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1. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

   https://doi.org/10.1107/S2052252522006418  

   Moreno-Chicano, Tadeo ; Carey, Leiah M. ; Axford, Danny ; Beale, John H. ; Doak, R. Bruce ; Duyvesteyn, Helen M. ; Ebrahim, Ali ; Henning, Robert W. ; Monteiro, Diana C. ; Myles, Dean A. ; et al ( September 2022 , IUCrJ)

   Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B. 

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2. Hubbard Brook Experimental Forest: Soil Freezing Study (SFS) In Situ Measurements of Snow and Soil Frost Depth

   https://doi.org/10.6073/pasta/207b884c7510aca0aa9bf2c5ed93e432  

   Templer, Pamela H ; Socci, Anne ; Campbell, John L ( January 2021 , Environmental Data Initiative)

   Climate models for the northeastern United States (U.S.) over the next century predict an increase in air temperature between 2.8 and 4.3 °C and a decrease in the average number of days per year when a snowpack will cover the forest floor (Hayhoe et al. 2007, 2008; Campbell et al. 2010). Studies of forest dynamics in seasonally snow-covered ecosystems have been primarily conducted during the growing season, when most biological activity occurs. However, in recent years considerable progress has been made in our understanding of how winter climate change influences dynamics in these forests. The snowpack insulates soil from below-freezing air temperatures, which facilitates a significant amount of microbial activity. However, a smaller snowpack and increased depth and duration of soil frost amplify losses of dissolved organic C and NO3- in leachate, as well as N2O released into the atmosphere. The increase in nutrient loss following increased soil frost cannot be explained by changes in microbial activity alone. More likely, it is caused by a decrease in plant nutrient uptake following increases in soil frost. We conducted a snow-removal experiment at Hubbard Brook Experimental Forest to determine the effects of a smaller winter snowpack and greater depth and duration of soil frost on trees, soil microbes, and arthropods. A number of publications have been based on these data: Comerford et al. 2013, Reinmann et al. 2019, Templer 2012, and Templer et al. 2012. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station. Campbell JL, Ollinger SV, Flerchinger GN, Wicklein H, Hayhoe K, Bailey AS. Past and projected future changes in snowpack and soil frost at the Hubbard Brook Experimental Forest, New Hampshire, USA. Hydrological Processes. 2010; 24:2465–2480. Comerford DP, PG Schaberg, PH Templer, AM Socci, JL Campbell, and KF Wallin. 2013. Influence of experimental snow removal on root and canopy physiology of sugar maple trees in a northern hardwood forest. Oecologia 171:261-269. Hayhoe K, Wake CP, Huntington TG, Luo LF, Schwartz MD, Sheffield J, et al. Past and future changes in climate and hydrological indicators in the US Northeast. Climate Dynamics. 2007; 28:381–407. Hayhoe, K., Wake, C., Anderson, B. et al. Regional climate change projections for the Northeast USA. Mitig Adapt Strateg Glob Change 13, 425–436 (2008). https://doi.org/10.1007/s11027-007-9133-2. Reinmann AB, J Susser, EMC Demaria, PH Templer. 2019. Declines in northern forest tree growth following snowpack decline and soil freezing.  Global Change Biology 25:420-430. Templer PH. 2012. Changes in winter climate: soil frost, root injury, and fungal communities (Invited). Plant and Soil 35: 15-17 Templer PH , AF Schiller, NW Fuller, AM Socci, JL Campbell, JE Drake, and TH Kunz. 2012. Impact of a reduced winter snowpack on litter arthropod abundance and diversity in a northern hardwood forest ecosystem. Biology and Fertility of Soils 48:413-424. 

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3. Establishing a Theoretical Landscape for Identifying Basal Plane Active 2D Metal Borides (MBenes) toward Nitrogen Electroreduction

   https://doi.org/10.1002/adfm.202008056  

   Guo, Xiangyu ; Lin, Shiru ; Gu, Jinxing ; Zhang, Shengli ; Chen, Zhongfang ; Huang, Shiping ( November 2020 , Advanced Functional Materials)

