The human brainome: network analysis identifies \u3ci\u3eHSPA2\u3c/i\u3e as a novel Alzheimer’s disease target

Our hypothesis is that changes in gene and protein expression are crucial to the development of late-onset Alzheimer’s disease. Previously we examined how DNA alleles control downstream expression of RNA transcripts and how those relationships are changed in late-onset Alzheimer’s disease. We have now examined how proteins are incorporated into networks in two separate series and evaluated our outputs in two different cell lines. Our pipeline included the following steps: (i) predicting expression quantitative trait loci; (ii) determining differential expression; (iii) analysing networks of transcript and peptide relationships; and (iv) validating effects in two separate cell lines. We performed all our analysis in two separate brain series to validate effects. Our two series included 345 samples in the first set (177 controls, 168 cases; age range 65–105; 58% female; KRONOSII cohort) and 409 samples in the replicate set (153 controls, 141 cases, 115 mild cognitive impairment; age range 66–107; 63% female; RUSH cohort). Our top target is heat shock protein family A member 2 (HSPA2), which was identified as a key driver in our two datasets. HSPA2 was validated in two cell lines, with overexpression driving further elevation of amyloid-B40 and amyloid-B42 levels in APP mutant cells, as well as significant elevation of microtubule associated protein tau and phosphorylated-tau in a modified neuroglioma line. This work further demonstrates that studying changes in gene and protein expression is crucial to understanding late onset disease and further nominates HSPA2 as a specific key regulator of late-onset Alzheimer’s disease processes

The human brainome: network analysis identifies HSPA2 as a novel Alzheimer's disease target

Our hypothesis is that changes in gene and protein expression are crucial to the development of late-onset Alzheimer's disease. Previously we examined how DNA alleles control downstream expression of RNA transcripts and how those relationships are changed in late-onset Alzheimer's disease. We have now examined how proteins are incorporated into networks in two separate series and evaluated our outputs in two different cell lines. Our pipeline included the following steps: (i) predicting expression quantitative trait loci; (ii) determining differential expression; (iii) analysing networks of transcript and peptide relationships; and (iv) validating effects in two separate cell lines. We performed all our analysis in two separate brain series to validate effects. Our two series included 345 samples in the first set (177 controls, 168 cases; age range 65-105; 58% female; KRONOSII cohort) and 409 samples in the replicate set (153 controls, 141 cases, 115 mild cognitive impairment; age range 66-107; 63% female; RUSH cohort). Our top target is heat shock protein family A member 2 (HSPA2), which was identified as a key driver in our two datasets. HSPA2 was validated in two cell lines, with overexpression driving further elevation of amyloid-b40 and amyloid-b42 levels in APP mutant cells, as well as significant elevation of microtubule associated protein tau and phosphorylated-tau in a modified neuroglioma line. This work further demonstrates that studying changes in gene and protein expression is crucial to understanding late onset disease and further nominates HSPA2 as a specific key regulator of late-onset Alzheimer's disease processes

Molecular specificity of substrate recognition and activation in cytochrome P-450(CAM)

The mechanisms by which biological macromolecules recognize small molecules are of fundamental relevance to the maintenance of living systems and the chemistry of noncovalent bonding. Hydrogen bonding and hydrophobic interactions have been implicated in binding and activation of hydrocarbon substrates by cytochrome P-450\sb{\rm cam}. The dependence of the reaction efficiency and specificity on the structural complementarity in the P-450\sb{\rm cam}-substrate complex suggests that the active site structure is of paramount importance in mediating catalysis. Cytochrome P-450\sb{\rm cam} was used as a model system to elucidate the role of specific active site residues in substrate recognition and to engineer enzyme-substrate interactions for novel specificities.Active site mutations of hydrophobic and hydrogen bonding residues were designed to alter the efficiency and specificity of aliphatic hydroxylation by changing the position and orientation of the substrate in the active site. Steric effects were assessed by engineering hydrophobic side chains at multiple sites around the perimeter of the binding pocket such that the access of the substrate to the heme is predicted to be either inhibited or enhanced. Ethylbenzene and a series of chlorinated ethanes were used to show that the position of steric bulk in the active site is correlated with the catalytic efficiency of the enzyme under both oxidative and reductive reaction conditions. Thus, the orientation of the substrate in the active site was altered in a predictable manner by the modulating the topology of the active site cavity. The uncoupling of reducing equivalents was strongly dependent on the oxidase branch point in the reaction, indicating that reaction efficiency at the level of the putative (FeO) \sp{3+} is controlled by substrate access to the iron. Polar contributions to substrate recognition were evaluated by the design of a hydrogen bond switch, which effected the expected changes in hydroxylation regiospecificity with (1R)- and(1S)-norcamphor. In general, active site design of hydrophobic contacts and polar interactions resulted in the expected perturbations in the P-450\sb{\rm cam} catalyzed reaction, suggesting that protein engineering for enhanced enzyme activity and specificity is a viable approach to the pursuit of novel catalysts.U of I OnlyETDs are only available to UIUC Users without author permissio

