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16S rRNA based identification of _Aeromonas sp. kumar_ by constructing phylogenetic tree and identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar Nature Precedings
P. Kumar; C. M. Ramakritinan; A. K. Kumaraguru.
A bacterial strain, designated _Aeromonas sp. kumar_, was isolated from a water sample collected from Red tide Bloom occurred in the region of Gulf of Mannar region, Puthumadam Coast, India and the strain was identified using 16S rRNA based identification. During the sample collection, microbiology analysis was done to study the morphology of the bacteria. Pure culture of strain was maintained through out the study. DNA was isolated and sequenced using 16S rRNA primers. A length of 1452 nucleotide was sequenced and was put in public data base for obtaining accession number. The sequence was studied using MEGA 4, to estimate the evolutionary distances and to construct the Phylogenetic tree. Along with that Regulatory elements and Transcription factors were...
Tipo: Manuscript Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3898/version/1
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17 years of integrated research, monitoring, and management of HWA and hemlock ecosystems at Delaware Water Gap National Recreation Area Nature Precedings
Richard Evans.
Delaware Water Gap National Recreation Area (“the park”) covers 28,000 ha along the Delaware River in Pennsylvania and New Jersey. Eastern hemlock forests cover 2,200 ha (8%) of the park, and are often associated with trout streams and scenic waterfalls. Activities like trout fishing, bird watching, and hiking are concentrated in hemlock forests, and many of these areas are officially designated as “Outstanding Natural Features” having “high intrinsic or unique values.” In 1989 hemlock woolly adelgid (HWA) was detected in the park, and since 1993 the park has conducted a program to address the threats that hemlock woolly adelgid and hemlock decline poses to park resources. This program...
Tipo: Presentation Palavras-chave: Ecology.
Ano: 2011 URL: http://precedings.nature.com/documents/5520/version/1
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3D model of lamprey estrogen receptor with estradiol and 15[alpha]-hydroxy-estradiol Nature Precedings
Michael E. Baker; David J. Chang; Charlie Chandsawangbhuwana.
Lamprey, a basal vertebrate, contains orthologs of the estrogen receptor (ER), progesterone receptor and corticoid receptor. A perplexing property of lamprey is that 15[alpha]-hydroxy-steroids are active steroids. For example, 15[alpha]-hydroxy-estradiol [15[alpha]-OH-E2] is the estrogen, instead of estradiol (E2). To investigate how 15[alpha]-OH-E2 binds lamprey ER, we constructed a 3D model of the lamprey ER with E2 and 15[alpha]-OH-E2. Our 3D model shows that S[delta] on Met-409 can form a hydrogen bond with the 15[alpha]-hydroxyl on 15[alpha]-OH-E2. In human ER[alpha], the corresponding residue Ile-424 has a van der Waals contact with 15[alpha]-OH-E2. BLAST analysis of GenBank indicates that among vertebrate ERs, only lamprey ER contains a...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2768/version/1
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A bestiary of non-linear functions for growth analysis Nature Precedings
C. E. Timothy Paine; Toby Marthews; Deborah Vogt; Drew Purves; Mark Rees; Andy Hector; Lindsay Turnbull.
Plant growth is an essential ecological process, integrating across scales from physiology to community dynamics. Predicting the growth of plants is essential to understand a wide range of ecological issues, including competition, plant-herbivore interactions and ecosystem functioning.
A challenge in modeling plant growth is that growth rates almost universally decrease with increasing size, for a variety of reasons. Traditional analyses of growth are hampered by the need to remain within the structures of linear models, which handle this slowing poorly. We demonstrate the implementation of a variety of non-linear models that are more appropriate for modeling plant growth than are the traditional, linear,...
Tipo: Presentation Palavras-chave: Ecology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5257/version/1
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A biosystematic basis for pelagic biodiversity Naturalis
Spoel, S. van der.
