AIM: To conduct the first global‐scale investigation of soil nematode assemblages using a standardized approach to quantify how environmental and climatic variables influence family assemblage ...structure in nematodes and determine whether nematode families have restricted distributions. LOCATION: Global. METHODS: We collected soil nematodes within four 10 m × 10 m plots distributed evenly along a 900‐m transect at each of 12 sites representing multiple ecosystem types across a latitudinal gradient (68° N to 77° S) on six continents. We assigned > 28,000 individuals to family level and trophic group morphologically. RESULTS: We recorded a total of 43 nematode families, but sites varied considerably in family richness (1–30). Families differed in their ranges with 12 families occurring at 10 or more sites, while 14 families occurred at three or fewer sites. Total nematode and trophic group abundances were generally related to soil characteristics, including bulk density and soil moisture, but we found no good predictor of family richness, diversity or evenness at the plot level. Family richness, diversity and evenness were considerably lower in the high‐latitude polar desert than elsewhere, but only family diversity showed a significant, albeit weak, latitudinal gradient. Nematode assemblage composition was quite strongly related to climate: 65% and 58% of the variation in assemblage composition across sites could be accounted for by mean annual rainfall and temperature, respectively. MAIN CONCLUSIONS: Nematode families display macroecological patterns similar to other organisms, such as a positive abundance–range size relationship and restricted distribution of some families. Local nematode abundances were related to soil characteristics, but we found no relationships between family richness and environmental or climatic variables. Family composition was related to mean annual rainfall and temperature, suggesting that climate is a good predictor of local assemblage structure. As a result, climate change may have a significant impact on nematode assemblages, with potential implications for ecosystem functioning.
Selective halogenation is necessary for a range of fine chemical applications, including the development of therapeutic drugs. While synthetic processes to achieve C-H halogenation require harsh ...conditions, enzymes such as nonheme iron halogenases carry out some types of C-H halogenation, i.e., chlorination or bromination, with ease, while others, i.e., fluorination, have never been observed in natural or engineered nonheme iron enzymes. Using density functional theory and correlated wave function theory, we investigate the differences in structural and energetic preferences of the smaller fluoride and the larger chloride or bromide intermediates throughout the catalytic cycle. Although we find that the energetics of rate-limiting hydrogen atom transfer are not strongly impacted by fluoride substitution, the higher barriers observed during the radical rebound reaction for fluoride relative to chloride and bromide contribute to the difficulty of C-H fluorination. We also investigate the possibility of isomerization playing a role in differences in reaction selectivity, and our calculations reveal crucial differences in terms of isomer energetics of the key ferryl intermediate between fluoride and chloride/bromide intermediates. While formation of monodentate isomers believed to be involved in selective catalysis is shown for chloride and bromide intermediates, we find that formation of the fluoride monodentate intermediate is not possible in our calculations, which lack additional stabilizing interactions with the greater protein environment. Furthermore, the shorter Fe-F bonds are found to increase isomerization reaction barriers, suggesting that incorporation of residues that form a halogen bond with F and elongate Fe-F bonds could make selective C-H fluorination possible in nonheme iron halogenases. Our work highlights the differences between the fluoride and chloride/bromide intermediates and suggests potential steps toward engineering nonheme iron halogenases to enable selective C-H fluorination.
Ocular delivery of lipid nanoparticle (LNPs) packaged mRNA can enable efficient gene delivery and editing. We generated LNP variants through the inclusion of positively charged-amine-modified ...polyethylene glycol (PEG)-lipids (LNPa), negatively charged-carboxyl-(LNPz) and carboxy-ester (LNPx) modified PEG-lipids, and neutral unmodified PEG-lipids (LNP). Subretinal injections of LNPa containing Cre mRNA in the mouse show tdTomato signal in the retinal pigmented epithelium (RPE) like conventional LNPs. Unexpectedly, LNPx and LNPz show 27% and 16% photoreceptor transfection, respectively, with striking localization extending from the photoreceptor synaptic pedicle to the outer segments, displaying pan-retinal distribution in the photoreceptors and RPE. LNPx containing Cas9 mRNA and sgAi9 leads to the formation of an oval elongated structure with a neutral charge resulting in 16.4% editing restricted to RPE. Surface modifications of LNPs with PEG variants can alter cellular tropism of mRNA. LNPs enable genome editing in the retina and in the future can be used to correct genetic mutations that lead to blindness.
