Search Results (461)

Isotopic investigations focused on determining the mobility and provenance of ancient human civilizations and sourcing of archeological artifacts continue to gain prominence in archeology. Most studies focus on the premise that the geographic variation in isotope systems of interest (e.g., Sr, Pb, Nd, O) in the natural environment is recorded in both human hard tissues of local individuals and raw materials sourced for artifacts within the same region. The introduction of multi-collection–inductively coupled plasma mass spectrometry (MC-ICP-MS) and laser ablation systems are techniques that consume smaller sample sizes compared to previous mass spectrometric approaches due to their higher ionization efficiency and increased sensitivity. This development has facilitated the isotopic measurement of trace elements present at low abundances (e.g., Pb, Nd, <1-to-low ppm range) particularly in human tooth enamel. Accurate interpretation of any isotope ratio measurement for the proveniencing of such low-abundance samples requires the adequate evaluation of post-mortem diagenetic alteration. A synopsis of practices currently in use for identifying post-mortem alteration in human archeological samples is discussed here. Post-mortem shifts in radiogenic isotope signatures resulting from secondary alteration are distinct from those potentially related to the impact of climate change on the bioavailable budgets for these elements. This topic is of interest to the archeological community and discussed here in the context of Holocene-aged samples from burial sites within the Nile River Valley System, and preferred dust source areas from the neighboring Sahara Desert. Full article

Tumor heterogeneity encompasses genetic, epigenetic, and phenotypic diversity, impacting treatment response and resistance. Spatial heterogeneity occurs both inter- and intra-lesionally, while temporal heterogeneity results from clonal evolution. High-throughput technologies like next-generation sequencing (NGS) enhance tumor characterization, but conventional biopsies still do not adequately capture genetic heterogeneity. Liquid biopsy (LBx), analyzing circulating tumor DNA (ctDNA), provides a minimally invasive alternative, offering real-time tumor evolution insights and identifying resistance mutations overlooked by tissue biopsies. This study evaluates the capability of LBx to capture tumor heterogeneity by comparing genetic profiles from multiple metastatic lesions and LBx samples. Eight patients from the Augsburger Longitudinal Plasma Study with various types of cancer provided 56 postmortem tissue samples, which were compared against pre-mortem LBx-derived circulating-free DNA sequenced by NGS. Tissue analyses revealed significant mutational diversity (4–12 mutations per patient, VAFs: 1.5–71.4%), with distinct intra- and inter-lesional heterogeneity. LBx identified 51 variants (4–17 per patient, VAFs: 0.2–31.1%), which overlapped with mutations from the tissue samples by 33–92%. Notably, 22 tissue variants were absent in LBx, whereas 18 LBx-exclusive variants were detected (VAFs: 0.2–2.8%). LBx effectively captures tumor heterogeneity, but should be used in conjunction with tissue biopsies for comprehensive genetic profiling. Full article

The increasing demand for food to meet the needs of the planet’s growing population requires, among other factors, greater and improved meat production. Meat quality is determined by key consumer-preferred traits, particularly tenderness, juiciness, and flavor. Recently, interest has grown in analyzing the genes associated with these phenotypic characteristics. Single-nucleotide polymorphisms (SNPs) are common genomic variations in cattle and represent the most widely used molecular markers. Research on SNP variation is now a major focus of genomic studies aimed at improving meat quality. Leptin levels reflect the amount of adipose tissue in meat, also known as marbling. Several SNPs in the leptin gene and its receptor have been linked to this meat quality trait. Similarly, SNPs in the calpain/calpastatin system play a significant role in postmortem muscle proteolysis and pork tenderness. This review examines these genetic variants as markers involved in the expression of phenotypic traits in meat products and explores their mechanisms of action. Additionally, it provides insights into the genetic variants associated with production-related characteristics. Full article