Biodiversity can be considered to be a human appreciation of the biological entity diversity. Diversity can be expressed numerically on the basis of taxa found, but it can also be expressed as the contribution of a specimen to the diversity, for which a formula is proposed. Diversity is the sum of the taxonomic or numerical diversity, and the ecological, genetical, historical, and phylogenetic diversity. Moreover, each group, or larger taxon, has its own characteristic diversity. These types of diversity are considered separately. One formula is tentatively proposed to calculate the overall diversity. Diversity in nature is variable, which is demonstrated in a diagram for comparison with societyinduced diversity changes. Diversity in the pelagic fluctuates...
Tipo: Article / Letter to the editor Palavras-chave: Biodiversity; Diversity calculation; Ecology; Pelagic; Phylogeny.
Ano: 1994 URL: http://www.repository.naturalis.nl/record/504018
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A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers Nature Precedings
Fucheng Zhang; Zhonghe Zhou; Xing Xu; Xiaolin Wang; Corwin Sullivan.
Recent coelurosaurian discoveries have greatly enriched our knowledge of the dinosaur-bird transition, but all reported taxa close to this transition are from relatively well-known coelurosaurian groups^1-3^. Here we report a new basal avialan, Epidexipteryx hui gen. et sp. nov., from the Middle-Late Jurassic of Inner Mongolia, China. This new species is characterized by an unexpected combination of characters seen in several different theropod groups, particularly the Oviraptorosauria. Phylogenetic analysis shows it to be the sister taxon to Epidendrosaurus^4,5^, forming a new clade at the base of Avialae^6^. Epidexipteryx also possesses two pairs of elongate ribbon-like tail feathers (ETFs), and its limbs lack contour feathers for flight. This finding...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2326/version/1
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A black, non-troglomorphic amphibian from the karst of Slovenia: Proteus anguinus parkelj n. ssp. (Urodela: Proteidae) Naturalis
Sket, B.; Arntzen, J.W..
A morphologically distinct cavernicolous salamander Proteus anguinus from southeastern Slovenia (Bela Krajina) is described as P. a. parkelj ssp. n. It differs from P. a. anguinus in a dark pigmentation, fully developed eyes, a skull with broader and shorter bones and fewer teeth, a voluminous jaw musculature that gives the head a bulky appearance, a proportionally longer trunk with a higher number of vertebrae, shorter extremities, and a shorter tail. Most of these traits are considered to be plesiomorphic character states. An allozyme analysis over 40 loci has shown the new dark pigmented taxon to be genetically similar to a white and troglomorphic neighbouring population from Stična (DNei = 0.23). Both populations in turn are genetically dissimilar to a...
Tipo: Article / Letter to the editor Palavras-chave: Urodela; Proteus; Taxonomy; Morphology; Allozyme analysis; Ecology; Distribution.
Ano: 1994 URL: http://www.repository.naturalis.nl/record/503865
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A decline in pollinator dependent vegetable crop productivity in India indicates pollination limitation and consequent agro-economic crises. Nature Precedings
Parthiba Basu; Ritam Bhattacharya; Pietro Ianetta.
Approximately 70% of the tropical crop species depend on pollinators for optimum yields (Roubik, 1995, Klein 2007). The economic value of such pollinated crops to India is $726 million and India is the world's second largest vegetable producer (Sidhu, 2005). This status has been underpinned by large-scale changes in land-use and pesticide dependency (Fazal, 2000; Shaw & Satish, 2007). A method (c.f. Aizen et al. 2008) that partitions crops into categories depending on their relative pollinator dependence (Index of pollinator dependence, DI) was applied to analysis of vegetable yields for India over 45 years (1963-2008) using FAO data. This has revealed that since 1993, relative yields of crop production has either flattened or declined,...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2011 URL: http://precedings.nature.com/documents/6044/version/1
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A Fresh Look at Energy, Materials, and Labor in Agriculture Nature Precedings
Aaron W. Baum; Tadeusz Patzek; Martin Bender; Steve Renich; Wes Jackson.
An understanding of agriculture's energy, material, and labor requirements is essential for achieving economic and ecological sustainability, and for assessing the effectiveness of relevant policy decisions (biofuel subsidies, regulations, labeling, etc.). Previous studies of energy, materials, and labor use in farming have been based on either unverified voluntary reporting or test plots, rather than on the high-resolution measurements of mass and energy flows. Here we present a recursive analysis of 1.25 million data points describing in unprecedented detail the resource transactions on a 60 ha farm functioning for over 6 years. This analysis highlights the importance of accounting for all types of materials, as well as capital equipment,...
