput Illumina 16S rRNA gene MiSeq sequencing platform. Microorganisms belonging to Enterobacter, Desulfovibrio and Enterococcus, which are capable of bidirectional extracellular electron transfer, were found to be the dominant members in all biofilms. Neither the polarity nor the position of the electrodes obviously altered the microbial community structures. This study provides a feasible strategy to build electrode active biofilms in a BES for azo dye wastewater treatment and gives great inspirations to bring this technology closer to application.

Development, standardization and validation of nuclear based technologies for estimating microbial protein supply in ruminant livestock for improving productivity

International Nuclear Information System (INIS)

Makkar, H.P.S.

2004-01-01

The primary constraint to livestock production in developing countries is the scarcity and fluctuating quantity and quality of the year-round feed supply. These countries experience serious shortages of animal feeds and fodders of the conventional type. Natural forages are very variable both in quality and quantity, conventional agro-industrial by-products are scarce and vary seasonal, and grains are required almost exclusively for human consumption. The small farmers in developing countries have limited resources available to them for feeding their ruminant livestock. Poor nutrition results in low rates of reproduction and production as well as increased susceptibility to disease and mortality. Providing adequate good-quality feed to livestock to raise and maintain their productivity is a major challenge to agricultural scientists and policy makers all over the world. Recent advances in ration balancing include manipulation of feed to increase the quantity and quality of protein and energy delivered to the small intestine. Selection of feeds based on high efficiency of microbial protein synthesis in the rumen along with the high dry matter digestibility, and development of feeding strategies based on high efficiency as well as high microbial protein synthesis in the rumen will lead to higher supply of protein post-ruminally. The strategy for improving production has therefore been to maximize the efficiency of utilization of available feed resources in the rumen by providing optimum conditions for microbial growth and thereby supplementing dietary nutrients to complement and balance the products of rumen digestion to the animal's requirement

Exploitation of the host cell ubiquitin machinery by microbial effector proteins.

Science.gov (United States)

Lin, Yi-Han; Machner, Matthias P

2017-06-15

Pathogenic bacteria are in a constant battle for survival with their host. In order to gain a competitive edge, they employ a variety of sophisticated strategies that allow them to modify conserved host cell processes in ways that favor bacterial survival and growth. Ubiquitylation, the covalent attachment of the small modifier ubiquitin to target proteins, is such a pathway. Ubiquitylation profoundly alters the fate of a myriad of cellular proteins by inducing changes in their stability or function, subcellular localization or interaction with other proteins. Given the importance of ubiquitylation in cell development, protein homeostasis and innate immunity, it is not surprising that this post-translational modification is exploited by a variety of effector proteins from microbial pathogens. Here, we highlight recent advances in our understanding of the many ways microbes take advantage of host ubiquitylation, along with some surprising deviations from the canonical theme. The lessons learned from the in-depth analyses of these host-pathogen interactions provide a fresh perspective on an ancient post-translational modification that we thought was well understood.This article is part of a Minifocus on Ubiquitin Regulation and Function. For further reading, please see related articles: 'Mechanisms of regulation and diversification of deubiquitylating enzyme function' by Pawel Leznicki and Yogesh Kulathu ( J. Cell Sci. 130 , 1997-2006). 'Cell scientist to watch - Mads Gyrd-Hansen' ( J. Cell Sci. 130 , 1981-1983). © 2017. Published by The Company of Biologists Ltd.

Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage.

Science.gov (United States)

Aida, Azrina A; Hatamoto, Masashi; Yamamoto, Masamitsu; Ono, Shinya; Nakamura, Akinobu; Takahashi, Masanobu; Yamaguchi, Takashi

2014-11-01

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Extracellular Proteins Limit the Dispersal of BiogenicNanoparticles

Energy Technology Data Exchange (ETDEWEB)

Moreau, John W.; Weber, Peter K.; Martin, Michael C.; Gilbert,Benjamin; Hutcheon, Ian D.; Banfield, Jillian F.

2007-04-27

High spatial-resolution secondaryion microprobespectrometry, synchrotron radiation Fourier-transform infraredspectroscopy and polyacrylamide gel analysis demonstrate the intimateassociation of proteins with spheroidal aggregates of biogenic zincsulfide nanocrystals, an example of extracellular biomineralization.Experiments involving synthetic ZnS nanoparticles and representativeamino acids indicate a driving role for cysteine in rapid nanoparticleaggregation. These findings suggest that microbially-derivedextracellular proteins can limit dispersal of nanoparticulatemetal-bearing phases, such as the mineral products of bioremediation,that may otherwise be transported away from their source by subsurfacefluid flow.

Quantum localization and protein-assisted vibrational energy flow in cofactors

International Nuclear Information System (INIS)

Leitner, David M

2010-01-01

Quantum effects influence vibrational dynamics and energy flow in biomolecules, which play a central role in biomolecule function, including control of reaction kinetics. Lifetimes of many vibrational modes of proteins and their temperature dependence, as determined by quantum golden-rule-based calculations, exhibit trends consistent with experimental observation and distinct from estimates based on classical modeling. Particularly notable are quantum coherence effects that give rise to localization of vibrational states of sizable organic molecules in the gas phase. Even when such a molecule, for instance a cofactor, is embedded in a protein, remnants of quantum localization survive that influence vibrational energy flow and its dependence on temperature. We discuss these effects on the mode-damping rates of a cofactor embedded in a protein, using the green fluorescent protein chromophore as a specific example. We find that for cofactors of this size embedded in their protein and solvent environment at room temperature a golden-rule calculation often overestimates the mode-damping rate.

Microbial glycoproteomics

DEFF Research Database (Denmark)

Halim, Adnan; Anonsen, Jan Haug

2017-01-01

Mass spectrometry-based "-omics" technologies are important tools for global and detailed mapping of post-translational modifications. Protein glycosylation is an abundant and important post translational modification widespread throughout all domains of life. Characterization of glycoproteins...... and research in this area is rapidly accelerating. Here, we review recent developments in glycoproteomic technologies with a special focus on microbial protein glycosylation....

Protein synthesis inhibitors attenuate water flow in vasopressin-stimulated toad urinary bladder

International Nuclear Information System (INIS)

Hoch, B.S.; Ast, M.B.; Fusco, M.J.; Jacoby, M.; Levine, S.D.

1988-01-01

Vasopressin stimulates the introduction of aggregated particles, which may represent pathways for water flow, into the luminal membrane of toad urinary bladder. It is not known whether water transport pathways are degraded on removal from membrane or whether they are recycled. The authors examined the effect of the protein synthesis inhibitors cycloheximide and puromycin using repeated 30-min cycles of vasopressin followed by washout of vasopressin, all in the presence of an osmotic gradient, a protocol that maximizes aggregate turnover. High dose cycloheximide inhibited flow immediately. Low dose cycloheximide did not affect initial flow. In the absence of vasopressin, inhibition did not develop. Despite the inhibition of flow in vasopressin-treated tissues, the cAMP-dependent protein kinase ratio was elevated in cycloheximide-treated tissues, suggesting modulation at a distal site in the stimulatory cascade. [ 14 C]urea permeability was not inhibited by cycloheximide. Puromycin also inhibited water flow by the fourth challenge with vasopressin. The data suggest that protein synthesis inhibitors attenuate flow at a site that is distal to cAMP-dependent protein kinase. However, the reversal of inhibition in MIX-treated tissues suggests that the water pathway can be fully manifested given suitable stimulation. They conclude that either large stores of the transport system are available or that the transport system is extensively recycled on retrieval from the membrane

Flow Analysis of a Rising Crude Oil Micro-Droplet Affected by Attached Microbial Streamers

Science.gov (United States)

Amaro, Matthew; White, Andrew; Jalali, Maryam; Sheng, Jian

2017-11-01

Microfluidic experiments show bacteria flowing past a pinned crude oil droplet produce microbial aggregates and streamers on the oil-water interface. High speed DIC microscopy at 1000 fps for 1 sec with a sampling interval of 10 min captures the evolving flow and bacterial motility as well as adhesion, aggregation and streamer events. With bacteria as tracers, velocity measurements are acquired with in-house PIV-assisted PTV software. Flow fields with spatial resolution 2.5 μm are measured around an O(100) μm drop in a 700 ×700 μm window. Full budgets of the 2D Navier-Stokes equation are faithfully resolved to determine pressure gradients by performing the balance over a control volume enclosing the droplet. Pressure gradients are integrated over the border of the control region to obtain pressure profiles at the leading and trailing edges. A momentum balance can be used to determine the drag induced by the drop and any attached streamers. Cases with and without streamers and their differing flow features are presented. Additionally streamers produce nonzero curl in the pressure gradient field providing a tool for identifying the position of otherwise invisible streamers. Ongoing experiments and future applications of the tools presented here will be discussed. Funded by GoMRI, NSF, ARO.

Hydrodynamics of microbial filter feeding.

Science.gov (United States)

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

2017-08-29

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

Directory of Open Access Journals (Sweden)

Mallette Natasha

2009-12-01

Full Text Available Abstract Background Three methods were developed for the application of stoichiometry-based network analysis approaches including elementary mode analysis to the study of mass and energy flows in microbial communities. Each has distinct advantages and disadvantages suitable for analyzing systems with different degrees of complexity and a priori knowledge. These approaches were tested and compared using data from the thermophilic, phototrophic mat communities from Octopus and Mushroom Springs in Yellowstone National Park (USA. The models were based on three distinct microbial guilds: oxygenic phototrophs, filamentous anoxygenic phototrophs, and sulfate-reducing bacteria. Two phases, day and night, were modeled to account for differences in the sources of mass and energy and the routes available for their exchange. Results The in silico models were used to explore fundamental questions in ecology including the prediction of and explanation for measured relative abundances of primary producers in the mat, theoretical tradeoffs between overall productivity and the generation of toxic by-products, and the relative robustness of various guild interactions. Conclusion The three modeling approaches represent a flexible toolbox for creating cellular metabolic networks to study microbial communities on scales ranging from cells to ecosystems. A comparison of the three methods highlights considerations for selecting the one most appropriate for a given microbial system. For instance, communities represented only by metagenomic data can be modeled using the pooled method which analyzes a community's total metabolic potential without attempting to partition enzymes to different organisms. Systems with extensive a priori information on microbial guilds can be represented using the compartmentalized technique, employing distinct control volumes to separate guild-appropriate enzymes and metabolites. If the complexity of a compartmentalized network creates an

Complete genome sequence of Klebsiella pneumoniae J1, a protein-based microbial flocculant-producing bacterium.

Science.gov (United States)

Pang, Changlong; Li, Ang; Cui, Di; Yang, Jixian; Ma, Fang; Guo, Haijuan

2016-02-20

Klebsiella pneumoniae J1 is a Gram-negative strain, which belongs to a protein-based microbial flocculant-producing bacterium. However, little genetic information is known about this species. Here we carried out a whole-genome sequence analysis of this strain and report the complete genome sequence of this organism and its genetic basis for carbohydrate metabolism, capsule biosynthesis and transport system. Copyright © 2016 Elsevier B.V. All rights reserved.

New concepts of microbial treatment processes for the nitrogen removal: effect of protein and amino acids degradation.

Science.gov (United States)

González-Martínez, Alejandro; Calderón, Kadiya; González-López, Jesús

2016-05-01

High concentrations of proteins and amino acids can be found in wastewater and wastewater stream produced in anaerobic digesters, having shown that amino acids could persist over different managements for nitrogen removal affecting the nitrogen removal processes. Nitrogen removal is completely necessary because of their implications and the significant adverse environmental impact of ammonium such as eutrophication and toxicity to aquatic life on the receiving bodies. In the last decade, the treatment of effluents with high ammonium concentration through anammox-based bioprocesses has been enhanced because these biotechnologies are cheaper and more environmentally friendly than conventional technologies. However, it has been shown that the presence of important amounts of proteins and amino acids in the effluents seriously affects the microbial autotrophic consortia leading to important losses in terms of ammonium oxidation efficiency. Particularly the presence of sulfur amino acids such as methionine and cysteine has been reported to drastically decrease the autotrophic denitrification processes as well as affect the microbial community structure promoting the decline of ammonium oxidizing bacteria in favor of other phylotypes. In this context we discuss that new biotechnological processes that improve the degradation of protein and amino acids must be considered as a priority to increase the performance of the autotrophic denitrification biotechnologies.

Quantitative physiology of Penicillium cyclopium grown on whey for production of microbial protein

Energy Technology Data Exchange (ETDEWEB)

Kim, J H; Libuchi, S; Lebeault, J M

1981-01-01

A filamentous fungus, Penicillium cyclopium, capable of growing on deproteinized whey was isolated and characterized for the purpose of production of microbial protein. This organism has a maximum specific growth rate of 0.2/hour at pH 3.0 to 4.5 and 28 degrees C in a medium containing only ammonium nitrogen and deproteinized whey. The yield coefficients are 0.68 g biomass/g lactose, 12.0 g biomass/g nitrogen, and 2.10 g biomass/g oxygen respectively. Crude protein and total nucleic acid contents of this organism are 47.5% and 7.4% (dry cell weight basis), respectively. The profile of essential amino acids show that it could be a good source of animal feed or food protein. However there are several advantages in using fungal cells (Spicer 1971); their amino acid profile is better, the recovery of biomass from the culture broth is much easier, their filamentous structure facilitates production of texturized foodstuffs without extraction and spinning, and they are already accepted as foods in many parts of the world. The authors have selected a filamentous fungus, Penicillium cyclopium which grows fast on deproteinized whey and has a high protein content. This paper describes the quantitative physiology of this organism and the amino acid profile of its protein. (Refs. 19).

In vitro microbial protein synthesis, ruminal degradation and post-ruminal digestibility of crude protein of dairy rations containing Quebracho tannin extract.

Science.gov (United States)

Castro-Montoya, J; Westreicher-Kristen, E; Henke, A; Diaby, M; Susenbeth, A; Dickhoefer, U

2018-02-01

This study evaluated the effects of Quebracho tannin extract (QTE) on in vitro ruminal fermentation, chemical composition of rumen microbes, ruminal degradation and intestinal digestibility of crude protein (iCPd). Three treatments were tested, the control (basal diet without QTE), the basal diet with 15 g QTE/kg dry matter (DM) and the basal diet with 30 g QTE/kg DM. The basal diet contained (g/kg DM): 339 grass silage, 317 maize silage and 344 concentrate. In vitro gas production kinetic was determined using the Hohenheim gas test (Experiment 1). The Ankom RF technique, a batch system with automatic gas pressure recordings, was used to determine in vitro production of short-chain fatty acids (SCFA) and ammonia-nitrogen concentration (NH 3 -N), as well as nitrogen and purine bases content in liquid-associated microbes (LAM) and in a residue of undegraded feed and solid-associated microbes (Feed+SAM) (Experiment 2). Ruminal degradation and iCPd were determined using the nylon bag technique and the mobile nylon bag technique, respectively (Experiment 3). Gas production (Experiment 1), total SCFA and NH 3 -N (Experiment 2) decreased with increasing QTE levels. Microbial mass and composition of LAM were not affected by QTE, but total mass of Feed+SAM linearly increased, likely due to decreased substrate degradation with increasing QTE levels. The total amount of N in microbial mass and undegraded feed after the in vitro incubation increased with increasing QTE levels, suggesting a potential greater N flow from the rumen to the duodenum. In contrast to in vivo studies with the same QTE, no effects were detected on ruminal effective degradability and iCPd, when using the nylon bag techniques. Based on the in vitro procedures, QTE increased the supply of N post-rumen; however, some evidence of a decreased fibre degradation were also observed. Therefore, the benefit of adding QTE to diets of cattle is still questionable. © 2017 Blackwell Verlag GmbH.

Defining microbial community composition and seasonal variation in a sewage treatment plant in India using a down-flow hanging sponge reactor.

Science.gov (United States)

Nomoto, Naoki; Hatamoto, Masashi; Hirakata, Yuga; Ali, Muntjeer; Jayaswal, Komal; Iguchi, Akinori; Okubo, Tsutomu; Takahashi, Masanobu; Kubota, Kengo; Tagawa, Tadashi; Uemura, Shigeki; Yamaguchi, Takashi; Harada, Hideki

2018-05-01

The characteristics of the microbial community in a practical-scale down-flow hanging sponge (DHS) reactor, high in organic matter and sulfate ion concentration, and the seasonal variation of the microbial community composition were investigated. Microorganisms related to sulfur oxidation and reduction (2-27%), as well as Leucobacter (7.50%), were abundant in the reactor. Anaerobic bacteria (27-38% in the first layer) were also in abundance and were found to contribute to the removal of organic matter from the sewage in the reactor. By comparing the Simpson index, the abundance-based coverage estimator (ACE) index, and the species composition of the microbial community across seasons (summer/dry, summer/rainy, autumn/dry, and winter/dry), the microbial community was found to change in composition only during the winter season. In addition to the estimation of seasonal variation, the difference in the microbial community composition along the axes of the DHS reactor was investigated for the first time. Although the abundance of each bacterial species differed along both axes of the reactor, the change of the community composition in the reactor was found to be greater along the vertical axis than the horizontal axis of the DHS reactor.

Rumen microbial protein supply as estimated from purine derivative excretion on sheep receiving faba beans (vicia faba as supplement delivered at different feeding frequencies

Directory of Open Access Journals (Sweden)

Asmuddin Natsir

2008-06-01

Full Text Available Rapid and extensive degradation of faba beans (Vicia faba by ruminal microbes can result in substantial and undesirable N loss from the rumen. The purpose of this study was to test the hypothesis that offering faba beans as a supplement more than once a day to sheep receiving a combination of oaten chaff and lucerne chaff as a basal diet will increase microbial protein supply to the intestines. The experiment was conducted in a Latin square design (4 x 4 using four mature merino sheep. The treatments were: T0 = basal diet ad libitum + nil supplements, T1 = T0 + faba beans (FB fed once daily, T2 = T0 + FB fed twice daily, T3 = T0 + FB fed 8 times daily. The basal diet was given once per day at 09:00 in the morning while FB were given at the rate of approximately 0.5% of live body weight and delivered according to the treatment protocol. Urinary excretion of purine derivative (PD was used to estimate microbial protein supply. The results indicated that even though treatment statistically had no effects on total urine output, PD excretion in the urine, PD absorbed, estimated microbial N supply, and the efficiency of rumen microbial protein synthesis, provision of supplement to sheep numerically improved microbial N supply by 92% compared to that of control group. However, there were no differences within the supplemented group. Therefore, it is concluded that feeding faba beans more than once a day was unnecessary.

Protein Stable Isotope Fingerprinting (P-SIF): Multidimensional Protein Chromatography Coupled to Stable Isotope-Ratio Mass Spectrometry

Science.gov (United States)

Pearson, A.; Bovee, R. J.; Mohr, W.; Tang, T.

2012-12-01

As metagenomics increases our insight into microbial community diversity and metabolic potential, new approaches are required to determine the biogeochemical expression of this potential within ecosystems. Because stable isotopic analysis of the major bioactive elements (C, N) has been used historically to map flows of substrates and energy among macroscopic food webs, similar principles may apply to microbes. To address this challenge, we have developed a new analytical approach called Protein Stable Isotope Fingerprinting (P-SIF). P-SIF generates natural stable isotopic fingerprints of microbial individual or community proteomes. The main advantage of P-SIF is the potential to bridge the gap between diversity and function, thereby providing a window into the "black box" of environmental microbiology and helping to decipher the roles of uncultivated species. Our method implements a three-way, orthogonal scheme to separate mixtures of whole proteins into subfractions dominated by single or closely-related proteins. Protein extracts first are isoelectrically focused in a gel-free technique that yields 12 fractions separated over a gradient of pH 3-10. Each fraction then is separated by size-exclusion chromatography into 20 pools, ranging from >100kD to ~10kD. Finally, each of these pools is subjected to HPLC and collected in 40 time-slices based on protein hydrophobicity. Theoretical calculation reveals that the true chromatographic resolution of the total scheme is 5000, somewhat less than the 9600 resulting fractions. High-yielding fractions are subjected to δ13C analysis by spooling-wire microcombustion irMS (SWiM-irMS) optimized for samples containing 1-5 nmol carbon. Here we will present the method, results for a variety of pure cultures, and preliminary data for a sample of mixed environmental proteins. The data show the promise of this method for unraveling the metabolic complexity hidden within microbial communities.

Synthetic Electric Microbial Biosensors

Science.gov (United States)

2017-06-10

domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited.   Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home   September, 2014

Multiple paths of electron flow to current in microbial electrolysis cells fed with low and high concentrations of propionate

KAUST Repository

Rao, Hari Ananda

2016-03-03

Microbial electrolysis cells (MECs) provide a viable approach for bioenergy generation from fermentable substrates such as propionate. However, the paths of electron flow during propionate oxidation in the anode of MECs are unknown. Here, the paths of electron flow involved in propionate oxidation in the anode of two-chambered MECs were examined at low (4.5 mM) and high (36 mM) propionate concentrations. Electron mass balances and microbial community analysis revealed that multiple paths of electron flow (via acetate/H2 or acetate/formate) to current could occur simultaneously during propionate oxidation regardless of the concentration tested. Current (57–96 %) was the largest electron sink and methane (0–2.3 %) production was relatively unimportant at both concentrations based on electron balances. At a low propionate concentration, reactors supplemented with 2-bromoethanesulfonate had slightly higher coulombic efficiencies than reactors lacking this methanogenesis inhibitor. However, an opposite trend was observed at high propionate concentration, where reactors supplemented with 2-bromoethanesulfonate had a lower coulombic efficiency and there was a greater percentage of electron loss (23.5 %) to undefined sinks compared to reactors without 2-bromoethanesulfonate (11.2 %). Propionate removal efficiencies were 98 % (low propionate concentration) and 78 % (high propionate concentration). Analysis of 16S rRNA gene pyrosequencing revealed the dominance of sequences most similar to Geobacter sulfurreducens PCA and G. sulfurreducens subsp. ethanolicus. Collectively, these results provide new insights on the paths of electron flow during propionate oxidation in the anode of MECs fed with low and high propionate concentrations.

Continuous protein concentration via free-flow moving reaction boundary electrophoresis.

Science.gov (United States)

Kong, Fanzhi; Zhang, Min; Chen, Jingjing; Fan, Liuyin; Xiao, Hua; Liu, Shaorong; Cao, Chengxi

2017-07-28

In this work, we developed the model and theory of free-flow moving reaction boundary electrophoresis (FFMRB) for continuous protein concentration for the first time. The theoretical results indicated that (i) the moving reaction boundary (MRB) can be quantitatively designed in free-flow electrophoresis (FFE) system; (ii) charge-to-mass ratio (Z/M) analysis could provide guidance for protein concentration optimization; and (iii) the maximum processing capacity could be predicted. To demonstrate the model and theory, three model proteins of hemoglobin (Hb), cytochrome C (Cyt C) and C-phycocyanin (C-PC) were chosen for the experiments. The experimental results verified that (i) stable MRBs with different velocities could be established in FFE apparatus with weak acid/weak base neutralization reaction system; (ii) proteins of Hb, Cyt C and C-PC were well concentrated with FFMRB; and (iii) a maximum processing capacity and recovery ratio of Cyt C enrichment were 126mL/h and 95.5% respectively, and a maximum enrichment factor was achieved 12.6 times for Hb. All of the experiments demonstrated the protein concentration model and theory. In contrast to other methods, the continuous processing ability enables FFMRB to efficiently enrich diluted protein or peptide in large volume solution. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331).

Science.gov (United States)

Yanagawa, Katsunori; Breuker, Anja; Schippers, Axel; Nishizawa, Manabu; Ijiri, Akira; Hirai, Miho; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2014-10-01

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Isolation of monodisperse nanodisc-reconstituted membrane proteins using free flow electrophoresis

DEFF Research Database (Denmark)

Justesen, Bo Højen; Laursen, Tomas; Weber, Gerhard

2013-01-01

Free flow electrophoresis is used for rapid and high-recovery isolation of homogeneous preparations of functionally active membrane proteins inserted into nanodiscs. The approach enables isolation of integral and membrane anchored proteins and is also applicable following introduction of, e...

Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

International Nuclear Information System (INIS)

Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz

2002-01-01

Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. 32 P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

Energy Technology Data Exchange (ETDEWEB)

Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)

2002-07-01

Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. {sup 32} P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

Microbial Diversity and Lipid Abundance in Microbial Mats from a Sulfidic, Saline, Warm Spring in Utah, USA

Science.gov (United States)

Gong, J.; Edwardson, C.; Mackey, T. J.; Dzaugis, M.; Ibarra, Y.; Course 2012, G.; Frantz, C. M.; Osburn, M. R.; Hirst, M.; Williamson, C.; Hanselmann, K.; Caporaso, J.; Sessions, A. L.; Spear, J. R.

