Impact of Coastal Erosion and Sedimentation along the Northern Coast of Sinai Peninsula

Coastal engineering activities during the past five decades have resulted in considerable shoreline change along the northern coast of Sinai Peninsula. In the west of El Arish Power Plant, sediment accretion has reached the tip of the breakwater of the cooling water intake basin necessitating extensive dredging inside the basin. In the east of El Arish Harbor, the shoreline is continuously retreating. Previous activities to mitigate the erosion have not succeeded. For example, the groin field in the east of the El Arish Harbor has transferred the problem to the neighboring beaches farther downcoast. In this study predominant coastal processes affecting the erosion of the Sinai northern coastline were investigated. Wave-induced longshore currents were found to be responsible for transporting the littoral drift along the coastline. Longshore sediment transport, from Port Said to Ashqelon, was quantified and the general patterns of erosion-accretion were determined by looking upon the gradients between transport rates along the coast. Particular emphasis was placed on shoreline change due to perturbations introduced by infrastructure sited at the coastline near El Arish. The shoreline change at El Arish Power Plant and Harbor were modeled using the coastal evolution model GENESIS. Having understood the coastal processes driving the shoreline change at these two locations, appropriate remedial measures were proposed to mitigate the problem. In this regard, a combination of hard and soft coastal engineering methods are presented to alleviate the dredging problem at the power plant while sand-bypassing/beach-nourishment is suggested as an effective sustainable solution to the erosion problem in the east of El Arish Harbor

In-Depth Transcriptome Analysis Reveals Novel TARs and Prevalent Antisense Transcription in Human Cell Lines

Several recent studies have indicated that transcription is pervasive in regions outside of protein coding genes and that short antisense transcripts can originate from the promoter and terminator regions of genes. Here we investigate transcription of fragments longer than 200 nucleotides, focusing on antisense transcription for known protein coding genes and intergenic transcription. We find that roughly 12% to 16% of all reads that originate from promoter and terminator regions, respectively, map antisense to the gene in question. Furthermore, we detect a high number of novel transcriptionally active regions (TARs) that are generally expressed at a lower level than protein coding genes. We find that the correlation between RNA-seq data and microarray data is dependent on the gene length, with longer genes showing a better correlation. We detect high antisense transcriptional activity from promoter, terminator and intron regions of protein-coding genes and identify a vast number of previously unidentified TARs, including putative novel EGFR transcripts. This shows that in-depth analysis of the transcriptome using RNA-seq is a valuable tool for understanding complex transcriptional events. Furthermore, the development of new algorithms for estimation of gene expression from RNA-seq data is necessary to minimize length bias

Decadal Scale Variability of Larsen Ice Shelf Melt Captured by Antarctic Peninsula Ice Core

In this study, we used the stable water isotope record (δ18O) from an ice core drilled in Palmer Land, southern Antarctic Peninsula (AP). Utilizing δ18O we identified two climate regimes during the satellite era. During the 1979–1998 positive interdecadal Pacific oscillation (IPO) phase, a low-pressure system north of the Weddell Sea drove southeasterly winds that are associated with an increase in warm air mass intrusion onto the Larsen shelves, which melted and a decreased sea ice concentration in the Weddell Sea/increase in the Bellingshausen Sea. This climate setting is associated with anomaly low δ18O values (compared with the latter IPO period). There is significantly more melt along the northern AP ice shelf margins and on the Larsen D and southern Larsen C during the 1979–1998 IPO positive phase. The IPO positive climatic setting was coincidental with the Larsen A ice shelf collapse. In contrast, during the IPO negative phase (1999–2011), northerly winds caused a reduction in sea ice in the Bellingshausen Sea/Drake Passage region. Moreover, a Southern Ocean north of the Weddell Sea high-pressure system caused low-latitude warm humid air over the tip and east of the AP, a setting that is associated with increased northern AP snowfall, a high δ18O anomaly, and less prone to Larsen ice shelf melt

Ice Core Chronologies from the Antarctic Peninsula: The Palmer, Jurassic, and Rendezvous Age-Scales

