Changes in gene expression during induction of the carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii

The regulation of genes by CO[subscript]2 concentration in wild type and mutants of the unicellular green alga Chlamydomonas reinhardtii was studied. This and other algal species can photosynthesize efficiently under limiting concentrations of CO[subscript]2 due to the activities of a CO[subscript]2 concentrating mechanism and carbonic anhydrase. A cDNA copy of the gene that codes for a periplasmic carbonic anhydrase (perCA) was isolated and used to study regulation of perCA synthesis in a cell wall-deficient mutant (CW-15). Over-expression of perCA in CW-15, relative to wild type, was found at the levels of enzyme activity, protein content, and mRNA abunDance; This regulation may be attributed to the inability of the mutant to retain perCA protein in the periplasmic space owing to the absence of an intact cell wall. Further, these findings suggest the cells can perceive and control (at the level of transcript abundance) perCA protein content;Another mutant, CIA-5, which lacks all components known to be required for CO[subscript]2 accumulation, was found to not accumulate perCA transcripts in response to limiting CO[subscript]2. In addition, transcript for the cabII-1 gene, which codes for one of the light harvesting chlorophyll binding proteins of photosystem II, was found to increase in abundance in response to limiting CO[subscript]2 in wild type cells but not in the CIA-5 mutant;Finally, the control by CO[subscript]2 concentration over synthesis of the large (L) and small (S) subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase was investigated. In vivo protein labeling experiments indicated that both subunits were made at lower rates (or were more rapidly turned-over) in cells exposed to limiting CO[subscript]2 for 4 to 8 hours than in 24 hour-limiting CO[subscript]2-adapted cells or in cells cultured under elevated CO[subscript]2. Involvement of adjustment in mRNA pool size in contributing to this response was ruled-out. Using in vivo pulse-chase protein labelings it was determined that, in cells exposed to limiting CO[subscript]2 for 4 hours, translation of L and S transcripts was arrested

Levels and Patterns of Genetic Diversity in the Rare and Endangered Cumberland Stitchwort, \u3cem\u3eMinuartia cumberlandensis\u3c/em\u3e (Caryophyllaceae)

Sequences of a highly variable nuclear gene (G3pdh) were used to characterize genetic diversity within and among populations of the endangered rockhouse endemic, Minuartia cumberlandensis (Wofford and Kral) McNeill (Caryophyllaceae), and compared to a widespread and abundant related species, M. glabra (Michaux) McNeill. By reconstructing phylogenetic relationships among G3pdh variants (haplotypes) and observing the geographical distribution of those ordered variants, an attempt was made to gauge the effects of historical and contemporary population processes acting within the species, particularly those with potential implications for long-term conservation. Both M. cumberlandensis and M. glabra were found to have high overall genetic (haplotype) diversity. In M. cumberlandensis, most of this variation was distributed among populations rather than within them (FST = 0.63), while in M. glabra the inverse was true, with variation largely within populations (FST = 0.22). This pattern suggests significant divergence among populations of M. cumberlandensis, likely caused by a reduced influence of gene flow relative to genetic drift. Observed heterozygosity in populations of M. cumberlandensis was significantly reduced relative to M. glabra, suggesting the effects of inbreeding within small populations. Minuartia. cumberlandensis maintains broad genetic polymorphism among populations, with genetic similarities between many populations likely resulting from persistent ancestral alleles rather than ongoing gene flow. Lineages of haplotypes with significantly restricted geographical ranges provide further evidence for restricted gene flow among populations of M. cumberlandensis. The bulk of genetic diversity in M. cumberlandensis is maintained within the largest, densest cluster of populations, which occurs primarily in Pickett County, with outlying populations having relatively low, though still significant, portions of the overall diversity in the species. Because of the small overall number of outlying populations, and the unique genetic makeup of each, all occurrences should be given the strongest possible protection from further human habitat disturbance. It is likely that M. cumberlandensis has persisted in its current location through cyclical changes in climate during the Pleistocene, and if protected from habitat destruction and population decimation, it may fare well in the face of future climate change

