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101.
Erin R. Vogel Mark E. Harrison Astri Zulfa Timothy D. Bransford Shauhin E. Alavi Simon Husson Helen Morrogh-Bernard Santiano Twentinolosa Firtsman Sri Suci Utami-Atmoko Maria A. van Noordwijk Wartika Rosa Farida 《PloS one》2015,10(10)
Bottom-up regulatory factors have been proposed to exert a strong influence on mammalian population density. Studies relating habitat quality to population density have typically made comparisons among distant species or communities without considering variation in food quality among localities. We compared dietary nutritional quality of two Bornean orangutan populations with differing population densities in peatland habitats, Tuanan and Sabangau, separated by 63 km. We hypothesized that because Tuanan is alluvial, the plant species included in the orangutan diet would be of higher nutritional quality compared to Sabangau, resulting in higher daily caloric intake in Tuanan. We also predicted that forest productivity would be greater in Tuanan compared to Sabangau. In support of these hypotheses, the overall quality of the diet and the quality of matched dietary items were higher in Tuanan, resulting in higher daily caloric intake compared to Sabangau. These differences in dietary nutritional quality may provide insights into why orangutan population density is almost two times greater in Tuanan compared to Sabangau, in agreement with a potentially important influence of diet quality on primate population density. 相似文献
102.
Josephine Sahner Sri Wilarso Budi Henry Barus Nur Edy Marike Meyer Marife D. Corre Andrea Polle 《PloS one》2015,10(9)
Conversion of tropical forests into intensely managed plantations is a threat to ecosystem functions. On Sumatra, Indonesia, oil palm (Elaeis guineensis) plantations are rapidly expanding, displacing rain forests and extensively used rubber (Hevea brasiliensis) agro-forests. Here, we tested the influence of land use systems on root traits including chemical traits (carbon, nitrogen, mineral nutrients, potentially toxic elements [aluminium, iron] and performance traits (root mass, vitality, mycorrhizal colonization). Traits were measured as root community-weighed traits (RCWTs) in lowland rain forests, in rubber agro-forests mixed with rain forest trees, in rubber and oil palm plantations in two landscapes (Bukit Duabelas and Harapan, Sumatra). We hypothesized that RCWTs vary with land use system indicating increasing transformation intensity and loss of ecosystem functions. The main factors found to be related to increasing transformation intensity were declining root vitality and root sulfur, nitrogen, carbon, manganese concentrations and increasing root aluminium and iron concentrations as well as increasing spore densities of arbuscular mycorrhizas. Mycorrhizal abundance was high for arbuscular and low for ectomycorrhizas and unrelated to changes in RCWTs. The decline in RCWTs showed significant correlations with soil nitrogen, soil pH and litter carbon. Thus, our study uncovered a relationship between deteriorating root community traits and loss of ecosystem functionality and showed that increasing transformation intensity resulted in decreasing root nutrition and health. Based on these results we suggest that land management that improves root vitality may enhance the ecological functions of intense tropical production systems. 相似文献
103.
104.
The number of high-dimensional datasets recording multiple aspects of a single phenomenon is increasing in many areas of science, accompanied by a need for mathematical frameworks that can compare multiple large-scale matrices with different row dimensions. The only such framework to date, the generalized singular value decomposition (GSVD), is limited to two matrices. We mathematically define a higher-order GSVD (HO GSVD) for N≥2 matrices D(i)∈R(m(i) × n), each with full column rank. Each matrix is exactly factored as D(i)=U(i)Σ(i)V(T), where V, identical in all factorizations, is obtained from the eigensystem SV=VΛ of the arithmetic mean S of all pairwise quotients A(i)A(j)(-1) of the matrices A(i)=D(i)(T)D(i), i≠j. We prove that this decomposition extends to higher orders almost all of the mathematical properties of the GSVD. The matrix S is nondefective with V and Λ real. Its eigenvalues satisfy λ(k)≥1. Equality holds if and only if the corresponding eigenvector v(k) is a right basis vector of equal significance in all matrices D(i) and D(j), that is σ(i,k)/σ(j,k)=1 for all i and j, and the corresponding left basis vector u(i,k) is orthogonal to all other vectors in U(i) for all i. The eigenvalues λ(k)=1, therefore, define the "common HO GSVD subspace." We illustrate the HO GSVD with a comparison of genome-scale cell-cycle mRNA expression from S. pombe, S. cerevisiae and human. Unlike existing algorithms, a mapping among the genes of these disparate organisms is not required. We find that the approximately common HO GSVD subspace represents the cell-cycle mRNA expression oscillations, which are similar among the datasets. Simultaneous reconstruction in the common subspace, therefore, removes the experimental artifacts, which are dissimilar, from the datasets. In the simultaneous sequence-independent classification of the genes of the three organisms in this common subspace, genes of highly conserved sequences but significantly different cell-cycle peak times are correctly classified. 相似文献
105.
106.
