A Miniature Orthogonal Injection Ion Funnel (MO-IF) Providing Enhanced Performance for the Miniature Mass Spectrometer

The sensitivity of the miniature mass spectrometer (mini-MS) is largely restricted by the ion transmission in rough vacuum region. Even though various "in-line" ion transfer devices have improved mini-MS sensitivity, the severe dynamic gas is still weakening the efficiency of ion transmission in this region. Inspired by the "off-axis" ion funnel design in the lab-scale mass spectrometers, a miniature orthogonal injection ion funnel (MO-IF) was developed in this study for the mini-MS with a continuous atmospheric pressure interface. Capable of directing injected ions by 90° and then transport them forward to the downstream skimmer, the MO-IF enabled the separation of ions from the dynamic gas flow jetted out of the inlet capillary. The key factors were optimized for the MO-IF, including the effects of RF amplitude, DC electric fields, and the position of the repeller. Under optimized conditions, the MO-IF minimized the negative effects of dynamic gas and improved the ion transmission efficiency by ∼2-fold in comparison with the in-line injection ion funnel. As a result, a lower limit of detection of 0.5 ng/mL were obtained with good linearity for hypaconitine. Additionally, the MO-IF further decreased the buffer gas pressure in the second vacuum chamber and improved the mass resolution by 1.1-1.5 times at different scan rates.

Crosslinking-induced patterning of MOFs by direct photo- and electron-beam lithography

Metal-organic frameworks (MOFs) with diverse chemistry, structures, and properties have emerged as appealing materials for miniaturized solid-state devices. The incorporation of MOF films in these devices, such as the integrated microelectronics and nanophotonics, requires robust patterning methods. However, existing MOF patterning methods suffer from some combinations of limited material adaptability, compromised patterning resolution and scalability, and degraded properties. Here we report a universal, crosslinking-induced patterning approach for various MOFs, termed as CLIP-MOF. Via resist-free, direct photo- and electron-beam (e-beam) lithography, the ligand crosslinking chemistry leads to drastically reduced solubility of colloidal MOFs, permitting selective removal of unexposed MOF films with developer solvents. This enables scalable, micro-/nanoscale (≈70 nm resolution), and multimaterial patterning of MOFs on large-area, rigid or flexible substrates. Patterned MOF films preserve their crystallinity, porosity, and other properties tailored for targeted applications, such as diffractive gas sensors and electrochromic pixels. The combined features of CLIP-MOF create more possibilities in the system-level integration of MOFs in various electronic, photonic, and biomedical devices.

Development of a hypoxia-activated red-emission fluorescent probe for in vivo tumor microenvironment imaging and anti-tumor therapy

Hypoxia, a significant feature of the tumor microenvironment, is closely associated with tumor growth, metastasis, and drug resistance. In the field of tumor microenvironment analysis, accurately imaging and quantifying hypoxia - a critical factor associated with tumor progression, metastasis, and resistance to therapy - remains a significant challenge. Herein, a hypoxia-activated red-emission fluorescent probe, ODP, for in vivo imaging of hypoxia in the tumor microenvironment is presented. Among various imaging methods, optical imaging is particularly convenient due to its rapid response and high sensitivity. The ODP probe specifically targets nitroreductase (AzoR), an enzyme highly expressed in hypoxic cells, playing a vital role by catalyzing the cleavage of azo bonds. The optical properties of ODP exhibited excellent performance in terms of fluorescence enhancement, fluorescence lifetime (0.81 ns), and detection limit (0.86 µM) in response to SDT. Cell imaging experiments showed that ODP could effectively detect and image intracellular hypoxia and the imaging capability of ODP was studied under various conditions including cell migration, antioxidant treatment, and different incubation times. Through comprehensive in vitro and in vivo experiments, including cellular imaging and mouse tumor models, this work demonstrates the efficacy of ODP in accurately detecting and imaging hypoxia. Moreover, ODP's potential in inducing apoptosis in cancer cells offers a promising avenue for integrating diagnostic and therapeutic strategies in cancer treatment. This innovative approach not only contributes to the understanding and assessment of tumor hypoxia but also opens new possibilities for targeted cancer therapy.

Identification and structural analysis of dimeric chicken complement component 3d and its binding with chicken complement receptor 2

Complement component 3d (C3d), the final cleavage product of complement component C3, interacts with CR2 and thus plays a crucial role in linking the innate and adaptive immune systems. Additionally, human C3d executes various functions in its dimeric form, which is more effective than its monomeric form. In this study, we aimed to explored whether chicken C3d (chC3d) exhibits similar characteristics, namely dimerization and binding of dimeric chC3d to chicken CR2 (chCR2). We investigated the interaction and co-localization of chC3d with itself using coimmunoprecipitation and confocal laser scanning microscopy, respectively. Then, dimeric chC3d was detected using native polyacrylamide gel electrophoresis and western blotting, and its equilibrium dissociation constant KD (827 nM) was determined using surface plasmon resonance. Finally, the interaction modes of dimeric chC3d were identified using molecular docking simulations, which revealed that dimeric chC3d could crosslink with chCR2 receptor. Overall, our findings will facilitate future explorations of the chicken complement system.

Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila

Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.

A New Biocontrol Agent Bacillus velezensis SF334 against Rubber Tree Fungal Leaf Anthracnose and Its Genome Analysis of Versatile Plant Probiotic Traits

Natural rubber is an important national strategic and industrial raw material. The leaf anthracnose of rubber trees caused by the Colletotrichum species is one of the important factors restricting the yields of natural rubber. In this study, we isolated and identified strain Bacillus velezensis SF334, which exhibited significant antagonistic activity against both C. australisinense and C. siamense, the dominant species of Colletotrichum causing rubber tree leaf anthracnose in the Hainan province of China, from a pool of 223 bacterial strains. The cell suspensions of SF334 had a significant prevention effect for the leaf anthracnose of rubber trees, with an efficacy of 79.67% against C. siamense and 71.8% against C. australisinense. We demonstrated that SF334 can lead to the lysis of C. australisinense and C. siamense mycelia by causing mycelial expansion, resulting in mycelial rupture and subsequent death. B. velezensis SF334 also harbors some plant probiotic traits, such as secreting siderophore, protease, cellulase, pectinase, and the auxin of indole-3-acetic acid (IAA), and it has broad-spectrum antifungal activity against some important plant pathogenic fungi. The genome combined with comparative genomic analyses indicated that SF334 possesses most genes of the central metabolic and gene clusters of secondary metabolites in B. velezensis strains. To our knowledge, this is the first time a Bacillus velezensis strain has been reported as a promising biocontrol agent against the leaf anthracnose of rubber trees caused by C. siamense and C. australisinense. The results suggest that B. velezensis could be a potential candidate agent for the leaf anthracnose of rubber trees.