Tipo: Manuscript Palavras-chave: Ecology; Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/4291/version/1
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A generic approach for representing complex structures in biological models Nature Precedings
Robert I. Muetzelfeldt.
Increasingly, the biological modelling community is looking for ways of handling complex and possibly dynamic structures in their models. On the one hand, the pathway-modelling groups (SBML and CellML) seek to move up levels of organisation, while on the other hand the "Virtual X" communities (where X is some organism or organ) need to represent the organisational structure within their object of study. To date, various approaches have been proposed, such as the SBML Level 3 'comp', 'spatial', 'array' and 'dyn' extension packages, and domain-specific elements in languages such as NeuroML, but there is no generic approach intended to be adopted by the various...
Tipo: Presentation Palavras-chave: Ecology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/5188/version/1
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A Meta-analysis of Studies on Plant Growth Rate and Allocation to Roots and Shoots Nature Precedings
Daniel R. Taub.
I performed a meta-analysis of studies examining the relationships among nutrient availability, plant growth rate and allocation to roots vs. shoots. Species characteristic of high fertility habits grew faster than species characteristic of less fertile habitats. While species were highly plastic in root/shoot ratio, there was a strong correlation in root/shoot across fertility levels when plants were grown across fertility gradients. This suggests that the proportional mass allocation to roots is a consistent characteristic of individual species relative to other species. There was no consistent relationship between allocation to roots and either growth rate or the fertility of habitats that species typically are found in.
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/185/version/1
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A model explaining some bryozoan colonies Nature Precedings
Dawid Mazurek.
Although the colonialism surely developed independently in Graptolithoidea and Bryozoa, both groups share similar patterns of astogeny. One of the common features is the presence of morphological gradients. Many attempts at its explanation were made for more than a half of the century. This paper discusses a new model of the late astogeny in some bryozoan colonies, showing a cyclic reappearance of secondary zones of astogenetic change and astogenetic repetition that cannot be explained by the single morphogen gradient theory.
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2008 URL: http://precedings.nature.com/documents/1585/version/1
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A model of nematode dynamics in the Westerschelde Estuary OMA
Li, J.; Vincx, M.; Herman, P.M.J..
We developed a time dynamic model to investigate the temporal dynamics of nematode community in the brackish zone of the Westerschelde Estuary. The biomass of four nematode feeding groups observed from March 1991 to February 1992 is used to calibrate the model. Using environmental data as the input, the model predicts the temporal modification and interrelation of four nematode feeding groups. Nematodes achieve a dominant position in the community because of their lower loss rate (in respiration, excretion and natural death). Predators which are deposit-feeding macrobenthos control the variations of dominant nematodes, such as omnivores and non-selective deposit feeders. Food availability causes modification only for rare nematodes such as epigrowth...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Diatoms; Ecology; Food; Light; Marine nematodes; Meiobenthos; Population dynamics; Predation; Respiration; Temperature; Nematoda [Nematodes].
Ano: 1996 URL: http://www.vliz.be/nl/open-marien-archief?module=ref&refid=7284
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A new approach to generating research-quality data through citizen science: The USA National Phenology Monitoring System Nature Precedings
Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Lisa Benton; Theresa M. Crimmins; Mark Losleben; Andrew D. Richardson; Alyssa Rosemartin; Mark D. Schwartz; Kathryn A. Thomas; Jake F. Weltzin; Bruce E. Wilson.
Phenology is one of the most sensitive biological responses to climate change, and recent changes in phenology have the potential to shake up ecosystems. In some cases, it appears they already are. Thus, for ecological reasons it is critical that we improve our understanding of species’ phenologies and how these phenologies are responding to recent, rapid climate change. Phenological events like flowering and bird migrations are easy to observe, culturally important, and, at a fundamental level, naturally inspire human curiosity— thus providing an excellent opportunity to engage citizen scientists. The USA National Phenology Network has recently initiated a national effort to encourage people at different levels of...