   To achieve efficient ammonia synthesis via electrochemical nitrogen reduction reaction (NRR), a qualified catalyst should have both high specific activity and large active surface area. However, integrating these two merits into one single material remains a big challenge due to the difficulty in balancing multiple reaction intermediates. Here, it is demonstrated that the boron‐analogues of MXenes, namely “MBenes”, could cope with the challenge and achieve the high activity and large reaction region simultaneously toward NRR. Using extensive density functional theory computations and taking 16 MBenes as representatives, it is identified that seven MBenes (CrB, MoB, WB, Mo₂B, V₃B₄, CrMnB₂, and CrFeB₂) not only have intrinsic basal plane activity for NRR with limiting potentials ranging from −0.22 to −0.82 V, but also possess superior capability of suppressing the competitive hydrogen evolution reaction. Particularly, different from the MXenes whose surface oxidation may block the active sites, once oxidized, these MBenes can catalyze NRR via the self‐activating process, reducing O*/OH* into H₂O* under reaction conditions, and favoring the N₂electroreduction. As a result, the exceptional activity and selectivity, high active area (≈10¹⁹m⁻²), and antioxidation nature render these MBenes as pH‐universal catalysts for NH₃production without introducing any dopants and defects.

    

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4. Response of diatom communities to climate and human disturbance: A 4200-year record from Costa Rica

   https://doi.org/10.1177/09596836231197775  

   Bitting, Madeleine ; Johanson, Erik N ; Haberyan, Kurt A ; Horn, Sally P ( December 2023 , The Holocene)

   This study integrates diatom analysis with existing records of pollen, charcoal, elemental composition, and stable light isotopes to expand upon the 4200-year history of human activity and climate change from Laguna Los Mangos in southern Pacific Costa Rica. We counted diatoms in peroxide-treated samples and analyzed community composition using cluster analysis, revealing four distinct assemblage zones with diatom variability most closely correlated with phosphorus, titanium, and organic content. The earliest assemblage (Zone D, 4150–3430 cal yr BP) was dominated by Encyonema silesiacum and Nitzschia incognita and aligned with a period of deforestation, erosion, and abundant macrophytes. Gomphonema affine proliferated in Zone C (3430–2450 cal yr BP), reflecting increased pH and productivity likely caused by agriculture-induced nutrient loading. We attributed the preservation gap from 3290 to 2970 cal yr BP in Zone C to silica depletion and erosional deposition that induced decline in diatom abundance by diluting valve concentrations in lake sediments. Nitzschia incognita and G. affine became the dominant taxa in Zone B (2450–1400 cal yr BP), likely reflecting eutrophy, increasing conductivity, and drying climate. Dominance of Diadesmis confervacea indicated reduced lake level in Zone A (1400 cal yr BP–modern) at the onset of the Terminal Classic Drought (TCD). A hiatus in the record indicates lake desiccation from 950 to 450 cal yr BP. During the Little Ice Age (LIA), diatoms reflect conditions similar to Zone B indicating increased lake level, circumneutral pH, and eutrophy. Refilling of the lake indicates increased precipitation during the LIA despite evidence of severe regional drought reported at other sites. Variable precipitation during this period likely resulted from the combined effects of Spanish contact, agricultural collapse, forest recovery, and shifts in Atlantic and Pacific climate forcing mechanisms. Overall, the Los Mangos diatom record reflects shallow, slightly alkaline, eutrophic conditions influenced by nutrient enrichment, erosion, and deforestation associated with maize agriculture.

    

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5. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock

   https://doi.org/10.1128/aem.00548-23  

   Mitchell, Stephanie L. ; Kearns, Daniel B. ; Carlson, Erin E. ( December 2023 , Applied and Environmental Microbiology)

   Bose, Arpita (Ed.)

   Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape maintenance, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Apparently-redundant proteins can be important for enabling an organism to cope with environmental stressors. In this study, we evaluated the consequence of environmental pH on PBP enzymatic activity inBacillus subtilis. Our data show that a subset of PBPs inB. subtilischange activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are favored for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed inStreptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly-redundant periplasmic enzymes.

   Microbes adapt to ever-changing environments and thrive over a vast range of conditions. While bacterial genomes are relatively small, significant portions encode for “redundant” functions. Apparent redundancy is especially pervasive in bacterial proteins that reside outside of the inner membrane. While conditions within the cytoplasm are carefully controlled, those of the periplasmic space are largely determined by the cell’s exterior environment. As a result, proteins within this environmentally exposed region must be capable of functioning under a vast array of conditions, and/or there must be several similar proteins that have evolved to function under a variety of conditions. This study examines the activity of a class of enzymes that is essential in cell wall construction to determine if individual proteins might be adapted for activity under particular growth conditions. Our results indicate that a subset of these proteins are preferred for growth under alkaline conditions, while others are readily dispensable.

    

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