Abstract：
:Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect's gut, and Lotmaria.
journal_name
Genes (Basel)journal_title
Genesauthors
Sereno D,Dorkeld F,Akhoundi M,Perrin Pdoi
10.3390/genes9080418subject
Has Abstractpub_date
2018-08-20 00:00:00issue
8issn
2073-4425pii
genes9080418journal_volume
9pub_type
杂志文章相关文献
Genes文献大全abstract：:Neurofibromatosis type 1 (NF1) is a cancer predisposition syndrome that results from dominant loss-of-function mutations mainly in the NF1 gene. Large rearrangements are present in 5-10% of affected patients, generally encompass NF1 neighboring genes, and are correlated with a more severe NF1 phenotype. Evident genoty...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10110839
更新日期：2019-10-24 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：:Model-based clustering with finite mixture models has become a widely used clustering method. One of the recent implementations is MCLUST. When objects to be clustered are summary statistics, such as regression coefficient estimates, they are naturally associated with estimation errors, whose covariance matrices can o...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11020185
更新日期：2020-02-10 00:00:00
abstract：:Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes2040748
更新日期：2011-10-28 00:00:00
abstract：:Colorectal cancer is the fourth most common neoplasia in Europe, where it accounts for 28.2 new cases per 100,000 inhabitants. In an effort to decrease the incidence of this disease, various prevention measures are being studied, one of which are anthocyanin-rich foods. Anthocyanins are potent antioxidant flavonoids m...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9030133
更新日期：2018-03-01 00:00:00
abstract：:Mitochondrial dynamics are known to have an important role in so-called age-related diseases, including cancer. Mitochondria is an organelle involved in many key cellular functions and responds to physiologic or stress stimuli by adapting its structure and function. Perhaps the most important structural changes involv...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes9020115
更新日期：2018-02-21 00:00:00
abstract：:Ubiquitous exposure to bisphenol A (BPA), an endocrine disruptor (ED), has raised concerns for both human and ecosystem health. Epigenetic factors, including microRNAs (miRNAs), are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebr...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes8100269
更新日期：2017-10-13 00:00:00
abstract：:Olfaction, which is mediated by olfactory receptor (OR) genes, is essential in the daily life of fish, especially in foraging. However, Chinese perch (Siniperca chuatsi) is believed to prey with reliance on vision and lateral sensation, but not on olfaction. Therefore, understanding the evolutionary dynamics of the Ch...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10020178
更新日期：2019-02-25 00:00:00
abstract：:Chlorella is a popular microalga with robust physiological and biochemical characteristics, which can be cultured under various conditions. The exploration of the small RNA content of Chlorella could improve strategies for the enhancement of metabolite production from this microalga. In this study, stress was introduc...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11101131
更新日期：2020-09-25 00:00:00
abstract：:A 9-month old male Jack Russell Terrier started showing paraparesis of the hindlimbs after a walk. Hospitalized, the dog went into cardiac arrest, and later died. Necroscopic examination revealed a severe thickness of the diaphragm, esophagus, and base of the tongue, leading to the diagnosis of muscular dystrophy. The...
journal_title：Genes
pub_type：
doi：10.3390/genes11101175
更新日期：2020-10-08 00:00:00
abstract：:Y-chromosomal (Y-DNA) haplogroups are more widely used in population genetics than in genetic epidemiology, although associations between Y-DNA haplogroups and several traits, including cardiometabolic traits, have been reported. In apparently homogeneous populations defined by principal component analyses, there is s...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9010045
更新日期：2018-01-22 00:00:00
abstract：:RNA-binding proteins (RBPs) are important regulators of cellular functions, playing critical roles on the survival of bacteria and in the case of pathogens, on their interaction with the host. RBPs are involved in transcriptional, post-transcriptional, and translational processes. However, except for model organisms l...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11020231
更新日期：2020-02-21 00:00:00
abstract：:Wnt is a complex signaling pathway involved in the regulation of crucial biological functions such as development, proliferation, differentiation and migration of cells, mainly stem cells, which are virtually present in all embryonic and adult tissues. Conversely, dysregulation of Wnt signal is implicated in developme...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes9020105
更新日期：2018-02-17 00:00:00
abstract：:The dog population of Southern East Asia is unique in harboring virtually the full range of the universal mtDNA gene pool, and consequently, it has the highest genetic diversity worldwide. Despite this, limited research has been performed on dog genetics within this region. Here we present the first comprehensive stud...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11030253
更新日期：2020-02-27 00:00:00
abstract：:B chromosomes are enigmatic heritable elements found in the genomes of numerous plant and animal species. Contrary to their broad distribution, most B chromosomes are non-essential. For this reason, they are regarded as genome parasites. In order to be stably transmitted through generations, many B chromosomes exhibit...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes10020123