2012-12-01

The microbial diversity of Stinking Springs, a sulfidic, saline, warm spring northeast of the Great Salt Lake was investigated. The measured pH, temperature, salinity, and sulfide concentration along the flow path ranged from 6.64-7.77, 40-28° C, 2.9-2.2%, and 250 μM to negligible, respectively. Five sites were selected along the flow path and within each site microbial mats were dissected into depth profiles based on the color and texture of the mat layers. Genomic DNA was extracted from each layer, and the 16S rRNA gene was amplified and sequenced on the Roche 454 Titanium platform. Fatty acids were also extracted from the mat layers and analyzed by liquid chromatography and mass spectrometry. The mats at Stinking Springs were classified into roughly two morphologies with respect to their spatial distribution: loose, sometimes floating mats proximal to the spring source; and thicker, well-laminated mats distal to the spring source. Loosely-laminated mats were found in turbulent stream flow environments, whereas well-laminated mats were common in less turbulent sheet flows. Phototrophs, sulfur oxidizers, sulfate reducers, methanogens, other bacteria and archaea were identified by 16S rRNA gene sequences. Diatoms, identified by microscopy and lipid analysis were found to increase in abundance with distance from the source. Methanogens were generally more abundant in deeper mat laminae. Photoheterotrophs were found in all mat layers. Microbial diversity increased significantly with depth at most sites. In addition, two distinct microbial streamers were identified and characterized at the two fast flowing sites. These two streamer varieties were dominated by either cyanobacteria or flavobacteria. Overall, our genomic and lipid analysis suggest that the physical and chemical environment is more predictive of the community composition than mat morphology. Site Map

Microbial Protein Production and Nitrogen Balance of Local Steer Fed Ammoniated Rice Straws Added

Directory of Open Access Journals (Sweden)

H Hindratiningrum

2009-05-01

Full Text Available The objective of the experiment was to investigate the kind of energy source feedstuffs on nutrient balance and microbial protein synthesis in local male beef cattle fed with ammoniated rice straws Twenty steers Peranakan Ongole (PO with average age 1-2 years old were used. They were divided 5 groups based on initial body weight as block. Therefore, Completely Randomised Block Design (CBRD was used for this experiment. Data were analysed by analysis variance and continued honestly significant different (HSD to test the differences between means. The result showed that the range MCP and eficiency MCP were 154,61 g/d until 226,54 g/d and 54,08 gMCP/kg DOMR until 62,64 gMCP/kg DOMR. The range of nitrogen balance were 72,28 gram until 111,67 gram. MCP and efficiency MCP were not affected (P>0,05 by the treatments but balance of nitrogen was affected (P<0,05. Diet containing fresh cassava waste as energy source (R2 was lower (P<0,05 than R1 and R4 while between R1,R3 and R4 was similar. This results indicate that feed source of energy (rice brand, wet cassava waste, dry cassava waste and corn can be used in steers with rice straw ensilage as forage. (Animal Production 11(2: 116-121 (2009 Key Words : Microbial protein production, nitrogen balance, rice straw, ensilage

Flow cytometric assessment of microbial abundance in the near-field area of seawater reverse osmosis concentrate discharge

KAUST Repository

Van Der Merwe, Riaan

2014-06-01

The discharge of concentrate and other process waters from seawater reverse osmosis (SWRO) plant operations into the marine environment may adversely affect water quality in the near-field area surrounding the outfall. The main concerns are the increase in salt concentration in receiving waters, which results in a density increase and potential water stratification near the outfall, and possible increases in turbidity, e.g., due to the discharge of filter backwash waters. Changes in ambient water quality may affect microbial abundance in the area, for example by hindering the photosynthesis process or disrupting biogenesis. It is widely accepted that marine biodiversity is lower in more extreme conditions, such as high salinity environments. As aquatic microbial communities respond very rapidly to changes in their environment, they can be used as indicators for monitoring ambient water quality. The objective of this study was to assess possible changes in microbial abundance as a result of concentrate discharge into the near-field area (<. 25. m) surrounding the outfall of the King Abdullah University of Science and Technology (KAUST) SWRO plant. Flow cytometric (FCM) analysis was conducted in order to rapidly determine microbial abundance on a single-cell level in 107 samples, taken by diving, from the discharge area, the intake area and two control sites. FCM analysis combined the measurement of distinct scatter of cells and particles, autofluorescence of cyanobacteria and algae, and fluorescence after staining of nucleic acids with SYBR® Green for a total bacterial count. The results indicate that changes in microbial abundance in the near-field area of the KAUST SWRO outfall are minor and appear to be the result of a dilution effect rather than a direct impact of the concentrate discharge. © 2014 Elsevier B.V.

Effect of protein supplementation on ruminal parameters and microbial community fingerprint of Nellore steers fed tropical forages.

Science.gov (United States)

Bento, C B P; Azevedo, A C; Gomes, D I; Batista, E D; Rufino, L M A; Detmann, E; Mantovani, H C

2016-01-01

In tropical regions, protein supplementation is a common practice in dairy and beef farming. However, the effect of highly degradable protein in ruminal fermentation and microbial community composition has not yet been investigated in a systematic manner. In this work, we aimed to investigate the impact of casein supplementation on volatile fatty acids (VFA) production, specific activity of deamination (SAD), ammonia concentration and bacterial and archaeal community composition. The experimental design was a 4×4 Latin square balanced for residual effects, with four animals (average initial weight of 280±10 kg) and four experimental periods, each with duration of 29 days. The diet comprised Tifton 85 (Cynodon sp.) hay with an average CP content of 9.8%, on a dry matter basis. Animals received basal forage (control) or infusions of pure casein (230 g) administered direct into the rumen, abomasum or divided (50 : 50 ratio) in the rumen/abomasum. There was no differences (P>0.05) in ruminal pH and microbial protein concentration between supplemented v. non-supplemented animals. However, in steers receiving ruminal infusion of casein the SAD and ruminal ammonia concentration increased 33% and 76%, respectively, compared with the control. The total concentration of VFA increased (P0.05) in species richness and diversity of γ-proteobacteria, firmicutes and archaea between non-supplemented Nellore steers and steers receiving casein supplementation in the rumen. However, species richness and the Shannon-Wiener index were lower (Pruminal and postruminal protein supplementation on metabolic activities of rumen microbes and the composition of bacterial and archaeal communities in the rumen of steers.

Biogas production from protein-rich biomass: fed-batch anaerobic fermentation of casein and of pig blood and associated changes in microbial community composition.

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Etelka Kovács

Full Text Available It is generally accepted as a fact in the biogas technology that protein-rich biomass substrates should be avoided due to inevitable process inhibition. Substrate compositions with a low C/N ratio are considered difficult to handle and may lead to process failure, though protein-rich industrial waste products have outstanding biogas generation potential. This common belief has been challenged by using protein-rich substrates, i.e. casein and precipitated pig blood protein in laboratory scale continuously stirred mesophilic fed-batch biogas fermenters. Both substrates proved suitable for sustained biogas production (0.447 L CH4/g protein oDM, i.e. organic total solids in high yield without any additives, following a period of adaptation of the microbial community. The apparent key limiting factors in the anaerobic degradation of these proteinaceous materials were the accumulation of ammonia and hydrogen sulfide. Changes in time in the composition of the microbiological community were determined by next-generation sequencing-based metagenomic analyses. Characteristic rearrangements of the biogas-producing community upon protein feeding and specific differences due to the individual protein substrates were recognized. The results clearly demonstrate that sustained biogas production is readily achievable, provided the system is well-characterized, understood and controlled. Biogas yields (0.45 L CH4/g oDM significantly exceeding those of the commonly used agricultural substrates (0.25-0.28 L CH4/g oDM were routinely obtained. The results amply reveal that these high-energy-content waste products can be converted to biogas, a renewable energy carrier with flexible uses that can replace fossil natural gas in its applications. Process control, with appropriate acclimation of the microbial community to the unusual substrate, is necessary. Metagenomic analysis of the microbial community by next-generation sequencing allows a precise determination of the

Biogas Production from Protein-Rich Biomass: Fed-Batch Anaerobic Fermentation of Casein and of Pig Blood and Associated Changes in Microbial Community Composition

Science.gov (United States)

Kovács, Etelka; Wirth, Roland; Maróti, Gergely; Bagi, Zoltán; Rákhely, Gábor; Kovács, Kornél L.

2013-01-01

It is generally accepted as a fact in the biogas technology that protein-rich biomass substrates should be avoided due to inevitable process inhibition. Substrate compositions with a low C/N ratio are considered difficult to handle and may lead to process failure, though protein-rich industrial waste products have outstanding biogas generation potential. This common belief has been challenged by using protein-rich substrates, i.e. casein and precipitated pig blood protein in laboratory scale continuously stirred mesophilic fed-batch biogas fermenters. Both substrates proved suitable for sustained biogas production (0.447 L CH4/g protein oDM, i.e. organic total solids) in high yield without any additives, following a period of adaptation of the microbial community. The apparent key limiting factors in the anaerobic degradation of these proteinaceous materials were the accumulation of ammonia and hydrogen sulfide. Changes in time in the composition of the microbiological community were determined by next-generation sequencing-based metagenomic analyses. Characteristic rearrangements of the biogas-producing community upon protein feeding and specific differences due to the individual protein substrates were recognized. The results clearly demonstrate that sustained biogas production is readily achievable, provided the system is well-characterized, understood and controlled. Biogas yields (0.45 L CH4/g oDM) significantly exceeding those of the commonly used agricultural substrates (0.25-0.28 L CH4/g oDM) were routinely obtained. The results amply reveal that these high-energy-content waste products can be converted to biogas, a renewable energy carrier with flexible uses that can replace fossil natural gas in its applications. Process control, with appropriate acclimation of the microbial community to the unusual substrate, is necessary. Metagenomic analysis of the microbial community by next-generation sequencing allows a precise determination of the alterations in

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

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Kuczmarski Thomas A

2006-10-01

Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

Effects of Synchronization of Carbohydrate and Protein Supply in Total Mixed Ration with Korean Rice Wine Residue on Ruminal Fermentation, Nitrogen Metabolism and Microbial Protein Synthesis in Holstein Steers

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Min Yu Piao

2012-11-01

Full Text Available Three Holstein steers in the growing phase, each with a ruminal cannula, were used to test the hypothesis that the synchronization of the hourly rate of carbohydrate and nitrogen (N released in the rumen would increase the amount of retained nitrogen for growth and thus improve the efficiency of microbial protein synthesis (EMPS. In Experiment 1, in situ degradability coefficients of carbohydrate and N in feeds including Korean rice wine residue (RWR were determined. In Experiment 2, three total mixed ration (TMR diets having different rates of carbohydrate and N release in the rumen were formulated using the in situ degradability of the feeds. All diets were made to contain similar contents of crude protein (CP and neutral detergent fiber (NDF but varied in their hourly pattern of nutrient release. The synchrony index of the three TMRs was 0.51 (LS, 0.77 (MS and 0.95 (HS, respectively. The diets were fed at a restricted level (2% of the animal’s body weight in a 3×3 Latin-square design. Synchronizing the hourly supply of energy and N in the rumen did not significantly alter the digestibility of dry matter, organic matter, crude protein, NDF or acid detergent fiber (ADF (p>0.05. The ruminal NH3-N content of the LS group at three hours after feeding was significantly higher (p0.05. In addition, the purine derivative (PD excretion in urine and microbial-N production (MN among the three groups were not significantly different (p>0.05. In conclusion, synchronizing dietary energy and N supply to the rumen did not have a major effect on nutrient digestion or microbial protein synthesis (MPS in Holstein steers.

Effects of concentrate replacement by feed blocks on ruminal fermentation and microbial growth in goats and single-flow continuous-culture fermenters.

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Molina-Alcaide, E; Pascual, M R; Cantalapiedra-Hijar, G; Morales-García, E Y; Martín-García, A I

2009-04-01

The effect of replacing concentrate with 2 different feed blocks (FB) on ruminal fermentation and microbial growth was evaluated in goats and in single-flow continuous-culture fermenters. Diets consisted of alfalfa hay plus concentrate and alfalfa hay plus concentrate with 1 of the 2 studied FB. Three trials were carried out with 6 rumen-fistulated Granadina goats and 3 incubation runs in 6 single-flow continuous-culture fermenters. Experimental treatments were assigned randomly within each run, with 2 repetitions for each diet. At the end of each in vivo trial, the rumen contents were obtained for inoculating the fermenters. For each incubation run, the fermenters were inoculated with ruminal fluid from goats fed the same diet supplied to the corresponding fermenter flask. The average pH values, total and individual VFA, and NH(3)-N concentrations, and acetate:propionate ratios in the rumen of goats were not affected (P >or= 0.10) by diet, whereas the microbial N flow (MNF) and efficiency were affected (P fermenters, the diet affected pH (Por= 0.05), and total (P=0.02), NH(3) (P=0.005), and non-NH(3) (P=0.02) N flows, whereas the efficiency of VFA production was not affected (P=0.75). The effect of diet on MNF and efficiency depended on the bacterial pellet used as a reference. An effect (Pfermenter contents and effluent were similar (P=0.05). Differences (Pfermentation variables and bacterial pellet compositions were found. Partial replacement of the concentrate with FB did not greatly compromise carbohydrate fermentation in unproductive goats. However, this was not the case for MNF and efficiency. Differences between the results obtained in vivo and in vitro indicate a need to identify conditions in fermenters that allow better simulation of fermentation, microbial growth, and bacterial pellet composition in vivo. Reduced feeding cost could be achieved with the inclusion of FB in the diets of unproductive goats without altering rumen fermentation.

Effects of the source of energy and minerals on microbial protein synthesis in rumen using 35S as indicator. Part of a coordinated programme on tracer techniques in studies on the use of non-protein nitrogen in ruminants

International Nuclear Information System (INIS)

Durant, M.

1976-05-01

Part I. The effect of the nature of carbohydrates and minerals on microbial growth in vitro was studied in vitro to intensify rumen microbial protein synthesis from non-protein nitrogen, using phosphorus incorporation (PR). The nature of starch greatly influences urea utilization. Among the tropical tubers studied, yam Cayenesis and canna Edulis give lower urea utilization than cassava and yam Dumetorum. However, this can be improved by processing. The effects are greatest when the proportion of urea to processed cereal is ca. 4-5%. S-addition as sulfate improves urea utilization with both natural and purified diets. Part II. Results from the Jouy and Ghent laboratories were analyzed statistically, to check the accuracy of the 32 P method for estimating microbial growth, using protein-free substrates. The linear relationship between PR and every other variable was studied. Two multivariate analyses, principal components and multiple regression, were applied. Net NH 3 utilization was predicted using the equations for substrates with proteins likely to be degraded. This method appears more accurate than using the N/P ratio in microflora. Equations should only be used under the specific experiments described

A human monocytic NF-κB fluorescent reporter cell line for detection of microbial contaminants in biological samples.

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Claire Battin

Full Text Available Sensing of pathogens by innate immune cells is essential for the initiation of appropriate immune responses. Toll-like receptors (TLRs, which are highly sensitive for various structurally and evolutionary conserved molecules derived from microbes have a prominent role in this process. TLR engagement results in the activation of the transcription factor NF-κB, which induces the expression of cytokines and other inflammatory mediators. The exquisite sensitivity of TLR signalling can be exploited for the detection of bacteria and microbial contaminants in tissue cultures and in protein preparations. Here we describe a cellular reporter system for the detection of TLR ligands in biological samples. The well-characterized human monocytic THP-1 cell line was chosen as host for an NF-ᴋB-inducible enhanced green fluorescent protein reporter gene. We studied the sensitivity of the resultant reporter cells for a variety of microbial components and observed a strong reactivity towards TLR1/2 and TLR2/6 ligands. Mycoplasma lipoproteins are potent TLR2/6 agonists and we demonstrate that our reporter cells can be used as reliable and robust detection system for mycoplasma contaminations in cell cultures. In addition, a TLR4-sensitive subline of our reporters was engineered, and probed with recombinant proteins expressed in different host systems. Bacterially expressed but not mammalian expressed proteins induced strong reporter activity. We also tested proteins expressed in an E. coli strain engineered to lack TLR4 agonists. Such preparations also induced reporter activation in THP-1 cells highlighting the importance of testing recombinant protein preparations for microbial contaminations beyond endotoxins. Our results demonstrate the usefulness of monocytic reporter cells for high-throughput screening for microbial contaminations in diverse biological samples, including tissue culture supernatants and recombinant protein preparations. Fluorescent reporter

Physical degradation of proteins in well-defined fluid flows studied within a four-roll apparatus.

Science.gov (United States)

Simon, S; Krause, H J; Weber, C; Peukert, W

2011-12-01

In most applications of biotechnology and downstream processing proteins are exposed to fluid stresses in various flow configurations which often lead to the formation of unwanted protein aggregates. In this paper we present physical degradation experiments for proteins under well-defined flow conditions in a four-roll apparatus. The flow field was characterized numerically by computational fluid dynamics (CFD) and experimentally by particle image velocimetry (PIV). The local shear strain rate as well as the local shear and elongation rate was used to characterize the hydrodynamic stress environment acting on the proteins. Lysozyme was used as a model protein and subjected to well-defined fluid stresses in high and low stress environment. By using in situ turbidity measurements during stressing the aggregate formation was monitored directly in the fluid flow. An increase in absorbance at 350 nm was attributed to a higher content of visible particles (>1 µm). In addition to lysozyme, the formation of aggregates was confirmed for two larger proteins (bovine serum albumin and alcohol dehydrogenase). Thus, the presented experimental setup is a helpful tool to monitor flow-induced protein aggregation with high reproducibility. For instance, screening experiments for formulation development of biopharmaceuticals for fill and finish operations can be performed in the lab-scale in a short time-period if the stress distributions in the application are transferred and applied in the four-roll mill. Copyright © 2011 Wiley Periodicals, Inc.

Effects of Synchronicity of Carbohydrate and Protein Degradation on Rumen Fermentation Characteristics and Microbial Protein Synthesis

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J. K. Seo

2013-03-01

Full Text Available A series of in vitro studies were carried out to determine i the effects of enzyme and formaldehyde treatment on the degradation characteristics of carbohydrate and protein sources and on the synchronicity of these processes, and ii the effects of synchronizing carbohydrate and protein supply on rumen fermentation and microbial protein synthesis (MPS in in vitro experiments. Untreated corn (C and enzyme-treated corn (EC were combined with soy bean meal with (ES and without (S enzyme treatment or formaldehyde treatment (FS. Six experimental feeds (CS, CES, CFS, ECS, ECES and ECFS with different synchrony indices were prepared. Highly synchronous diets had the greatest dry matter (DM digestibility when untreated corn was used. However, the degree of synchronicity did not influence DM digestibility when EC was mixed with various soybean meals. At time points of 12 h and 24 h of incubation, EC-containing diets showed lower ammonia-N concentrations than those of C-containing diets, irrespective of the degree of synchronicity, indicating that more efficient utilization of ammonia-N for MPS was achieved by ruminal microorganisms when EC was offered as a carbohydrate source. Within C-containing treatments, the purine base concentration increased as the diets were more synchronized. This effect was not observed when EC was offered. There were significant effects on VFA concentration of both C and S treatments and their interactions. Similar to purine concentrations, total VFA production and individual VFA concentration in the groups containing EC as an energy source was higher than those of other groups (CS, CES and CFS. The results of the present study suggested that the availability of energy or the protein source are the most limiting factors for rumen fermentation and MPS, rather than the degree of synchronicity.

What is microbial community ecology?

Science.gov (United States)

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Rumen microbial protein synthesis and nitrogen efficiency as affected by tanniferous and non-tanniferous forage legumes incubated individually or together in Rumen Simulation Technique.

Science.gov (United States)

Grosse Brinkhaus, Anja; Bee, Giuseppe; Schwarm, Angela; Kreuzer, Michael; Dohme-Meier, Frigga; Zeitz, Johanna O

2018-03-01

A limited availability of microbial protein can impair productivity in ruminants. Ruminal nitrogen efficiency might be optimised by combining high-quality forage legumes such as red clover (RC), which has unfavourably high ruminal protein degradability, with tanniferous legumes like sainfoin (SF) and birdsfoot trefoil (BT). Silages from SF and from BT cultivars [Bull (BB) and Polom (BP)] were incubated singly or in combination with RC using the Rumen Simulation Technique (n = 6). The tanniferous legumes, when compared to RC, changed the total short-chain fatty acid profile by increasing propionate proportions at the expense of butyrate. Silage from SF contained the most condensed tannins (CTs) (136 g CT kg -1 dry matter) and clearly differed in various traits from the BT and RC silages. The apparent nutrient degradability (small with SF), microbial protein synthesis, and calculated content of potentially utilisable crude protein (large with SF) indicated that SF had the greatest efficiency in ruminal protein synthesis. The effects of combining SF with RC were mostly linear. The potential of sainfoin to improve protein supply, demonstrated either individually or in combination with a high-performance forage legume, indicates its potential usefulness in complementing protein-deficient ruminant diets and high-quality forages rich in rumen-degradable protein. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Electrochemical study of multi-electrode microbial fuel cells under fed-batch and continuous flow conditions

KAUST Repository

Ren, Lijiao

2014-07-01

Power production of four hydraulically connected microbial fuel cells (MFCs) was compared with the reactors operated using individual electrical circuits (individual), and when four anodes were wired together and connected to four cathodes all wired together (combined), in fed-batch or continuous flow conditions. Power production under these different conditions could not be made based on a single resistance, but instead required polarization tests to assess individual performance relative to the combined MFCs. Based on the power curves, power produced by the combined MFCs (2.12 ± 0.03 mW, 200 ω) was the same as the summed power (2.13 mW, 50 ω) produced by the four individual reactors in fed-batch mode. With continuous flow through the four MFCs, the maximum power (0.59 ± 0.01 mW) produced by the combined MFCs was slightly lower than the summed maximum power of the four individual reactors (0.68 ± 0.02 mW). There was a small parasitic current flow from adjacent anodes and cathodes, but overall performance was relatively unaffected. These findings demonstrate that optimal power production by reactors hydraulically and electrically connected can be predicted from performance by individual reactors. © 2013 Elsevier B.V. All rights reserved.

Interaction of unsaturated fat or coconut oil with monensin in lactating dairy cows fed 12 times daily. I. Protozoal abundance, nutrient digestibility, and microbial protein flow to the omasum.

Science.gov (United States)

Reveneau, C; Karnati, S K R; Oelker, E R; Firkins, J L

2012-04-01

Monensin (tradename: Rumensin) should reduce the extent of amino acid deamination in the rumen, and supplemental fat should decrease protozoal abundance and intraruminal N recycling. Because animal-vegetable (AV) fat can be biohydrogenated in the rumen and decrease its effectiveness as an anti-protozoal agent, we included diets supplemented with coconut oil (CNO) to inhibit protozoa. In a 6 × 6 Latin square design with a 2 × 3 factorial arrangement of treatments, 6 rumen-cannulated cows were fed diets without or with Rumensin (12 g/909 kg) and either no fat (control), 5% AV fat, or 5% CNO. The log10 concentrations (cells/mL) of total protozoa were not different between control (5.97) and AV fat (5.95) but were decreased by CNO (4.79; main effect of fat source). Entodinium and Dasytricha decreased as a proportion of total cells from feeding CNO, whereas Epidinium was unchanged in total abundance and thus increased proportionately. Total volatile fatty acid concentration was not affected by diet, but the acetate:propionate ratio decreased for CNO (1.85) versus control (2.95) or AV fat (2.58). Feeding CNO (23.8%) decreased ruminal neutral detergent fiber digestibility compared with control (31.1%) and AV fat (30.5%). The total-tract digestibility of NDF was lower for CNO (45.8%) versus control (57.0%) and AV fat (54.6%), with no difference in apparent organic matter digestibility (averaging 69.8%). The omasal flows of microbial N and non-ammonia N were lower for CNO versus control and AV fat, but efficiency of microbial protein synthesis was not affected. The dry matter intake was 4.5 kg/d lower with CNO, which decreased milk production by 3.1 kg/d. Main effect means of dry matter intake and milk yield tended to decrease by 0.7 and 1.2 kg/d, respectively, when Rumensin was added. Both percentage and production of milk fat decreased for CNO (main effect of fat source). An interaction was observed such that AV decreased milk fat yield more when combined with Rumensin

Effect of sulfur supplements on cellulolytic rumen micro-organisms and microbial protein synthesis in cattle fed a high fibre diet.

Science.gov (United States)

McSweeney, C S; Denman, S E

2007-11-01

To examine the effect of sulfur-containing compounds on the growth of anaerobic rumen fungi and the fibrolytic rumen bacteria Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes in pure culture and within the cattle rumen. The effect of two reduced sulfur compounds, 3-mercaptopropionic acid (MPA) or 3-mercapto-1-propanesulfonic acid as the sole S source on growth of pure fibroyltic fungal and bacterial cultures showed that these compounds were capable of sustaining growth. An in vivo trial was then conducted to determine the effect of sulfur supplements (MPA and sodium sulfate) on microbial population dynamics in cattle fed the roughage Dichanthium aristatum. Real-time PCR showed significant increases in fibrolytic bacterial and fungal populations when cattle were supplemented with these compounds. Sulfate supplementation leads to an increase in dry matter intake without a change in whole tract dry matter digestibility. Supplementation of low S-containing diets with either sodium sulfate or MPA stimulates microbial growth with an increase in rumen microbial protein supply to the animal. Through the use of real-time PCR monitoring, a better understanding of the effect of S supplementation on discrete microbial populations within the rumen is provided.