The influence of soft tissue structures, including ligaments spanning one or more intervertebral junctions and the nuchal ligament, on motion of the equine cervical joints remains unclear. The present study addressed this using four post-mortem horse specimens extending from head to withers with all ligaments intact. Three-dimensional kinematics was obtained from markers on the head and bone-anchored markers on each cervical and the first thoracic vertebra during rotation, lateral bending, flexion and extension of the whole head, and neck segment. Yaw, pitch, and roll angles in 8 cervical joints (total 32) were calculated. Flexion and extension were expressed mainly as pitch in 27 and 22 joints, respectively. Rotation appeared as predominantly roll in 13 joints, whereas lateral bending was represented as predominantly yaw in 1 and as roll or pitch in all other joints. Significant correlations between yaw, pitch, and roll were observed at individual cervical joints in 97% of all measurements, with the atlanto-occipital joint showing complete (100%) correlation. Most non-significant correlations occurred at the C5–C6 joint, while C6–C7 exhibited significantly lower correlation coefficients compared to other levels. The overall movement of the head and neck is not replicated at individual cervical joint levels and should be considered when evaluating equine necks in vivo. Full article

Background: Human metapneumovirus (hMPV) is a respiratory pathogen that causes illness ranging from mild upper respiratory tract infections to severe pneumonia, particularly in individuals with comorbidities. Fatal cases of hMPV-induced hemorrhagic pneumonia are rare and likely under-reported. Diagnosis is often delayed due to overlapping symptoms with other respiratory viruses and the rapid progression of the disease. Case presentation: We report the case of a 55-year-old man with a complex medical history, including liver cirrhosis and diabetes mellitus, who developed acute viral pneumonia. Initial symptoms appeared three days before a sudden clinical deterioration marked by shortness of breath, hemoptysis, and respiratory failure. A nasopharyngeal swab taken on the third day of illness tested positive for hMPV by qRT-PCR. The patient died the following day. Postmortem molecular testing confirmed hMPV in lung tissue and alveolar contents. Autopsy revealed bilateral hemorrhagic pneumonia with regional lymphadenopathy. Histopathological examination showed alveolar hemorrhage, multinucleated cells, neutrophilic infiltration, activated autophagy in macrophages, and numerous cytoplasmic eosinophilic viral inclusions. Conclusions: This is the first documented case of fatal hMPV pneumonia in Armenia. It highlights the potential severity of hMPV in adults with chronic health conditions and emphasizes the need for timely molecular diagnostics. Postmortem identification of characteristic viral inclusions may serve as a cost-effective histopathological marker of hMPV-associated lung pathology. Full article

Bone tissue is one of the most remarkable examples of biological plasticity within the human body, with a high regenerative capacity and adaptation following traumatic injuries. This process is conducted through a series of complex and interlinked molecular mechanisms, which will be summarized in this study. The temporal progression of bone healing follows relatively predictable phases, characterized by variation in the concentration and/or activity of biomolecules such as BMP, VEGF, MMPs. The molecular understanding of bone plasticity and regeneration has potentially significant implications in forensic sciences. They were not extensively studied and implemented in practical, forensic environments, mainly due to their high costs and limited availability. However, they have potential uses in areas, such as the interpretation of skeletal trauma, the estimation of the post-traumatic intervals, the postmortem interval, or the differentiation between ante-, peri-, and postmortem injuries to the bone. Full article

