The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights.

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Antagonistic regulation of target genes by the SISTER OF TM3-JOINTLESS2 complex in tomato inflorescence branching.

Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)-SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)-have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.

ASYMMETRIC LEAVES 2 and ASYMMETRIC LEAVES 2-LIKE are partially redundant genes and essential for fruit development in tomato.

Fruit size and shape are controlled by genes expressed during the early developmental stages of fruit. Although the function of ASYMMETRIC LEAVES 2 (AS2) in promoting leaf adaxial cell fates has been well characterized in Arabidopsis thaliana, the molecular mechanisms conferring freshy fruit development as a spatial-temporal expression gene in tomato pericarp remain unclear. In the present study, we verified the transcription of SlAS2 and SlAS2L, two homologs of AS2, in the pericarp during early fruit development. Disruption of SlAS2 or SlAS2L caused a significant decrease in pericarp thickness as a result of a reduction in the number of pericarp cell layers and cell area, leading to smaller tomato fruit size, which revealed their critical roles in tomato fruit development. In addition, leaves and stamens exhibited severe morphological defects in slas2 and slas2l single mutants, as well as in the double mutants. These results demonstrated the redundant and pleiotropic functions of SlAS2 and SlAS2L in tomato fruit development. Yeast two-hybrid and split-luciferase complementation assays showed that both SlAS2 and SlAS2L physically interact with SlAS1. Molecular analyses further indicated that SlAS2 and SlAS2L regulate various downstream genes in leaf and fruit development, and that some genes participating in the regulation of cell division and cell differentiation in the tomato pericarp are affected by these genes. Our findings demonstrate that SlAS2 and SlAS2L are vital transcription factors required for tomato fruit development.

Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes.

High-resolution spatial and temporal maps of gene expression have facilitated a comprehensive understanding of animal development and evolution. In nematodes, the small body size represented a major challenge for such studies, but recent advancements have helped overcome this limitation. Here, we have implemented single worm transcriptomics (SWT) in the nematode model organism Pristionchus pacificus to provide a high-resolution map of the developmental transcriptome. We selected 38 time points from hatching of the J2 larvae to young adults to perform transcriptome analysis over 60 h of postembryonic development. A mean sequencing depth of 4.5 million read pairs allowed the detection of more than 23,135 (80%) of all genes. Nearly 3000 (10%) genes showed oscillatory expression with discrete expression levels, phases, and amplitudes. Gene age analysis revealed an overrepresentation of ancient gene classes among oscillating genes, and around one-third of them have 1:1 orthologs in C. elegans One important gene family overrepresented among oscillating genes is collagens. Several of these collagen genes are regulated by the developmental switch gene eud-1, indicating a potential function in the regulation of mouth-form plasticity, a key developmental process in this facultative predatory nematode. Together, our analysis provides (1) an updated protocol for SWT in nematodes that is applicable to many microscopic species, (2) a 1- to 2-h high-resolution catalog of P. pacificus gene expression throughout postembryonic development, and (3) a comparative analysis of oscillatory gene expression between the two model organisms P. pacificus and C. elegans and associated evolutionary dynamics.

Tomato APETALA2 family member SlTOE1 regulates inflorescence branching by repressing SISTER OF TM3.

Inflorescence architecture directly impacts yield potential in most crops. As a model of sympodial plants, tomato (Solanum lycopersicum) inflorescence exhibits highly structural plasticity. However, the genetic regulatory network of inflorescence architecture in tomato remains unclear. Here, we investigated a modulator of inflorescence branching in tomato, TARGET OF EAT1 (SlTOE1), an APETALA2 (AP2) family member found to be predominantly expressed in the floral meristem (FM) of tomato. sltoe1 knockout mutants displayed highly branched inflorescences and defective floral organs. Transcriptome analysis revealed that SISTER OF TM3 (STM3) and certain floral development-related genes were upregulated in the flower meristem of sltoe1. SlTOE1 could directly bind the promoters of STM3 and Tomato MADS-box gene 3 (TM3) to repress their transcription. Simultaneous mutation of STM3 and TM3 partially restored the inflorescence branching of the sltoe1cr mutants, suggesting that SlTOE1 regulates inflorescence development, at least in part through an SlTOE1STM3/TM3 module. Genetic analysis showed that SlTOE1 and ENHANCER OF JOINTLESS 2 (EJ2) additively regulate tomato inflorescence branching; their double mutants showed more extensive inflorescence branching. Our findings uncover a pathway controlling tomato inflorescence branching and offer deeper insight into the functions of AP2 subfamily members.

