damage	ARP staining: detects abasic sites (aldehyde-reactive probe), ARP reacts with a ring-opened sugar moiety resulting from the loss of a base in the DNA (abasic sites). → further confirmed using a conventional quantitative ELISA-based method (Fig. 2b). qPCR: detects broad DNA damage (various forms of DNA damage have the propensity to slow down or block DNA polymerase progression (26). mtDNA sample with the least mtDNA damage will produce the greatest amount of PCR product (26). Method: amplification of a PCR fragment specific to the mitochondrial genome. (patent Andolina et al. PCT No: PCT / US2016 / 050773: The amount of amplified DNA product is a direct measurement of the lesion frequency. The larger the number of lesions , the less full – length reaction product is produced , and thus lower fluorescence is observed The QPCR-based assay simultaneously assesses a wide variety of DNA damage, single and double-strand breaks; it may also detect DNA repair intermediates (Ayala-Torres et al., 2000; Furda et al., 2012a; Santos et al., 2006). On the other hand, the assay does not detect all forms of DNA damage, only those that impede or stop DNA polymerase progression. Moreover, it does not provide information of the specific type(s) of DNA damage present in a sample. (Dölle, 2016 #1416) Copy number and deletion analysis were performed simultaneously in the same neuron, using a duplex real-time PCR. To assess mtDNA SNVs down to very-low heteroplasmy levels, we performed PCR amplification and ultra-deep sequencing [commercial kit] Detroit R&D https://www.cosmobio.co.jp/product/detail/dna-damage-analysis-kit-drd.asp?entry_id=16826 This kit can be used on blood (Plasma(사용논문: (Al Amir Dache, 2020 #1513), ), cells and tissues from humans, mice and rats. In vitro and in vivo. Another advantage of this approach is that, unlike the Comet and 8-OHdG assays, it is possible to detect a variety of mtDNA, including defects and mutations. This innovative approach uses 8.8 kb (human), 8.2 kb (mouse), and 8.4 kb (rat) lengths of mitochondrial DNA for 14-18 cycles of qPCR, followed by amplification and quantification using real-time PCR. Otake: It is based on quantification of 8.8 kb mitochondrial DNA qPCR. Abasic or lesion site in mtDNA would lower amplification efficiency in PCR reaction (Qi, 2023 #2429) PCR-based assay (Mito DNAox): ↑ in PD PBMC Y = Fmin + ((Fmax − Fmin) / (1 + 10^(C50−x)·Slope))	(Greenamyre patent), rat whole blood (Sanders, 2014 #1422) ↑PD Rat blood Plasma(사용논문: (Al Amir Dache, 2020 #1513)	(#1411) ↑in PD patient SN and Rat brain
Methyl mtDNA	DNA methylation is a well-known epigenetic mechanism that regulates nuclear gene transcription. Mjff funds this Many healthy humans harbour low levels (<1%) of mtDNA point mutations, including both inherited and acquired mutations. Standard detection method: Bisulfite genomic sequencing (methylation-specific PCR)		(Blanch, 2016 #1355) ↓ (SN, N=10), TaqMan PCR
cytokine	[FGF-21] is a regulator of glucose and fatty acid metabolism in the body. FGF-21 is present in the brain, including SN, and is expressed by glial cells in culture.6 In dopaminergic neurons, FGF-21 increases the levels of peroxisome proliferator–activated receptor gamma coactivator 1-alpha (PGC-1α) and enhances mitochondrial respiratory function.6 PGC-1α is a mitochondrial master regulator that is downregulated in PD.7 [GDF-15]: review {Fujita, 2016 #1341} is predominantly expressed in the liver.8 In the brain, its most prominent site of synthesis is the choroid plexus, which secretes GDF-15 into the CSF from where the molecule can penetrate through the ependymal layer into the parenchyma.9	(Maetzler, 2016 #1340) ↑ in PDD, PDND, DLB (but overlap with HC)	-Serum level shows no change in LOPD (n=84) or EOPD (n=37) (Davis et al., 2020, PMID: 32190419) -GDF15: ↑ (but ⇄ overlap)in Spd (n=36, H&Y 4.2.6 )Miyaue, 2020 #1339)

(Davis, 2020 #1090) panel A — Biomarker concentration (pg/mL) box plots for FGF-21 and GDF-15 across Control / PD / EOPD / LOPD with significance bars p=0.0049 and p=0.001.