[Short-term outcomes of the TRIANGLE operation after neoadjuvant chemotherapy in locally advanced pancreatic cancer]

Objective: To investigate the safety and efficacy of the TRIANGLE operation after neoadjuvant chemotherapy in locally advanced pancreatic cancer(LAPC). Methods: This study is a retrospective case series analysis. Between January 2020 and December 2022, a total of 103 patients were diagnosed as LAPC who underwent neoadjuvant chemotherapy at the Pancreas Center, the First Affiliated Hospital of Nanjing Medical University. Among them, 26 patients (25.2%) underwent the TRIANGLE operation. There were 15 males and 11 females,with a age of (59±7) years (range: 49 to 74 years). The pre-treatment serum CA19-9(M(IQR)) was 248.8(391.6)U/ml (range: 0 to 1 428 U/ml),and the serum carcinoembryonic antigen was 4.1(3.8)μg/L(range: 1.4 to 13.4 μg/L). The neoadjuvant chemotherapy regimens included: mFOLFIRINOX regimen in 6 cases(23.1%), GnP regimen in 14 cases(53.8%), and mFOLFIRINOX+GnP regimen in 6 cases(23.1%). The follow-up duration extended until June 2023 or until the occurrence of the patient's death or loss to follow-up. The Kaplan-Meier method was employed to estimate the 1-year and 3-year overall survival rates. Results: After neoadjuvant chemotherapy,CA19-9 levels decreased by 92.3(40.1)%(range:2.1% to 97.7%). Evaluation of the response to treatment revealed 13 cases(50.0%) of stable disease,11 cases(42.3%) of partial response,and 2 cases(7.7%) of complete response. The surgical operation consisted of 12 cases(46.2%) of pancreaticoduodenectomy,12 cases(46.2%) of distal pancreatectomy,and 2 cases(7.7%) of total pancreatectomy. Margin determination was based on the "standardised pathology protocol" and the "1 mm" principle. No R2 and R1(direct) resections were observed,while the R0 resection rate was 61.5%(16/26), and the R1(1 mm) resection rate was 38.5%(10/26).The R1(1 mm) resection rates for the anterior margin,posterior margin,transected margin,portal vein groove margin,and uncinate margin were 23.1%(6/26),19.2%(5/26),12.5%(3/24),2/14, and 1/12, respectively. The overall postoperative complication rate was 57.8%(15/26),with major complications including grade B/C pancreatic fistula 25.0%(6/24,excluding 2 cases of total pancreatectomy),delayed gastric emptying in 23.1%(6/26),wound complications 11.5%(3/26),postoperative hemorrhage 7.7%(2/26), chylous fistula 7.7%(2/26) and bile fistula 3.8%(1/26). No reoperation was performed during the perioperative period(<90 days). One patient died on the 32nd day postoperatively due to a ruptured pseudoaneurysm. A total of 25 patients were followed up,with a follow-up time of 21(24)months(range: 8 to 42 months). During the follow-up period,8 cases(32.0%) died due to tumor recurrence and metastasis,while 17 patients(68.0%) remained alive,including 11 cases of disease-free survival,5 cases of distant metastasis,and 1 case of local recurrence. The overall survival rates at 1- and 3-year after the initiation of neoadjuvant chemotherapy were 95.8% and 58.9%, respectively. The overall survival rates at 1- and 3-year after surgery were 77.7% and 57.8%, respectively. Conclusion: Performing pancreatoduodenectomy according to the Heidelberg triangle protocol in LAPC patients after neoadjuvant chemotherapy might increase the R0 resection rate without increasing perioperative mortality or the incidence of major postoperative complications.

Vapor-assisted synthesis of the MOF-74 metal-organic framework family from zinc, cobalt, and magnesium oxides

In this work, we investigate the vapor-assisted synthesis of the metal-organic framework MOF-74 starting from three metal oxides (ZnO, CoO, and MgO). Depending on the nature of the added vapor (H2O, DMF, DMSO), the metal oxide, and the temperature, the outcome of the reaction can be directed towards the desired porous phase. Ex situ and in situ XRD measurements reveal the formation of an intermediate phase during the reaction of MgO with H4dobdc, while the MOF-74 phase forms directly for ZnO and CoO. The reduced CO2 uptake of the resulting materials compared to solvothermally prepared MOFs might be offset by the convenience of the presented route and the promise of a high space time yield.

[Distal pancreatectomy with celiac axis resection for pancreatic body cancer: a single center review of 89 consecutive cases]

Objective: To investigate the clinical efficacy of distal pancreatectomy with celiac axis resection(DP-CAR). Methods: A total of 89 consecutive patients (50 males and 39 females) who were diagnosed with pancreatic body cancer and underwent DP-CAR in Pancreas Center,First Affiliated Hospital of Nanjing Medical University between September 2013 and June 2022 were retrospectively reviewed. There were 50 males and 39 females,with age(M(IQR)) of 63(12) years(range:43 to 81 years). Perioperative parameters,pathology results and follow-up data of these patients were analyzed,χ2 or Fisher's test for categorical data while the Wilcoxon test for quantitative data. Survival results were estimated by the Kaplan-Meier survival method. Results: Among 89 cases,cases combined with portal vein-superior mesenteric vein or organ resection accounted for 22.5% (20/89) and 42.7% (38/89),respectively. The operative time,blood loss and postoperative hospital stay were 270 (110) minutes,300 (300) ml and 13 (10) days,respectively. The overall morbidity rate was 67.4% (60/89) while the major morbidity was 11.2% (10/89). The increase rate in transient liver enzymes was 42.7% (38/89),3.4% (3/89) for liver failure,53.9% (48/89) for clinically relevant postoperative pancreatic fistula,1.1% (1/89) for bile leak,3.4% (3/89) for chylous leak of grade B and C,11.2% (10/89) for abdominal infection,9.0% (8/89) for postoperative hemorrhage of grade B and C,4.5% (4/89) for delayed gastric emptying,6.7% (6/89) for deep vein thrombosis,3.4% (3/89) for reoperation,4.5% (4/89)for hospital mortality,7.9% (7/89) for 90-day mortality. The pathological type was pancreatic cancer for all 89 cases and pancreatic ductal adenocarcinoma made up 92.1% (82/89). The tumor size was 4.8(2.0) cm, ranging from 1.5 to 12.0 cm. The number of lymph nodes harvested was 14 (13)(range:2 to 33),with a positive lymph node rate of 13.0% (24.0%). The resection R0 rate was 30.0% (24/80) and the R1 (<1 mm) rate was 58.8% (47/80). The median overall survival time was 21.3 months (95%CI: 15.6 to 24.3) and the median disease-free survival time was 19.1 months (95%CI: 11.7 to 25.1). The overall survival at 1-year and 2-year were 69.60% and 39.52%. The median survival time of 58 patients with adjuvant chemotherapy was 24.3 months (95%CI: 17.8 to 32.3) while that of 13 patients without any kind of adjuvant therapy was 8.4 months (95%CI: 7.3 to 22.3). Seven patients accepted neoadjuvant chemotherapy and there was no significant morbidity among them,with a resection rate of R0 of 5/7. Conclusion: DP-CAR is safe and feasible for selective cases,which could be more valuable in improving long-term survival when combined with (neo) adjuvant therapy.

Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications

The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.

A chromosome-scale genome and proteome draft of Tremella fuciformis

In this study, we first reported a high-quality chromosome-scale genome of Tremella fuciformis using Pacbio HiFi sequencing combining Hi-C technology. According to 21.6 Gb PacBio HiFi reads and 18.1 Gb Hi-C valid reads, we drafted a T. fuciformis genome of 27.38 Mb assigned to 10 chromosomes, with the contig N50 of 2.28 Mb, GC content of 56.51 %, BUSCOs completeness of 93.1 % and consensus quality value of 33.7. The following annotation of genomic components predicted 5,171 repeat sequences, 283 RNAs, and 10,150 protein-coding genes. Next, the intracellular proteins at three differential life stages of T. fuciformis (conidium, hyphal and fruiting body) were identified by the shot-gun proteomics. 6,823 canonical proteins (68.1 % of predicted proteome) have been identified with protein FDR cut-off of 0.01, establishing the first proteome draft of predicted protein-coding genes of T. fuciformis. Finally, 24 T. fuciformis polysaccharides (TPS) biosynthesis-related genes in mycelia were identified by comparative transcriptomics and proteomics, which may be more active than in conidium and revealed the TPS biosynthesis process in mycelia. This present study elucidated T. fuciformis genome composition and organization, drafted its associated proteome, and provided a genome-view of TPS biosynthesis, which will be a powerful platform for biological and genetic studies in T. fuciformis.

