Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato.

Sweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.

Molecular Mechanisms of Mercury-Sensitive Aquaporins.

Aquaporins are transmembrane channels that allow for the passive permeation of water and other small molecules across biological membranes. Their channel activities are sensitive to mercury ions. Intriguingly, while most aquaporins are inhibited by mercury ions, several aquaporins are activated by mercury ions. The molecular basis of the opposing aquaporin regulation by mercury remains poorly understood. Herein, we investigated AqpZ inhibition and AQP6 activation upon binding of mercury ions using solid-state NMR (ssNMR) and molecular dynamics (MD) simulations. Based on the structure of the Hg-AqpZ complex constructed by MD simulations and ssNMR, we identified that the pore closure was caused by mercury-induced conformational changes of the key residue R189 in the selectivity filter region, while pore opening was caused by conformational changes of residues H181 and R196 in the selectivity filter region in AQP6. Both conformational changes were caused by the disruption of the H-bond network of R189/R196 by mercury. The molecular details provided a structural basis for mercury-mediated functional changes in aquaporins.

Microbial degradation and valorization of poly(ethylene terephthalate) (PET) monomers.

The polyethylene terephthalate (PET) is one of the major plastics with a huge annual production. Alongside with its mass production and wide applications, PET pollution is threatening and damaging the environment and human health. Although mechanical or chemical methods can deal with PET, the process suffers from high cost and the hydrolyzed monomers will cause secondary pollution. Discovery of plastic-degrading microbes and the corresponding enzymes emerges new hope to cope with this issue. Combined with synthetic biology and metabolic engineering, microbial cell factories not only provide a promising approach to degrade PET, but also enable the conversion of its monomers, ethylene glycol (EG) and terephthalic acid (TPA), into value-added compounds. In this way, PET wastes can be handled in environment-friendly and more potentially cost-effective processes. While PET hydrolases have been extensively reviewed, this review focuses on the microbes and metabolic pathways for the degradation of PET monomers. In addition, recent advances in the biotransformation of TPA and EG into value-added compounds are discussed in detail.

Low-Concentration C2 H6 Capture Enabled by Size Matching in the Ultramicropore.

Low-concentration ethane capture is crucial for environmental protection and natural gas purification. The ideal physisorbent with strong C2 H6 interaction and large C2 H6 uptake at low-concentration level has rarely been reported, due to the large pKa value and small quadrupole moment of C2 H6 . Herein, we demonstrate the perfectly size matching between the ultramicropore (pore size of 4.6 Å) and ethane (kinetic diameter of 4.4 Å) in a nickel pyridine-4-carboxylate metal-organic framework (IISERP-MOF2), which enables the record-breaking performance for low concentration C2 H6 capture. IISERP-MOF2 exhibits the large C2 H6 adsorption enthalpy of 56.7 kJ/mol, and record-high C2 H6 uptake at low pressure of 0.01-0.1 bar and 298 K (1.8 mmol/g at 0.01 bar). Molecule simulations and C2 H6 -loading crystal structure analysis revealed that the maximized interaction sites in IISERP-MOF2 with ethane molecule originates the strong C2 H6 adsorption. The dynamic breakthrough experiments for gas mixtures of C2 H6 /N2 (1/999, v/v) and C2 H6 /CH4 (5/95, v/v) proved the excellent low-concentration C2 H6 capture performance.

[Quality evaluation of Gastrodiae Rhizoma standard decoction based on UPLC fingerprint and quantitative analysis multi-components method].

To establish the quantitative analysis multi-components with a single-marker(QAMS) method for six components and fingerprint of standard decoction of Gastrodiae Rhizoma, verify the accuracy and feasibility of the method, and evaluate the quality of standard decoction. Based on UPLC with gastrodin as the internal standard, relative correction factors of p-hydroxybenzyl alcohol, parishin E, parishin B, parishin C, parishin A and gastrodin were determined by investigating the column temperature, flow rate, chromatographic columns and multi-point concentration correction. The total contents in 18 batches of standard decoction of Gastrodiae Rhizoma and the similarity were determined to calculate the similarity. The results of standard curve method, external standard one-point method and quantitative analysis multi-components with a single-marker(QAMS) were compared, and the results showed that there was no significant difference among these three methods. By analyzing the results of standard decoctions from different origins, it can be seen that the quality of Gastrodia standard decoctions derived from Anhui and Yunnan was better, followed by Shaanxi and Hubei, and relatively poor in Gansu, with similarities all above 0.90 in the fingerprints. Therefore, the QAMS method that can measure the contents of gastrodin, p-hydroxybenzyl alcohol, parishin E, parishin B, parishin C and parishin A in standard decoction of Gastrodiae Rhizoma combined with fingerprint is accurate, feasible and fast, which can be used to evaluate the quality of standard decoction of Gastrodiae Rhizoma, and also provide a reference for the research on the quality standards of raw materials for Gastrodiae Rhizoma prepared slices and alike.

