An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.

We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.

Engineering homoeologs provide a fine scale for quantitative traits in polyploid.

Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR-Cas9-mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad-spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops.

Induction of Autophagy and Its Role in Peripheral Nerve Regeneration after Peripheral Nerve Injury.

No matter what treatment is used after nerve transection, a complete cure is impossible, so basic and clinical research is underway to find a cure. As part of this research, autophagy is being investigated for its role in nerve regeneration. Here, we review the existing literature regarding the involvement and significance of autophagy in peripheral nerve injury and regeneration. A comprehensive literature review was conducted to assess the induction and role of autophagy in peripheral nerve injury and subsequent regeneration. Studies were included if they were prospective or retrospective investigations of autophagy and facial or peripheral nerves. Articles not mentioning autophagy or the facial or peripheral nerves, review articles, off-topic articles, and those not written in English were excluded. A total of 14 peripheral nerve studies that met these criteria, including 11 involving sciatic nerves, 2 involving facial nerves, and 1 involving the inferior alveolar nerve, were included in this review. Studies conducted on rats and mice have demonstrated activation of autophagy and expression of related factors in peripheral nerves with or without stimulation of autophagy-inducing factors such as rapamycin, curcumin, three-dimensional melatonin nerve scaffolds, CXCL12, resveratrol, nerve growth factor, lentinan, adipose-derived stem cells and melatonin, basic fibroblast growth factor, and epothilone B. Among the most studied of these factors in relation to degeneration and regeneration of facial and sciatic nerves are LC3II/I, PI3K, mTOR, Beclin-1, ATG3, ATG5, ATG7, ATG9, and ATG12. This analysis indicates that autophagy is involved in the process of nerve regeneration following facial and sciatic nerve damage. Inadequate autophagy induction or failure of autophagy responses can result in regeneration issues after peripheral nerve damage. Animal studies suggest that autophagy plays an important role in peripheral nerve degeneration and regeneration.

Newly Discovered Alleles of the Tomato Antiflorigen Gene SELF PRUNING Provide a Range of Plant Compactness and Yield.

In tomato cultivation, a rare natural mutation in the flowering repressor antiflorigen gene SELF-PRUNING (sp-classic) induces precocious shoot termination and is the foundation in determinate tomato breeding for open field production. Heterozygous single flower truss (sft) mutants in the florigen SFT gene in the background of sp-classic provide a heterosis-like effect by delaying shoot termination, suggesting the subtle suppression of determinacy by genetic modification of the florigen-antiflorigen balance could improve yield. Here, we isolated three new sp alleles from the tomato germplasm that show modified determinate growth compared to sp-classic, including one allele that mimics the effect of sft heterozygosity. Two deletion alleles eliminated functional transcripts and showed similar shoot termination, determinate growth, and yields as sp-classic. In contrast, amino acid substitution allele sp-5732 showed semi-determinate growth with more leaves and sympodial shoots on all shoots. This translated to greater yield compared to the other stronger alleles by up to 42%. Transcriptome profiling of axillary (sympodial) shoot meristems (SYM) from sp-classic and wild type plants revealed six mis-regulated genes related to the floral transition, which were used as biomarkers to show that the maturation of SYMs in the weaker sp-5732 genotype is delayed compared to sp-classic, consistent with delayed shoot termination and semi-determinate growth. Assessing sp allele frequencies from over 500 accessions indicated that one of the strong sp alleles (sp-2798) arose in early breeding cultivars but was not selected. The newly discovered sp alleles are potentially valuable resources to quantitatively manipulate shoot growth and yield in determinate breeding programs, with sp-5732 providing an opportunity to develop semi-determinate field varieties with higher yields.

Role of the WNT/ß-catenin/ZKSCAN3 Pathway in Regulating Chromosomal Instability in Colon Cancer Cell lines and Tissues.

