Minimal Influence of [NiFe] Hydrogenase on Hydrogen Isotope Fractionation in H_2-Oxidizing Cupriavidus necator

Fatty acids produced by H_2-metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons for such a depletion are not known, but are often assumed to involve the strong D-depletion of H_2. Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H_2-consuming, chemoautotrophic conditions and measured the isotopic compositions of its fatty acids. In parallel with the wild type, two mutants of this strain, each lacking one of two key hydrogenase enzymes, were also grown and measured. In all three strains, fractionations between fatty acids and water ranged from -173‰ to -235‰, and averaged -217‰, -196‰, and -226‰, respectively, for the wild type, SH- mutant, and MBH- mutant. There was a modest increase in δD as a result of loss of the soluble hydrogenase enzyme. Fractionation curves for all three strains were constructed by growing parallel cultures in waters with δD_(water) values of approximately -25‰, 520‰, and 1100‰. These curves indicate that at least 90% of the hydrogen in fatty acids is derived from water, not H_2. Published details of the biochemistry of the soluble and membrane-bound hydrogenases confirm that these enzymes transfer electrons rather than intact hydride (H-) ions, providing no direct mechanism to connect the isotopic composition of H_2 to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H_2 plays little or no direct role in controlling lipid δD values. The observed fractionations must instead result from isotope effects in the reduction of NAD(P)H by reductases with flavin prosthetic groups, which transfer two electrons and acquire H+ (or D+) from solution. Parallels to NADPH reduction in photosynthesis may explain why D/H fractionations in C. necator are nearly identical to those in many photoautotrophic algae and bacteria. We conclude that strong D-depletion is not a diagnostic feature of chemoautotrophy

Marine Methane Biogeochemistry Investigated with Isotope-based Studies in the Field and the Laboratory

The ocean is a dynamic environment for methane’s biogeochemical processes. Three major processes take center stage: biological methanogenesis, anaerobic methane oxidation, and aerobic methane oxidation. These three key methane biogeochemical processes are intricately balanced within the oceanic environment, resulting in minimal methane escaping into the atmosphere. This dissertation aims to integrate fieldwork with laboratory research, combining investigative tools such as chemical measurements, radiotracer incubations, anaerobic cultivation, and stable isotope probing. The objective is to probe the behaviors of aerobic methane oxidation in relation to the ocean’s oxygen availability and isotopic signatures during methanogenesis from methyl-based compounds.Chapters 1 and 2 of my dissertation delve into the effectiveness and efficiency of aerobic methane oxidation in the ocean’s water column. The Santa Barbara Basin (SBB) is known for experiencing seasonal deoxygenation and reoxygenation cycles, resulting in fluctuating methane concentrations in the deep water column. In chapter 1, my study comprehensively investigated this seasonal cycle through a nine-month period of repeated sampling and measurement of key parameters associated with methane biogeochemistry in the deep waters of the SBB. These parameters include oxygen, nitrate, methane concentrations, and the rate of aerobic methane oxidation. My findings revealed a sequential pattern. First, a decline in oxygen concentration was observed to precede a decrease in nitrate concentration. Second, the accumulation of methane followed, with a marked decline in both oxygen and nitrate levels. Finally, changes in the methane oxidation rate, which reflects the activity of the methanotroph community, occurred subsequently, albeit with a slight time lag. I also discovered that the rate of methane oxidation is primarily dependent on the availability of methane within the water column. Furthermore, my research uncovered that the transient methane pulse accompanying the observed oxygen depletion in the SBB triggered the development of a persistent methanotrophic community, even after methane concentrations had returned to normal levels – an ecological memory effect. In Chapter 2, beyond the analysis of observed trends, I utilized methane concentrations, methane oxidation rates, and vertical methane diffusion to calculate the minimum methane source required for the deep water column. This computation was conducted across a range of contrasting environmental conditions, ultimately revealing that anoxic conditions demand a greater influx of methane into the water column. A comparison to data collected during a 2023 oceanic research expedition revealed an even greater demand for methane input, in the presence of well-established and persistent anoxic conditions. Chapter 3 of my dissertation is dedicated to investigating mechanistic underpinnings of stable carbon isotope fractionations during methylotrophic methanogenesis by marine archaea. Understanding these mechanistic underpinnings enables the inclusion of methylotrophic methanogenesis in isotopically informed biogeochemical reaction networks for anaerobic environments. This study included wild type methylotrophic methanogens as well as a mutant strain in which the reduction of methylated substrates is coupled to hydrogen oxidation or acetate oxidation, providing further mechanistic insight of isotopic variations originating at the reaction branch point

Segment Shards: Cross-Prompt Adversarial Attacks against the Segment Anything Model

Foundation models play an increasingly pivotal role in the field of deep neural networks. Given that deep neural networks are widely used in real-world systems and are generally susceptible to adversarial attacks, securing foundation models becomes a key research issue. However, research on adversarial attacks against the Segment Anything Model (SAM), a visual foundation model, is still in its infancy. In this paper, we propose the prompt batch attack (PBA), which can effectively attack SAM, making it unable to capture valid objects or even generate fake shards. Extensive experiments were conducted to compare the adversarial attack performance among optimizing without prompts, optimizing all prompts, and optimizing batches of prompts as in PBA. Numerical results on multiple datasets show that the cross-prompt attack success rate (ASR∗) of the PBA method is 17.83% higher on average, and the attack success rate (ASR) is 20.84% higher. It is proven that PBA possesses the best attack capability as well as the highest cross-prompt transferability. Additionally, we introduce a metric to evaluate the cross-prompt transferability of adversarial attacks, effectively fostering research on cross-prompt attacks. Our work unveils the pivotal role of the batched prompts technique in cross-prompt adversarial attacks, marking an early and intriguing exploration into this area against SAM