Overexpression of rice aquaporin OsPIP1;2 improves yield by enhancing mesophyll CO2 conductance and phloem sucrose transport.

Aquaporins are involved in CO2 transport from the leaf intercellular air space to the chloroplast, which contributes to CO2 assimilation. However, the mechanism of CO2 transport by rice (Oryza sativa L.) aquaporins is unknown. Here, we investigated the function of the aquaporin OsPIP1;2 in CO2 diffusion-associated photosynthesis and phloem sucrose transport. Moreover, the grain yield of rice lines overexpressing OsPIP1;2 was determined. OsPIP1;2 was localized to the plasma membrane and the relative expression of OsPIP1;2 was approximately 5-fold higher in leaves in the presence of an elevated CO2 concentration. Overexpression of OsPIP1;2 increased mesophyll conductance by approximately 150% compared with wild-type (WT) rice. The OsPIP1;2-overexpressing lines had higher biomass than the WT, possibly due to increased phloem sucrose transport. In addition, the grain yield of OsPIP1;2-overexpressing lines was approximately 25% higher than that of the WT in three-season field experiments, due to the increased numbers of effective tillers and spikelets per panicle. Our results suggest that OsPIP1;2 modulates rice growth and grain yield by facilitating leaf CO2 diffusion, which increases both the net CO2 assimilation rate and sucrose transport.

Light-Induced Printing of Protein Structures on Membranes in Vitro.

Reconstituting functional modules of biological systems in vitro is an important yet challenging goal of bottom-up synthetic biology, in particular with respect to their precise spatiotemporal regulation. One of the most desirable external control parameters for the engineering of biological systems is visible light, owing to its specificity and ease of defined application in space and time. Here we engineered the PhyB-PIF6 system to spatiotemporally target proteins by light onto model membranes and thus sequentially guide protein pattern formation and structural assembly in vitro from the bottom up. We show that complex micrometer-sized protein patterns can be printed on time scales of seconds, and the pattern density can be precisely controlled by protein concentration, laser power, and activation time. Moreover, when printing self-assembling proteins such as the bacterial cytoskeleton protein FtsZ, the targeted assembly into filaments and large-scale structures such as artificial rings can be accomplished. Thus, light mediated sequential protein assembly in cell-free systems represents a promising approach to hierarchically building up the next level of complexity toward a minimal cell.

[Research progress on antidepressant effects of Sini San based on three progressive levels of "single herb, herb-pair, and complicated Chinese herbal formula"].

Depression is a kind of mental illness accompanied by complex etiology and pathogenesis in clinic. With the quickening pace of circadian rhythm and increase of life pressure in modern society, the incidence of depression is increasing year by year. Nowadays, some typical antidepressant Western medicines, such as selective serotonin re-uptake inhibitors (SSRI) and tricyclic antidepressants (TCA), have been used as the main therapeutic drugs in clinic. Unfortunately, administration of these drugs will result in severe adverse reactions, slow treatments, and low cure rates, thus obviously they can not be used for a long term. Sini San, which originated from Treatise on Febrile Diseases written by Zhang zhongjing, is a prescription widely applied in clinic for curing mental illness and also a basic Chinese herbal formula for modern treatment of depression. This article would review the research progress on antidepressant effects of Sini San based on single herbs of Bupleuri Radix and Paeoniae Radix Alba, herb-pair of Bupleuri Radix-Paeoniae Radix Alba, and formula of Sini San, providing directions and ideas for future research on complicated Chinese herbal formulae.

Amino acids as co-amorphous excipients for tackling the poor aqueous solubility of valsartan.