Zinc finger protein with KRAB and SCAN domains 3 (ZKSCAN3) acts as an oncogenic transcription factor in human malignant tumors, including colon and prostate cancer. However, most of the ZKSCAN3-induced carcinogenic mechanisms remain unknown. In this study, we identified ZKSCAN3 as a downstream effector of the oncogenic Wnt/ß-catenin signaling pathway, using RNA sequencing and ChIP analyses. Activation of the Wnt pathway by recombinant Wnt gene family proteins or the GSK inhibitor, CHIR 99021 upregulated ZKSCAN3 expression in a ß-catenin-dependent manner. Furthermore, ZKSCAN3 upregulation suppressed the expression of the mitotic spindle checkpoint protein, Mitotic Arrest Deficient 2 Like 2 (MAD2L2) by inhibiting its promoter activity and eventually inducing chromosomal instability in colon cancer cells. Conversely, deletion or knockdown of ZKSCAN3 increased MAD2L2 expression and delayed cell cycle progression. In addition, ZKSCAN3 upregulation by oncogenic WNT/ß-catenin signaling is an early event of the adenoma-carcinoma sequence in colon cancer development. Specifically, immunohistochemical studies (IHC) were performed using normal (NM), hyperplastic polyps (HPP), adenomas (AD), and adenocarcinomas (AC). Their IHC scores were considerably different (61.4 in NM; 88.4 in HPP; 189.6 in AD; 246.9 in AC). In conclusion, ZKSCAN3 could be responsible for WNT/ß-catenin-induced chromosomal instability in colon cancer cells through the suppression of MAD2L2 expression.

NOP53 Suppresses Autophagy through ZKSCAN3-Dependent and -Independent Pathways.

Autophagy is an evolutionally conserved process that recycles aged or damaged intracellular components through a lysosome-dependent pathway. Although this multistep process is propagated in the cytoplasm by the orchestrated activity of the mTOR complex, phosphatidylinositol 3-kinase, and a set of autophagy-related proteins (ATGs), recent investigations have suggested that autophagy is tightly regulated by nuclear events. Thus, it is conceivable that the nucleolus, as a stress-sensing and -responding intranuclear organelle, plays a role in autophagy regulation, but much is unknown concerning the nucleolar controls in autophagy. In this report, we show a novel nucleolar-cytoplasmic axis that regulates the cytoplasmic autophagy process: nucleolar protein NOP53 regulates the autophagic flux through two divergent pathways, the ZKSCAN3-dependent and -independent pathways. In the ZKSCAN3-dependent pathway, NOP53 transcriptionally activates a master autophagy suppressor ZKSCAN3, thereby inhibiting MAP1LC3B/LC3B induction and autophagy propagation. In the ZKSCAN3-independent pathway, NOP53 physically interacts with histone H3 to dephosphorylate S10 of H3, which, in turn, transcriptionally downregulates the ATG7 and ATG12 expressions. Our results identify nucleolar protein NOP53 as an upstream regulator of the autophagy process.

Potential risk of exposure to heavy metals from co-processing of secondary wastes in the Republic of Korea.

The co-processing of secondary wastes during ordinary Portland cement (OPC) can result in high heavy metal concentrations in OPC products. However, earlier studies have not evaluated the concentrations of heavy metals (HMs) in OPC as a function of secondary input materials. Further, the health risk assessment (HRA) model has, thus far, has not been employed to assess the potential health risks associated with secondary raw materials and secondary fuels in OPC. Hence, to address these knowledge gaps, herein, monthly data for six HMs in the input materials and fuels from seven OPC manufacturers in the Republic of Korea were analyzed and modeled. Pb and Cu concentrations were found to be approximately 10-200 and 4-200 times higher than those of the other HMs, respectively. Furthermore, maximum Pb and Cu concentrations were 2-3 and 2-5 times higher than those reported in other countries, respectively. The quantity of input material had a significant influence on the observed patterns, and secondary raw materials, secondary additives, and secondary fuels were also determined to be important. Based on HRA assessment, although the risk levels were within permissible ranges, carcinogenic hazards attributable to Cr and Pb were not negligible. The results can aid in informed decision making and in implementing effective measures for managing risks associated with HMs in the OPC industry, thereby ameliorating threats to human health and environment.

