Genetic requirements for cell division in a genomically minimal cell.

Genomically minimal cells, such as JCVI-syn3.0, offer a platform to clarify genes underlying core physiological processes. Although this minimal cell includes genes essential for population growth, the physiology of its single cells remained uncharacterized. To investigate striking morphological variation in JCVI-syn3.0 cells, we present an approach to characterize cell propagation and determine genes affecting cell morphology. Microfluidic chemostats allowed observation of intrinsic cell dynamics that result in irregular morphologies. A genome with 19 genes not retained in JCVI-syn3.0 generated JCVI-syn3A, which presents morphology similar to that of JCVI-syn1.0. We further identified seven of these 19 genes, including two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, which are required together to restore a phenotype similar to that of JCVI-syn1.0. This result emphasizes the polygenic nature of cell division and morphology in a genomically minimal cell.

Conformational Changes of CFTR upon Phosphorylation and ATP Binding.

The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from an ATP-binding cassette transporter. CFTR channel gating is strictly coupled to phosphorylation and ATP hydrolysis. Previously, we reported essentially identical structures of zebrafish and human CFTR in the dephosphorylated, ATP-free form. Here, we present the structure of zebrafish CFTR in the phosphorylated, ATP-bound conformation, determined by cryoelectron microscopy to 3.4 Å resolution. Comparison of the two conformations shows major structural rearrangements leading to channel opening. The phosphorylated regulatory domain is disengaged from its inhibitory position; the nucleotide-binding domains (NBDs) form a "head-to-tail" dimer upon binding ATP; and the cytoplasmic pathway, found closed off in other ATP-binding cassette transporters, is cracked open, consistent with CFTR's unique channel function. Unexpectedly, the extracellular mouth of the ion pore remains closed, indicating that local movements of the transmembrane helices can control ion access to the pore even in the NBD-dimerized conformation.

Sperm bauplan and function and underlying processes of sperm formation and selection.

The spermatozoon is a highly differentiated and polarized cell, with two main structures: the head, containing a haploid nucleus and the acrosomal exocytotic granule, and the flagellum, which generates energy and propels the cell; both structures are connected by the neck. The sperm's main aim is to participate in fertilization, thus activating development. Despite this common bauplan and function, there is an enormous diversity in structure and performance of sperm cells. For example, mammalian spermatozoa may exhibit several head patterns and overall sperm lengths ranging from ∼30 to 350 µm. Mechanisms of transport in the female tract, preparation for fertilization, and recognition of and interaction with the oocyte also show considerable variation. There has been much interest in understanding the origin of this diversity, both in evolutionary terms and in relation to mechanisms underlying sperm differentiation in the testis. Here, relationships between sperm bauplan and function are examined at two levels: first, by analyzing the selective forces that drive changes in sperm structure and physiology to understand the adaptive values of this variation and impact on male reproductive success and second, by examining cellular and molecular mechanisms of sperm formation in the testis that may explain how differentiation can give rise to such a wide array of sperm forms and functions.

Generating interstitial water within the persisting tetrahedral H-bond network explains density increase upon compressing liquid water.

Despite its ubiquitous nature, the atomic structure of water in its liquid state is still controversially debated. We use a combination of X-ray Raman scattering spectroscopy in conjunction with ab initio and path integral molecular dynamics simulations to study the local atomic and electronic structure of water under high pressure conditions. Systematically increasing fingerprints of non-hydrogen-bonded H[Formula: see text]O molecules in the first hydration shell are identified in the experimental and computational oxygen K-edge excitation spectra. This provides evidence for a compaction mechanism in terms of a continuous collapse of the second hydration shell with increasing pressure via generation of interstitial water within locally tetrahedral hydrogen-bonding environments.

Scaling of the morphology of African cities.

