| 1. |
- Wang, Xin-Ping, et al.
(författare)
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Effects of surface characteristics on infiltration patterns in an arid shrub desert
- 2007
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Ingår i: Hydrological Processes. - : Wiley. - 1099-1085 .- 0885-6087. ; 21:1, s. 72-79
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Tidskriftsartikel (refereegranskat)abstract
- Precipitation is often the sole source of water replenishment in arid and semi-arid areas and, thus, plays a pertinent role in sustaining desert ecosystems. Revegetation over 40 years using mainly Artemisia ordosica and Caragana korshinskii at Shapotou Desert Experimental Research Station near Lanzhou, China, has established a dwarf-shrub and microbiotic soil crust cover on the stabilized sand dunes. The redistribution of infiltrated moisture through percolation, root extraction, and evapotranspiration pathways was investigated. Three sets of time-domain reflectometry (TDR) probes were inserted horizontally at 5, 10, 15, 20, 30 and 40 cm depths below the ground surface in a soil pit. The three sets of TDR probes were installed in dwarf-shrub sites of A. ordosica and C. korshinskii community with and without a microbiotic soil crust cover, and an additional set was placed in a bare sand dune area that had neither vegetation nor a microbiotic soil crust present. Volumetric soil moisture content was recorded at hourly intervals and used in the assessment of infiltration for the different surface covers. Infiltration varied greatly, from 7.5 cm to more than 45 cm, depending upon rainfall quantity and soil surface conditions. In the shrub community area without microbiotic soil crust cover, infiltration increased due to preferential flow associated with root tunnels. The microbiotic soil crust cover had a significant negative influence on the infiltration for small rainfall events (similar10 mm), restricting the infiltration depth to less than 20 cm and increasing soil moisture content just beneath the soil profile of 10 cm, whereas it was not as strong or clear for larger rainfall events (similar60 mm). For small rainfall events, the wetting front depth for the three kinds of surface cover was as follows: shrub community without microbiotic soil crust > bare area > shrub community with microbiotic soil crust. In contrast, for large rainfall events, infiltration was similar in shrub communities with and without microbiotic soil crust cover, but significantly higher than measured in the bare area. Soil water extraction by roots associated with evapotranspiration restricted the wetting front penetration after 1 to 3 h of rainfall. Copyright © 2006 John Wiley & Sons, Ltd.
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| 2. |
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| 3. |
- Chi, Zhi-Hong, et al.
(författare)
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Zinc transporter 7 is located in the cis-Golgi apparatus of mouse choroid epithelial cells.
- 2006
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Ingår i: Neuroreport. - : Ovid Technologies (Wolters Kluwer Health). - 0959-4965. ; 17:17, s. 1807-11
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Tidskriftsartikel (refereegranskat)abstract
- The cellular localization of zinc transporter 7 protein in the mouse choroid plexus was examined in this study. Zinc transporter 7 immunoreactive cells were detected in the third, lateral, and fourth ventricles of CD-1 mouse brain. Distinct zinc transporter 7 immunoreactivity was concentrated in the perinuclear regions of the positive cells. The results from zinc autometallography showed that zinc-positive grains were also predominantly located in the perinuclear areas. Ultrastructural localization showed that zinc transporter 7 immunostaining was predominantly present in the membrane and cisternae of the cis-Golgi networks and some vesicle compartments. The results support the notion that zinc transporter 7 may participate in the transport of the cytoplasmic zinc into the Golgi apparatus, and may be involved in local packaging of zinc-binding proteins in the mouse choroid plexus.
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| 4. |
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| 5. |
- Hong, Xin, et al.
