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Search Results: 1 - 10 of 181273 matches for " William F Martin "
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Early evolution without a tree of life
William F Martin
Biology Direct , 2011, DOI: 10.1186/1745-6150-6-36
Abstract: This article was reviewed by Dan Graur, W. Ford Doolittle, Eugene V. Koonin and Christophe Malaterre.Biology currently lacks a robust and comprehensive description of early evolution. We should aim to fill that void, but in a language that operates with biology and chemistry, not with branching patterns in phylogenetic trees, versions of which based on informational genes are called the tree of life. Genomes attest unequivocally to the abundance of lateral gene transfer in microbial chromosome history, but current thinking on early evolution is still largely couched in the conceptual framework of trees. When it comes to getting a fuller grasp of microbial evolution, trees might be standing in the way more than they are actually helping us at the moment, because i) the overall relatedness of prokaryotic genomes is not properly described by any single tree, and ii) the relationship of eukaryotes to prokaryotes is also not tree-like in nature because the endosymbiotic origins of organelles introduces lineage mergers and genetic amalgamation into the evolutionary process. If we aim to deliver to science and society a complete picture of early evolution, then at some point we have to incorporate the origin of life into the larger picture of things, too, which means linking microbial evolution to the elements on early Earth. Overall those are fairly tall orders, but we have to start somewhere.Getting a better picture of early evolution is important for understanding our place in the larger scheme of things. Yet the further back we look in time, the less we know about the course of life's history. The evolutionary history of organisms visible to the naked eye -- plants and animals -- has a recurrently branching phylogeny that can be more or less accurately represented in the mathematical image of a bifurcating tree. Darwin's mechanisms of natural variation and natural selection were inferred from observations of macroscopic life, and those two mechanisms are still sufficie
Dietary protein intake and renal function
William F Martin, Lawrence E Armstrong, Nancy R Rodriguez
Nutrition & Metabolism , 2005, DOI: 10.1186/1743-7075-2-25
Abstract: Dietary protein intake can modulate renal function [1] and its role in renal disease has spawned an ongoing debate in the literature. At the center of the controversy is the concern that habitual consumption of dietary protein in excess of recommended amounts promotes chronic renal disease through increased glomerular pressure and hyperfiltration [2,3]. Media releases often conclude that, "too much protein stresses the kidney" [4]. The real question, however, is whether research in healthy individuals supports this notion. In fact, studies suggest that hyperfiltration in response to various physiological stimuli is a normal adaptative mechanism [5-10].The purpose of this paper is to review the available evidence regarding the effects of protein intake on renal function with particular emphasis on renal disease. This review will consider research regarding the role of dietary protein in chronic kidney disease, normal renal function and kidney stone formation and evaluate the collective body of literature to ascertain whether habitual consumption of dietary protein in excess of what is recommended warrants a health concern in terms of the initiation and promotion of renal disease. In the following review, high protein (HP) diets will be defined as a daily consumption of greater than or equal to 1.5 g/kg/day, which is almost twice the current Recommended Dietary Allowance but within the range of current Dietary Reference Intakes (DRIs) for protein [11]. The Institute of Medicine DRI report concluded that there was insufficient scientific evidence for recommendations of an upper limit of protein intake but suggested an acceptable macronutrient distribution range of 10–35% of total energy for protein intake [11].While the optimal ratio of macronutrient intake for adults has typically focused on fat and carbohydrate [12], contemporary discussions include the role of dietary protein [13-15]. This is particularly true given the recent popularity of high protein diets in wei
Structural organization and interactions of transmembrane domains in tetraspanin proteins
Oleg V Kovalenko, Douglas G Metcalf, William F DeGrado, Martin E Hemler
BMC Structural Biology , 2005, DOI: 10.1186/1472-6807-5-11