This review paper presents a comprehensive overview of DNA preservation in hard tissues (bones and teeth) for applications in forensic and archaeogenetic analyses. It presents bone structure, DNA location in bones and teeth, and extensive information about postmortem DNA location and preservation. Aged bones are a challenging biological material for DNA isolation due to their low DNA content, degraded DNA, and the potential presence of PCR inhibitors. In addition, the binding of DNA to the mineral matrix necessitates the inclusion of a demineralization process in extraction, and its contribution to the resulting increase in both DNA quality and quantity is explained. Guidelines and recommendations on bone sample selection to obtain higher DNA yields are discussed in terms of past, recent, and possible future recommendations. Interskeletal and intraskeletal differences in DNA yield are also explained. Recent studies have shown that current recommendations for the genetic identification of skeletal remains, including femurs, tibias, and teeth, may not be the most effective sampling approach. Moreover, when mass disasters and mass graves with commingled skeletal remains are considered, there is a greater possibility that the recommended set of skeletal elements will not be available for sampling and subsequent genetic testing. This review highlights interskeletal and intraskeletal variability in DNA yield, with a focus on studies conducted on poorly preserved skeletal remains, including both postwar (1945) victims from Slovenia and ancient human skeletons. Special emphasis is placed on anatomical differences and potential mechanisms influencing DNA preservation, as demonstrated in research on both modern and historical skeletons. Finally, the petrous part of the temporal bone and tooth cementum were reviewed in greater detail because they have been recognized as an optimal sampling type in both ancient DNA studies and routine forensic case analyses. Our experiences with the Second World War and archaeological petrous bones are discussed and compared to those of other bone types. Full article

The postmortem interval (PMI), defined as the time elapsed between death and the discovery or examination of the body, is a crucial parameter in forensic science for estimating the time of death. There are many ways to measure the PMI, such as Henssge’s nomogram, which uses rectal temperature measurement; livor mortis; rigor mortis; and forensic entomology. However, these methods are usually affected by various conditions in the surrounding environment. The purpose of the present study was to compare molecular genetics and histological changes in the brain and skeletal muscle tissues of SD rats over increasing periods of time after death. For the PMIs, we considered 0 h, 6 h, 12 h, 24 h, 36 h, 48 h, 4 days, 6 days, 8 days, 10 days, 14 days, and 21 days and compared them at 4 °C and 26 °C. Hematoxylin and Eosin (H&E) staining was performed to observe tissue changes. Morphological tissue changes were observed in cells for up to 21 days at 4 °C, and cell destruction was visually confirmed after 14 days at 26 °C. Total RNA (tRNA) was isolated from each tissue sample, and complementary DNA (cDNA) was synthesized. A reverse transcription quantitative PCR (RT-qPCR) SYBR Green assay targeting three types of housekeeping genes, including Gapdh, Sort1, B2m, and 5S rRNA, was performed. The results showed that Gapdh and 5S rRNA were highly stable and could be better RNA targets for estimating the PMI in brain and skeletal muscle tissues. Conversely, Sort1 and B2m showed poor stability and low expression levels. In conclusion, these molecular biomarkers could be used as auxiliary indicators of the PMI in human, depending on the stability of the marker. Full article

Understanding how sample type may influence the probability of influenza A virus (IAV) sequencing and isolation success can help improve the use of diagnostic tests and refine surveillance strategies in swine populations. The objective of this study was to evaluate the probability of success for IAV hemagglutinin (HA) and neuraminidase (NA) Sanger sequencing and virus isolation in Madin–Darby Canine Kidney (MDCK) cells across different porcine sample types submitted to the Iowa State University Veterinary Diagnostic Laboratory (ISU VDL) from 2018 to 2024. Antemortem and postmortem sample types were selected and analyzed based on reverse transcription real-time polymerase chain reaction (RT-rtPCR) cycle threshold (Ct) values. The Ct values corresponding to 95%, 75%, and 50% probabilities of sequencing or virus isolation success were determined for each sample type. For antemortem samples, a 95% probability of success for HA Sanger sequencing on nasal swabs exhibited a Ct value of 27.8 from 1046 samples and 23.6 for NA sequencing based on 66 nasal swabs. Using oral fluids, HA and NA Sanger sequencing success was at Ct values of 27.3 from 3446 samples and 22.1 from 137 samples, respectively. For postmortem samples, lung tissue had the highest number of sequences for the HA and NA, with Ct values of 25.7 and 21.5, respectively. For a 95% probability of successful virus isolation, nasal swabs demonstrated a Ct value of 21.1 from 647 samples, while lungs had a Ct value of 18.7 from 5892 samples. This study determined that nasal swabs and lung tissue had the highest probability of IAV gene sequencing and virus isolation success, while oral fluids, a common swine diagnostic sample type that is easy to collect and welfare-friendly, can be effective for gene sequencing when using lower IAV RT-rtPCR Ct values, i.e., ≤27.3. These results provide practical expectations for successful IAV HA and NA gene sequencing and virus isolation at 95%, 75%, and 50% probabilities based on sample type and RT-rtPCR Ct values to improve diagnostic testing strategies in swine populations. Full article