Long interspersed nuclear element-1 (L1) is a retrotransposable element that autonomously replicates in the human genome, resulting in DNA damage and genomic instability. Activation of L1 in ...senescent cells triggers a type I interferon response and age-associated inflammation. Two open reading frames encode an ORF1 protein functioning as messenger RNA chaperone and an ORF2 protein providing catalytic activities necessary for retrotransposition. No function has been identified for the conserved, disordered N-terminal region of ORF1. Using microscopy and NMR spectroscopy, we demonstrate that ORF1 forms liquid droplets in vitro in a salt-dependent manner and that interactions between its N-terminal region and coiled-coil domain are necessary for phase separation. Mutations disrupting blocks of charged residues within the N-terminus impair phase separation, whereas some mutations within the coiled-coil domain enhance phase separation. Demixing of the L1 particle from the cytosol may provide a mechanism to protect the L1 transcript from degradation.
Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in ...static cell types. How super-enhancers are established during cell differentiation remains obscure.
Here, by developing an unbiased approach to systematically analyze the evolving landscape of super-enhancers during cell differentiation in multiple lineages, we discover a general trend where super-enhancers emerge through three distinct temporal patterns: conserved, temporally hierarchical, and de novo. The three types of super-enhancers differ further in association patterns in target gene expression, functional enrichment, and 3D chromatin organization, suggesting they may represent distinct structural and functional subtypes. Furthermore, we dissect the enhancer repertoire within temporally hierarchical super-enhancers, and find enhancers that emerge at early and late stages are enriched with distinct transcription factors, suggesting that the temporal order of establishment of elements within super-enhancers may be directed by underlying DNA sequence. CRISPR-mediated deletion of individual enhancers in differentiated cells shows that both the early- and late-emerged enhancers are indispensable for target gene expression, while in undifferentiated cells early enhancers are involved in the regulation of target genes.
In summary, our analysis highlights the heterogeneity of the super-enhancer population and provides new insights to enhancer functions within super-enhancers.
A fast and efficient search function across the database has been a core component for a number of data-intensive tasks in machine learning, IoT applications, and inference. However, the conventional ...digital machines implementing the search functionality with repetitive arithmetic operations suffer from the energy efficiency and performance degradation due to the significant data transfer between the storage and processing units in the Von Neumann architecture. Ternary content addressable memories (TCAMs) are an essential hardware form of computing-in-memory (CiM) designs that aim to overcome the data transfer bottlenecks by implementing the parallel associative search function within the memory blocks. While most state-of-the-art TCAM designs focus on improving the information density by harnessing compact nonvolatile memories (NVMs), little efforts have been spent on optimizing the energy efficiency of the NVM-based TCAM. In this article, by exploiting the ferroelectric FET (FeFET) as a representative NVM, we propose an NOR-type 2FeFET-1T and an NAND-type 2FeFET-2T TCAM designs that enable highly energy-efficient associative search by reducing the associated precharge overheads. We then propose a hybrid ferroelectric NAND-NOR (HFNN) TCAM design to further improve the energy efficiency. An HFNN-based segmented architecture is proposed to reduce the search delay and energy by search operation pipeline. Evaluation results suggest that the proposed 2FeFET-1T, 2FeFET-2T and HFNN TCAM design consume <inline-formula> <tex-math notation="LaTeX">3.03\times </tex-math></inline-formula>, <inline-formula> <tex-math notation="LaTeX">8.08\times </tex-math></inline-formula>, and <inline-formula> <tex-math notation="LaTeX">226.92\times </tex-math></inline-formula> less search energy than the conventional 16T complementary metal oxide semiconductor (CMOS) TCAM, respectively. Application benchmarking shows that our proposed 2FeFET-1T/2FeFET-2T/HFNN TCAM can save, on average, 45.2%/50.6%/57.5% the GPU energy consumption as compared to the conventional GPU.
Complete encapsulation of nucleic acids by lipid-based nanoparticles (LNPs) is often thought to be one of the main prerequisites for successful nucleic acid delivery, as the lipid environment ...protects mRNA from degradation by external nucleases and assists in initiating delivery processes. However, delivery of mRNA via a preformed vesicle approach (PFV-LNPs) defies this precondition. Unlike traditional LNPs, PFV-LNPs are formed via a solvent-free mixing process, leading to a superficial mRNA localization. While demonstrating low encapsulation efficiency in the RiboGreen assay, PFV-LNPs improved delivery of mRNA to the retina by up to 50% compared to the LNP analogs across several benchmark formulations, suggesting the utility of this approach regardless of the lipid composition. Successful mRNA and gene editors' delivery is observed in the retinal pigment epithelium and photoreceptors and validated in mice, non-human primates, and human retinal organoids. Deploying PFV-LNPs in gene editing experiments result in a similar extent of gene editing compared to analogous LNP (up to 3% on genomic level) in the Ai9 reporter mouse model; but, remarkably, retinal tolerability is significantly improved for PFV-LNP treatment. The study findings indicate that the LNP formulation process can greatly influence mRNA transfection and gene editing outcomes, improving LNP treatment safety without sacrificing efficacy.
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