Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin

Although nucleosome remodeling is essential to transcriptional regulation in eukaryotes, little is known about its genome-wide behavior. Since a number of nucleosome positioning maps in vivo have been recently determined, we examined if their comparisons might be used for obtaining a genome-wide profile of nucleosome remodeling. Using seven yeast maps, the local variability of nucleosomes, measured by the entropy, was significantly higher in a set of reported unstable nucleosomes. The binding sites of four transcription factors, known as the remodeling factors, were distinctively high both in entropy and linker ratio, whereas those of Yhp1, their potential inhibitor, showed the lowest values in both of them. Taken together, our map shows the general information of nucleosome dynamics reasonably well. The “nucleosome dynamics” map provides the new significant correlation with the degree of expression variety instead of their intensity. Furthermore, the associations with gene function and histone modification were also discussed here

Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.</jats:p

A middle holocene steppe bison and paleoenvironments from the versleuce meadows, Whitehorse, Yukon, Canada

A partial skeleton of a bison was recovered during residential house construction in Whitehorse, Yukon, Canada. The specimen represents a young (estimated 6 year old) bison individual that died, was partially scavenged by carnivores, and subsequently buried by calcareous silt sediment in a pond or small lake during the middle Holocene, ~5400 years ago. Palaeoenvironmental data, including molluscs, pollen, vascular plant, and bryophyte macrofossils demonstrate that the small waterbody was surrounded by white spruce dominated boreal forest. Morphometric analysis of the skeleton reveals that its taxonomic affinity is ambiguous, likely owing to it representing an ontogenetically young individual, though it does share some cranial and horn core characteristics of named species such as Bison occidentalis or Bison priscus. Mitochondrial genomic data confirm that this bison belongs to Clade 2A (northern clade), which represents Pleistocene steppe bison (B. cf. priscus) in Beringia through the Holocene and is not represented in living bison species. These data further demonstrate that northern steppe bison population survived the late Pleistocene extinction event, persisted locally in southern Yukon into the Holocene, and are best characterized as a species with a high degree of morphological variability and ecological flexibility

A middle holocene steppe bison and paleoenvironments from the versleuce meadows, Whitehorse, Yukon, Canada

A partial skeleton of a bison was recovered during residential house construction in Whitehorse, Yukon, Canada. The specimen represents a young (estimated 6 year old) bison individual that died, was partially scavenged by carnivores, and subsequently buried by calcareous silt sediment in a pond or small lake during the middle Holocene, ~5400 years ago. Palaeoenvironmental data, including molluscs, pollen, vascular plant, and bryophyte macrofossils demonstrate that the small waterbody was surrounded by white spruce dominated boreal forest. Morphometric analysis of the skeleton reveals that its taxonomic affinity is ambiguous, likely owing to it representing an ontogenetically young individual, though it does share some cranial and horn core characteristics of named species such as Bison occidentalis or Bison priscus. Mitochondrial genomic data confirm that this bison belongs to Clade 2A (northern clade), which represents Pleistocene steppe bison (B. cf. priscus) in Beringia through the Holocene and is not represented in living bison species. These data further demonstrate that northern steppe bison population survived the late Pleistocene extinction event, persisted locally in southern Yukon into the Holocene, and are best characterized as a species with a high degree of morphological variability and ecological flexibility