Toward the optical tongue: flow-through sensing of tannin-protein interactions based on FTIR spectroscopy.

Science.gov (United States)

Edelmann, Andrea; Lendl, Bernhard

2002-12-11

The interaction of polyphenols (tannins) with proline-rich proteins (gelatin) has been studied using an automated flow injection system with Fourier transform infrared spectroscopic detection to gain insight into chemical aspects related to astringency. In the perception of astringency, a major taste property in red wines and other beverages such as beer, tea, or fruit juices, an interaction between proline-rich salivary proteins and tannins present in the sample takes place. To study this interaction, agarose beads carrying gelatin (a proline-rich protein) were placed in the IR flow cell in such a way that the beads were probed by the IR beam. Using an automated flow system, we injected samples in a carrier stream and flushed over the proteins in a highly reproducible manner. Simultaneously, any retardation due to tannin-protein interactions taking place inside the flow cell was monitored by infrared spectroscopy. Tannins of different sources (grapes, wooden barrels, formulations used in wine making) were investigated, and their flow-through behavior was characterized. Significant differences in their affinity toward gelatin could be observed. Furthermore, because of small but characteristic differences in the IR spectrum, it is possible to distinguish condensed from hydrolyzable tannins. Nonastringent substances such as alcohols, sugars, and acids did not show retention on gelatin. The selectivity of the flow-through sensor was also demonstrated on the example of red and white wine. In contrast to white wine, where no interaction could be observed, in red wine a major interaction of the red wine tannins was found.

Detection of site specific glycosylation in proteins using flow cytometry†

Science.gov (United States)

Jayakumar, Deepak; Marathe, Dhananjay D.; Neelamegham, Sriram

2009-01-01

We tested the possibility that it is possible to express unique peptide probes on cell surfaces and detect site-specific glycosylation on these peptides using flow cytometry. Such development can enhance the application of flow cytometry to detect and quantify post-translational modifications in proteins. To this end, the N-terminal section of the human leukocyte glycoprotein PSGL-1 (P-selectin glycoprotein ligand-1) was modified to contain a poly-histidine tag followed by a proteolytic cleavage site. Amino acids preceding the cleavage site have a single O-linked glycosylation site. The recombinant protein called PSGL-1 (HT) was expressed on the surface of two mammalian cell lines, CHO and HL-60, using a lentiviral delivery approach. Results demonstrate that the N-terminal portion of PSGL-1 (HT) can be released from these cells by protease, and the resulting peptide can be readily captured and detected using cytometry-bead assays. Using this strategy, the peptide was immunoprecipitated onto beads bearing mAbs against either the poly-histidine sequence or the human PSGL-1. The carbohydrate epitope associated with the released peptide was detected using HECA-452 and CSLEX-1, monoclonal antibodies that recognize the sialyl Lewis-X epitope. Finally, the peptide released from cells could be separated and enriched using nickel chelate beads. Overall, such an approach that combines recombinant protein expression with flow cytometry, may be useful to quantify changes in site-specific glycosylation for basic science and clinical applications. PMID:19735085

Soluble Protein Analysis using a Compact Bench-top Flow Cytometer

Science.gov (United States)

Pappas, Dimitri; Kao, Shib-Hsin; Cyr, Johnathan

2004-01-01

Future space exploration missions will require analytical technology capable of providing both autonomous medical care to the crew and investigative capabilities to researchers. While several promising candidate technologies exist for further development, flow cytometry is an attractive technology as it offers both crew health (blood cell count, leukocyte differential, etc.) and a wide array of biochemistry and immunology assays. research settings, the application of this technique to soluble protein analysis is also possible. Proteomic beads using fluorescent dyes for optical encoding were used to monitor six cytokines simultaneously in cell medium of cell cultures in stationary and rotating cell culture systems. The results of this work demonstrate that a compact flow cytometer, such as a system proposed for space flight, can detect a variety of soluble proteins for crew health and biotechnology experiments during long-term missions.

Uses of antimicrobial genes from microbial genome

Science.gov (United States)

Sorek, Rotem; Rubin, Edward M.

2013-08-20

We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

Carbon input increases microbial nitrogen demand, but not microbial nitrogen mining in boreal forest soils

Science.gov (United States)

Wild, Birgit; Alaei, Saeed; Bengtson, Per; Bodé, Samuel; Boeckx, Pascal; Schnecker, Jörg; Mayerhofer, Werner; Rütting, Tobias

2016-04-01

Plant primary production at mid and high latitudes is often limited by low soil N availability. It has been hypothesized that plants can indirectly increase soil N availability via root exudation, i.e., via the release of easily degradable organic compounds such as sugars into the soil. These compounds can stimulate microbial activity and extracellular enzyme synthesis, and thus promote soil organic matter (SOM) decomposition ("priming effect"). Even more, increased C availability in the rhizosphere might specifically stimulate the synthesis of enzymes targeting N-rich polymers such as proteins that store most of the soil N, but are too large for immediate uptake ("N mining"). This effect might be particularly important in boreal forests, where plants often maintain high primary production in spite of low soil N availability. We here tested the hypothesis that increased C availability promotes protein depolymerization, and thus soil N availability. In a laboratory incubation experiment, we added 13C-labeled glucose to a range of soil samples derived from boreal forests across Sweden, and monitored the release of CO2 by C mineralization, distinguishing between CO2 from the added glucose and from the native, unlabeled soil organic C (SOC). Using a set of 15N pool dilution assays, we further measured gross rates of protein depolymerization (the breakdown of proteins into amino acids) and N mineralization (the microbial release of excess N as ammonium). Comparing unamended control samples, we found a high variability in C and N mineralization rates, even when normalized by SOC content. Both C and N mineralization were significantly correlated to SOM C/N ratios, with high C mineralization at high C/N and high N mineralization at low C/N, suggesting that microorganisms adjusted C and N mineralization rates to the C/N ratio of their substrate and released C or N that was in excess. The addition of glucose significantly stimulated the mineralization of native SOC in soils

Multi-electrode continuous flow microbial electrolysis cell for biogas production from acetate

Energy Technology Data Exchange (ETDEWEB)

Rader, Geoffrey K.; Logan, Bruce E. [Department of Civil and Environmental Engineering, Penn State University, University Park, PA 16802 (United States)

2010-09-15

Most microbial electrolysis cells (MECs) contain only a single set of electrodes. In order to examine the scalability of a multiple-electrode design, we constructed a 2.5 L MEC containing 8 separate electrode pairs made of graphite fiber brush anodes pre-acclimated for current generation using acetate, and 304 stainless steel mesh cathodes (64 m{sup 2}/m{sup 3}). Under continuous flow conditions and a one day hydraulic retention time, the maximum current was 181 mA (1.18 A/m{sup 2}, cathode surface area; 74 A/m{sup 3}) within three days of operation. The maximum hydrogen production (day 3) was 0.53 L/L-d, reaching an energy efficiency relative to electrical energy input of {eta}{sub E} = 144%. Current production remained relatively steady (days 3-18), but the gas composition dramatically shifted over time. By day 16, there was little H{sub 2} gas recovered and methane production increased from 0.049 L/L-d (day 3) to 0.118 L/L-d. When considering the energy value of both hydrogen and methane, efficiency relative to electrical input remained above 100% until near the end of the experiment (day 17) when only methane gas was being produced. Our results show that MECs can be scaled up primarily based on cathode surface area, but that hydrogen can be completely consumed in a continuous flow system unless methanogens can be completely eliminated from the system. (author)

Multi-electrode continuous flow microbial electrolysis cell for biogas production from acetate

KAUST Repository

Rader, Geoffrey K.; Logan, Bruce E.

2010-01-01

Most microbial electrolysis cells (MECs) contain only a single set of electrodes. In order to examine the scalability of a multiple-electrode design, we constructed a 2.5 L MEC containing 8 separate electrode pairs made of graphite fiber brush anodes pre-acclimated for current generation using acetate, and 304 stainless steel mesh cathodes (64 m2/m3). Under continuous flow conditions and a one day hydraulic retention time, the maximum current was 181 mA (1.18 A/m2, cathode surface area; 74 A/m 3) within three days of operation. The maximum hydrogen production (day 3) was 0.53 L/L-d, reaching an energy efficiency relative to electrical energy input of ηE = 144%. Current production remained relatively steady (days 3-18), but the gas composition dramatically shifted over time. By day 16, there was little H2 gas recovered and methane production increased from 0.049 L/L-d (day 3) to 0.118 L/L-d. When considering the energy value of both hydrogen and methane, efficiency relative to electrical input remained above 100% until near the end of the experiment (day 17) when only methane gas was being produced. Our results show that MECs can be scaled up primarily based on cathode surface area, but that hydrogen can be completely consumed in a continuous flow system unless methanogens can be completely eliminated from the system. © 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.

Multi-electrode continuous flow microbial electrolysis cell for biogas production from acetate

KAUST Repository

Rader, Geoffrey K.

2010-09-01

Most microbial electrolysis cells (MECs) contain only a single set of electrodes. In order to examine the scalability of a multiple-electrode design, we constructed a 2.5 L MEC containing 8 separate electrode pairs made of graphite fiber brush anodes pre-acclimated for current generation using acetate, and 304 stainless steel mesh cathodes (64 m2/m3). Under continuous flow conditions and a one day hydraulic retention time, the maximum current was 181 mA (1.18 A/m2, cathode surface area; 74 A/m 3) within three days of operation. The maximum hydrogen production (day 3) was 0.53 L/L-d, reaching an energy efficiency relative to electrical energy input of ηE = 144%. Current production remained relatively steady (days 3-18), but the gas composition dramatically shifted over time. By day 16, there was little H2 gas recovered and methane production increased from 0.049 L/L-d (day 3) to 0.118 L/L-d. When considering the energy value of both hydrogen and methane, efficiency relative to electrical input remained above 100% until near the end of the experiment (day 17) when only methane gas was being produced. Our results show that MECs can be scaled up primarily based on cathode surface area, but that hydrogen can be completely consumed in a continuous flow system unless methanogens can be completely eliminated from the system. © 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.

A new method for tracing flows of nitrogen and carbon through bacteria and algae in aquatic microbial communities: Analysis of 15N- and 13C-incorporation into D-alanine and other hydrolysable amino acids

NARCIS (Netherlands)

Veuger, B.

2006-01-01

Nitrogen flows through bacteria and algae in aquatic microbial communities are an important part of the nitrogen cycle, which plays a central role in aquatic ecosystems. However, work on uptake and retention of nitrogen in bacteria versus algae in natural microbial communities has long been hampered

Microbial Energy Conversion

Energy Technology Data Exchange (ETDEWEB)

Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

2006-10-01

production. Research should focus on the actions of enzymes and enzyme complexes within the context of the whole cell, how they’re regulated, where they’re placed, and what they interact with. Better modeling tools are needed to facilitate progress in microbial energy transformations. Models of metabolic dynamics, including levels of reductants and regulation of electron flow need to be improved. Global techno-economic models of microbial energy conversion systems, which seek to simultaneously describe the resource flows into and out of a system as well as its economics, are needed and should be made publicly available on the internet. Finally, more emphasis needs to be placed on multidisciplinary education and training and on cooperation between disciplines in order to make the most of microbial energy conversion technologies and to meet the research needs of the future.

Microbial protein and blood parameters of goats fed with licury cake

Directory of Open Access Journals (Sweden)

Máikal Souza Borja

2014-02-01

Full Text Available The objective of this study was to determine the ideal level of licury cake in the diet of Boer goats through microbial synthesis estimated based on the presence of purine derivatives in the urine and on blood urea and glucose parameters. Twenty uncastrated one-year-old ¾ Boer goats with an average body weight of 18 kg were distributed in a completely randomized design. Each animal was confined to a one m2 suspended stall with access to water ad libitum. The diets were formulated in accordance with the NRC (2007, and the ingredients were: 50% Tifton-85 (Cynodon sp hay, corn meal, soybean meal, premixed vitamin and mineral supplement, and licury cake. The treatments were: 1 0% of the goat’s total diet composed of licury cake (DM basis, 2 15% of the total diet composed of licury cake, 3 30% of the diet composed of licury cake, and 4 45% of the diet composed of licury cake. The experiment lasted for 17 days. The first 10 days were used to adapt the animals to the diets and facilities. The inclusion of the licury cake in the goat’s diets reduced the levels of blood nitrogen and glucose. Urinary excretion decreased linearly with the inclusion of licury cake in the diet. The inclusion of licury cake in the goat’s diets also caused a linear reduction in the excretion of allantoin, xanthine and hypoxanthine and total purine derivative (PD in urine samples. Based on the microbial protein production and blood parameters of goats fed with licury cake, up to 15% of the goat diet may be composed of licury cake.

Coexpression of multidrug resistance involve proteins: a flow cytometric analysis.

Science.gov (United States)

Boutonnat, J; Bonnefoix, T; Mousseau, M; Seigneurin, D; Ronot, X

1998-01-01

Cross resistance to multiple natural cytotoxic products represents a major obstacle in myeloblastic acute leukaemia (AML). Multidrug resistance (MDR) often involves overexpression of plasma membrane drug transporter P-glycoprotein (PGP) or the resistance associated protein (MRP). Recently, a protein overexpressed in a non-PGP MDR lung cancer cell line and termed lung resistance related protein (LRP) was identified. These proteins are known to be associated with a bad prognosis in AML. We have developed a triple indirect labelling analysed by flow cytometry to detect the coexpression of these proteins. Since no cell line expressing all three antigens is known, we mixed K562 cells (resistant to Adriblastine, PGP+, MRP-, LRP-) with GLC4 cells (resistant to Adriblastine, PGP-, MRP+, LRP+) to create a model system to test the method. The antibodies used were UIC2 for PGP, MRPm6 for MRP and LRP56 for LRP. They were revealed by Fab'2 coupled with Fluoresceine-isothiocyanate, Phycoerythrin or Tricolor with isotype specificity. Cells were fixed and permeabilized after PGP labelling because MRPm6 and LRP56 recognize intracellular epitopes. PGP and LRP were easily detected. MRP is expressed at relatively low levels and was more difficult to detect because in the triple labelling the non specific staining was higher than in a single labelling. Despite the increased background in the triple labelling we were able to detect coexpression of PGP, MRP, LRP by flow cytometry. This method appears to be very useful to detect coexpression of markers in AML. Such coexpression could modify the therapeutic approach with revertants.

Maximum flow approach to prioritize potential drug targets of Mycobacterium tuberculosis H37Rv from protein-protein interaction network.

Science.gov (United States)

Melak, Tilahun; Gakkhar, Sunita

2015-12-01

In spite of the implementations of several strategies, tuberculosis (TB) is overwhelmingly a serious global public health problem causing millions of infections and deaths every year. This is mainly due to the emergence of drug-resistance varieties of TB. The current treatment strategies for the drug-resistance TB are of longer duration, more expensive and have side effects. This highlights the importance of identification and prioritization of targets for new drugs. This study has been carried out to prioritize potential drug targets of Mycobacterium tuberculosis H37Rv based on their flow to resistance genes. The weighted proteome interaction network of the pathogen was constructed using a dataset from STRING database. Only a subset of the dataset with interactions that have a combined score value ≥770 was considered. Maximum flow approach has been used to prioritize potential drug targets. The potential drug targets were obtained through comparative genome and network centrality analysis. The curated set of resistance genes was retrieved from literatures. Detail literature review and additional assessment of the method were also carried out for validation. A list of 537 proteins which are essential to the pathogen and non-homologous with human was obtained from the comparative genome analysis. Through network centrality measures, 131 of them were found within the close neighborhood of the centre of gravity of the proteome network. These proteins were further prioritized based on their maximum flow value to resistance genes and they are proposed as reliable drug targets of the pathogen. Proteins which interact with the host were also identified in order to understand the infection mechanism. Potential drug targets of Mycobacterium tuberculosis H37Rv were successfully prioritized based on their flow to resistance genes of existing drugs which is believed to increase the druggability of the targets since inhibition of a protein that has a maximum flow to

Towards generation of bioactive peptides from meat industry waste proteins: Generation of peptides using commercial microbial proteases.

Science.gov (United States)

Ryder, Kate; Bekhit, Alaa El-Din; McConnell, Michelle; Carne, Alan

2016-10-01

Five commercially available food-grade microbial protease preparations were evaluated for their ability to hydrolyse meat myofibrillar and connective tissue protein extracts to produce bioactive peptides. A bacterial-derived protease (HT) extensively hydrolysed both meat protein extracts, producing peptide hydrolysates with significant in vitro antioxidant and ACE inhibitor activities. The hydrolysates retained bioactivity after simulated gastrointestinal hydrolysis challenge. Gel permeation chromatography sub-fractionation of the crude protein hydrolysates showed that the smaller peptide fractions exhibited the highest antioxidant and ACE inhibitor activities. OFFGEL electrophoresis of the small peptides of both hydrolysates showed that low isoelectric point peptides had antioxidant activity; however, no consistent relationship was observed between isoelectric point and ACE inhibition. Cell-based assays indicated that the hydrolysates present no significant cytotoxicity towards Vero cells. The results indicate that HT protease hydrolysis of meat myofibrillar and connective tissue protein extracts produces bioactive peptides that are non-cytotoxic, should be stable in the gastrointestinal tract and may contain novel bioactive peptide sequences. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of Mechanical Properties of Microbial Biofilms

Science.gov (United States)

Callison, Elizabeth; Gose, James; Perlin, Marc; Ceccio, Steven

2017-11-01

The physical properties of microbial biofilms grown subject to shear flows determine the form and mechanical characteristics of the biofilm structure, and consequently, the turbulent interactions over and through the biofilm. These biofilms - sometimes referred to as slime - are comprised of microbial cells and extracellular polymeric substance (EPS) matrices that surround the multicellular communities. Some of the EPSs take the form of streamers that tend to oscillate in flows, causing increased turbulent mixing and drag. As the presence of EPS governs the compliance and overall stability of the filamentous streamers, investigation of the mechanical properties of biofilms may also inform efforts to understand hydrodynamic performance of fouled systems. In this study, a mixture of four diatom genera was grown under turbulent shear flow on test panels. The mechanical properties and hydrodynamic performance of the biofilm were investigated using rheology and turbulent flow studies in the Skin-Friction Flow Facility at the University of Michigan. The diatoms in the mixture of algae were identified, and the elastic and viscous moduli were determined from small-amplitude oscillations, while a creep test was used to evaluate the biofilm compliance.

Improved means and methods for expressing recombinant proteins

NARCIS (Netherlands)

Poolman, Berend; Martinez Linares, Daniel; Gul, Nadia

2014-01-01

The invention relates to the field of genetic engineering and the production of recombinant proteins in microbial host cells. Provided is a method for enhanced expression of a recombinant protein of interest in a microbial host cell, comprising providing a microbial host cell wherein the function of

Application of biocathode in microbial fuel cells: cell performance and microbial community

Energy Technology Data Exchange (ETDEWEB)

Guo-Wei, Chen [Pusan National Univ. (Korea). Dept. of Environmental Engineering; Hefei Univ. of Technology (China). School of Civil Engineering; Choi, Soo-Jung; Lee, Tae-Ho; Lee, Gil-Young; Cha, Jae-Hwan; Kim, Chang-Won [Pusan National Univ. (Korea). Dept. of Environmental Engineering

2008-06-15

Instead of the utilization of artificial redox mediators or other catalysts, a biocathode has been applied in a two-chamber microbial fuel cell in this study, and the cell performance and microbial community were analyzed. After a 2-month startup, the microorganisms of each compartment in microbial fuel cell were well developed, and the output of microbial fuel cell increased and became stable gradually, in terms of electricity generation. At 20 ml/min flow rate of the cathodic influent, the maximum power density reached 19.53 W/m{sup 3}, while the corresponding current and cell voltage were 15.36 mA and 223 mV at an external resistor of 14.9 {omega}, respectively. With the development of microorganisms in both compartments, the internal resistance decreased from initial 40.2 to 14.0 {omega}, too. Microbial community analysis demonstrated that five major groups of the clones were categorized among those 26 clone types derived from the cathode microorganisms. Betaproteobacteria was the most abundant division with 50.0% (37 of 74) of the sequenced clones in the cathode compartment, followed by 21.6% (16 of 74) Bacteroidetes, 9.5% (7 of 74) Alphaproteobacteria, 8.1% (6 of 74) Chlorobi, 4.1% (3 of 74) Deltaproteobacteria, 4.1% (3 of 74) Actinobacteria, and 2.6% (2 of 74) Gammaproteobacteria. (orig.)

In-Drift Microbial Communities

Energy Technology Data Exchange (ETDEWEB)

D. Jolley

2000-11-09

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

In-Drift Microbial Communities

International Nuclear Information System (INIS)

Jolley, D.

2000-01-01

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses

Nonfeed application of rendered animal proteins for microbial production of eicosapentaenoic acid by the fungus Pythium irregulare.

Science.gov (United States)

Liang, Yi; Garcia, Rafael A; Piazza, George J; Wen, Zhiyou

2011-11-23

Rendered animal proteins are well suited for animal nutrition applications, but the market is maturing, and there is a need to develop new uses for these products. The objective of this study is to explore the possibility of using animal proteins as a nutrient source for microbial production of omega-3 polyunsaturated fatty acids by the microalga Schizochytrium limacinum and the fungus Pythium irregulare. To be absorbed by the microorganisms, the proteins needed to be hydrolyzed into small peptides and free amino acids. The utility of the protein hydrolysates for microorganisms depended on the hydrolysis method used and the type of microorganism. The enzymatic hydrolysates supported better cell growth performance than the alkali hydrolysates did. P. irregulare displayed better overall growth performance on the experimental hydrolysates compared to S. limacinum. When P. irregulare was grown in medium containing 10 g/L enzymatic hydrolysate derived from meat and bone meal or feather meal, the performance of cell growth, lipid synthesis, and omega-3 fatty acid production was comparable to the that of culture using commercial yeast extract. The fungal biomass derived from the animal proteins had 26-29% lipid, 32-34% protein, 34-39% carbohydrate, and industrial microorganisms which can produce omega-3 fatty acids for making omega-3-fortified foods or feeds.

Soil Microbes and soil microbial proteins: interactions with clay minerals

International Nuclear Information System (INIS)

Spence, A.; Kelleher, B. P.

2009-01-01

Bacterial enumeration in soil environments estimates that the population may reach approximately 10 1 0 g - 1 of soil and comprise up to 90% of the total soil microbial biomass. Bacteria are present in soils as single cells or multicell colonies and often strongly adsorb onto mineral surfaces such as sand and clay. The interactions of microbes and microbial biomolecules with these minerals have profound impacts on the physical, chemical and biological properties of soils. (Author)

Microbial Invasion vs. Tick Immune Regulation.

