scholarly journals Improving access to endogenous DNA in ancient bones and teeth

2015 ◽  
Author(s):  
Peter de Barros Damgaard ◽  
Ashot Margaryan ◽  
Hannes Schroeder ◽  
Ludovic Orlando ◽  
Eske Willerslev ◽  
...  
Keyword(s):  
Standard Procedure ◽  
Genomic Research ◽  
Limiting Factor ◽  
Digestion Time ◽  
Bone Material ◽  
Tropical Environments ◽  
Molecular Complexity ◽  
A Minor ◽  
Methodological Guidelines ◽  
Digestion Step

Poor DNA preservation is the most limiting factor in ancient genomic research. In the vast majority of ancient bones and teeth, endogenous DNA molecules only represent a minor fraction of the whole DNA extract, rendering traditional shot-gun sequencing approaches cost-ineffective for whole-genome characterization. Based on ancient human bone samples from temperate and tropical environments, we show that an initial EDTA-based enzymatic 'pre-digestion' of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we identify the optimal pre-digestion time and document an average increase of 2.7 times in the endogenous DNA fraction after 1 hour of pre-digestion. With longer pre-digestion times, the increase is asymptotic while molecular complexity decreases. We repeated the experiment with n=21 and t=15-30', and document a significant increase in endogenous DNA content (one-sided paired t-test: p=0.009). We advocate the implementation of a short pre-digestion step as a standard procedure in ancient DNA extractions from bone material. Finally, we demonstrate on 14 ancient teeth that crushed cementum of the roots contains up to 14 times more endogenous DNA than the dentine. Our presented methodological guidelines considerably advance the ability to characterize ancient genomes.

Ingestion and elemental budgets for Linuche unguiculata, a scyphomedusa with zooxanthellae

2005 ◽  
Vol 85 (3) ◽  
pp. 613-625 ◽  
Author(s):  
Patricia Kremer
Keyword(s):  
Egg Production ◽  
Tissue Growth ◽  
Gut Contents ◽  
Digestion Time ◽  
Dissolved Nutrients ◽  
Nitrogen And Phosphorus ◽  
Prey Concentration ◽  
Laboratory Results ◽  
Experimental Feeding ◽  
A Minor

Specific rations for the zooxanthellae-bearing medusa, Linuche unguiculata, were calculated using two approaches: (a) gut contents of field collected medusae combined with experimental measurements of digestion time; and (b) experimental feeding studies combined with estimates of ambient prey biomass. Estimates of specific daily ration from gut contents averaged 5% for carbon, 6% for nitrogen, and 4% for phosphorus for the dominant size of medusae. Of the 868 medusae examined, 86% contained recognizable prey with an average of 3.6 items per medusa. Copepods dominated the gut contents (51%) as well as the ambient zooplankton prey (82%), but there was an over-representation of shelled prey, larval molluscs and foraminifera, in the gut (33%) compared with their availability (4%). Digestion times for crustaceans ranged from 1—4 h with longer times for larger prey. Ambient prey concentrations in areas of abundant L. unguiculata ranged from 0.2—4.0 prey l-1, with an average of 1.7 and no measurable day—night differences. There were also no measurable day—night differences in ingestion rates for field or laboratory fed medusae. Feeding studies showed a linear relationship between ingestion and prey concentration up to 400 prey l-1. Rations determined from experimental feeding studies were higher but less than double the ration estimates based on field gut contents. Specific ration decreased with increased medusa size in both field and laboratory results. Heterotrophy was calculated to be a major source of both nitrogen and phosphorus, but only a minor source of carbon. Elemental budgets for carbon, nitrogen and phosphorus were calculated using measured inputs of photosynthesis, ingestion, and dissolved nutrients and measured outputs of respiration, excretion, reproduction and tissue growth. Total measured outputs balanced the inputs, within the uncertainty associated with egg production.