Snow as structural habitat for wolverines in a changing Arctic

Dissertation (Ph.D.) University of Alaska Fairbanks, 2022Arctic snowpack provides critical wintertime habitat for animals to facilitate thermoregulation and avoid predators. Wolverines (Gulo gulo) are iconic among such animals, relying on snow burrows for resting sites and reproductive dens. Most of the knowledge regarding this mesocarnivore's association with snow, however, has so far originated in more southerly latitudes. In this dissertation, I investigated Arctic wolverines' behaviors associated with snow, focusing on how specific snow properties influence resting, habitat selection, and avoiding predators. Motivated by the paucity of published descriptions of wolverine resting burrows and reproductive dens on tundra, I first described terrain features and architecture of such sites. I found that resting burrows typically consist of a single tunnel leading to a resting chamber, sometimes associated with non-snow structure such as stream cutbanks and river shelf ice. By contrast, reproductive dens typically consist of longer tunnels associated with snowdrift-forming terrain. Second, I used GPS collar data from 21 adult wolverines, coupled with snowpack information at 10 meter pixel resolution, to evaluate wolverine habitat selection and movement response to snow depth, density, and melt status. I found that wolverines select deeper, denser snow, except when snow is melting, likely reflecting resting site use. Third, I developed a machine learning model to classify wolverine behaviors using tri-axial accelerometers based on direct observations of three captive wolverines, and applied this model to free-living wolverines in Arctic Alaska. I found that the model performs better when allowed to predict behaviors as "unknown," and that it accurately predicts resting, food handling, running, and scanning surroundings. Finally, based in part on this classification model, I evaluated the extent to which wolverines' use of snow burrows and surface beds for resting sites is influenced by thermoregulatory needs versus predation avoidance. I found evidence in support of both demands driving resting behavior; wolverines trade thermoregulation off against predation avoidance by resting on the snow surface on warm, sunny days, but use snow burrows on cold, dark days to meet both demands simultaneously. Collectively, this dissertation demonstrates the importance of Arctic snowpack to wolverines, a topic of increasing importance as the snow season shortens with climate change, and serves as a model for investigating behavioral processes associated with snow among other species.National Science Foundation Graduate Research Fellowship Program, Wildlife Conservation Society, Wilburforce Foundation, M.J. Murdock Charitable Trust, The Wolverine Foundation, the University of Alaska Fairbanks Erich Follmann Memorial Student Research FundChapter 1: Introduction -- Chapter 2: Terrain features and architecture of wolverine (Gulo gulo) resting burrows and reproductive dens on Arctic tundra -- Chapter 3: Spatiotemporally variable snow properties drive habitat use of an Arctic mesopredator -- Chapter 4: Accounting for unknown behaviors of free-living animals in accelerometer-based classification models: demonstration on a wide-ranging mesopredator -- Chapter 5: Trade-off between predation risk and behavioural thermoregulation drives resting behaviour in a cold-adapted mesocarnivore -- Chapter 6: Conclusion -- Appendices

QuakeMigrate: a Modular, Open-Source Python Package for Automatic Earthquake Detection and Location

Detecting and locating microearthquakes from continuous waveform records is the fundamental step in microseismic processing. Dense local networks and arrays have introduced the possibility to detect large numbers of far weaker events, but when viewed on seismic records from individual stations their waveforms are often obscured by noise. Furthermore, areas of interest for microseismic monitoring often feature extremely high event rates, highlighting the limitations of traditional techniques based on phase picking and association. In order to maximise the new insights gained, we require fully automated techniques which can exploit modern recordings to produce highly complete earthquake catalogues containing few artefacts. QuakeMigrate is a new modular, open-source Python package providing a framework to efficiently, automatically and robustly detect and locate microseismicity. The user inputs continuous seismic data, a velocity model or pre-calculated look-up table and list of station locations. Instead of reducing the raw waveforms to discrete time picks, they are transformed (by amplitude, frequency and/or polarisation analysis) to continuous functions representing the probability of a particular phase arrival through time. These ‘onset functions’ from stations across the network are then migrated according to a travel-time look-up table and stacked to perform a grid-search for coherent sources of energy in the subsurface. This enables detection of earthquakes at close to or below the signal-to-noise ratio at individual stations, and implicitly associates phase arrivals even at very small inter-event times. We demonstrate the flexibility and power of this approach with examples of basal icequakes detected at the Rutford Ice Stream, Antarctica, dike- and caldera-collapse induced seismicity at Bárðarbunga central volcano, Iceland, and the aftershock sequence from a M5 earthquake at Mt. Kinabalu, northern Borneo. The modular nature of the workflow and wide range of automatic plotting options makes parameter choice straightforward, and robust event location uncertainty statistics facilitate filtering to produce a robust catalogue. QuakeMigrate also outputs phase picks and local magnitude estimates, with an architecture designed to promote further community-driven extension in future

A common polymorphism in SNCA is associated with accelerated motor decline in GBA-Parkinson's disease.

A growing number of genetic susceptibility factors have been identified for Parkinson’s disease (PD). The combination of inherited risk variants is likely to affect not only risk of developing PD but also its clinical course. Variants in the GBA gene are particularly common, being found in approximately 5 to 10% of patients, and they lead to more rapid disease progression1. However, the effect of concomitant genetic risk factors on disease course in GBA-PD is not known.The CamPaIGN study has received financial support from the Wellcome Trust, the Medical Research Council, Parkinson’s UK and the Patrick Berthoud Trust. CHWG is supported by an RCUK/UKRI Innovation Fellowship awarded by the Medical Research Council. RAB is supported by the Wellcome Trust Stem Cell Institute (Cambridge). TBS received financial support from the Cure Parkinson’s Trust. The study is also supported by the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre Dementia and Neurodegeneration Theme (reference number 146281). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. CRS' work is supported in part by NIH grants R01AG057331, U01NS100603, R01AG057331, and the American Parkinson Disease Association. Illumina MEGA Chip genotyping was made possible by a philanthropic investment from Dooley LLC (to Brigham & Women's Hospital and CRS)

Motor complications in Parkinson's disease: 13-year follow-up of the CamPaIGN cohort.

