The tectonic influence on the last 1500-year infill history of a deep lake located on the North Anatolian Fault: Lake Sapanca (N-W Turkey)

Lake Sapanca on the North Anatolian Fault zone (NW Turkey) is a pull-apart basin at the junction between the İzmit-Sapanca fault segment, the Sakarya segment and the westernmost end of the Mudurnu Valley fault. Multiproxy analyses of a 586-cm-long sediment core taken in the lake centre have revealed a complex history of earthquake events. The radiocarbon chronology, affected by reworking of plant remains, suggests that the sediment sequence retrieved from the centre of the lake covers approximately the last 1500 years. The bottom metre of the sequence is a gley soil indicating that at least the eastern half of the lake was a wetland, a prolongation of the floodplain between the lake and River Sakarya, that has collapsed to form the modern deep lake. A series of sedimentological and palynological indicators have been used to highlight four major episodes of mass movements linked to earthquakes. The short existence of the eastern part of the lake highlights the complexity of the morphology of the Sakarya Straight, a possible past connection between the Gulf of İzmit and the Black Sea

Recent high-energy marine events in the sediments of the Lagoa de Óbidos and Martinhal (Portugal): Recognition, age and likely causes

© 2012 Author(s) - This work is distributed under the Creative Commons Attribution 3.0 License.This article has been made available through the Brunel Open Access Publishing Fund.A key issue in coastal hazards research is the need to distinguish sediments deposited by past extreme storms from those of past tsunamis. This study contributes to this aim by investigating patterns of sedimentation associated with extreme coastal flood events, in particular, within the Lagoa de Óbidos (Portugal). The recent stratigraphy of this coastal lagoon was studied using a wide range of techniques including visual description, grain-size analysis, digital and x-ray photography, magnetic susceptibility and geochemical analysis. The sequence was dated by 14C, 210Pb and Optically Stimulated Luminescence. Results disclose a distinctive coarser sedimentary unit, within the top of the sequence studied, and shown in quartz sand by the enrichment of elements with marine affinity (e.g., Ca and Na) and carbonates. The unit fines upwards and inland, thins inland and presents a sharp erosive basal contact. A noticeable post-event change in the sedimentary pattern was observed. The likely agent of sedimentation is discussed here and the conceivable association with the Great Lisbon tsunami of AD 1755 is debated, while a comparison is attempted with a possibly synchronous deposit from a tsunami in Martinhal (Algarve, Portugal). The possibility of a storm origin is also discussed in the context of the storminess of the western Portuguese coast and the North Atlantic Oscillation. This study highlights certain characteristics of the sedimentology of the deposits that may have a value in the recognition of extreme marine inundation signatures elsewhere in the world.This article is made available through the Brunel Open Access Publishing Fund

Boron content of Lake Ulubat sediment: A key to interpret the morphological history of NW Anatolia, Turkey

Freshwater Lake Ulubat (c. 1.5 m deep and c. 138 km2) receives sediment from a 10.414 km2 area in the seismically active Susurluk Drainage Basin (SDB) of NW Turkey. The B and trace element contents of the lake infill seem to be a link between the fresh landforms of the SDB and the lacustrine sediment. Deposition in Lake Ulubat has been 1.60 cm.a-1 for the last 50 a according to radionucleides; however the sedimentation rate over the last millennium was 0.37 cm.a-1 based on 14C dating. The B content of the lacustrine infill displays a slight increase at 0.50 m and a drastic increase at 4 m depth occurring c. 31 a and c. 1070 a ago respectively. Probably the topmost change corresponds to the start of open mining in the SDB and the second one to the natural trenching of borate ore-deposits. These dates also show indirectly a 1.4 cm.a-1 erosion rate during the last millennium as the borate beds were trenched up to 15 m. By extrapolation, it is possible to establish that the formation of some of the present morphological features of the southern Marmara region, especially river incision, began in the late Pleistocene, and developed especially over the last 75 ka

Wind control on the accumulation of heavy metals in sediment of Lake Ulubat, Anatolia, Turkey

Freshwater Lake Ulubat (zmean = 1.5-2.0 m and Area = ~138 km2), NW Anatolia, Turkey was filled in by fine-to-medium-grain silts during the late Holocene. Deposition in Lake Ulubat has been 1.6 cm yr-1 for the last 50 years, but the sedimentation rate over the last ~1,600 years was lower (0.37 mm yr-1). The organic matter and carbonate contents of the infill show cyclic changes that reflect environmental fluctuations. The silt-dominated lithology and the vertically uniform heavy metal distributions are probably due to wind-controlled sedimentation in the lake. Heterogeneous mud, derived from a large, mountainous drainage basin, is deposited in the lake mostly during summer, June to October, when conditions are hot and calm. Winter months are stormier and sediments are re-suspended due to the shallow water depth and the effect of waves on the lake bottom. It is likely that re-suspended sediments, particularly fine-grained particles, together with the heavy metals, are transported out of the lake via the outlet, especially during periods of high lake level. This resuspension and removal process probably caused the lake sediments to become silt-dominated and depleted in heavy metals. The role of broad shallow lakes in sequestering sediments and heavy metals can be described more accurately when wind data are considered. Such information may also be helpful for land-use planning in downstream areas