While viral pathogens are often subdivided into neurotropic and non-neurotropic categories, systemic inflammation caused by non-neurotropic viruses still possesses the ability to alter the central nervous system (CNS). Studies of CNS disease induced by viral infection, whether neurotropic or not, are presented with a unique set of challenges. First, because brain biopsies are rarely necessary to diagnose viral-associated neurological disorders, antemortem tissue samples are not readily available for study and human pathological studies must rely on end-stage, postmortem evaluations. Second, in vitro models fail to fully capture the nuances of an intact immune system, necessitating the use of animal models to fully characterize pathogenesis and identify potential therapeutic approaches. Non-human primates (NHP) represent a particularly attractive animal model in that they overcome many of the limits posed by more distant species and most closely mirror human disease pathogenesis and susceptibility. Here, we review NHP infection models of viruses known to infect and/or replicate within cells of the CNS, including West Nile virus, the equine encephalitis viruses, Zika virus, and herpesviruses, as well as those known to alter the immune status of the brain in the absence of significant CNS penetrance, including human immunodeficiency virus (HIV) in the current era of combination antiretroviral therapy (cART) and the coronavirus of severe acute respiratory syndrome (SARS)-CoV−2. This review focuses on viruses with an established role in causing CNS disease, including encephalitis, meningitis, and myelitis and NHP models of viral infection that are directly translatable to the human condition through relevant routes of infection, comparable disease pathogenesis, and responses to therapeutic intervention. Full article

Amyotrophic lateral sclerosis (ALS) is characterized by upper and lower motor neuron failure and poor prognosis. This study performed a meta-analysis of gene expression datasets that compared bulk-processed post-mortem spinal cord from ALS and control (CTL) patients. The analysis included 569 samples (454 ALS, 115 CTL) from 348 individuals (262 ALS, 86 CTL). Patterns of differential expression bias, related to mRNA abundance, gene length and GC content, were discernable from individual studies but attenuated by meta-analysis. A total of 213 differentially expressed genes (DEGs) were identified (144 ALS-increased, 69 ALS-decreased). ALS-increased DEGs were most highly expressed by microglia and associated with MHC class II, immune response and leukocyte activation. ALS-decreased DEGs were abundantly expressed by mature oligodendrocytes (e.g., the MOL5 phenotype) and associated with myelin production, plasma membrane and sterol metabolism. Comparison to spatial transcriptomics data showed that DEGs were prominently expressed in white matter, with increased DEG expression strongest in the ventral/lateral white matter. These results highlight white matter as the spinal cord region most strongly associated with the shifts in mRNA abundance observed in bulk-processed tissues. These shifts can be explained by attrition of mature oligodendrocytes and an ALS-emergent microglia phenotype that is partly shared among neurodegenerative conditions. Full article

Chronic kidney disease (CKD) significantly affects canine health, but the precise cellular mechanisms of this condition remain elusive. In this study, we used single-cell RNA sequencing (scRNA-seq) to profile renal cellular gene expression in a canine model of X-linked hereditary nephropathy (XLHN). Dogs with this condition exhibit juvenile-onset CKD similar to that seen in human Alport syndrome. Post-mortem renal cortical tissues from an affected male dog and a heterozygous female dog were processed to obtain single-cell suspensions. In total, we recovered up to 13,190 cells and identified 11 cell types, including major kidney cells and immune cells. Differential gene expression analysis comparing the affected male and heterozygous female dogs identified cell-type specific pathways that differed in a subpopulation of proximal tubule cells. These pathways included the integrin signaling pathway and the pathway for inflammation mediated by chemokine and cytokine signaling. Additionally, using machine learning-empowered digital cytometry, we deconvolved bulk mRNA-seq data from a previous canine study, revealing changes in cell type proportions across CKD stages. These results underline the utility of single-cell methodologies and digital cytometry in veterinary nephrology. Full article