更新日期：2019-02-08 00:00:00
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：:Chinese kale is a native vegetable in Southern China and the flowering stalk is the most commonly used edible part due to its high glucosinolate content and other nutritional qualities. The GTR protein played important roles in the glucosinolate transport process. In this study, three BocGTR1 genes were cloned from Ch...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10030202
更新日期：2019-03-08 00:00:00
abstract：:Cancers can be categorized into two groups: those whose frequency increases with age, and those resulting from errors during mammalian development. The first group is linked to DNA replication through the accumulation of genetic mutations that occur during proliferation of developmentally acquired stem cells that give...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes8020045
更新日期：2017-01-25 00:00:00
abstract：:The actin depolymerizing factor (ADF) proteins have growth, development, defense-related and growth regulatory functions in plants. The present study used genome-wide analysis to investigate ADF family genes in tomato. Eleven tomato ADF genes were identified and differential expression patterns were found in different...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes7100079
更新日期：2016-09-29 00:00:00
abstract：:Aging is a complex multi-layered phenomenon. The study of aging in humans is based on the use of biological material from hard-to-gather tissues and highly specific cohorts. The introduction of cell reprogramming techniques posed promising features for medical practice and basic research. Recently, a growing number of...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes9010039
更新日期：2018-01-16 00:00:00
abstract：:Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbr...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11030281
更新日期：2020-03-06 00:00:00
abstract：:Trees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptually defined as a s...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes11090995
更新日期：2020-08-25 00:00:00
abstract：:Cancer is the second deadliest disease listed by the WHO. One of the major causes of cancer disease is tobacco and consumption possibly due to its main component, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). A plethora of studies have been conducted in the past aiming to decipher the association of NNK with o...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10080564
更新日期：2019-07-26 00:00:00
abstract：:Despite a considerable body of published research on hepatitis B in Bangladesh, researchers continue to lament the lack of reliable information about hepatitis B virus (HBV) infection epidemiology. The present review aims to provide a comprehensive survey of the literature with particular focus on a number of epidemio...
journal_title：Genes
pub_type： 杂志文章,评审
doi：10.3390/genes9110541
更新日期：2018-11-08 00:00:00
abstract：:The filamenting temperature-sensitive Z proteins (FtsZs) play an important role in plastid division. In this study, three FtsZ genes were isolated from the cassava genome, and named MeFtsZ1, MeFtsZ2-1, and MeFtsZ2-2, respectively. Based on phylogeny, the MeFtsZs were classified into two groups (FtsZ1 and FtsZ2). MeFts...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes8120391
更新日期：2017-12-15 00:00:00
abstract：:The wall-associated kinase (WAK) and wall-associated kinase like (WAKL) is a subfamily of receptor-like kinases associated with the cell wall, which have been suggested as sensors of the extracellular environment and triggers of intracellular signals. However, these proteins have not yet been comprehensively analyzed ...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11101186
更新日期：2020-10-12 00:00:00
abstract：BACKGROUND:Radiation induces DNA double-strand breaks (DSBs), and chromosome aberrations (CA) form during the DSBs repair process. Several methods have been used to model the repair kinetics of DSBs including the bi-exponential model, i.e., N(t) = N1exp(-t/τ1) + N2exp(-t/τ2), where N(t) is the number of breaks at time ...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes10110936
更新日期：2019-11-16 00:00:00
abstract：:Background: The C34T polymorphism (rs 17602729) in adenosine monophosphate deaminase 1 gene (AMPD1) is associated with muscular energy metabolism in exercise. However, the role of its potential modifying impact on exercise-induced changes in obesity related parameters is unknown. The aim of the study was to determine ...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11050558
更新日期：2020-05-16 00:00:00
abstract：:Perennial agriculture has been proposed as an option to improve the sustainability of cropping systems, by increasing the efficiency of resource use, while also providing ecosystem services. Neo-domestication, the contemporary domestication of plants that have not previously been used in agriculture, can be used to ge...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes9090422
更新日期：2018-08-21 00:00:00
abstract：BACKGROUND:Anthocyanin pigmentation characterizes a number of tissues of Citrus and its relatives. The gain and loss of pigmentation is intriguing and is inherited variously among species. METHODS:Citrus germplasm was used to investigate the anthocyanin pigmentation of tissues never before considered, including stamen...
journal_title：Genes
pub_type： 杂志文章
doi：10.3390/genes11070807
更新日期：2020-07-16 00:00:00
