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1.
J Colloid Interface Sci ; 674: 841-851, 2024 Jun 29.
Article in English | MEDLINE | ID: mdl-38955015

ABSTRACT

Due to the complexity of regulatory networks of disease-related biomarkers, developing simple, sensitive, and accurate methods has remained challenging for precise diagnosis. Herein, an "AND" logic gates DNA molecular machine (LGDM) was constructed, which was powered by the catalytic hairpin assembly (CHA). It was coupled with dual-emission CdTe quantum dots (QDs)-based cation exchange reaction (CER) for label-free, sensitive, and ratiometric fluorescence detection of APE1 and miRNA biomarkers. Benefiting from synergistic signal amplification strategies and a ratiometric fluorometric output mode, this LGDM enables accurate logic computing with robust and significant output signals from weak inputs. It offers improved sensitivity and selectivity even in cell extracts. Using dual-emission spectra CdTe QDs, with a ratiometric signal output mode, ensured good stability and effectively prevented false-positive signals from intrinsic biological interferences compared to the approach relying on a single signal output mode, which enabled the LGDM to achieve rapid, efficient, and accurate natural drug screening against APE1 inhibitors in vitro and cells. The developed method provides impetus to streamline research related to miRNA and APE1, offering significant promise for widespread application in drug development and clinical analysis.

2.
J Hum Evol ; 192: 103519, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38843697

ABSTRACT

An ape partial postcranial skeleton (KNM-NP 64631) was recovered during the 2015-2021 field seasons at Napudet, a Middle Miocene (∼13 Ma) locality in northern Kenya. Bony elements representing the shoulder, elbow, hip, and ankle joints, thoracic and lumbar vertebral column, and hands and feet, offer valuable new information about the body plan and positional behaviors of Middle Miocene apes. Body mass estimates from femoral head dimensions suggest that the KNM-NP 64631 individual was smaller-bodied (c. 13-17 kg) than some Miocene taxa from eastern Africa, including Ekembo nyanzae, and probably Equatorius africanus or Kenyapithecus wickeri, and was more comparable to smaller-bodied male Nacholapithecus kerioi individuals. Similar to many Miocene apes, the KNM-NP 64631 individual had hip and hallucal tarsometatarsal joints reflecting habitual hindlimb loading in a variety of postures, a distal tibia with a large medial malleolus, an inflated humeral capitulum, probably a long lumbar spine, and a long pollical proximal phalanx relative to femoral head dimensions. The KNM-NP 64631 individual departs from most Early Miocene apes in its possession of a more steeply beveled radial head and deeper humeral zona conoidea, reflecting enhanced supinating-pronating abilities at the humeroradial joint. The KNM-NP 64631 individual also differs from Early Miocene Ekembo heseloni in having a larger elbow joint (inferred from radial head size) relative to the mediolateral width of the lumbar vertebral bodies and a more asymmetrical talar trochlea, and in these ways recalls inferred joint proportions for, and talocrural morphology of, N. kerioi. Compared to most Early Miocene apes, the KNM-NP 64631 individual likely relied on more forelimb-dominated arboreal behaviors, perhaps including vertical climbing (e.g., extended elbow, hoisting). Moreover, the Napudet ape partial postcranial skeleton suggests that an arboreally adapted body plan characterized by relatively large (here, based on joint size) forelimbs, but lacking orthograde suspensory adaptations, may not have been 'unusual' among Middle Miocene apes.


Subject(s)
Fossils , Hominidae , Animals , Kenya , Fossils/anatomy & histology , Hominidae/anatomy & histology , Male , Female , Anthropology, Physical , Biological Evolution
3.
Biosensors (Basel) ; 14(6)2024 May 27.
Article in English | MEDLINE | ID: mdl-38920578

ABSTRACT

A fluorogenic aptamer (FA)-based hybridization chain reaction (HCR) could provide a sensitive and label-free signal amplification method for imaging molecules in living cells. However, existing FA-HCR methods usually face some problems, such as a complicated design and significant background leakage, which greatly limit their application. Herein, we developed an FA-centered HCR (FAC-HCR) method based on a remote toehold-mediated strand displacement reaction. Compared to traditional HCRs mediated by four hairpin probes (HPs) and two HPs, the FAC-HCR displayed significantly decreased background leakage and improved sensitivity. Furthermore, the FAC-HCR was used to test a non-nucleic acid target, apurinic/apyrimidinic endonuclease 1 (APE1), an important BER-involved endonuclease. The fluorescence analysis results confirmed that FAC-HCR can reach a detection limit of 0.1174 U/mL. By using the two HPs for FAC-HCR with polyetherimide-based nanoparticles, the activity of APE1 in living cells can be imaged. In summary, this study could provide a new idea to design an FA-based HCR and improve the performance of HCRs in live cell imaging.