Co-amorphization has recently been shown to be a promising approach for stabilizing amorphous drugs and improving the dissolution rate of poorly water-soluble drugs. In this study, three basic amino acids were chosen as small molecular weight excipients to interact with the drug to form co-amorphous combinations. The co-amorphous combinations of valsartan (VAL) with l-histidine, l-arginine, and l-lysine were prepared by vibrational ball milling. Solid-state characterization with X-ray powder diffraction and differential scanning calorimetry (DSC) revealed that all of the co-amorphous mixtures were homogeneous. The molecular interactions of the co-amorphous mixtures were investigated through the glass transition temperature (Tg) in the DSC measurements and Fourier transform infrared spectroscopy. The drug remained chemically stable during the milling process, and the co-amorphous formulations were generally physically stable over at least 3 months at 40 °C under dry conditions. The dissolution rate of all of the co-amorphous mixtures was significantly increased over that of the amorphous VAL alone. The results of this study demonstrated the potential of amino acids as small molecular weight excipients in co-amorphous formulations to improve the drug solubility and dissolution rate.

[Research progress of Baizhu Shaoyao powder in treating ulcerative colitis].

Ulcerative colitis is a chronic, nonspecific and complex intestinal disease. The current clinical treatment guideline of this disease recommends a variety of options with oral western medicines, such as aminosalicylic acids, glucocorticosteroids, and immunosuppressors. However, due to their unstable therapeutic effects, high toxicities, and strong drug dependence, they are not suitable for long-term administration. Baizhu Shaoyao powder, a traditional Chinese medicinal prescription, is clinically and commonly used for tonifying spleen and softening liver as well as eliminating dampness and relieving diarrhea. Recent researches suggest that Baizhu Shaoyao powder has significant effect in the treatment of ulcerative colitis. This article reviewed the research progress on the curative effect and action mechanism of Baizhu Shaoyao powder in treating ulcerative colitis, and provided the ideas and directions for its further research in future.

[A new strategy for exploring herb-pair investigation with a case study on Astragali Radix-Corni Fructus in treatment of diabetic nephropathy].

As the smallest unit of traditional Chinese medicinal formula compatibility, herb-pair has the basic characteristic of traditional Chinese medicinal formula compatibility. In recent years, herb-pair investigation has attracted much attention, which is an indispensable part of modernization of traditional Chinese medicine. With the decrease of the efficiency in the discovery of new drug, how to discover new drugs from traditional Chinese medicinal herb-pair has also been a bottleneck for the research and development of drug. The authors reviewed the domestic and foreign literatures in the latest years and summarized the current situations and the existing problems of herb-pair study. Based on these investigations, the authors innovatively proposed a novel concept of "precision herb-pair". Difference from traditional Chinese medicinal herb-pair or formulae with extensive roles and unclear efficacies, "precision herb-pair" belongs to a developed new mini herb-pair formula with an exact treatment and a relatively clear composition based on a certain specific disease. In addition, the authors also proposed a new strategy of "herb-pair - screen of multiple constituents based on column separation and in vitro cell viability - fuzzy target recognition pharmacology - re-evaluation of precision herb-pair", and successfully applied it to the development of a precision herb-pair from Astragali Radix-Corni Fructus in treatment of diabetic nephropathy. This proposed new strategy is simple, easy to carry out, and has a wide application, and can offer references and thoughts for the modern investigation of herb-pair and the research and development of new drug.

Aquaporins and membrane diffusion of CO2 in living organisms.

BACKGROUND: Determination of CO2 diffusion rates in living cells revealed inconsistencies with existing models about the mechanisms of membrane gas transport. Mainly, these discrepancies exist in the determined CO2 diffusion rates of bio-membranes, which were orders of magnitudes below those for pure lipid bilayers or theoretical considerations as well as in the observation that membrane insertion of specific aquaporins was rescuing high CO2 transport rates. This effect was confirmed by functional aquaporin protein analysis in heterologous expression systems as well as in bacteria, plants and partly in mammals. SCOPE OF REVIEW: This review summarizes the arguments in favor of and against aquaporin facilitated membrane diffusion of CO2 and reports about its importance for the physiology of living organisms. MAJOR CONCLUSIONS: Most likely, the aquaporin tetramer forming an additional fifth pore is required for CO2 diffusion facilitation. Aquaporin tetramer formation, membrane integration and disintegration could provide a mechanism for regulation of cellular CO2 exchange. The physiological importance of aquaporin mediated CO2 membrane diffusion could be shown for plants and cyanobacteria and partly for mammals. GENERAL SIGNIFICANCE: Taking the mentioned results into account, consequences for our current picture of cell membrane transport emerge. It appears that in some or many instances, membranes might not be as permeable as it was suggested by current bio-membrane models, opening an additional way of controlling the cellular influx or efflux of volatile substances like CO2. This article is part of a Special Issue entitled Aquaporins.