(författare)
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Intron size, abundance, and distribution within untranslated regions of genes
- 2006
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:12, s. 2392-2404
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Tidskriftsartikel (refereegranskat)abstract
- Most research concerning the evolution of introns has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes. Here, we directly determined intron size, abundance, and distribution in UTRs of genes using full-length cDNA libraries and complete genome sequences for four species,Arabidopsis thaliana, Drosophila melanogaster, human, and mouse. Overall intron occupancy (introns/exon kbp) is lower in 5′ UTRs than CDSs, but intron density (intron occupancy in regions containing introns) tends to be higher in 5′ UTRs than in CDSs. Introns in 5′ UTRs are roughly twice as large as introns in CDSs, and there is a sharp drop in intron size at the 5′ UTR-CDS boundary. We propose a mechanistic explanation for the existence of selection for larger intron size in 5′ UTRs, and outline several implications of this hypothesis. We found introns to be randomly distributed within 5′ UTRs, so long as a minimum required exon size was assumed. Introns in 3′ UTRs were much less abundant than in 5′ UTRs. Though this was expected for human and mouse that have intron-dependent nonsense-mediated decay (NMD) pathways that discourage the presence of introns within the 3′ UTR, it was also true for A. thaliana and D. melanogaster, which may lack intron-dependent NMD. Our findings have several implications for theories of intron evolution and genome evolution in general.
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| 6. |
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| 7. |
- Lynch, Michael, et al.
(författare)
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NMD and the evolution of eukaryotic gene structure
- 2006
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Ingår i: Nonsense-Mediated mRNA Decay. - : Landes Bioscience/Eurekah.com. ; , s. 197-211
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Bokkapitel (refereegranskat)abstract
- All cells are confronted with undesirable transcripts derived from mutant alleles, but the production of aberrant transcripts from otherwise normal DNA may be an even greater challenge. The substantial fraction of problematical transcripts containing premature termination codons (PTCs) are subject to elimination by the nonsense-mediated mRNA decay (NMD) pathway. Phylogenetic analysis suggests that NMD and the exon junction complex (EJC) upon which it depends in mammals (see chapter by Maquat) are ancient, raising the possibility of an early association of NMD with introns. This may help explain why introns were able to proliferate to an apparently considerable degree in the stem eukaryote, despite the mutational burden that introns impose upon their host genes. A long-term evolutionary asso- ciation between NMD and introns also provides a possible explanation for the nonrandom spatial distribution of introns in the genes of multicellular species and for an apparent slow- down (and possible stabilization) of intron colonization in modern species. Several lineages, all of which are nearly devoid of ancestral introns, appear to have lost NMD and the EJC, and these taxa have exceptionally simple genomic features that minimize the chances of producing erroneous transcripts. Validation of these ideas will require empirical work on the degree of coordination between NMD, the EJC, and the locations of introns in a wide array of genes distributed across diverse phylogenetic lineages.
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| 8. |
- Lynch, Michael, et al.
(författare)
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The evolution of transcription-initiation sites
- 2005
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 22:4, s. 1137-1146
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Tidskriftsartikel (refereegranskat)abstract
- Unlike the situation in prokaryotes, most eukaryotic messenger RNAs contain a moderately long 5′ untranslated region (UTR). Such leader sequences impose a burden on eukaryotic genes by providing substrate for the mutational origin of premature translation-initiation codons, which generally result in defective proteins. To gain an insight into the expansion of 5′ UTRs in eukaryotic genomes, we present a simple null model in which the evolution of transcription-initiation sites is entirely driven by the stochastic mutational flux of core-promoter sequences and premature translation-initiation codons. This model yields results consistent with a variety of heretofore disconnected observations, including the form of length distributions of 5′ UTRs, the relatively low variance in UTR features among distantly related eukaryotes, the universal reliance on relatively simple core-promoter sequences, and the elevated density of introns in the 5′ UTR. We suggest that the reduced effective population sizes of most eukaryotes impose a population-genetic environment conducive to the movement of core promoters to random positions, subject to the constraint imposed by the upstream accumulation of premature translation-initiation codons. If this hypothesis is correct, then selection for gene-specific regulatory features need not be invoked to explain either the origin of lengthy eukaryotic 5′ UTRs or the 1,000-fold range of 5′-UTR lengths among genes within species. Nevertheless, once permanently established, expanded 5′ UTRs may have provided a novel substrate for the evolution of mechanisms for posttranscriptional regulation of eukaryotic gene expression. These results provide a further example of how an increase in the power of random genetic drift can passively promote the evolution of forms of gene architecture that ultimately facilitate the evolution of organismal complexity.
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| 9. |
- Nugent, Chris, et al.
