Sustainable development of megadeltas worldwide has recently been the focus of international socioeconomic and environmental concerns. Long-term geomorphic sustainability of deltas is crucial for ...sustaining coastal resources and marine ecosystems. The modern Yellow River Delta (YRD), which has been developed since 1855, is increasingly facing erosion threats under natural and human-induced changes. Utilizing long-term hydrological data, remote-sensing satellite images and bathymetric survey data, the transition processes of the modern YRD (including both the subaerial and subaqueous delta) during 1855–2015 from the perspective of morphodynamics are examined. The results show that over the past 160 years, the evolution of the Yellow River subaerial delta is under rapid accretion before 2000, and transitioned to slight erosion state after 2000, which is believed to be associated with the reduced sediment supply. Correspondingly, the Yellow River subaqueous delta is also believed to transition from the accretion into net erosion since 2000, with a net volume change rate of −1.5 × 108 m3/yr. As the primary source for deltaic deposits, at least 2.6 × 108 t/yr of sediment supply is required to sustain the erosion-accretion balance of both the subaerial and subaqueous delta. Compared with the previous research, we present that the 160-year morphological evolution of the modern deltaic system is strongly influenced by the reduction of sediment input. Within this time frame the changes in the partition of sediment load among frequent migrations of the deltaic channel could have a direct impact on variations of the long-term erosion-deposition patterns of the modern YRD. Extreme events of storm surges and frequent strong winds caused significant short-term fluctuations in the erosion/deposition of the subaqueous delta that would affect long-term changes. The insights gained from this study may help to set scientific guidelines for the sustainable development of other river deltas worldwide that are subject to climate change and human interventions.
•The 160-year morphological evolution of the modern YRD is quantitatively analyzed.•The modern YRD has transitioned from the accretion to net erosion state since 2000.•The modern deltaic system is strongly influenced by insufficient sediment supply.•Frequent channel migrations have a direct impact on variations of deltaic morphology.•Extreme storm events can affect long-term changes in the deltaic transition.
Suspended particulate matter (SPM) is the primary component of coastal waters. The spatiotemporal dynamics of SPM has an important influence on water bio-optical properties, pollutant diffusion, ...landform evolution, and carbon, oxygen, and nutrient cycles. This study presents the spatial distribution of monthly average SPM concentrations from 2017 to 2020 in the abandoned Diaokouhe and Shenxiangou distributary mouths of the Yellow River Delta (YRD). The SPM concentrations were derived based on 161 Landsat-8 OLI and Sentinel-2A/B MSI satellite images. Accuracy assessment using the synchronous in-situ measurements (R2 = 0.91, root mean square error (RMSE) = 38.79 mg/L, and relative percentage difference (RPD) = 23.45%) and cross comparison between SPM concentrations derived from the two sensors (R2 = 0.97, RPD = 8.77%) showed convincing performances. Our results show that the monthly average SPM is characterized by significant seasonality, with a higher concentration and wider range in dry seasons compared to that in wet seasons. The spatial distributions of SPM are closely associated with coastal water depths. The SPM concentration in the Shenxiangou mouth is always lower than that of the shallower Diaokouhe mouth. The long-term seabed erosion provides a continuous supply of sediment. Wind-wave forces explain the seasonal variations of SPM by inducing the resuspension of bottom sediments. The residual currents control the transportation of SPM to the offshore and to the east. The artificial groins located between the two river mouths show obvious sediment trapping effects. Moreover, the interception capability of impermeable groins is considerably better than that of permeable groins.
•Landsat-8 OLI and Sentinel-2A/B MSI are combined to estimate SPM.•Seasonal variation of SPM in the abandoned distributary mouths of YRD is obtained.•The impact of environment factors, as well as artificial groins, on the spatiotemporal dynamics of SPM are discussed.
The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing ...technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Nonlinear unloading plays an important role in predicting springback during plastic forming process. To improve the accuracy of springback prediction which could provide a guide for precision ...forming, uniaxial tensile tests and uniaxial loading-unloading-loading tensile tests on SUS304 stainless steel were carried out. The flow stress mathematical model and chord modulus mathematical model were calibrated according to the test results. A constant elastic modulus three-point bending finite element model (E0FEMB) and a constant elastic modulus roll forming finite element model (E0FEMR) were established in MSC.MARC. The chord modulus was output by the PLOTV subroutine to determine the mean modulus of different regions, and the mean modulus three-point bending finite element model (E¯cFEMB) and the mean modulus roll forming finite element model (E¯cFEMR) were defined. The constant modulus finite element model (E0FEM) simulation results and the mean modulus finite element model (E¯cFEM) simulation results were compared with the three-point bending tests and roll forming tests test results. The difference between the simulation results and the test results was small, indicating that the mean modulus was feasible to predict the springback, which verified the suitability of the E¯cFEM.
Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent ...datasets generated by deep-sequencing and high-density tiling arrays, and we discovered an array of well-positioned nucleosomes flanking sites occupied by the insulator binding protein CTCF across the human genome. These nucleosomes are highly enriched for the histone variant H2A.Z and 11 histone modifications. The distances between the center positions of the neighboring nucleosomes are largely invariant, and we estimate them to be 185 bp on average. Surprisingly, subsets of nucleosomes that are enriched in different histone modifications vary greatly in the lengths of DNA protected from micrococcal nuclease cleavage (106-164 bp). The nucleosomes enriched in those histone modifications previously implicated to be correlated with active transcription tend to contain less protected DNA, indicating that these modifications are correlated with greater DNA accessibility. Another striking result obtained from our analysis is that nucleosomes flanking CTCF sites are much better positioned than those downstream of transcription start sites, the only genomic feature previously known to position nucleosomes genome-wide. This nucleosome-positioning phenomenon is not observed for other transcriptional factors for which we had genome-wide binding data. We suggest that binding of CTCF provides an anchor point for positioning nucleosomes, and chromatin remodeling is an important component of CTCF function.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Eukaryotic gene transcription is accompanied by acetylation and methylation of nucleosomes near promoters, but the locations and roles of histone modifications elsewhere in the genome remain unclear. ...We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are marked by trimethylation of Lys4 of histone H3 (H3K4), whereas enhancers are marked by monomethylation, but not trimethylation, of H3K4. We developed computational algorithms using these distinct chromatin signatures to identify new regulatory elements, predicting over 200 promoters and 400 enhancers within the 30-Mb region. This approach accurately predicted the location and function of independently identified regulatory elements with high sensitivity and specificity and uncovered a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2). Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide a new tool for the functional annotation of the human genome.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of Saccharomyces cerevisiae ...whose nucleosome binding affinities have been experimentally determined (Yuan et al. 2005) to train a support vector machine to identify the nucleosome formation potential of any given sequence of DNA. The DNA sequences whose nucleosome formation potential are most accurately predicted are those that contain strong nucleosome forming or inhibiting signals and are found within nucleosome length stretches of genomic DNA with continuous nucleosome formation or inhibition signals. We have accurately predicted the experimentally determined nucleosome positions across a well-characterized promoter region of S. cerevisiae and identified strong periodicity within 199 center-aligned mononucleosomes studied recently (Segal et al. 2006) despite there being no periodicity information used to train the support vector machine. Our analysis suggests that only a subset of nucleosomes are likely to be positioned by intrinsic sequence signals. This observation is consistent with the available experimental data and is inconsistent with the proposal of a nucleosome positioning code. Finally, we show that intrinsic nucleosome positioning signals are both more inhibitory and more variable in promoter regions than in open reading frames in S. cerevisiae.
The ability to derive a whole-genome map of transcription-factor binding sites (TFBS) is crucial for elucidating gene regulatory networks. Herein, we describe a robust approach that couples chromatin ...immunoprecipitation (ChIP) with the paired-end ditag (PET) sequencing strategy for unbiased and precise global localization of TFBS. We have applied this strategy to map p53 targets in the human genome. From a saturated sampling of over half a million PET sequences, we characterized 65,572 unique p53 ChIP DNA fragments and established overlapping PET clusters as a readout to define p53 binding loci with remarkable specificity. Based on this information, we refined the consensus p53 binding motif, identified at least 542 binding loci with high confidence, discovered 98 previously unidentified p53 target genes that were implicated in novel aspects of p53 functions, and showed their clinical relevance to p53-dependent tumorigenesis in primary cancer samples.
River dynamics and sediment budget play a crucial role in shaping geomorphic variability of river channels and deltaic environments. Basin-scale human activities, including dam construction, induce ...alterations in river flow and sediment dynamics in the downstream channels and to the delta, and quantification of sediment source shift along downstream fluvial-deltaic systems is often uncertain. This study analyzed the river regime changes and sediment dynamics of a typical sediment-laden fluvial-deltaic system—the lower Yellow River (LYR) and the Yellow River Delta (YRD) —to assess the integrated effects of dam impoundment and dam-based river regulation schemes on downstream hydrogeomorphic transition processes. The Xiaolangdi (XLD) Reservoir, which was completed in 2000 with a total storage of 12.7 km3, is the final reservoir located in the middle Yellow River and plays an important role in flood control and energy supply. Following the full operation of XLD Reservoir, the relationship between water and sediment in the LYR became more balanced, with a drastic decline of sediment input and seasonal migrations of floodwaters. The interannual variability of water levels at downstream hydrological stations indicated a geomorphic transition in the LYR from net deposition to erosion state. The building of the XLD Reservoir caused a downstream shift of river-originated sediment source and 48% of the total sediment delivered to the YRD was derived from the LYR. However, the reduced sediment delivery since 2000 has still triggered net land loss regarding the YRD system, with a strong spatial variability which is dominated by the reduced accretion at the active delta front and erosion at the abandoned river mouth and coastal engineering zone. Compared with other environmental factors, the construction of upstream dams contributed the most to the decline of downstream sediment delivery over the past decades. The challenge for sustainable sediment management is the gradual decline of scouring efficiency as the riverbed sediment is coarsening. Our study suggests that future river regulation strategies should consider the geomorphic sustainability of both the LYR and the YRD system.
The protooncogene MYC encodes the c-Myc transcription factor that regulates cell growth, cell proliferation, cell cycle, and apoptosis. Although deregulation of MYC contributes to tumorigenesis, it ...is still unclear what direct Myc-induced transcriptomes promote cell transformation. Here we provide a snapshot of genome-wide, unbiased characterization of direct Myc binding targets in a model of human B lymphoid tumor using ChIP coupled with pair-end ditag sequencing analysis (ChIP-PET). Myc potentially occupies >4,000 genomic loci with the majority near proximal promoter regions associated frequently with CpG islands. Using gene expression profiles with ChIP-PET, we identified 668 direct Myc-regulated gene targets, including 48 transcription factors, indicating that Myc is a central transcriptional hub in growth and proliferation control. This first global genomic view of Myc binding sites yields insights of transcriptional circuitries and cis regulatory modules involving Myc and provides a substantial framework for our understanding of mechanisms of Myc-induced tumorigenesis.