Abstract：
:The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.
journal_name
Genes (Basel)journal_title
Genesauthors
Ferrari G,Lischer HEL,Neukamm J,Rayo E,Borel N,Pospischil A,Rühli F,Bouwman AS,Campana MGdoi
10.3390/genes9090436subject
Has Abstractpub_date
2018-08-31 00:00:00issue
9issn
2073-4425pii
genes9090436journal_volume
9pub_type
杂志文章相关文献
Genes文献大全abstract：BACKGROUND:Engineering apomixis in sexually reproducing plants has been long desired because of the potential to fix hybrid vigor. Validating the functionality of genes originated from apomictic species that contribute to apomixis upon transfer to sexually reproducing species is an important step. The PsASGR-BABYBOOM-l...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11091072
更新日期：2020-09-12 00:00:00
abstract：:The prevalence of the so-called diseases of affluence, such as type 2 diabetes or hypertension, has increased dramatically in the last two generations. Although genome-wide association studies (GWAS) have discovered hundreds of genes involved in disease etiology, the sudden increase in disease incidence suggests a maj...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9080411
更新日期：2018-08-14 00:00:00
abstract：:Leafminer insects of the genus Liriomyza are small flies whose larvae feed on the internal tissue of some of the most important crop plants for the human diet. Several of these pest species are highly uniform from the morphological point of view, meaning molecular data represents the only reliable taxonomic tool usefu...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9110554
更新日期：2018-11-15 00:00:00
abstract：:One of the hallmarks of cancer cells is their indefinite replicative potential, made possible by the activation of a telomere maintenance mechanism (TMM). The majority of cancers reactivate the reverse transcriptase, telomerase, to maintain their telomere length but a minority (10% to 15%) utilize an alternative lengt...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes11020133
更新日期：2020-01-27 00:00:00
abstract：:In human pre-mRNA splicing, infrequent errors occur resulting in erroneous splice products as shown in a genome-wide approach. One characteristic subgroup consists of products lacking one cassette exon. The noise in the splicing process, represented by those misspliced products, can be increased by cold shock treatmen...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes2030562
更新日期：2011-08-02 00:00:00
abstract：:During CRISPR/Cas9 mediated genome editing, site-specific double strand breaks are introduced and repaired either unspecific by non-homologous end joining (NHEJ) or sequence dependent by homology directed repair (HDR). Whereas NHEJ-based generation of gene knock-out is widely performed, the HDR-based knock-in of speci...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9060296
更新日期：2018-06-13 00:00:00
abstract：:Rapeseed contains glucosinolates, a toxic group of sulfur-containing glucosides, which play critical roles in defense against herbivores and microbes. However, the presence of glucosinolates in rapeseed reduces the value of the meal as feed for livestock. We performed association mapping of seed glucosinolate (GS) con...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes6041215
更新日期：2015-11-18 00:00:00
abstract：:Single-cell RNA-seq (scRNA-seq) is quite prevalent in studying transcriptomes, but it suffers from excessive zeros, some of which are true, but others are false. False zeros, which can be seen as missing data, obstruct the downstream analysis of single-cell RNA-seq data. How to distinguish true zeros from false ones i...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11050532
更新日期：2020-05-11 00:00:00
abstract：:Prader-Willi syndrome (PWS) is a complex multisystemic condition caused by a lack of paternal expression of imprinted genes from the 15q11.2-q13 region. Limited literature exists on the association between molecular classes, growth hormone use, and the prevalence of psychiatric phenotypes in PWS. In this study, we ana...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11111250
更新日期：2020-10-23 00:00:00
abstract：:MicroRNAs (miRNAs) are short, single-stranded, non-coding RNA molecules that act as post-transcriptional gene regulators. They can inhibit target protein-coding genes, through repressing messenger RNA (mRNA) translation or promoting their degradation. miRNAs were initially found to be originated from nuclear genome an...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes5040865
更新日期：2014-09-26 00:00:00
abstract：:Pulmonary hypertension (PH) is a serious disorder with high morbidity and mortality rate. We analyzed the right-ventricular systolic pressure (RVSP), right-ventricular hypertrophy (RVH), lung histology, and transcriptomes of six-week-old male rats with PH induced by (1) hypoxia (HO), (2) administration of monocrotalin...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11020126
更新日期：2020-01-23 00:00:00
abstract：:Novel coat colour phenotypes often emerge during domestication, and there is strong evidence of genetic selection for the two main genes that control base coat colour in horses-ASIP and MC1R. These genes direct the type of pigment produced, red pheomelanin (MC1R) or black eumelanin (ASIP), as well as the relative conc...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11060606
更新日期：2020-05-30 00:00:00
abstract：:Ehlers-Danlos syndrome (EDS) comprises clinically heterogeneous connective tissue disorders with diverse molecular etiologies. The 2017 International Classification for EDS recognized 13 distinct subtypes caused by pathogenic variants in 19 genes mainly encoding fibrillar collagens and collagen-modifying or processing...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10020135