Retinal Vessel Density and Retinal Nerve Fiber Layer Thickness: A Prospective Study of One-Year Follow-Up of Patients with Parkinson's Disease

Objective

This study aims to compare the superficial vascular density from the macular region and the retinal nerve fiber layer (RNFL) thickness from the optic disc region between Parkinson's disease (PD) patients and controls.

Methods

We enrolled 56 idiopathic PD patients, totaling 86 eyes (PD group), and 45 sex- and age-matched healthy individuals, amounting to 90 eyes (control group). All subjects underwent examination using Zeiss wide-field vascular optical coherence tomography (OCT) (Cirrus HD-OCT 5000 Carl Zeiss, Germany), with a scanning range of 3 mm × 3 mm. We divided the images into two concentric circles with diameters of 1 mm and 3 mm at the macular fovea's center. Patients with PD were evaluated during their "off" phase using the Unified Parkinson's Disease Rating Scale III (UPDRS-III) and the Hoehn-Yahr scale (H-Y scale) to assess disease severity.

Results

The PD group exhibited significantly lower RNFL thickness (106.13±12.36 μm) compared to the control group (115.95±11.37 μm, P < 0.05). Similarly, the superficial retinal vessel length density was significantly lower in the PD group (20.7 [19.62, 22.17] mm-1) than in the control group (21.79±1.16 mm-1, P < 0.05). Correlation analysis revealed a negative correlation between RNFL thickness and UPDRS III score (rs=-0.036, P=0.037), and RNFL thickness tended to decrease with increasing severity of movement disorders. However, during the 6 and 12-month follow-up of some PD patients, we observed no progressive thinning of the RNFL or decreased superficial vascular density.

Conclusion

PD patients show retinal structural damage characterized by RNFL thinning and reduced retinal vessel length density. However, RNFL thickness did not correlate with vascular density nor did it decrease with the disease's progression.

Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila

Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.

Antagonistic transcriptome profile reveals potential mechanisms of action on Xanthomonas oryzae pv. oryzicola by the cell-free supernatants of Bacillus velezensis 504, a versatile plant probiotic bacterium

Bacterial leaf streak (BLS) of rice is a severe disease caused by the bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) that has gradually become the fourth major disease on rice in some rice-growing regions in southern China. Previously, we isolated a Bacillus velezensis strain 504 that exhibited apparent antagonistic activity against the Xoc wild-type strain RS105, and found that B. velezensis 504 was a potential biocontrol agent for BLS. However, the underlying mechanisms of antagonism and biocontrol are not completely understood. Here we mine the genomic data of B. velezensis 504, and the comparative transcriptomic data of Xoc RS105 treated by the cell-free supernatants (CFSs) of B. velezensis 504 to define differentially expressed genes (DEGs). We show that B. velezensis 504 shares over 89% conserved genes with FZB42 and SQR9, two representative model strains of B. velezensis, but 504 is more closely related to FZB42 than SQR9, as well as B. velezensis 504 possesses the secondary metabolite gene clusters encoding the essential anti-Xoc agents difficidin and bacilysin. We conclude that approximately 77% of Xoc RS105 coding sequences are differentially expressed by the CFSs of B. velezensis 504, which significantly downregulates genes involved in signal transduction, oxidative phosphorylation, transmembrane transport, cell motility, cell division, DNA translation, and five physiological metabolisms, as well as depresses an additional set of virulence-associated genes encoding the type III secretion, type II secretion system, type VI secretion system, type IV pilus, lipopolysaccharides and exopolysaccharides. We also show that B. velezensis 504 is a potential biocontrol agent for bacterial blight of rice exhibiting relative control efficiencies over 70% on two susceptible cultivars, and can efficiently antagonize against some important plant pathogenic fungi including Colletotrichum siamense and C. australisinense that are thought to be the two dominant pathogenic species causing leaf anthracnose of rubber tree in Hainan province of China. B. velezensis 504 also harbors some characteristics of plant growth-promoting rhizobacterium such as secreting protease and siderophore, and stimulating plant growth. This study reveals the potential biocontrol mechanisms of B. velezensis against BLS, and also suggests that B. velezensis 504 is a versatile plant probiotic bacterium.

Current advances in the molecular regulation of abiotic stress tolerance in sorghum via transcriptomic, proteomic, and metabolomic approaches

Sorghum (Sorghum bicolor L. Moench), a monocot C4 crop, is an important staple crop for many countries in arid and semi-arid regions worldwide. Because sorghum has outstanding tolerance and adaptability to a variety of abiotic stresses, including drought, salt, and alkaline, and heavy metal stressors, it is valuable research material for better understanding the molecular mechanisms of stress tolerance in crops and for mining new genes for their genetic improvement of abiotic stress tolerance. Here, we compile recent progress achieved using physiological, transcriptome, proteome, and metabolome approaches; discuss the similarities and differences in how sorghum responds to differing stresses; and summarize the candidate genes involved in the process of responding to and regulating abiotic stresses. More importantly, we exemplify the differences between combined stresses and a single stress, emphasizing the necessity to strengthen future studies regarding the molecular responses and mechanisms of combined abiotic stresses, which has greater practical significance for food security. Our review lays a foundation for future functional studies of stress-tolerance-related genes and provides new insights into the molecular breeding of stress-tolerant sorghum genotypes, as well as listing a catalog of candidate genes for improving the stress tolerance for other key monocot crops, such as maize, rice, and sugarcane.

Chromosome-level wild Hevea brasiliensis genome provides new tools for genomic-assisted breeding and valuable loci to elevate rubber yield

The rubber tree (Hevea brasiliensis) is grown in tropical regions and is the major source of natural rubber. Using traditional breeding approaches, the latex yield has increased by sixfold in the last century. However, the underlying genetic basis of rubber yield improvement is largely unknown. Here, we present a high-quality, chromosome-level genome sequence of the wild rubber tree, the first report on selection signatures and a genome-wide association study (GWAS) of its yield traits. Population genomic analysis revealed a moderate population divergence between the Wickham clones and wild accessions. Interestingly, it is suggestive that H. brasiliensis and six relatives of the Hevea genus might belong to the same species. The selective sweep analysis found 361 obvious signatures in the domesticated clones associated with 245 genes. In a 15-year field trial, GWAS identified 155 marker-trait associations with latex yield, in which 326 candidate genes were found. Notably, six genes related to sugar transport and metabolism, and four genes related to ethylene biosynthesis and signalling are associated with latex yield. The homozygote frequencies of the causal nonsynonymous SNPs have been greatly increased under selection, which may have contributed to the fast latex yield improvement during the short domestication history. Our study provides insights into the genetic basis of the latex yield trait and has implications for genomic-assisted breeding by offering valuable resources in this new domesticated crop.