A large proportion of Africa's infrastructure is yet to be built. Where and how these new buildings are constructed matters since today's decisions will last for decades. The resulting morphology of cities has lasting implications for a city's energy needs. Estimating and projecting these needs has always been challenging in Africa due to the lack of data. Yet, given the sweeping urbanization expected in Africa over the next three decades, this obstacle must be overcome to guide cities toward a trajectory of sustainability and resilience. Based on the location and surface of nearly 200 million buildings on the continent, we estimate the interbuilding distance of almost six thousand cities. Buildings' footprint data enable the construction of urban form indicators to compare African cities' elongation, sprawl, and emptiness. We establish the BASE model, where the mean distance between buildings is a functional relation to the number of Buildings and their average Area, as well as the Sprawl and the Elongation of its spatial arrangement. The mean distance between structures in cities-our proxy for its energy demands related to mobility-grows faster than the square root of its population, resulting from the combined impact of a sublinear growth in the number of buildings and a sublinear increase in building size and sprawl. We estimate that when a city doubles its population, it triples its energy demand from transport.

A retrotransposon insertion in the Mao1 promoter results in erect pubescence and higher yield in soybean.

Adaptive changes in crops contribute to the diversity of agronomic traits, which directly or indirectly affect yield. The change of pubescence form from appressed to erect is a notable feature during soybean domestication. However, the biological significance and regulatory mechanism underlying this transformation remain largely unknown. Here, we identified a major-effect locus, PUBESCENCE FORM 1 (PF1), the upstream region of Mao1, that regulates pubescence form in soybean. The insertion of a Ty3/Gypsy retrotransposon in PF1 can recruit the transcription factor GAGA-binding protein to a GA-rich region, which up-regulates Mao1 expression, underpinning soybean pubescence evolution. Interestingly, the proportion of improved cultivars with erect pubescence increases gradually with increasing latitude, and erect-pubescence cultivars have a higher yield possibly through a higher photosynthetic rate and photosynthetic stability. These findings open an avenue for molecular breeding through either natural introgression or genome editing toward yield improvement and productivity.

Universal interpretations of vocal music.

Despite the variability of music across cultures, some types of human songs share acoustic characteristics. For example, dance songs tend to be loud and rhythmic, and lullabies tend to be quiet and melodious. Human perceptual sensitivity to the behavioral contexts of songs, based on these musical features, suggests that basic properties of music are mutually intelligible, independent of linguistic or cultural content. Whether these effects reflect universal interpretations of vocal music, however, is unclear because prior studies focus almost exclusively on English-speaking participants, a group that is not representative of humans. Here, we report shared intuitions concerning the behavioral contexts of unfamiliar songs produced in unfamiliar languages, in participants living in Internet-connected industrialized societies (n = 5,516 native speakers of 28 languages) or smaller-scale societies with limited access to global media (n = 116 native speakers of three non-English languages). Participants listened to songs randomly selected from a representative sample of human vocal music, originally used in four behavioral contexts, and rated the degree to which they believed the song was used for each context. Listeners in both industrialized and smaller-scale societies inferred the contexts of dance songs, lullabies, and healing songs, but not love songs. Within and across cohorts, inferences were mutually consistent. Further, increased linguistic or geographical proximity between listeners and singers only minimally increased the accuracy of the inferences. These results demonstrate that the behavioral contexts of three common forms of music are mutually intelligible cross-culturally and imply that musical diversity, shaped by cultural evolution, is nonetheless grounded in some universal perceptual phenomena.

On Viazovska's modular form inequalities.

Viazovska proved that the [Formula: see text] lattice sphere packing is the densest sphere packing in [Formula: see text] dimensions. Her proof relies on two inequalities between functions defined in terms of modular and quasimodular forms. We give a direct proof of these inequalities that does not rely on computer calculations.

Non-B-form DNA tends to form in centromeric regions and has undergone changes in polyploid oat subgenomes.

