Alternative outlets for sustaining photosynthetic electron transport during dark-to-light transitions.

Environmental stresses dramatically impact the balance between the production of photosynthetically derived energetic electrons and Calvin-Benson-Bassham cycle (CBBC) activity; an imbalance promotes accumulation of reactive oxygen species and causes cell damage. Hence, photosynthetic organisms have developed several strategies to route electrons toward alternative outlets that allow for storage or harmless dissipation of their energy. In this work, we explore the activities of three essential outlets associated with Chlamydomonas reinhardtii photosynthetic electron transport: (i) reduction of O2 to H2O through flavodiiron proteins (FLVs) and (ii) plastid terminal oxidases (PTOX) and (iii) the synthesis of starch. Real-time measurements of O2 exchange have demonstrated that FLVs immediately engage during dark-to-light transitions, allowing electron transport when the CBBC is not fully activated. Under these conditions, we quantified maximal FLV activity and its overall capacity to direct photosynthetic electrons toward O2 reduction. However, when starch synthesis is compromised, a greater proportion of the electrons is directed toward O2 reduction through both the FLVs and PTOX, suggesting an important role for starch synthesis in priming/regulating CBBC and electron transport. Moreover, partitioning energized electrons between sustainable (starch; energetic electrons are recaptured) and nonsustainable (H2O; energetic electrons are not recaptured) outlets is part of the energy management strategy of photosynthetic organisms that allows them to cope with the fluctuating conditions encountered in nature. Finally, unmasking the repertoire and control of such energetic reactions offers new directions for rational redesign and optimization of photosynthesis to satisfy global demands for food and other resources

Lakeside View: Sociocultural Responses to Changing Water Levels of Lake Turkana, Kenya

Throughout the Holocene, Lake Turkana has been subject to drastic changes in lake levels and the subsistence strategies people employ to survive in this hot and arid region. In this paper, we reconstruct the position of the lake during the Holocene within a paleoclimatic context. Atmospheric forcing mechanisms are discussed in order to contextualize the broader landscape changes occurring in eastern Africa over the last 12,000 years. The Holocene is divided into five primary phases according to changes in the strand-plain evolution, paleoclimate, and human subsistence strategies practiced within the basin. Early Holocene fishing settlements occurred adjacent to high and relatively stable lake levels. A period of high-magnitude oscillations in lake levels ensued after 9,000 years BP and human settlements appear to have been located close to the margins of the lake. Aridification and a final regression in lake levels ensued after 5,000 years BP and human communities were generalized pastoralists-fishers-foragers. During the Late Holocene, lake levels may have dropped below their present position and subsistence strategies appear to have been flexible and occasionally specialized on animal pastoralism. Modern missionary and government outposts have encouraged the construction of permanent settlements in the region, which are heavily dependent on outside resources for their survival. Changes in the physical and cultural environments of the Lake Turkana region have been closely correlated, and understanding the relationship between the two variables remains a vital component of archaeological research

Lakeside View: Sociocultural Responses to Changing Water Levels of Lake Turkana, Kenya

Throughout the Holocene, Lake Turkana has been subject to drastic changes in lake levels and the subsistence strategies people employ to survive in this hot and arid region. In this paper, we reconstruct the position of the lake during the Holocene within a paleoclimatic context. Atmospheric forcing mechanisms are discussed in order to contextualize the broader landscape changes occurring in eastern Africa over the last 12,000 years. The Holocene is divided into five primary phases according to changes in the strand-plain evolution, paleoclimate, and human subsistence strategies practiced within the basin. Early Holocene fishing settlements occurred adjacent to high and relatively stable lake levels. A period of high-magnitude oscillations in lake levels ensued after 9,000 years BP and human settlements appear to have been located close to the margins of the lake. Aridification and a final regression in lake levels ensued after 5,000 years BP and human communities were generalized pastoralists-fishers-foragers. During the Late Holocene, lake levels may have dropped below their present position and subsistence strategies appear to have been flexible and occasionally specialized on animal pastoralism. Modern missionary and government outposts have encouraged the construction of permanent settlements in the region, which are heavily dependent on outside resources for their survival. Changes in the physical and cultural environments of the Lake Turkana region have been closely correlated, and understanding the relationship between the two variables remains a vital component of archaeological research

Water Level History of Lake Turkana, Kenya and Hydroclimate Variability during the African Humid Period