Subject(s)
Aptamers, Nucleotide , Biosensing Techniques , DNA-(Apurinic or Apyrimidinic Site) Lyase , Nucleic Acid Hybridization , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Humans , Fluorescent Dyes
4.
Aging (Albany NY) ; 16(12): 10435-10445, 2024 06 14.
Article in English | MEDLINE | ID: mdl-38885059

ABSTRACT

BACKGROUND: Non-small cell lung cancer (NSCLC) represents a highly immunogenic malignancy. Immunologic tolerance facilitated by myeloid-derived suppressor cells (MDSCs) is implicated in primary or secondary resistance mechanisms in NSCLC. The potential role of APE1 in regulating NSCLC metastasis by targeting MDSCs remains uncertain. METHODS: This study utilized a plasmid, Plxpsp-mGM-CSF, to induce elevated granulocyte-macrophage colony-stimulating factor (GM-CSF) expression in A549 cells. Tumor transplantation experiments involved A549, A549+GM-CSF, and A549+GM-CSF-siAPE1 cell lines. Evaluation encompassed MDSCs, Treg cells, IgG, CD3, and CD8 levels. RESULTS: Notably, lung cancer tissues and cells displayed markedly reduced APE1 expression. siAPE1 transfection significantly curtailed tumor growth compared to the A549+GM-CSF group. APE1 knockdown orchestrated immune system modulation in lung tumor mice, characterized by diminished MDSCs but augmented Treg cells, IgG, CD3, and CD8. Additionally, APE1 knockdown led to reduced levels of pro-MDSC cytokines (HGF, CCL5, IL-6, CCL12) and a concurrent upregulation of the anti-MDSC cytokine IL-1ra. Furthermore, APE1 knockdown impeded cell viability in both A549 and H1650 cells. CONCLUSIONS: Transplantation of A549-GM-CSF amplified MDSC levels, fostering accelerated tumor growth, while mitigating MDSC levels through APE1 knockdown hindered tumor progression and alleviated inflammatory infiltration in lung cancer tissues. Strategies targeting the APE1/MDSC axis offer a promising approach for lung cancer prevention and treatment, presenting novel insights for NSCLC management.


Subject(s)
Carcinoma, Non-Small-Cell Lung , DNA-(Apurinic or Apyrimidinic Site) Lyase , Granulocyte-Macrophage Colony-Stimulating Factor , Lung Neoplasms , Myeloid-Derived Suppressor Cells , Myeloid-Derived Suppressor Cells/immunology , Myeloid-Derived Suppressor Cells/metabolism , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Carcinoma, Non-Small-Cell Lung/immunology , Carcinoma, Non-Small-Cell Lung/metabolism , Animals , Lung Neoplasms/genetics , Lung Neoplasms/immunology , Lung Neoplasms/pathology , Lung Neoplasms/secondary , Lung Neoplasms/metabolism , Humans , Mice , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Granulocyte-Macrophage Colony-Stimulating Factor/metabolism , Granulocyte-Macrophage Colony-Stimulating Factor/genetics , A549 Cells , Gene Knockdown Techniques , Neoplasm Metastasis , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/metabolism , Male , Female
6.
J Biol Chem ; 300(6): 107337, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38705397

ABSTRACT

APE2 plays important roles in the maintenance of genomic and epigenomic stability including DNA repair and DNA damage response. Accumulating evidence has suggested that APE2 is upregulated in multiple cancers at the protein and mRNA levels and that APE2 upregulation is correlative with higher and lower overall survival of cancer patients depending on tumor type. However, it remains unknown how APE2 protein abundance is maintained and regulated in cells. Here, we provide the first evidence of APE2 regulation via the posttranslational modification ubiquitin. APE2 is poly-ubiquitinated via K48-linked chains and degraded via the ubiquitin-proteasome system where K371 is the key residue within APE2 responsible for its ubiquitination and degradation. We further characterize MKRN3 as the E3 ubiquitin ligase for APE2 ubiquitination in cells and in vitro. In summary, this study offers the first definition of the APE2 proteostasis network and lays the foundation for future studies pertaining to the posttranslational modification regulation and functions of APE2 in genome integrity and cancer etiology/treatment.