Science.gov (United States)

Sonenshine, Daniel E; Macaluso, Kevin R

2017-01-01

Ticks transmit a greater variety of pathogenic agents that cause disease in humans and animals than any other haematophagous arthropod, including Lyme disease, Rocky Mountain spotted fever, human granulocytic anaplasmosis, babesiosis, tick-borne encephalitis, Crimean Congo haemorhagic fever, and many others (Gulia-Nuss et al., 2016). Although diverse explanations have been proposed to explain their remarkable vectorial capacity, among the most important are their blood feeding habit, their long term off-host survival, the diverse array of bioactive molecules that disrupt the host's natural hemostatic mechanisms, facilitate blood flow, pain inhibitors, and minimize inflammation to prevent immune rejection (Hajdušek et al., 2013). Moreover, the tick's unique intracellular digestive processes allow the midgut to provide a relatively permissive microenvironment for survival of invading microbes. Although tick-host-pathogen interactions have evolved over more than 300 million years (Barker and Murrell, 2008), few microbes have been able to overcome the tick's innate immune system, comprising both humoral and cellular processes that reject them. Similar to most eukaryotes, the signaling pathways that regulate the innate immune response, i.e., the Toll, IMD (Immunodeficiency) and JAK-STAT (Janus Kinase/ Signal Transducers and Activators of Transcription) also occur in ticks (Gulia-Nuss et al., 2016). Recognition of pathogen-associated molecular patterns (PAMPs) on the microbial surface triggers one or the other of these pathways. Consequently, ticks are able to mount an impressive array of humoral and cellular responses to microbial challenge, including anti-microbial peptides (AMPs), e.g., defensins, lysozymes, microplusins, etc., that directly kill, entrap or inhibit the invaders. Equally important are cellular processes, primarily phagocytosis, that capture, ingest, or encapsulate invading microbes, regulated by a primordial system of thioester-containing proteins

Microbial Invasion vs. Tick Immune Regulation

Directory of Open Access Journals (Sweden)

Daniel E. Sonenshine

2017-09-01

Full Text Available Ticks transmit a greater variety of pathogenic agents that cause disease in humans and animals than any other haematophagous arthropod, including Lyme disease, Rocky Mountain spotted fever, human granulocytic anaplasmosis, babesiosis, tick-borne encephalitis, Crimean Congo haemorhagic fever, and many others (Gulia-Nuss et al., 2016. Although diverse explanations have been proposed to explain their remarkable vectorial capacity, among the most important are their blood feeding habit, their long term off-host survival, the diverse array of bioactive molecules that disrupt the host's natural hemostatic mechanisms, facilitate blood flow, pain inhibitors, and minimize inflammation to prevent immune rejection (Hajdušek et al., 2013. Moreover, the tick's unique intracellular digestive processes allow the midgut to provide a relatively permissive microenvironment for survival of invading microbes. Although tick-host-pathogen interactions have evolved over more than 300 million years (Barker and Murrell, 2008, few microbes have been able to overcome the tick's innate immune system, comprising both humoral and cellular processes that reject them. Similar to most eukaryotes, the signaling pathways that regulate the innate immune response, i.e., the Toll, IMD (Immunodeficiency and JAK-STAT (Janus Kinase/ Signal Transducers and Activators of Transcription also occur in ticks (Gulia-Nuss et al., 2016. Recognition of pathogen-associated molecular patterns (PAMPs on the microbial surface triggers one or the other of these pathways. Consequently, ticks are able to mount an impressive array of humoral and cellular responses to microbial challenge, including anti-microbial peptides (AMPs, e.g., defensins, lysozymes, microplusins, etc., that directly kill, entrap or inhibit the invaders. Equally important are cellular processes, primarily phagocytosis, that capture, ingest, or encapsulate invading microbes, regulated by a primordial system of thioester

The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems

Science.gov (United States)

Besmer, Michael D.; Weissbrodt, David G.; Kratochvil, Bradley E.; Sigrist, Jürg A.; Weyland, Mathias S.; Hammes, Frederik

2014-01-01

Fluorescent staining coupled with flow cytometry (FCM) is often used for the monitoring, quantification and characterization of bacteria in engineered and environmental aquatic ecosystems including seawater, freshwater, drinking water, wastewater, and industrial bioreactors. However, infrequent grab sampling hampers accurate characterization and subsequent understanding of microbial dynamics in all of these ecosystems. A logic technological progression is high throughput and full automation of the sampling, staining, measurement, and data analysis steps. Here we assess the feasibility and applicability of automated FCM by means of actual data sets produced with prototype instrumentation. As proof-of-concept we demonstrate examples of microbial dynamics in (i) flowing tap water from a municipal drinking water supply network and (ii) river water from a small creek subject to two rainfall events. In both cases, automated measurements were done at 15-min intervals during 12–14 consecutive days, yielding more than 1000 individual data points for each ecosystem. The extensive data sets derived from the automated measurements allowed for the establishment of baseline data for each ecosystem, as well as for the recognition of daily variations and specific events that would most likely be missed (or miss-characterized) by infrequent sampling. In addition, the online FCM data from the river water was combined and correlated with online measurements of abiotic parameters, showing considerable potential for a better understanding of cause-and-effect relationships in aquatic ecosystems. Although several challenges remain, the successful operation of an automated online FCM system and the basic interpretation of the resulting data sets represent a breakthrough toward the eventual establishment of fully automated online microbiological monitoring technologies. PMID:24917858

A hybrid clustering approach to recognition of protein families in 114 microbial genomes

Directory of Open Access Journals (Sweden)

Gogarten J Peter

2004-04-01

Full Text Available Abstract Background Grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses (e.g., homology-based prediction of structure or function. Standard clustering methods such as single-linkage clustering capture a history of cluster topologies as a function of threshold, but in practice their usefulness is limited because unrelated sequences join clusters before biologically meaningful families are fully constituted, e.g. as the result of matches to so-called promiscuous domains. Use of the Markov Cluster algorithm avoids this non-specificity, but does not preserve topological or threshold information about protein families. Results We describe a hybrid approach to sequence-based clustering of proteins that combines the advantages of standard and Markov clustering. We have implemented this hybrid approach over a relational database environment, and describe its application to clustering a large subset of PDB, and to 328577 proteins from 114 fully sequenced microbial genomes. To demonstrate utility with difficult problems, we show that hybrid clustering allows us to constitute the paralogous family of ATP synthase F1 rotary motor subunits into a single, biologically interpretable hierarchical grouping that was not accessible using either single-linkage or Markov clustering alone. We describe validation of this method by hybrid clustering of PDB and mapping SCOP families and domains onto the resulting clusters. Conclusion Hybrid (Markov followed by single-linkage clustering combines the advantages of the Markov Cluster algorithm (avoidance of non-specific clusters resulting from matches to promiscuous domains and single-linkage clustering (preservation of topological information as a function of threshold. Within the individual Markov clusters, single-linkage clustering is a more-precise instrument, discerning sub-clusters of biological relevance. Our hybrid approach thus provides a computationally efficient

Engineered, highly reactive substrates of microbial transglutaminase enable protein labeling within various secondary structure elements.

Science.gov (United States)

Rachel, Natalie M; Quaglia, Daniela; Lévesque, Éric; Charette, André B; Pelletier, Joelle N

2017-11-01

Microbial transglutaminase (MTG) is a practical tool to enzymatically form isopeptide bonds between peptide or protein substrates. This natural approach to crosslinking the side-chains of reactive glutamine and lysine residues is solidly rooted in food and textile processing. More recently, MTG's tolerance for various primary amines in lieu of lysine have revealed its potential for site-specific protein labeling with aminated compounds, including fluorophores. Importantly, MTG can label glutamines at accessible positions in the body of a target protein, setting it apart from most labeling enzymes that react exclusively at protein termini. To expand its applicability as a labeling tool, we engineered the B1 domain of Protein G (GB1) to probe the selectivity and enhance the reactivity of MTG toward its glutamine substrate. We built a GB1 library where each variant contained a single glutamine at positions covering all secondary structure elements. The most reactive and selective variants displayed a >100-fold increase in incorporation of a recently developed aminated benzo[a]imidazo[2,1,5-cd]indolizine-type fluorophore, relative to native GB1. None of the variants were destabilized. Our results demonstrate that MTG can react readily with glutamines in α-helical, β-sheet, and unstructured loop elements and does not favor one type of secondary structure. Introducing point mutations within MTG's active site further increased reactivity toward the most reactive substrate variant, I6Q-GB1, enhancing MTG's capacity to fluorescently label an engineered, highly reactive glutamine substrate. This work demonstrates that MTG-reactive glutamines can be readily introduced into a protein domain for fluorescent labeling. © 2017 The Protein Society.

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment.

Science.gov (United States)

Besmer, Michael D; Epting, Jannis; Page, Rebecca M; Sigrist, Jürg A; Huggenberger, Peter; Hammes, Frederik

2016-12-07

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality - particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL -1 . The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.

Detection of Intracellular Factor VIII Protein in Peripheral Blood Mononuclear Cells by Flow Cytometry

Directory of Open Access Journals (Sweden)

Gouri Shankar Pandey

2013-01-01

Full Text Available Flow cytometry is widely used in cancer research for diagnosis, detection of minimal residual disease, as well as immune monitoring and profiling following immunotherapy. Detection of specific host proteins for diagnosis predominantly uses quantitative PCR and western blotting assays. In this study, we optimized a flow cytometry-based detection assay for Factor VIII protein in peripheral blood mononuclear cells (PBMCs. An indirect intracellular staining (ICS method was standardized using monoclonal antibodies to different domains of human Factor VIII protein. The FVIII protein expression level was estimated by calculating the mean and median fluorescence intensities (MFI values for each monoclonal antibody. ICS staining of transiently transfected cell lines supported the method's specificity. Intracellular FVIII protein expression was also detected by the monoclonal antibodies used in the study in PBMCs of five blood donors. In summary, our data suggest that intracellular FVIII detection in PBMCs of hemophilia A patients can be a rapid and reliable method to detect intracellular FVIII levels.

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

Science.gov (United States)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

Effects of cinnamaldehyde and garlic oil on rumen microbial fermentation in a dual flow continuous culture.

Science.gov (United States)

Busquet, M; Calsamiglia, S; Ferret, A; Cardozo, P W; Kamel, C

2005-07-01

Eight continuous culture fermentors inoculated with ruminal liquor from heifers fed a 50:50 alfalfa hay:concentrate diet (17.6% crude protein, 28.0% neutral detergent fiber) were used in 3 replicated periods to study the effects of cinnamaldehyde (CIN) and garlic oil (GAR) on rumen microbial fermentation. Treatments were no additive (negative control); 1.25 mg/L (MON) and 12.5 mg/L (MON10) of the ionophore antibiotic monensin (positive control); 31.2 mg/L CIN (CIN) and 312 mg/L (CIN10) of CIN; and 31.2 mg/L GAR (GAR) and 312 mg/L (GAR10) of GAR (Allium sativa). The MON10 caused expected changes in microbial fermentation patterns (a decrease in fiber digestion, ammonia N concentration, and proportions of acetate and butyrate; an increase in the proportion of propionate; and a trend to increase small peptide plus AA N concentration). The CIN decreased the proportion of acetate and branch-chained volatile fatty acids (VFA) and increased the proportion of propionate; CIN10 decreased the proportion of acetate and increased the proportion of butyrate compared with the control. The GAR10 increased the proportion of propionate and butyrate and decreased the proportion of acetate and branch-chained VFA compared with the control. The GAR10 also increased the small peptide plus amino acid N concentration, although no effects were observed on large peptides or ammonia N concentrations. The CIN and GAR10 resulted in similar effects as monensin, with the exception of the effects on the molar proportion of butyrate, which suggests that they might have a different mode of action in affecting in vitro microbial fermentation.

Microbial proteomics: a mass spectrometry primer for biologists

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Graham Ciaren

2007-08-01

Full Text Available Abstract It is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level. In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.

Microbial protein synthesis and concentration of urea in dairy heifers fed diets with cactus forage Opuntia

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Maria do Socorro Mercês Aguiar

2015-04-01

Full Text Available The objective was to analyze the influence of increasing levels of forage cactus Opuntia in the diet on the nitrogen balance, the concentrations of urea in urine and plasma and microbial protein synthesis in dairy heifers ¾ Holstein-zebu confined. twenty four heifers were used with initial body weight of 163.00 ± 18 kg, with 8 months old and distributed in a completely randomized design with four treatments and six replications. It was used sorghum silage, concentrate and increasing levels of forage cactus Opuntia in the diet (0, 200, 400 and 600 g kg-1. The nitrogen intake, feces and urine, digested and retained with the addition of forage cactus in the diet showed decreasing linear effect. Nitrogen balance was influenced by the inclusion of forage cactus in the diet of dairy heifers through the values observed for the digested and retained nitrogen, which can be related to similar effects found for the consumption of nitrogen and the nitrogen excretion in feces and urine. Nitrogen digested percentage of intake and nitrogen retention as a percentage of ingested and digested showed no difference with the inclusion of forage cactus in the diet. The concentration of urea nitrogen in the urine of heifers had a quadratic effect point of maximum excretion level of 275.80 g kg-1 of forage cactus in the diet. Consequently, the excretion of urea nitrogen and urea excretion showed similar effect with maximum points excretion levels of 293.75 and 319.00 g kg-1 of forage in the diet. The concentration of ureic nitrogen in plasma showed no difference, with an average value of 13.19 mg dL-1. Synthesis of nitrogen and microbial crude protein adjusted to the quadratic model. The microbial efficiency was not influenced by the inclusion of forage cactus in replacement of sorghum silage and concentrate. The urine volume similar to the treatments, with an average of 5.90 liters of urine per day, proving that the creatinine excretion in urine was not influenced

Elimination of pyraclostrobin by simultaneous microbial degradation coupled with the Fenton process in microbial fuel cells and the microbial community.

Science.gov (United States)

Zhao, Huanhuan; Kong, Chui-Hua

2018-06-01

The elimination of pyraclostrobin by simultaneous microbial degradation and Fenton oxidation was achieved in a microbial fuel cell (MFC) system. After 12 h of incubation, the removal rate of pyraclostrobin was 1.4 mg/L/h at the anode and 1.7 mg/L/h at the cathode. The pyraclostrobin concentration was less than the detection limit (0.1 mg/L) after 72 h at the anode and 24 h at the cathode. The air flow rate, temperature, and pH of the catholyte had significant effects on the generation of H 2 O 2 . The maximum production of H 2 O 2 was 1.2 mg/L after reaction for 20 h during the Fenton process. Microbial community analysis indicated that functional bacteria in the genera Chryseobacterium, Stenotrophomonas, Arcobacter, and Comamonas were predominant in the anodic biofilm. In conclusion, the MFC-Fenton system provides an effective approach for treating environmental contaminants. Copyright © 2018 Elsevier Ltd. All rights reserved.

Estimation of rumen microbial protein production from purine derivatives in urine. A laboratory manual for the FAO/IAEA co-ordinated research programme on development, standardization and validation of nuclear based technologies for measuring microbial protein supply in ruminant livestock for improving productivity

International Nuclear Information System (INIS)

1997-05-01

This laboratory manual contains the methodologies used in the standardization and validation of the urine purine derivative technique for estimating microbial protein supply to the rumen. It includes descriptions of methods that involve both radioactive and stable isotopes as well as non isotopic techniques such as chemical assays, since it has been recognised that while isotopic trace techniques provide a powerful tool for nutrition research they can not and should not be used in isolation. Refs, figs, tabs

16S rRNA targeted DGGE fingerprinting of microbial communities

NARCIS (Netherlands)

Tzeneva, V.A.; Heilig, G.H.J.; Vliet, van W.M.; Akkermans, A.D.L.; Vos, de W.M.; Smidt, H.

2008-01-01

The past decades have seen the staggering development of molecular microbial ecology as a discipline that uses the detection of so-called biomarkers to monitor microbial communities in environment samples. A variety of molecules can be used as biomarkers, including cell-wall components, proteins,

Deep subsurface microbial processes

Science.gov (United States)

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

Evaluation of some feedstuffs with special emphasis on the effect of nitrate and other non-protein nitrogen fractions on ruminal microbial metabolism

International Nuclear Information System (INIS)

Nikolic, J.A.

1988-01-01

Green herbage grown under widely different conditions was examined for nitrate content. The mean value was 0.14% (range 0.01-0.32%) NO 3 -N in the dry matter (DM). It was concluded that the cut green fodder would induce high levels of blood methaemoglobin when fed to ruminants in mixed diets. Nevertheless, experiments in vitro indicated that relatively small amounts of dietary nitrate induced considerable microbial nitrate reducing activity in rumen contents. Moreover, nitrate reduction to ammonia was accompanied by alterations in microbial sulphur and energy metabolism. A technique for determining organic matter digestibility (OMD) in vitro was standardized and used to evaluate the potential nutritive value of some fruit wastes. Studies on apple pomace silage indicated that added urea did not significantly increase the silage protein content but remained as a potential source of non-protein nitrogen for rumen microorganisms. Apple pomace ensiled alone or preferably with other ingredients was acceptable to sheep and cattle, particularly as a supplement to their winter rations. (author). 27 refs, 2 figs, 5 tabs

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

International Nuclear Information System (INIS)

Wang, Yifeng; Papenguth, Hans W.

2000-01-01

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

Energy Technology Data Exchange (ETDEWEB)

WANG,YIFENG; PAPENGUTH,HANS W.

2000-05-04

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance.

Science.gov (United States)

Bokulich, Nicholas A; Bergsveinson, Jordyn; Ziola, Barry; Mills, David A

2015-03-10

Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments.

Microbial Flocculant for Nature Soda

Energy Technology Data Exchange (ETDEWEB)

Qin, Peiyong; Zhang, Tong; Chen, Cuixian

2004-03-31

Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculant was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.

Green fluorescent protein (GFP) leakage from microbial biosensors provides useful information for the evaluation of the scale-down effect

DEFF Research Database (Denmark)

Delvigne, Frank; Brognaux, Alison; Francis, Frédéric

2011-01-01

Mixing deficiencies can be potentially detected by the use of a dedicated whole cell microbial biosensor. In this work, a csiE promoter induced under carbon-limited conditions was involved in the elaboration of such biosensor. The cisE biosensor exhibited interesting response after up and down......-shift of the dilution rate in chemostat mode. Glucose limitation was accompanied by green fluorescent protein (GFP) leakage to the extracellular medium. In order to test the responsiveness of microbial biosensors to substrate fluctuations in large-scale, a scale-down reactor (SDR) experiment was performed. The glucose...... fluctuations were characterized at the single cell level and tend to decrease the induction of GFP. Simulations run on the basis of a stochastic hydrodynamic model have shown the variability and the frequencies at which biosensors are exposed to glucose gradient in the SDR. GFP leakage was observed to a great...

The relationship between odd- and branched-chain fatty acids and microbial nucleic acid bases in rumen

Directory of Open Access Journals (Sweden)

Keyuan Liu

2017-11-01

Full Text Available Objective This study aims to identify the relationship between odd- and branched-chain fatty acids (OBCFAs and microbial nucleic acid bases in the rumen, and to establish a model to accurately predict microbial protein flow by using OBCFA. Methods To develop the regression equations, data on the rumen contents of individual cows were obtained from 2 feeding experiments. In the first experiment, 3 rumen-fistulated dry dairy cows arranged in a 3×3 Latin square were fed diets of differing forage to concentration ratios (F:C. The second experiment consisted of 9 lactating Holstein dairy cows of similar body weights at the same stage of pregnancy. For each lactation stage, 3 cows with similar milk production were selected. The rumen contents were sampled at 4 time points of every two hours after morning feeding 6 h, and then to analyse the concentrations of OBCFA and microbial nucleic acid bases in the rumen samples. Results The ruminal bacteria nucleic acid bases were significantly influenced by feeding diets of differing forge to concentration ratios and lactation stages of dairy cows (p<0.05. The concentrations of OBCFAs, especially odd-chain fatty acids and C15:0 isomers, strongly correlated with the microbial nucleic acid bases in the rumen (p<0.05. The equations of ruminal microbial nucleic acid bases established by ruminal OBCFAs contents showed a good predictive capacity, as indicated by reasonably low standard errors and high R-squared values. Conclusion This finding suggests that the rumen OBCFA composition could be used as an internal marker of rumen microbial matter.

Organic priority substances and microbial processes in river sediments subject to contrasting hydrological conditions.

Science.gov (United States)

Zoppini, Annamaria; Ademollo, Nicoletta; Amalfitano, Stefano; Casella, Patrizia; Patrolecco, Luisa; Polesello, Stefano

2014-06-15

Flood and drought events of higher intensity and frequency are expected to increase in arid and semi-arid regions, in which temporary rivers represent both a water resource and an aquatic ecosystem to be preserved. In this study, we explored the variation of two classes of hazardous substances (Polycyclic Aromatic Hydrocarbons and Nonylphenols) and the functioning of the microbial community in river sediments subject to hydrological fluctuations (Candelaro river basin, Italy). Overall, the concentration of pollutants (∑PAHs range 8-275ngg(-1); ∑NPs range 299-4858ngg(-1)) suggests a moderate degree of contamination. The conditions in which the sediments were tested, flow (high/low) and no flow (wet/dry/arid), were associated to significant differences in the chemical and microbial properties. The total organic carbon contribution decreased together with the stream flow reduction, while the contribution of C-PAHs and C-NPs tended to increase. NPs were relatively more concentrated in sediments under high flow, while the more hydrophobic PAHs accumulated under low and no flow conditions. Passing from high to no flow conditions, a gradual reduction of microbial processes was observed, to reach the lowest specific bacterial carbon production rates (0.06fmolCh(-1)cell(-1)), extracellular enzyme activities, and the highest doubling time (40h) in arid sediments. In conclusion, different scenarios for the mobilization of pollutants and microbial processes can be identified under contrasting hydrological conditions: (i) the mobilization of pollutants under high flow and a relatively higher probability for biodegradation; (ii) the accumulation of pollutants during low flow and lower probability for biodegradation; (iii) the drastic reduction of pollutant concentrations under dry and arid conditions, probably independently from the microbial activity (abiotic processes). Our findings let us infer that a multiple approach has to be considered for an appropriate water

Evaluation of the Weevil-damaged Sweet Potato as Substrate for Microbial Protein Obtaining

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Lic. Antonio Montes-de-Oca-Olivares

2015-11-01

Full Text Available The production of microbial protein from agricultural and agroindustrial wastes is an important way to supply the demand of this essential nutritional principle. Sweet potato (Ipomea batata tubercles damaged by weevil (Cylas formicarius are considered a waste due to their unpleasant flavor. This research deal in the characterization of sweet potato damaged by weevil, as an alternative substratefor the culture of the fodder yeast Candida utilis. It was found that the damaged tubercle had a similar composition that the healthy one, concerning dry matter, total reducing sugars, nitrogen and minerals; the high content of reducing sugars (30-40 % dry weight recommends the use of this waste as a substrate for single cell protein production. Several fungal strains were assayed to enzymatic degradation of sweet potato polysaccharides; from these ones, Aspergillus oryzae H/28-1 and Neurospora sp. were the more actives to release reducing sugars to the culture medium, being the last one the more prominent. Theyeast Candida utilis showed a satisfactory growth in media formulated in basis to weevil-damaged sweet potato, reaching reducing sugar consumptions over 80 % and biomass yields of 37-58 %; addition of urea as nitrogen source improved both parameters of the growth. The fermentation’s end-product acquired a pleasant flavor, which suggests a better palatability.

A multi-platform flow device for microbial (co- cultivation and microscopic analysis.

Directory of Open Access Journals (Sweden)

Matthijn C Hesselman

Full Text Available Novel microbial cultivation platforms are of increasing interest to researchers in academia and industry. The development of materials with specialized chemical and geometric properties has opened up new possibilities in the study of previously unculturable microorganisms and has facilitated the design of elegant, high-throughput experimental set-ups. Within the context of the international Genetically Engineered Machine (iGEM competition, we set out to design, manufacture, and implement a flow device that can accommodate multiple growth platforms, that is, a silicon nitride based microsieve and a porous aluminium oxide based microdish. It provides control over (co-culturing conditions similar to a chemostat, while allowing organisms to be observed microscopically. The device was designed to be affordable, reusable, and above all, versatile. To test its functionality and general utility, we performed multiple experiments with Escherichia coli cells harboring synthetic gene circuits and were able to quantitatively study emerging expression dynamics in real-time via fluorescence microscopy. Furthermore, we demonstrated that the device provides a unique environment for the cultivation of nematodes, suggesting that the device could also prove useful in microscopy studies of multicellular microorganisms.

Feeding strategies for groundwater enhanced biodenitrification in an alluvial aquifer: Chemical, microbial and isotope assessment of a 1D flow-through experiment

Energy Technology Data Exchange (ETDEWEB)

Vidal-Gavilan, G., E-mail: georginavidal@biorem.cat [D D' ENGINY BIOREM S.L., Madrazo 68, bxs., 08006 Barcelona (Spain); Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristallografia, Mineralogia i Dipòsits MInerals, Universitat de Barcelona, Martí i Franquès s/n, 08028 Barcelona (Spain); Carrey, R., E-mail: rcarrey@ub.edu [Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristallografia, Mineralogia i Dipòsits MInerals, Universitat de Barcelona, Martí i Franquès s/n, 08028 Barcelona (Spain); Solanas, A., E-mail: asolanas@ub.edu [Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Avgda. Diagonal 645, 08028 Barcelona (Spain); Soler, A., E-mail: albertsolergil@ub.edu [Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristallografia, Mineralogia i Dipòsits MInerals, Universitat de Barcelona, Martí i Franquès s/n, 08028 Barcelona (Spain)

2014-10-01

Nitrate-removal through enhanced in situ biodenitrification (EISB) is an existing alternative for the recovery of groundwater quality, and is often suggested for use in exploitation wells pumping at small flow-rates. Innovative approaches focus on wider-scale applications, coupling EISB with water-management practices and new monitoring tools. However, before this approach can be used, some water-quality issues such as the accumulation of denitrification intermediates and/or of reduced compounds from other anaerobic processes must be addressed. With such a goal, a flow-through experiment using 100 mg-nitrate/L groundwater was built to simulate an EISB for an alluvial aquifer. Heterotrophic denitrification was induced through the periodic addition of a C source (ethanol), with four different C addition strategies being evaluated to improve the quality of the denitrified water. Chemical, microbial and isotope analyses of the water were performed. Biodenitrification was successfully stimulated by the daily addition of ethanol, easily achieving drinking water standards for both nitrate and nitrite, and showing an expected linear trend for nitrogen and oxygen isotope fractionation, with a εN/εO value of 1.1. Nitrate reduction to ammonium was never detected. Water quality in terms of remaining C, microbial counts, and denitrification intermediates was found to vary with the experimental time, and some secondary microbial respiration processes, mainly manganese reduction, were suspected to occur. Carbon isotope composition from the remaining ethanol also changed, from an initial enrichment in {sup 13}C-ethanol compared to the value of the injected ethanol (− 30.6‰), to a later depletion, achieving δ{sup 13}C values well below the initial isotope composition (to a minimum of − 46.7‰). This depletion in the heavy C isotope follows the trend of an inverse fractionation. Overall, our results indicated that most undesired effects on water quality may be controlled

Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

Science.gov (United States)

Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

2014-06-17

Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. Copyright © 2014 John Wiley & Sons, Inc.

Specialized microbial databases for inductive exploration of microbial genome sequences

Directory of Open Access Journals (Sweden)

Cabau Cédric

2005-02-01

Full Text Available Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis associated to related organisms for comparison.

