Becoming Human:An Ancient Genome Perspective

Writing a commentary in the 50th anniversary issue of Cell,Profs.FU Qiaomei and E.Andrew Bennett,both from the Institute of Vertebrate Paleontology and Paleoanthropology(IVPP)of the Chinese Academy of Sciences,explored the contribution of paleogenomics to the evolution of modern humans.

Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips

To understand how differentially methylated genes（DMGs）might affect the pathogenesis of Kashin-Beck disease（KBD）.Genome-wide methylation profiling of whole blood from 12matched KBD and controls pairs was performed using a high-resolution Infinium 450 K methylation array.In total,97 CpG sites were differentially

From human genome epidemiology to systems epidemiology:current progress and future perspective

The recent progress in human genome epidemiology(HuGE) is already having a profound impact on the practice of medicine and public health.First,the success of genome-wide association studies has greatly expanded the direction and content of epidemiological researches,including revealing new genetic mechanisms of complex diseases,identifying new targets for therapeutic interventions,and improving application in early screening of high-risk populations.At the same time,large-scale genomic studies make it possible to efficiently explore the gene-environment interactions,which will help better understand the biological pathways of complex diseases and identify individuals who may be more susceptible to diseases.Additionally,the emergence of systems epidemiology aims to integrate multi-omics together with epidemiological data to create a systems network that can comprehensively characterize the diverse range of factors contributing to disease development.These progress will help to apply HuGE findings into practice to improve the health of individuals and populations.

CHINESE HUMAN GENOME PROJECT (HGP) MADE SIGNIFICANT PROGRESS

The first stage of HGP in China (Jan. 1994～Jun. 1997) was sponsored by the National Natural Science Foundation of China in the form of a principle project (total funding: 3,750,000 RMB) entitled "Study on gene structure of some loci in the genome of Chinese nationalities". After 3 and half years’ collaborative work by 19 groups and about 200 scientists distributed in 16 participating labs, coordinated by Prof. Bo-Qing QIANG of the Institute of Basic Medical Sciences, Chinese

The Human Genome Map

ON April 14, 2003, scientists from China, the United States. Japan, Germany, France and Britain announced they had completed sequence mapping of the human genome, marking the end of the Human Genome Project （HGP） started in 1990. Yang Huanming, an academician from the Chinese Academy of Sciences （CAS） and Chairman of the Shenzhen branch of the Beijing Genomics Institute （BGI）. led the group of Chinese experts that contributed to the project. The Chinese team played an integral part in the research unti August 26, 2001.

Identification of TSS in the Human Genome Based on a RBF Neural Network

The identification of functional motifs in a DNA sequence is fundamentally a statistical pattern recognition problem. This paper introduces a new algorithm for the recognition of functional transcription start sites （TSSs） in human genome sequences, in which a RBF neural network is adopted, and an improved heuristic method for a 5-tuple feature viable construction, is proposed and implemented in two RBFPromoter and ImpRBFPromoter packages developed in Visual C＋＋ 6.0. The algorithm is evaluated on several different test sequence sets. Compared with several other promoter recognition programs, this algorithm is proved to be more flexible, with stronger learning ability and higher accuracy.

The effects of human genome DNA on spinal cord neurons of the embryonic mouse in vitro

objective: To study the effects of human genome DNA on the cultured spinal cord neurons of em bryonic mouse. Methods: The human genome DNA was added to the culture medium of the spinal cord neu rons of embryonic mouse. Eight days later, MTT assay, NSE immunocytochemical staining and image analy sis were proformed to examine the viabilities and the neurites lengths of the neurons. Results: The neurite length of the experimental group was significantly Ionger than that of the control group, but no marked dif ference was found between the viabilities of the neurons of the experimental groups and that of the control ones. Conclusiou: Human genome DNA has no effects on the viabilities of the cultured neurons but can pro mote the neurite growth.

Genome-wide comparison inferred the origin and evolution of B-cell epitopes on the proteins of human influenza A virus

The novel strain H1N1 caused the outbreak of first pandemic influenza in 21 century. Now it is a common component of current seasonal influenza viruses. The recent transmission and plentiful genome sequences available provided a good opportunity to study the origin and evolution of epitopes on the proteins of human influenza virus. In the present study, the B-cell epitope compositions in the pandemic strains, circulating traditional seasonal strains, swine strains as well as highly virulent avian strain H5N1 were identified with the aid of the Immune Epitope DataBase (IEDB) and were compared at genomic level. A total of 14210 distinct sequences down-loaded from NCBI database were used for analysis. Some epitopes on proteins HA or NA, not conserved in recent seasonal strains, were found in 2009 pandemic strains but existed in the early human strains (1919-1935). The pandemic strain shared higher conserved epitopes with “bird flu” virus H5N1than classic human seasonal strains. The epitopes that could exist at common antigenic regions of HA protein are needed to further identify. The genetic exchanges between human and swine population by transmission was very active but the princepal side of the transmission could be from swine to human. These results provided valuable information on influenza A virus evolution and transmission by means of epitope analysis at genomic level.