Sequential Sol-Gel Self-Assembly and Nonclassical Gel-Crystal Transformation of the Metal-Organic Framework Gel

Metal-organic framework (MOF) gel, an emerging subtype of MOF structure, is unique in formation and function; however, its evolutionary process remains elusive. Here, the evolution of a model gel-based MOF, UiO-66(Zr) gel, is explored by demonstrating its sequential sol-gel self-assembly and nonclassical gel-crystal transformation. The control of the sol-gel process enables the observation and characterization of structures in each assembly stage (phase-separation, polycondensation, and hindered-crystallization) and facilitates the preparation of hierarchical materials with giant mesopores. The gelation mechanism is tentatively attributed to the formation of zirconium oligomers. By further utilizing the pre-synthesized gel, the nonclassical gel-crystal transformation is achieved by the modulation in an unconventional manner, which sheds light on crystal intermediates and distinct crystallization motions ("growth and splitting" and "aggregation and fusion"). The overall sol-gel and gel-crystal evolutions of UiO-66(Zr) enrich self-assembly and crystallization domains, inspire the design of functional structures, and demand more in-depth research on the intermediates in the future.

Risk factors of delayed gastric emptying in patients after pancreaticoduodenectomy: a comprehensive systematic review and meta-analysis

BACKGROUND

Delayed gastric emptying (DGE) is a common complication after pancreaticoduodenectomy (PD) or pylorus preserving pancreaticoduodenectomy (PPPD). However, its risk factors are still unclear. This meta-analysis aimed to identify the potential risk factors of DGE among patients undergoing PD or PPPD.

METHODS

We searched PubMed, EMBASE, Web of Science, Cochrane Library, Google Scholar and ClinicalTrial.gov for studies that examined the clinical risk factors of DGE after PD or PPPD from inception through July 31, 2022. We pooled odds ratios (ORs) with 95% confidence intervals (CIs) using random-effects or fixed-effects models. We also performed heterogeneity, sensitivity, and publication bias analyses.

RESULTS

The study included a total of 31 research studies, which involved 9205 patients. The pooled analysis indicated that out of 16 non-surgical related risk factors, three risk factors were found to be associated with an increased incidence of DGE. These risk factors were older age (OR 1.37, P=0.005), pre-operative biliary drainage (OR 1.34, P=0.006), and soft pancreas texture (OR 1.23, P=0.04). On the other hand, patients with dilated pancreatic duct (OR 0.59, P=0.005) had a decreased risk of DGE. Among 12 operation related risk factors，more blood loss (OR 1.33, P=0.01), post-operative pancreatic fistula (POPF) (OR 2.09, P<0.001), intra-abdominal collection (OR 3.58 , P=0.001), and intra-abdominal abscess (OR 3.06, P<0.0001) were more likely to cause DGE. However, our data also revealed 20 factors did not support stimulative factors influencing DGE.

CONCLUSION

Age, pre-operative biliary drainage, pancreas texture, pancreatic duct size, blood loss, POPF, intra-abdominal collection and intra-abdominal abscess are significantly associated with DGE. This meta-analysis may have utility in guiding clinical practice for improvements for screening patients with high risk of DGE and selecting appropriate treatment measure.

Identification and Characterization of chCR2, a Protein That Binds Chicken Complement Component 3d

Complement receptor type 2 (CR2) is an important membrane molecule expressed on B cells and follicular dendritic cells. Human CR2 has been shown to play a critical role in bridging the innate complement-mediated immune response with adaptive immunity by binding complement component 3d (C3d). However, the chicken CR2 (chCR2) gene has not been identified or characterized. In this study, unannotated genes that contain short consensus repeat (SCR) domains were analyzed based on RNA sequencing data for chicken bursa lymphocytes, and a gene with &gt;80% homology to CR2 from other bird species was obtained. The gene consisted of 370 aa and was much smaller than the human CR2 gene because 10–11 SCRs were missing. The gene was then demonstrated as a chCR2 that exhibited high binding activity to chicken C3d. Further studies revealed that chCR2 interacts with chicken C3d through a binding site in its SCR1–4 region. An anti-chCR2 mAb that recognizes the epitope 258CKEISCVFPEVQ269 was prepared. Based on the anti-chCR2 mAb, the flow cytometry and confocal laser scanning microscopy experiments confirmed that chCR2 was expressed on the surface of bursal B lymphocytes and DT40 cells. Immunohistochemistry and quantitative PCR analyses further indicated that chCR2 is predominantly expressed in the spleen, bursa, and thymus, as well as in PBLs. Additionally, the expression of chCR2 varied according to the infectious bursal disease virus infection status. Collectively, this study identified and characterized chCR2 as a distinct immunological marker in chicken B cells.

Toward Exploring and Utilizing the Nutritional and Functional Properties of Cereal Crops

Cereal crops are of great importance in the development of human civilization and fall into two groups, major crops and minor crops [...].

Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila

Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila because Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by determining Tet DNA-binding sites throughout the genome and by mapping the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC-modified sites can be found along the entire transcript and are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are frequently involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and are sensitized to reduced levels of slit. Both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs, primarily in developing nerve cells.

Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics

RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.

The association between paraspinal muscle degeneration and osteoporotic vertebral compression fracture severity in postmenopausal women

BACKGROUND

According to reports in the literature, osteoporotic vertebral compression fracture (OVCF) is associated with paraspinal muscle degeneration; however, the association between the severity of OVCF and paraspinal muscle degeneration is not clear.

OBJECTIVE

The purpose of this study was to investigate the association between paraspinal muscle degeneration and OVCF severity in postmenopausal women.

METHODS

Three hundred and seventy-six MRI images from 47 patients were collected and analyzed. Sagittal and axial coronal T2-weighted images were used to measure the fractured vertebra sagittal cross-sectional area (FSCSA), the adjacent normal vertebral body sagittal cross-sectional area (NSCSA), paraspinal muscle cross-sectional area (CSA), and the fat cross-sectional area (FCSA). The ratio of fractured vertebra compressed sagittal cross-sectional area (RCSA) and fatty infiltration ratio (FIR) was subsequently calculated. The formulas for RCSA and FIR calculations are as follows: RCSA = (NSCSA-FSCSA)/NSCSA; FIR = FCSA/CSA. RCSA and FIR represent the severity of OVCF and paraspinal muscle degeneration, respectively.

RESULTS

The correlation between paraspinal muscle degeneration and OVCF severity was analyzed using the Pearson correlation, and multiple regression analysis was performed to explore related risk factors. OVCF severity was closely associated with paraspinal muscle degeneration (L3/4 FIR r= 0.704, P< 0.05; L4/5 FIR r= 0.578, P< 0.05; L5/S1 FIR r= 0.581, P< 0.05). Multiple regression analysis demonstrated that the risk factor for OVCF severity was L3/4 FIR (β= 0.421, P= 0.033).

CONCLUSION

OVCF severity was associated with the FIR of paraspinal muscles, and L3/4 FIR was a predictive factor for OVCF severity in postmenopausal women.

CircSTX6 promotes pancreatic ductal adenocarcinoma progression by sponging miR-449b-5p and interacting with CUL2

BACKGROUND

circular RNAs (circRNAs) have been reported to play crucial roles in the biology of different cancers. However, little is known about the function of circSTX6 (hsa_circ_0007905) in pancreatic ductal adenocarcinoma (PDAC).

METHODS

circSTX6, a circRNA containing exons 4, 5, 6 and 7 of the STX6 gene, was identified by RNA sequencing and detected by quantitative reverse transcription PCR (qRT-PCR). The biological function of circSTX6 was assessed in vitro and in vivo. The relationship between circSTX6 and miR-449b-5p was confirmed by biotin-coupled circRNA capture, fluorescence in situ hybridization (FISH) and luciferase reporter assays. The interaction of circSTX6 with Cullin 2 (CUL2) was verified by RNA-protein RNA pull-down, RNA immunoprecipitation (RIP) and western blotting assays.