更新日期：2019-02-12 00:00:00
abstract：:The nitrogen use efficiency (NUE) of crop plants is limited and enhancing it in rice, a major cereal crop, would be beneficial for farmers and the environment alike. Here we report the genome-wide transcriptome analysis of two rice genotypes, IR 64 (IR64) and Nagina 22 (N22) under optimal (+N) and chronic starvation (...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9040206
更新日期：2018-04-11 00:00:00
abstract：:Our current knowledge of B chromosome biology has been augmented by an increase in the number and diversity of species observed to carry B chromosomes as well as the use of next-generation sequencing for B chromosome genomic analysis. Within the genus Drosophila, B chromosomes have been observed in a handful of specie...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes9100470
更新日期：2018-09-27 00:00:00
abstract：:Microaneurysms (MAs) are the earliest detectable diabetic retinopathy (DR) lesions. Thus, the ability to automatically detect MAs is critical for the early diagnosis of DR. However, achieving the accurate and reliable detection of MAs remains a significant challenge due to the size and complexity of retinal fundus ima...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10100817
更新日期：2019-10-17 00:00:00
abstract：:Eimeria tenella (E. tenella) is one of the most frequent and pathogenic species of protozoan parasites of the genus Eimeria that exclusively occupies the cecum, exerting a high economic impact on the poultry industry. To investigate differentially expressed genes (DEGs) in the cecal tissue of Jinghai yellow chickens i...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10060420
更新日期：2019-05-31 00:00:00
abstract：:Engineered yeast are an important production platform for the biosynthesis of high-value compounds with medical applications. Recent years have witnessed several new developments in this area, largely spurred by advances in the field of synthetic biology and the elucidation of natural metabolic pathways. This minirevi...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes9070340
更新日期：2018-07-06 00:00:00
abstract：:A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [...]. ...
journal_title：Genes
pub_type： 社论
doi：10.3390/genes11030245
更新日期：2020-02-26 00:00:00
abstract：:The scale of genetic methods are presently being expanded: forensic genetic assays previously were limited to tens of loci, but now technologies allow for a transition to forensic genomic approaches that assess thousands to millions of loci. However, there are subtle distinctions between genetic assays and their genom...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes12020185
更新日期：2021-01-27 00:00:00
abstract：:The grizzly bear (Ursus arctos ssp. horribilis) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9120598
更新日期：2018-11-30 00:00:00
abstract：:The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal ...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes12020129
更新日期：2021-01-20 00:00:00
abstract：:High-throughput technologies have allowed researchers to obtain genome-wide data from a wide array of experimental model systems. Unfortunately, however, new data generation tends to significantly outpace data re-utilization, and most high throughput datasets are only rarely used in subsequent studies or to generate n...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10060423
更新日期：2019-06-01 00:00:00
abstract：:The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. Afte...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9040213
更新日期：2018-04-16 00:00:00
abstract：:Approximately 150 fungal species are considered as primary pathogens of humans and animals[...]. ...
journal_title：Genes
pub_type： 社论
doi：10.3390/genes10020136
更新日期：2019-02-12 00:00:00
abstract：:Self/foreign discrimination by the innate immune system depends on receptors that identify molecular patterns as associated to pathogens. Among others, this group includes endosomal Toll-like receptors, among which Toll-like receptors (TLR) 3, 7, 8, and 13 recognize and discriminate mammalian from microbial, potential...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes10020092
更新日期：2019-01-29 00:00:00
abstract：:Fig wasps are a peculiar group of insects which, for millions of years, have inhabited the enclosed syconia of fig trees. Considering the relatively closed and dark environment of fig syconia, we hypothesize that the fig wasps' oxidative phosphorylation (OXPHOS) pathway, which is the main oxygen consumption and adenos...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11111353
更新日期：2020-11-15 00:00:00
abstract：:Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11010033
更新日期：2019-12-27 00:00:00
abstract：:We employed Illumina 450 K Infinium microarrays to profile DNA methylation (DNAm) in neuronal nuclei separated by fluorescence-activated sorting from the postmortem orbitofrontal cortex (OFC) of heroin users who died from heroin overdose (N = 37), suicide completers (N = 22) with no evidence of heroin use and from con...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes8060152
更新日期：2017-05-30 00:00:00
abstract：:Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are separately domesticated from their wild ancestors Oryza rufipogon and Oryza barthii, which are very sensitive to daylength. In the process of domestication, some traits that are favorable for the natural survival of wild rice such as seed dormancy and s...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes9100489
更新日期：2018-10-10 00:00:00
