Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.     

Subspecies in Przewalski’s gazelle Procapra przewalskii and its conservation implication

Przewalski’s gazelle Procapra przewalskii is an endangered species endemic to China. A question remains about subspecific variation in this species. Skulls of Przewalski’s gazelle collected from its current remnant ranges around the Qinghai Lake in combination with those collected prior to the 20th century were measured and analyzed using Hierarchical Cluster Analysis in order to clarify the question. Unexpectedly, P. p. diversicornis, extirpated from its historic range, has spread to the Qinghai Lake region where it has replaced nominotypical P. p. przewalskii and is now restricted to a few small isolated populations around the lake. We discuss the causes of this unexpected replacement. In this study, we discuss the possibility of a new form, possibly a new subspecies, in the Guide Basin, adjacent to Qinghai Lake; it is unclear whether the new form has long existed and was only discovered in recent years, or whether it evolved in recent times due to the geographical isolation and anthropogenic landscape features. The study sheds light on the processes of microevolution and subspeciation in Procapra przewalskii, and based on the findings, we propose measures for conservation strategies for Przewalski’s gazelle.     

Biogenically driven organic contribution to marine aerosol

Marine aerosol contributes significantly to the global aerosol load and consequently has an important impact on both the Earth's albedo and climate. So far, much of the focus on marine aerosol has centred on the production of aerosol from sea-salt and non-sea-salt sulphates. Recent field experiments, however, have shown that known aerosol production processes for inorganic species cannot account for the entire aerosol mass that occurs in submicrometre sizes. Several experimental studies have pointed to the presence of significant concentrations of organic matter in marine aerosol. There is some information available about the composition of organic matter, but the contribution of organic matter to marine aerosol, as a function of aerosol size, as well as its characterization as hydrophilic or hydrophobic, has been lacking. Here we measure the physical and chemical characteristics of submicrometre marine aerosol over the North Atlantic Ocean during plankton blooms progressing from spring through to autumn. We find that during bloom periods, the organic fraction dominates and contributes 63% to the submicrometre aerosol mass (about 45% is water-insoluble and about 18% water-soluble). In winter, when biological activity is at its lowest, the organic fraction decreases to 15%. Our model simulations indicate that organic matter can enhance the cloud droplet concentration by 15% to more than 100% and is therefore an important component of the aerosol-cloud-climate feedback system involving marine biota.     

Accurate whole human genome sequencing using reversible terminator chemistry

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.     

Clay minerals in surface sediments of the Pearl River drainage basin and their contribution to the South China Sea

Clay minerals have played a significant role in the study of the East Asian monsoon evolution in the South China Sea by being able to track oceanic current variations and to reveal contemporaneous paleoclimaUc changes prevailing in continental source areas. As one of the most important rivers inputting terrigenous matters to the northern South China Sea, the Pearl River was not previously paid attention to from the viewpoint of clay mineralogy. This paper presents a detailed study on clay minerals in surface sediments collected from the Pearl River drainage basin （including all three main channels, various branches, and the Lingdingyang in the estuary） by using the X-ray diffraction （XRD） method. The results indicate that the clay mineral assemblage consists dominantly of kaolinite （35%-65%）, lesser abundance of chlorite （20%-35%） and illite （12%-42%）, and very scare smectite occurrences （generally 〈5%）. Their respective distribution does not present any obvious difference throughout the Pearl River drainage basin. However, downstream the Pearl River to the northern South China Sea, the clay mineral assemblage varies significantly： kaolinite decreases gradually, smecUte and illite increase gradually. Additionally, illite chemistry index steps down and illite crystallinity steps up. These variations indicate the contribution of major kaolinite, lesser illite and chlorite, and very scarce smecUte to the northern South China Sea from the Pearl River drainage basin. The maximum contribution of clay minerals from the Pearl River is 72% to the northern margin and only 15% to the northern slope of the South China Sea. In both glacials and interglacials, kaolinite indicates that the ability of mechanical erosion occurred in the Pearl River drainage basin.