RESULTS

circSTX6 was frequently upregulated in PDAC tissues, and circSTX6 overexpression promoted tumor proliferation and metastasis both in vitro and in vivo. Furthermore, circSTX6 expression was associated with tumor differentiation and N stage. Mechanistically, circSTX6 regulated the expression of non-muscle myosin heavy chain 9 (MYH9) by sponging miR-449b-5p. Moreover, circSTX6 was confirmed to participate in the ubiquitin-dependent degradation of hypoxia-inducible factor 1-alpha (HIF1A) by interacting with CUL2 and subsequently accelerating the transcription of MYH9.

CONCLUSIONS

Our findings indicate that circSTX6 facilitates proliferation and metastasis of PDAC cells by regulating the expression of MYH9 through the circSTX6/miR-449b-5p axis and circSTX6/CUL2/HIF1A signaling pathway. Therefore, circSTX6 could serve as a potential therapeutic target for the treatment of PDAC.

CA9-Related Acidic Microenvironment Mediates CD8+ T Cell Related Immunosuppression in Pancreatic Cancer

PURPOSE

This study aims to integrate pancreatic cancer TCGA, GEO, and single-cell RNA-sequencing (scRNA-seq) datasets, and explore the potential prognostic markers and underlying mechanisms of the immune microenvironment of pancreatic cancer through bioinformatics methods, in vitro and in vivo assays.

METHODS

Expression data and clinicopathological data of pancreatic cancer TCGA, GEO (GSE131050), single cell sequencing (PAAD_CRA001160) dataset were downloaded. We used R/Bioconductor edgeR for differential expression analysis. ClusterProfiler was utilized to perform GO enrichment analysis on differentially expressed genes. The online software CIBERSORT was used to reanalyze the mRNA expression data of pancreatic cancer. CellRanger, RunPCA, FindNeighbors, FindClusters, RunTSNE and RunUMAP were used to perform preprocessing, cell clustering and expression profile analysis on single-cell sequencing data sets. We analyzed intracellular pH with or without CA9 inhibitor SLC-0111. Indirect co-culture model of human pancreatic cancer cell lines and healthy individual-derived PBMCs were used to determine the effect of CA9-related Acidic Microenvironment on CD8+ T cells.

RESULTS

The CIBERSORT analysis of TCGA pancreatic cancer transcriptome sequencing data showed that among the 22 immune microenvironment components, CD8+ T cell infiltration was significantly correlated with the prognosis of pancreatic cancer patients. The differential expression analysis of the TCGA data grouped by the level of CD8+ T cell infiltration indicates that the expression of carbonic anhydrase 9 (CA9) is the most significant, and the survival analysis suggests that CA9 is associated with the overall survival of pancreatic cancer. TCGA data and GEO data set GSE131050 expression correlation analysis suggests that CA9 and CD8 expression are closely related. Pancreatic cancer single-cell sequencing data set PAAD_CRA001160 analysis results show that CA9 is mainly expressed in pancreatic cancer cell clusters, and the expression of the cancer cell subgroup CA9 in the single-cell data set is correlated with CD8+ T cell infiltration.

CONCLUSION

Pancreatic cancer cells may inhibit the infiltration of CD8+ T cells through CA9. Further exploration of its related mechanisms can be used to explore the immune escape pathway of pancreatic cancer and provides new perspectives immune targeted therapy.

[Comparative clinical efficacy analysis of pancreatoduodenectomy for distal bile duct and pancreatic head cancer: a report of 1 005 cases]

Objective: To compare and analyze the clinical efficacy of pancreaticoduodenectomy for distal bile duct cancer and pancreatic head cancer. Methods: Clinical data of 1 005 patients who underwent pancreaticoduodenectomy and postoperative pathological examination confirmed the diagnosis of distal bile duct cancer and pancreatic head cancer at the Pancreas Center of the First Affiliated Hospital of Nanjing Medical University from January 2016 to December 2020 were analyzed retrospectively. There were 112 cases in the distal bile duct cancer group, 71 males and 41 females,with age (M(IQR)) of 65(15) years(range: 40 to 87 years); 893 cases in the pancreatic head cancer group, 534 males and 359 females,with age of 64(13)years(range: 16 to 91 years). The differences between clinicopathological characteristics and postoperative overall survival of the two groups were analyzed by χ² test, Fisher's exact probability method, rank sum test or log-rank test, respectively. The difference in postoperative overall survival between the two groups was compared using Kaplan-Meier method after propensity score matching (1∶1). Results: Compared with the pancreatic head cancer group,the distal bile duct cancer group had shorter operative time (240.0(134.0) minutes vs. 261.0(97.0) minutes, Z=2.712, P=0.007),less proportion of combined venous resection (4.5% (5/112) vs. 19.4% (173/893), χ²=15.177,P<0.01),smaller tumor diameter (2.0(1.0) cm vs. 3.0(1.5) cm,Z=10.567,P<0.01),higher well/moderate differentiation ratio (51.4% (56/112) vs. 38.0% (337/893), χ²=7.328, P=0.007),fewer positive lymph nodes (0(1) vs. 1(3), Z=5.824, P<0.01),and higher R0 resection rate (77.7% (87/112) vs. 38.3%(342/893), χ²=64.399, P<0.01),but with a higher incidence of overall postoperative complications (50.0% (56/112) vs. 36.3% (324/892), χ²=7.913,P=0.005),postoperative pancreatic fistula (28.6% (32/112) vs. 13.9% (124/893), χ²=16.318,P<0.01),and postoperative abdominal infection (21.4% (24/112) vs. 8.6% (77/892), χ²=18.001,P<0.01). After propensity score matching, there was no statistical difference in postoperative overall survival time between patients in the distal bile duct cancer group and the pancreatic head cancer group (50.6 months vs. 35.1 months,Z=1.640,P=0.201),and multifactorial analysis showed that tumor site was not an independent risk factor affecting the prognosis of patients in both groups after matching (HR=0.73,95%CI:0.43 to 1.23,P=0.238). Conclusions: Patients with distal bile duct cancer are more likely to benefit from early diagnosis and surgical treatment than patients with pancreatic head cancer,but with a relative higher postoperative complication rates. The different tumor origin site is not an independent risk factor for prognosis of patients with distal bile duct cancer and pancreatic head cancer after propensity score matching.

Prevalence of Germline Sequence Variations Among Patients With Pancreatic Cancer in China

IMPORTANCE

A higher incidence of pancreatic cancer has been reported in the Chinese population compared with the White population, but genetic differences are unknown to date. Large-sample germline testing for both familial and sporadic pancreatic cancers has been conducted predominantly in White populations, whereas similar studies in Chinese populations are limited.

OBJECTIVE

To assess the prevalence of germline sequence variations in patients with pancreatic diseases in China.

DESIGN, SETTING, AND PARTICIPANTS

This genetic association study was a case series that included genetic data from patients with pancreatic ductal adenocarcinoma (PDAC) or non-PDAC pancreatic diseases seen at The First Affiliated Hospital of Nanjing Medical University in Nanjing, China, between January 2006 and December 2017 (Nanjing cohort). Comparator group data were obtained for a US cohort from Johns Hopkins Hospital (JHH), a population from East Asia from the Exome Aggregation Consortium (ExAC) database, and the larger population from China from the ChinaMAP database. Data were updated and analyzed in July 2021.

MAIN OUTCOMES AND MEASURES

Next-generation sequencing technology was used to examine the prevalence of deleterious variations in 59 genes of the included Chinese patients with DNA extracted from peripheral blood samples. The Fisher exact test was used to assess differences among the frequencies of germline variations in the study patients vs the comparator groups.