Subject(s)
DNA-(Apurinic or Apyrimidinic Site) Lyase , Ubiquitination , Humans , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , Ubiquitin/metabolism , Protein Processing, Post-Translational , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , HEK293 Cells , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/genetics , Proteolysis , Endonucleases , Multifunctional Enzymes
7.
Int J Mol Sci ; 25(10)2024 May 09.
Article in English | MEDLINE | ID: mdl-38791183

ABSTRACT

Apurinic/apyrimidinic endonuclease 1 (APE1) is involved in DNA repair and transcriptional regulation mechanisms. This multifunctional activity of APE1 should be supported by specific structural properties of APE1 that have not yet been elucidated. Herein, we applied atomic force microscopy (AFM) to characterize the interactions of APE1 with DNA containing two well-separated G-rich segments. Complexes of APE1 with DNA containing G-rich segments were visualized, and analysis of the complexes revealed the affinity of APE1 to G-rich DNA sequences, and their yield was as high as 53%. Furthermore, APE1 is capable of binding two DNA segments leading to the formation of loops in the DNA-APE1 complexes. The analysis of looped APE1-DNA complexes revealed that APE1 can bridge G-rich segments of DNA. The yield of loops bridging two G-rich DNA segments was 41%. Analysis of protein size in various complexes was performed, and these data showed that loops are formed by APE1 monomer, suggesting that APE1 has two DNA binding sites. The data led us to a model for the interaction of APE1 with DNA and the search for the specific sites. The implication of these new APE1 properties in organizing DNA, by bringing two distant sites together, for facilitating the scanning for damage and coordinating repair and transcription is discussed.


Subject(s)
DNA-(Apurinic or Apyrimidinic Site) Lyase , DNA , Microscopy, Atomic Force , Protein Binding , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry , DNA/metabolism , DNA/chemistry , Humans , Binding Sites , DNA Repair
8.
Cell Cycle ; 23(5): 602-612, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38717991

ABSTRACT

Gastric cancer is a highly immunogenic malignancy. Immune tolerance facilitated by myeloid-derived suppressor cells (MDSCs) has been implicated in gastric cancer resistance mechanisms. The potential role of APE1 in regulating gastric cancer metastasis by targeting MDSCs remains uncertain. In this study, the plasmid Plxpsp-mGM-CSF was used to induce high expression of granulocyte-macrophage colony-stimulating factor (GM-CSF) in GES-1 cells. For tumor transplantation experiments, AGS, AGS+GM-CSF and AGS+GM-CSF-siAPE1 cell lines were established by transfection, followed by subcutaneous implantation of tumor cells. MDSCs, Treg cells, IgG, CD3 and CD8 levels were assessed. Transfection with siAPE1 significantly inhibited tumor growth compared to the AGS+GM-CSF group. APE1 gene knockdown modulated the immune system in gastric cancer mice, characterized by a decrease in MDSCs and an increase in Treg cells, IgG, CD3 and CD8. In addition, APE1 gene knockdown resulted in decreased levels of pro-MDSC cytokines (HGF, CCL5, IL-6, CCL12). Furthermore, APE1 gene knockdown inhibited proliferation, migration and invasion of AGS and MKN45 cells. AGS-GM-CSF cell transplantation increased MDSC levels and accelerated tumor growth, whereas APE1 knockdown reduced MDSC levels, inhibited tumor growth and attenuated inflammatory infiltration in gastric cancer tissues. Strategies targeting the APE1/MDSC axis offer a promising approach to the prevention and treatment of gastric cancer, providing new insights into its management.