Centromeres are the specialized regions of the chromosomes that direct faithful chromosome segregation during cell division. Despite their functional conservation, centromeres display features of rapidly evolving DNA and wide evolutionary diversity in size and organization. Previous work found that the noncanonical B-form DNA structures are abundant in the centromeres of several eukaryotic species with a possible implication for centromere specification. Thus far, systematic studies into the organization and function of non-B-form DNA in plants remain scarce. Here, we applied the oat system to investigate the role of non-B-form DNA in centromeres. We conducted chromatin immunoprecipitation sequencing using an antibody to the centromere-specific histone H3 variant (CENH3); this accurately positioned oat centromeres with different ploidy levels and identified a series of centromere-specific sequences including minisatellites and retrotransposons. To define genetic characteristics of oat centromeres, we surveyed the repeat sequences and found that dyad symmetries were abundant in oat centromeres and were predicted to form non-B-DNA structures in vivo. These structures including bent DNA, slipped DNA, Z-DNA, G-quadruplexes, and R-loops were prone to form within CENH3-binding regions. Dynamic conformational changes of predicted non-B-DNA occurred during the evolution from diploid to tetraploid to hexaploid oat. Furthermore, we applied the single-molecule technique of AFM and DNA:RNA immunoprecipitation with deep sequencing to validate R-loop enrichment in oat centromeres. Centromeric retrotransposons exhibited strong associations with R-loop formation. Taken together, our study elucidates the fundamental character of non-B-form DNA in the oat genome and reveals its potential role in centromeres.

The shapeshifting Helicobacter pylori: From a corkscrew to a ball.

There is growing evidence that bacterial morphology is closely related to their lifestyle. The helical Helicobacter pylori relies on its unique shape for survival and efficient colonization of the human stomach. Yet, they have been observed to transform into another distinctive morphology, the spherical coccoid. Despite being hypothesized to be involved in the persistence and transmission of this species, years of effort in deciphering the roles of the coccoid form remain fruitless since contrasting observations regarding its lifestyle were reported. Here, we discuss the two forms of H. pylori with a focus on the coccoid form, the molecular mechanism behind its morphological transformation, and experimental approaches to further develop our understanding of this phenomenon. We also propose a putative mechanism of the coccoid formation in H. pylori through induction of a type-I toxin-antitoxin (TA) system recently shown to influence the morphology of this species.

Both mOTS-words and pOTS-words prefer emoji stimuli over text stimuli during a lexical judgment task.

The visual word form area in the occipitotemporal sulcus (here OTS-words) is crucial for reading and shows a preference for text stimuli. We hypothesized that this text preference may be driven by lexical processing. Hence, we performed three fMRI experiments (n = 15), systematically varying participants' task and stimulus, and separately evaluated middle mOTS-words and posterior pOTS-words. Experiment 1 contrasted text with other visual stimuli to identify both OTS-words subregions. Experiment 2 utilized an fMRI adaptation paradigm, presenting compound words as texts or emojis. In experiment 3, participants performed a lexical or color judgment task on compound words in text or emoji format. In experiment 2, pOTS-words, but not mOTS-words, showed fMRI adaptation for compound words in both formats. In experiment 3, both subregions showed higher responses to compound words in emoji format. Moreover, mOTS-words showed higher responses during the lexical judgment task and a task-stimulus interaction. Multivariate analyses revealed that distributed responses in pOTS-words encode stimulus and distributed responses in mOTS-words encode stimulus and task. Together, our findings suggest that the function of the OTS-words subregions goes beyond the specific visual processing of text and that these regions are flexibly recruited whenever semantic meaning needs to be assigned to visual input.

Satellite mapping of urban built-up heights reveals extreme infrastructure gaps and inequalities in the Global South.