The protective effects of electroacupuncture on intestinal barrier lesions in IBS and UC model

Abstract Irritable bowel syndrome (IBS) and ulcerative colitis (UC) are two intestinal diseases with different pathological changes. Electroacupuncture (EA) at Zusanli (ST36) on both IBS and UC is widely used in clinic practice. But it is unclear whether acupuncture at one acupoint can treat two different intestinal diseases at different layers of intestinal barrier. To address this question, we explored three intestinal barrier lesions in IBS and UC mice with the aid of transcriptome data analysis and studied the efficacy of EA at ST36 on them. The transcriptome data analysis showed that both UC and IBS had disrupted intestinal barrier in various layers. And both UC and IBS had epithelial barrier lesions with reduction of ZO-1, Occludin and Claudin-1, while UC rather than IBS had the destruction of the mucus barrier with less MUC2 expression. As to the vascular barrier, UC showed a higher CD31 level and mesenteric blood flow reduction, while IBS showed a lower PV-1 level. EA at ST36 can significantly improve the above lesions of intestinal barrier of IBS and UC. Our results gave more details about the comprehensive protective effect of EA for UC and IBS. We guess the effect of acupuncture may be a kind of homeostasis regulation

Time series of oxygen, nitrate, methane concentrations and methane oxidation rates of the Santa Barbara Basin deep water column from 2019-2020 (BASIN project)

Dataset: Time Series Water Column ParametersTime series of water column parameters (oxygen, nitrate, methane concentrations and methane oxidation rates) are sampled and measured to show the changes related to methane biogeochemistry during a deoxygenation and reoxygenation event in the deep Santa Barbara water column (440-583m). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/872703NSF Division of Ocean Sciences (NSF OCE) OCE-1829981, NSF Division of Ocean Sciences (NSF OCE) OCE-183003

Initial Methane Concentration Alteration Experiment Data of the Deep Santa Barbara Basin Water Column from October 2019 (BASIN project)

Dataset: Initial Methane Concentration Alteration DataA methane concentration alteration experiment was performed to test the influence of methane concentration on methane oxidation rate. Together with the oxygen concentration alteration experiment, the purpose of this experiment was to test the assumption that methane oxidation in the Santa Barbara Basin deep water column follows first order kinetics. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/872652NSF Division of Ocean Sciences (NSF OCE) OCE-1829981, NSF Division of Ocean Sciences (NSF OCE) OCE-183003

Initial Oxygen Concentration Alteration Experiment Data of the Deep Santa Barbara Basin Water Column from October 2019 (BASIN project)

Dataset: Initial Oxygen Concentration Alteration DataAn oxygen concentration alteration experiment was performed to test the influence of oxygen concentration on methane oxidation rate. Together with the methane concentration alteration experiment, the purpose of this experiment was to test the assumption that methane oxidation in the Santa Barbara Basin deep water column follows first order kinetics. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/872665NSF Division of Ocean Sciences (NSF OCE) OCE-1829981, NSF Division of Ocean Sciences (NSF OCE) OCE-183003

Time course experiment related data to validate incubation duration for methane oxidation rate measurement of the deep Santa Barbara Basin water column from September 2019 (BASIN project)

Dataset: Time Course Experiment DataThis time course experiment was performed to test if the uptake rate of 3H-CH4 is linear over the chosen incubation time (3 days) for the seawater samples. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/872687NSF Division of Ocean Sciences (NSF OCE) OCE-1829981, NSF Division of Ocean Sciences (NSF OCE) OCE-183003

Insights into the mechanism and kinetics of dissolution of aluminoborosilicate glasses in acidic media: Impact of high ionic field strength cations

Achieving thinner and higher performance display/substrate glasses and transparent glass-ceramics with tunable properties requires a precise control of acid-etching process, thus necessitating a comprehensive understanding of glass composition–structure–dissolution behavior relationships in acidic medium. Unfortunately, the literature on this subject has been focused only on a narrow set of glass chemistries. Therefore, consensus on the mechanisms that govern the acidic dissolution of multicomponent silicate glasses over a broad compositional space is still lacking. The present work employs a suite of state-of-the-art spectroscopic techniques, including 1D and 2D NMR, TEM-EELS, ICP-OES, and XPS, to provide an insight into the mechanism and kinetics of corrosion of alkali/alkaline-earth aluminoborosilicate glasses (comprising high field strength cations – HFSCs, i.e., La3+, Ti4+, Zr4+ and Nb5+) in acidic media (HCl; pH = 2). Incorporating the HFSCs into the glasses induces significant structural changes in their network, thus, impacting the forward rate dissolution kinetics. Based on the results, we hypothesize that the glasses dissolve at pH = 2 through an ‘interfacial dissolution – re-precipitation mechanism (IDPM)’ and ‘in-situ recondensation’ coupled pattern, wherein the IDPM results in a Si-rich alteration layer, followed by local recondensation occurring due to limited kinetics near the interfacial solution between the uncorroded glass surface and the outer alteration layer