Subject(s)
DNA-(Apurinic or Apyrimidinic Site) Lyase , Granulocyte-Macrophage Colony-Stimulating Factor , Myeloid-Derived Suppressor Cells , Stomach Neoplasms , Stomach Neoplasms/pathology , Stomach Neoplasms/genetics , Stomach Neoplasms/immunology , Stomach Neoplasms/metabolism , Animals , Myeloid-Derived Suppressor Cells/metabolism , Cell Line, Tumor , Humans , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , Mice , Granulocyte-Macrophage Colony-Stimulating Factor/metabolism , Granulocyte-Macrophage Colony-Stimulating Factor/genetics , Gene Knockdown Techniques , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/metabolism , Neoplasm Metastasis , Mice, Inbred BALB C , Cytokines/metabolism , Cell Proliferation/genetics
9.
Biodivers Data J ; 12: e120314, 2024.
Article in English | MEDLINE | ID: mdl-38707255

ABSTRACT

Siamangs (Symphalangussyndactylus) are native to Peninsular Malaysia, Sumatra and southern Thailand and their taxonomical classification at subspecies level remains unclear. Morphologically, two subspecies were proposed as early as 1908 by Thomas namely Symphalangus s.syndactylus and Symphalanguss.continentis. Thus, this study aims to clarify the Siamang subspecies status, based on mtDNA D-loop sequences. Faecal samples were collected from wild Siamang populations at different localities in Peninsular Malaysia. A 600-bp sequence of the mitochondrial D-loop region was amplified from faecal DNA extracts and analysed along with GenBank sequences representing Symphalangus sp., Nomascus sp., Hylobates sp., Hoolock sp. and outgroups (Pongopygmaeus, Macacafascicularis and Papiopapio). The molecular phylogenetic analysis in this study revealed two distinct clades formed by S.s.syndactylus and S.s.continentis which supports the previous morphological delineation of the existence of two subspecies. Biogeographical analysis indicated that the Sumatran population lineage was split from the Peninsular Malaysian population lineage and a diversification occurrred in the Pliocene era (~ 3.12 MYA) through southward expansion. This postulation was supported by the molecular clock, which illustrated that the Peninsular Malaysian population (~ 1.92 MYA) diverged earlier than the Sumatran population (~ 1.85 MYA). This is the first study to use a molecular approach to validate the subspecies statuses of S.s.syndactylus and S.s.continentis. This finding will be useful for conservation management, for example, during Siamang translocation and investigations into illegal pet trade and forensics involving Malayan and Sumatran Siamangs.

10.
Rinsho Shinkeigaku ; 64(4): 272-279, 2024 Apr 24.
Article in Japanese | MEDLINE | ID: mdl-38508734

ABSTRACT

We analyzed 20 patients diagnosed with autoimmune neurological diseases with seizure predominance. In these patients, we examined the usefulness of Antibody Prevalence in Epilepsy and Encephalopathy (APE2) score and Antibodies Contributing to Focal Epilepsy Signs and Symptoms (ACES) score in autoimmune encephalitis (AE) for facilitating early treatment. APE2 score was positive in 19 of 20 patients. ACES score was positive in 15 of 20 patients, and 4 of 5 of the patients with negative ACES score did not have AE. Comprehensive assessment including the use of the above scores is desirable in the early stage of AE.


Subject(s)
Autoantibodies , Encephalitis , Seizures , Humans , Autoantibodies/blood , Male , Female , Middle Aged , Encephalitis/immunology , Encephalitis/diagnosis , Encephalitis/therapy , Adult , Aged , Seizures/etiology , Seizures/immunology , Hashimoto Disease/immunology , Hashimoto Disease/diagnosis , Hashimoto Disease/complications , Biomarkers/blood , Early Medical Intervention , Young Adult , Adolescent , Aged, 80 and over , Severity of Illness Index
11.
Cell Mol Life Sci ; 81(1): 113, 2024 Mar 04.
Article in English | MEDLINE | ID: mdl-38436697

ABSTRACT

APE1 is an essential gene involved in DNA damage repair, the redox regulation of transcriptional factors (TFs) and RNA processing. APE1 overexpression is common in cancers and correlates with poor patient survival. Stress granules (SGs) are phase-separated cytoplasmic assemblies that cells form in response to environmental stresses. Precise regulation of SGs is pivotal to cell survival, whereas their dysregulation is increasingly linked to diseases. Whether APE1 engages in modulating SG dynamics is worthy of investigation. In this study, we demonstrate that APE1 colocalizes with SGs and promotes their formation. Through phosphoproteome profiling, we discover that APE1 significantly alters the phosphorylation landscape of ovarian cancer cells, particularly the phosphoprofile of SG proteins. Notably, APE1 promotes the phosphorylation of Y-Box binding protein 1 (YBX1) at S174 and S176, leading to enhanced SG formation and cell survival. Moreover, expression of the phosphomutant YBX1 S174/176E mimicking hyperphosphorylation in APE1-knockdown cells recovered the impaired SG formation. These findings shed light on the functional importance of APE1 in SG regulation and highlight the importance of YBX1 phosphorylation in SG dynamics.


