Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes are primarily carried by complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. From 56 metagenomes spanning all three major ODZs, we use genome-resolved metagenomics to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 metagenome-assembled genomes presents the largest collection of pelagic ODZ microbes and reveals a clearer picture of the nitrogen cycling community within this environment.

Marine oxygen-deficient zones represent a natural source of nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent. To investigate controls on N2O production, the responses of ammonia oxidation (AO) to nitrite (NO2-) and N2O with respect to oxygen (O-2), ammonium (NH4+) and NO2- concentrations were evaluated using N-15 - NH4+ tracer incubations in the Eastern Tropical North Pacific. Within the oxycline, additions of NH4+ and O-2 stimulated N2O production according to Michaelis-Menten kinetics, indicating that both substrates were limiting, and that N2O production, even if the exact mechanisms remain uncertain, is mediated by predictable kinetics. Low half-saturation constants for NH4+ (12-28 nM) and O-2 (460 +/- 130 nM) during N2O production indicate that AO communities are well adapted to low concentrations of both substrates. Hybrid N2O formation (i.e., from one (NH4+)-N-15 , and one unlabeled nitrogen (N) source, e.g., NO2-, NO) accounted for similar to 90% of the N2O production from NH4+ and was robust across the different O-2 , NO2+, and NH4+ conditions. Lack of response to variable substrate concentrations implies that the unlabeled N source was not limiting for N2O production. Although both O-2 and NH4+ were key modulators of N2O production rates, N2O yield (N2O produced per NO2- produced) seemed to be controlled solely by O-2 . The N2O yield increased when O-2 concentrations dropped below the half-saturation concentration for AO to NO2+ (<1.4 mu M), the range where NO2- production decreased faster than N2O production. Our study shows that O-2 control on N2O yield from AO is robust across stations and depths.

SummaryThe chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the prediction of A/B compartment prediction from Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, that enables fast and memory-efficient determination of A/B compartments at high resolution even in dataset with low sequencing depth.Availabilitygithub.com/scoutzxb/CscoreToolContactxzheng@carnegiescience.edu

The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in aiding these studies. We approached assembling the Sciara genome using multiple sequencing technologies: PacBio, Oxford Nanopore MinION, and Illumina. To find an optimal assembly using these datasets, we generated 44 Illumina assemblies using 7 short-read assemblers and 50 long-read assemblies of PacBio and MinION sequence data using 6 long-read assemblers. We ranked assemblies using a battery of reference-free metrics, and scaffolded a subset of the highest-ranking assemblies using BioNano Genomics optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. Moreover, we anchored nearly half of the Sciara genome sequence into chromosomes. Finally, we used the signal level of both the PacBio and Oxford Nanopore data to explore the presence or absence of DNA modifications in the Sciara genome since DNA modifications may play a role in imprinting in Sciara, as they do in mammals. These data serve as the foundation for future research by the growing community studying the unique features of this emerging model system.

Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long non-coding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, and Tetrahymena models, but not in parasitic protozoa, including clinically relevant human parasites. Here, using the protozoan parasite, Trypanosoma brucei (T. brucei) as a model, we have identified the interactome of T. brucei TERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors of TbTERT, highlighting unique features of T. brucei telomerase biology. These unique interactions with TbTERT, suggest mechanistic differences in telomere maintenance between T. brucei and other eukaryotes.

This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.

As moderately volatile elements, isotopes of Rb and K can trace volatilization processes in planetary bod-ies. Rubidium isotopic data are however very scarce, especially for non-carbonaceous meteorites. Here, we report combined Rb and K isotopic data (d87/85Rb and d41/39 Kappa) for 7 ordinary, 6 enstatite, and 4 Martian meteorite falls to understand the causes for the variations in volatile abundances and isotopic compositions. Bulk Rb and K isotopic compositions of planetary bodies are estimated to be (Table 1): Mars +0.10 +/- 0.03 T. for Rb and-0.26 +/- 0.05 T. for K, bulk OCs-0.120.15-0.24 T. for Rb and-0.720.28 -0.41 T. for K, bulk ECs 0.020.29-0.26 T. for Rb and-0.330.37-0.23 T. for K. The bulk K isotopic compositions of subgroup OCs are estimated to be-0.720.26-0.55 T. for H chondrites,-0.710.23 -0.39T.for L chondrites, and-0.770.63-0.30 T. for LL chondrites. A broad correlation between the Rb and K isotopic compositions of planetary bodies is observed. The correlation follows a slope that is consistent with kinetic evaporation and condensation processes, suggesting volatility-controlled mass-dependent isotope fractionation (as opposed to nucle-osynthetic anomalies).Individual ordinary and enstatite chondrites show large Rb and K isotopic variations (-1.02 to +0.29 T. for Rb and-0.91 to-0.15 T. for K). Samples of lower metamorphic grades display correlated elemental and isotopic fractionations between Rb and K, while samples of higher metamorphic grades show great scatter, suggesting that chondrite parent-body processes have decoupled the two elements and their iso-topes at the sample scale. Several processes could have contributed to the observed isotopic variations of Rb and K, including (i) chondrule "nugget effect", (ii) volatilization during parent-body thermal metamor-phism (heat-induced vaporization and gas transport within parent bodies), (iii) thermal diffusion during parent-body metamorphism, and (iv) impact/shock heating. Quantitative modeling of the first two pro-cesses suggests that neither of them could produce isotopic variations large enough to explain the observed isotopic variations. Volatilization during parent-body thermal metamorphism [the scenario (ii)], which has been commonly invoked to explain the isotopic variations of volatile elements, is gas transport-limited and its effect on isotopic fractionations of moderately volatile elements should be neg-ligible. Modeling of diffusion processes suggests that (iii) could produce K isotopic variation comparable to the observed variation. The large isotopic variations in non-carbonaceous meteorites are thus most likely due to diffusive redistribution of K and Rb during metamorphism and/or shock-induced heating and vaporization.(c) 2023 Elsevier Ltd. All rights reserved.

BACKGROUND: Many animals and plants acquire their coevolved symbiotic partners shortly post-embryonic development. Thus, during embryogenesis, cellular features must be developed that will promote both symbiont colonization of the appropriate tissues, as well as persistence at those sites. While variation in the degree of maturation occurs in newborn tissues, little is unknown about how this variation influences the establishment and persistence of host-microbe associations.

HD 53143 is a mature Sun-like star and host to a broad disk of dusty debris, including a cold outer ring of planetesimals near 90 au. Unlike most other inclined debris disks imaged at visible wavelengths, the cold disk around HD 53143 appears as disconnected "arcs" of material, with no forward-scattering side detected to date. We present new, deeper Hubble Space Telescope Imaging Spectrograph coronagraphic observations of the HD 53143 debris disk and show that the forward-scattering side of the disk remains undetected. By fitting our KLIP-reduced observations via forward modeling with an optically thin disk model, we show that fitting the visible wavelength images with an azimuthally symmetric disk with unconstrained orientation results in an unphysical edge-on orientation that is at odds with recent ALMA observations, while constraining the orientation to that observed by ALMA results in nearly isotropically scattering dust. We show that the HD 53143 host star exhibits significant stellar variations due to spot rotation and revisit age estimates for this system.