Tyrosine Phosphorylation of the Kv2.1 Channel Contributes to Injury in Brain Ischemia.

In brain ischemia, oxidative stress induces neuronal apoptosis, which is mediated by increased activity of the voltage-gated K+ channel Kv2.1 and results in an efflux of intracellular K+. The molecular mechanisms underlying the regulation of Kv2.1 and its activity during brain ischemia are not yet fully understood. Here this study provides evidence that oxidant-induced apoptosis resulting from brain ischemia promotes rapid tyrosine phosphorylation of Kv2.1. When the tyrosine phosphorylation sites Y124, Y686, and Y810 on the Kv2.1 channel are mutated to non-phosphorylatable residues, PARP-1 cleavage levels decrease, indicating suppression of neuronal cell death. The tyrosine residue Y810 on Kv2.1 was a major phosphorylation site. In fact, cells mutated Y810 were more viable in our study than were wild-type cells, suggesting an important role for this site during ischemic neuronal injury. In an animal model, tyrosine phosphorylation of Kv2.1 increased after ischemic brain injury, with an observable sustained increase for at least 2 h after reperfusion. These results demonstrate that tyrosine phosphorylation of the Kv2.1 channel in the brain may play a critical role in regulating neuronal ischemia and is therefore a potential therapeutic target in patients with brain ischemia.

Complications in patients with intramedullary nails: a case series from a single Cambodian surgical clinic.

PURPOSE: Since its development in 1999, the SIGN nail has been used in over 190,000 surgeries spanning 55 countries. To date, however, evaluation of SIGN nail outcomes has been limited to small prospective studies or large retrospective studies using SIGN's online database. This study uses the experience of a single, independent Cambodian surgical clinic to characterize common complications, provide commentary on ways to reduce the risk of those complications, and determine whether several observed nail fractures were due to metallurgic defects. METHODS: Clinic medical records were queried to identify complications in patients with SIGN nails. Data was abstracted including age, sex, mechanism of injury, and latency between injury, primary implantation, and presentation with a complication. Two nails that fractured in vivo were analyzed by light microscopy, scanning electron microscopy, and polarized light microscopy after chemical etching. RESULTS: Fifty-four complications in 51 patients were identified. The most common complications were non-union (n = 26, 48%), infection (n = 16, 30%), flexion limitation (n = 11, 20%), nail fracture (n = 4, 7%), delayed union (n = 4, 7%), and malunion (n = 4, 7%). Other complications included broken or floating screws. Fractography revealed that two of the fractured nails most likely failed by fatigue followed by fast fracture at the site of non-union. We found no evidence of intrinsic nail defects. We identified multiple inconsistencies between SIGN's database and independent clinic records. CONCLUSIONS: Non-union and infection were common relative to all complications. Based on radiographic review, risk for non-union and malunion can be minimized by selecting an appropriate nail diameter, using multiple interlocking screws, and employing the correct implant and approach for fracture morphology when using SIGN nails. Nail fractures were unlikely to be caused by metallurgical flaws. Further study is necessary to determine the appropriate management of non-unions based on radiographic and clinical factors.

Specificity Assessment of CRISPR Genome Editing of Oncogenic EGFR Point Mutation with Single-Base Differences.

In CRISPR genome editing, CRISPR proteins form ribonucleoprotein complexes with guide RNAs to bind and cleave the target DNAs with complete sequence complementarity. CRISPR genome editing has a high potential for use in precision gene therapy for various diseases, including cancer and genetic disorders, which are caused by DNA mutations within the genome. However, several studies have shown that targeting the DNA via sequence complementarity is imperfect and subject to unintended genome editing of other genomic loci with similar sequences. These off-target problems pose critical safety issues in the therapeutic applications of CRISPR technology, with particular concerns in terms of the genome editing of pathogenic point mutations, where non-mutant alleles can become an off-target with only a one-base difference. In this study, we sought to assess a novel CRISPR genome editing technique that has been proposed to achieve a high specificity by positioning the mismatches within the protospacer adjacent motif (PAM) sequence. To this end, we compared the genome editing specificities of the PAM-based and conventional methods on an oncogenic single-base mutation in the endothelial growth factor receptor (EGFR). The results indicated that the PAM-based method provided a significantly increased genome editing specificity for pathogenic mutant alleles with single-base precision.