Subject(s)
DNA-(Apurinic or Apyrimidinic Site) Lyase , Ovarian Neoplasms , Stress Granules , Y-Box-Binding Protein 1 , Female , Humans , Endodeoxyribonucleases , Ovarian Neoplasms/genetics , Phosphorylation , Stress Granules/metabolism , Y-Box-Binding Protein 1/genetics , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism
12.
Epilepsy Behav ; 154: 109737, 2024 May.
Article in English | MEDLINE | ID: mdl-38518672

ABSTRACT

PURPOSE: Immune-mediated seizures are rare but are increasingly recognized as an etiology of seizures resistant to anti-seizure medications (ASMs). Antibody Prevalence in Epilepsy 2 (APE2) and Response to Immunotherapy in Epilepsy 2 (RITE2) scores were developed recently to identify patients who may be seropositive for serum central nervous system (CNS) specific antibodies (Ab) and may benefit from immunotherapy (Dubey et al. 2018). The goal of this study was to apply APE2 and RITE2 scores to an independent cohort of patients with seizures secondary to autoimmune encephalitis (AE) and to further verify the sensitivity and specificity of the scores. PRINCIPAL RESULTS: We conducted a retrospective study at Stanford University Hospital between 2008 and 2021 and included patients who had acute seizures and AE using diagnostic criteria from Graus (n = 34 definite AE, 10 probable AE, and 12 possible AE) (Graus et al. 2016). Patients were excluded if they did not have a serum Ab panel investigated or had alternate diagnoses (n = 55). APE2 and RITE2 scores were calculated based on clinical and diagnostic data (n = 56). Serum Ab were positive in 73 % of patients, in which 63 % cases carried CNS specific Ab. An APE2 score ≥ 4 had a sensitivity of 97 % and specificity of 14 % to predict a positive serum CNS specific Ab. A RITE2 score ≥ 7 had a sensitivity of 93 % and specificity of 60 % to predict seizure responsiveness to immunotherapy. CONCLUSION: APE2 and RITE2 scores had high sensitivities but low specificities to predict seropositivity and seizure responsiveness to immunotherapy in patients with autoimmune encephalitis with seizures.


Subject(s)
Encephalitis , Seizures , Humans , Female , Male , Adult , Seizures/blood , Seizures/etiology , Seizures/diagnosis , Middle Aged , Retrospective Studies , Encephalitis/complications , Encephalitis/blood , Encephalitis/immunology , Encephalitis/diagnosis , Hashimoto Disease/complications , Hashimoto Disease/blood , Aged , Sensitivity and Specificity , Autoantibodies/blood , Young Adult , Immunotherapy/methods , Adolescent
13.
FEBS J ; 291(13): 2849-2875, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38401056

ABSTRACT

The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is an essential enzyme of the base excision repair pathway of non-distorting DNA lesions. In response to genotoxic treatments, APE1 is highly secreted (sAPE1) in association with small-extracellular vesicles (EVs). Interestingly, its presence in the serum of patients with hepatocellular or non-small-cell-lung cancers may represent a prognostic biomarker. The mechanism driving APE1 to associate with EVs is unknown, but is of paramount importance in better understanding the biological roles of sAPE1. Because APE1 lacks an endoplasmic reticulum-targeting signal peptide, it can be secreted through an unconventional protein secretion endoplasmic reticulum-Golgi-independent pathway, which includes an endosome-based secretion of intraluminal vesicles, mediated by multivesicular bodies (MVBs). Using HeLa and A549 cell lines, we investigated the role of endosomal sorting complex required for transport protein pathways (either-dependent or -independent) in the constitutive or trichostatin A-induced secretion of sAPE1, by means of manumycin A and GW 4869 treatments. Through an in-depth biochemical analysis of late-endosomes (LEs) and early-endosomes (EEs), we observed that the distribution of APE1 on density gradient corresponded to that of LE-CD63, LE-Rab7, EE-EEA1 and EE-Rab 5. Interestingly, the secretion of sAPE1, induced by cisplatin genotoxic stress, involved an autophagy-based unconventional secretion requiring MVBs. The present study enlightens the central role played by MVBs in the secretion of sAPE1 under various stimuli, and offers new perspectives in understanding the biological relevance of sAPE1 in cancer cells.