The Historical Position and Value Dimensions of Human Rights Civilization

Human beings are the mainstay and the ultimate goal of civilization.The history of human civilization is a continuous struggle to realize the respect,liberation,protection,and development of humanity.Human rights are an achievement of humanity and a symbol of progress,and the human rights civilization is an important component of human civilization.Understanding and interpreting human rights from the perspective of human rights civilization means that human rights are not only a concept or an idea but also a grand historical and long-term social practice.Up to now,the development of human rights civilization has roughly experienced four awakening eras:initialization,revolution,popularization,and globalization.In terms of its value dimensions,it has the characteristics of progressiveness,diversity,commonality,inclusiveness,indivisibility,openness,and so on.The historical position of human rights civilization and the development of its value dimensions have shown to the world that human rights are the common wealth of humanity,and human rights belong to all mankind;human rights are historical,concrete,and developmental;the concept of human rights is constantly evolving,and its connotations and categories are constantly expanding;achieving the free and well-rounded development of every person is the highest value realm of human rights civilization.The Chinese modernization endows Chinese civilization with modern strength and opens up new horizons for human rights civilization.The new pattern of human rights civilization to be created by Chinese modernization not only possesses the common characteristics of human rights civilization but also enjoys Chinese characteristics based on its own national conditions,enriching and developing the diversity of human rights civilization for all mankind.

Pioneering a New Realm of Human Rights Civilization in the Chinese Path to Modernization——An Overview of the Symposium on“The Chinese Path to Modernization and the Promotion of Free and Comprehensive Human Development”

On October 14,2023,a symposium themed“The Chinese Path to Modernization and the Promotion of Free and Comprehensive Human Development”was held in Changchun,Jilin Province,China.More than fifty experts,scholars,and researchers from national institutions and universities engaged in discussions and exchanges on human rights on the Chinese path to modernization,including the path,practice,knowledge systems,and civilization forms of human rights.This symposium played a significant role in advancing the construction of the disciplinary system,academic system,and discourse system of human rights in China.

Revisiting the Spirit of the UDHR and Discussing Human Rights Development——Summary of Views from the Seminar Commemorating the 75th Anniversary of the Universal Declaration of Human Rights

On December 4,2023,the China Society for Human Rights Studies hosted a seminar in Beijing commemorating the 75^(th) Anniversary of the Universal Declaration of Human Rights.Participants discussed topics such as the significance of the Universal Declaration of Human Rights,China’s theories and practices in respecting and safeguarding human rights,the three global initiatives and global human rights governance,human rights protection in the digital age,and telling Chinese stories of human rights in the new era.The discussions led to a broad consensus and achieved positive results.

From Human Genome and Gut Microbiome to Personalized Cancer Nutrition

In attempts to improve the quality of life for both healthy and diseased patients,dietary and lifestyle guidelines have been formulated by numerous organizations.However,dietary and lifestyle changes are often insufficient to prevent or cure diseases.Of note,the development of cancer has been shown to be closely related to an individual’s dietary and xenobiotic intake.Interestingly,studies have shown that different people have different reactions to the same dietary interventions.The development of genomic and gut microbiome technologies has started to illuminate internal causes of many of the above phenomena.Variations in the genome affect an individual’s metabolism and the bioavailability of nutrients.Variations in the bacterial colonization lead to different functional potentials for the microbe,differences in metabolite production and modulation of the host’s metabolism.Quantifying and incorporating these factors into a comprehensive individualized nutrition plan may enable cancer patients to receive rational and effective nutritional treatment.

On the Protection of the Rights of Future Generations in the Context of Human Germline Genome Editing

Human germline genome editing has inherent risks in the use of the technologies, as well as unknown genetic and social risks. The application of such technologies by the present generations will adversely affect human dignity, right to life and health, right to biological information integrity, genetic autonomy and other specific rights of future generations. Legal protection should be provided for the rights of future generations affected by human germline genome editing, which is supported by the theories of intergenerational equity,the intergenerational social contract and an intergenerational community with a shared future for human beings. In spite of the continuously improved regulation of germline genome editing in China, the attention paid to the rights of future generations remains insufficient.Learning from international legislation, in combination with the current research and applications of germline genome editing, China can strengthen the protection of the rights of future generations in the context of human germline gene editing from three aspects: clarifying the principles and contents regarding the rights protection of future generations, strengthening the oversight of germline genome editing,and promoting the implementation of laws and regulations such as the Biosecurity Law.

