Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.Peer reviewedFinal Published versio

Plant Flavonoids on Oxidative Stress-Mediated Kidney Inflammation

© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Simple Summary: Increased stress is often observed in patients with kidney diseases, contributing to renal injury progression. Flavonoids are naturally occurring plant compounds with known health benefits, including antiapoptotic, anti-inflammatory, and antioxidant properties. Flavonoids can protect the kidney by improving antioxidant status, ameliorating excess reactive oxygen species levels, and acting as Nrf2-mediators in generating antioxidant responses in the body. Flavonoids also modulate inflammatory markers, exert anti-inflammatory effects, and protect the cells from apoptotic cell death in the kidney. Interestingly, few clinical trials have reported a direct correlation between a flavonoid-rich diet and better kidney disease prognosis. However, flavonoids have a low bioavailability in the body, making it essential to understand better their molecular mechanism of action. We suggest that a flavonoid-rich diet could have promising nephroprotective effects and beneficial outcomes in treating patients with kidney diseases. Abstract: The kidney is susceptible to reactive oxygen species-mediated cellular injury resulting in glomerulosclerosis, tubulointerstitial fibrosis, tubular cell apoptosis, and senescence, leading to renal failure, and is a significant cause of death worldwide. Oxidative stress-mediated inflammation is a key player in the pathophysiology of various renal injuries and diseases. Recently, flavonoids’ role in alleviating kidney diseases has been reported with an inverse correlation between dietary flavonoids and kidney injuries. Flavonoids are plant polyphenols possessing several health benefits and are distributed in plants from roots to leaves, flowers, and fruits. Dietary flavonoids have potent antioxidant and free-radical scavenging properties and play essential roles in disease prevention. Flavonoids exert a nephroprotective effect by improving antioxidant status, ameliorating excessive reactive oxygen species (ROS) levels, and reducing oxidative stress, by acting as Nrf2 antioxidant response mediators. Moreover, flavonoids play essential roles in reducing chemical toxicity. Several studies have demonstrated the effects of flavonoids in reducing oxidative stress, preventing DNA damage, reducing inflammatory cytokines, and inhibiting apoptosis-mediated cell death, thereby preventing or improving kidney injuries/diseases. This review covers the recent nephroprotective effects of flavonoids against oxidative stress-mediated inflammation in the kidney and their clinical advancements in renal therapy.Peer reviewe

Détection et identification de l'ADN dégradé (nouvelles approches moléculaires et biophysiques)

Species identification is a key issue in many topical fields such as food forensics, medicine, paleontology, etc.. In processed products (animal or plant), identification based on morphological characters is not possible because no diagnostic test is available, hence the need to use identification methods based on DNA amplification by PCR (DNA barcoding). However, in degraded substrates, this molecule is sometimes unavailable to PCR due to the presence of inhibitors and / or chemical modifications that block the activity of Taq polymerase. In the first part, this thesis develops a methodology for extracting and amplifying DNA from leather, taken as a model of a product which is highly resistant to molecular analysis due to the treatments used in its manufacture. Indeed, the DNA in worked skin is highly degraded, chemically modified and more specifically it is co-extracted with inhibitors of PCR (dyes and tannins). In addition to the important applications in fraud prevention and biodiversity protection, restoration of historical musical instruments was an important goal of our approach. As new enzymatic treatments (DNA repair) are currently limited to already amplifiable DNA substrates, it is necessary to develop a new approach for DNA inaccessible by PCR. Thus, the second part of this thesis develops a new non-enzymatic method. This physical detection of DNA is based on vibrational Raman spectroscopy (SERRS, Surface Enhanced Resonant Raman Spectroscopy). In the future, this approach could replace the PCR, and be applied for rapid and reliable molecular diagnosis, especially in medical tests.L'identification des espèces est une question essentielle dans de nombreux domaines actuels comme l'agro-alimentaire, la médecine, la paléontologie, etc. Dans les produits transformés (d origine animale ou végétale), l identification basée sur des caractères morphologiques n est pas possible car aucun critère diagnostique n est accessible, d où la nécessité d utilisation de méthodes d identification basées sur l amplification de l ADN par PCR (DNA barcoding). Cependant, dans des substrats dégradés, cette molécule est parfois inaccessible à la PCR en raison de la présence d inhibiteurs et/ou de modifications chimiques bloquant l activité de la Taq polymérase. Dans une première partie, cette thèse développe une méthodologie d extraction et d amplification de l ADN à partir des cuirs, pris comme modèle des produits les plus réfractaires à l analyse moléculaire, du fait des traitements utilisés lors de leurs fabrication. En effet, l'ADN présent dans la peau travaillée est fortement dégradé et chimiquement modifié et en particulier il est co-extrait avec des inhibiteurs de la PCR (colorants et tanins). Outre des applications importantes dans la répression des fraudes et la protection de la biodiversité, la restauration des instruments historiques de musique a été un objectif important de notre approche. Comme les nouveaux traitements enzymatiques (réparation de l ADN) sont pour l instant limités aux substrats d ADN déjà amplifiables, il est donc nécessaire de développer une nouvelle approche pour l ADN inaccessible par la PCR. Dans ce but, la deuxième partie de cette thèse développe une nouvelle méthode non enzymatique. Il s agit d une détection physique de l ADN, basée sur la spectroscopie vibrationnelle Raman (SERRS, Surface Enhanced Resonant Raman Spectroscopy). Dans l avenir, cette approche pourrait remplacer la PCR, et être appliquée pour les diagnostics moléculaires rapides et fiables, en particulier pour les analyses médicales.LYON-ENS Sciences (693872304) / SudocSudocFranceF