The relationship between odd- and branched-chain fatty acids and microbial nucleic acid bases in rumen.

Science.gov (United States)

Liu, Keyuan; Hao, Xiaoyan; Li, Yang; Luo, Guobin; Zhang, Yonggen; Xin, Hangshu

2017-11-01

This study aims to identify the relationship between odd- and branched-chain fatty acids (OBCFAs) and microbial nucleic acid bases in the rumen, and to establish a model to accurately predict microbial protein flow by using OBCFA. To develop the regression equations, data on the rumen contents of individual cows were obtained from 2 feeding experiments. In the first experiment, 3 rumen-fistulated dry dairy cows arranged in a 3×3 Latin square were fed diets of differing forage to concentration ratios (F:C). The second experiment consisted of 9 lactating Holstein dairy cows of similar body weights at the same stage of pregnancy. For each lactation stage, 3 cows with similar milk production were selected. The rumen contents were sampled at 4 time points of every two hours after morning feeding 6 h, and then to analyse the concentrations of OBCFA and microbial nucleic acid bases in the rumen samples. The ruminal bacteria nucleic acid bases were significantly influenced by feeding diets of differing forge to concentration ratios and lactation stages of dairy cows (pacids and C15:0 isomers, strongly correlated with the microbial nucleic acid bases in the rumen (pacid bases established by ruminal OBCFAs contents showed a good predictive capacity, as indicated by reasonably low standard errors and high R-squared values. This finding suggests that the rumen OBCFA composition could be used as an internal marker of rumen microbial matter.

Rumen Microbial Protein Production in Rumen-Simulating-Technique (RUSITEC) Using 15N-Urea Nitrogen, as Influenced By Hay and Barley Ratios in Feed

International Nuclear Information System (INIS)

Al-Masri, M. R.; Abel, HJ.; Steinberg, W.

2004-01-01

Metabolism of dietary nitrogen using labeled 15 N and the changes in the microbial protein mass and NH3-N were studied in five rumen-simulating-technique(RUSITEC)-fermenters, which were run simultaneously in three identically repeated experiments. Each experiment consisted of a 6-day adaptation period followed directly by a 3-day collection period. The feed of the fermenters (G1, G2, G3, G4 and G5) varied in the ratio of barley. The barley increased by 20% between the fermenters. Grass hay+barley (g/d) in the feed of the fermenters was 10+2 (G1), 8+4 (G2), 6+6 (G3), 4+8 (G4) and 2+10 (G5). The results indicated that there were no significant (P>0.05) changes in the amounts of microbial nitrogen (92-118 mg/d) and microbial mass syntheses which were (mg/d): 1154 (G1), 1063 (G2), 1152 (G3), 1127 (G4) and 1362 (G5). Increasing the proportion of barley in the fermenters (G4 and G5) decreased NH3-N amounts (G2 and G3) significantly (P<0.05). The energy was not efficiently used in G5 having a lower ratio of the microbial nitrogen and microbial mass to the total short chain fatty acids than that other fermenters. (authors)

Strategies for targeting tetraspanin proteins: potential therapeutic applications in microbial infections.

Science.gov (United States)

Hassuna, Noha; Monk, Peter N; Moseley, Gregory W; Partridge, Lynda J

2009-01-01

The identification of novel targets and strategies for therapy of microbial infections is an area of intensive research due to the failure of conventional vaccines or antibiotics to combat both newly emerging diseases (e.g. viruses such as severe acute respiratory syndrome (SARS) and new influenza strains, and antibiotic-resistant bacteria) and entrenched, pandemic diseases exemplified by HIV. One clear approach to this problem is to target processes of the host organism rather than the microbe. Recent data have indicated that members of the tetraspanin superfamily, proteins with a widespread distribution in eukaryotic organisms and 33 members in humans, may provide such an approach. Tetraspanins traverse the membrane four times, but are distinguished from other four-pass membrane proteins by the presence of conserved charged residues in the transmembrane domains and a defining 'signature' motif in the larger of the two extracellular domains (the EC2). They characteristically form promiscuous associations with one another and with other membrane proteins and lipids to generate a specialized type of microdomain: the tetraspanin-enriched microdomain (TEM). TEMs are integral to the main role of tetraspanins as 'molecular organizers' involved in functions such as membrane trafficking, cell-cell fusion, motility, and signaling. Increasing evidence demonstrates that tetraspanins are used by intracellular pathogens as a means of entering and replicating within human cells. Although previous investigations focused mainly on viruses such as hepatitis C and HIV, it is now becoming clear that other microbes associate with tetraspanins, using TEMs as a 'gateway' to infection. In this article we review the properties and functions of tetraspanins/TEMs that are relevant to infective processes and discuss the accumulating evidence that shows how different pathogens exploit these properties in infection and in the pathogenesis of disease. We then investigate the novel and exciting

Free flow electrophoresis separation and AMS quantitation of 14C-naphthalene-protein adducts

International Nuclear Information System (INIS)

Buchholz, Bruce A.; Haack, Kurt W.; Sporty, Jennifer L.; Buckpitt, Alan R.; Morin, Dexter

2010-01-01

Naphthalene is a volatile aromatic hydrocarbon to which humans are exposed from a variety of sources including mobile air sources and cigarette smoke. Naphthalene produces dose-(concentration)dependent injury to airway epithelial cells of murine lung which is observed at concentrations well below the current occupational exposure standard. Toxicity is dependent upon the cytochrome P450 mediated metabolic activation of the parent substrate to unstable metabolites which become bound covalently to tissue proteins. Nearly 70 proteins have been identified as forming adducts with reactive naphthalene metabolites using in vitro systems but very little work has been conducted in vivo because reasonably large amounts (100 μCi) of 14 C labeled parent compound must be administered to generate detectable adduct levels on storage phosphor screens following separation of labeled proteins by 2D gel electrophoresis. The work described here was done to provide proof of concept that protein separation by free flow electrophoresis followed by AMS detection of protein fractions containing protein bound reactive metabolites would provide adducted protein profiles in animals dosed with trace quantities of labeled naphthalene. Mice were administered 200 mg/kg naphthalene intraperitoneally at a calculated specific activity of 2 DPM/nmol (1 pCi/nmol) and respiratory epithelial tissue was obtained by lysis lavage 4 h post injection. Free flow electrophoresis (FFE) separates proteins in the liquid phase over a large pH range (2.5-11.5) using low molecular weight acids and bases to modify the pH. The apparatus separates fractions into standard 96-well plates that can be used in other protein analysis techniques. The buffers of the fractions have very high carbon content, however, and need to be dialyzed to yield buffers compatible with 14 C-AMS. We describe the processing techniques required to couple FFE to AMS for quantitation of protein adducts.

Free flow electrophoresis separation and AMS quantitation of 14C-naphthalene-protein adducts

Science.gov (United States)

Buchholz, Bruce A.; Haack, Kurt W.; Sporty, Jennifer L.; Buckpitt, Alan R.; Morin, Dexter

2010-04-01

Naphthalene is a volatile aromatic hydrocarbon to which humans are exposed from a variety of sources including mobile air sources and cigarette smoke. Naphthalene produces dose-(concentration)dependent injury to airway epithelial cells of murine lung which is observed at concentrations well below the current occupational exposure standard. Toxicity is dependent upon the cytochrome P450 mediated metabolic activation of the parent substrate to unstable metabolites which become bound covalently to tissue proteins. Nearly 70 proteins have been identified as forming adducts with reactive naphthalene metabolites using in vitro systems but very little work has been conducted in vivo because reasonably large amounts (100 μCi) of 14C labeled parent compound must be administered to generate detectable adduct levels on storage phosphor screens following separation of labeled proteins by 2D gel electrophoresis. The work described here was done to provide proof of concept that protein separation by free flow electrophoresis followed by AMS detection of protein fractions containing protein bound reactive metabolites would provide adducted protein profiles in animals dosed with trace quantities of labeled naphthalene. Mice were administered 200 mg/kg naphthalene intraperitoneally at a calculated specific activity of 2 DPM/nmol (1 pCi/nmol) and respiratory epithelial tissue was obtained by lysis lavage 4 h post injection. Free flow electrophoresis (FFE) separates proteins in the liquid phase over a large pH range (2.5-11.5) using low molecular weight acids and bases to modify the pH. The apparatus separates fractions into standard 96-well plates that can be used in other protein analysis techniques. The buffers of the fractions have very high carbon content, however, and need to be dialyzed to yield buffers compatible with 14C-AMS. We describe the processing techniques required to couple FFE to AMS for quantitation of protein adducts.

Effect of peristalsis in balance of intestinal microbial ecosystem

Science.gov (United States)

Mirbagheri, Seyed Amir; Fu, Henry C.

2017-11-01

A balance of microbiota density in gastrointestinal tracts is necessary for health of the host. Although peristaltic flow made by intestinal muscles is constantly evacuating the lumen, bacterial density stay balanced. Some of bacteria colonize in the secreted mucus where there is no flow, but the rest resist the peristaltic flow in lumen and maintain their population. Using a coupled two-dimensional model of flow induced by large amplitude peristaltic waves, bacterial motility, reproduction, and diffusion, we address how bacterial growth and motility combined with peristaltic flow affect the balance of the intestinal microbial ecosystem.

Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways.

Science.gov (United States)

Atkinson, Joshua T; Campbell, Ian; Bennett, George N; Silberg, Jonathan J

2016-12-27

The ferredoxin (Fd) protein family is a structurally diverse group of iron-sulfur proteins that function as electron carriers, linking biochemical pathways important for energy transduction, nutrient assimilation, and primary metabolism. While considerable biochemical information about individual Fd protein electron carriers and their reactions has been acquired, we cannot yet anticipate the proportion of electrons shuttled between different Fd-partner proteins within cells using biochemical parameters that govern electron flow, such as holo-Fd concentration, midpoint potential (driving force), molecular interactions (affinity and kinetics), conformational changes (allostery), and off-pathway electron leakage (chemical oxidation). Herein, we describe functional and structural gaps in our Fd knowledge within the context of a sequence similarity network and phylogenetic tree, and we propose a strategy for improving our understanding of Fd sequence-function relationships. We suggest comparing the functions of divergent Fds within cells whose growth, or other measurable output, requires electron transfer between defined electron donor and acceptor proteins. By comparing Fd-mediated electron transfer with biochemical parameters that govern electron flow, we posit that models that anticipate energy flow across Fd interactomes can be built. This approach is expected to transform our ability to anticipate Fd control over electron flow in cellular settings, an obstacle to the construction of synthetic electron transfer pathways and rational optimization of existing energy-conserving pathways.

Theory of microbial genome evolution

Science.gov (United States)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

Factors Affecting Microbial Contamination of Market Eggs: A Review

Directory of Open Access Journals (Sweden)

Svobodová J.

2015-01-01

Full Text Available The aim of the review was to analyze the ways of microbial contamination, the protective mechanism of egg, and factors that affect the quantity of contamination and microbial penetration. Eggs can be contaminated during their formation in the infected reproductive organs of hens or after laying, when eggs are exposed to contaminated environment. The eggs are equipped against microbial contamination by several protective mechanisms comprising the presence of cuticle, eggshell, eggshell membranes, occurrence of some antibacterial proteins, and high pH value of albumen. There are several factors that affect the quantity of microbial contamination and penetration such as species of bacteria, the amount of microorganisms, storage conditions, quality of eggshell or number of pores.

Microbial network for waste activated sludge cascade utilization in an integrated system of microbial electrolysis and anaerobic fermentation

DEFF Research Database (Denmark)

Liu, Wenzong; He, Zhangwei; Yang, Chunxue

2016-01-01

in an integrated system of microbial electrolysis cell (MEC) and anaerobic digestion (AD) for waste activated sludge (WAS). Microbial communities in integrated system would build a thorough energetic and metabolic interaction network regarding fermentation communities and electrode respiring communities...... to Firmicutes (Acetoanaerobium, Acetobacterium, and Fusibacter) showed synergistic relationship with exoelectrogensin the degradation of complex organic matter or recycling of MEC products (H2). High protein and polysaccharide but low fatty acid content led to the dominance of Proteiniclasticum...... biofilm. The overall performance of WAS cascade utilization was substantially related to the microbial community structures, which in turn depended on the initial pretreatment to enhance WAS fermentation. It is worth noting that species in AD and MEC communities are able to build complex networks...

Personalizing Protein Nourishment

Science.gov (United States)

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

Microbial links and element flows in nested detrital food-webs.

NARCIS (Netherlands)

Pokarzhevskii, A.D.; van Straalen, N.M.; Zaboev, D.P.; Zaitsev, A.S.

2003-01-01

Microbial links are obligate in any food chain in soil, because detritivorous animals derive essential amino acids and other resources from microorganisms. To degrade recalcitrant substrates such as cellulose, soil animals do not produce their own cellulase, but they use cellulases derived from gut

Predicting Structure and Function for Novel Proteins of an Extremophilic Iron Oxidizing Bacterium

Science.gov (United States)

Wheeler, K.; Zemla, A.; Banfield, J.; Thelen, M.

2007-12-01

provide details for a working hypothesis of electron flow within the biofilm's major bacterium. Nearly 7% of the novel proteins contain tetratrico peptide repeat (TPR) modules, a protein-protein interaction domain that participates in signal transduction and a wide variety of other cellular functions. Like many biofilms, the various organisms in this community use unknown mechanisms to communicate, relying upon each other for survival. Especially interesting is evidence that most of these novel TPR proteins are located in the extracellular or membrane fractions, suggesting their role in intracellular communication. (1) Ram et al, 2005, Science 308:1915-20, "Community Proteomics of a Natural Microbial Biofilm" (2) Zemla et al, 2005, Nucleic Acids Res 33 (Web Server issue):W111-5, "AS2TS system for protein structure modeling and analysis" This work was funded by the DOE Genomics: GTL Program and was performed under the auspices of the DOE by the University of California, Lawrence Livermore National Laboratory under contract W-7405-Eng-48.

Versatile microbial surface-display for environmental remediation and biofuels production

Energy Technology Data Exchange (ETDEWEB)

Wu, Cindy H.; Mulchandani, Ashok; Chen, wilfred

2008-02-14

Surface display is a powerful technique that utilizes natural microbial functional components to express proteins or peptides on the cell exterior. Since the reporting of the first surface-display system in the mid-1980s, a variety of new systems have been reported for yeast, Gram-positive and Gram-negative bacteria. Non-conventional display methods are emerging, eliminating the generation of genetically modified microorganisms. Cells with surface display are used as biocatalysts, biosorbents and biostimulants. Microbial cell-surface display has proven to be extremely important for numerous applications ranging from combinatorial library screening and protein engineering to bioremediation and biofuels production.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Science.gov (United States)

Huntemann, Marcel; Ivanova, Natalia N; Mavromatis, Konstantinos; Tripp, H James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M; Kyrpides, Nikos C

2015-01-01

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

Removal of Microbial Contamination from Surface by Plasma

Science.gov (United States)

Feng, Xinxin; Liu, Hongxia; Shen, Zhenxing; Wang, Taobo

2018-01-01

Microbial contamination is closely associated with human and environmental health, they can be tested on food surfaces, medical devices, packing material and so on. In this paper the removal of the microbial contamination from surface using plasma treatment is investigated. The Escherichia coli (E. coli) has been chosen as a bio-indicator enabling to evaluate the effect of plasma assisted microbial inactivation. Oxygen gas was as the working gas. The plasma RF power, plasma exposition time, gas flow and the concentration of organic pollutant were varied in order to see the effect of the plasma treatment on the Gram-negative germ removal. After the treatment, the microbial abatement was evaluated by the standard plate count method. This proved a positive effect of the plasma treatment on Gram-negative germ removal. The kinetics and mathematical model of removal were studied after plasma treatment, and then the removing course of E. coli was analyzed. This work is meaningful for deepening our understanding of the fundamental scientific principles regarding microbial contamination from surface by plasma.

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

Energy Technology Data Exchange (ETDEWEB)

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

2015-05-29

Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.

A multi-parametric approach assessing microbial viability and organic matter characteristics during managed aquifer recharge.

Science.gov (United States)

Kim, Hyun-Chul; Noh, Jin Hyung; Chae, So-Ryong; Choi, Jaewon; Lee, Yunho; Maeng, Sung Kyu

2015-08-15

Soil column (SC) experiments were conducted to investigate the feasibility of using silver nanoparticles (AgNPs) as microbial inhibitors; the microbial viability affecting the degradation of pharmaceutically active compounds (PhACs) and the characteristics of organic matter during managed aquifer recharge were specifically evaluated. Natural surface water samples treated with AgNPs (0, 2.5, 5, and 10 mg L(-1)) were continually fed into the soil columns for 2 years. The adverse impact of AgNPs on the cell membrane integrity and microbial enzymatic activity was quantitatively determined using flow cytometry and adenosine triphosphate analysis. The increase in AgNP concentration in the feed water (up to 10 mg L(-1)) resulted in a corresponding deterioration in the performance of the managed aquifer recharge (MAR), with respect to the removal of organic carbon, oxidation of nitrogenous compounds, and PhAC attenuation. The fluorescence excitation-emission matrices of feed water and treated water showed the favorable removal of protein-like substances compared to humic-like substances regardless of the AgNP concentrations; however, the extent of removed fractions decreased noticeably when the microbial viability was lowered via AgNP treatment. The biological oxidation of organic nitrogen was almost completely inhibited when 10 mg L(-1) AgNP was added during soil passage. The attenuation of bezafibrate, ketoprofen, diclofenac, clofibric acid, and gemfibrozil was strongly associated with the significant deterioration in biodegradation as a result of AgNP activity. Copyright © 2015 Elsevier B.V. All rights reserved.

Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model.

Science.gov (United States)

Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

2016-10-06

Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks. The basic idea is to estimate the steady-state network flow between nodes that belong to different PPI networks based on a Markov random walk model. The random walker is designed to make random moves to adjacent nodes within a PPI network as well as cross-network moves between potential orthologous nodes with high sequence similarity. Based on this Markov random walk model, we estimate the steady-state network flow - or the long-term relative frequency of the transitions that the random walker makes - between nodes in different PPI networks, which can be used as a probabilistic score measuring their potential correspondence. Subsequently, the estimated scores can be used for detecting orthologous proteins in conserved functional modules through network alignment. Through evaluations based on multiple real PPI networks, we demonstrate that the proposed scheme leads to improved alignment results that are biologically more meaningful at reduced computational cost, outperforming the current state-of-the-art algorithms. The source code and datasets can be downloaded from http://www.ece.tamu.edu/~bjyoon/CUFID .

Continuous flow electrophoretic separation of proteins and cells from mammalian tissues

Science.gov (United States)

Hymer, W. C.; Barlow, Grant H.; Blaisdell, Steven J.; Cleveland, Carolyn; Farrington, Mary Ann; Feldmeier, Mary; Hatfield, J. Michael; Lanham, J. Wayne; Grindeland, Richard; Snyder, Robert S.

1987-01-01

This paper describes an apparatus for continuous flow electrophoresis (CFE), designed to separate macromolecules and cells at conditions of microgravity. In this CFE, buffer flows upward in a 120-cm long flow chamber, which is 16-cm wide x 3.0-mm thick in the microgravity version (and 6-cm wide x 1.5-mm thick in the unit-gravity laboratory version). Ovalbumin and rat serum albumin were separated in space (flight STS-4) with the same resolution of the two proteins achieved at 25 percent total w/v concentration that was obtained in the laboratory at 0.2 percent w/v concentration. Rat anterior pituitary cells, cultured human embryonic kidney cells, and canine Langerhans cells were separated into subpopulations (flight STS-8) more effectively than in unit gravity, with comparable resolution having been achieved at 100 times the concentration possible on earth.

Metabolizable protein systems in ruminant nutrition: A review

Directory of Open Access Journals (Sweden)

Lalatendu Keshary Das

2014-08-01

Full Text Available Protein available to ruminants is supplied by both microbial and dietary sources. Metabolizable protein (MP is the true protein which is absorbed by the intestine and supplied by both microbial protein and protein which escapes degradation in the rumen; the protein which is available to the animal for maintenance, growth, fetal growth during gestation, and milk production. Thus, the concept of balancing ruminant rations basing on only dietary crude protein (CP content seems erroneous. In India, ruminant rations are still balanced for digestible CP and total digestible nutrients for protein and energy requirements, respectively. Traditional feed analysis methods such as proximate analysis and detergent analysis consider feed protein as a single unit and do not take into account of the degradation processes that occur in rumen and passage rates of feed fractions from rumen to intestine. Therefore, the protein requirement of ruminants should include not only the dietary protein source, but also the microbial CP from rumen. The MP systems consider both the factors, thus predict the protein availability more accurately and precisely. This system is aptly designed to represent the extent of protein degradation in the rumen and the synthesis of microbial protein as variable functions. Feed protein fractions, i.e., rumen degradable protein and rumen undegradable protein play vital roles in meeting protein requirements of rumen microbes and host animal, respectively. With the advent of sophisticated nutrition models such as Cornell net carbohydrate and protein system, National Research Council, Agricultural Research Council, Cornell Penn Miner Dairy and Amino Cow; ration formulation has moved from balancing diets from CP to MP, a concept that describes the protein requirements of ruminantsat intestinal level, and which is available to animals for useful purposes.

The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

Energy Technology Data Exchange (ETDEWEB)

Methe, Barbara [J. Craig Venter Inst. (JCVI), Rockville, MD (United States); Lipton, Mary [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mahadevan, Krishna [Univ. of Toronto, ON (Canada)

2016-08-31

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives of this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling

Metaproteomics: Harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

Science.gov (United States)

Hettich, Robert L.; Pan, Chongle; Chourey, Karuna; Giannone, Richard J.

2013-01-01

Summary The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample. PMID:23469896

Free flow electrophoresis separation and AMS quantitation of {sup 14}C-naphthalene-protein adducts

Energy Technology Data Exchange (ETDEWEB)

Buchholz, Bruce A., E-mail: bbuchholz@llnl.go [Center for AMS, LLNL, 7000 East Avenue, Livermore, CA 94551 (United States); Haack, Kurt W.; Sporty, Jennifer L. [Center for AMS, LLNL, 7000 East Avenue, Livermore, CA 94551 (United States); Buckpitt, Alan R.; Morin, Dexter [Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, CA 95616 (United States)

2010-04-15

Naphthalene is a volatile aromatic hydrocarbon to which humans are exposed from a variety of sources including mobile air sources and cigarette smoke. Naphthalene produces dose-(concentration)dependent injury to airway epithelial cells of murine lung which is observed at concentrations well below the current occupational exposure standard. Toxicity is dependent upon the cytochrome P450 mediated metabolic activation of the parent substrate to unstable metabolites which become bound covalently to tissue proteins. Nearly 70 proteins have been identified as forming adducts with reactive naphthalene metabolites using in vitro systems but very little work has been conducted in vivo because reasonably large amounts (100 muCi) of {sup 14}C labeled parent compound must be administered to generate detectable adduct levels on storage phosphor screens following separation of labeled proteins by 2D gel electrophoresis. The work described here was done to provide proof of concept that protein separation by free flow electrophoresis followed by AMS detection of protein fractions containing protein bound reactive metabolites would provide adducted protein profiles in animals dosed with trace quantities of labeled naphthalene. Mice were administered 200 mg/kg naphthalene intraperitoneally at a calculated specific activity of 2 DPM/nmol (1 pCi/nmol) and respiratory epithelial tissue was obtained by lysis lavage 4 h post injection. Free flow electrophoresis (FFE) separates proteins in the liquid phase over a large pH range (2.5-11.5) using low molecular weight acids and bases to modify the pH. The apparatus separates fractions into standard 96-well plates that can be used in other protein analysis techniques. The buffers of the fractions have very high carbon content, however, and need to be dialyzed to yield buffers compatible with {sup 14}C-AMS. We describe the processing techniques required to couple FFE to AMS for quantitation of protein adducts.

[Progress in expression and molecular modification of microbial transglutaminase].

Science.gov (United States)

Liu, Song; Zhang, Dongxu; Du, Guocheng; Chen, Jian

2011-12-01

Microbial transglutaminase, which could catalyze the cross-linking of many proteins or non-protein materials, has been widely used in food, pharmaceutical and textile industry. To enhance the yield of the enzyme and establish corresponding platform for molecular modification, the researchers of Japanese Ajinomoto began to construct the recombinant strain producing transglutaminase in the 1990s. So far, the enzyme has been successfully expressed in different expression systems. Some of the recombinant strains are more productive than wild strains. Recently, progress has been made in the molecular modification of microbial transglutaminase, and the activity, thermo-stability and specificity of the enzyme are improved. This review briefly summarized and analyzed the strategies involved in these studies, and noted its trends.

Flow of nucleic acids from the rumen and recovery of purine derivatives in the urine of cattle and buffaloes

International Nuclear Information System (INIS)

Soejono, M.; Yusiati, L.M.; Bachrudin, Z.; Budhi, S.P.S.; Widyobroto, B.P.; Utomo, R.

