Isotopic clumping in wood as a proxy for photorespiration in trees.

Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO2]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups (R-O-CH3) in wood. Most methoxyl C-H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue 13CH2D correlates with temperature (18-28 °C) and atmospheric [CO2] (280-1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO2] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood.

The Effect of Location of a Unicortical Defect on the Mechanical Properties of Rabbit Tibiae: A Model of the Distal Jig Pin Hole in Tibial Plateau Levelling Osteotomy.

OBJECTIVE: The aim of this study was to determine the effect of a unicortical defect at either the mid-diaphysis (MD) or distal metaphysis (DM) on the torsional properties of tibiae in an in vitro rabbit model, and to further examine optimal distal jig pin position for the canine tibial plateau levelling osteotomy (TPLO) procedure. STUDY DESIGN: Thirty-eight tibiae from 19 skeletally mature female New Zealand White rabbits were assigned to one of three groups; Group 1: intact, Group 2: MD defect and Group 3: DM defect. Defects were created using a 1.6 mm Ellis pin. Pure torsion was applied to each sample and peak torque and angular displacement recorded. RESULTS: All tibiae fractured in a spiral configuration. Fracture lines involved the defect in 33% of the MD samples and 0% of the DM samples. No differences were detected for peak torque and stiffness between groups. However, energy (mean ± standard deviation) was significantly reduced (p = 0.028) in the MD group (0.18 ± 0.07) relative to the intact tibia group (0.31 ± 0.14). Angle was also significantly reduced (p = 0.040) in the MD group (0.17 ± 0.05) compared with the intact group (0.23 ± 0.07). Placement of a DM defect had no significant effect on mechanical properties of the rabbit tibiae. CONCLUSION: Defects placed in the MD significantly reduced energy and angle in comparison to intact samples. No significant difference in peak torque or stiffness was observed between groups. If canine tibiae were similarly affected, our findings suggest jig pin placement in the DM to have a lesser effect on the torsional properties of the tibiae.

Massive formation of early diagenetic dolomite in the Ediacaran ocean: Constraints on the "dolomite problem".

Paleozoic and Precambrian sedimentary successions frequently contain massive dolomicrite [CaMg(CO3)2] units despite kinetic inhibitions to nucleation and precipitation of dolomite at Earth surface temperatures (<60 °C). This paradoxical observation is known as the "dolomite problem." Accordingly, the genesis of these dolostones is usually attributed to burial-hydrothermal dolomitization of primary limestones (CaCO3) at temperatures of >100 °C, thus raising doubt about the validity of these deposits as archives of Earth surface environments. We present a high-resolution, >63-My-long clumped-isotope temperature (TΔ47) record of shallow-marine dolomicrites from two drillcores of the Ediacaran (635 to 541 Ma) Doushantuo Formation in South China. Our T∆47 record indicates that a majority (87%) of these dolostones formed at temperatures of <100 °C. When considering the regional thermal history, modeling of the influence of solid-state reordering on our TΔ47 record further suggests that most of the studied dolostones formed at temperatures of <60 °C, providing direct evidence of a low-temperature origin of these dolostones. Furthermore, calculated δ18O values of diagenetic fluids, rare earth element plus yttrium compositions, and petrographic observations of these dolostones are consistent with an early diagenetic origin in a rock-buffered environment. We thus propose that a precursor precipitate from seawater was subsequently dolomitized during early diagenesis in a near-surface setting to produce the large volume of dolostones in the Doushantuo Formation. Our findings suggest that the preponderance of dolomite in Paleozoic and Precambrian deposits likely reflects oceanic conditions specific to those eras and that dolostones can be faithful recorders of environmental conditions in the early oceans.

Identifying ERBB2 Activating Mutations in HER2-Negative Breast Cancer: Clinical Impact of Institute-Wide Genomic Testing and Enrollment in Matched Therapy Trials.

PURPOSE: The yield of comprehensive genomic profiling in recruiting patients to molecular-based trials designed for small subgroups has not been fully evaluated. We evaluated the likelihood of enrollment in a clinical trial that required the identification of a specific genomic change based on our institute-wide genomic tumor profiling. PATIENTS AND METHODS: Using genomic profiling from archived tissue samples derived from patients with metastatic breast cancer treated between 2011 and 2017, we assessed the impact of systematic genomic characterization on enrollment in an ongoing phase II trial (ClinicalTrials.gov identifier: NCT01670877). Our primary aim was to describe the proportion of patients with a qualifying ERBB2 mutation identified by our institutional genomic panel (OncoMap or OncoPanel) who enrolled in the trial. Secondary objectives included median time from testing result to trial registration, description of the spectrum of ERBB2 mutations, and survival. Associations were calculated using Fisher's exact test. RESULTS: We identified a total of 1,045 patients with metastatic breast cancer without ERBB2 amplification who had available genomic testing results. Of these, 42 patients were found to have ERBB2 mutation and 19 patients (1.8%) were eligible for the trial on the basis of the presence of an activating mutation, 18 of which were identified by OncoPanel testing. Fifty-eight percent of potentially eligible patients were approached, and 33.3% of eligible patients enrolled in the trial guided exclusively by OncoPanel testing. CONCLUSION: More than one half of eligible patients were approached for trial participation and, significantly, one third of those were enrolled in NCT01670877. Our data illustrate the ability to enroll patients in trials of rare subsets in routine clinical practice and highlight the need for these broadly based approaches to effectively support the success of these studies.

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

Factors Associated With Delays in Chemotherapy Initiation Among Patients With Breast Cancer at a Comprehensive Cancer Center.

BACKGROUND: National guidelines endorse time-dependent quality metrics for breast cancer care. We examined factors associated with delays in chemotherapy initiation at an NCI-Designated Comprehensive Cancer Center. PATIENTS AND METHODS: We identified 523 patients who received postoperative adjuvant chemotherapy between January 2011 and December 2013 at our center. We defined 28 days from last definitive surgery (LDS) to chemotherapy as the target time frame, and an unacceptable delay in chemotherapy initiation (UCD) as greater than 42 days from LDS. Multivariate regression models were used to identify factors associated with UCD and the impact of Oncotype DX testing in patients with hormone receptor (HR)-positive breast cancer. RESULTS: Median days between LDS and chemotherapy initiation was 34 (interquartile range, 15), with 30% of patients starting within 28 days of LDS and 26.9% having UCD. Tumor characteristics such as subtype and stage affected UCD; patients with HR-positive or HER2-positive tumors were more likely to be delayed compared with those with triple-negative breast cancer. Patients with stage I disease, those undergoing mastectomy with or without immediate reconstruction, and those whose pathology sign-out was greater than 10 days postoperatively were more likely to be delayed. A higher proportion of UCD was found in HR-positive patients (31%) for whom Oncotype DX testing was ordered compared with those in whom it was not ordered (20%). CONCLUSIONS: This study provides insight into subpopulations that may be at risk to experience delays in chemotherapy initiation, directing interventions to improve the timeliness of care.