Redox Processes affecting the spent fuel source-term

The source term from spent fuel dissolution is subject to considerable uncertainties, both with respect to the presence and extent of oxidative dissolution processes of the spent fuel itself and the coupling with processes associated with the iron canister. Related problems to be examined in this work package are the representativeness and reliability of laboratory data with respect to the impact of unavoidable minor concentrations of oxygen also in inert-gas boxes used, the potential reactivity and its outcome of hydrogen from container corrosion in combination with high burn-up spent fuel, possible galvanic coupling of spent fuel and container material and the retention of redox sensitive radionuclides by relevant minerals, especially by steel container corrosion products. A set of investigations has been conducted with the aim of getting better insight into redox processes determining spent fuel and iron canister corrosion. ITU reports on studies on spent fuel in presence of corroding Fe, on corrosion of spent fuel in presence of H2 and on fuel corrosion studies on thin film model systems. The redox reactivity of doped UO2 in view of effects on the reactivity towards H2O2 has been studied at KTH. The reductive trapping of actinides in container corrosion products during spent fuel corrosion is investigated by INE. Studsvik reports on the redox chemistry at the near field of repository and the influences of iron canister material and hydrogen. Redox conditions near waste packages were studied by NRI.JRC.E.5-Nuclear chemistr

The human brainome: network analysis identifies \u3ci\u3eHSPA2\u3c/i\u3e as a novel Alzheimer’s disease target

Our hypothesis is that changes in gene and protein expression are crucial to the development of late-onset Alzheimer’s disease. Previously we examined how DNA alleles control downstream expression of RNA transcripts and how those relationships are changed in late-onset Alzheimer’s disease. We have now examined how proteins are incorporated into networks in two separate series and evaluated our outputs in two different cell lines. Our pipeline included the following steps: (i) predicting expression quantitative trait loci; (ii) determining differential expression; (iii) analysing networks of transcript and peptide relationships; and (iv) validating effects in two separate cell lines. We performed all our analysis in two separate brain series to validate effects. Our two series included 345 samples in the first set (177 controls, 168 cases; age range 65–105; 58% female; KRONOSII cohort) and 409 samples in the replicate set (153 controls, 141 cases, 115 mild cognitive impairment; age range 66–107; 63% female; RUSH cohort). Our top target is heat shock protein family A member 2 (HSPA2), which was identified as a key driver in our two datasets. HSPA2 was validated in two cell lines, with overexpression driving further elevation of amyloid-B40 and amyloid-B42 levels in APP mutant cells, as well as significant elevation of microtubule associated protein tau and phosphorylated-tau in a modified neuroglioma line. This work further demonstrates that studying changes in gene and protein expression is crucial to understanding late onset disease and further nominates HSPA2 as a specific key regulator of late-onset Alzheimer’s disease processes

Cholesterol Ester Oxidation by Mycobacterial Cytochrome P450

Mycobacteria share a common cholesterol degradation pathway initiated by oxidation of the alkyl side chain by enzymes of cytochrome P450 (CYP) families 125 and 142. Structural and sequence comparisons of the two enzyme families revealed two insertions into the N-terminal region of the CYP125 family (residues 58–67 and 100–109 in the CYP125A1 sequence) that could potentially sterically block the oxidation of the longer cholesterol ester molecules. Catalytic assays revealed that only CYP142 enzymes are able to oxidize cholesteryl propionate, and although CYP125 enzymes could oxidize cholesteryl sulfate, they were much less efficient at doing so than the CYP142 enzymes. The crystal structure of CYP142A2 in complex with cholesteryl sulfate revealed a substrate tightly fit into a smaller active site than was previously observed for the complex of CYP125A1 with 4-cholesten-3-one. We propose that the larger CYP125 active site allows for multiple binding modes of cholesteryl sulfate, the majority of which trigger the P450 catalytic cycle, but in an uncoupled mode rather than one that oxidizes the sterol. In contrast, the more unhindered and compact CYP142 structure enables enzymes of this family to readily oxidize cholesteryl esters, thus providing an additional source of carbon for mycobacterial growth

Application of HB17, an Arabidopsis class II homeodomain-leucine zipper transcription factor, to regulate chloroplast number and photosynthetic capacity

Transcription factors are proposed as suitable targets for the control of traits such as yield or food quality in plants. This study reports the results of a functional genomics research effort that identified ATHB17, a transcription factor from the homeodomain-leucine zipper class II family, as a novel target for the enhancement of photosynthetic capacity. It was shown that ATHB17 is expressed natively in the root quiescent centre (QC) from Arabidopsis embryos and seedlings. Analysis of the functional composition of genes differentially expressed in the QC from a knockout mutant (athb17-1) compared with its wild-type sibling revealed the over-representation of genes involved in auxin stimulus, embryo development, axis polarity specification, and plastid-related processes. While no other phenotypes were observed in athb17-1 plants, overexpression of ATHB17 produced a number of phenotypes in Arabidopsis including enhanced chlorophyll content. Image analysis of isolated mesophyll cells of 35S::ATHB17 lines revealed an increase in the number of chloroplasts per unit cell size, which is probably due to an increase in the number of proplastids per meristematic cell. Leaf physiological measurements provided evidence of improved photosynthetic capacity in 35S::ATHB17 lines on a per unit leaf area basis. Estimates of the capacity for ribulose-1,5-bisphosphate-saturated and -limited photosynthesis were significantly higher in 35S::ATHB17 lines

O2‐06‐01: The Human Brainome: Human Brain Genome, Transcriptome, and Proteome Integration

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153287/1/alzjjalz201606424.pd