Tipo: Poster Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/3695/version/1
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A new approach to generating research-quality phenology data: The USA National Phenology Monitoring System Nature Precedings
Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Bruce E. Wilson; Jake F. Weltzin; the rest of the USA-NPN Protocol Development Team.
The USA National Phenology Network (www.usanpn.org) has recently initiated a national effort to encourage people at different levels of expertise—from backyard naturalists to professional scientists—to observe phenology and contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology and associated phenological responses to climate change. Many phenological observation protocols identify specific single dates at which individual phenological events are observed, but the scientific usefulness of long-term phenological observations can be improved with a more carefully structured protocol. At the USA-NPN we have developed a new approach that...
Tipo: Poster Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/3695/version/2
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A New General Allometric Biomass Model Nature Precedings
Wei Sheng Zeng; Shou Zheng Tang.
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(≈2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2011 URL: http://precedings.nature.com/documents/6704/version/1
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A New General Allometric Biomass Model Nature Precedings
Wei Sheng Zeng; Shou Zheng Tang.
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(~2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M and D...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2011 URL: http://precedings.nature.com/documents/6704/version/2
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A practical field guide to weeds of rice in Asia. International Rice Research Institute
Caton, B.P.; Mortimer, M.; Hill, J.E.; International Rice Research Institute..
116 p. : col. ill.
Tipo: Book Palavras-chave: Weeds; Botany; Ecology; Cultural Control; Guide books; Asia.
Ano: 2004 URL: http://hdl.handle.net/123456789/1018
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A review of Chorthippus species with angled pronotal lateral keels from Greece with special reference to transitional populations between some Peloponnesean taxa (Orthoptera, Acrididae) Naturalis
Willemse, F.; Helversen, O. von; Odé, B..
This paper presents a summary of the current knowledge on the systematics of the Greek taxa of Chorthippus, morphologically characterised by angled lateral pronotal keels (usually grouped as Glyptobothrus). Prior to this paper, based on traditional morphology, ten taxa of Chorthippus with angled lateral pronotal keels were recognized from Greece. Based on morphology as well as (and more importantly so) bioacoustics thirteen Greek taxa are now recognised. With addition of a few additional related taxa that occur only outside Greece, all are treated in this paper: Chorthippus apricarius apricarius (Linnaeus, 1758), C. vagans vagans (Eversmann, 1848) (not in Greece), C. v. cypriotus (Uvarov, 1936) stat. nov. [Cyprus], C. v. africanus Nadig, 1981 [N. Africa],...
Tipo: Article / Letter to the editor Palavras-chave: Chorthippus; Glyptobothrus; Greece; Acrididae; Orthoptera; Morphology; Bioacoustics; Taxonomy; Variability; Transitional or hybrid populations; Phylogeny; Evolution; Palaeobiogeography; Key; Distribution; Ecology; 42.75.
Ano: 2009 URL: http://www.repository.naturalis.nl/record/314191
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A revision of the Heteropteryginae (Insecta: Phasmida: Bacillidae) of Borneo, with the description of a new genus and ten new species Naturalis
Bragg, P.E..
The three tribes of Heteropteryginae Kirby, 1896 occurring in Borneo are nocturnal, and ground dwelling species, easily found in both primary and secondary rainforest. The subfamily is reviewed, with keys and redescriptions of all Bornean species; one new species of a predominantly Bornean genus is described from the Philippines. Lectotypes have been selected for a number of species. The eggs of 17 species are described and illustrated. Distribution maps are given for all species. Many of the species have been collected by the author and reared in the United Kingdom; some observations on their natural history and behaviour are included. In the tribe Heteropterygini the synonymy has been re-examined with a revision to the status of several taxa. The five...
Tipo: Article / Letter to the editor Palavras-chave: Phasmida; Heteropteryginae; Distribution; Ecology; Borneo; New genus; Spinodares; New species; Dares; Datames; Lectotypes.; 42.75.
Ano: 1998 URL: http://www.repository.naturalis.nl/record/317712
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