Role of the JNK Pathway in Varicella-Zoster Virus Lytic Infection and Reactivation.

Mechanisms of neuronal infection by varicella-zoster virus (VZV) have been challenging to study due to the relatively strict human tropism of the virus and the paucity of tractable experimental models. Cellular mitogen-activated protein kinases (MAPKs) have been shown to play a role in VZV infection of nonneuronal cells, with distinct consequences for infectivity in different cell types. Here, we utilize several human neuronal culture systems to investigate the role of one such MAPK, the c-Jun N-terminal kinase (JNK), in VZV lytic infection and reactivation. We find that the JNK pathway is specifically activated following infection of human embryonic stem cell-derived neurons and that this activation of JNK is essential for efficient viral protein expression and replication. Inhibition of the JNK pathway blocked viral replication in a manner distinct from that of acyclovir, and an acyclovir-resistant VZV isolate was as sensitive to the effects of JNK inhibition as an acyclovir-sensitive VZV isolate in neurons. Moreover, in a microfluidic-based human neuronal model of viral latency and reactivation, we found that inhibition of the JNK pathway resulted in a marked reduction in reactivation of VZV. Finally, we utilized a novel technique to efficiently generate cells expressing markers of human sensory neurons from neural crest cells and established a critical role for the JNK pathway in infection of these cells. In summary, the JNK pathway plays an important role in lytic infection and reactivation of VZV in physiologically relevant cell types and may provide an alternative target for antiviral therapy.IMPORTANCE Varicella-zoster virus (VZV) has infected over 90% of people worldwide. While primary infection leads to the typically self-limiting condition of chickenpox, the virus can remain dormant in the nervous system and may reactivate later in life, leading to shingles or inflammatory diseases of the nervous system and eye with potentially severe consequences. Here, we take advantage of newer stem cell-based technologies to study the mechanisms by which VZV infects human neurons. We find that the c-Jun N-terminal kinase (JNK) pathway is activated by VZV infection and that blockade of this pathway limits lytic replication (as occurs during primary infection). In addition, JNK inhibition limits viral reactivation, exhibiting parallels with herpes simplex virus reactivation. The identification of the role of the JNK pathway in VZV infection of neurons reveals potential avenues for the development of alternate antiviral drugs.

c-Jun N-terminal kinase regulates the nucleoplasmic translocation and stability of nucleolar GLTSCR2 protein.

Glioblastoma tumor suppressive candidate region gene 2 (GLTSCR2) is a nucleolar protein that participates in critical cellular processes including the DNA damage response, cell cycle regulation, and inhibition of MYC-induced transforming activity. Irrespective of these important physiological and pathological functions, the mechanisms that regulate GLTSCR2 expression, and its nucleolar-nucleoplasmic translocation, are largely unknown. HeLa cells were treated with various protein kinase inhibitors and subjected to immunocytochemical or immunoblot assays for GLTSCR2. Protein stability was determined by the cycloheximide chase or ubiquitination assays. Oligomer status was analyzed by immunoprecipitation. Inhibiting c-jun N-terminal kinase (JNK) phosphorylation activity on c-jun by SP600125, or adding a c-jun peptide, induced the nucleoplasmic translocation of GLTSCR2 from the nucleolus and enhanced protein degradation through the proteasome-polyubiquitination pathway. These effects may have resulted from reducing the binding affinity between GLTSCR2 monomers. These data indicate that JNK, and its phosphorylation target c-jun, are prerequisites for the nucleolar distribution of GLTSCR2 and maintenance of its protein stability. Overall, GLTSCR2 is crucial for normal cellular function as well as for preventing the development or progression of cancer. The JNK-c-jun axis is indispensible for regulating the activities of GLTSCR2.

Vector radiative transfer in a multilayer medium by natural element method.