Information on urban built-up infrastructure is essential to understand the role of cities in shaping environmental, economic, and social outcomes. The lack of data on built-up heights over large areas has limited our ability to characterize urban infrastructure and its spatial variations across the world. Here, we developed a global atlas of urban built-up heights circa 2015 at 500-m resolution from the Sentinel-1 Ground Range Detected satellite data. Results show extreme gaps in per capita urban built-up infrastructure in the Global South compared with the global average, and even larger gaps compared with the average levels in the Global North. Per capita urban built-up infrastructures in some countries in the Global North are more than 30 times higher than those in the Global South. The results also show that the built-up infrastructure in 45 countries in the Global North combined, with ∼16% of the global population, is roughly equivalent to that of 114 countries in the Global South, with ∼74% of the global population. The inequality in urban built-up infrastructure, as measured by an inequality index, is large in most countries, but the largest in the Global South compared with the Global North. Our analysis reveals the scale of infrastructure demand in the Global South that is required in order to meet sustainable development goals.

Form Factor-Free Boron Nitride Nanotube-Agarose Composites for Neutron Shielding.

Boron nitride nanotubes (BNNTs) have remarkable mechanical and thermal properties and are suitable for neutron shielding due to boron. Because BNNTs exist in bundled and stiff shapes, limiting their practical applications, however, it is essential to improve their formability and processability. In this study, we demonstrate form-factor-free BNNTs and agarose composites for use in neutron shielding for the first time; they are fabricated by mixing hydrophilic agarose with noncovalently functionalized water-soluble BNNTs (p-BNNTs). The mechanical properties of the agarose/p-BNNT composite films surpass those of conventional commodity plastics. When the p-BNNT concentration increased, the neutron linear attenuation coefficient of the composite film increases from 0.574 ± 0.010 to 0.765 ± 0.062 mm-1, which is comparable to that of conventional rigid shielding materials. In particular, the addition of 10 wt % p-BNNTs to agarose results in excellent form-factor flexibility, neutron shielding, and mechanical properties, thus rendering it a promising candidate for the nuclear industry.

Variability in Chromosome 1 of Select Moroccan Pyrenophora teres f. teres Isolates Overcomes a Highly Effective Barley Chromosome 6H Source of Resistance.

Barley net form net blotch (NFNB) is a destructive foliar disease caused by Pyrenophora teres f. teres. Barley line CIho5791, which harbors the broadly effective chromosome 6H resistance gene Rpt5, displays dominant resistance to P. teres f. teres. To genetically characterize P. teres f. teres avirulence/virulence on the barley line CIho5791, we generated a P. teres f. teres mapping population using a cross between the Moroccan CIho5791-virulent isolate MorSM40-3 and the avirulent reference isolate 0-1. Full genome sequences were generated for 103 progenies. Saturated chromosome-level genetic maps were generated, and quantitative trait locus (QTL) mapping identified two major QTL associated with P. teres f. teres avirulence/virulence on CIho5791. The most significant QTL mapped to chromosome (Ch) 1, where the virulent allele was contributed by MorSM40-3. A second QTL mapped to Ch8; however, this virulent allele was contributed by the avirulent parent 0-1. The Ch1 and Ch8 loci accounted for 27 and 15% of the disease variation, respectively, and the avirulent allele at the Ch1 locus was epistatic over the virulent allele at the Ch8 locus. As a validation, we used a natural P. teres f. teres population in a genome-wide association study that identified the same Ch1 and Ch8 loci. We then generated a new reference quality genome assembly of parental isolate MorSM40-3 with annotation supported by deep transcriptome sequencing of infection time points. The annotation identified candidate genes predicted to encode small, secreted proteins, one or more of which are likely responsible for overcoming the CIho5791 resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Global patterns and drivers of plant-soil microbe interactions.

Plant-soil feedback (PSF) is an important mechanism determining plant community dynamics and structure. Understanding the geographic patterns and drivers of PSF is essential for understanding the mechanisms underlying geographic plant diversity patterns. We compiled a large dataset containing 5969 observations of PSF from 202 studies to demonstrate the global patterns and drivers of PSF for woody and non-woody species. Overall, PSF was negative on average and was influenced by plant attributes and environmental settings. Woody species PSFs did not vary with latitude, but non-woody PSFs were more negative at higher latitudes. PSF was consistently more positive with increasing aridity for both woody and non-woody species, likely due to increased mutualistic microbes relative to soil-borne pathogens. These findings were consistent between field and greenhouse experiments, suggesting that PSF variation can be driven by soil legacies from climates. Our findings call for caution to use PSF as an explanation of the latitudinal diversity gradient and highlight that aridity can influence plant community dynamics and structure across broad scales through mediating plant-soil microbe interactions.