Enhanced biogas recovery by applying post-digestion in large-scale centralized biogas plants

2006 ◽  
Vol 54 (2) ◽  
pp. 237-244 ◽  
Author(s):  
I. Angelidaki ◽  
A. Heinfelt ◽  
L. Ellegaard
Keyword(s):  
Particulate Matter ◽  
Large Scale ◽  
Biogas Production ◽  
Stable Process ◽  
Particulate Material ◽  
Limiting Factor ◽  
Biogas Plants ◽  
Temperature Levels ◽  
Rate Limiting ◽  
Digestion Step

The main objective of this study was to investigate the degradation efficiency of centralized biogas plants and provide guidance for the design of more efficient digester and post-digestion systems. These centralized biogas plants in Denmark digest manure together with organic waste from the food industry to generate biogas, which is used for electricity and thermal energy. A total of 20 such plants are currently active in Denmark, most of which were included in the investigation. From the plants, samples were obtained from various steps of the process. Samples were analysed and the residual biogas potential determined by batch post-digestion at various temperature levels. Results were correlated with plant characteristics and production statistics in order to judge the efficiency of various digestion concepts. A simplified model based on a two-step biogas production process was developed and experimental data were used to determine kinetic constants. Experimental results and analysis combined with model simulations showed that the residual biogas potential in the main digestion step effluent is originating mainly from undegraded particulate matter in the biomass. For thermophilic plants 93% of the residual biogas potential was originating from particulate matter and 88% for the mesophilic biogas plants. This indicates that the residual biogas potential is mainly due to insufficient retention time in the main digestion step for hydrolysis of particulate material and that the hydrolysis step is the methane yield limiting factor, while conversion of soluble material such as VFA is the rate limiting factor critical for achieving a stable process.

scholarly journals Oral administration of deuterium-labelled polyamines to sucking rat pups: luminal uptake, metabolic fate and effects on gastrointestinal maturation

1997 ◽  
Vol 78 (4) ◽  
pp. 639-654 ◽  
Author(s):  
Bernard Dorhout ◽  
Anet Van Faassen ◽  
Christien M. Van Beusekom ◽  
Anneke W. Kingma ◽  
Elly De Hoog ◽  
...  
Keyword(s):  
Diamine Oxidase ◽  
Physiological Saline ◽  
Organ Distribution ◽  
Limiting Factor ◽  
Mass Fragmentography ◽  
Metabolic Fate ◽  
Rat Pups ◽  
Stimulation Of Erythropoiesis ◽  
A Minor ◽  
Gut Maturation

Non-physiological amounts of oral polyamines have been reported to induce precocious gut maturation in rat pups. The aim of the present study was to investigate organ distribution and metabolic fate of orally administered stable-isotopically labelled polyamines in rat pups. Pups received tetradeuterium-labelled putrescine (Pu-d4; 3 μmol), spermidine (Sd-d4; 5 μmol), spermine (Sp-d4; 3 μmol), or physiological saline twice daily on postnatal days 7–10 or 12–15. They were killed on days 10 and 15. We determined activities of ileal lactase (EC3.2.1.23), maltase (EC3.2.1.20), sucrase (EC3.2.1.48) and diamine oxidase (EC1.4.3.6) and established villus and crypt lengths. Polyamines and their labelling percentages in organs were determined by GC and mass fragmentography. Treatments did not affect growth rate, but caused lower weights of liver, kidneys and heart. Maltase activity increased, lactase decreased, whereas sucrase and diamine oxidase did not change. Villus and crypt lengths increased. Organ polyamine pools were labelled to different extents. Irrespective of the orally administered polyamine, all organs contained Pu-d4, Sd-d4 and Sp-d4. Administered Pu-d4 and Sd-d4 were recovered mainly as Sd-d4, whereas Sp-d4 was recovered as Sp-d4 and Sd-d4. Total polyamines in a caecum, colon and erythrocytes increased, but increases were only to a minor extent with regard to labelled polyamines. Our data confirm precocious gut maturation by exogenous polyamines. Putrescine appears to be the limiting factor. The exogenous polyamines were distributed among all investigated organs. They are not only used for the synthesis of higher polyamines, but also retroconverted to their precursors. Changes in erythrocyte polyamine contents suggest precocious stimulation of erythropoiesis.

scholarly journals 341 Overcoming Seed Dormancy in Winecups, Callirhoe involucrata