Deni Pranowo Nuryono Ali Agus Sri Wedhastri Elisabeth Viktoria Reiter Ebrahim Razzazi-Fazeli Jürgen Zentek 《Mycotoxin Research》2013,29(3):135-139
Samples from large (100–200 tons) batches of palm kernel cake (PKC, n?=?20) and copra meal (CM, n?=?13) were collected at production facilities of four Indonesian feed mill manufacturers and analysed for aflatoxin B1 (AFB1) by ELISA. Recoveries using spiked samples ranged from 86 to 113 %, with relative standard deviations of <9 % (PKC) and <6 % (CM). All batches were positive for AFB1: in PKC, at levels of 5.8–93.1 μg/kg (mean 49 μg/kg), and in CM, at levels of 1.1–147 μg/kg (mean 38.1 μg/kg). AFB1 levels were, in most batches, below the maximum level (100 μg/kg) recommended by the National Standardisation Agency, Republic of Indonesia. However, about half of the batches exceeded both the European Union and USA regulations for AFB1 in animal feed. In conclusion, serious efforts are necessary to control production, storage and shipment of palm kernel cake and copra meal for feed purposes, and clearly not only for products intended for export but also to reduce AFB1 levels in domestic Indonesian feed. 相似文献
107.
Mycobacterium leprae is closely related to Mycobacterium tuberculosis, yet causes a very different illness. Detailed genomic comparison between these two species of mycobacteria reveals that the decaying M. leprae genome contains less than half of the M. tuberculosis functional genes. The reduction of genome size and accumulation of pseudogenes in the M. leprae genome is thought to result from multiple recombination events between related repetitive sequences, which provided the impetus to investigate the recombination-like activities of RecA protein. In this study, we have cloned, over-expressed and purified M. leprae RecA and compared its activities with that of M. tuberculosis RecA. Both proteins, despite being 91% identical at the amino acid level, exhibit strikingly different binding profiles for single-stranded DNA with varying GC contents, in the ability to catalyze the formation of D-loops and to promote DNA strand exchange. The kinetics and the extent of single-stranded DNA-dependent ATPase and coprotease activities were nearly equivalent between these two recombinases. However, the degree of inhibition exerted by a range of ATP:ADP ratios was greater on strand exchange promoted by M. leprae RecA compared to its M. tuberculosis counterpart. Taken together, our results provide insights into the mechanistic aspects of homologous recombination and coprotease activity promoted by M. lepare RecA, and further suggests that it differs from the M. tuberculosis counterpart. These results are consistent with an emerging concept of DNA-sequence influenced structural differences in RecA nucleoprotein filaments and how these differences reflect on the multiple activities associated with RecA protein. 相似文献
108.
Michael Kessler Yann Clough Ramadhanil Pitopang Daniela Leitner Sri S. Tjitrosoedirdjo 《Biotropica》2011,43(6):755-762
Tropical secondary forest and agroforestry systems have been identified as important refuges for the local species diversity of birds and other animal groups, but little is known about the importance of these systems for terrestrial herbs. In particular, few studies report how the conversion from tropical forest to technified cacao plantation affects the species richness and the community structure of herbs. We conducted surveys in 43 cacao plantations along the border of the Lore Lindu National Park in Central Sulawesi, ranging from agroforests to technified cacao, categorizing the plantations as rustic cacao, planted shade cacao, and technified cacao. We recorded 91 herb species. Of the 74 species determined to species level, 21 were also found in natural forests, while 53 were recorded only in agricultural habitats. Araceae was the most forest‐dependent plant family while Asteraceae included the highest number of nonforest species. Overall, the presence of forest species was confined to moderately intensively managed rustic and planted shaded plantations. Distance from the forest, which has been identified as a crucial parameter for the diversity and composition of other taxa in cacao agroforests, only played a minimal role for herbs. Our study suggests that native forest herbs maybe more vulnerable to forest conversion than animal groups. The intensification of cacao plantation management increases the presence of weedy species to the detriment of native forest species. 相似文献
109.
Shevin R. Feroz Saharuddin B. Mohamad Zarith S. D. Bakri Sri N. A. Malek Saad Tayyab 《PloS one》2013,8(10)
Interaction of a pharmacologically important flavonoid, pinostrobin (PS) with the major transport protein of human blood circulation, human serum albumin (HSA) has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 105 M−1 at 25°C) between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol−1 K−1 and ΔH = −15.48 kJ mol−1) and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow’s site I, located at subdomain IIA, and was well supported by the molecular modelling data. 相似文献
110.
Dumbala Srinivas Reddy Pooja Bhatnagar-Mathur Katamreddy Sri Cindhuri Kiran K. Sharma 《PloS one》2013,8(10)
The quantitative real-time PCR (qPCR) based techniques have become essential for gene expression studies and high-throughput molecular characterization of transgenic events. Normalizing to reference gene in relative quantification make results from qPCR more reliable when compared to absolute quantification, but requires robust reference genes. Since, ideal reference gene should be species specific, no single internal control gene is universal for use as a reference gene across various plant developmental stages and diverse growth conditions. Here, we present validation studies of multiple stably expressed reference genes in cultivated peanut with minimal variations in temporal and spatial expression when subjected to various biotic and abiotic stresses. Stability in the expression of eight candidate reference genes including ADH3, ACT11, ATPsyn, CYP2, ELF1B, G6PD, LEC and UBC1 was compared in diverse peanut plant samples. The samples were categorized into distinct experimental sets to check the suitability of candidate genes for accurate and reliable normalization of gene expression using qPCR. Stability in expression of the references genes in eight sets of samples was determined by geNorm and NormFinder methods. While three candidate reference genes including ADH3, G6PD and ELF1B were identified to be stably expressed across experiments, LEC was observed to be the least stable, and hence must be avoided for gene expression studies in peanut. Inclusion of the former two genes gave sufficiently reliable results; nonetheless, the addition of the third reference gene ELF1B may be potentially better in a diverse set of tissue samples of peanut. 相似文献