(författare)
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Assessing the impact of individual sensor reliability within smart living environments
- 2008
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Ingår i: IEEE International Conference onAutomation Science and Engineering. - Piscataway, NJ : IEEE Communications Society. - 9781424420223 ; , s. 685-690
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Konferensbidrag (refereegranskat)abstract
- The potential of smart living environments to provide a form of independent living for the ageing population is becoming more recognised. These environments are comprised of sensors which are used to assess the state of the environment, some form of information management to process the sensor data and finally a suite of actuators which can be used to change the state of the environment. When providing a form of support which may impinge upon the well being of the end user it is essential that a high degree of reliability can be maintained. Within this paper we present an information management framework to process sensor based data within smart environments. Based on this framework we assess the impact of sensor reliability on the classification of activities of daily living. From this assessment we show how it is possible to identify which sensors within a given set of experiments can be considered to be the most critical and as such consider how this information may be used to propose a set of guidelines which may be adopted for managing sensor reliability from a practical point of view.
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| 10. |
- Scofield, Douglas, et al.
(författare)
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Position of the final intron in full-length transcripts : Determined by NMD?
- 2007
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 24:4, s. 896-899
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Tidskriftsartikel (refereegranskat)abstract
- Nonsense-mediated decay (NMD) pathways for detection and degradation of transcripts containing premature termination (stop) codons (PTCs) are ubiquitous among the eukaryotes. NMD uses the presence of a second signal downstream of a termination codon to distinguish a PTC from a true stop codon. In mammals and perhaps other eukaryotes, the second signal is a protein complex closely associated with exon–exon junctions formed after removal of spliceosomal introns. A valid transcript in such species must have its 3′-most intron positioned so as not to serve as a second signal relative to the true stop. This requirement has been termed the “55-bp rule”, in reference to the position within the 3′ untranslated region (3′ UTR) of valid transcripts downstream of which introns should not be found. However, as more information has become available, it is apparent that the 55-bp rule still holds in species with NMD pathways, which are not intron dependent. To clarify the applicability of the 55-bp rule, we constructed a large database of 3′-most intron positions within full-length transcripts from 4 eukaryotes, 2 of which (human and mouse) use intron positions for NMD, 1 of which (Drosophila melanogaster) does not, and 1 of which (Arabidopsis thaliana) may not use intron positions. Surprisingly, we found intron numbers to be sharply reduced within 3′ UTRs in comparison to coding sequences starting immediately downstream of true stop, rather than 55 bp; this strong threshold existed for all 4 species. We suggest that a more general mechanism—higher rates of intron inclusion within 3′ UTRs—is better able to explain this threshold. We propose that 3′ UTRs are better able to tolerate loss of intron integrity than other gene regions, due to the generally greater length of conserved sequences important within 3′ UTR exons. This mechanism may also help to explain the roughly 3 times greater length of 3′ UTRs in comparison to 5′ UTRs.
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| 11. |
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| 12. |
- Thinh, N.Q., et al.
(författare)
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Properties of Ga-interstitial defects in AlxGa 1-xNyP1-y
- 2005
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 71:12
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Tidskriftsartikel (refereegranskat)abstract
- A detailed account of the experimental results from optically detected magnetic resonance (ODMR) studies of grown-in defects in (Al)GaNP alloys, prepared by molecular beam epitaxy, is presented. The experimental procedure and an in-depth analysis by a spin Hamiltonian lead to the identification of two Gai defects (Gai-A and Gai-B). New information on the electronic properties of these defects and the recombination processes leading to the observation of the ODMR signals will be provided. These defects are deep-level defects. In conditions when the defect is directly involved in radiative recombination of the near-infrared photoluminescence band, the energy level of the Gai-B defect was estimated to be deeper than ~1.2 eV from either the conduction or valence band edge. In most cases, however, these defects act as nonradiative recombination centers, reducing the efficiency of light emission from the alloys. They can thus undermine the performance of potential photonic devices. High thermal stability is observed for these defects. ©2005 The American Physical Society.
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| 13. |
- Vorona, Igor, et al.