2004-01-01

An experiment was conducted to determine the flow of nucleic acids from the rumen to duodenum. Two duodenal-cannulated each of male Ongole cattle and buffaloes aged three to four years were used and fed a mixture of king grass and rice bran (70:30 DM basis). At 95% and 60% of the voluntary intake in three weeks each before morning feeding period. Cr-mordanted alfalfa was used as a marker. The excretion of allantoin, uric acid, purine derivatives, and creatinine and the PDC index were higher in cattle than buffaloes at both levels of intake (P < 0.05). There were no difference between cattle and buffaloes with regard to the flow of RNA when expressed on digestible organic matter intake (DOMI), flow rate of RNA/kg DOMI, or flow rate of crude protein/kg DOMI. It can be concluded that the differences in urine excretion of purine derivatives between cattle and buffalo is not due to the differences in the amount of rumen microbial protein synthesis, but due to differences in purine metabolism between cattle and buffaloes. (author)

Purine derivative excretion and microbial protein synthesis in sheep ...

African Journals Online (AJOL)

In a 3 x 3 Latin square design experiment, urinary excretions of purine derivatives (allantoin N, Uric acid N, Xanthine + Hypoxanthine N) were measured and used to estimate microbial N yield in 9 sheep fed roughage- based diet supplemented with 0, 150 and 300g DM grass silage respectively. Daily urinary excretions of ...

Flow-through Column Experiments and Modeling of Microbially Mediated Cr(VI) Reduction at Hanford 100H

Science.gov (United States)

Yang, L.; Molins, S.; Beller, H. R.; Brodie, E. L.; Steefel, C.; Nico, P. S.; Han, R.

2010-12-01

Microbially mediated Cr(VI) reduction at the Hanford 100H area was investigated by flow-through column experiments. Three separate experiments were conducted to promote microbial activities associated with denitrification, iron and sulfate reduction, respectively. Replicate columns packed with natural sediments from the site under anaerobic environment were injected with 5mM Lactate as the electron donor and 5 μM Cr(VI) in all experiments. Sulfate and nitrate solutions were added to act as the main electron acceptors in the respective experiments, while iron columns relied on the indigenous sediment iron (and manganese) oxides as electron acceptors. Column effluent solutions were analyzed by IC and ICP-MS to monitor the microbial consumption/conversion of lactate and the associated Cr(VI) reduction. Biogeochemical reactive transport modeling was performed to gain further insights into the reaction mechanisms and Cr(VI) bioreduction rates. All experimental columns showed a reduction of the injected Cr(VI). Columns under denitrifying conditions showed the least Cr(VI) reduction at early stages (simulations indicated that biomass growth completely depleted influent ammonium, and called for an additional source of N to account for the measured reduction rates. Iron columns were the least active with undetectable consumption of the injected lactate, slowest cell growth, and the smallest change in Cr(VI) concentrations during the course of the experiment. In contrast, columns under sulfate-reducing/fermentative conditions exhibited the greatest Cr(VI) reduction capacity. Two sulfate columns evolved to complete lactate fermentation with acetate and propionate produced in the column effluent after 40 days of experiments. These fermenting columns showed a complete removal of injected Cr(VI), visible precipitation of sulfide minerals, and a significant increase in effluent Fe and Mn concentrations. Reactive transport simulations suggested that direct reduction of Cr(VI) by

Flow induced dispersion analysis rapidly quantifies proteins in human plasma samples

DEFF Research Database (Denmark)

Poulsen, Nicklas N; Andersen, Nina Z; Østergaard, Jesper

2015-01-01

Rapid and sensitive quantification of protein based biomarkers and drugs is a substantial challenge in diagnostics and biopharmaceutical drug development. Current technologies, such as ELISA, are characterized by being slow (hours), requiring relatively large amounts of sample and being subject...... to cumbersome and expensive assay development. In this work a new approach for quantification based on changes in diffusivity is presented. The apparent diffusivity of an indicator molecule interacting with the protein of interest is determined by Taylor Dispersion Analysis (TDA) in a hydrodynamic flow system...... in a blood plasma matrix), fully automated, and being subject to a simple assay development. FIDA is demonstrated for quantification of the protein Human Serum Albumin (HSA) in human plasma as well as for quantification of an antibody against HSA. The sensitivity of the FIDA assay depends on the indicator...

A microbial trigger for gelled polymers

Energy Technology Data Exchange (ETDEWEB)

Bailey, S.; Bryant, R.; Zhu, T.

1995-12-31

A process using a microbially gelled biopolymer was developed and used to modify permeability in coreflood experiments. Alkaline-soluble curdlan biopolymer was mixed with microbial nutrients and acid-producing alkaliphilic bacteria, and injected into Berea sandstone cores. Concurrent bottle tests with the polymer solution were incubated beside the core. Polymer in the bottle tests formed rigid gel in 2-5 days at 27{degree}C. After 7 days incubation, 25-35 psi fluid pressure was required to begin flow through the cores. Permeability of the cores was decreased from 852 md to 2.99 md and from 904 md to 4.86 md, respectively, giving residual resistance factors of 334 and 186.

Whey protein isolate edible films with essential oils incorporated to improve the microbial quality of poultry.

Science.gov (United States)

Fernández-Pan, Idoya; Mendoza, Mauricio; Maté, Juan I

2013-09-01

Whey protein isolate edible films with oregano or clove essential oils (EOs) incorporated as natural antimicrobials have been developed, with the aim of enhancing the microbial quality of poultry. The effectiveness of the films was determined against both the whole and selected microbiota developed during different periods of cold storage on the surface of skinless chicken breast. Tests were conducted by using both turbidimetric and agar disc diffusion methods. The antimicrobial edible films developed showed high effectiveness against the main spoilers developed on the surface of skinless chicken breasts cold-stored for 8 days. The films based on oregano EO showed greater effectiveness than those based on clove EO. Still, clove EO could be part of an effective antimicrobial edible film. Enterobacteriaceae was the most susceptible to the effect of the films when lower concentrations of EO were incorporated. The largest inhibition surfaces obtained were provoked by films with the highest concentration of oregano EO incorporated against lactic acid bacteria. The antimicrobial edible films developed in this study inhibited the growth of the microbial populations that developed through storage of the chicken breast and caused its spoilage. The results of this research have direct application in the food industry to enhance the control of the development of spoilers such as Pseudomonas spp. or lactic acid bacteria. © 2013 Society of Chemical Industry.

Microbial enzyme activity, nutrient uptake and nutrient limitation in forested streams

Science.gov (United States)

Brian H. Hill; Frank H. McCormick; Bret C. Harvey; Sherri L. Johnson; Melvin L. Warren; Colleen M. Elonen

2010-01-01

The flow of organic matter and nutrients from catchments into the streams draining them and the biogeochemical transformations of organic matter and nutrients along flow paths are fundamental processes instreams (Hynes,1975; Fisher, Sponseller & Heffernan, 2004). Microbial biofilms are often the primary interface for organic matter and nutrient uptake and...

Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions

Energy Technology Data Exchange (ETDEWEB)

Anderson, Lindsey N.; Koech, Phillip K.; Plymale, Andrew E.; Landorf, Elizabeth V.; Konopka, Allan; Collart, Frank; Lipton, Mary S.; Romine, Margaret F.; Wright, Aaron T.

2016-02-02

The rapid completion of microbial genomes is inducing a conundrum in functional gene discovery. Novel methods are critically needed to shorten the gap between characterizing a microbial genome and experimentally validating bioinformatically-predicted functions. Of particular importance are transport mechanisms, used to shuttle nutrients and metabolites across cell mem-branes, such as B vitamins, which are indispensable to metabolic reactions crucial to the survival of diverse microbes ranging from members of environmental microbial communities to human pathogens. Methods to accurately assign function and specificity for a wide range of experimentally unidentified and/or predicted membrane-embedded transport proteins, and characterization of intra-cellular enzyme-cofactor/nutrient associations are needed to enable a significantly improved understanding of microbial biochemis-try and physiology, how microbes associate with others, and how they sense and respond to environmental perturbations. Chemical probes derived from B vitamins B1, B2, and B7 have allowed us to experimentally address the aforementioned needs by identifying B vitamin transporters and intracellular protein-cofactor associations through live cell labeling of the filamentous anoxygenic pho-toheterotroph, Chloroflexus aurantiacus J-10-fl, known for both B vitamin biosynthesis and environmental salvage. Our probes provide a unique opportunity to directly link cellular activity and protein function back to ecosystem and/or host dynamics by iden-tifying B vitamin transport and disposition mechanisms required for survival.

Flow of light energy in benthic photosynthetic microbial mats

Energy Technology Data Exchange (ETDEWEB)

Al-Najjar, Mohammad Ahmad A.

2010-12-15

The work in this thesis demonstrates the assessment of the energy budget inside microbial mat ecosystems, and the factors affecting light utilization efficiency. It presents the first balanced light energy budget for benthic microbial mat ecosystems, and shows how the budget and the spatial distribution of the local photosynthetic efficiencies within the euphotic zone depend on the absorbed irradiance (Jabs). The energy budget was dominated by heat dissipation on the expense of photosynthesis. The maximum efficiency of photosynthesis was at light limiting conditions When comparing three different marine benthic photosynthetic ecosystems (originated from Abu-Dhabi, Arctic, and Exmouth Gulf in Western Australia), differences in the efficiencies were calculated. The results demonstrated that the maximum efficiency depended on mat characteristics affecting light absorption and scattering; such as, photopigments ratio and distribution, and the structural organization of the photosynthetic organisms relative to other absorbing components of the ecosystem (i.e., EPS, mineral particles, detritus, etc.). The maximum efficiency decreased with increasing light penetration depth, and increased with increasing the accessory pigments (phycocyanin and fucoxanthin)/chlorophyll ratio. Spatial heterogeneity in photosynthetic efficiency, pigment distribution, as well as light acclimation in microbial mats originating from different geographical locations was investigated. We used a combined pigment imaging approach (variable chlorophyll fluorescence and hyperspectral imaging), and fingerprinting approach. For each mat, the photosynthetic activity was proportional to the local pigment concentration in the photic zone, but not for the deeper layers and between different mats. In each mat, yield of PSII and E1/2 (light acclimation) generally decreased in parallel with depth, but the gradients in both parameters varied greatly between samples. This mismatch between pigments concentration

Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells

DEFF Research Database (Denmark)

Weiss Nielsen, Martin; Sternberg, Claus; Molin, Søren

2011-01-01

well-defined conditions(2,3). The system consists of a flow cell that serves as growth chamber for the biofilm. The flow cell is supplied with nutrients and oxygen from a medium flask via a peristaltic pump and spent medium is collected in a waste container. This construction of the flow system allows......Many microbial cells have the ability to form sessile microbial communities defined as biofilms that have altered physiological and pathological properties compared to free living microorganisms. Biofilms in nature are often difficult to investigate and reside under poorly defined conditions(1...... a continuous supply of nutrients and administration of e.g. antibiotics with minimal disturbance of the cells grown in the flow chamber. Moreover, the flow conditions within the flow cell allow studies of biofilm exposed to shear stress. A bubble trapping device confines air bubbles from the tubing which...

Acetate enhances startup of a H₂-producing microbial biocathode.

Science.gov (United States)

Jeremiasse, Adriaan W; Hamelers, Hubertus V M; Croese, Elsemiek; Buisman, Cees J N

2012-03-01

H(2) can be produced from organic matter with a microbial electrolysis cell (MEC). To decrease MEC capital costs, a cathode is needed that is made of low-cost material and produces H(2) at high rate. A microbial biocathode is a low-cost candidate, but suffers from a long startup and a low H(2) production rate. In this study, the effects of cathode potential and carbon source on microbial biocathode startup were investigated. Application of a more negative cathode potential did not decrease the startup time of the biocathode. If acetate instead of bicarbonate was used as carbon source, the biocathode started up more than two times faster. The faster startup was likely caused by a higher biomass yield for acetate than for bicarbonate, which was supported by thermodynamic calculations. To increase the H(2) production rate, a flow through biocathode fed with acetate was investigated. This biocathode produced 2.2 m(3) H(2) m(-3)  reactor day(-1) at a cathode potential of -0.7 V versus NHE, which was seven times that of a parallel flow biocathode of a previous study. Copyright © 2011 Wiley Periodicals, Inc.

Microbial bioenergetics of coral-algal interactions

Directory of Open Access Journals (Sweden)

Ty N.F. Roach

2017-06-01

Full Text Available Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify

Mechanistic Understanding of Microbial Plugging for Improved Sweep Efficiency

Energy Technology Data Exchange (ETDEWEB)

Steven Bryant; Larry Britton

2008-09-30

Microbial plugging has been proposed as an effective low cost method of permeability reduction. Yet there is a dearth of information on the fundamental processes of microbial growth in porous media, and there are no suitable data to model the process of microbial plugging as it relates to sweep efficiency. To optimize the field implementation, better mechanistic and volumetric understanding of biofilm growth within a porous medium is needed. In particular, the engineering design hinges upon a quantitative relationship between amount of nutrient consumption, amount of growth, and degree of permeability reduction. In this project experiments were conducted to obtain new data to elucidate this relationship. Experiments in heterogeneous (layered) beadpacks showed that microbes could grow preferentially in the high permeability layer. Ultimately this caused flow to be equally divided between high and low permeability layers, precisely the behavior needed for MEOR. Remarkably, classical models of microbial nutrient uptake in batch experiments do not explain the nutrient consumption by the same microbes in flow experiments. We propose a simple extension of classical kinetics to account for the self-limiting consumption of nutrient observed in our experiments, and we outline a modeling approach based on architecture and behavior of biofilms. Such a model would account for the changing trend of nutrient consumption by bacteria with the increasing biomass and the onset of biofilm formation. However no existing model can explain the microbial preference for growth in high permeability regions, nor is there any obvious extension of the model for this observation. An attractive conjecture is that quorum sensing is involved in the heterogeneous bead packs.

Measurement of the rate of bacterial protein synthesis in rumen. Part of a coordinated programme on tracer techniques in studies on the use of non-protein nitrogen in ruminants

International Nuclear Information System (INIS)

Leng, R.A.

1975-10-01

A technique has been developed to differentiate between rumen microbial and dietary protein at the duodenum. Mature whethers fitted with rumen, duodenal and ileal cannulas were fed protein poor diets with added urea, casein and formaldehyde treated casein. These contained 0.30, 1.54, 3.26 and 3.26 % N respectively. The isotopes 35 S or 15 N were infused into the rumen to label microbial protein so that microbial protein could be differentiated from dietary protein. By using the 35 S or 15 N system to mark microbes, it was found that 40% of the formaldehyde treated protein is fermented in the rumen and about 10% is lost in the feces. This indicates that approximately 50% of the protected protein was utilized by the sheep

Effects of incorporation of whey protein concentrate on physicochemical, texture, and microbial evaluation of developed cookies

Directory of Open Access Journals (Sweden)

Safa Hamid Wani

2015-12-01

Full Text Available Whey Protein concentrate (WPC was incorporated into cookies at different levels (0, 2, 4, and 6%. Cookies were analyzed for physicochemical, color, textural, microbial, and sensory attributes. Physicochemical analysis revealed that 6% WPC supplemented cookies shows maximum protein content (13.22%, moisture content (11.33%, fat content (23.08%, and ash content (2.02% as compared to control. However, control sample shows significantly different (p ≤ 0.05 value for crude fiber and carbohydrate content. Maximum thickness (9.63 mm, diameter (44.06 mm, and weight (9.10 g were found for control and these decreased significantly (p ≤ 0.05 with increase in WPC supplementation level in cookies. Cookie supplemented with 4% WPC showed maximum overall acceptability (4.76. Texture analysis revealed that 6% WPC supplemented cookie shows maximum cutting force (55.3 N. Lightness (L* value of cookies decreased from 67.32 to 57.94. Where as a* and b* value increased from 0.37 to 3.57 and 25.35 to 27.54, respectively. The total plate count of cookie samples was under acceptable limits.

Biodegradation of phenol in batch and continuous flow microbial fuel cells with rod and granular graphite electrodes.

Science.gov (United States)

Moreno, Lyman; Nemati, Mehdi; Predicala, Bernardo

2018-01-01

Phenol biodegradation was evaluated in batch and continuous flow microbial fuel cells (MFCs). In batch-operated MFCs, biodegradation of 100-1000 mg L -1 phenol was four to six times faster when graphite granules were used instead of rods (3.5-4.8 mg L -1  h -1 vs 0.5-0.9 mg L -1  h -1 ). Similarly maximum phenol biodegradation rates in continuous MFCs with granular and single-rod electrodes were 11.5 and 0.8 mg L -1  h -1 , respectively. This superior performance was also evident in terms of electrochemical outputs, whereby continuous flow MFCs with granular graphite electrodes achieved maximum current and power densities (3444.4 mA m -3 and 777.8 mW m -3 ) that were markedly higher than those with single-rod electrodes (37.3 mA m -3 and 0.8 mW m -3 ). Addition of neutral red enhanced the electrochemical outputs to 5714.3 mA m -3 and 1428.6 mW m -3 . Using the data generated in the continuous flow MFC, biokinetic parameters including μ m , K S , Y and K e were determined as 0.03 h -1 , 24.2 mg L -1 , 0.25 mg cell (mg phenol) -1 and 3.7 × 10 -4  h -1 , respectively. Access to detailed kinetic information generated in MFC environmental conditions is critical in the design, operation and control of large-scale treatment systems utilizing MFC technology.

Growing and analyzing biofilms in flow chambers

DEFF Research Database (Denmark)

Tolker-Nielsen, Tim; Sternberg, Claus

2011-01-01

This unit describes the setup of flow chamber systems for the study of microbial biofilms, and methods for the analysis of structural biofilm formation. Use of flow chambers allows direct microscopic investigation of biofilm formation. The biofilms in flow chambers develop under hydrodynamic......, and disassembly and cleaning of the system. In addition, embedding and fluorescent in situ hybridization of flow chamber-grown biofilms are addressed....

Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

DEFF Research Database (Denmark)

Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

2016-01-01

An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal...... derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff...... between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used...

Shifts in microbial populations in Rusitec fermenters as affected by the type of diet and impact of the method for estimating microbial growth (15N v. microbial DNA).

Science.gov (United States)

Mateos, I; Ranilla, M J; Saro, C; Carro, M D

2017-11-01

Rusitec fermenters are in vitro systems widely used to study ruminal fermentation, but little is known about the microbial populations establishing in them. This study was designed to assess the time evolution of microbial populations in fermenters fed medium- (MC; 50% alfalfa hay : concentrate) and high-concentrate diets (HC; 15 : 85 barley straw : concentrate). Samples from solid (SOL) and liquid (LIQ) content of fermenters were taken immediately before feeding on days 3, 8 and 14 of incubation for quantitative polymerase chain reaction and automated ribosomal intergenic spacer analysis analyses. In SOL, total bacterial DNA concentration and relative abundance of Ruminococcus flavefaciens remained unchanged over the incubation period, but protozoal DNA concentration and abundance of Fibrobacter succinogenes, Ruminococcus albus and fungi decreased and abundance of methanogenic archaea increased. In LIQ, total bacterial DNA concentration increased with time, whereas concentration of protozoal DNA and abundance of methanogens and fungi decreased. Diet×time interactions were observed for bacterial and protozoal DNA and relative abundance of F. succinogenes and R. albus in SOL, as well as for protozoal DNA in LIQ. Bacterial diversity in SOL increased with time, but no changes were observed in LIQ. The incubated diet influenced all microbial populations, with the exception of total bacteria and fungi abundance in LIQ. Bacterial diversity was higher in MC-fed than in HC-fed fermenters in SOL, but no differences were detected in LIQ. Values of pH, daily production of volatile fatty acids and CH4 and isobutyrate proportions remained stable over the incubation period, but other fermentation parameters varied with time. The relationships among microbial populations and fermentation parameters were in well agreement with those previously reported in in vivo studies. Using 15N as a microbial marker or quantifying total microbial DNA for estimating microbial protein synthesis

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

Science.gov (United States)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

Microbial genome analysis: the COG approach.

Science.gov (United States)

Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2017-09-14

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion.

Science.gov (United States)

Zhao, Chunhui; Mu, Hui; Zhao, Yuxiao; Wang, Liguo; Zuo, Bin

2018-02-01

This study firstly evaluated the microbial role when choosing the acclimated anaerobic granular sludge (AGS) and waste activated sludge (WAS) as microbial and nutritional regulators to improve the biomethanation of fruit and vegetable wastes (FVW). Results showed that the enriched hydrogenotrophic methanogens, and Firmicutes and Spirochaeta in the AGS were responsible for the enhanced methane yield. A synthetic waste representing the mixture of WAS and FVW was then used to investigate the influences of different substrate composition on methane generations. The optimal mass ratio of carbohydrate/protein/cellulose was observed to be 50:45:5, and the corresponding methane yield was 411mL/g-VS added . Methane kinetic studies suggested that the modified Gompertz model fitted better with those substrates of carbohydrate- than protein-predominated. Parameter results indicated that the maximum methane yield and production rate were enhanced firstly and then reduced with the decreasing carbohydrate and increasing protein percentages; the lag phase time however increased continuously. Copyright © 2017 Elsevier Ltd. All rights reserved.

Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

Science.gov (United States)

Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

2007-12-01

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms

Effects of nonstructural carbohydrates and protein sources on intake, apparent total tract digestibility, and ruminal metabolism in vivo and in vitro with high-concentrate beef cattle diets.

Science.gov (United States)

Rotger, A; Ferret, A; Calsamiglia, S; Manteca, X

2006-05-01

To investigate the effects of synchronizing nonstructural carbohydrate (NSC) and protein degradation on intake and rumen microbial fermentation, four ruminally fistulated Holstein heifers (BW = 132.3 +/- 1.61 kg) fed high-concentrate diets were assigned to a 4 x 4 Latin square design with a 2 x 2 factorial arrangement of treatments studied in vivo and in vitro with a dual-flow continuous culture system. Two NSC sources (barley and corn) and 2 protein sources [soybean meal (SBM) and sunflower meal (SFM)] differing in their rate and extent of ruminal degradation were combined resulting in a synchronized rapid fermentation diet (barley-SFM), a synchronized slow fermentation diet (corn-SBM), and 2 unsynchronized diets with a rapidly and a slowly fermenting component (barley-SBM, and corn-SFM). In vitro, the fermentation profile was studied at a constant pH of 6.2, and at a variable pH with 12 h at pH 6.4 and 12 h at pH 5.8. Synchronization tended to result in greater true OM digestion (P = 0.072), VFA concentration (P = 0.067), and microbial N flow (P = 0.092) in vitro, but had no effects on in vivo fermentation pattern or on apparent total tract digestibility. The NSC source affected the efficiency of microbial protein synthesis in vitro, tending to be greater (P = 0.07) for barley-based diets, and in vivo, the NSC source tended to affect intake. Dry matter and OM intake tended to be greater (P > or = 0.06) for corn- than barley-based diets. Ammonia N concentration was lower in vitro (P = 0.006) and tended to be lower in vivo (P = 0.07) for corn- than barley-based diets. In vitro, pH could be reduced from 6.4 to 5.8 for 12 h/d without any effect on ruminal fermentation or microbial protein synthesis. In summary, ruminal synchronization seemed to have positive effects on in vitro fermentation, but in vivo recycling of endogenous N or intake differences could compensate for these effects.

Determination of rumen microbial growth in vitro form 32P-labelled phosphate incorporation

International Nuclear Information System (INIS)

Nevel, C.J. Van; Demeyer, D.I.

1977-01-01

The extracellular phosphate pool in incubations of rumen fluid or washed cell suspensions of mixed rumen bacteria (WCS) was labelled with 32 P. From the constant extracellular phosphate pool specific activity and the amount of radioactivity incorporated during incubation, the amount of P incorporated in the microbial fraction was calculated. From the value for nitrogen: P determined in microbial matter, the amount of N incorporated was calculated as a measure of microbial growth. Incorporation of soluble non-protein-N in incubations devoid of substrate protein was 50 and 80% of the values obtained using isotope method for rumen fluid and WCS respectively. Incorporation of 32 P in P-containing microbial components (mainly nucleic acids) was compared with net synthesis of these components in incubations of WCS. When N incorporation, calculated from results obtained using isotope method in incubations with rumen fluid, was compared with the amount of carbohydrate substrate fermented and the type of fermentation, values between 18.3 and 44.6 g N incorporated kg of organic matter fermented were obtained. The use of isotopes for determination of rumen microbial growth in vitro is critically discussed. (author)

Study of performances, stability and microbial characterization of a Sequencing Batch Biofilter Granular Reactor working at low recirculation flow.

Science.gov (United States)

De Sanctis, Marco; Beccari, Mario; Di Iaconi, Claudio; Majone, Mauro; Rossetti, Simona; Tandoi, Valter

2013-02-01

The Sequencing Batch Biofilter Granular Reactor (SBBGR) is a promising wastewater treatment technology characterized by high biomass concentration in the system, good depuration performance and low sludge production. Its main drawback is the high energy consumption required for wastewater recirculation through the reactor bed to ensure both shear stress and oxygen supply. Therefore, the effect of low recirculation flow on the long-term (38 months) performance of a laboratory scale SBBGR was studied. Both the microbial components of the granules, and their main metabolic activities were evaluated (heterotrophic oxidation, nitrification, denitrification, fermentation, sulphate reduction and methanogenesis). The results indicate that despite reduced recirculation, the SBBGR system maintained many of its advantageous characteristics. Copyright © 2012 Elsevier Ltd. All rights reserved.