Soluble CD27 as a predictive biomarker for intra-tumoral CD70/CD27 interaction in nasopharyngeal carcinoma.

In CD70-expressing tumors, the interaction of CD70 on tumor cells with its lymphocyte receptor, CD27, is thought to play a role in immunosuppression in the tumor microenvironment and elevated serum levels of soluble CD27 (sCD27). Previous studies showed that CD70 is expressed in nasopharyngeal carcinoma (NPC), an Epstein-Barr virus (EBV)-related malignancy. However, the association between intratumoral CD70/CD27 expression and serum levels of sCD27 in NPC remains unclear. In the present study, we show that CD70 is primarily expressed by tumor cells in NPC and that CD27-positive lymphocytes infiltrate around tumor cells. NPC patients with CD27-positive lymphocytes had significantly better prognosis than patients lacking these cells. In addition, high CD70 expression by tumor cells tended to be correlated with shorter survival in NPC patients with CD27-positive lymphocytes. Serum sCD27 levels were significantly increased in patients with NPC and provided good diagnostic accuracy for discriminating patients from healthy individuals. The concentration of serum sCD27 in patients with CD70-positive NPC with CD27-positive lymphocytes was significantly higher than in patients with tumors negative for CD70 and/or CD27, indicating that the intratumoral CD70/CD27 interaction boosts the release of sCD27. Furthermore, positive expression of CD70 by NPC cells was significantly correlated with EBV infection. Our results suggest that CD70/CD27-targeted immunotherapies may be promising treatment options and that sCD27 may become an essential tool for evaluating the applicability of these therapies by predicting the intratumoral CD70/CD27 interaction in NPC.

The transition from vision to language: Distinct patterns of functional connectivity for subregions of the visual word form area.

Reading entails transforming visual symbols to sound and meaning. This process depends on specialized circuitry in the visual cortex, the visual word form area (VWFA). Recent findings suggest that this text-selective cortex comprises at least two distinct subregions: the more posterior VWFA-1 is sensitive to visual features, while the more anterior VWFA-2 processes higher level language information. Here, we explore whether these two subregions also exhibit different patterns of functional connectivity. To this end, we capitalize on two complementary datasets: Using the Natural Scenes Dataset (NSD), we identify text-selective responses in high-quality 7T adult data (N = 8), and investigate functional connectivity patterns of VWFA-1 and VWFA-2 at the individual level. We then turn to the Healthy Brain Network (HBN) database to assess whether these patterns replicate in a large developmental sample (N = 224; age 6-20 years), and whether they relate to reading development. In both datasets, we find that VWFA-1 is primarily correlated with bilateral visual regions. In contrast, VWFA-2 is more strongly correlated with language regions in the frontal and lateral parietal lobes, particularly the bilateral inferior frontal gyrus. Critically, these patterns do not generalize to adjacent face-selective regions, suggesting a specific relationship between VWFA-2 and the frontal language network. No correlations were observed between functional connectivity and reading ability. Together, our findings support the distinction between subregions of the VWFA, and suggest that functional connectivity patterns in the ventral temporal cortex are consistent over a wide range of reading skills.

Animal models as windows into the pathogenesis of myopia: Illuminating new directions for vision health.

