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Does the 43 bp sequence from an 800,000 year old cretan dwarf elephantid really rewrite the textbook on mammoths?

ABSTRACT: Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al (2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 year old fossil of the Cretan pigmy elephant (Elephas creticus). According to the authors of this study, a deep taxonomic revision of Cretan dwarf elephants would be needed, as the sequence exhibits clear affinities with woolly mammoth haplotypes. However, we point here many aspects that seriously weaken the strength of the ancient DNA evidence reported.

SUBMITTER: Orlando L

PROVIDER: S-EPMC2373798 | biostudies-literature | 2007 Feb

REPOSITORIES: biostudies-literature

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Does the 43 bp sequence from an 800,000 year old cretan dwarf elephantid really rewrite the textbook on mammoths?

Orlando Ludovic L Pagés Marie M Calvignac Sébastien S Hughes Sandrine S Hänni Catherine C

Biology letters 20070201 1

Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al (2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 yea ...[more]

PMID: 17443966

Similar Datasets

800,000 year old mammoth DNA, modern elephant DNA or PCR artefact?

Project description:Poulakakis and colleagues (Poulakakis et al. 2006: Biol. Lett. 2, 451-454), report the recovery of 'authentic' mammoth DNA from an 800,000-year-old fragment of bone excavated on the island of Crete. In light of results from other ancient DNA studies that indicate how DNA survival is unlikely in samples, which are recovered from warm environments and are relatively old (e.g. more than 100,000 years), these findings come as a great surprise. Here, we show that problems exist with the methodological approaches used in the study. First, the nested PCR technique as reported is nonsensical--one of the second round 'nested' primers falls outside the amplicon of the first round PCR. More worryingly, the binding region of one of the first round primers (Elcytb320R) falls within the short 43 base pair reported mammoth sequence, specifically covering two of the three reportedly diagnostic Elephas polymorphisms. Finally, we demonstrate using a simple BLAST search in GenBank that the claimed 'uniquely derived character state' for mammoths is in fact also found within modern elephants.

| S-EPMC2373799 | biostudies-literature

Million-year-old DNA sheds light on the genomic history of mammoths.

Project description:Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

| S-EPMC7116897 | biostudies-literature

Acute cataract development in a 43-year-old woman after an ultrasound eyelid-tightening procedure.

Project description:PurposeThe purpose of this article is to describe a severe side effect presentation of a bilateral cataract after treatment with intense focused ultrasound (IFUS) and subsequent uneventful cataract surgery.ObservationsA 43-year-old woman presented to the emergency room with decreased visual acuity several hours after undergoing an eyelid-tightening procedure using IFUS. The patient's vision was decreased (R>L), a result of an acute cataract, which had an unusual appearance and consistency. Several weeks later, visual acuity had decreased further in the right eye to 20/400 and the patient underwent uneventful laser-assisted cataract surgery with intraocular lens implantation, which resulted in full visual recovery.Conclusions and importanceThis case emphasizes the need for particular attention to possible side effects resulting from periocular IFUS, including severe ocular impact requiring surgical intervention.

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Quantitative DIA-Based proteomics of three-year-old and two-year-old Eriocheir sinensis

Project description:Comparative analysis of quantitative DIA-Based proteomics between three-year-old and two-year-old Eriocheir sinensis

2024-04-16 | PXD051511 |

Asynchronous Bilateral Renal Infarction and Thrombophilia With Associated Gene Mutations in a 43-Year-Old Man: A Case Report.

Project description:Renal infarction (RI) is frequently misdiagnosed or diagnosed late because of its rarity and nonspecific clinical presentation, which may result in irreversible damage to the renal parenchyma or increase the risk of other embolic events affecting additional organs. Multiple causal mechanisms and cases of idiopathic RI have been reported, but the causal factors are not clear in most cases.Here, we report the case of a patient with heterochronic bilateral RI caused by thrombophilia. Although he had several risk factors for hypercoagulation disorders, two gene mutations-MTHFR 677 C>T and PLG 1858G>A-were identified by genome sequencing of the entire exome. The findings suggest the possibility of a synergistic relationship between the two gene mutations.Thus, screening for gene mutations may provide additional clues for clarifying the cause of RI and thrombophilia.

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Five-year-old 'Wink' grape cultivar

Project description:microRNAs(miRNAs) play critical regulatory roles mainly through cleaving targeted mRNAs or repressing gene translation during plant developments. Grapevine is amongst the most economically important fruit crops with whole genome available, and the study on grapevine miRNAs (Vv-miRNAs) have also been emphasized. However, the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development has not been studied well, especially on a transcriptome-wide level. Here, six small RNA (sRNA) and mRNA libraries from various grapevine tissues were constructed for Illumina and Degradome sequencing. Subsequently, the spatiotemporal variation in the Vv-miRNAs’ regulation on their target genes was systematically analyzed. Totally, 242 known and 132 novel Vv-miRNAs were identified, and 193 target mRNAs including 103 for known and 90 for novel miRNAs were validated in one or more of tissues examined. The interesting finding was that over 50% of novel miRNAs were expressed exclusively in flowers or berries where they had tissue-specific cleavage roles on their target genes, especially, the breadth of their cleavage sites in flower tissues. Moreover, six novel miRNAs in berries were found to response to exogenous gibberellin (GA) and/or ethylene by real time RT-PCR (qRT-PCR) analysis, confirming their regulatory functions during berry development. Other finding was that about 93.6% of the known miRNAs possessed the high conservation in various tissues where their expression levels exhibited some dynamic variations during grapevine development. Significantly, it was found the phenomena that some Vv-miRNA families exist one key member that act as the main regulator of their target genes during grapevine development.