Expression of hepatitis B virus genes in early embryonic cells originated from hamster ova and human spermatozoa transfected with the complete viral genome

Aim： To detect the expression of hepatitis B virus （HBV） genes （HB S and C genes） in early embryonic cells after introducing motile human sperm carrying HBV DNA into zona-free hamster oocytes via the in vitro fertilization （IVF） technique. Methods： Human sperm-mediated HBV genes were delivered into zona-free hamster oocytes by the IVF method. Polymerase chain reaction （PCR） was used to detect HB S and pre-Core/Core （pre-C/C） coding genes both in one- and two-cell embryos. Reverse transcription-PCR （RT-PCR） analysis was used to study the expression of the two genes. Fluorescence in situ hybridization （FISH） analysis using the full-length HBV DNA as the hybridization probe was performed to confirm the integration of viral DNA in the host embryonic genome. Results： Both HB S and pre-C/C coding genes are present and transcribed in one- and two-cell embryos originated from hamster ova IVF with human spermatozoa carrying HBV DNA sequences. Conclusion： Sperm-mediated HBV genes are able to replicate and express themselves in early embryonic cells. These results provide direct evidence that HBV DNA could transmit vertically to the next generation via the male germ line.

Haploidization of Human Diploid Metaphase Cells: Is This Genome Reductive Mechanism Opperational in Near-Haploid Leukemia?

The present study presents cytogenetics/cytology of haploidization in the origin of a new, fast growing diploid, small cell-type (F-dPCs). The sequence of events was haploid groupings of the chromosomes in normal, human metaphase cells, followed by genomic doubling to homozygousdiploidy. These events were responses to DNA replication stress fromamino acid glutamine deprivation. Importantly, these homozygous cells outgrew normal fibroblasts in 2 - 3 passages—they had gained proliferative advantage (GPA), presumably from loss (LOH) of tumor suppressor genes. They were morphologically changed cells with rounded nuclei that grew in a “streaming” growth pattern and with changed form and size of mitosis, similar to some hyperplasias. The grouping of the chromosomes in metaphase cells was asymmetric with a narrow range around the median (23) (no micro-nuclei), suggesting genetic control. The root-origin of haploidization was evidenced by maternal and paternal genomes occupying separate territories in metaphase cells, which assumedly permitted independent segregations of bichromatid chromosomes. In near-haploid ALL-L1 leukemia the loss of virtually, whole chromosomal complements was judged by SNP array analyses, as a primary event before genomic doubling to hyperdiploidy with LOH. From the present data such specific, non-random loss of chromosomes strongly suggested, a haploidization process capable of genomic doubling, as observed for the “birth” of the small, F-dPCs. This suggestion was supported by this type of leukemia being the L1-type, where L1 signifies small cells. The possibility now exists that a tumorigenic process can be initiated directly from diploid cells through haploid (near-haploid) distributed chromosomes in normal metaphase cells. This event followed by monosomic doublings to UPDs would lead to massive LOH and a return to para-diploidy, a frequent occurrence in many types of tumors. The present simple, cultural derivations of the extraordinary F-dPCs allow GPA-identification and experimental manipulations, perhaps relevant in a vaccine program.

Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGEN^TMBio-IT Processor for Precision Medicine

Slow speed of the Next-Generation sequencing data analysis, compared to the latest high throughput sequencers such as HiSeq X system, using the current industry standard genome analysis pipeline, has been the major factor of data backlog which limits the real-time use of genomic data for precision medicine. This study demonstrates the DRAGEN Bio-IT Processor as a potential candidate to remove the “Big Data Bottleneck”. DRAGENTM accomplished the variant calling, for ~40× coverage WGS data in as low as ~30 minutes using a single command, achieving the over 50-fold data analysis speed while maintaining the similar or better variant calling accuracy than the standard GATK Best Practices workflow. This systematic comparison provides the faster and efficient NGS data analysis alternative to NGS-based healthcare industries and research institutes to meet the requirement for precision medicine based healthcare.

Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome

INTRODUCTIONNuclearpseudogenesofmitochondrial(mt)DNAwereinitiallydiscoveredintheearly80's[1--6].However,mechanismsforthegenerationofmtDNApseudogenesarestillnotclearandmayvaryindifferentcases.BothRNA--[7--8]andDNAmediated[9--11]processeshavebeensugges...

Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family

Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.

Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.