Background/Objectives: A growing body of evidence is amassing in the literature suggesting a correlation between Alzheimer’s disease (AD) and thrombotic vascular complications, which led to the suggestive hypothesis that thrombosis may contribute to AD onset and progression by damaging the neurovasculature and reducing the cerebral blood flow. In turn, low cerebral blood flow is likely to contribute to neurodegeneration by reducing nutrient and oxygen supply and impairing toxic metabolite removal from the brain tissue. Methods: We searched the literature for studies in animal models of AD or patients diagnosed with the disease that reported circulating markers of platelet hyperactivity or hypercoagulation, or histological evidence of brain vascular thrombosis. Results: Platelet hyperactivity and hypercoagulability have been described in multiple animal models of AD, and histological evidence of neurovascular thrombosis has also been reported. Similarly, clinical studies on patients with AD showed circulating markers of platelet hyperactivity and hypercoagulation, or histological evidence of neurovascular thrombosis collected from post-mortem brain tissue samples. Conclusions: Taken together, a convincing picture is emerging that suggests a strong correlation between systemic or neurovascular thrombosis and AD. Nonetheless, a mechanistic role for haemostasis dysregulation and neurovascular damage in the onset or the progression of AD remains to be proven. Future research should focus on this important question in order to clarify the mechanisms underlying AD and identify a treatment for this disease. Full article

This review presents an in-depth analysis of the synergistic role of molecular biology in advancing forensic entomology. The study discusses how insects associated with decomposing bodies provide critical data for estimating the post-mortem interval (PMI), and how molecular techniques improve species identification and trace analysis. The manuscript examines DNA-based methods such as RAPD, RFLP, and mitochondrial sequencing, along with innovative applications like gene expression profiling and entomotoxicology analysis. Additionally, it presents real case studies illustrating how molecular data from insects can be used not only to estimate PMI but also to identify victims or suspects through human DNA retrieved from insect tissues. These advances confirm the fundamental role of molecular biology in strengthening the reliability and applicability of forensic entomology in legal contexts. Full article

Background/Objectives: End-of-life (EOL) HIV cure research, which studies HIV persistence through pre- and post-mortem tissue collection, has focused primarily on people living with HIV (PLWH) with a prognosis of six months or less. However, the perspectives of long-term survivors (LTS) diagnosed before the advent of effective antiretroviral treatment (ART) remain underexplored. Understanding their motivations and concerns about EOL cure research is essential for creating inclusive and ethical research frameworks. Methods: Between 2023 and 2024, we conducted in-depth qualitative interviews with 16 PLWH aged 60 and older from diverse backgrounds across the United States, recruited through community-based organizations and HIV networks. We used inductive thematic analysis to explore LTS’ perspectives on EOL HIV research. Results: Participants included cisgender men (56.25%) and women (43.75%) with diverse racial identities. While participants supported EOL HIV cure research, their willingness to participate varied, influenced by awareness, logistics, and ethical concerns. Altruism-motivated participation, but misconceptions about procedures and concerns over bodily integrity represented potential barriers. Some viewed blood draws and leukaphereses as routine, while others expressed hesitancy with biopsies and post-mortem tissue retrieval. HIV stigma, historical mistrust, and cultural beliefs also played a role in willingness to participate. LTS emphasized the need for decentralized research sites, travel support, and financial safeguards. Conclusions: To include LTS in EOL HIV cure research, a community-driven approach is needed, focusing on clear communication, ethical considerations, logistical support, and linkages to EOL care. Addressing misconceptions and building trust, particularly within groups traditionally underrepresented in research, is essential to expanding participation. Full article