Robust bistatic ghost imaging with no physical synchronization.

Ghost imaging (GI) requires each echo from the object being correctly matched with the corresponding illuminiation pattern. We proposed a way for such matching with no physical synchronization towards bistatic configuration. The illumination is dually encoded in spatial and time domain. With aperiodic waveform and progressive correlation, the echoes can be correctly located and images can be obtained. In the experiments, our scheme is verified under different levels of signal to noise ratios, as well as different intensity of crosstalk. Ghost imaging with two transmitters and one receiver is also demonstrated. With our method, it is also possible to improve the imaging speed with multiple sources.

Satellite NO2 Retrieval Complicated by Aerosol Composition over Global Urban Agglomerations: Seasonal Variations and Long-Term Trends (2001-2018).

Tropospheric nitrogen dioxide (NO2) poses a serious threat to the environmental quality and public health. Satellite NO2 observations have been continuously used to monitor NO2 variations and improve model performances. However, the accuracy of satellite NO2 retrieval depends on the knowledge of aerosol optical properties, in particular for urban agglomerations accompanied by significant changes in aerosol characteristics. In this study, we investigate the impacts of aerosol composition on tropospheric NO2 retrieval for an 18 year global data set from Global Ozone Monitoring Experiment (GOME)-series satellite sensors. With a focus on cloud-free scenes dominated by the presence of aerosols, individual aerosol composition affects the uncertainties of tropospheric NO2 columns through impacts on the aerosol loading amount, relative vertical distribution of aerosol and NO2, aerosol absorption properties, and surface albedo determination. Among aerosol compositions, secondary inorganic aerosol mostly dominates the NO2 uncertainty by up to 43.5% in urban agglomerations, while organic aerosols contribute significantly to the NO2 uncertainty by -8.9 to 37.3% during biomass burning seasons. The possible contrary influences from different aerosol species highlight the importance and complexity of aerosol correction on tropospheric NO2 retrieval and indicate the need for a full picture of aerosol properties. This is of particular importance for interpreting seasonal variations or long-term trends of tropospheric NO2 columns as well as for mitigating ozone and fine particulate matter pollution.

Size-Resolved Molecular Characterization of Water-Soluble Organic Matter in Atmospheric Particulate Matter from Northern China.

Atmospheric particulate matter (PM) affects visibility, climate, biogeochemical cycles and human health. Water-soluble organic matter (WSOM) is an important component of PM. In this study, PM samples with size-resolved measurements at aerodynamic cut-point diameters (Dp) of 0.01-18µm were collected in the rural area of Baoding and the urban area of Dalian, Northern China. Non-targeted analysis was adopted for the characterization of the molecule constitutes of WSOM in different sized particles using Fourier transform-ion cyclotron resonance mass spectrometry. Regardless of the location, the composition of WSOM in Aitken mode particles (aerodynamic diameter < 0.05 µm) was similar. The WSOM in accumulation mode particles (0.05-2 µm) in Baoding was predominantly composed of CHO compounds (84.9%), which were mainly recognized as lignins and lipids species. However, S-containing compounds (64.2%), especially protein and carbohydrates species, accounted for most of the WSOM in the accumulation mode particles in Dalian. The CHO compounds (67.6%-79.7%) contributed the most to the WSOM in coarse mode particles (> 2 µm) from both sites. Potential sources analysis indicated the WSOM in Baoding were mainly derived from biomass burning and oxidation reactions, while the WSOM in Dalian arose from coal combustion, oxidation reactions, and regional transport.

Clinical features and treatment of heterotopic pancreas in children: a multi-center retrospective study.

