Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Dehydration Versus Deamination of N-Terminal Glutamine in Collision-Induced Dissociation of Protonated Peptides

Some of the most prominent “neutral losses” in peptide ion fragmentation are the loss of ammonia and water from N-terminal glutamine. These processes are studied by electrospray ionization mass spectrometry in singly- and doubly-protonated peptide ions undergoing collision-induced dissociation in a triple quadrupole and in an ion trap instrument. For this study, four sets of peptides were synthesized: (1) QLLLPLLLK and similar peptides with K replaced by R, H, or L, and Q replaced by a number of amino acids, (2) QLnK (n = 0, 1, 3, 5, 7, 9, 11), (3) QLnR (n = 0, 1, 3, 5, 7, 9), and (4) QLn (n = 1, 2, 3, 4, 8). The results for QLLLPLLLK and QLLLPLLLR show that the singly protonated ions undergo loss of ammonia and to a smaller extent loss of water, whereas the doubly protonated ions undergo predominant loss of water. The fast fragmentation next to P (forming the y5 ion) occurs to a larger extent than the neutral losses from the singly protonated ions but much less than the water loss from the doubly protonated ions. The results from these and other peptides show that, in general, when N-terminal glutamine peptides have no “mobile protons”, that is, the number of charges on the peptide is no greater than the number of basic amino acids (K, R, H), deamination is the predominant neutral loss fragmentation, but when mobile protons are present the predominant process is the loss of water. Both of these processes are faster than backbone fragmentation at the proline. These results are rationalized on the basis of resonance stabilization of the two types of five-membered ring products that would be formed in the neutral loss processes; the singly protonated ion yields the more stable neutral pyrrolidinone ring whereas the doubly protonated ion yields the protonated aminopyrroline ring (see Schemes). The generality of these trends is confirmed by analyzing an MS/MS spectra library of peptides derived from tryptic digests of yeast. In the absence of mobile protons, glutamine deamination is the most rapid neutral loss process. For peptides with mobile protons, dehydration from glutamine is far more rapid than from any other amino acid. Most strikingly, end terminal glutamine is by far the most labile source of neutral loss in excess-proton peptides, but not highly exceptional when mobile protons are not available. In addition, rates of deamination are faster in lysine versus arginine C-terminus peptides and 20 times faster in positively charged than negatively charged peptides, demonstrating that these formal neutral loss reactions are not “neutral reactions” but depend on charge state and stability

A new species of the genus Soriculus (Soricidae, Eulipotyphla, Mammalia) from Medog in the eastern Himalaya

Himalayan shrews of the genus Soriculus (Soricidae, Eulipotyphla), currently represented by four nominal species, are endemic to the Himalayas and the Gaoligong Mountains. In April 2022 and April 2023, a total of 10 specimens of Soriculus were collected from Beibeng and Damu, Medog County, Tibet, China. The morphology of the specimens was compared with the four recognised species of the genus Soriculus. Additionally, two mitochondrial (Cyt b and 12S) and three nuclear (APOB, BRCAI and RAG2) genes were sequenced to test the phylogenetic relationships of these specimens with the other species. Our results indicate that these specimens represent a distinct species, Soriculus beibengensis sp. nov., which is formally described here. The new species is distinguished from the other Soriculus species by the combination of darker pelages, smaller size, the relatively stubby nasal and the widened posterior processes of incisors. Phylogenetic analyses revealed the new species is sister to S. minor. The p–distance of Cyt b gene between S. beibengensis sp. nov. and other nominal Soriculus species ranges from 9.1–16.3%. This new species has a known distribution at an elevation of 1,500–2,125 m in Medog County, Tibet, China. The discovery of this new species from Medog County has important implications for interpreting small mammal biogeographic patterns in the eastern Himalaya and the mountain chains of south-west China

Plasmapause surface wave oscillates the magnetosphere and diffuse aurora

Energy circulation in geospace lies at the heart of space weather research. In the inner magnetosphere, the steep plasmapause boundary separates the cold dense plasmasphere, which corotates with the planet, from the hot ring current/plasma sheet outside. Theoretical studies suggested that plasmapause surface waves related to the sharp inhomogeneity exist and act as a source of geomagnetic pulsations, but direct evidence of the waves and their role in magnetospheric dynamics have not yet been detected. Here, we show direct observations of a plasmapause surface wave and its impacts during a geomagnetic storm using multi-satellite and ground-based measurements. The wave oscillates the plasmapause in the afternoon-dusk sector, triggers sawtooth auroral displays, and drives outward-propagating ultra-low frequency waves. We also show that the surface-wave-driven sawtooth auroras occurred in more than 90% of geomagnetic storms during 2014-2018, indicating that they are a systematic and crucial process in driving space energy dissipation

Ameliorants improve saline-alkaline soils on a large scale in northern Jiangsu Province, China

In order to improve the coastal saline-alkali soil in north Jiangsu Province, the effects of a newly-developed ameliorant was compared with gypsum and cow manure in field trials in coastal saline soil in Dafeng County, China. Measurements included soil electrical conductivity, pH, soil nutrients, the plant (Salicornia europea L.) growth and ion concentration in stems and roots. The three ameliorants and their combinations improved soil physical and chemical properties and increased the plant height and stem diameter in the order of cow dung > gypsum > new ameliorant. During the experimental period, the soil electrical conductivity of the optimum combination decreased initially and then increased, but was lower than that in the other treatments. Compared with the control, the pH value in the optimum treatment increased by 10.4%, 9.2% and 5.2% in 0-5, 5-20 and 20-40 cm soil layers, respectively. The content of soil organic matter in the three soil layers increased by 22%, 28% and 10%, respectively. The total potassium content in different soil layers increased by 23%, 26% and 26%, respectively. In the optimal treatment, the height of S. europea increased by 32% and stem diameter by 20% compared with control. The K+ and Ca2+ concentration in roots and stems of S. europaea was significantly higher in the optimum treatment compared with control. The optimum combination (in t/ha) was: the new ameliorant 45, gypsum 18 and cow dung 300. (C) 2015 Elsevier B.V. All rights reserved.In order to improve the coastal saline-alkali soil in north Jiangsu Province, the effects of a newly-developed ameliorant was compared with gypsum and cow manure in field trials in coastal saline soil in Dafeng County, China. Measurements included soil electrical conductivity, pH, soil nutrients, the plant (Salicornia europea L.) growth and ion concentration in stems and roots. The three ameliorants and their combinations improved soil physical and chemical properties and increased the plant height and stem diameter in the order of cow dung > gypsum > new ameliorant. During the experimental period, the soil electrical conductivity of the optimum combination decreased initially and then increased, but was lower than that in the other treatments. Compared with the control, the pH value in the optimum treatment increased by 10.4%, 9.2% and 5.2% in 0-5, 5-20 and 20-40 cm soil layers, respectively. The content of soil organic matter in the three soil layers increased by 22%, 28% and 10%, respectively. The total potassium content in different soil layers increased by 23%, 26% and 26%, respectively. In the optimal treatment, the height of S. europea increased by 32% and stem diameter by 20% compared with control. The K+ and Ca2+ concentration in roots and stems of S. europaea was significantly higher in the optimum treatment compared with control. The optimum combination (in t/ha) was: the new ameliorant 45, gypsum 18 and cow dung 300. (C) 2015 Elsevier B.V. All rights reserved