(författare)
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Magnetic resonance signatures of grown-in defects in GaInNP alloys grown on a GaAs substrate
- 2005
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 86:22, s. 222110-
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Tidskriftsartikel (refereegranskat)abstract
- Dilute-nitride Ga0.44In0.56NyP1-y alloys with y=0-0.02, grown on a GaAs substrate using gas-source molecular beam epitaxy, are studied by the optically detected magnetic resonance (ODMR) technique. Grown-in paramagnetic defects were found to act as centers of nonradiative recombination. Resolved hyperfine structure for one of the detected ODMR signals suggests involvement of a Ga-interstitial or an As-antisite in the structure of the related defect. © 2005 American Institute of Physics.
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| 14. |
- Wang, Xin, et al.
(författare)
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Engineering Nanomaterial Surfaces for Biomedical Applications
- 2009
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Ingår i: Experimental biology and medicine. - : SAGE Publications. - 1535-3702 .- 1535-3699. ; 234:10, s. 1128-1139
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Tidskriftsartikel (refereegranskat)abstract
- Nanomaterials, possessing unique physical and chemical properties, have attracted much interest and generated wide varieties of applications. Recent investigations of functionalized nanomaterials have expanded into the biological area, providing a versatile platform in biomedical applications such as biomolecular sensing, biological imaging, drug delivery and disease therapy. Bio-functions and bio-compatibility of nanomaterials are realized by introducing synthetic ligands or natural biomolecules onto nanomaterials, and combining ligand-receptor biological interactions with intrinsic nanomaterial properties. Common strategies of engineering nanomaterial surfaces involve physisorption or chemisorption of desired ligands. We developed a phollochemically initiated surface coupling chemistry, bringing versatility and simplicity to nanomaterial functionalization. The method was applied to attach underivatized carbohydrates efficiently on gold and iron oxide nanoparticles, and the resulting glyconanoparticles were successfully used as a sensitive biosensing system probing specific interactions between carbohydrates and proteins as well as bacteria. Exp Biol Med 234:1128-1139, 2009
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| 15. |
- Yang, Han-Xin, et al.
(författare)
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Diversity-optimized cooperation on complex networks
- 2009
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American physical society. - 1063-651X .- 1095-3787. ; 79:5, s. 056107-
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Tidskriftsartikel (refereegranskat)abstract
- We propose a strategy for achieving maximum cooperation in evolutionary games on complex networks. Each individual is assigned a weight that is proportional to the power of its degree, where the exponent α is an adjustable parameter that controls the level of diversity among individuals in the network. During the evolution, every individual chooses one of its neighbors as a reference with a probability proportional to the weight of the neighbor, and updates its strategy depending on their payoff difference. It is found that there exists an optimal value of α, for which the level of cooperation reaches maximum. This phenomenon indicates that, although high-degree individuals play a prominent role in maintaining the cooperation, too strong influences from the hubs may counterintuitively inhibit the diffusion of cooperation. Other pertinent quantities such as the payoff, the cooperator density as a function of the degree, and the payoff distribution are also investigated computationally and theoretically. Our results suggest that in order to achieve strong cooperation on a complex network, individuals should learn more frequently from neighbors with higher degrees, but only to a certain extent.
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| 16. |
- Yang, Han-Xin, et al.
(författare)
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Effects of social diversity on the emergence of global consensus in opinion dynamics
- 2009
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American Physical Society. - 1063-651X .- 1095-3787. ; 80:4, s. 046108-046112
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Tidskriftsartikel (refereegranskat)abstract
- We propose a variant of the voter model by introducing the social diversity in the evolution process. Each individual is assigned a weight that is proportional to the power of its degree, where the power exponent α is an adjustable parameter that controls the level of diversity among individuals in the network. At each time step, a pair of connected individuals, say i and j, are randomly selected to update their opinions. The probability pi of choosing is opinion as their common opinion is proportional to is weight. We consider the scale-free topology and concentrate on the efficiency of reaching the final consensus, which is significant in characterizing the self-organized systems. Interestingly, it is found that there exists an optimal value of α, leading to the shortest consensus time. This phenomenon indicates that, although a strong influence of high-degree individuals is helpful for quick consensus achievement, over strong influence inhibits the convergence process. Other quantities, such as the probability of an individual’s initial opinion becomes the final opinion as a function of degree, the evolution of the number of opinion clusters, as well as the relationship between average consensus time and the network size, are also studied. Our results are helpful for better understanding the role of degree heterogeneity of the individuals in the opinion dynamics.