RESULTS

A total of 1009 patients with PDAC (627 [62.1%] male; mean [SD] age, 62.8 [10.2] years) and 885 with non-PDAC diseases (477 [53.9%] male; mean [SD] age, 52.0 [15.9] years) from the Nanjing cohort were included for genetic analysis; all were Han Chinese individuals. Pathogenic variations were detected in 63 patients with PDAC (6.2%; 95% CI, 4.7%-7.7%). Variations in BRCA2 (odds ratio [OR], 3.2; 95% CI, 1.4-7.7; P = .008) and PALB2 (OR, 5.2; 95% CI, 1.6-17.0; P = .007) were significantly associated with pancreatic risk in the Nanjing cohort. Pathogenic variants of genes associated with homologous recombination DNA damage repair, including ATM, BRCA1/2, PALB2, BRIP1, FANCA, FANCC, RAD51D, and XRCC2, were found in 34 patients with PDAC (3.4%). No Ashkenazi Jewish-specific BRCA2 variation (p.Ser1982fs) was detected. The odds ratio of a SPINK1 variation in patients with PDAC was 3.2 (95% CI, 1.8-5.7; P < .001) in the Nanjing cohort compared with the ExAC cohort. Variations in the pancreatic secretory enzyme genes CPA1 and CPB1 were not detected in the Nanjing cohort.

CONCLUSIONS AND RELEVANCE

In this genetic association study, sporadic pancreatic cancer was associated with pathogenic germline variations in a cohort from China. These findings provide insights into the genetic background of pancreatic cancer in the Han Chinese population with PDAC.

Vapor-Phase Processing of Metal-Organic Frameworks

ConspectusPorous metal-organic frameworks (MOFs), formed from organic linkers and metal nodes, have attracted intense research attention. Because of their high specific surface areas, uniform and adjustable pore sizes, and versatile physicochemical properties, MOFs have shown disruptive potential in adsorption, catalysis, separation, etc. For many of these applications, MOFs are synthesized solvothermally as bulk powders and subsequently shaped as pellets or extrudates. Other applications, such as membrane separations and (opto)electronics, require the implementation of MOFs as (patterned) thin films. Most thin-film formation methods are adapted from liquid-phase synthesis protocols. Precursor transport and nucleation are difficult to control in these cases, often leading to particle formation in solution. Moreover, the use of solvents gives rise to environmental and safety challenges, incompatibility issues with some substrates, and corrosion issues in the case of dissolved metal salts. In contrast, vapor-phase processing methods have the merits of environmental friendliness, control over thickness and conformality, scalability in production, and high compatibility with other workflows.In this Account, we outline some of our efforts and related studies in the development and application of vapor-phase processing of crystalline MOF materials (MOF-VPP). We first highlight the advances and mechanisms in the vapor-phase deposition of MOFs (MOF-VPD), mainly focusing on the reactions between a linker vapor and a metal-containing precursor layer. The characteristics of the obtained MOFs (thickness, porosity, crystallographic phase, orientation, etc.) and the correlation of these properties with the deposition parameters (precursors, temperatures, humidity, post-treatments, etc.) are discussed. Some in situ characterization methods that contributed to a fundamental understanding of the involved mechanisms are included in the discussion. Second, four vapor-phase postsynthetic functionalization (PSF) methods are summarized: linker exchange, guest loading, linker grafting, and metalation. These approaches eliminate potential solubility issues and enable fast diffusion of reactants and guests as well as a high loading or degree of exchange. Vapor-phase PSF provides a platform to modify the MOF porosity or even introduce new functionalities (e.g., luminescence photoswitching and catalytic activity). Third, since vapor-phase processing methods enable the integration of MOF film deposition into a (micro)fabrication workflow, they facilitate a range of applications with improved performance (low-k dielectrics, sensors, membrane separations, etc.). Finally, we provide a discussion on the limitations, challenges, and further opportunities for MOF-VPP. Through the discussion and analysis of the vapor-phase processing strategies as well as the underlying mechanisms in this Account, we hope to contribute to the development of the controllable synthesis, functionalization, and application of MOFs and related materials.

Identification of FEZ2 as a potential oncogene in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the common malignant tumors with high lethal rate and poor prognosis. Dysregulation of many genes have been reported to be involved in the occurrence and development of PDAC. However, as a highly conserved gene in eukaryotes, the role of Fasciculation and Elongation protein Zeta 2 (FEZ2) in pancreatic cancer progression is not clear. In this study, we identified the oncogenic effect of FEZ2 on PDAC. By mining of The Cancer Genome Atlas (TCGA) database, we found that FEZ2 was upregulated in PDAC tissues and FEZ2 expression was negatively regulated by its methylation. Moreover, high expression and low methylation of FEZ2 correlated with poor prognosis in PDAC patients. Besides, we found that FEZ2 could promote PDAC cells proliferation, migration and 5-FU resistance in vitro. Furthermore, Gene pathway enrichment analysis demonstrated a positive correlation between Wnt signaling activation and FEZ2 expression in PDAC patients. Western blot showed that FEZ2 knockdown significantly suppressed β-catenin expression. Collectively, our finding revealed that FEZ2 functioned as a potential oncogene on PDAC progression and migration, and the expression of FEZ2 had guidance value for the treatment and chemotherapy program of PDAC patients.

The transcriptional dynamics during de novo shoot organogenesis of Ma bamboo (Dendrocalamus latiflorus Munro): implication of the contributions of the abiotic stress response in this process

De novo shoot organogenesis is an important biotechnological tool for fundamental studies in plant. However, it is difficult in most bamboo species, and the genetic control of this highly dynamic and complicated regeneration process remains unclear. In this study, based on an in-depth analysis at the cellular level, the shoot organogenesis from calli of Ma bamboo (Dendrocalamus latiflorus Munro) was divided into five stages. Subsequently, single-molecule long-read isoform sequencing of tissue samples pooled from all five stages was performed to generate a full-length transcript landscape. A total of 83 971 transcripts, including 73 209 high-quality full-length transcripts, were captured, which served as an annotation reference for the subsequent RNA sequencing analysis. Time-course transcriptome analysis of samples at the abovementioned five stages was conducted to investigate the global gene expression atlas showing genome-wide expression of transcripts during the course of bamboo shoot organogenesis. K-means clustering analysis and stage-specific transcript identification revealed important dynamically expressed transcription regulators that function in bamboo shoot organogenesis. The majority of abiotic stress-responsive genes altered their expression levels during this process, and further experiments demonstrated that exogenous application of moderate but not severe abiotic stress increased the shoot regeneration efficiency. In summary, our study provides an overview of the genetic flow dynamics during bamboo shoot organogenesis. Full-length cDNA sequences generated in this study can serve as a valuable resource for fundamental and applied research in bamboo in the future.

Development and validation of a ferroptosis-related prognostic model in pancreatic cancer

BACKGROUND

The purpose of this study was to identify ferroptosis-related genes (FRGs) associated with the prognosis of pancreatic cancer and to construct a prognostic model based on FRGs.

METHODS

Based on pancreatic cancer data obtained from The Cancer Genome Atlas database, we established a prognostic model from 232 FRGs. A nomogram was constructed by combining the prognostic model and clinicopathological features. Gene Expression Omnibus datasets and tissue samples obtained from our center were utilized to validate the model. The relationship between risk score and immune cell infiltration was explored by CIBERSORT and TIMER.