The present chronology of East African paleoclimate suggests the transitions associated with the African Humid Period (AHP) at ca. 15 and 5 ka were binary. Previous studies have indicated water levels for Lake Turkana as relatively unchanging at ~88 to 98 m above present level for the AHP, and infer outflow into the White Nile Basin. This interpretation is reinforced by many proxy-inferences for East African hydroclimate, which suggest ubiquitous wet conditions between ca. 11.5 and 6 cal. ka. Also, previous studies suggest that peak water levels for Lake Turkana resulted from precipitation delivered by a strengthened African monsoon and were amplified by overflow from adjacent lake basins. This study presents an intensive sedimentologic investigation of the western strand plain of Lake Turkana. New AMS 14C ages on seventeen freshwater gastropod and bivalve shells taken from littoral deposits provide chronologic control. This reconstruction of water level for Lake Turkana is based on these results, which are combined with previous ages that have been ranked systematically. Water level of Lake Turkana may have varied by ± 60 m at least ten times, potentially reaching the outlet elevation at ca.11.3, 10.3, 9.0, 6.3 and 5.1 cal. ka. Inferences on the source of moisture to sustain these many high stands are based on isotopic data on leaf wax (δDwax), various metrics of runoff and associated sea surface temperature (SST) records from the Indian and the Atlantic oceans. Multiple water level oscillations, possibly to the outlet sill elevation, between 14.5 and 8.5 cal. ka are associated with intervals of elevated Atlantic-derived moisture flux to East Africa, and a zonally variable CAB. After ca. 7.5 cal. ka, water level oscillations may be linked to rising SSTs in the Western Indian Ocean, and moisture delivered by the East African Monsoon. In turn, evidence from relict beach landforms supports low lake levels associated with Heinrich Event 1, the Younger Dryas, the 8.2 ka meltwater event and mid-Holocene aridity for East Africa post 4.5 ka. These regressions are attributed to intervals of suppressed SSTs for the Eastern Atlantic Ocean, and limited westerly moisture flux to East Africa

Expanding Coverage of the Chemical Exposome Using Novel Data Acquisition and Computational Tools

The chemical exposome encompasses the sum of all exposures during an individual’s lifetime. This group of compounds, when combined with genetic traits, determine chronic disease, thus, to fully understand human health issues, it is imperative to improve exposome measurements to match genomic technologies. My dissertation focuses on expanding the coverage of the chemical exposome and developing tools and techniques that will increase the reliability of untargeted mass spectrometry based studies. In Chapter 1, I address the many challenges faced when trying to measure all compounds contained within the chemical exposome. Exposome compounds cover a large range of biological concentration, many different structural classes, and are extensively modified in the body via detoxification pathways. I explore the potential strategies researchers can employ to address these difficulties, from instrumental acquisition and sample preparation, to compound identification and other data processing tools. In Chapter 2, I discuss the utilization of hydrogen-deuterium exchange (HDX) for identifying unknown compounds in metabolomics and exposomics studies. HDX is a method by which all of the acidic protons in a compound are exchanged with deuterium prior to mass spectrometric analysis with the goal of using the resulting mass shift to illuminate potential substructures. In this work, we compared the efficacy of different deuterium incorporation methods, explored the filtering potential of this method on 253 test compounds and large chemical databases, and identified 101 compounds in mouse mammary tumors. The results of this study show that HDX can alleviate researchers’ reliance on mass spectral databases for identifying compounds in biological samples. Chapter 3 focuses on an untargeted exposomics method that was developed to measure chemical exposures that influence female reproductive health. In the human body, xenobiotic compounds are transformed through metabolism to increase polarity and allow for excretion in the urine. These transformations commonly consist of phase I hydroxylation reactions mediated by CYP450 enzymes and phase II conjugations mediated by transferases. In the urine, the most common conjugate forms are glucuronides and sulfates. Our urinary exposomics method takes advantage of this knowledge. By using B-glucuronidase/aryl sulfatase, we can cleave the phase II conjugates into their phase I forms, and easily extract these less polar analytes from the polar urinary matrix. This method was used to measure exposure compounds in 50 women from Orange County, CA at three different time points. The compound measurements were then used to build linear mixed effects models to predict the chemical variables that influence hormonally derived endocrine endpoints. Models were built for menstrual cycle length, cycle peak luteinizing hormone, follicular estrone-1,3-glucuronide, and estrone-1,3-glucuronide slope. Chemical variables that had not previously been associated with reproductive function were identified for each of these endocrine endpoints. These models illuminate novel chemical exposures for future causative studies on reproductive health

Regularization in Bifactor-(S-1)-Models

Supplementary materials for the article "Regularization Methods in Bifactor-(S-1) Models with Explanatory Variables