Abstract: Among 28 human tetraspanin proteins, the TM1-3 sequences display a distinct heptad repeat motif (abcdefg)n. In TM1, position a is occupied by structurally conserved bulky residues and position d contains highly conserved Asn and Gly residues. In TM2, position a is occupied by conserved small residues (Gly/Ala/Thr), and position d has a conserved Gly and two bulky aliphatic residues. In TM3, three a positions of the heptad repeat are filled by two leucines and a glutamate/glutamine residue, and two d positions are occupied by either Phe/Tyr or Val/Ile/Leu residues. No heptad motif is apparent in TM4 sequences. Mutations of conserved glycines in human CD9 (Gly25 and Gly32 in TM1; Gly67 and Gly74 in TM2) caused aggregation of mutant proteins inside the cell. Modeling of the TM1-TM2 interface in CD9, using a novel algorithm, predicts tight packing of conserved bulky residues against conserved Gly residues along the two helices. The homodimeric interface of CD9 was mapped, by disulfide cross-linking of single-cysteine mutants, to the vicinity of residues Leu14 and Phe17 in TM1 (positions g and c) and Gly77, Gly80 and Ala81 in TM2 (positions d, g and a, respectively). Mutations of a and d residues in both TM1 and TM2 (Gly25, Gly32, Gly67 and Gly74), involved in intramolecular TM1-TM2 interaction, also strongly diminished intermolecular interaction, as assessed by cross-linking of Cys80.Our results suggest that tetraspanin intra- and intermolecular interactions are mediated by conserved residues in adjacent, but distinct regions of TM1 and TM2. A key structural element that defines TM1-TM2 interaction in tetraspanins is the specific packing of bulky residues against small residues.Tetraspanins constitute a large family of integral membrane proteins, characteristically containing 4, 6 or 8 conserved cysteine residues in the large extracellular loop (including the CCG and PxxCC motifs), which form disulfide bonds, and several conserved polar residues in the intracellular loo
A systematic review of existing national priorities for child health research in sub-Saharan Africa
George H Swingler, James H Irlam, William M Macharia, Félix Tietche, Martin M Meremikwu
Health Research Policy and Systems , 2005, DOI: 10.1186/1478-4505-3-7
Abstract: Collaborators from a purposive sample of 20 WHO-AFRO Region countries, assisted by key informants from a range of governmental, non-governmental, research and funding organisations and universities, identified and located potentially eligible prioritisation documents. Included documents were those published between 1990 and 2002 from national or nationally accredited institutions describing national health research priorities for child health, alone or as part of a broader report in which children were a clearly identifiable group. Laboratory, clinical, public health and policy research were included. Two reviewers independently assessed eligibility for inclusion and extracted data.Eight of 33 potentially eligible reports were included. Five reports focused on limited areas of child health. The remaining three included child-specific categories in reports of general research priorities, with two such child-specific categories limited to reproductive health. In a secondary analysis of Essential National Health Research reports that included children, though not necessarily as an identifiable group, the reporting of priorities varied markedly in format and numbers of priorities listed, despite a standard recommended approach. Comparison and synthesis of reported priorities was not possible.Few systematically developed national research priorities for child health exist in sub-Saharan Africa. Children's interests may be distorted in prioritisation processes that combine all age groups. Future development of priorities requires a common reporting framework and specific consideration of childhood priorities.Africa experiences a huge burden of childhood disease in a context of limited resources for health care and research. Sixty five percent of the burden of disease in sub-Saharan Africa in 1990 was attributable to childhood conditions [1]. In 2001 28 of the 30 countries with the highest under-5 mortality rates were in Africa, and the under-5 mortality rate for sub-Sahar
Insulin sensitivity is normalized in the third generation (F3) offspring of developmentally programmed insulin resistant (F2) rats fed an energy-restricted diet
Daniel C Benyshek, Carol S Johnston, John F Martin, William D Ross
Nutrition & Metabolism , 2008, DOI: 10.1186/1743-7075-5-26
Abstract: Female Sprague Dawley rats (F0) were mated with control males and protein malnourished during pregnancy/lactation. F1 offspring were then weaned to adequate but energy-restricted diets into adulthood. F1 dams were fed energy-restricted diets throughout pregnancy/lactation. F2 offspring were also fed energy-restricted diets post weaning. F2 pregnant dams were maintained as described above. Their F3 offspring were split into two groups; one was maintained on the energy-restricted diet, the other was maintained on an adequate diet consumed ad libitum post weaning.F2 animals fed energy-restricted diets were insulin resistant (p < 0.05), while the insulin sensitivity of their F3 offspring equaled and surpassed that of controls on both the energy-restricted and adequate ad libitum postweaning diets (p < 0.05).Maternal energy-restriction did not consistently program reduced insulin sensitivity in offspring over three consecutive generations. The reasons for this remain unclear. It is possible that the intergenerational transmission of developmentally programmed insulin resistance is determined in part by the relative insulin sensitivity of the mother during pregnancy/lactation.An increasing number of experimental animal studies have demonstrated the intergenerational effects of developmental programming on a variety of phenotypic traits, including birth weight, blood pressure, and glucose metabolism. While the investigation of the multigenerational effects of developmentally programmed traits is widening, very few studies have explored the potential for these traits to be transmitted beyond the second (F2) generation, or with post weaning diets other than adequate-control [1]. A recent study reported that glucose metabolism is altered in the adequately-nourished offspring (F1 through F3 generation) of dams (F0) malnourished during gestation and lactation [2]. Here we extend those findings with a pilot study examining the intergenerational effects of energy-restricted diets
Gender impacts the post-exercise substrate and endocrine response in trained runners
Lisa M Vislocky, P Courtney Gaine, Matthew A Pikosky, William F Martin, Nancy R Rodriguez
Journal of the International Society of Sports Nutrition , 2008, DOI: 10.1186/1550-2783-5-7
Abstract: After consuming a euenergetic diet (1.8 g·kg-1·d-1 protein, 26% fat, 58% carbohydrates, 42.8 ± 1.2 kcal/kg body weight) for 8 days, blood was collected from trained male (n = 6, 21 yrs, 70 kg, 180 cm, 9% body fat, VO2peak 78.0 ± 3.4 mL·kg FFM-1·min-1) and female (n = 6, 23 y, 66 kg, 170 cm, 29% body fat, VO2peak 71.6 ± 4.5 mL·kg FFM-1·min-1) endurance runners at rest and during recovery from a 75 min run at 70% VO2peak. Circulating levels of glucose, lactate, free fatty acids (FFAs), insulin, cortisol, growth hormone (GH), and free insulin-like growth factor I (IGF-I) were measured.During the recovery period, females experienced increases in glucose, lactate and insulin while no changes were noted in men (P < 0.05). Males experienced increases in GH and decreases in IGF-I levels respectively (P < 0.05) while no changes were observed in females. FFA levels increased during recovery from endurance exercise, but changes were not different between genders.These data further document gender differences in substrate and endocrine changes during a prolonged recovery period following endurance exercise. Future studies are needed to evaluate the effect of differing diets and nutritional supplements on these gender-specific post-exercise substrate and endocrine differences.Fat and carbohydrates are the primary fuel sources used by muscle during aerobic exercise [1]. Intramyocellular triglycerides (IMTGs) and plasma free fatty acids (FFAs) are the primary sources of fat while muscle glycogen and blood glucose are the major sources of carbohydrates provided to working muscle. Endogenous protein is not a major fuel source during exercise [2]. While protein oxidation will increase as exercise intensity increases [3] and/or individuals become glycogen depleted [4], its contribution to total energy production remains minimal. In general, the relative contribution of each substrate to energy production is complicated by many factors such as exercise intensity, duration, subject trai
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
Lemay Danielle G,Martin William F,Hinrichs Angie S,Rijnkels Monique
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-253
Abstract: Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST) which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The software is available at http://docpollard.org/software.html
Detection of circular polarization in light scattered from photosynthetic microbes
William B. Sparks,James Hough,Thomas A. Germer,Feng Chen,Shiladitya DasSarma,Priya DasSarma,Frank T. Robb,Nadine Manset,Ludmilla Kolokolova,Neill Reid,F. Duccio Macchetto,William Martin
Physics , 2009, DOI: 10.1073/pnas.0810215106
Abstract: The identification of a universal biosignature that could be sensed remotely is critical to the prospects for success in the search for life elsewhere in the universe. A candidate universal biosignature is homochirality, which is likely to be a generic property of all biochemical life. Due to the optical activity of chiral molecules, it has been hypothesized that this unique characteristic may provide a suitable remote sensing probe using circular polarization spectroscopy. Here, we report the detection of circular polarization in light scattered by photosynthetic microbes. We show that the circular polarization appears to arise from circular dichroism of the strong electronic transitions of photosynthetic absorption bands. We conclude that circular polarization spectroscopy could provide a powerful remote sensing technique for generic life searches.
