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1. Comparison of δ ¹³ C analyses of individual foraminifer ( Orbulina universa ) shells by secondary ion mass spectrometry and gas source mass spectrometry

   https://doi.org/10.1002/rcm.9658  

   Wycech, Jody_B; Kelly, Daniel_Clay; Kozdon, Reinhard; Ishida, Akizumi; Kitajima, Kouki; Spero, Howard_J; Valley, John_W (November 2023, Rapid Communications in Mass Spectrometry)

   Abstract RationaleThe use of secondary ion mass spectrometry (SIMS) to perform micrometer‐scalein situcarbon isotope (δ¹³C) analyses of shells of marine microfossils called planktic foraminifers holds promise to explore calcification and ecological processes. The potential of this technique, however, cannot be realized without comparison to traditional whole‐shell δ¹³C values measured by gas source mass spectrometry (GSMS). MethodsPaired SIMS and GSMS δ¹³C values measured from final chamber fragments of the same shell of the planktic foraminiferOrbulina universaare compared. The SIMS–GSMS δ¹³C differences (Δ¹³C_SIMS‐GSMS) were determined via paired analysis of hydrogen peroxide‐cleaned fragments of modern cultured specimens and of fossil specimens from deep‐sea sediments that were either untreated, sonicated, and cleaned with hydrogen peroxide or vacuum roasted. After treatment, fragments were analyzed by a CAMECA IMS 1280 SIMS instrument and either a ThermoScientific MAT‐253 or a Fisons Optima isotope ratio mass spectrometer (GSMS). ResultsPaired analyses of cleaned fragments of cultured specimens (n = 7) yield no SIMS–GSMS δ¹³C difference. However, paired analyses of untreated (n = 18) and cleaned (n = 12) fragments of fossil shells yield average Δ¹³C_SIMS‐GSMSvalues of 0.8‰ and 0.6‰ (±0.2‰, 2 SE), respectively, while vacuum roasting of fossil shell fragments (n = 11) removes the SIMS–GSMS δ¹³C difference. ConclusionsThe noted Δ¹³C_SIMS‐GSMSvalues are most likely due to matrix effects causing sample–standard mismatch for SIMS analyses but may also be a combination of other factors such as SIMS measurement of chemically bound water. The volume of material analyzed via SIMS is ~10⁵times smaller than that analyzed by GSMS; hence, the extent to which these Δ¹³C_SIMS‐GSMSvalues represent differences in analyte or instrument factors remains unclear. 

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2. Condensin I ^DC , H4K20me1, and perinuclear tethering maintain X chromosome repression in C. elegans

   https://doi.org/10.1101/2024.04.05.588224  

   Trombley, Jessica; Rakozy, Audry I; Jash, Eshna; Csankovszki, Györgyi (April 2024, bioRxiv)

   Abstract Dosage compensation inCaenorhabditis elegansequalizes X-linked gene expression between XX hermaphrodites and XO males. The process depends on a condensin- containing dosage compensation complex (DCC), which binds the X chromosomes in hermaphrodites to repress gene expression. Condensin I^DCand an additional five DCC components must be present on the X during early embryogenesis in hermaphrodites to establish dosage compensation. However, whether the DCC’s continued presence is required to maintain the repressed state once established is unknown. Beyond the role of condensin I^DCin X chromosome compaction, additional mechanisms contribute to X- linked gene repression. DPY-21, a non-condensin I^DCDCC component, is an H4K20me2/3 demethylase whose activity enriches the repressive histone mark, H4 lysine 20 monomethylation, on the X chromosomes. In addition, CEC-4 tethers H3K9me3-rich chromosomal regions to the nuclear lamina, which also contributes to X- linked gene repression. To investigate the necessity of condensin I^DCduring the larval and adult stages of hermaphrodites, we used the auxin-inducible degradation system to deplete the condensin I^DCsubunit DPY-27. While DPY-27 depletion in the embryonic stages resulted in lethality, DPY-27 depleted larvae and adults survive. In these DPY-27 depleted strains, condensin I^DCwas no longer associated with the X chromosome, the X became decondensed, and the H4K20me1 mark was gradually lost, leading to X-linked gene derepression. These results suggest that the stable maintenance of dosage compensation requires the continued presence of condensin I^DC. A loss-of-function mutation incec-4, in addition to the depletion of DPY-27 or the genetic mutation ofdpy- 21, led to even more significant increases in X-linked gene expression, suggesting that tethering heterochromatic regions to the nuclear lamina helps stabilize repression mediated by condensin I^DCand H4K20me1. Author SummaryIn some organisms, whether an individual becomes male, female, or hermaphrodite is determined by the number of their sex chromosomes. In the nematodeCaenorhabditis elegans, males have one X chromosome, whereas hermaphrodites have two X chromosomes. This difference in the number of X chromosomes is crucial for deciding whether an individual becomes a hermaphrodite or a male. However, having two X chromosomes can lead to problems because it results in different gene expression levels, resulting in hermaphrodite lethality. To solve this issue, many organisms undergo a process called dosage compensation. Dosage compensation inC. elegansis achieved by a group of proteins known as the dosage compensation complex (DCC), which includes a protein called DPY-27. The function of DPY-27 is essential during early embryonic development. This study shows that in contrast to early embryonic development, larvae and adults can still survive when DPY-27 is missing. In these worms, all known mechanisms involved in dosage compensation are disrupted and the X is no longer repressed. Our results suggest that the maintenance of dosage compensation in nematodes is an active process, and that it is essential for survival when the organism is developing, but once fully developed, the process becomes dispensable. 