Subject(s)
DNA Repair , DNA-(Apurinic or Apyrimidinic Site) Lyase , Protein Transport , Humans , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , HeLa Cells , Endosomes/metabolism , A549 Cells , Extracellular Vesicles/metabolism , Extracellular Vesicles/genetics , Endosomal Sorting Complexes Required for Transport/metabolism , Endosomal Sorting Complexes Required for Transport/genetics , Multivesicular Bodies/metabolism , Excision Repair , Hydroxamic Acids
14.
Int J Biol Macromol ; 262(Pt 1): 129902, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38307426

ABSTRACT

In situ imaging of microRNA (miRNA) content and distribution is valuable for monitoring tumor progression. However, tumor specific in situ imaging remains a challenge due to low miRNA abundance, lack of biological compatibility, and poor specificity. In this study, we designed a DNA tetrahedral framework complex with hairpins (DTF-HPAP) consisting of an apurinic/apyrimidinic site (AP site) that could be specifically recognized and cleaved by apurinic/apyrimidinic endonuclease 1 (APE1). Efficient and specific in situ imaging of miR-21 in tumors was thus achieved through catalytic hairpin assembly (CHA) reaction. In this study, DTF-HPAP was successfully constructed to trigger the cumulative amplification of fluorescence signal in situ. The specificity, sensitivity and serum stability of DTF-HPAP were verified in vitro, and DTF-HPAP could be easily taken up by cells, acting as a biosensor to detect tumors in mice. Furthermore, we verified the ability of DTF-HPAP to specifically image miR-21 in tumors, and demonstrated its capability for tumor-specific imaging in clinical samples.


Subject(s)
Biosensing Techniques , MicroRNAs , Neoplasms , Mice , Animals , MicroRNAs/genetics , Endonucleases , Catalysis , Biosensing Techniques/methods
15.
Trends Ecol Evol ; 39(5): 456-466, 2024 May.
Article in English | MEDLINE | ID: mdl-38302324

ABSTRACT

We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.


Subject(s)
Biological Evolution , Extinction, Biological , Fossils , Hominidae , Animals , Africa , Genome , Genomics , Hominidae/genetics , Phylogeny
16.
Proc Biol Sci ; 291(2016): 20232345, 2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38351806

ABSTRACT

Joking draws on complex cognitive abilities: understanding social norms, theory of mind, anticipating others' responses and appreciating the violation of others' expectations. Playful teasing, which is present in preverbal infants, shares many of these cognitive features. There is some evidence that great apes can tease in structurally similar ways, but no systematic study exists. We developed a coding system to identify playful teasing and applied it to video of zoo-housed great apes. All four species engaged in intentionally provocative behaviour, frequently accompanied by characteristics of play. We found playful teasing to be characterized by attention-getting, one-sidedness, response looking, repetition and elaboration/escalation. It takes place mainly in relaxed contexts, has a wide variety of forms, and differs from play in several ways (e.g. asymmetry, low rates of play signals like the playface and absence of movement-final 'holds' characteristic of intentional gestures). As playful teasing is present in all extant great ape genera, it is likely that the cognitive prerequisites for joking evolved in the hominoid lineage at least 13 million years ago.


Subject(s)
Hominidae , Humans , Infant , Animals , Cognition , Gestures , Attention
17.
Proc Natl Acad Sci U S A ; 121(6): e2220392121, 2024 Feb 06.
Article in English | MEDLINE | ID: mdl-38305758