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 450F-451
Author(s):  
Dianne Oakley ◽  
Julie Laufmann ◽  
James Klett ◽  
Harrison Hughes
Keyword(s):  
Hydrogen Peroxide ◽  
Gibberellic Acid ◽  
Seed Dormancy ◽  
Seed Coat ◽  
Practical Method ◽  
Boiling Water ◽  
Limiting Factor ◽  
Water Leaching ◽  
Hard Seed ◽  
A Minor

Propagation of Winecups [Callirhoe involucrata (Torrey & A. Gray)] for use as a landscape ornamental has been impeded by a lack of understanding of the seed dormancy and a practical method for overcoming it. As with many members of the Malvaceae family, C. involucrata produces hard seed. In the populations tested, it accounted for 90% of an average sample. Impermeability, however, is not the only limiting factor to germination. Three disparate populations of seed, representing two different collection years have been investigated using moist pre-chilling, boiling water, leaching, gibberellic acid, hydrogen peroxide and mechanical and chemical scarification methods. Scarifying in concentrated sulfuric acid stimulates germination of some seed fractions and causes embryonic damage in others, suggesting variation in seed coat thickness. Similar results were obtained using a pressurized air-scarifier; the hard seed coat of some seed fractions were precisely scarified while others were physically damaged using the same psi/time treatment. Placing seed in boiling water increases germination from 4%, 7%, and 18 % to 23%, 25%, and 77% in the three populations, respectively. Leaching for 24/48 h in cold (18 °C) aerated water or for 24 h in warm (40 °C) aerated water showed only a minor increase over the control. Pre-chilling at 5 °C for 30, 60, and 90 days showed no improvement over the control. Gibberellic acid-soaked blotters improved germination at 400 ppm to 20%, 10%, and 41%; at 500 ppm germination was reduced. Soaking seed for 24 h in a 3% concentration of hydrogen peroxide did not effect germination; at a 30% concentration germination was reduced. The considerable variation in seed dormancy expression may be a function of differences in environmental factors during development or seed age.

The Influence of Nutrient Availability on the Ecosystem Behaviour of a Salt Water Lake

1984 ◽  
Vol 16 (1-2) ◽  
pp. 121-130 ◽  
Author(s):  
I de Vries ◽  
M F Veul
Keyword(s):  
Primary Production ◽  
Salt Lake ◽  
Salt Water ◽  
Point Of View ◽  
Limiting Factor ◽  
Dynamic Calculation ◽  
Nitrogen And Phosphorus ◽  
A Minor ◽  
Minor Extent ◽  
Lake Grevelingen

The influence of the availability of silicon, nitrogen and phosphorus on the behaviour of the ecosystem in the salt Lake Grevelingen is evaluated. Quantification of the nutrientcycling is essentially based on a dynamic calculation of detritus formation resulting from mortality of phytoplankton and microphytobenthos, including mineralization as function of temperature and substrate concentration. Also changes of the dissolved inorganic nutrientpools resulting from primary production, mineralization and net loading are dynamically ca1culated. Silicon and nitrogen are reversibly fixed in bottomdetritus during the summer halfyear, which implies that primary production depends on the balance between accumulation of detritus in the bottom and mineralization. In contrast the dynamics of phosphorus depend only to a minor extent on primary production and net loading. The net yearly load of nitrogen equals the amount of nitrogen present in the waterphase during the winterperiod. However winter concentrations do not increase and nitrogen remains a limiting factor for primary production. 3-4 g N/m2/year is apparently removed from the lake by denitrification. The environmental factors enabling denitrification are important for consolidation of the ecosystem behaviour. From a management point of view stratification which inhibits denitrification, should be avoided.

scholarly journals Predicting the Cost and Pace of Pharmacogenomic Advances: An Evidence-Based Study

2013 ◽  
Vol 59 (4) ◽  
pp. 649-657 ◽  
Author(s):  
Ramy Arnaout ◽  
Thomas P Buck ◽  
Paulvalery Roulette ◽  
Vikas P Sukhatme
Keyword(s):  
Monte Carlo Model ◽  
Adverse Outcomes ◽  
Data Driven ◽  
Genomic Research ◽  
Limiting Factor ◽  
Single Digit ◽  
Genomic Variants ◽  
Prescription Drug Use ◽  
Priming Phase ◽  
The Cost

