PCNA Ubiquitination Is Important, But Not Essential for Translesion DNA Synthesis in Mammalian Cells

Translesion DNA synthesis (TLS) is a DNA damage tolerance mechanism in which specialized low-fidelity DNA polymerases bypass replication-blocking lesions, and it is usually associated with mutagenesis. In Saccharomyces cerevisiae a key event in TLS is the monoubiquitination of PCNA, which enables recruitment of the specialized polymerases to the damaged site through their ubiquitin-binding domain. In mammals, however, there is a debate on the requirement for ubiquitinated PCNA (PCNA-Ub) in TLS. We show that UV-induced Rpa foci, indicative of single-stranded DNA (ssDNA) regions caused by UV, accumulate faster and disappear more slowly in Pcna(K164R/K164R) cells, which are resistant to PCNA ubiquitination, compared to Pcna(+/+) cells, consistent with a TLS defect. Direct analysis of TLS in these cells, using gapped plasmids with site-specific lesions, showed that TLS is strongly reduced across UV lesions and the cisplatin-induced intrastrand GG crosslink. A similar effect was obtained in cells lacking Rad18, the E3 ubiquitin ligase which monoubiquitinates PCNA. Consistently, cells lacking Usp1, the enzyme that de-ubiquitinates PCNA exhibited increased TLS across a UV lesion and the cisplatin adduct. In contrast, cells lacking the Rad5-homologs Shprh and Hltf, which polyubiquitinate PCNA, exhibited normal TLS. Knocking down the expression of the TLS genes Rev3L, PolH, or Rev1 in Pcna(K164R/K164R) mouse embryo fibroblasts caused each an increased sensitivity to UV radiation, indicating the existence of TLS pathways that are independent of PCNA-Ub. Taken together these results indicate that PCNA-Ub is required for maximal TLS. However, TLS polymerases can be recruited to damaged DNA also in the absence of PCNA-Ub, and perform TLS, albeit at a significantly lower efficiency and altered mutagenic specificity

Hominin reactions to herbivore distribution in the Lower Palaeolithic of the Southern Levant

We explore the relationship between the edaphic potential of soils and the mineral properties of the underlying geology as a means of mapping the differential productivity of different areas of the Pleistocene landscape for large herbivores. These factors strongly control the health of grazing animals irrespective of the particular types of vegetation growing on them, but they have generally been neglected in palaeoanthropological studies in favour of a more general emphasis on water and vegetation, which provide an incomplete picture. Taking the Carmel-Galilee-Golan region as an example, we show how an understanding of edaphic potential provides insight into how animals might have exploited the environment. In order to simplify the analysis, we concentrate on the Lower Palaeolithic period and the very large animals that dominate the archaeofaunal assemblages of this period. Topography and the ability of soils to retain water also contribute to the differential productivity and accessibility of different regions and to patterns of seasonal movements of the animals, which are essential to ensure a supply of healthy fodder throughout the year, especially for large animals such as elephants, which require substantial regions of good grazing and browsing. Other animals migrating in groups have similar needs. The complex topography of the Southern Levant with frequent sudden and severe changes in gradient, and a wide variety of landforms including rocky outcrops, cliffs, gorges, and ridges, places major limits on these patterns of seasonal movements. We develop methods of mapping these variables, based on the geology and our substantial field experience, in order to create a framework of landscape variation that can be compared with the locations and contents of archaeological sites to suggest ways in which early hominins used the variable features of the landscape to target animal prey, and we extend the analysis to the consideration of smaller mammals that were exploited more intensively after the disappearance of the elephants. We consider some of the ways in which this regional-scale approach can be further tested and refined, and advocate the development of such studies as an essential contribution to understanding the wider pattern of hominin dispersal

A Spatial Distribution Study of Faunal Remains from Two Lower Magdalenian Occupation Levels in El Mirón Cave, Cantabria, Spain

Abstract: Human behaviour can be reconstructed by analysing specific activities and campsite organization using spatial analysis. The dense occupation layers of the Lower Cantabrian Magdalenian in the Northern Spain reveal varied aspects of Upper Palaeolithic lifeways, including evidence of specific localized activities. The outer vestibule of El Mirón cave has a particularly rich and intact Lower Magdalenian occupation horizon, Levels 15–17. The excavations in the outer vestibule “Cabin” area of the site revealed excellent bone preservation. Artefacts and faunal remains were individually recorded and sediments water-screened to yield a large sample of archaeological finds and spatial data. Zooarchaeological analysis provided the taxonomic, anatomic and taphonomic determination of the faunal individual finds. Smaller animal remains were categorized and counted; special attention was given to the identification of anthropogenic modifications such as burnt bones or bone flakes. These small refuse items are considered to be useful, in situ indicators of localized activities. The spatial distribution analysis of this dense and complex palimpsest of El Mirón Lower Cantabrian Magdalenian layers required GIS based methods including density analysis, heatmaps and cluster analysis. Based on the spatial distribution of Level 15 and 16 faunal remains, different activity areas were identified comprising hearth, working and dropping zones. These results imply the deliberately segregated use of space within the Lower Cantabrian Magdalenian site area, in which bone-processing activities played a central rol

The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well

Opportunism or aquatic specialization? Evidence of freshwater fish exploitation at Ohalo II- A waterlogged Upper Paleolithic site.

Analysis of ca. 17,000 fish remains recovered from the late Upper Paleolithic/early Epi-Paleolithic (LGM; 23,000 BP) waterlogged site of Ohalo II (Rift Valley, Israel) provides new insights into the role of wetland habitats and the fish inhabiting them during the evolution of economic strategies prior to the agricultural evolution. Of the current 19 native fish species in Lake Kinneret (Sea of Galilee), eight species were identified at Ohalo II, belonging to two freshwater families: Cyprinidae (carps) and Cichlidae (St. Peter fish). Employing a large set of quantitative and qualitative criteria (NISP, species richness, diversity, skeletal element representation, fragmentation, color, spatial distribution, etc.), we demonstrate that the inhabitants of Ohalo II used their knowledge of the breeding behavior of different species of fish, for year-round intensive exploitation

Frequency (NISP), percentage, and survival index (SI) calculated for cranial and postcranial bones, according to the studied loci at Ohalo II.

<p>Frequency (NISP), percentage, and survival index (SI) calculated for cranial and postcranial bones, according to the studied loci at Ohalo II.</p

Correspondence analysis of taxonomic groups’ relative abundance (%) in the natural accumulation and at Loci 1, 3, 7, and 8.

<p>Correspondence analysis of taxonomic groups’ relative abundance (%) in the natural accumulation and at Loci 1, 3, 7, and 8.</p

Ohalo II fish remains taxonomic composition, species richness and diversity, by studied loci (taxonomic abundance (%) is calculated according to the different taxonomic levels: Family, genus and species, and therefore the total NISP varies).

<p>Ohalo II fish remains taxonomic composition, species richness and diversity, by studied loci (taxonomic abundance (%) is calculated according to the different taxonomic levels: Family, genus and species, and therefore the total NISP varies).</p

Frequency (NISP) of colors and signs of burning recorded on fish remains from Ohalo II, according to the studied loci.

<p>Frequency (NISP) of colors and signs of burning recorded on fish remains from Ohalo II, according to the studied loci.</p