OBJECTIVE: Heterotopic pancreas, an uncommon condition in children, can present with diagnostic and treatment challenges. This study aimed to evaluate the clinical features and treatment options for this disorder in pediatric patients. METHODS: We conducted a retrospective analysis, including patients diagnosed with heterotopic pancreas at four tertiary hospitals between January 2000 and June 2022. Patients were categorized into symptomatic and asymptomatic groups based on clinical presentation. Clinical parameters, including age at surgery, lesion size and site, surgical or endoscopic approach, pathological findings, and outcome, were statistically analyzed. RESULTS: The study included 88 patients with heterotopic pancreas. Among them, 22 were symptomatic, and 41 were aged one year or younger. The heterotopic pancreas was commonly located in Meckel's diverticulum (46.59%), jejunum (20.45%), umbilicus (10.23%),ileum (7.95%), and stomach (6.82%). Sixty-six patients had concomitant diseases. Thirty-three patients had heterotopic pancreas located in the Meckel's diverticulum, with 80.49% of cases accompanied by gastric mucosa heterotopia (GMH). Patients without accompanying GMH had a higher prevalence of heterotopic pancreas-related symptoms (75%). Treatment modalities included removal of the lesions by open surgery, laparoscopic or laparoscopic assisted surgery, or endoscopic surgery based on patient's age, the lesion site and size, and coexisting diseases. CONCLUSIONS: Only one-fourth of the patients with heterotopic pancreas presented with symptoms. Those located in the Meckel's diverticulum have commonly accompanying GMH. Open surgical, laparoscopic surgical or endoscopic resection of the heterotopic pancreas is recommended due to potential complications. Future prospective multicenter studies are warranted to establish rational treatment options.

Distributed NN-Based Formation Control of Multi-Agent Systems: A Reduced-Order Appointed-Time Observer Approach.

Although the formation control of multi-agent systems has been widely investigated from various aspects, the problem is still not well resolved, especially for the case of distributed output-feedback formation controller design without input information exchange among neighboring agents. Using relative output information, this paper presents a novel distributed reduced-order estimation of the formation error at a predefined time. Based on the proposed distributed observer, a neural-network-based formation controller is then designed for multi-agent systems with connected graphs. The results are verified by both theoretical demonstration and simulation example.

Retrospective review of acute post-tracheostomy complications and contributing risk factors.

OBJECTIVE: Tracheostomy is performed for various indications ranging from prolonged ventilation to airway obstruction. Many factors may play a role in the incidence of complications in the immediate post-operative period including patient-related factors. Chronic obstructive pulmonary disease and asthma are some of the most common pulmonary pathologies in the United States. The relationship between obstructive pulmonary diseases and acute post-tracheostomy complications has been incompletely studied. DESIGN: A retrospective chart review was designed in order to answer these objectives. Medical records were reviewed for the technique used, complications, and contributing patient factors. Post-operative complications were defined as any tracheostomy-related adverse event occurring within 14 days. SETTING: The study took place at an academic comprehensive cancer. PARTICIPANTS: Inclusion criteria included patients from January 2017 through December 2018 who underwent a tracheostomy. Exclusion criteria included presence of stomaplasty, total laryngectomy, and tracheostomies performed at outside hospitals. MAIN OUTCOME MEASURES: Patient factors examined included demographics, comorbidities, and body mass index with the primary outcome measured being the rate of tracheostomy complications. RESULTS: The most common indication for tracheostomy among the 321 patients that met inclusion criteria was airway obstruction or a head and neck cancer surgical procedure. Obstructive sleep apnea was associated with acute complications in bivariate analysis (29.4% complications, p = .003). Chronic obstructive pulmonary disease and asthma were not associated with acute complications in bivariate analysis (11.6% complications, p = .302). Among the secondary outcomes measured, radiation was associated with early complications occurring in post-operative days 0-6 (1.1%, p = .029). CONCLUSION: Patients with obstructive sleep apnea may have a higher risk of acute post-tracheostomy complications that might be due to the patient population at risk for obstructive sleep apnea. Patients with obstructive pulmonary pathologies such as asthma or chronic obstructive pulmonary disorder did not have an elevated risk of complications which is clinically significant when considering the utility of ventilation and tracheostomy in the management of acute respiratory failure secondary to these conditions.

Residual levels and health risk assessment of trace metals in Chinese resident diet.

