A genetic association study of glutamine-encoding DNA sequence structures, somatic CAG expansion, and DNA repair gene variants, with Huntington disease clinical outcomes

Background: Huntington disease (HD) is caused by an unstable CAG/CAA repeat expansion encoding a toxic polyglutamine tract. Here, we tested the hypotheses that HD outcomes are impacted by somatic expansion of, and polymorphisms within, the HTT CAG/CAA glutamine-encoding repeat, and DNA repair genes. Methods: The sequence of the glutamine-encoding repeat and the proportion of somatic CAG expansions in blood DNA from participants inheriting 40 to 50 CAG repeats within the TRACK-HD and Enroll-HD cohorts were determined using high-throughput ultra-deep-sequencing. Candidate gene polymorphisms were genotyped using kompetitive allele-specific PCR (KASP). Genotypic associations were assessed using time-to-event and regression analyses. Findings: Using data from 203 TRACK-HD and 531 Enroll-HD participants, we show that individuals with higher blood DNA somatic CAG repeat expansion scores have worse HD outcomes: a one-unit increase in somatic expansion score was associated with a Cox hazard ratio for motor onset of 3·05 (95% CI = 1·94 to 4·80, p = 1·3 × 10−6). We also show that individual-specific somatic expansion scores are associated with variants in FAN1 (pFDR = 4·8 × 10-6), MLH3 (pFDR = 8·0 × 10−4), MLH1 (pFDR = 0·004) and MSH3 (pFDR = 0·009). We also show that HD outcomes are best predicted by the number of pure CAGs rather than total encoded-glutamines. Interpretation: These data establish pure CAG length, rather than encoded-glutamine, as the key inherited determinant of downstream pathophysiology. These findings have implications for HD diagnostics, and support somatic expansion as a mechanistic link for genetic modifiers of clinical outcomes, a driver of disease, and potential therapeutic target in HD and related repeat expansion disorders

Soil Organic Carbon Isotope Tracing in Sorghum under Ambient CO2 and Free-Air CO2 Enrichment (FACE)

As atmospheric carbon dioxide concentrations, [CO2Air ], continue their uncontrolled rise, the capacity of soils to accumulate or retain carbon is uncertain. Free-air CO2 enrichment (FACE) experiments have been conducted to better understand the plant, soil and ecosystem response to elevated [CO2 ], frequently employing commercial CO2 that imparts a distinct isotopic signal to the system for tracing carbon. We conducted a FACE experiment in 1998 and 1999, whereby sorghum (C4 photosynthetic pathway) was grown in four replicates of four treatments using a split-strip plot design: (i) ambient CO2 /ample water (365 µmol mol−1, “Control–Wet”), (ii) ambient CO2 /water stress (“Control–Dry”), (iii) CO2-enriched (560 µmol mol−1, “FACE–Wet”), and (iv) CO2-enriched/water stressed (“FACE–Dry”). The stable-carbon isotope composition of the added CO2 (in FACE treatments) was close to that of free atmosphere background values, so the subsequent similar13 C-enriched carbon signal photosynthetically fixed by C4 sorghum plants could be used to trace the fate of carbon in both FACE and control treatments. Measurement of soil organic carbon content (SOC (%) = gC/ gdry soil × 100%) and δ13 C at three depths (0–15, 15–30, and 30–60 cm) were made on soils from the beginning and end of the two experimental growing seasons. A progressive ca. 0.5‰–1.0‰ δ13 C increase in the upper soil SOC in all treatments over the course of the experiment indicated common entry of new sorghum carbon into the SOC pools. The 0–15 cm SOC in FACE treatments was13 C-enriched relative to the Control by ca. 1‰, and according to isotopic mass balance, the fraction of the new sorghum-derived SOC in the Control–Wet treatment at the end of the second season was 8.4%, 14.2% in FACE–Wet, 6.5% in Control–Dry, and 14.2% in FACE–Dry. The net SOC enhancement resulting from CO2 enrichment was therefore 5.8% (or 2.9% y−1 of experiment) under ample water and 7.7% (3.8% y−1 of experiment) under limited water, which matches the pattern of greater aboveground biomass increase with elevated [CO2Air ] under the Dry treatment, but no parallel isotopic shifts were found in deeper soils. However, these increased fractions of new carbon in SOC at the end of the experiment do not necessarily mean an increase in total SOC content, because gravimetric measurements of SOC did not reveal a significant increase under elevated [CO2Air ], at least within the limits of SOC-content error bars. Thus, new carbon gains might be offset by pre-experiment carbon losses. The results demonstrate successful isotopic tracing of carbon from plants to soils in this sorghum FACE experiment showing differences between FACE and Control treatments, which suggest more dynamic cycling of SOC under elevated [CO2Air ] than in the Control treatment. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Thermodynamic benchmark study using Biacore technology

A total of 22 individuals participated in this benchmark study to characterize the thermodynamics of small-molecule inhibitor-enzyme interactions using Biacore instruments. Participants were provided with reagents (the enzyme carbonic anhydrase II, which was immobilized onto the sensor surface, and four sulfonamide-based inhibitors) and were instructed to collect response data from 6 to 36 °C. van't Hoff enthalpies and entropies were calculated from the temperature dependence of the binding constants. The equilibrium dissociation and thermodynamic constants determined from the Biacore analysis matched the values determined using isothermal titration calorimetry. These results demonstrate that immobilization of the enzyme onto the sensor surface did not alter the thermodynamics of these interactions. This benchmark study also provides insights into the opportunities and challenges in carrying out thermodynamic studies using optical biosensor