The vector radiative transfer problem in a vertically multilayer scattering medium with spatial changes in the index of refraction is solved by the natural element method (NEM). The top boundary of the multilayer medium is irradiated by a collimated beam. In our model, the angular space is discretized by the discrete ordinates approach, and the spatial discretization is conducted by the Galerkin weighted residuals approach. In the solution procedure, the collimated component for the Stokes parameters is first solved by NEM, and then it is embedded into the vector radiative transfer equation for the diffuse component as a source term. To keep the consistency of the directions in all the layers, angular interpolation of the Stokes parameters at the interfaces is adopted. The NEM approach for the collimated component is first validated. Then, the classical coupled atmosphere-water system irradiated by different states of collimated beam is examined to verify the numerical performance of the method. Numerical results show that the NEM is accurate, flexible, and effective in solving polarized radiative transfer in a multilayer medium. Finally, polarized radiative transfer in a four-layer system is investigated and analyzed.

Cellular stage specific functional analysis of REX1: In human embryonic stem cells.

As transcription and translation are dynamic and can vary among the cell types and conditions, proteomics may reveal the tissue-specific functions of a protein, more relevant to its genuine functions on cellular mechanisms. The new proteome analysis by Son et al. [Proteomics 2015, 15, 2220-2229] identified the functions of the pluripotency marker protein, REX1 in hESCs, and unraveling its regulatory network orchestrating pluripotency. Compared to the previous transcriptome analysis that showed mechanisms irrelevant to pluripotency, Son et al. employed a proteome analysis determined convincing and meaningful mechanisms of REX. In addition to demonstrating the biological importance of REX1, this research by Son et al. is also a compelling example of the conceptual significance of connecting proteomics with stem cell biology.

Characterization of wastes from construction and demolition sector.

In Republic of Korea, construction and demolition (C&D) waste accounts for 49.9% of the total waste. In the present work, the mineralogical composition, the concentrations of 11 heavy metals, 19 PAH, and 7 polychlorinated biphenyl (PCB) congeners present in the 6 broad category (9 subcategories) of C&D hazardous waste were discussed along with their leaching characteristics. In concrete/mixed cement waste, the concentrations of As, Cr(6+), Hg, and Zn were in the range of 1.76-7.86, ND-1.63, 0.026-0.047, and 110.90-280.17 mg/kg, respectively. The asphalt waste sample A1 possessed relatively high concentrations of phenanthrene, fluoranthene, pyrene, benz(a)anthracene, benzo(a)pyrene, and indeno(1,2,3-cd)pyrene comparing to the other samples and it contains 0.08-0.1% of coal tar. Hazardous nature of the C&D wastes greatly depends on the source of the collection. Zn concentration was above 1000 mg/kg for road asphalt waste samples A4 and A5. Total PCB concentration were high in the soil waste sample S1 (130 µg/kg) as it was the excavated soil obtained from the premises of an oil station. Leaching of As, Ba, CN(-), and F(-) were observed in most of the C&D waste samples.

Stem Cell-Based Approaches in Parkinson's Disease Research.

Parkinson's disease (PD) is a neurodegenerative condition characterized by the loss of midbrain dopaminergic neurons, leading to motor symptoms. While current treatments provide limited relief, they don't alter disease progression. Stem cell technology, involving patient-specific stem cell-derived neurons, offers a promising avenue for research and personalized regenerative therapies. This article reviews the potential of stem cell-based research in PD, summarizing ongoing efforts, their limitations, and introducing innovative research models. The integration of stem cell technology and advanced models promises to enhance our understanding and treatment strategies for PD.

Microfluidics-based condensation bioaerosol sampler for multipoint airborne virus monitoring.