Preoperative prediction of conversion from laparoscopic rectal resection to open surgery: a clinical study of conversion scoring of laparoscopic rectal resection to open surgery.

OBJECTIVE: The objectives of this paper were to establish a model for the conversion of laparoscopic rectal resection to open surgery and to predict possible conversion before surgery. METHODS: The clinical data of 602 cases of laparoscopic rectal resection were retrospectively assessed. Risk factors associated with conversion of laparoscopic rectal resection to open rectal surgery were identified by logistic regression analysis. Also, a scoring system was created to calculate a score for the conversion of laparoscopic rectal resection to predict possible conversion for patients who underwent laparoscopic rectal resection before surgery. RESULTS: A total of 90 patients required conversion (total conversion rate = 14.95%). The established model included six variables: male gender, surgical experience (≤25 cases), history of abdominal surgery, body mass index ≥ 28, tumor diameter ≥ 6 cm, and tumor invasion or metastasis, for which 6, 4, 5, 10, 15, and 21 points were assigned, respectively. A patient with a total score >14.5 points was considered to have a high probability of conversion, whereas a patient with a total score <14.5 points was considered at a low risk. CONCLUSION: Preoperative determination of conversion score may predict possible conversion of laparoscopic rectal resection and thus reduce unnecessary open rectal surgery.

Comparative proteomic profiles of the normal and aganglionic hindgut in human Hirschsprung disease.

BACKGROUND: Hirschsprung disease (HSCR) is the third most common congenital disorder of the gastrointestinal tract. This study aims to elucidate changes in protein expression between the normal and aganglionic hindgut in human HSCR. METHODS: The biopsies were obtained from the normal and aganglionic hindgut in human HSCR, and the comparative proteomics were analyzed by mass spectrometry (MS)-based two-dimensional gel electrophoresis (2DE). RESULTS: A total of 932-986 protein spots were identified in each of the gut segments, among which 30 spots had at least an eightfold difference in volume (%). Of the 30 differentially expressed spots, 15 proteins were identified via sequence analysis. Among these 15 proteins, eight were upregulated and seven were downregulated in the aganglionic group. The well-represented classes included biomarkers of enteric ganglions, extracellular matrix proteins, LIM domain proteins, serum proteins, and other pleiotropic proteins. Five proteins were selected and verified by western blotting and real-time PCR, and the results were consistent with the results of 2DE. CONCLUSION: MS-based 2DE can help to identify pathological relevant proteins in HSCR; it defines an extensive protein catalog of the normal and aganglionic hindgut and may constitute the basis to understand pathophysiological mechanisms related to the HSCR.

Decreased enteric fatty acid amide hydrolase activity is associated with colonic inertia in slow transit constipation.

BACKGROUND: Constipation is one of the most common chronic digestive complaints. Gastrointestinal transit studies have divided it into three patterns: normal transit, slow transit constipation (STC), and outlet obstruction. It has been demonstrated that STC patients respond poorly to standard therapies, and the etiology of STC remains poorly understood. Animal studies have also shown that fatty acid amide hydrolase (FAAH) controls intestinal motility through its putative receptors or non-receptor-mediated pathways. However, the role of FAAH in STC has not been elaborated. METHODS: A case series was carried out on thirty-two STC patients fulfilling the Rome II criteria and on 24 controls. All of the subjects underwent a laparotomy in Shengjing Hospital. Colonic specimens were obtained and used for FAAH expression analysis, enzyme activity assay, and cannabinoid detection. RESULTS: FAAH immunoreactivity occurred in the enteric neurons and in the surface epithelial and glands. The expression level and enzyme activity of FAAH in the STC group were both significantly lower than those in the control group (P < 0.05). The amounts of anandamide, 2-arachidonylglycerol, and palmitoylethanolamide, which are negatively correlated with enzyme activity, were significantly higher in the constipation group than that in the control group. In the STC group, cannabinoid receptor type 1 immunoreactivity occurred predominantly in the submucosal and myenteric fibers that were obviously strong and wave-like in their appearance. Enteric ganglions decreased or disappeared. CONCLUSIONS: The tone of the enteric cannabinoids system is disturbed in STC, and the decreased enteric FAAH activity contributes to colonic inertia in STC.