BACKGROUND Adverse outcomes associated with prescription drug use are common and costly. Many adverse outcomes can be avoided through pharmacogenomics: choosing and dosing of existing drugs according to a person's genomic variants. Finding and validating associations between outcomes and genomic variants and developing guidelines for avoiding drug-related adverse outcomes will require further research; however, no data-driven estimates yet exist for the time or money required for completing this research. METHODS We identified examples of associations between adverse outcomes and genomic variants. We used these examples to estimate the time and money required to identify and confirm other associations, including the cost of failures, and to develop and validate pharmacogenomic dosing guidelines for them. We built a Monte Carlo model to estimate the time and financial costs required to cut the overall rate of drug-related adverse outcomes by meaningful amounts. We analyzed the model's predictions for a broad range of assumptions. RESULTS AND CONCLUSIONS Our model projected that the development of guidelines capable of cutting overall drug-related adverse outcomes by 25%–50% with current approaches will require investment of single-digit billions of dollars and take 20 years. The model forecasts a pump-priming phase of 5–7 years, which would require expenditures of hundreds of millions of dollars, with little apparent return on investment. The single most important parameter was the extent to which genomic variants cause adverse outcomes. The size of the labor force was not a limiting factor. A “50 000 Pharmacogenomes Project” could speed progress. Our approach provides a template for other areas of genomic research.

scholarly journals Certain contentious issues related to the suspended sentence

Crimen ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 235-254
Author(s):  
Veljko Delibašić ◽  
Tijana Kostić
Keyword(s):  
Criminal Code ◽  
General Purpose ◽  
Public Prosecutor ◽  
Limiting Factor ◽  
Criminal Sanction ◽  
The Public ◽  
Criminal Sanctions ◽  
Material Conditions ◽  
Adherence Monitoring ◽  
A Minor

This paper addresses the issue of suspended sentence since it is a criminal sanction frequently applied in Serbia and statutory provisions regulating suspended sentence are also subject to frequent modification which altogether emphasizes the need of its continuous study. Within the general purpose of criminal sanctions, the purpose of a suspended sentence is to avoid imposing the sentence on an offender for a minor offence in cases when it can be reasonably expected that a warning with a threatened sentence shall suffice to prevent the offender from perpetrating other crimes. Suspended sentence can be granted only when the offender has been sentenced to less than two years imprisonment, however, on condition (which was tightened in 2019) that the crime does not fall within the category of criminal offences for which an eight-year prison sentence (before it was 10 years) or longer can be delivered. Subjective reasons due to which suspended sentence cannot be granted have been also extended, so therefore, suspended sentence can be granted only if more than five years have elapsed from the time the judgment became final by which the offender was sentenced either to imprisonment or was pronounced a suspended sentence for a crime with premeditated intent. In view of the fact that a fine is still a form of punishment and, accordingly, a stricter criminal sanction than suspended sentence which is a non-custodial measure meaning a more lenient sanction, it would be quite acceptable if the legislator, as a limiting factor, also envisaged a fine for a crime with premediated intent. As regards a five year term calculated from the finality of judgment, a better solution would be that the period be calculated from the day of the sentence being served, prescribed or the day a pardon has been granted, i.e. from the day when the adherence monitoring period to probation conditions has expired. Furthermore, recently introduced statutory solutions would result in decrease in the number of suspended sentences in criminal sanctions structure. When it comes to suspended sentence supervision order, as it is rarely applied, it is necessary that minimum effort be invested in providing material conditions and human resources for carrying out this sanction which was found to be effective in many countries. A serious omission of legislators is that the Criminal Procedure Code, when defining the institution of hearing for pronouncing a criminal sanction, leaves an option to the public prosecutor to propose passing of a suspended sentence with determining fine, which is contrary to the Criminal Code. This omission should be corrected by giving priority to the Criminal Code i.e. by excluding the option for the public prosecutor to propose such a sanction.