To facilitate rapid monitoring of airborne viruses, they must be collected with high efficiency and concentrated in a small volume of a liquid sample. In addition, the development of low-cost miniaturized samplers is essential for multipoint monitoring. Thus, in an attempt to fulfill these requirements, this study developed a microfluidic condensation bioaerosol sampler (MCBS). The developed sampler comprised two parts: a virus growth section and a virus droplet-to-liquid sample conversion section, each of which was fabricated on a chip using microfluidic technology. The condensation nucleus growth technique used in the virus growth section grew nanometer-sized airborne viruses into micro-sized droplets, making it possible to collection of viruses easier and with high efficiency. In addition, the virus droplet-to-liquid sample conversion section controlled the transport of droplets based on electrowetting technology. This enabled the collected airborne viruses to be concentrated in tens of microliters of the liquid sample. To evaluate the performance of both the sections, the virus dropletization, virus collection efficiency, and virus droplet-to-liquid sample conversion efficiency were evaluated through quantitative experiments. H1N1 and HCOV-229E viruses were used to conduct quantitative experiments on MCBS. We could obtain virus liquid samples with at 72.8- and 89.9-times higher concentration through 1:1 evaluation with a commercial sampler. Thus, the developed sampler facilitated efficient collection and concentration of airborne viruses in a compact, cost-effective manner. This is expected to facilitate rapid and accurate multipoint monitoring of viral aerosols.

Expression of ChAT, Iba-1, and nNOS in the Central Nervous System following Facial Nerve Injury.

Facial nerve injury can cause significant functional impairment, impacting both the peripheral and central nervous systems. The present study evaluated changes in facial motor function, numbers of cholinergic neurons and microglia, and nNOS levels in the facial nucleus of the central nervous system (CNS) following peripheral facial nerve injury. Facial nerve function, as determined by eyeblink and whisker-movement reflexes, was evaluated at baseline and 1, 2, 3, 4, 8, and 12 weeks after inducing facial nerve injury through compression or axotomy. The expression of choline acetyltransferase (ChAT), ionized calcium-binding adaptor molecule 1 (Iba-1), and neuronal nitric oxide synthase (nNOS) in the facial nucleus of the CNS was analyzed 2, 4, and 12 weeks after peripheral facial nerve injury. Compression-induced facial nerve injury was found to lead to temporary facial motor impairment, whereas axotomy resulted in persistent impairment. Moreover, both compression and axotomy reduced ChAT expression and increased Iba-1 and nNOS expression in the facial nucleus, indicating upregulation of an inflammatory response and neurodegeneration. These results indicate that, compared with compression-induced injury, axotomy-induced facial nerve injury results in greater facial motor dysfunction and more persistent microglial and nitric oxide activation in the facial nucleus of the CNS.

Generation of an induced pluripotent stem cell line (PNUYHi002-A) from a patient with Alzheimer's disease carrying PRNP M232R variant.

We generated a human induced pluripotent stem cell (iPSC) line from the peripheral blood mononuclear cells isolated from a 59-year-old male patient with Alzheimer's disease (AD). The iPSC line was meticulously characterized to confirm its pluripotency, absence of transgenes, and normal karyotype. The unexpected discovery of the M232R variant in PRNP makes this cell line a valuable resource for investigating AD pathogenesis.

Autophagy Genes and Otitis Media Outcomes.

Otitis media (OM) is a common cause of hearing loss in children that requires corrective surgery. Various studies have investigated the pathomechanisms and treatment of OM. Autophagy, an essential cellular recycling and elimination mechanism implicated in various diseases, is known to play an important role in the pathogenesis of OM. Here, we conducted a literature review on autophagy in OM, highlighting the relationship between expression patterns of autophagy-related factors and pathophysiological and clinical aspects of OM. We summarized the existing research results on the expression of autophagy-related factors in acute OM (AOM), OM with effusion (OME), chronic OM (COM) with cholesteatoma, and COM without cholesteatoma (CholeOM) in animals and humans. Autophagy-related factors are expressed in the middle ear mucosa or fluid of AOM, effusion of OME, granulation tissue of COM, and cholesteatoma of CholeOM. Among ATGs and other autophagy-related factors, the most extensively studied in relation to the pathogenesis of OM are mTOR, LC3II/I, PI3K, Beclin-1, FLIP, Akt, and Rubicon. Expression of autophagy-related factors is associated with AOM, OME, COM, and CholeOM. Inadequate expression of these factors or a decrease/increase in autophagy responses can result in OM, underscoring the critical role of ATGs and related factors in the pathogenesis of OM.