ABSTRACT

Germline colonization by retroviruses results in the formation of endogenous retroviruses (ERVs). Most colonization's occurred millions of years ago. However, in the Australo-Papuan region (Australia and New Guinea), several recent germline colonization events have been discovered. The Wallace Line separates much of Southeast Asia from the Australo-Papuan region restricting faunal and pathogen dispersion. West of the Wallace Line, gibbon ape leukemia viruses (GALVs) have been isolated from captive gibbons. Two microbat species from China appear to have been infected naturally. East of Wallace's Line, the woolly monkey virus (a GALV) and the closely related koala retrovirus (KoRV) have been detected in eutherians and marsupials in the Australo-Papuan region, often vertically transmitted. The detected vertically transmitted GALV-like viruses in Australo-Papuan fauna compared to sporadic horizontal transmission in Southeast Asia and China suggest the GALV-KoRV clade originates in the former region and further models of early-stage genome colonization may be found. We screened 278 samples, seven bat and one rodent family endemic to the Australo-Papuan region and bat and rodent species found on both sides of the Wallace Line. We identified two rodents (Melomys) from Australia and Papua New Guinea and no bat species harboring GALV-like retroviruses. Melomys leucogaster from New Guinea harbored a genomically complete replication-competent retrovirus with a shared integration site among individuals. The integration was only present in some individuals of the species indicating this retrovirus is at the earliest stages of germline colonization of the Melomys genome, providing a new small wild mammal model of early-stage genome colonization.


Subject(s)
Chiroptera , Endogenous Retroviruses , Gammaretrovirus , Marsupialia , Animals , Leukemia Virus, Gibbon Ape/genetics , New Guinea , Gammaretrovirus/genetics , Murinae/genetics , Marsupialia/genetics , Germ Cells
18.
BMC Genom Data ; 25(1): 21, 2024 Feb 21.
Article in English | MEDLINE | ID: mdl-38383300

ABSTRACT

BACKGROUND: GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. RESULTS: On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human. CONCLUSION: In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms.


Subject(s)
Hominidae , Animals , Humans , Hominidae/genetics , Genome/genetics , Y Chromosome , Genomics
19.
Talanta ; 272: 125747, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38364557

ABSTRACT

MicroRNA (miRNA) is involved in the progression of Alzheimer's disease (AD) and emerges as a promising AD biomarker and therapeutic target. Therefore, there is an urgent need to develop convenient and precise miRNA detection methods for AD diagnosis. Herein, a dual-signal amplification strategy based on rolling circle amplification and APE1-assisted amplification for miRNA analysis for early diagnosis of AD was proposed. The strategy consisted of dumbbell-shaped probe (DP) as amplification template and a reporter probe (RP) with an AP site modification. In the presence of the target miRNA, the miRNAs bound to the toehold domain of DP and DP was activated into a circular template. Then, RCA reaction was triggered, producing a large number of long-stranded products containing repeated sequences. After RCA, APE1 enzyme recognized and removed AP site in the complex of RCA/RP products. By coupling RCA with APE1-assisted amplification, this method has high sensitivity with the limit of detection (LOD) of 1.82 fM. Moreover, by using DP as template for RCA reaction, high specificity can be achieved. By detecting miR-206 in serum using this method, the expression of miR-206 can be accurately distinguished between AD patients and healthy individuals, indicating that this method has broad application prospects in clinical diagnosis.


Subject(s)
Alzheimer Disease , MicroRNAs , Humans , MicroRNAs/genetics , MicroRNAs/analysis , Alzheimer Disease/diagnosis , Alzheimer Disease/genetics , Limit of Detection , Early Diagnosis , Nucleic Acid Amplification Techniques/methods
20.
Braz. j. med. biol. res ; 57: e13250, fev.2024. graf
Article in English | LILACS-Express | LILACS | ID: biblio-1557307

ABSTRACT

Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/REF-1) is a multifunctional protein acting on cellular signaling pathways, including DNA repair and redox activities. APE1/REF-1 has emerged as a target for cancer therapy, and its role in breast cancer models would reveal new strategies for cancer therapy. APX2009 is a specific APE1/REF-1 redox inhibitor whose anticancer properties have not been described in breast cancer cells. Here, we investigated the effect of the APX2009 treatment in the breast cancer cell lines MDA-MB-231 and MCF-7. Breast cancer cell lines were cultured, and WST1 and colony formation assays were performed to evaluate cell proliferation. Annexin V-FITC/7-AAD and LDH-Glo™ assays were performed to evaluate cell death. The wound healing assay and Matrigel transwell assay were performed after APX2009 treatment to evaluate the cellular migration and invasion processes, respectively. Our findings demonstrated that APX2009 treatment decreased breast cancer cell proliferative, migratory, and invasive properties. Furthermore, it induced apoptosis in both cell lines. Our study is the first to show the effects of APX2009 treatment on apoptosis in a breast cancer cell. Therefore, this study suggested that APX2009 treatment is a promising anticancer molecule for breast cancer.

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