Machine learning approach to gene essentiality prediction: a review

2021 ◽  
Author(s):  
Olufemi Aromolaran ◽  
Damilare Aromolaran ◽  
Itunuoluwa Isewon ◽  
Jelili Oyelade
Keyword(s):  
Machine Learning ◽  
Gene Ontology ◽  
Prediction Models ◽  
Essential Gene ◽  
Standard Procedure ◽  
Essential Genes ◽  
Limiting Factor ◽  
Learning Approach ◽  
Gene Essentiality ◽  
Machine Learning Approach

Abstract   Essential genes are critical for the growth and survival of any organism. The machine learning approach complements the experimental methods to minimize the resources required for essentiality assays. Previous studies revealed the need to discover relevant features that significantly classify essential genes, improve on the generalizability of prediction models across organisms, and construct a robust gold standard as the class label for the train data to enhance prediction. Findings also show that a significant limitation of the machine learning approach is predicting conditionally essential genes. The essentiality status of a gene can change due to a specific condition of the organism. This review examines various methods applied to essential gene prediction task, their strengths, limitations and the factors responsible for effective computational prediction of essential genes. We discussed categories of features and how they contribute to the classification performance of essentiality prediction models. Five categories of features, namely, gene sequence, protein sequence, network topology, homology and gene ontology-based features, were generated for Caenorhabditis elegans to perform a comparative analysis of their essentiality prediction capacity. Gene ontology-based feature category outperformed other categories of features majorly due to its high correlation with the genes’ biological functions. However, the topology feature category provided the highest discriminatory power making it more suitable for essentiality prediction. The major limiting factor of machine learning to predict essential genes conditionality is the unavailability of labeled data for interest conditions that can train a classifier. Therefore, cooperative machine learning could further exploit models that can perform well in conditional essentiality predictions. Short abstract Identification of essential genes is imperative because it provides an understanding of the core structure and function, accelerating drug targets’ discovery, among other functions. Recent studies have applied machine learning to complement the experimental identification of essential genes. However, several factors are limiting the performance of machine learning approaches. This review aims to present the standard procedure and resources available for predicting essential genes in organisms, and also highlight the factors responsible for the current limitation in using machine learning for conditional gene essentiality prediction. The choice of features and ML technique was identified as an important factor to predict essential genes effectively.

scholarly journals Diversity of Rhizobia and Importance of Their Interactions with Legume Trees for Feasibility and Sustainability of the Tropical Agrosystems

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 206 ◽  
Author(s):  
Emanoel G. Moura ◽  
Cristina S. Carvalho ◽  
Cassia P. C. Bucher ◽  
Juliana L. B. Souza ◽  
Alana C. F. Aguiar ◽  
...  
Keyword(s):  
Acacia Mangium ◽  
Gliricidia Sepium ◽  
Common Species ◽  
Humid Tropics ◽  
Limiting Factor ◽  
Tropical Environments ◽  
Legume Trees ◽  
Sustainable Agricultural Systems ◽  
Biological Nitrogen ◽  
N Use

Symbiotic biological nitrogen fixation (BNF) is a complex process that involves rhizobia, a diverse group of α and β-proteobacteria bacteria, and legume species. Benefits provided by BNF associated with legume trees in tropical environments include improvements to efficiency of nitrogen (N) use, increase of soil carbon sequestration, stabilization of soil organic matter, decrease of soil penetration resistance, and improvement of soil fertility. All these benefits make BNF a crucial ecosystem service to the sustainability of tropical agriculture. Due to the importance of this ecological process and the high diversity of rhizobia, these bacteria have been extensively characterized worldwide. Currently, over 400 species of rhizobia are known, distributed into seven families. In the humid tropics, Leucaena leucocephala, Acacia mangium, Gliricidia sepium, and Clitoria fairchildiana are four of the most common species used by family farmers to create sustainable agricultural systems. These four legumes perform symbiosis with different groups of rhizobia. Exploring BNF could help to enable sustainable intensification of agriculture in the humid tropics, mainly because it can increase N use efficiency in an environment where N is a limiting factor to plant growth.

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