RESULTS

The prognostic model was established based on four FRGs (ENPP2, ATG4D, SLC2A1 and MAP3K5), and the risk score was demonstrated to be an independent risk factor in pancreatic cancer (HR 1.648, 95% CI 1.335-2.035, p < 0.001). Based on the median risk score, patients were divided into a high-risk group and a low-risk group. The low-risk group had a better prognosis than the high-risk group. In the high-risk group, patients treated with chemotherapy had a better prognosis. The nomogram showed that the model was the most important element. Gene set enrichment analysis identified three key pathways, namely, TGFβ signaling, HIF signaling pathway and the adherens junction. The prognostic model may be associated with infiltration of immune cells such as M0 macrophages, M1 macrophages, CD4 + T cells and CD8 + T cells.

CONCLUSION

The ferroptosis-related prognostic model can be employed to predict the prognosis of pancreatic cancer. Ferroptosis is an important marker, and immunotherapy may be a potential therapeutic target for pancreatic cancer.

Surface-Mounted Metal-Organic Frameworks: Past, Present, and Future Perspectives

Metal-organic frameworks (MOFs) are an emerging class of porous materials composed of organic linkers and metal centers/clusters. The integration of MOFs onto the solid surface as thin films/coatings has spurred great interest, thanks to leveraging control over their morphology (such as size- and shape-regulated crystals) and orientation, flexible processability, and easy recyclability. These aspects, in synergy, promise a wide range of applications, including but not limited to gas/liquid separations, chemical sensing, and electronics. Dozens of innovative methods have been developed to manipulate MOFs on various solid substrates for academic studies and potential industrial applications. Among the developed deposition methods, the liquid-phase epitaxial layer-by-layer (LPE-LbL) method has demonstrated its merits over precise control of the thickness, roughness, homogeneity, and orientations, among others. Herein, we discuss the major developments of surface-mounted MOFs (SURMOFs) in LbL process optimization, summarizing the SURMOFs' performance in different applications, and put forward our perspective on the future of SURMOFs in terms of advances in the formulation, applications, and challenges. Finally, future prospects and challenges with respect to SURMOFs growth will be discussed, keeping the focus on their widening applications.

Influences of Psychological Intervention on Negative Emotion, Cancer-Related Fatigue and Level of Hope in Lung Cancer Chemotherapy Patients Based on the PERMA Framework

Background:

Psychological status is a decisive factor for regulating the lung cancer chemotherapy patients’ levels of fatigue and hope. Using the PERMA (Positive Emotion, Engagement, Relationships, Meaning, and Accomplishment) framework. We aimed to explore the influences of the psychological intervention on the patients’ negative emotion, cancer-related fatigue, and level of hope.

Method:

A total of 100 lung cancer chemotherapy patients admitted in Wuhan No.4 Hospital, China, from Jan 2018 to Aug 2019 were enrolled as research objects divided into the control group and observation group. Positive psychological intervention using the PERMA framework was given to the observation group. The scores of Post-Traumatic Growth Inventory (PTGI), Self-rating Anxiety Scale (SAS), Self-rating Depression Scale (SDS), Cancer Fatigue Scale (CFS), and Herth Hope Index (HHI) were evaluated and compared in the two groups.

Results:

After the intervention, PTGI score in the observation group is higher than that in the control group, whereas the SAS and SDS scores are lower in the observation group than in the control group, and the differences are statistically significant (P<0.05). Score of each CFS dimension and total CFS score in the observation group are all lower than those in the control group, with statistically significant differences (P<0.05). Score of each HHI dimension and total HHI score are higher than those in the control group, and the differences are statistically significant (P<0.05).

Conclusion:

Positive psychological intervention using the PERMA framework can improve the emotional and fatigue state of lung cancer chemotherapy patients and elevate their level of hope.

WISP1 Protects Against Chondrocyte Senescence and Apoptosis by Regulating αvβ3 and PI3K/Akt Pathway in Osteoarthritis

Our study aimed at validating the effect of WISP1 on osteoarthritis (OA) and the pathway involved in the WISP1-induced protection against OA. The expression of WISP1 was measured by immunohistochemical analyses. We found that WISP1 expression was shown to be upregulated within human OA cartilage compared with controls. WISP1 expression was related to knee OA severity. rhWISP1 inhibited OA chondrocyte senescence and apoptosis in vitro, which was reversed by the αvβ3 antibody and PI3K/Akt inhibitor LY294002. WISP1 overexpression induced by knee injection of LiCI could also prevent the senescence and apoptosis of rat chondrocytes. Safranin-O staining and Mankin score revealed that WISP1 overexpression can protect rat chondrocytes from degeneration. Nearly opposite results were obtained in the treatment of ICG-001 and siRNA-WISP1 in vivo. These data strongly suggest that WISP1 can protect against the senescence and apoptosis of chondrocytes via modulating the αvβ3 receptor and PI3K/Akt signaling pathway within OA. Therefore, the development of specific activators of WISP1 may present the value of an underlying OA treatment.

Template-Mediated Control over Polymorphism in the Vapor-Assisted Formation of Zeolitic Imidazolate Framework Powders and Films

The landscape of possible polymorphs for some metal-organic frameworks (MOFs) can pose a challenge for controlling the outcome of their syntheses. Demonstrated here is the use of a template to control in the vapor-assisted formation of zeolitic imidazolate framework (ZIF) powders and thin films. Introducing a small amount of either ethanol or dimethylformamide vapor during the reaction between ZnO and 4,5-dichloroimidazole vapor results in the formation of the porous ZIF-71 phase, whereas other conditions lead to the formation of the dense ZIF-72 phase or amorphous materials. Time-resolved in situ small-angle X-ray scattering reveals that the porous phase is metastable and can be transformed into its dense polymorph. This transformation is avoided through the introduction of template vapor. The porosity of the resulting ZIF powders and films was studied by N₂ and Kr physisorption, as well as positron annihilation lifetime spectroscopy. The templating principle was demonstrated for other members of the ZIF family as well, including the ZIF-7 series, ZIF-8_Cl, and ZIF-8_Br.

Role of MALAT1 in gynecological cancers: Pathologic and therapeutic aspects

Gynecological cancers, including breast, ovarian, uterine, vaginal, cervical and vulvar cancers are among the major threats to modern life, particularly to female health. Long non-coding RNAs (lncRNAs) play critical roles in normal development of organisms, as well as the tumorigenesis process, and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a large infrequently spliced lncRNA, which have been implicated in different gynecological cancers. MALAT1 is overexpressed in breast, ovarian, cervical and endometrial cancers, which initiates cancer progression by inducing changes in the expression of several anti-apoptotic and epithelial-to-mesenchymal transition-related genes. Targeting MALAT1 is an important strategy to combat gynecological cancers, and application of RNA-interference technology and chemotherapeutic process are crucial to target and minimize MALAT1 activity. The present review discusses the role of MALAT1 in gynecological cancers, and potential strategies to target this lncRNA to develop cancer therapeutics. However, further clinical studies are required to determine the prognostic potential of MALAT1 in gynecological cancers.

Sub-adventitial divestment technique for resecting artery-involved pancreatic cancer: a retrospective cohort study

PURPOSE

To introduce sub-adventitial divestment technique (SDT), a procedure to remove the tumor while preserving the artery during curative pancreatectomy. Peri-operative safety profile was also evaluated.

METHODS

In a single center consecutive series of pancreatectomy for pancreatic cancer, the outcome of patients who had pancreatectomy with SDT was compared to standard pancreatic surgery.