A prenylated dsRNA sensor protects against severe COVID-19

INTRODUCTION Interferons (IFNs) are cytokines that are rapidly deployed in response to invading pathogens. By initiating a signaling cascade that stimulates the expression of hundreds of genes, IFNs create an antiviral state in host cells. Because IFNs heavily influence COVID-19 outcomes, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication can be inhibited by the antiviral state, it is important to understand how the individual antiviral effectors encoded by IFN-stimulated genes (ISGs) inhibit SARS-CoV-2. RATIONALE We hypothesized that IFN-stimulated antiviral effectors can inhibit SARS-CoV-2, and that variation at the loci encoding these defenses underlies why some people are more susceptible to severe COVID-19. RESULTS We used arrayed ISG expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1) consistently inhibited SARS-CoV-2 in different contexts. Using CRISPR-Cas9, we found that endogenous OAS1 makes a substantial contribution to the antiviral state by recognizing short stretches of double-stranded RNA (dsRNA) and activating RNase L. We globally mapped where OAS1 binds to SARS-CoV-2 viral RNAs and found that OAS1 binding is remarkably specific, with two conserved stem loops in the SARS-CoV-2 5′-untranslated region (UTR) constituting the principal viral target. OAS1 expression was readily detectable at the sites of infection in individuals who died of COVID-19, and specific OAS1 alleles are known to be associated with altered susceptibility to infection and severe disease. It had previously been reported that alleles containing a common splice-acceptor single nucleotide polymorphism in OAS1 (Rs10774671) were associated with less severe COVID-19. We determined that people with at least one allele with a G at this position could express a prenylated form of OAS1 (p46), whereas other individuals could not. Using a series of mutants, we found that C-terminal prenylation was necessary for OAS1 to initiate a block to SARS-CoV-2. Furthermore, confocal microscopy revealed that prenylation targeted OAS1 to perinuclear structures rich in viral dsRNA, whereas non-prenylated OAS1 was diffusely localized and unable to initiate a detectable block to SARS-CoV-2 replication. The realization that prenylation is essential for OAS1-mediated sensing of SARS-CoV-2 allowed us to examine the transcriptome of infected patients and investigate whether there was a link between the expression of prenylated OAS1 and SARS-CoV-2 disease progression. Analysis of the OAS1 transcripts from 499 hospitalized COVID-19 patients revealed that expressing prenylated OAS1 was associated with protection from severe COVID-19. Because prenylated OAS1 was so important in human cases, we wanted to determine whether horseshoe bats, the likely source of SARS-CoV-2, possessed the same defense. When we examined the genomic region where the prenylation signal should reside, retrotransposition of a long terminal repeat sequence had ablated this signal, preventing the expression of prenylated anti-CoV OAS1 in these bats. CONCLUSION C-terminal prenylation targets OAS1 to intracellular sites rich in viral dsRNA, which are likely the SARS-CoV-2 replicative organelles. Once in the right place, OAS1 binds to dsRNA structures in the SARS-CoV-2 5′-UTR and initiates a potent block to SARS-CoV-2 replication. Thus, the correct targeting of OAS1 and the subsequent inhibition of SARS-CoV-2 likely underpins the genetic association of alleles containing a G at Rs10774671 with reduced susceptibility to infection and severe disease in COVID-19. Moreover, the conspicuous absence of this antiviral defense in horseshoe bats potentially explains why SARS-CoV-2 is so sensitive to this defense in humans

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

On 24th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses

A prenylated dsRNA sensor protects against severe COVID-19

Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that OAS1, through RNase L, potently inhibits SARS-CoV-2. We show that a common splice-acceptor SNP (Rs10774671) governs whether people express prenylated OAS1 isoforms that are membrane-associated and sense specific regions of SARS-CoV-2 RNAs, or only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. Importantly, in hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting this antiviral defense is a major component of a protective antiviral response

A saturated map of common genetic variants associated with human height

Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes(1). Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel(2)) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10-20% (14-24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.A large genome-wide association study of more than 5 million individuals reveals that 12,111 single-nucleotide polymorphisms account for nearly all the heritability of height attributable to common genetic variants

A saturated map of common genetic variants associated with human height.

Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10-20% (14-24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries

Environmental catastrophes in Mauritania, the desert and the coast (Volume of abstracts and field guide)

Abstracts from the conference volume can be accessed via the link below