[Abstract unavailable

Comprehensive identification and cataloging of copy number variations (CNVs) is required to provide a complete view of human genetic variation. The resolution of CNV detection in previous experimental designs has been limited to tens or hundreds of kilobases. Here we present PennCNV, a hidden Markov model (HMM) based approach, for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources of information, including total signal intensity and allelic intensity ratio at each SNP marker, the distance between neighboring SNPs, the allele frequency of SNPs, and the pedigree information where available. We applied PennCNV to genotyping data generated for 112 HapMap individuals; on average, we detected ∼27 CNVs for each individual with a median size of ∼12 kb. Excluding common rearrangements in lymphoblastoid cell lines, the fraction of CNVs in offspring not detected in parents (CNV-NDPs) was 3.3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping.

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A remarkable feature of modern silicon electronics is its ability to remain functionally and physically invariant, almost indefinitely for many practical purposes. Here, we introduce a silicon-based technology that offers the opposite behavior: it gradually vanishes over time, in a well-controlled, programmed manner. Devices that are ‘transient’ in this sense create application possibilities that cannot be addressed with conventional electronics, such as active implants that exist for medically useful timeframes, but then completely dissolve and disappear via resorption by the body. We report a comprehensive set of materials, manufacturing schemes, device components and theoretical design tools for a complementary metal oxide semiconductor (CMOS) electronics of this type, together with four different classes of sensors and actuators in addressable arrays, two options for power supply and a wireless control strategy. A transient silicon device capable of delivering thermal therapy in an implantable mode and its demonstration in animal models illustrate a system-level example of this technology.

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within-and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.Asian cultivated rice is grown worldwide and comprises the staple food for half of the global population. It is envisaged that by the year 2035 1 feeding this growing population will necessitate that an additional 112 million metric tons of rice be produced on a smaller area of land, using less water and under more fluctuating climatic conditions, which will require that future rice cultivars be higher yielding and resilient to multiple abiotic and biotic stresses. The foundation of the continued improvement of rice cultivars is the rich genetic diversity within domesticated populations and wild relatives [2][3][4] . For over 2,000 years, two major types of O. sativa-O. sativa Xian group (here referred to as Xian/Indica (XI) and also known as , Hsien or Indica) and O. sativa Geng Group (here referred to as Geng/Japonica (GJ) and also known as , Keng or Japonica)-have historically been recognized [5][6][7] . Varied degrees of post-reproductive barriers exist between XI and GJ rice accessions 8 ; this differentiation between XI and GJ rice types and the presence of different varietal groups are well-documented at isozyme and DNA levels 6,9 . Two other distinct groups have also been recognized using molecular markers 10 ; one of these encompasses the Aus, Boro and Rayada ecotypes from Bangladesh and India (which we term the circum-Aus group (cA)) and the other comprises the famous Basmati and Sadri aromatic varieties (which we term the circum-Basmati group (cB)).Approximately 780,000 rice accessions are available in gene banks worldwide 11 . To enable the more efficient use of these accessions in future rice improvement, the Chinese Academy of Agricultural Sciences, BGI-Shenzhen and International Rice Research Institute sequenced over 3,000 rice genomes (3K-RG) as part of the 3,000 Rice Genomes Project 12. Here we present analyses of genetic variation in the 3K-RG that focus on important aspects of O. sativa diversity, single nucleotide polymorphisms (SNPs) and structural variation (deletions, duplications, inversions and translocations). We also construct a species pangenome consisting of 'core...

The gut microbiota benefits humans via short-chain fatty acid (SCFA) production from carbohydrate fermentation, and deficiency in SCFA production is associated with type 2 diabetes mellitus (T2DM). We conducted a randomized clinical study of specifically designed isoenergetic diets, together with fecal shotgun metagenomics, to show that a select group of SCFA-producing strains was promoted by dietary fibers and that most other potential producers were either diminished or unchanged in patients with T2DM. When the fiber-promoted SCFA producers were present in greater diversity and abundance, participants had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production. Promotion of these positive responders diminished producers of metabolically detrimental compounds such as indole and hydrogen sulfide. Targeted restoration of these SCFA producers may present a novel ecological approach for managing T2DM.

AbstractBackgroundAs the number of patients increases, there is a growing understanding of the form of pneumonia sustained by the 2019 novel coronavirus (SARS-CoV-2), which has caused an outbreak in China. Up to now, clinical features and treatment of patients infected with SARS-CoV-2 have been reported in detail. However, the relationship between SARS-CoV-2 and coagulation has been scarcely addressed. Our aim is to investigate the blood coagulation function of patients with SARS-CoV-2 infection.MethodsIn our study, 94 patients with confirmed SARS-CoV-2 infection were admitted in Renmin Hospital of Wuhan University. We prospectively collect blood coagulation data in these patients and in 40 healthy controls during the same period.ResultsAntithrombin values in patients were lower than that in the control group (p < 0.001). The values of D-dimer, fibrin/fibrinogen degradation products (FDP), and fibrinogen (FIB) in all SARS-CoV-2 cases were substantially higher than those in healthy controls. Moreover, D-dimer and FDP values in patients with severe SARS-CoV-2 infection were higher than those in patients with milder forms. Compared with healthy controls, prothrombin time activity (PT-act) was lower in SARS-CoV-2 patients. Thrombin time in critical SARS-CoV-2 patients was also shorter than that in controls.ConclusionsThe coagulation function in patients with SARS-CoV-2 is significantly deranged compared with healthy people, but monitoring D-dimer and FDP values may be helpful for the early identification of severe cases.

SUMMARY B lymphocytes have critical roles as positive and negative regulators of immunity. Their inhibitory function has so far been associated primarily with interleukin (IL)-10 because B cell-derived IL-10 can protect against autoimmune disease and increase susceptibility to pathogens1,2. Here, we identify IL-35-producing B cells as novel key players in the negative regulation of immunity. Mice in which only B cells did not express IL-35 lost their ability to recover from the T cell-mediated demyelinating autoimmune disease experimental autoimmune encephalomyelitis (EAE). In contrast, these mice displayed a strikingly improved resistance to infection with the intracellular bacterial pathogen Salmonella typhimurium, as shown by their superior containment of the bacterial growth and their prolonged survival both after primary infection, and upon secondary challenge after vaccination, compared to control mice. The increased immunity found in mice lacking IL-35 production by B cells was associated with a higher activation of macrophages and inflammatory T cells, as well as an enhanced stimulatory function of B cells as antigen-presenting cells (APC). During Salmonella infection IL-35- and IL-10-producing B cells corresponded to two largely distinct sets of surface-IgM+CD138hiTACI+CXCR4+CD1dintTim1int plasma cells expressing the transcription factor Blimp1. During EAE CD138+ plasma cells were also the major source of B cell-derived IL-35 and IL-10. Collectively, our data unravel the importance of IL-35-producing B cells in regulation of immunity, and highlight IL-35 production by B cells as a novel therapeutic target for autoimmune and infectious diseases. More generally, this study emphasizes the central role of activated B cells, particularly plasma cells, and their production of cytokines in the regulation of immune responses in health and disease.