Large-scale metal contamination across the food web is an intractable problem due to increasing pollutant emissions, atmospheric transport, and dry and wet deposition of elements. The present study focus on several trace metals that are rarely studied but have special toxicity, including tin (Sn), antimony (Sb), gold (Au), hafnium (Hf), palladium (Pd), platinum (Pt), ruthenium (Ru), tellurium (Te) and iridium (Ir). We investigated trace metals residues and distribution characteristics, and further evaluated the potential health risks from major daily food intakes in 33 cities in China. Sn, Sb, Ir, Hf, and Au were frequently detected in food samples with the concentrations ranged from ND (not detected) to 24.78 µg/kg ww (wet weight). Eggs exhibited the highest residual level of all detected metals (13.70 ± 14.70 µg/kg ww in sum), while the lowest concentrations were observed in vegetables (0.53 ± 0.17 µg/kg ww in sum). Sn accounting for more than 50% of the total trace metals concentration in both terrestrial and aquatic animal origin foods. In terrestrial plant origin foods, Sn and Ir were the most abundant elements. Hf and Au were the most abundant elements in egg samples. In addition, Sb and Ir showed a clear trophic dilution effect in terrestrial environments, while in aquatic ecosystems, Sn, Hf, and Au exhibited obvious trophic amplification effects. The calculated average estimated daily intake (EDI) via food consumption in five regions of China was 0.09 µg/(kg·day), implying the health risk of aforementioned elements was acceptable.

Indirect spectrum measurement via random phase modulation and detection in temporal domain.

Spectroscopy continues to provide possibilities for a deeper understanding of fundamental physical phenomena. Traditional spectral measurement method, dispersive Fourier transformation, is always limited by its realization condition (detection in the temporal far-field). Inspired by Fourier ghost imaging, we put forward an indirect spectrum measurement to overcome the limitation. The spectrum information is reconstructed via random phase modulation and near-field detection in the time domain. Since all operations are realized in the near-field region, the required length of dispersion fiber and optical loss are greatly reduced. Considering the application in spectroscopy, the length of required dispersion fiber, the spectrum resolution, the range of spectrum measurement and the requirement on bandwidth of photodetector are investigated.

The Bax inhibitor GmBI-1α interacts with a Nod factor receptor and plays a dual role in the legume-rhizobia symbiosis.

The gene networks surrounding Nod factor receptors that govern the symbiotic process between legumes and rhizobia remain largely unexplored. Here, we identify 13 novel GmNFR1α-associated proteins by yeast two-hybrid screening, and describe a potential interacting protein, GmBI-1α. GmBI-1α had the highest positive correlation with GmNFR1α in a co-expression network analysis, and its expression at the mRNA level in roots was enhanced by rhizobial infection. Moreover, GmBI-1α-GmNFR1α interaction was shown to occur in vitro and in vivo. The GmBI-1α protein was localized to multiple subcellular locations, including the endoplasmic reticulum and plasma membrane. Overexpression of GmBI-1α increased the nodule number in transgenic hairy roots or transgenic soybean, whereas down-regulation of GmBI-1α transcripts by RNA interference reduced the nodule number. In addition, the nodules in GmBI-1α-overexpressing plants became smaller in size and infected area with reduced nitrogenase activity. In GmBI-1α-overexpressing transgenic soybean, the elevated GmBI-1α also promoted plant growth and suppressed the expression of defense signaling-related genes. Infection thread analysis of GmBI-1α-overexpressing plants showed that GmBI-1α promoted rhizobial infection. Collectively, our findings support a GmNFR1α-associated protein in the Nod factor signaling pathway and shed new light on the regulatory mechanism of GmNFR1α in rhizobial symbiosis.

Regulatory pathway underpinning the development of encephalitis after simian immunodeficiency virus infection in rhesus macaques (Macaca mulatta).

BACKGROUND: Simian immunodeficiency virus (SIV) infection in rhesus macaques (Macaca mulatta) can lead to the development of SIV encephalitis (SIVE), which is closely related to human immunodeficiency virus (HIV)-induced dementia. METHODS: This was done by analyzing SIV and SIVE encephalitis in infected M. mulatta hippocampus samples from two microarray data sets, identifying two groups of common differentially expressed genes and predicting associated protein interactions. RESULTS: We found that eight genes-MX1, B2M, IFIT1, TYMP, STAT1, IFI44, ISG15, and IFI27-affected the negative regulation of biological processes, hepatitis C and Epstein-Barr viral infection, and the toll-like receptor signaling pathway, which mediate the development of encephalitis after SIV infection. In particular, STAT1 played a central role in the process by regulating biopathological changes during the development of SIVE. CONCLUSION: These findings provide a new theoretical basis for the treatment of encephalopathy after HIV infection by targeting STAT1.