RESULTS

From June 2014 to June 2016, 72 patients had pancreatectomy with SDT and 235 had standard surgery. Tumor stage was T4 in all 72 (100%) tumors removed using SDT compared to four (2%) with standard pancreatectomy (p < 0.001). All 72 (100%) tumors in the SDT group were stage III compared to 24 (10%) in the standard surgery group (p < 0.001). Both groups had a high proportion of poorly differentiated tumors (52 (72%) and 163 (69%) respectively) and perineural tumor invasion (62 (86%) and 186 (79%) respectively). R1 (< 1 mm) was found in 24 (86%) of 28 tumors in the SDT group, and in 72 (60%) out of 120 standard pancreatectomy tumors (p = 0.01). Complications occurred in 29 (40%) of the SDT group and in 88 (37%) of the standard group. The in-hospital mortality was four (6%) in the SDT group and one (0.4%) in the standard group (p = 0.01), with a 90-day mortality of 5 (8%)/60 and 6 (3%)/209 (p = 0.07) respectively.

CONCLUSIONS

The sub-adventitial divestment technique appeared to be an effective surgical technique to remove the tumor while preserving the artery. This approach warrants further validation in prospective studies.

Direct X-ray and electron-beam lithography of halogenated zeolitic imidazolate frameworks

Metal-organic frameworks (MOFs) offer disruptive potential in micro- and optoelectronics because of the unique properties of these microporous materials. Nanoscale patterning is a fundamental step in the implementation of MOFs in miniaturized solid-state devices. Conventional MOF patterning methods suffer from low resolution and poorly defined pattern edges. Here, we demonstrate the resist-free, direct X-ray and electron-beam lithography of MOFs. This process avoids etching damage and contamination and leaves the porosity and crystallinity of the patterned MOFs intact. The resulting high-quality patterns have excellent sub-50-nm resolution, and approach the mesopore regime. The compatibility of X-ray and electron-beam lithography with existing micro- and nanofabrication processes will facilitate the integration of MOFs in miniaturized devices.

Study on the Effect of Nano Albumin Paclitaxel Combined with Carboplatin in the Treatment of Lung Squamous Cell Carcinoma

This study aims to compare the efficacy and side effects of albumin-binding paclitaxel plus carboplatin (NAB PC) and paclitaxel plus carboplatin (PC) in the first-line treatment of advanced non-small cell lung cancer (NSCLC). A total of 60 patients with advanced NSCLC diagnosed by histopathology or cytology were randomly divided into nab PC group (albumin-binding paclitaxel 130 mg/mL, D1, D; carboplatin AUC = 6, D1) and PC group (paclitaxel 175 mg/mL, D1; carboplatin AUC = 6, D1), one cycle every three weeks. RECIST 1.1 standard was used to evaluate the short-term objective efficacy, and who acute and subacute toxicity classification standard was used to evaluate the toxicity. The total effective rate (RR) and disease control rate (DCR) of NAB PC group were 40.0% and 80.0%, respectively, which were higher than 23.3% and 60.0% of the PC group, respectively. This difference was statistically significant (p < 0.05). In squamous cell carcinoma, the RR of NAB PC group and PC group were 57.1% (8/14) and 23.1% (3/13) respectively, with a statistically significant difference (p < 0.05); in non-squamous cell carcinoma, the RR of the two groups were 25.0% (4/16) and 23.3% (4/17) without statistical significance (p > 0.05). The median progression free survival time of the NAB PC group and PC group was 6.5 and 5.9 months, respectively, with no significant difference (p>0.05). No significant difference arose in the incidence of grade III-IV toxicity between the two groups (p > 0.05). The incidence of neutropenia in the NAB PC group was higher than that in the PC group (p < 0.05). The therapeutic effect of paclitaxel combined with carboplatin in the treatment of advanced NSCLC is better, the effect of paclitaxel combined with carboplatin is better, and the side effects can be tolerated, which is worthy of clinical application. Patients are more satisfied with their care.

Toward the Genetic Basis and Multiple QTLs of Kernel Hardness in Wheat

Kernel hardness is one of the most important single traits of wheat seed. It classifies wheat cultivars, determines milling quality and affects many end-use qualities. Starch granule surfaces, polar lipids, storage protein matrices and Puroindolines potentially form a four-way interaction that controls wheat kernel hardness. As a genetic factor, Puroindoline polymorphism explains over 60% of the variation in kernel hardness. However, genetic factors other than Puroindolines remain to be exploited. Over the past two decades, efforts using population genetics have been increasing, and numerous kernel hardness-associated quantitative trait loci (QTLs) have been identified on almost every chromosome in wheat. Here, we summarize the state of the art for mapping kernel hardness. We emphasize that these steps in progress have benefitted from (1) the standardized methods for measuring kernel hardness, (2) the use of the appropriate germplasm and mapping population, and (3) the improvements in genotyping methods. Recently, abundant genomic resources have become available in wheat and related Triticeae species, including the high-quality reference genomes and advanced genotyping technologies. Finally, we provide perspectives on future research directions that will enhance our understanding of kernel hardness through the identification of multiple QTLs and will address challenges involved in fine-tuning kernel hardness and, consequently, food properties.

Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data

Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3′ untranslated regions (3′UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3′UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3′UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3′UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3′UTRs. Importantly, the high-confidence alternative 3′UTR genes significantly overlapped with the genesets that are associated with RNA N⁶-methyladenosine (m⁶A) modification, suggesting a clear indication between alternative 3′UTR and m⁶A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3′UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3′UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3′UTRs and their genotype specificity.

Age Estimation in Han Adults by Thin-Layer CT Scan of Cranial Sutures

Abstract

Objective To explore the value of degree of cranial suture closure in forensic adult age estimation by thin-layer CT scan and establish an adult age estimation model of the Han nationality. Methods Thin-layer CT scan samples of the heads of 220 healthy Sichuan Han adults （110 males, 110 females） aged 20 to 70 were collected, of which 20 samples （10 males, 10 females） were randomly selected as test samples. The sagittal suture, coronal suture （both left and right） and lambdoid suture （both left and right） were respectively and equally divided into 2 segments, and every segment was equally divided into 10 layers and the corresponding multiplanar reformation （MPR） images were selected. The closure of cranial sutures on MPR images was classified into the grades 1-7. The correlations between cranial sutures and age were analyzed to build regression equation for age estimation. Results The degree of closure of sagittal suture, coronal suture （both left and right） and lambdoid suture （both left and right） was positively correlated with age. The coefficient of determination （R²） of regression equation was 0.419 in males, 0.589 in females, and 0.522 in all samples. The results of the verification test showed that the mean absolute error （MAE） was 6.39 years in males, 6.16 years in females, and 6.29 years in all samples. Conclusion There was a higher accuracy in adult age estimation by thin-layer CT scan of cranial sutures. The age of Han nationality adults can be estimated by the degree of cranial sutures closure.

Using phage-assisted continuous evolution (PACE) to evolve human PD1

PD1/PDL1 pathway plays a critical role in cancer immune responses. The immune checkpoint inhibitors of PD1/PDL1 have been well explored and developed for immunotherapies of solid tumors. Recently, various monoclonal antibodies targeting the PD1/PDL1 pathway have emerged and achieved remarkable success in clinical trials. However, challenges with these monoclonal antibodies have appeared during cancer therapies, including predictors of response, patient selection, and innate resistance. Thus, a competitive antagonist of native PD1/PDL1, with smaller size and lower side-effect, is required for future cancer therapies. In this study, we utilized a protein evolution system of phage-assisted continuous evolution (PACE) to evolve PD1 continuously. Our results indicated that the newly evolved PD1 bound to PDL1 with higher affinity. The interactome analysis further suggested that these evolved PD1s exhibited higher specificity with PDL1. Therefore, these evolved PD1s may be applied as a new tool for tumor immunotherapy.