BACKGROUND: Long-term population-representative data on motor fluctuations and levodopa-induced dyskinesias in Parkinson's disease is lacking. METHODS: The Cambridgeshire Parkinson's Incidence from GP to Neurologist (CamPaIGN) cohort comprises incident PD cases followed for up to 13 years (n = 141). Cumulative incidence of motor fluctuations and levodopa-induced dyskinesias and risk factors were assessed using Kaplan-Meyer and Cox regression analyses. RESULTS: Cumulative incidence of motor fluctuations and levodopa-induced dyskinesias was 54.3% and 14.5%, respectively, at 5 years and 100% and 55.7%, respectively, at 10 years. Higher baseline UPDRS-total and SNCA rs356219(A) predicted motor fluctuations, whereas higher baseline Mini-mental State Examination and GBA mutations predicted levodopa-induced dyskinesias. Early levodopa use did not predict motor complications. Both early motor fluctuations and levodopa-induced dyskinesias predicted reduced mortality in older patients (age at diagnosis >70 years). CONCLUSIONS: Our data support the hypothesis that motor complications are related to the severity of nigrostriatal pathology rather than early levodopa use and indicate that early motor complications do not necessarily confer a negative prognosis. © 2019 International Parkinson and Movement Disorder Society.This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2013-R1A1A2010499). CWG is supported by a Medical Research Council Clinician Scientist Fellowship. The CamPaIGN study was supported by the Wellcome Trust, the Medical Research Council, the Patrick Berthoud Trust, and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre Dementia and Neurodegeneration Theme (Grant Reference Number 146281). RAB is an NIHR Senior Investigator

Risk stratification for venous thromboembolism in patients with testicular germ cell tumors

BACKGROUND:Patients with testicular germ cell tumors (TGCT) have an increased risk for venous thromboembolism (VTE). We identified risk factors for VTE in this patient cohort and developed a clinical risk model. METHODS:In this retrospective cohort study at the Medical University of Graz we included 657 consecutive TGCT patients across all clinical stages. A predictive model for VTE was developed and externally validated in 349 TGCT patients treated at the University Hospital Zurich. RESULTS:Venous thromboembolic events occurred in 34 (5.2%) patients in the Graz cohort. In univariable competing risk analysis, higher clinical stage (cS) and a retroperitoneal lymphadenopathy (RPLN) were the strongest predictors of VTE (p<0.0001). As the presence of a RPLN with more than 5cm in greatest dimension without coexisting visceral metastases is classified as cS IIC, we constructed an empirical VTE risk model with the following four categories (12-month-cumulative incidence): cS IA-B 8/463 patients (1.7%), cS IS-IIB 5/86 patients (5.9%), cS IIC 3/21 patients (14.3%) and cS IIIA-C 15/70 patients (21.4%). This risk model was externally validated in the Zurich cohort (12-month-cumulative incidence): cS IA-B (0.5%), cS IS-IIB (6.0%), cS IIC (11.1%) and cS IIIA-C (19.1%). Our model had a significantly higher discriminatory performance than a previously published classifier (RPLN-VTE-risk-classifier) which is based on the size of RPLN alone (AUC-ROC: 0.75 vs. 0.63, p = 0.007). CONCLUSIONS:According to our risk stratification, TGCT patients with cS IIC and cS III disease have a very high risk of VTE and may benefit from primary thromboprophylaxis for the duration of chemotherapy

Acute Motor Axonal Neuropathy in a Patient with Metastatic Pancreatic Neuroendocrine Tumor Receiving Chemotherapy with Capecitabine and Temozolomide: A Case Report

We report a case of a 37- year old female patient with metastatic pancreatic neuroendocrine tumor that developed acute motor axonal neuropathy after receiving chemotherapy with capecitabine and temozolomide. She had repeatedly progressed after several surgical resections of her liver metastases, other hepatic directed procedures, several sessions of peptide receptor radionuclide therapy and two systemic treatment lines. When we started a third line therapy with capecitabine (1500 mg absolute twice daily, day 1-14) and temozolomide (360 mg absolute in two divided doses on day 1-5) in a 28 days long cycle, she unexpectedly developed a progressive weakness of the upper and lower limbs and dysphagia. The diagnosis of acute motor axonal neuropathy was confirmed by nerve conduction studies. The patient`s condition improved rapidly after chemotherapy was stopped and plasma exchange (nine sessions) as well as a maintenance therapy with intravenous immunoglobulins was started. She was almost asymptomatic seven months after onset of symptoms. This case describes a previously unreported association between acute motor axonal neuropathy and chemotherapy with capecitabine and temozolomide