The bound state in the continuum in flexible terahertz metasurfaces enabled sensitive biosensing.

The combination of a flexible device and novel electromagnetic resonances offers new dimensions to manipulate electromagnetic waves and promises new device functionalities. In this study, we experimentally demonstrate a flexible metasurface that can support the bound state in the continuum (BIC) in the terahertz regime. The metasurface consists of toroidal dipole resonant units on top of the flexible polyimide substrate, which can support a terahertz Friedrich-Wintgen BIC resonance, and the resonance characteristics can be tuned by changing the parameters of the coupling unit among two resonant modes. The BIC resonances under different bending conditions are analyzed and compared, showing decent mechanical robustness. The sensing application is demonstrated by combining Fetal Bovine Serum with the flexible BIC metasurface. The measured minimum detectable concentration is 0.007 mg mL-1. Benefiting from the mechanical flexibility and BIC resonance characteristics, our approach can effectively manipulate terahertz waves and have potential applications in the realization of multifunctional and flexible photonic devices.

A pretreatment prediction model of grade 3 tumors classed by the IASLC grading system in lung adenocarcinoma.

PURPOSE: The new grading system for invasive nonmucinous lung adenocarcinoma (LUAD) in the 2021 World Health Organization Classification of Thoracic Tumors was based on a combination of histologically predominant subtypes and high-grade components. In this study, a model for the pretreatment prediction of grade 3 tumors was established according to new grading standards. METHODS: We retrospectively collected 399 cases of clinical stage I (cStage-I) LUAD surgically treated in Tianjin Chest Hospital from 2015 to 2018 as the training cohort. Besides, the validation cohort consists of 216 patients who were collected from 2019 to 2020. These patients were also diagnosed with clinical cStage-I LUAD and underwent surgical treatment at Tianjin Chest Hospital. Univariable and multivariable logistic regression analyses were used to select independent risk factors for grade 3 adenocarcinomas in the training cohort. The nomogram prediction model of grade 3 tumors was established by R software. RESULTS: In the training cohort, there were 155 grade 3 tumors (38.85%), the recurrence-free survival of which in the lobectomy subgroup was better than that in the sublobectomy subgroup (P = 0.034). After univariable and multivariable analysis, four predictors including consolidation-to-tumor ratio, CEA level, lobulation, and smoking history were incorporated into the model. A nomogram was established and internally validated by bootstrapping. The Hosmer-Lemeshow test result was χ2 = 7.052 (P = 0.531). The C-index and area under the receiver operating characteristic curve were 0.708 (95% CI: 0.6563-0.7586) for the training cohort and 0.713 (95% CI: 0.6426-0.7839) for the external validation cohort. CONCLUSIONS: The nomogram prediction model of grade 3 LUAD was well fitted and can be used to assist in surgical or adjuvant treatment decision-making.

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell.

Environment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has potential to shed light on the origin of novel traits and adaptation to environmental change. However, molecular studies are scarce, and little is known about molecular mechanisms associated with plasticity. We investigated the gene regulatory network controlling predatory vs. non-predatory dimorphism in the nematode Pristionchus pacificus and found that it consists of genes of extremely different age classes. We isolated mutants in the conserved nuclear hormone receptor nhr-1 with previously unseen phenotypic effects. They disrupt mouth-form determination and result in animals combining features of both wild-type morphs. In contrast, mutants in another conserved nuclear hormone receptor nhr-40 display altered morph ratios, but no intermediate morphology. Despite divergent modes of control, NHR-1 and NHR-40 share transcriptional targets, which encode extracellular proteins that have no orthologs in Caenorhabditis elegans and result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. Major morphological changes in this gland cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations. Thus, the origin of feeding plasticity involved novelty at the level of genes, cells and behavior.