Quantitative analysis of microbial biomass yield in aerobic bioreactor.

Science.gov (United States)

Watanabe, Osamu; Isoda, Satoru

2013-12-01

We have studied the integrated model of reaction rate equations with thermal energy balance in aerobic bioreactor for food waste decomposition and showed that the integrated model has the capability both of monitoring microbial activity in real time and of analyzing biodegradation kinetics and thermal-hydrodynamic properties. On the other hand, concerning microbial metabolism, it was known that balancing catabolic reactions with anabolic reactions in terms of energy and electron flow provides stoichiometric metabolic reactions and enables the estimation of microbial biomass yield (stoichiometric reaction model). We have studied a method for estimating real-time microbial biomass yield in the bioreactor during food waste decomposition by combining the integrated model with the stoichiometric reaction model. As a result, it was found that the time course of microbial biomass yield in the bioreactor during decomposition can be evaluated using the operational data of the bioreactor (weight of input food waste and bed temperature) by the combined model. The combined model can be applied to manage a food waste decomposition not only for controlling system operation to keep microbial activity stable, but also for producing value-added products such as compost on optimum condition. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Invited review: Essential oils as modifiers of rumen microbial fermentation.

Science.gov (United States)

Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

2007-06-01

Microorganisms in the rumen degrade nutrients to produce volatile fatty acids and synthesize microbial protein as an energy and protein supply for the ruminant, respectively. However, this fermentation process has energy (losses of methane) and protein (losses of ammonia N) inefficiencies that may limit production performance and contribute to the release of pollutants to the environment. Antibiotic ionophores have been very successful in reducing these energy and protein losses in the rumen, but the use of antibiotics in animal feeds is facing reduced social acceptance, and their use has been banned in the European Union since January 2006. For this reason, scientists have become interested in evaluating other alternatives to control specific microbial populations to modulate rumen fermentation. Essential oils can interact with microbial cell membranes and inhibit the growth of some gram-positive and gram-negative bacteria. As a result of such inhibition, the addition of some plant extracts to the rumen results in an inhibition of deamination and methanogenesis, resulting in lower ammonia N, methane, and acetate, and in higher propionate and butyrate concentrations. Results have indicated that garlic oil, cinnamaldehyde (the main active component of cinnamon oil), eugenol (the main active component of the clove bud), capsaicin (the active component of hot peppers), and anise oil, among others, may increase propionate production, reduce acetate or methane production, and modify proteolysis, peptidolysis, or deamination in the rumen. However, the effects of some of these essential oils are pH and diet dependent, and their use may be beneficial only under specific conditions and production systems. For example, capsaicin appears to have small effects in high-forage diets, whereas the changes observed in high-concentrate diets (increases in dry matter intake and total VFA, and reduction in the acetateto-propionate ratio and ammonia N concentration) may be beneficial

Does microbial cm-scale heterogeneity impact pesticide degradation in and leaching from loamy agricultural soils?

DEFF Research Database (Denmark)

Rosenbom, Annette Elisabeth; Binning, Philip John; Aamand, Jens

2014-01-01

matrix flow or preferential flow through a soil matrix with a wormhole. MCPA leached, within 250 days, below 1 metre only when degrader biomass was absent and preferential flow occurred. Both biodegradation in the plough layer and the microbially active lining of the wormhole contributed to reducing MCPA...

Effects of correcting in situ ruminal microbial colonization of feed particles on the relationship between ruminally undegraded and intestinally digested crude protein in concentrate feeds.

Science.gov (United States)

González, Javier; Mouhbi, Rabiaa; Guevara-González, Jesús Alberto; Arroyo, José María

2018-02-01

In situ estimates of ruminally undegraded protein (RUP) and intestinally digested protein (IDP) of ten concentrates, uncorrected or corrected for the ruminal microbial colonization, were used to examine the effects of this correction on the relationship between IDP and RUP values. Both variables were established for three rumen and duodenum cannulated wethers using 15 N labeling-techniques and considering measured rates of ruminal particle comminution (k c ) and outflow (k p ). A covariance analysis showed that the close relationship found between both variables (IDP = -0.0132 ± 0.00679 + 0.776 ± 0.0002 RUP; n = 60; P content in concentrates and industrial by-products can be predicted from RUP values, thus avoiding the laborious and complex procedure of determining intestinal digestibility; however, a larger sample of feeds is necessary to achieve more accurate predictions. The lack of influence of the correction for microbial contamination on the prediction observed in the present study increases the data available for this prediction. However, only the use of corrected values may provide an accurate evaluation. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Emulsion properties of pork myofibrillar protein in combination with microbial transglutaminase and calcium alginate under various pH conditions.

Science.gov (United States)

Hong, Geun Pyo; Min, Sang-Gi; Chin, Koo Bok

2012-01-01

In this study, the effects of microbial transglutaminase (MTG) and calcium alginate (CA) systems in combination with soybean oil on the emulsion properties of porcine myofibrillar protein (MP) were evaluated under various pH conditions. MTG was shown to improve emulsifying capacity and creaming stability, which increased with increasing pH values up to 6.5. The CA did not influence emulsifying capacity, but it improved the creaming stability of the MP-stabilized emulsions. Both MTG and CA enhanced the rheological properties, but their effects on the physical characteristics of the protein evidenced an opposite trend in relation to pH, i.e., the MTG system improved both the emulsion and gelling properties with increasing pH, whereas the CA system was effective when the pH was lowered. By combining the two MP gelling systems, a stable and pH-insensible emulsion could be produced. Copyright © 2011 Elsevier Ltd. All rights reserved.

Microbial degradation of dissolved proteins in seawater

International Nuclear Information System (INIS)

Hollibaugh, J.T.; Azam, F.

1983-01-01

An experimental protocol using radiolabeled proteins was developed to investigate the rates and mechanisms whereby dissolved proteins are degraded in natural marine plankton communities. The results of field observations and laboratory experiments indicate that proteins are degraded by a particle-bound, thermolabile system, presumably bacteria-associated enzymes, with an apparent half-saturation constant of ca. 25 μg bovine serum albumin (BSA) per liter. Gel permeation chromatography indicated that peptides of chain length intermediate between BSA and the final products of degradation (MW<700) do not accumulate in the medium. Competition experiments indicate that the system is relatively nonspecific. Turnover rates for the protein pool in samples collected in the Southern California Bight were of the same order of magnitude as the turnover rate of the L-leucine pool and were correlated with primary productivity, chlorophyll a concentrations, bacterial abundance and biomass, and L-leucine turnover rate. These data suggest that amino acids derived from proteins are utilized preferentially and do not completely mix with the amino acids in the bulk phase

Chemical composition and microbial load of cheese produced using ...

African Journals Online (AJOL)

Aframomum sceptrum) on the chemical composition and microbial load of cheese was evaluated in a Completely Randomized Design. Cheese produced with 1% bear berry (Aframomum sceptrum) had the highest (P < 0.05) crude protein content ...

Quantifying ruminal nitrogen metabolism using the omasal sampling technique in cattle--a meta-analysis.

Science.gov (United States)

Broderick, G A; Huhtanen, P; Ahvenjärvi, S; Reynal, S M; Shingfield, K J

2010-07-01

Mixed model analysis of data from 32 studies (122 diets) was used to evaluate the precision and accuracy of the omasal sampling technique for quantifying ruminal-N metabolism and to assess the relationships between nonammonia-N flow at the omasal canal and milk protein yield. Data were derived from experiments in cattle fed North American diets (n=36) based on alfalfa silage, corn silage, and corn grain and Northern European diets (n=86) composed of grass silage and barley-based concentrates. In all studies, digesta flow was quantified using a triple-marker approach. Linear regressions were used to predict microbial-N flow to the omasum from intake of dry matter (DM), organic matter (OM), or total digestible nutrients. Efficiency of microbial-N synthesis increased with DM intake and there were trends for increased efficiency with elevated dietary concentrations of crude protein (CP) and rumen-degraded protein (RDP) but these effects were small. Regression of omasal rumen-undegraded protein (RUP) flow on CP intake indicated that an average 32% of dietary CP escaped and 68% was degraded in the rumen. The slope from regression of observed omasal flows of RUP on flows predicted by the National Research Council (2001) model indicated that NRC predicted greater RUP supply. Measured microbial-N flow was, on average, 26% greater than that predicted by the NRC model. Zero ruminal N-balance (omasal CP flow=CP intake) was obtained at dietary CP and RDP concentrations of 147 and 106 g/kg of DM, corresponding to ruminal ammonia-N and milk urea N concentrations of 7.1 and 8.3mg/100mL, respectively. Milk protein yield was positively related to the efficiency of microbial-N synthesis and measured RUP concentration. Improved efficiency of microbial-N synthesis and reduced ruminal CP degradability were positively associated with efficiency of capture of dietary N as milk N. In conclusion, the results of this study indicate that the omasal sampling technique yields valuable estimates

Effect of Carbohydrate Sources and Levels of Cotton Seed Meal in Concentrate on Feed Intake, Nutrient Digestibility, Rumen Fermentation and Microbial Protein Synthesis in Young Dairy Bulls

Directory of Open Access Journals (Sweden)

M. Wanapat

2013-04-01

Full Text Available The objective of this study was to investigate the effect of levels of cottonseed meal with various carbohydrate sources in concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in dairy bulls. Four, 6 months old dairy bulls were randomly assigned to receive four dietary treatments according to a 2×2 factorial arrangement in a 4×4 Latin square design. Factor A was carbohydrate source; cassava chip (CC and cassava chip+rice bran in the ratio of 3:1 (CR3:1, and factor B was cotton seed meal levels in the concentrate; 109 g CP/kg (LCM and 328 g CP/kg (HCM at similar overall CP levels (490 g CP/kg. Bulls received urea-lime treated rice straw ad libitum and were supplemented with 10 g of concentrate/kg BW. It was found that carbohydrate source and level of cotton seed meal did not have significant effects on ruminal pH, ammonia nitrogen concentration, microbial protein synthesis or feed intake. Animals which received CC showed significantly higher BUN concentration, ruminal propionic acid and butyric acid proportions, while dry matter, organic matter digestibility, populations of total viable bacteria and proteolytic bacteria were lower than those in the CR3:1 treatment. The concentration of total volatile fatty acids was higher in HCM than LCM treatments, while the concentration of butyric acid was higher in LCM than HCM treatments. The population of proteolytic bacteria with the LCM treatments was higher than the HCM treatments; however other bacteria groups were similar among the different levels of cotton seed meal. Bulls which received LCM had higher protein digestibility than those receiving HCM. Therefore, using high levels of cassava chip and cotton seed meal might positively impact on energy and nitrogen balance for the microbial population in the rumen of the young dairy bull.

Effect of four local vegetable leaves on the protein and microbial ...

African Journals Online (AJOL)

5 were run. The processed beef samples were microbially and chemically analysed after treatment and during storage. Beef treated with leaves extracts revealed Staphylococcus aureus after 28 days of storage, while 49 days for those treated ...

Changes of microbial spoilage, lipid-protein oxidation and physicochemical properties during post mortem refrigerated storage of goat meat.

Science.gov (United States)

Sabow, Azad Behnan; Sazili, Awis Qurni; Aghwan, Zeiad Amjad; Zulkifli, Idrus; Goh, Yong Meng; Ab Kadir, Mohd Zainal Abidin; Nakyinsige, Khadijah; Kaka, Ubedullah; Adeyemi, Kazeem Dauda

2016-06-01

Examined was the effect of post mortem refrigerated storage on microbial spoilage, lipid-protein oxidation and physicochemical traits of goat meat. Seven Boer bucks were slaughtered, eviscerated and aged for 24 h. The Longissimus lumborum (LL) and Semitendinosus (ST) muscles were excised and subjected to 13 days post mortem refrigerated storage. The pH, lipid and protein oxidation, tenderness, color and drip loss were determined in LL while microbiological analysis was performed on ST. Bacterial counts generally increased with increasing aging time and the limit for fresh meat was reached at day 14 post mortem. Significant differences were observed in malondialdehyde (MDA) content at day 7 of storage. The thiol concentration significantly reduced as aging time increased. The band intensities of myosin heavy chain (MHC) and troponin-T significantly decreased as storage progressed, while actin remained relatively stable. After 14 days of aging, tenderness showed significant improvement while muscle pH and drip loss reduced with increase in storage time. Samples aged for 14 days had higher lightness (P goat meat. © 2016 Japanese Society of Animal Science.

Research of radiation-resistant microbial organisms

Energy Technology Data Exchange (ETDEWEB)

Kim, Dongho; Lim, Sangyong; Joe, Minho; Park, Haejoon; Song, Hyunpa; Im, Seunghun; Kim, Haram; Kim, Whajung; Choi, Jinsu; Park, Jongchun

2012-01-15

Many extremophiles including radiation-resistant bacteria Deinococcus radiodurans have special characteristics such as novel enzymes and physiological active substances different from known biological materials and are being in the spotlight of biotechnology science. In this research, basic technologies for the production of new genetic resources and microbial strains by a series of studies in radiation-resistant microbial organisms were investigated and developed. Mechanisms required for radiation-resistant in Deinococcus radiodurans were partly defined by analyzing the function of dinB, pprI, recG, DRA{sub 0}279, pprM, and two-component signal transduction systems. To apply genetic resource and functional materials from Deinococcus species, omics analysis in response to cadmium, construction of macroscopic biosensor, and characterization of carotenoids and chaperon protein were performed. Additionally, potential use of D. geothermalis in monosaccharide production from non-biodegradable plant materials was evaluated. Novel radiation resistant yeasts and bacteria were isolated and identified from environmental samples to obtain microbial and genomic resources. An optimal radiation mutant breeding method was set up for efficient and rapid isolation of target microbial mutants. Furthermore, an efficient ethanol producing mutant strain with high production yield and productivity was constructed using the breeding method in collaboration with Korea Research Institute of Bioscience and Biotechnology. Three Deinococcal bioindicators for radiation dosage confirmation after radiation sterilization process were developed. These results provide a comprehensive information for novel functional genetic elements, enzymes, and physiological active substances production or application. Eventually, industrial microbial cell factories based on radiation resistant microbial genomes can be developed and the technologies can be diffused to bioindustry continuously by this project.

Research of radiation-resistant microbial organisms

International Nuclear Information System (INIS)

Kim, Dongho; Lim, Sangyong; Joe, Minho; Park, Haejoon; Song, Hyunpa; Im, Seunghun; Kim, Haram; Kim, Whajung; Choi, Jinsu; Park, Jongchun

2012-01-01

Many extremophiles including radiation-resistant bacteria Deinococcus radiodurans have special characteristics such as novel enzymes and physiological active substances different from known biological materials and are being in the spotlight of biotechnology science. In this research, basic technologies for the production of new genetic resources and microbial strains by a series of studies in radiation-resistant microbial organisms were investigated and developed. Mechanisms required for radiation-resistant in Deinococcus radiodurans were partly defined by analyzing the function of dinB, pprI, recG, DRA 0 279, pprM, and two-component signal transduction systems. To apply genetic resource and functional materials from Deinococcus species, omics analysis in response to cadmium, construction of macroscopic biosensor, and characterization of carotenoids and chaperon protein were performed. Additionally, potential use of D. geothermalis in monosaccharide production from non-biodegradable plant materials was evaluated. Novel radiation resistant yeasts and bacteria were isolated and identified from environmental samples to obtain microbial and genomic resources. An optimal radiation mutant breeding method was set up for efficient and rapid isolation of target microbial mutants. Furthermore, an efficient ethanol producing mutant strain with high production yield and productivity was constructed using the breeding method in collaboration with Korea Research Institute of Bioscience and Biotechnology. Three Deinococcal bioindicators for radiation dosage confirmation after radiation sterilization process were developed. These results provide a comprehensive information for novel functional genetic elements, enzymes, and physiological active substances production or application. Eventually, industrial microbial cell factories based on radiation resistant microbial genomes can be developed and the technologies can be diffused to bioindustry continuously by this project

Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia

Energy Technology Data Exchange (ETDEWEB)

Orphan, Victoria Jeanne [California Inst. of Technology (CalTech), Pasadena, CA (United States). Division of Geological and Planetary Sciences

2014-11-26

Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet, our ability to effectively study symbionts in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in the form of new methodologies. Developing strategies that establish links between the identity of microorganisms and their metabolic potential, as well as techniques that can probe metabolic networks on a scale that captures individual molecule exchange and processing, is at the forefront of microbial ecology. Understanding the interactions between microorganisms on this level, at a resolution previously intractable, will lead to our greater understanding of carbon turnover and microbial community resilience to environmental perturbations. In this project, we studied an enigmatic syntrophic association between uncultured methane-oxidizing archaea and sulfate-reducing bacteria. This environmental archaeal-bacterial partnership represents a globally important sink for methane in anoxic environments. The specific goals of this project were organized into 3 major tasks designed to address questions relating to the ecophysiology of these syntrophic organisms under changing environmental conditions (e.g. different electron acceptors and nutrients), primarily through the development of microanalytical imaging methods which enable the visualization of the spatial distribution of the partners within aggregates, consumption and exchange of isotopically labeled substrates, and expression of targeted proteins identified via metaproteomics. The advanced tool set developed here to collect, correlate, and analyze these high resolution image and isotope-based datasets from methane-oxidizing consortia has the potential to be widely applicable for studying and modeling patterns of activity and interactions across a broad range of

Understanding Structural Features of Microbial Lipases–-An Overview

Directory of Open Access Journals (Sweden)

John Geraldine Sandana Mala

2008-01-01

Full Text Available The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ returns only 93 hits (as of September 2007 and, the NCBI database ( http://www.ncbi.nlm.nih.gov reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.

Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein.

Science.gov (United States)

Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

2016-11-08

An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

Science.gov (United States)

Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

2016-11-01

An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

Host-derived, pore-forming toxin-like protein and trefoil factor complex protects the host against microbial infection.

Science.gov (United States)

Xiang, Yang; Yan, Chao; Guo, Xiaolong; Zhou, Kaifeng; Li, Sheng'an; Gao, Qian; Wang, Xuan; Zhao, Feng; Liu, Jie; Lee, Wen-Hui; Zhang, Yun

2014-05-06

Aerolysins are virulence factors belonging to the bacterial β-pore-forming toxin superfamily. Surprisingly, numerous aerolysin-like proteins exist in vertebrates, but their biological functions are unknown. βγ-CAT, a complex of an aerolysin-like protein subunit (two βγ-crystallin domains followed by an aerolysin pore-forming domain) and two trefoil factor subunits, has been identified in frogs (Bombina maxima) skin secretions. Here, we report the rich expression of this protein, in the frog blood and immune-related tissues, and the induction of its presence in peritoneal lavage by bacterial challenge. This phenomena raises the possibility of its involvement in antimicrobial infection. When βγ-CAT was administrated in a peritoneal infection model, it greatly accelerated bacterial clearance and increased the survival rate of both frogs and mice. Meanwhile, accelerated Interleukin-1β release and enhanced local leukocyte recruitments were determined, which may partially explain the robust and effective antimicrobial responses observed. The release of interleukin-1β was potently triggered by βγ-CAT from the frog peritoneal cells and murine macrophages in vitro. βγ-CAT was rapidly endocytosed and translocated to lysosomes, where it formed high molecular mass SDS-stable oligomers (>170 kDa). Lysosomal destabilization and cathepsin B release were detected, which may explain the activation of caspase-1 inflammasome and subsequent interleukin-1β maturation and release. To our knowledge, these results provide the first functional evidence of the ability of a host-derived aerolysin-like protein to counter microbial infection by eliciting rapid and effective host innate immune responses. The findings will also largely help to elucidate the possible involvement and action mechanisms of aerolysin-like proteins and/or trefoil factors widely existing in vertebrates in the host defense against pathogens.

Performance of a pilot-scale continuous flow microbial electrolysis cell fed winery wastewater.

Science.gov (United States)

Cusick, Roland D; Bryan, Bill; Parker, Denny S; Merrill, Matthew D; Mehanna, Maha; Kiely, Patrick D; Liu, Guangli; Logan, Bruce E

2011-03-01

A pilot-scale (1,000 L) continuous flow microbial electrolysis cell was constructed and tested for current generation and COD removal with winery wastewater. The reactor contained 144 electrode pairs in 24 modules. Enrichment of an exoelectrogenic biofilm required ~60 days, which is longer than typically needed for laboratory reactors. Current generation was enhanced by ensuring adequate organic volatile fatty acid content (VFA/SCOD ≥ 0.5) and by raising the wastewater temperature (31 ± 1°C). Once enriched, SCOD removal (62 ± 20%) was consistent at a hydraulic retention time of 1 day (applied voltage of 0.9 V). Current generation reached a maximum of 7.4 A/m(3) by the planned end of the test (after 100 days). Gas production reached a maximum of 0.19 ± 0.04 L/L/day, although most of the product gas was converted to methane (86 ± 6%). In order to increase hydrogen recovery in future tests, better methods will be needed to isolate hydrogen gas produced at the cathode. These results show that inoculation and enrichment procedures are critical to the initial success of larger-scale systems. Acetate amendments, warmer temperatures, and pH control during startup were found to be critical for proper enrichment of exoelectrogenic biofilms and improved reactor performance.

Comparative proteomic analysis in pea treated with microbial consortia of beneficial microbes reveals changes in the protein network to enhance resistance against Sclerotinia sclerotiorum.

Science.gov (United States)

Jain, Akansha; Singh, Akanksha; Singh, Surendra; Singh, Vinay; Singh, Harikesh Bahadur

2015-06-15

Microbial consortia may provide protection against pathogenic ingress via enhancing plant defense responses. Pseudomonas aeruginosa PJHU15, Trichoderma harzianum TNHU27 and Bacillus subtilis BHHU100 were used either singly or in consortia in the pea rhizosphere to observe proteome level changes upon Sclerotinia sclerotiorum challenge. Thirty proteins were found to increase or decrease differentially in 2-DE gels of pea leaves, out of which 25 were identified by MALDI-TOF MS or MS/MS. These proteins were classified into several functional categories including photosynthesis, respiration, phenylpropanoid metabolism, protein synthesis, stress regulation, carbohydrate and nitrogen metabolism and disease/defense-related processes. The respective homologue of each protein identified was trapped in Pisum sativum and a phylogenetic tree was constructed to check the ancestry. The proteomic view of the defense response to S. sclerotiorum in pea, in the presence of beneficial microbes, highlights the enhanced protection that can be provided by these microbes in challenged plants. Copyright © 2015 Elsevier GmbH. All rights reserved.

Microchemostat - microbial continuous culture in a polymer-based, instrumented microbioreactor

DEFF Research Database (Denmark)

Zhang, Z.; Bocazzi, P.; Choi, H. G.

2006-01-01

-based microbioreactor system integrated with optical density (OD), pH, and dissolved oxygen (DO) real-time measurements for continuous cultivation of microbial cells. Escherichia coli (E. coli) cells are continuously cultured in a 150 mL, membrane-aerated, well-mixed microbioreactor fed by a pressure-driven flow......In a chemostat, microbial cells reach a steady state condition at which cell biomass production, substrates and the product concentrations remain constant. These features make continuous culture a unique and powerful tool for biological and physiological research. We present a polymer...

Microbial electrolytic capture, separation and regeneration of CO2 for biogas upgrading

DEFF Research Database (Denmark)

Jin, Xiangdan; Zhang, Yifeng; Li, Xiaohu

2017-01-01

challenges. In this study, an innovative microbial electrolytic system was developed to capture, separate and regenerate CO2 for biogas upgrading without external supply of chemicals, and potentially to treat wastewater. The new system was operated at varied biogas flow rates and external applied voltages....... CO2 was effectively separated from the raw biogas and the CH4 content in the outlet reached as high as 97.0±0.2% at the external voltage of 1.2 V and gas flow rate of 19.6 mL/h. Regeneration of CO2 was also achieved in the regeneration chamber with low pH (1.34±0.04). The relatively low electric...... and potentially expands the application of microbial electrochemical technologies....

Comparison of three 15N methods to correct for microbial contamination when assessing in situ protein degradability of fresh forages.

Science.gov (United States)

Kamoun, M; Ammar, H; Théwis, A; Beckers, Y; France, J; López, S

2014-11-01

The use of stable (15)N as a marker to determine microbial contamination in nylon bag incubation residues to estimate protein degradability was investigated. Three methods using (15)N were compared: (15)N-labeled forage (dilution method, LF), (15)N enrichment of rumen solids-associated bacteria (SAB), and (15)N enrichment of rumen liquid-associated bacteria (LAB). Herbage from forages differing in protein and fiber contents (early-cut Italian ryegrass, late-cut Italian ryegrass, and red clover) were freeze-dried and ground and then incubated in situ in the rumen of 3 steers for 3, 6, 12, 24, and 48 h using the nylon bag technique. The (15)N-labeled forages were obtained by fertilizing the plots where herbage was grown with (15)NH4 (15)NO3. Unlabeled forages (obtained from plots fertilized with NH4NO3) were incubated at the same time that ((15)NH4)2SO4 was continuously infused into the rumen of the steers, and then pellets of labeled SAB and LAB were isolated by differential centrifugation of samples of ruminal contents. The proportion of bacterial N in the incubation residues increased from 0.09 and 0.45 g bacterial N/g total N at 3 h of incubation to 0.37 and 0.85 g bacterial N/g total N at 48 h of incubation for early-cut and late-cut ryegrass, respectively. There were differences (P forage (late-cut ryegrass) was 0.51, whereas the corrected values were 0.85, 0.84, and 0.77 for the LF, SAB, and LAB methods, respectively. With early-cut ryegrass and red clover, the differences between uncorrected and corrected values ranged between 6% and 13%, with small differences among the labeling methods. Generally, methods using labeled forage or labeled SAB and LAB provided similar corrected degradability values. The accuracy in estimating the extent of degradation of protein in the rumen from in situ disappearance curves is improved when values are corrected for microbial contamination of the bag residue.