DNA for species identification in leather: Fraud detection and endangered species protection

International audienceIn this study, we focused on species identification in leather. Based on optimized extraction method combined with a panel of ultra-specific primers targeting short mitochondrial DNA fragments, we have developed a complete and efficient method that allows molecular identification of species origin in leather. Despite great advances in the fields of forensic, species identification in processed animal products is still very limited, not only because of classic problems as the tiny amount of DNA and/or DNA degradation, but also because of the critical problem of PCR inhibitors which are co-extracted with DNA molecules. In perspective, this study could be applied to detect frauds in particular in leather market and/or protect endangered species

Prevalence of Antibiotic-Resistant Bacteria in Domestic Water Storage Tanks in Sidon, Lebanon

Safe, accessible, and good water quality are essential characteristics for reducing various waterborne diseases. Since domestic water is the water most consumed by Lebanese people, cleaning household water tanks is important to prevent their exposure to pathogenic microorganisms. Generally, all the stages of the value chain of the Lebanese water sector are still imperfect. Thus, the domestic water should be regularly tested, especially in the impoverished landmarks where water quality is the worst. The aim of this study is to evaluate the physicochemical parameters and microbiological quality of the water in the storage tanks of homes in Sidon, Lebanon. Fifty water samples were collected aseptically from domestic water storage tanks. The microbiological assessment was performed using basic plating techniques. Identification of isolated bacteria was performed using MALDI-TOF-MS. Physicochemical parameters were assessed using titration, pH, and conductivity measurements. Antibiotic-susceptibility testing was performed using antibiotic disks. Screening for virulence genes in bacteria was carried out via polymerase chain reaction (PCR). Most of the physicochemical parameters were within the permissible limits of the World Health Organization (WHO) for drinking water. The heterotrophic plate count (HPC) varied between the water samples. The total coliform, fecal coliform, and Escherichia coli (E. coli) contaminate was 54%, 20%, and 16% in each of the samples, respectively. Other bacteria isolated from household water included intestinal Enterococcus faecalis (E. faecalis) (68%), Staphylococcus aureus (S. aureus) (68%), and Pseudomonas aeruginosa (P. aeruginosa) (22%). Other predominant isolates recovered from the samples were also identified. The bacterial isolates showed a prevalence of resistance and intermediate resistance against the tested antibiotic agents. Multi-resistant Staphylococcus aureus (MRSA) was detected in 21% of the collected S. aureus, using cefoxitin agent and mecA gene detection. A prevalence of virulence genes in both P. aeruginosa and S. aureus was also noticed. Our data show that Sidon domestic water is not suitable for either drinking or home applications

A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target

In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwichhybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a nonenzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and o

Detection of DNA Sequences Refractory to PCR Amplification Using a Biophysical SERRS Assay (Surface Enhanced Resonant Raman Spectroscopy)

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction - based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage

Combination of double-stranded R_5′/R_3′ molecules investigated in this study.

<p>N_5′/N_3′ is the original non-degraded molecule.</p><p>Combination of double-stranded R_5′/R_3′ molecules investigated in this study.</p

Specificity and co-contamination assays.

<p>All spectra were acquired in 1 acquisition of 30 s. (A) In black, negative control without target DNA. (B) In blue, <i>C. hircus</i>, negative control (5.10⁻⁸ M). (C) In green, signal from <i>R. rupicapra</i> (5.10⁻⁸ M). (D) In red, signal obtained from an equimolar mix of <i>R. rupicapra</i> and <i>C. hircus</i> DNA (5.10⁻⁸ M each).</p

Siglecs in Brain Function and Neurological Disorders

Siglecs (Sialic acid-binding immunoglobulin-type lectins) are a I-type lectin that typically binds sialic acid. Siglecs are predominantly expressed in immune cells and generate activating or inhibitory signals. They are also shown to be expressed on the surface of cells in the nervous system and have been shown to play central roles in neuroinflammation. There has been a plethora of reviews outlining the studies pertaining to Siglecs in immune cells. However, this review aims to compile the articles on the role of Siglecs in brain function and neurological disorders. In humans, the most abundant Siglecs are CD33 (Siglec-3), Siglec-4 (myelin-associated glycoprotein/MAG), and Siglec-11, Whereas in mice the most abundant are Siglec-1 (sialoadhesin), Siglec-2 (CD22), Siglec-E, Siglec-F, and Siglec-H. This review is divided into three parts. Firstly, we discuss the general biological aspects of Siglecs that are expressed in nervous tissue. Secondly, we discuss about the role of Siglecs in brain function and molecular mechanism for their function. Finally, we collate the available information on Siglecs and neurological disorders. It is intriguing to study this family of proteins in neurological disorders because they carry immunoinhibitory and immunoactivating motifs that can be vital in neuroinflammation