In this study, we present the age scales for three Antarctic Peninsula (AP) ice cores: Palmer, Rendezvous, and Jurassic. The three cores are all intermediate-depth cores, in the 133–141 m depth range. Non-sea-salt sulfate ([nssSO42−]) and hydrogen peroxide (H2O2) display marked seasonal variability suitable for annual-layer counting. The Palmer ice core covers 390 years, 1621–2011 C.E., and is one of the oldest AP cores. Rendezvous and Jurassic are lower elevation high-snow accumulation sites and therefore cover shorter intervals, 1843–2011 C.E. and 1874–2011 C.E., respectively. The age scales show good agreement with known volcanic age horizons. The three chronologies’ start and end dates of volcanic events are compared to the volcanic events in the published WAIS Divide core. The age difference for the Palmer age scale is ±6 months, Rendezvous ±9 months, and Jurassic ±7 months. Our results demonstrate the advantage of dating several cores from the same region at the same time. Additional confidence can be gained in the age scales by evaluating and finding synchronicity of [nssSO42−] peaks amongst the sites.</jats:p

Analysis of transcript and protein overlap in a human osteosarcoma cell line

<p>Abstract</p> <p>Background</p> <p>An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with <it>in situ </it>protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF).</p> <p>Results</p> <p>A large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies.</p> <p>Conclusion</p> <p>This suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.</p

Ice core chemistry database: an Antarctic compilation of sodium and sulfate records spanning the past 2000 years

Changes in sea ice conditions and atmospheric circulation over the Southern Ocean play an important role in modulating Antarctic climate. However, observations of both sea ice and wind conditions are limited in Antarctica and the Southern Ocean, both temporally and spatially, prior to the satellite era (1970 onwards). Ice core chemistry data can be used to reconstruct changes over annual, decadal, and millennial timescales. To facilitate sea ice and wind reconstructions, the CLIVASH2k (CLimate Variability in Antarctica and the Southern Hemisphere over the past 2000 years) working group has compiled a database of two species, sodium [Na+] and sulfate [SO2− 4 ], commonly measured ionic species. The database (https://doi.org/10.5285/9E0ED16E-F2AB4372-8DF3-FDE7E388C9A7; Thomas et al., 2022) comprises records from 105 Antarctic ice cores, containing records with a maximum age duration of 2000 years. An initial filter has been applied, based on evaluation against sea ice concentration, geopotential height (500 hPa), and surface wind fields to identify sites suitable for reconstructing past sea ice conditions, wind strength, or atmospheric circulation

The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development

It has long been known that trypanosomes regulate mitochondrial biogenesis during the life cycle of the parasite; however, the mitochondrial protein inventory (MitoCarta) and its regulation remain unknown. We present a novel computational method for genome-wide prediction of mitochondrial proteins using a support vector machine-based classifier with ∼90% prediction accuracy. Using this method, we predicted the mitochondrial localization of 468 proteins with high confidence and have experimentally verified the localization of a subset of these proteins. We then applied a recently developed parallel sequencing technology to determine the expression profiles and the splicing patterns of a total of 1065 predicted MitoCarta transcripts during the development of the parasite, and showed that 435 of the transcripts significantly changed their expressions while 630 remain unchanged in any of the three life stages analyzed. Furthermore, we identified 298 alternatively splicing events, a small subset of which could lead to dual localization of the corresponding proteins

The PE-PPE Domain in Mycobacterium Reveals a Serine α/β Hydrolase Fold and Function: An In-Silico Analysis

The PE and PPE proteins first reported in the genome sequence of Mycobacterium tuberculosis strain H37Rv are now identified in all mycobacterial species. The PE-PPE domain (Pfam ID: PF08237) is a 225 amino acid residue conserved region located towards the C-terminus of some PE and PPE proteins and hypothetical proteins. Our in-silico sequence analysis revealed that this domain is present in all Mycobacteria, some Rhodococcus and Nocardia farcinica genomes. This domain comprises a pentapeptide sequence motif GxSxG/S at the N-terminus and conserved amino acid residues Ser, Asp and His that constitute a catalytic triad characteristic of lipase, esterase and cutinase activity. The fold prediction and comparative modeling of the 3-D structure of the PE-PPE domain revealed a “serine α/β hydrolase” structure with a central β-sheet flanked by α-helices on either side. The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site. The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified. Our findings add to the growing list of serine hydrolases in mycobacterium, which are essential for the maintenance of their impermeable cell wall and virulence. These results provide the directions for the design of experiments to establish the function of PE and PPE proteins