Salinity-gradient energy driven microbial electrosynthesis of hydrogen peroxide

DEFF Research Database (Denmark)

Li, Xiaohu; Angelidaki, Irini; Zhang, Yifeng

2017-01-01

Hydrogen peroxide (H2O2) as a strong oxidant, is widely used in various chemical industries and environmental remediation processes. In this study, we developed an innovative method for cost-effective production of H2O2 by using a microbial reverse-electrodialysis electrolysis cell (MREC). In the......Hydrogen peroxide (H2O2) as a strong oxidant, is widely used in various chemical industries and environmental remediation processes. In this study, we developed an innovative method for cost-effective production of H2O2 by using a microbial reverse-electrodialysis electrolysis cell (MREC......). In the MREC, electrical potential generated by the exoelectrogens and the salinity-gradient between salt and fresh water were utilized to drive the high-rate H2O2 production. Operational parameters such as air flow rate, pH, cathodic potential, flow rate of salt and fresh water were investigated. The optimal...... H2O2 production was observed at salt and fresh water flow rate of 0.5 mL min−1, air flow rate of 12–20 mL min−1, cathode potential of −0.485 ± 0.025 V (vs Ag/AgCl). The maximum H2O2 accumulated concentration of 778 ± 11 mg L−1 was obtained at corresponding production rate of 11.5 ± 0.5 mg L−1 h−1...

Using water chemistry, isotopes and microbiology to evaluate groundwater sources, flow paths and geochemical reactions in the Death Valley flow system, USA

Energy Technology Data Exchange (ETDEWEB)

Thomas, James M.; Hershey, Ronald L. [Desert Research Institute, 2215 Raggio Pwky, Reno, NV, USA 89512 (United States); Moser, Duane P.; Fisher, Jenny C.; Reihle, Jessica; Wheatley, Alexandra [Desert Research Institute, 755 E. Flamingo Rd, Las Vegas, NV, USA 89130 (United States); Baldino, Cristi; Weissenfluh, Darrick [US Fish and Wildlife Service, Ash Meadows NWR, Amargosa Valley, NV, USA 89020 (United States)

2013-07-01

Springs of Ash Meadows and Furnace Creek (near or in Death Valley, CA) have nearly constant flow, temperature, chemistry, and similar δ{sup 2}H and δ{sup 18}O signatures. These factors indicate shared water sources and/or analogous geochemical reactions along similar flow paths. DNA-based (16S rRNA gene) microbial diversity assessments further illuminate these relationships. Whereas, all Ash Meadows springs share related archaea populations, variations in carbon-14 (Crystal Spring) and strontium isotopes, Na{sup +}, SO{sub 4}{sup 2-}, and methane concentrations (Big Spring), correspond with microbial differences within and between the two discharge areas. Similar geochemical signatures linking Ash Meadows and Furnace Creek springs appear to support a distinct end member at Big Spring in Ash Meadows, which is also supported by coincident enrichment in microbial methanogens and methanotrophs. Conversely, DNA libraries from a deep carbonate well (878 m) located between Ash Meadows and Furnace Creek (BLM-1), indicate no shared microbial diversity between Ash Meadows or Furnace Creek springs. (authors)

Velocity landscape correlation resolves multiple flowing protein populations from fluorescence image time series.

Science.gov (United States)

Pandžić, Elvis; Abu-Arish, Asmahan; Whan, Renee M; Hanrahan, John W; Wiseman, Paul W

2018-02-16

Molecular, vesicular and organellar flows are of fundamental importance for the delivery of nutrients and essential components used in cellular functions such as motility and division. With recent advances in fluorescence/super-resolution microscopy modalities we can resolve the movements of these objects at higher spatio-temporal resolutions and with better sensitivity. Previously, spatio-temporal image correlation spectroscopy has been applied to map molecular flows by correlation analysis of fluorescence fluctuations in image series. However, an underlying assumption of this approach is that the sampled time windows contain one dominant flowing component. Although this was true for most of the cases analyzed earlier, in some situations two or more different flowing populations can be present in the same spatio-temporal window. We introduce an approach, termed velocity landscape correlation (VLC), which detects and extracts multiple flow components present in a sampled image region via an extension of the correlation analysis of fluorescence intensity fluctuations. First we demonstrate theoretically how this approach works, test the performance of the method with a range of computer simulated image series with varying flow dynamics. Finally we apply VLC to study variable fluxing of STIM1 proteins on microtubules connected to the plasma membrane of Cystic Fibrosis Bronchial Epithelial (CFBE) cells. Copyright © 2018 Elsevier Inc. All rights reserved.

Microbial Profiling Of Cyanobacteria From VIT Lake

Directory of Open Access Journals (Sweden)

Swati Singh

2015-08-01

Full Text Available The application of molecular biological methods to study the diversity and ecology of micro-organisms in natural environments has been practice in mid-1980. The aim of our research is to access the diversity composition and functioning of complex microbial community found in VIT Lake. Molecular ecology is a new field in which microbes can be recognized and their function can be understood at the DNA or RNA level which is useful for constructing genetically modified microbes by recombinant DNA technology for reputed use in the environment. In this research first we will isolate cyanobacteria in lab using conventional methods like broth culture and spread plate method then we will analyze their morphology using various staining methods and DNA and protein composition using electrophoresis method. The applications of community profiling approaches will advance our understanding of the functional role of microbial diversity in VIT Lake controls on microbial community composition.

High flow ceramic pot filters

OpenAIRE

van Halem, D.; van der Laan, H.; Soppe, A. I.A.; Heijman, S.G.J.

2017-01-01

Ceramic pot filters are considered safe, robust and appropriate technologies, but there is a general consensus that water revenues are limited due to clogging of the ceramic element. The objective of this study was to investigate the potential of high flow ceramic pot filters to produce more water without sacrificing their microbial removal efficacy. High flow pot filters, produced by increasing the rice husk content, had a higher initial flow rate (6–19 L h−1), but initial LRVs for E. coli o...

Microbial diversity in a full-scale anaerobic reactor treating high ...

African Journals Online (AJOL)

Microbial characteristics in the up-flow anaerobic sludge blanket reactor (UASB) of a full-scale high concentration cassava alcohol wastewater plant capable of anaerobic hydrocarbon removal were analyzed using cultivation-independent molecular methods. Forty-five bacterial operational taxonomic units (OTUs) and 24 ...

Effects of concentrate proportion in the diet with or without Fusarium toxin-contaminated triticale on ruminal fermentation and the structural diversity of rumen microbial communities in vitro.

Science.gov (United States)

Boguhn, Jeannette; Neumann, Dominik; Helm, André; Strobel, Egbert; Tebbe, Christoph C; Dänicke, Sven; Rodehutscorda, Markus

2010-12-01

The objective of this study was to investigate the effects of the concentrate proportion and Fusarium toxin-contaminated triticale (FCT) in the diet on nutrient degradation, microbial protein synthesis and structure of the microbial community, utilising a rumen simulation technique and single-strand conformation polymorphism (SSCP) profiles based on PCR-amplified small subunit ribosomal RNA genes. Four diets containing 60% or 30% concentrates on a dry matter basis with or without FCT were incubated. The fermentation of nutrients and microbial protein synthesis was measured. On the last day of incubation, microbial mass was obtained from the vessel liquid, DNA was extracted and PCR-primers targeting archaea, fibrobacter, clostridia, bifidobacteria, bacillii, fungi, and bacteria were applied to separately study the individual taxonomic groups with SSCP. The concentrate proportion affected the fermentation and the microbial community, but not the efficiency of microbial protein synthesis. Neither the fermentation of organic matter nor the synthesis and composition of microbial protein was affected by FCT. The fermentation of detergent fibre fractions was lower in diets containing FCT compared to diets with uncontaminated triticale. Except for the clostridia group, none of the microbial groups were affected by presence of FCT. In conclusion, our results give no indication that the supplementation of FCT up to a deoxynivalenol concentration in the diet of 5 mg per kg dry matter affects the fermentation of organic matter and microbial protein synthesis. These findings are independent of the concentrate level in the diets. A change in the microbial community composition of the genus Clostridia may be the reason for a reduction in the cellulolytic activity.

Microbial Electrochemistry and its Application to Energy and Environmental Issues

Science.gov (United States)

Hastings, Jason Thomas

Microbial electrochemistry forms the basis of a wide range of topics from microbial fuel cells to fermentation of carbon food sources. The ability to harness microbial electron transfer processes can lead to a greener and cleaner future. This study focuses on microbial electron transfer for liquid fuel production, novel electrode materials, subsurface environments and removal of unwanted byproducts. In the first chapter, exocellular electron transfer through direct contact utilizing passive electrodes for the enhancement of bio-fuel production was tested. Through the application of microbial growth in a 2-cell apparatus on an electrode surface ethanol production was enhanced by 22.7% over traditional fermentation. Ethanol production efficiencies of close to 95% were achieved in a fraction of the time required by traditional fermentation. Also, in this chapter, the effect of exogenous electron shuttles, electrode material selection and resistance was investigated. Power generation was observed using the 2-cell passive electrode system. An encapsulation method, which would also utilize exocellular transfer of electrons through direct contact, was hypothesized for the suspension of viable cells in a conductive polymer substrate. This conductive polymer substrate could have applications in bio-fuel production. Carbon black was added to a polymer solution to test electrospun polymer conductivity and cell viability. Polymer morphology and cell viability were imaged using electron and optical microscopy. Through proper encapsulation, higher fuel production efficiencies would be achievable. Electron transfer through endogenous exocellular protein shuttles was observed in this study. Secretion of a soluble redox active exocellular protein by Clostridium sp. have been shown utilizing a 2-cell apparatus. Cyclic voltammetry and gel electrophoresis were used to show the presence of the protein. The exocellular protein is capable of reducing ferrous iron in a membrane separated

Role of macrophyte and effect of supplementary aeration in up-flow constructed wetland-microbial fuel cell for simultaneous wastewater treatment and energy recovery.

Science.gov (United States)

Oon, Yoong-Ling; Ong, Soon-An; Ho, Li-Ngee; Wong, Yee-Shian; Dahalan, Farrah Aini; Oon, Yoong-Sin; Lehl, Harvinder Kaur; Thung, Wei-Eng; Nordin, Noradiba

2017-01-01

This study investigates the role of plant (Elodea nuttallii) and effect of supplementary aeration on wastewater treatment and bioelectricity generation in an up-flow constructed wetland-microbial fuel cell (UFCW-MFC). Aeration rates were varied from 1900 to 0mL/min and a control reactor was operated without supplementary aeration. 600mL/min was the optimum aeration flow rate to achieve highest energy recovery as the oxygen was sufficient to use as terminal electron acceptor for electrical current generation. The maximum voltage output, power density, normalized energy recovery and Coulombic efficiency were 545.77±25mV, 184.75±7.50mW/m 3 , 204.49W/kg COD, 1.29W/m 3 and 10.28%, respectively. The variation of aeration flow rates influenced the NO 3 - and NH 4 + removal differently as nitrification and denitrification involved conflicting requirement. In terms of wastewater treatment performance, at 60mL/min aeration rate, UFCW-MFC achieved 50 and 81% of NO 3 - and NH 4 + removal, respectively. E. nuttallii enhanced nitrification by 17% and significantly contributed to bioelectricity generation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Imaging Flow Cytometry Analysis to Identify Differences of Survival Motor Neuron Protein Expression in Patients With Spinal Muscular Atrophy.

Science.gov (United States)

Arakawa, Reiko; Arakawa, Masayuki; Kaneko, Kaori; Otsuki, Noriko; Aoki, Ryoko; Saito, Kayoko

2016-08-01

Spinal muscular atrophy is a neurodegenerative disorder caused by the deficient expression of survival motor neuron protein in motor neurons. A major goal of disease-modifying therapy is to increase survival motor neuron expression. Changes in survival motor neuron protein expression can be monitored via peripheral blood cells in patients; therefore we tested the sensitivity and utility of imaging flow cytometry for this purpose. After the immortalization of peripheral blood lymphocytes from a human healthy control subject and two patients with spinal muscular atrophy type 1 with two and three copies of SMN2 gene, respectively, we used imaging flow cytometry analysis to identify significant differences in survival motor neuron expression. A bright detail intensity analysis was used to investigate differences in the cellular localization of survival motor neuron protein. Survival motor neuron expression was significantly decreased in cells derived from patients with spinal muscular atrophy relative to those derived from a healthy control subject. Moreover, survival motor neuron expression correlated with the clinical severity of spinal muscular atrophy according to SMN2 copy number. The cellular accumulation of survival motor neuron protein was also significantly decreased in cells derived from patients with spinal muscular atrophy relative to those derived from a healthy control subject. The benefits of imaging flow cytometry for peripheral blood analysis include its capacities for analyzing heterogeneous cell populations; visualizing cell morphology; and evaluating the accumulation, localization, and expression of a target protein. Imaging flow cytometry analysis should be implemented in future studies to optimize its application as a tool for spinal muscular atrophy clinical trials. Copyright © 2016 Elsevier Inc. All rights reserved.

Differences in microbial communities and performance between suspended and attached growth anaerobic membrane bioreactors treating synthetic municipal wastewater

KAUST Repository

Harb, Moustapha

2015-08-14

Two lab-scale anaerobic membrane bioreactors (AnMBRs), one up-flow attached-growth (UA) and another continuously stirred (CSTR), were operated under mesophilic conditions (35 °C) while treating synthetic municipal wastewater (800 mg L−1 COD). Each reactor was attached to both polyvinylidene fluoride (PVDF) and polyethersulfone (PES) microfiltration (MF) membranes in an external cross-flow configuration. Both reactors were started up and run under the same operating conditions for multiple steady-state experiments. Chemical oxygen demand (COD) removal rates were similar for both reactors (90–96%), but captured methane was found to be 11–18% higher for the CSTR than the UA reactor. Ion Torrent sequencing targeting 16S rRNA genes showed that several operational taxonomic units (OTUs) most closely related to fermentative bacteria (e.g., Microbacter margulisiae) were dominant in the suspended biomass of the CSTR, accounting for 30% of the microbial community. Conversely, methanogenic archaea (e.g., Methanosaeta) and syntrophic bacteria (e.g., Smithella propionica) were found in significantly higher relative abundances in the UA AnMBR as compared to the CSTR due to their affinity for surface attachment. Of the methanogens that were present in the CSTR sludge, hydrogenotrophic methanogens dominated (e.g., Methanobacterium). Measured EPS (both proteins and carbohydrates), which has been broadly linked to fouling, was determined to be consistently lower in the UA AnMBR membrane samples than in CSTR AnMBR membrane samples. Principal component analysis (PCA) based on HPLC profiles of soluble microbial products (SMPs) further demonstrated these differences between reactor types in replicate runs. The results of this study showed that reactor configuration can significantly impact the development of the microbial communities of AnMBRs that are responsible for both membrane and reactor performance.

Assessing marine microbial induced corrosion at Santa Catalina Island, California

Directory of Open Access Journals (Sweden)

Gustavo Antonio Ramírez

2016-10-01

Full Text Available High iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial-induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, California, USA, for periods of two and six months. Substrates consisted of mild steel – a major constituent of maritime infrastructure – and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting high-flux conditions; a stagnant condition; an active flow-through condition with seawater slowly pumped over the substrates; and an enrichment condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the two-month high flux incubations document coating of substrates with twisted stalks, resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria. Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all six month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that i high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of

On-chip determination of C-reactive protein using magnetic particles in continuous flow.

Science.gov (United States)

Phurimsak, Chayakom; Tarn, Mark D; Peyman, Sally A; Greenman, John; Pamme, Nicole

2014-11-04

We demonstrate the application of a multilaminar flow platform, in which functionalized magnetic particles are deflected through alternating laminar flow streams of reagents and washing solutions via an external magnet, for the rapid detection of the inflammatory biomarker, C-reactive protein (CRP). The two-step sandwich immunoassay was accomplished in less than 60 s, a vast improvement on the 80-300 min time frame required for enzyme-linked immunosorbent assays (ELISA) and the 50 min necessary for off-chip magnetic particle-based assays. The combination of continuous flow and a stationary magnet enables a degree of autonomy in the system, while a detection limit of 0.87 μg mL(-1) makes it suitable for the determination of CRP concentrations in clinical diagnostics. Its applicability was further proven by assaying real human serum samples and comparing those results to values obtained using standard ELISA tests.

The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet.

Science.gov (United States)

Mu, Chunlong; Yang, Yuxiang; Luo, Zhen; Guan, Leluo; Zhu, Weiyun

2016-03-01

A high-protein diet (HPD) can produce hazardous compounds and reduce butyrate-producing bacteria in feces, which may be detrimental to gut health. However, information on whether HPD affects intestinal function is limited. The aim of this study was to determine the impact of an HPD on the microbiota, microbial metabolites, and epithelial transcriptome in the colons of rats. Adult male Wistar rats were fed either a normal-protein diet (20% protein, 56% carbohydrate) or an HPD (45% protein, 30% carbohydrate) for 6 wk (n = 10 rats per group, individually fed). After 6 wk, the colonic microbiome, microbial metabolites, and epithelial transcriptome were determined. Compared with the normal-protein diet, the HPD adversely altered the colonic microbiota by increasing (P 0.7, P < 0.05) with genes and metabolites generally regarded as being involved in disease pathogenesis, suggesting these bacteria may mediate the detrimental effects of HPDs on colonic health. Our findings suggest that the HPD altered the colonic microbial community, shifted the metabolic profile, and affected the host response in the colons of rats toward an increased risk of colonic disease. © 2016 American Society for Nutrition.

Large-Scale, Continuous-Flow Production of Stressed Biomass (Desulfovibrio vulgaris Hildenborough)

Energy Technology Data Exchange (ETDEWEB)

Geller, Jil T.; Borglin, Sharon E.; Fortney, Julian L.; Lam, Bonita R.; Hazen, Terry C.; Biggin, Mark D.

2010-05-01

The Protein Complex Analysis Project (PCAP, http://pcap.lbl.gov/), focuses on high-throughput analysis of microbial protein complexes in the anaerobic, sulfate-reducing organism, DesulfovibriovulgarisHildenborough(DvH).Interest in DvHas a model organism for bioremediation of contaminated groundwater sites arises from its ability to reduce heavy metals. D. vulgarishas been isolated from contaminated groundwater of sites in the DOE complex. To understand the effect of environmental changes on the organism, midlog-phase cultures are exposed to nitrate and salt stresses (at the minimum inhibitory concentration, which reduces growth rates by 50percent), and compared to controls of cultures at midlogand stationary phases. Large volumes of culture of consistent quality (up to 100 liters) are needed because of the relatively low cell density of DvHcultures (one order of magnitude lower than E. coli, for example) and PCAP's challenge to characterize low-abundance membrane proteins. Cultures are grown in continuous flow stirred tank reactors (CFSTRs) to produce consistent cell densities. Stressor is added to the outflow from the CFSTR, and the mixture is pumped through a plug flow reactor (PFR), to provide a stress exposure time of 2 hours. Effluent is chilled and held in large carboys until it is centrifuged. A variety of analyses -- including metabolites, total proteins, cell density and phospholipidfatty-acids -- track culture consistency within a production run, and differences due to stress exposure and growth phase for the different conditions used. With our system we are able to produce the requisite 100 L of culture for a given condition within a week.

Growing and Analyzing Biofilms in Flow Chambers

DEFF Research Database (Denmark)

Tolker-Nielsen, Tim; Sternberg, Claus

2011-01-01

This unit describes the setup of flow chamber systems for the study of microbial biofilms, and methods for the analysis of structural biofilm formation. Use of flow chambers allows direct microscopic investigation of biofilm formation. The biofilms in flow chambers develop under hydrodynamic......, and disassembly and cleaning of the system. In addition, embedding and fluorescent in situ hybridization of flow chamber–grown biofilms are addressed. Curr. Protoc. Microbiol. 21:1B.2.1-1B.2.17. © 2011 by John Wiley & Sons, Inc....

A Lateral Flow Protein Microarray for Rapid and Sensitive Antibody Assays

Directory of Open Access Journals (Sweden)

Helene Andersson-Svahn

2011-11-01

Full Text Available Protein microarrays are useful tools for highly multiplexed determination of presence or levels of clinically relevant biomarkers in human tissues and biofluids. However, such tools have thus far been restricted to laboratory environments. Here, we present a novel 384-plexed easy to use lateral flow protein microarray device capable of sensitive (< 30 ng/mL determination of antigen-specific antibodies in ten minutes of total assay time. Results were developed with gold nanobeads and could be recorded by a cell-phone camera or table top scanner. Excellent accuracy with an area under curve (AUC of 98% was achieved in comparison with an established glass microarray assay for 26 antigen-specific antibodies. We propose that the presented framework could find use in convenient and cost-efficient quality control of antibody production, as well as in providing a platform for multiplexed affinity-based assays in low-resource or mobile settings.

Membrane fouling related to microbial community and extracellular polymeric substances at different temperatures.

Science.gov (United States)

Gao, Da-Wen; Wen, Zhi-Dan; Li, Bao; Liang, Hong

2013-09-01

An anoxic-aerobic membrane bioreactor was established to investigate the role of microorganisms and microbial metabolites in membrane fouling at different temperatures. The results showed that the membrane fouling cycle at 303, 293, and 283 K were 30, 29, and 5.5 days, respectively. Polysaccharides dominated the extracellular polymeric substances (EPS) and soluble microbial products (SMP) at 303 and 293 K, instead, proteins was the predominant composition of metabolites at 283 K. The correlation coefficient (r(2)) was calculated to identify the relationship between temperature (T), filtration resistance (R) and compositions of EPS and SMP. In biocake, the EPS polysaccharides (EPSc) was the most correlative factor to temperature (T) and filtration resistance (R); in mixed liquor, the ratio of SMP polysaccharides to proteins (SMPc/p) was the most correlative factor. The microbial community structure and the dominant species was the major reason causing the change of EPS and SMP composition. Copyright © 2013 Elsevier Ltd. All rights reserved.

Vibrational energy flow through the green fluorescent protein-water interface: communication maps and thermal boundary conductance.

Science.gov (United States)

Xu, Yao; Leitner, David M

2014-07-17

We calculate communication maps for green fluorescent protein (GFP) to elucidate energy transfer pathways between the chromophore and other parts of the protein in the ground and excited state. The approach locates energy transport channels from the chromophore to remote regions of the protein via residues and water molecules that hydrogen bond to the chromophore. We calculate the thermal boundary conductance between GFP and water over a wide range of temperature and find that the interface between the protein and the cluster of water molecules in the β-barrel poses negligible resistance to thermal flow, consistent with facile vibrational energy transfer from the chromophore to the β-barrel waters observed in the communication maps.

Compaction agent clarification of microbial lysates

Science.gov (United States)

DeWalt, Brad W.; Murphy, Jason C.; Fox, George E.; Willson, Richard C.

2003-01-01

Recombinant proteins are often purified from microbial lysates containing high concentrations of nucleic acids. Pre-purification steps such as nuclease addition or precipitation with polyethyleneimine or ammonium sulfate are normally required to reduce viscosity and to eliminate competing polyanions before anion exchange chromatography. We report that small polycationic compaction agents such as spermine selectively precipitate nucleic acids during or after Escherichia coli lysis, allowing DNA and RNA to be pelleted with the insoluble cell debris. Analysis by spectrophotometry and protein assay confirmed a significant reduction in the concentration of nucleic acids present, with preservation of protein. Lysate viscosity is greatly reduced, facilitating subsequent processing. We have used 5mM spermine to remove nucleic acids from E. coli lysate in the purification of a hexahistidine-tagged HIV reverse transcriptase.

Mechanistic model for microbial growth on hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Mallee, F M; Blanch, H W

1977-12-01

Based on available information describing the transport and consumption of insoluble alkanes, a mechanistic model is proposed for microbial growth on hydrocarbons. The model describes the atypical growth kinetics observed, and has implications in the design of large scale equipment for single cell protein (SCP) manufacture from hydrocarbons. The model presents a framework for comparison of the previously published experimental kinetic data.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Flow cytometry, fluorescent probes, and flashing bacteria

NARCIS (Netherlands)

Bunthof, C.J.

2002-01-01

Key words: fluorescent probes, flow cytometry, CSLM, viability, survival, microbial physiology, lactic acid bacteria, Lactococcus lactis , Lactobacillus plantarum , cheese, milk,