Metabolomics: lactate	serum lactate (Lactate stress test)		(Miyaue, 2020 #1339)= on lactate stress test (sPD)	(Obrenovitch, 1988 #1202) baboon with ischemia brain tissue: ↑ lactate
Metab imaging	MR spectroscopy: {Bowen, 1995 #1211} Spd, n=14, ↑ ratio of lactate to N-acetyl aspartate, with the greatest increase (3x) manifested by the subgroup(n = 4) with dementia, indicating an increase in cerebral lactate {Steele, 2017 #1089, {Stewart, 2021 #1343} review } dynamic nuclear polarization (DNP using ¹³C-MRS,). Js) DNP can use pyruvate (most widely used due to favoring technicalities), or lactate, or glucose (장점: permitting more directly study of the glycolytic pathway). Concept: hyperpolarization by DNP → ↑ sensitivity of exogenous agents → ↑ the sensitivity of the MRS with a ↑ spatial resolution to the millimeters and ↑ a temporal resolution at the subsecond range. IV injection of the hyperpolarized ¹³C-pyruvate results in appearance of ¹³C-lactate, ¹³C-alanine and ¹³C-bicarbonate resonance peaks depending on tissue, disease and the metabolic state. 단점: To date, a key limitation in the technique has been the short half-life of the hyperpolarization period (10–40 s for pyruvate; 51 s for glucose), necessitating the ensuing metabolic processes to occur rapidly, and resulting image generation to occur in 52 min (Brindle et al., 2011). 아식 못 슬성도임.
FDG PET	FDG-PET: Fluorodeoxyglucose, glucose analog,) Readily available The uptake of 18F-FDG by tissues is a marker for the tissue uptake of glucose, 18F-FDG is taken up by cells, phosphorylated by hexokinase (whose mitochondrial form is greatly elevated in rapidly growing malignant tumours),[20] and retained by tissues with high metabolic activity, such as most types of malignant tumours. {Steele, 2017 #1089: lacking the necessary sensitivity to identify substrates in low tissue concentrations, {Stewart, 2021 #1343} : FDG is routinely used for high sensitivity and specificity clinical PET imaging of glucose metabolism63, 단점: since FDG-6-phosphate does not undergo further glycolysis, FDG PET cannot probe metabolism beyond the first step of the glycolysis pathway. Cerebral glucose metabolic rate is considered a measure of synaptic activity given that the main metabolic activity of the brain relates to neurotransmission (Fowler & Volkow, 2001). Biggest problem: cannot distinguish cell loss, synaptic loss, or true hypometabolism [FDG PET in PD] {Ghaemi, 2002 #1872} Nine patients with MSA-P, 24 patients with PD, and seven healthy controls, FIG2. AND Table3, PD vs HC 안 차이, msa 만 ↓ {Antonini, 1997 #1873} , results: fig4 & table 2, PD에서 오히려 약간 ↑	Score diagram of subject scores derived from instrumental functional analyses of caudate nucleus and putamen score values in multiple systems atrophy, Parkinson's disease and seven normal control subjects (figure with three groups MSA (n=9), PD (n=24), Healthy controls (n=7)).
Phosphatidylethanolamine	MJFF is funding the study of blood Phosphatidylethanolamine (a MAM-linked phospholipid) level in PD patients.
N-formyl peptides (NFP)	MJFF is funding the study of blood, CSF and brain NFP levels in PD patients.
	See '2021 Katy Succinate_BM_TRAP1.pptx

MRS Imaging

Principle

• Magnetization transfer (MT)
  • Definition
    • the transfer of nuclear spin polarization and/or spin coherence from one population of nuclei to another population of nuclei, and to the use of these phenomena.[1]
      This pulse saturates protons bound to macromolecules but not those in free water. The saturated macromolecule-bound protons partially transfer their magnetization to protons in the hydration layer and free water.

Oxidative phoshorylation과 별도로) During periods of increased energy demand (e.g., exercise or muscle stimulation) or reduced mitochondrial ATP generation (e.g., ischemia or hypoxia), CK (creatine kinase) allows rapid transfer of the high-energy phosphate group in PCr (*phosphocreatine, 비상식량, =creatine phosphate (CP) , creatine molecule that serves as a rapidly mobilizable reserve of high-energy phosphates, ‘temporal energy buffer’) to ADP through its forward reaction, so ATP is generated.

	ATP generation	ATP consumption	CK REACTION	ATP resynthesis (during high energy demand)
?	mitochondria	Cytosol & cell membrane	Mitochondria	Cytosol
	Oxidative phosphorylation	ATP hydrolysis	PCr synthesis
ion	ADP + Pi + H⁺ → ATP + Cr ( → Adenine nucleotide translocator (ANT), =ADP/ATP translocase (ANT)=ADP/ATP carrier protein = mitochondrial ADP/ATP carrier (AAC) 에 의해 ATP 가 Cytosol 도 이동)	ATP + H2O→ ADP + Pi +energy	ATP + Cr(?)→ ADP + PCr + H (?)⁺ (→ then PCr leaves mitochondria)	ADP + PCr → ATP + Cr+ (→ then Pi 가 가서 glycolysis 등 함)
nsible	F1F0-ATPase (also known as H+-ATPase)	Na+/K+-ATPase	(Mitochondrial) CK	(cytosolic) CK
			The rates of CK reactions are much higher (~5 times) than the net rates of ATP synthesis and utilization in the human brain

Uncertain Spans

location	transcription	uncertainty
damage row / amplification fraction equation	reads Y = F_min + ((F_max − F_min) / (1 + 10^(C50−x)·Slope)) (preserved as a graphical formula in the source).	OCR rendering of the equation is approximate; the exponent layout in the source may differ slightly from the unicode rendering.
cytokine row / Maetzler 2016 #1340 cell	reads ↑ in PDD, PDND, DLB (but overlap with HC); abbreviations PDD/PDND/DLB are preserved verbatim from the source.	low confidence on whether PDND should be parsed as PDD-ND or as a separate clinical group label.
damage row / Greenamyre patent right-most cell	reads (Greenamyre patent), rat whole blood / (Sanders, 2014 #1422) ↑PD Rat blood / Plasma(사용논문: (Al Amir Dache, 2020 #1513) and (#1411) ↑in PD patient SN and Rat brain; cells contain Korean shorthand 사용논문 and unclear citation key arrangement.	citation keys reconstructed from visible fragments.
MRS Imaging table / question-mark row labels	left-most column shows partial labels e?, ion, nsible which appear to be tail-truncations of Where?, Reaction, Responsible in the source; preserved verbatim because the leading characters are cut off in the photo slice.	partial truncation at left edge of slice.