2021-08-24 | GSE182618 | GEO

23,000-year-old southern-Iberian

Project description:A 23,000-year-old southern-Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum

| PRJEB58642 | ENA

Abnormal macrophage response to microbial stimulus in a 43-year-old man with a severe form of atherosclerosis: a case report.

Project description:IntroductionNew evidence indicates infections are emerging as risk factors for atherosclerosis although their specific role in the development and progression of atherosclerosis is still unclear.Case presentationA 43-year-old Caucasian man who had been treated for four years for multiple sclerosis progressively manifested systemic hypertension, polycythemia, peripheral arterial occlusion with intermittent claudication, and persistent headaches. In 2006, an instrumental analysis (magnetic resonance imaging) of our patient revealed widespread fibrocalcific atherosclerotic lesions which accounted for all his current symptoms, including those related to microbial stimulus. Two particular aspects were of interest, namely a lack of conventional cardiovascular risk factors and a negative family history for cardiovascular events. His chemical blood tests all yielded negative findings although a low positive hepatitis C virus-ribonucleic acid titer was detected. The titer had progressively increased and worsening atherosclerosis threatened the life of our patient. Interferon therapy was not appropriate for our patient due to the severe adverse effects observed shortly after its administration.ConclusionsThe reaction of individual cells to infections may provide an explanation as to why individuals with a similar microbial burden, corrected for the presence of other risk factors, display a different susceptibility to developing or worsening atherosclerosis. The identification of susceptible individuals and the treatment even of silent infections may provide an additional tool against atherosclerosis and its clinical complications. The evaluation of cell susceptibility before and after the correction of risk factors may contribute to the assessment of the efficacy of drug therapy.

| S-EPMC2909247 | biostudies-literature

A Novel Distal 22Q11.21 Microduplication in a 43-Year-Old Male Patient with Mild Intellectual Disability, Social Cognitive Dysfunctions, and Anxiety.

Project description:ObjectiveThe chromosome region 22q11.2 is highly susceptible to genomic rearrangements. It has become clear that genomic instability extends distally to the commonly deleted/duplicated region (Low Copy Repeats [LCR] A-D) and that a clear difference exists between the phenotypic presentation of patients with rearrangements in the common region versus that in the distal region (LCR D-H), particularly with respect to developmental and somatic issues. Microdeletions in the 22q11.2 distal region are typically associated with congenital heart defects whereas distal 22q11.2 microduplications are infrequently described and present with a smaller duplicated region and a rather unspecified phenotype.MethodThe present paper provides detailed assessments of a middle-aged male with mild intellectual disability, elsewhere diagnosed with autism spectrum disorder. Because of persisting functional complaints, he was referred for second opinion to a specialized outpatient department.ResultsHigh resolution SNP-based array analysis demonstrated a ~1.5 Mb distal microduplication in chromosome 22 flanked by LCR region 22C and LCR22E encompassing among others the disease gene MAPK1. No remarkable facial dysmorphisms were noticed. Autism spectrum disorder was ruled out and it was concluded that the patient was primarily suffering from mild intellectual disability and social cognitive dysfunctions with anxieties and suspicious social interactions, to be understood as a disorder within the anxiety spectrum.ConclusionsThe pattern of psychological and psychiatric phenomena was discussed against the background of findings on psychopathology in the chromosome 22 region demarcated by LCR breakpoints C and E. It was suggested that alterations in the MAPK1 gene due to either a deletion or a duplication enhance the vulnerability to develop a psychiatric disorder within the anxiety spectrum.

| S-EPMC10712293 | biostudies-literature

Old age genetically confirmed frontotemporal lobar degeneration with TDP-43 has limbic predominant TDP-43 deposition.

Project description:AimsTo assess the burden of transactive response DNA-binding protein of 43 kDa (TDP-43) inclusions in a unique cohort of old-age patients with genetic frontotemporal lobar degeneration (gFTLD-TDP) and compare these patients with sporadic old-age individuals with TDP-43, either in the presence of Alzheimer's disease (AD-TDP) or in isolation (pure-TDP).MethodsThe brain bank at Mayo Clinic-Jacksonville was searched for cases ≥75 years old at death with TDP-43 extending into middle frontal cortex. Cases were split into the following groups: (1) gFTLD-TDP (n = 15) with progranulin (GRN)/C9ORF72 mutations; (2) AD-TDP (n = 10)-cases with median Braak neurofibrillary tangle (NFT) stage VI, Thal phase V; (3) pure-TDP (n = 10)-cases with median Braak NFT stage I, Thal phase I. Clinical data were abstracted; TDP-43 burden was calculated using digital pathology.ResultsAmnestic Alzheimer's dementia was the clinical diagnosis in ≥50% patients in each group. The distribution of TDP-43 burden in gFTLD-TDP and AD-TDP, but not pure-TDP, was limbic-predominant targeting CA1 and subiculum. Patients with gFTLD-TDP had higher burden in entorhinal cortex compared to AD-TDP. TDP-43 burden in middle frontal cortex did not differ between the three groups.ConclusionsIn old age it is challenging to clinically and pathologically differentiate gFTLD-TDP from AD-TDP and pure-TDP-43 based on burden. Like AD-TDP, old age gFTLD-TDP have a limbic predominant TDP-43 distribution. The finding that amnestic Alzheimer's dementia was the most common clinical diagnosis regardless of group suggests that TDP-43 directly and indirectly targets limbic regions.

| S-EPMC8576062 | biostudies-literature

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