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3. J ‐modulated ¹⁹ F‐ and ¹ H‐detected dual‐optimized inverted ¹ J _CC 1,n‐ADEQUATE: A universal ADEQUATE experiment

   https://doi.org/10.1002/mrc.5324  

   Crouch, Ronald C; Pelmuş, Marius; Raab, Jeffrey G; Tischenko, Evgeny; Frey, Michael; Wang, Yunyi; Reibarkh, Mikhail; Williamson, R Thomas; Martin, Gary E (March 2023, Magnetic Resonance in Chemistry)

   Abstract The recently reported¹⁹F‐detected dual‐optimized inverted¹J_CC1,n‐ADEQUATE experiment and the previously reported¹H‐detected version have been modified to incorporateJ‐modulation, making it feasible to acquire all 1,1‐ and 1,n‐ADEQUATE correlations as well as¹J_CCandⁿJ_CChomonuclear scalar couplings in a single experiment. The experiments are demonstrated usingN,N‐dimethylamino‐2,5,6‐trifluoro‐3,4‐phthalonitrile andN,N‐dimethylamino‐3,4‐phthalonitrile. 

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4. The Neumann function and the L ^p Neumann problem in chord-arc domains

   https://doi.org/10.1515/ans-2023-0171  

   Hofmann, Steve; Sparrius, Derek (February 2025, Advanced Nonlinear Studies)

   Abstract We construct the Neumann function in a 1-sided chord-arc domain (i.e., a uniform domain with an Ahlfors regular boundary), and establish size and Hölder continuity estimates up to the boundary. We then obtain a Kenig-Pipher type theorem, in whichL^psolvability of the Neumann problem is shown to yield solvability inL^qfor 1 <q<p, and in the Hardy spaceH¹, in 2-sided chord-arc domains, under suitable background hypotheses. 

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5. Alternate routes to mnm ⁵ s ² U synthesis in Gram-positive bacteria

   https://doi.org/10.1128/jb.00452-23  

   Jaroch, Marshall; Sun, Guangxin; Tsui, Ho-Ching Tiffany; Reed, Colbie; Sun, Jingjing; Jörg, Marko; Winkler, Malcolm E; Rice, Kelly C; Dziergowska, Agnieszka; Stich, Troy A; et al (April 2024, Journal of Bacteriology)

   Henkin, Tina M (Ed.)

   The wobble bases of tRNAs that decode split codons are often heavily modified. In bacteria, tRNA^{Glu, Gln, Asp}contains a variety of xnm⁵s²U derivatives. The synthesis pathway for these modifications is complex and fully elucidated only in a handful of organisms, including the Gram-negativeEscherichia coliK12 model. Despite the ubiquitous presence of mnm⁵s²U modification, genomic analysis shows the absence ofmnmCorthologous genes, suggesting the occurrence of alternate biosynthetic schemes for the conversion of cmnm⁵s²U to mnm⁵s²U. Using a combination of comparative genomics and genetic studies, a member of the YtqA subgroup of the radical Sam superfamily was found to be involved in the synthesis of mnm⁵s²U in bothBacillus subtilisandStreptococcus mutans. This protein, renamed MnmL, is encoded in an operon with the recently discovered MnmM methylase involved in the methylation of the pathway intermediate nm⁵s²U into mnm⁵s²U inB. subtilis. Analysis of tRNA modifications of bothS. mutansandStreptococcus pneumoniaeshows that growth conditions and genetic backgrounds influence the ratios of pathway intermediates owing to regulatory loops that are not yet understood. The MnmLM pathway is widespread along the bacterial tree, with some phyla, such as Bacilli, relying exclusively on these two enzymes. Although mechanistic details of these newly discovered components are not fully resolved, the occurrence of fusion proteins, alternate arrangements of biosynthetic components, and loss of biosynthetic branches provide examples of biosynthetic diversity to retain a conserved tRNA modification in Nature.IMPORTANCEThe xnm⁵s²U modifications found in several tRNAs at the wobble base position are widespread in bacteria where they have an important role in decoding efficiency and accuracy. This work identifies a novel enzyme (MnmL) that is a member of a subgroup of the very versatile radical SAM superfamily and is involved in the synthesis of mnm⁵s²U in several Gram-positive bacteria, including human pathogens. This is another novel example of a non-orthologous displacement in the field of tRNA modification synthesis, showing how different solutions evolve to retain U34 tRNA modifications. 

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