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| 17. |
- Zhang, Jin-Ting, et al.
(författare)
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Nuclear to cytoplasmic shift of p33ING1b protein from normal oral mucosa to oral squamous cell carcinoma in relation to clinicopathological variables
- 2008
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Ingår i: Journal of Cancer Research and Clinical Oncology. - : Springer Science and Business Media LLC. - 0171-5216 .- 1432-1335. ; 134:3, s. 421-426
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: p33ING1b, as a candidate tumour suppressor gene, has been found to be expressed a proportion of oral squamous cell carcinomas (OSCCs), however, its clinicopathological significance is not studied yet. Our aim was to investigate association of p33ING1b expression with clinicopathological variables and particularly interesting new cysteine-histidine rich protein (PINCH) in OSCCs. Methods: p33ING1b expression was immumohistochemically examined in 20 normal oral mucosa specimens and 49 OSCCs. Results: Normal squamous cells showed only p33ING1b nuclear expression (no cytoplasmic expression), with a rate of 90% positive cases. While 24% of OSCCs appeared cytoplasmic expression (11 of them with weak nuclear staining) and the rest tumours (76%) were negative for p33 ING1b. Furthermore, the cases having lymph node metastasis showed a higher frequency of positive cytoplasmic expression than those without metastasis (P = 0.03). The p33ING1b cytoplasmic expression was positively related to PINCH expression (P = 0.04), the cases positive for both proteins had a high rate of the metastasis (P = 0.03). Conclusions: The transfer of p33ING1b protein from the nucleus to the cytoplasm may result in loss of normal cellular function of the protein, which might play a role in the tumourigenesis and metastasis of OSCCs. © 2007 Springer-Verlag.
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| 18. |
- Zheng, Wei, et al.
(författare)
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Divalent metal transporter 1 is involved in amyloid precursor protein processing and A{beta} generation.
- 2009
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Ingår i: FASEB Journal. - : Wiley. - 1530-6860 .- 0892-6638. ; 23:12, s. 4207-4217
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Tidskriftsartikel (refereegranskat)abstract
- The amyloid-beta precursor protein (APP) and its pathogenic byproduct beta-amyloid peptide (Abeta) play central roles in the pathogenesis of Alzheimer's disease (AD). Reduction in levels of the potentially toxic Abeta is one of the most important therapeutic goals in AD. Recent studies have shown that bivalent metals such as iron, copper, and zinc are involved in APP expression, Abeta deposition, and senile plaque formation in the AD brain. However, the underlying mechanisms involved in abnormal homeostasis of bivalent metals in AD brain remain unclear. In the present study, we found that two isoforms of the divalent metal transporter 1 (DMT1), DMT1-IRE, and DMT1-nonIRE, were colocalized with Abeta in the plaques of postmortem AD brain. Using the APP/PS1 transgenic mouse model, we found that the levels of both DMT1-IRE and DMT1-nonIRE were significantly increased in the cortex and hippocampus compared with wild type-control. We further verified the proposed mechanisms by which DMT1 might be involved in APP processing and Abeta secretion by using the SH-SY5Y cell line stably overexpressing human APP Swedish mutation (APPsw) as a cell model. We found that overexpression of APPsw resulted in increased expression levels of both DMT1-IRE and DMT1-nonIRE in SH-SY5Y cells. Interestingly, silencing of endogenous DMT1 by RNA interference, which reduced bivalent ion influx, led to reductions of APP expression and Abeta secretion. These findings suggest both that DMT1 plays a critical role in ion-mediated neuropathogenesis in AD and that pharmacological blockage of DMT1 may provide novel therapeutic strategies against AD.-Zheng, W., Xin, N., Chi, Z.-H., Zhao, B.-L., Zhang, J., Li, J.-Y., Wang, Z.-Y. Divalent metal transporter 1 (DMT1) is involved in amyloid precursor protein processing and Abeta generation.
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