Thermoelectric power factor of a 70 nm Ni-nanowire in a magnetic field
Rüdiger Mitdank,Martin Handwerg,Corinna Steinweg,William T?llner,Mihaela Daub,Kornelius Nielsch,Saskia F. Fischer
Physics , 2011,
Abstract: Thermoelectric (TE) properties of a single nanowire (NW) are investigated in a microlab which allows the determination of the Seebeck coefficient S and the conductivity {\sigma}. A significiant influence of the magnetization of a 70 nm ferromagnetic Ni-NW on its power factor S^{2}{\sigma} is observed. We detected a strong magneto thermopower effect (MTP) of about 10% and an anisotropic magneto resistance (AMR) as a function of an external magnetic field B in the order of 1%. At T = 295 K and B = 0 T we determined the absolute value of S = - (19 \pm 2) {\mu}V/K. At zero field the figure of merit ZT \approx 0.02 was calculated using the Wiedemann-Franz-law for the thermal conductivity. The thermopower S increases considerably as a function of B up to 10% at B = 0.5 T, and with a magneto thermopower of \partialS/\partialB \approx - (3.8 \pm 0,5) {\mu}V/(K.T). The AMR and MTP are related by \partials/\partialr \approx -11 \pm 1 (\partials = \partialS/S). The TE efficiency increases in a transversal magnetic field (B =0.5T) due to an enhanced power factor by nearly 20%.
Evaluation of Best Management Practices in Millsboro Pond Watershed Using Soil and Water Assessment Tool (SWAT) Model  [PDF]
Aditya Sood, William F. Ritter
Journal of Water Resource and Protection (JWARP) , 2010, DOI: 10.4236/jwarp.2010.25047
Abstract: The Inland Bays in southern Delaware (USA) are facing eutrophication due to the nutrient loading from its watershed. The source of nutrients in the watershed is predominantly agriculture. The Millsboro Pond, a sub-watershed within the Inland Bays basin, was modeled using the Soil and Water Assessment Tool (SWAT) model. It was found that the contribution of ground water from outside the watershed had a signifi-cant impact on the hydrology of the region. Once the model was calibrated and validated, five management scenarios were implemented, one at a time, to measure its effectiveness in reducing the nutrient loading in the watershed. Among the Best Management Practices (BMPs), planting winter cover crops on the agricul-ture land was the most effective method in reducing the nutrient loads. The second most effective method was to provide grassland riparian zones. The BMPs alone were not able to achieve the nutrient load reduc-tion as required by the Total Maximum Daily Loads (TMDLs). Two extra scenarios that involved in replac-ing agriculture land with forest, first with deciduous trees and then with high yielding trees were considered. It is suggested that to achieve the required TMDL for the watershed, some parts of the agricultural land may have to be effectively converted into the managed forest with some high yielding trees such as hybrid poplar trees providing cellulose raw material for bio fuels. The remaining agriculture land should take up the prac-tice of planting winter cover crops and better nutrient management. Riparian zones, either in form of forest or grasslands, should be the final line of defense for reducing nutrient loading in the watershed.
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