The incidence of myopia, particularly high myopia, is increasing annually. Myopia has gradually become one of the leading causes of global blindness and is a considerable public-health concern. However, the pathogenesis of myopia remains unclear, and exploring the mechanism underlying myopia has become an urgent scientific priority. Creating animal models of myopia is important for studying the pathogenesis of refractive errors. This approach allows researchers to study and analyze the pathogenesis of myopia from aspects such as changes in refractive development, pathological changes in eye tissue, and molecular pathways related to myopia. This review summarizes the examples of animal models, methods of inducing myopia experimentally, and molecular signaling pathways involved in developing myopia-induced animal models. This review provides solid literature for researchers in the field of myopia prevention and control. It offers guidance in selecting appropriate animal models and research methods to fit their research objectives. By providing new insights and a theoretical basis for studying mechanisms of myopia, we detail how elucidated molecular pathways can be exploited to translate into safe and effective measures for myopia prevention and control.

Form-deprivation myopia promotes sclera M2-type macrophages polarization in mice.

PURPOSE: To explore the phenotype of sclera macrophages in form-deprivation (FD) myopia mice and the effects of M2 macrophage in FD myopia development. METHODS: C57BL/6 mice were under 2 weeks of unilateral FD treatment. and they were separated into two groups, including an intraperitoneally injected(IP) vehicle group and Panobinostat (LBH589) (10 mg/kg per body weight) treatment group. All biometric parameters were measured before and after treatments, and the type and density of sclera macrophages were identified by immunofluorescence and RT-qPCR. In vitro, we analyzed the M2 macrophage and primary human sclera fibroblast (HSF) co-culture system by using the transcriptome sequencing method. Gene ontology (GO) and KEGG enrichment analyses were used to pinpoint the biological functions and pathways associated with the identified Differentially Expressed Genes (DEGs). The hub genes were investigated using the STRING database and Cytoscape software and were confirmed using RT-qPCR. RESULTS: We found that the M2-type sclera macrophage density and expression increased in FD-treated eyes. The results showed that LBH589 inhibited the M2 macrophage polarization, and reduced FDM development. GO and KEGG analyses revealed that the DEGs were predominantly involved in the synthesis and breakdown of the extracellular matrix (ECM), as well as in pathways related to ECM-receptor interaction and the PI3K-Akt signaling pathway. Five hub genes (FN-1, MMP-2, COL1A1, CD44, and IL6) were identified, and RT-qPCR validated the variation in expression levels among these genes. CONCLUSION: M2 macrophage polarization occurred in the sclera in FDM mice. Panobinostat-mediated inhibition of M2 macrophage polarization may decrease FDM progression, as M2 macrophages are crucial in controlling ECM remodeling by HSFs.

Construction of a three-dimensional inflammation model of human bronchial epithelial cells BEAS-2B by using the self-assembling D-form peptide Sciobio-â ¢.

Human bronchial epithelial cells in the airway system, as the primary barrier between humans and the surrounding environment, assume a crucial function in orchestrating the processes of airway inflammation. Target to develop a new three-dimensional (3D) inflammatory model to airway system, and here we report a strategy by using self-assembling D-form peptide to cover the process. By testing physicochemical properties and biocompatibility of Sciobio-Ⅲ, we confirmed that it can rapidly self-assembles under the trigger of ions to form a 3D nanonetwork-like scaffold, which supports 3D cell culture including the cell strains like BEAS-2B cells. Subsequently, inflammation model was established by lipopolysaccharide (LPS), the expression of some markers of tumor necrosis factor-α (TNF-α), interleukin-1ß (IL-1ß), interleukin-6 (IL-6), and interleukin-8 (IL-8), the levels of relevant inflammatory factors were measured by RT-qPCR and the secretion profile of inflammatory cytokines by ELISA, are obtained the quite difference effects in 2D and 3D microenvironment, which suggested Sciobio-Ⅲ hydrogel is an ideal scaffold that create the microenvironment for 3D cell culture. Here we are success to establish a 3D inflammation model for airway system. This innovative model allows for rapid and accurate evaluation of drug metabolism and toxicological side effects, hope to use in drug screening for airway inflammatory diseases and beyond.