Co-translational association of cell-free expressed membrane proteins with supplied lipid bilayers.

Routine strategies for the cell-free production of membrane proteins in the presence of detergent micelles and for their efficient co-translational solubilization have been developed. Alternatively, the expression in the presence of rationally designed lipid bilayers becomes interesting in particular for biochemical studies. The synthesized membrane proteins would be directed into a more native-like environment and cell-free expression of transporters, channels or other membrane proteins in the presence of supplied artificial membranes could allow their subsequent functional analysis without any exposure to detergents. In addition, lipid-dependent effects on activity and stability of membrane proteins could systematically be studied. However, in contrast to the generally efficient detergent solubilization, the successful stabilization of membrane proteins with artificial membranes appears to be more difficult. A number of strategies have therefore been explored in order to optimize the co-translational association of membrane proteins with different forms of supplied lipid bilayers including liposomes, bicelles, microsomes or nanodiscs. In this review, we have compiled the current state-of-the-art of this technology and we summarize parameters which have been indicated as important for the co-translational association of cell-free synthesized membrane proteins with supplied membranes.

Cell-free Protein Synthesis System for Building Synthetic Cells.

The Cell-Free Protein Synthesis (CFPS) system has been widely employed to facilitate the bottom-up assembly of synthetic cells. It serves as the host for the core machinery of the Central Dogma, standing as an optimal chassis for the integration and assembly of diverse artificial cellular mimicry systems. Despite its frequent use in the fabrication of synthetic cells, establishing a tailored and robust CFPS system for a specific application remains a nontrivial challenge. In this methods paper, we present a comprehensive protocol for the CFPS system, routinely employed in constructing synthetic cells. This protocol encompasses key stages in the preparation of the CFPS system, including the cell extract, template preparation, and routine expression optimization utilizing a fluorescent reporter protein. Additionally, we show representative results by encapsulating the CFPS system within various micro-compartments, such as monolayer droplets, double-emulsion vesicles, and chambers situated atop supported lipid bilayers. Finally, we elucidate the critical steps and conditions necessary for the successful assembly of these CFPS systems in distinct environments. We expect that our approach will facilitate the establishment of good working practices among various laboratories within the continuously expanding synthetic cell community, thereby accelerating progress in the field of synthetic cell development.

Causal roles of gut microbiota in cholangiocarcinoma etiology suggested by genetic study.

BACKGROUND: Cholangiocarcinoma (CCA) is a highly malignant biliary tract cancer with poor prognosis. Previous studies have implicated the gut microbiota in CCA, but evidence for causal mechanisms is lacking. AIM: To investigate the causal relationship between gut microbiota and CCA risk. METHODS: We performed a two-sample mendelian randomization study to evaluate potential causal associations between gut microbiota and CCA risk using genome-wide association study summary statistics for 196 gut microbial taxa and CCA. Genetic variants were used as instrumental variables. Multiple sensitivity analyses assessed result robustness. RESULTS: Fifteen gut microbial taxa showed significant causal associations with CCA risk. Higher genetically predicted abundance of genus Eubacteriumnodatum group, genus Ruminococcustorques group, genus Coprococcus, genus Dorea, and phylum Actinobacteria were associated with reduced risk of gallbladder cancer and extrahepatic CCA. Increased intrahepatic CCA risk was associated with higher abundance of family Veillonellaceae, genus Alistipes, order Enterobacteriales, and phylum Firmicutes. Protective effects against CCA were suggested for genus Collinsella, genus Eisenbergiella, genus Anaerostipes, genus Paraprevotella, genus Parasutterella, and phylum Verrucomicrobia. Sensitivity analyses indicated these findings were reliable without pleiotropy. CONCLUSION: This pioneering study provides novel evidence that specific gut microbiota may play causal roles in CCA risk. Further experimental validation of these candidate microbes is warranted to consolidate causality and mechanisms.

Functional characterization of a novel aquaporin from Dictyostelium discoideum amoebae implies a unique gating mechanism.

The social amoeba Dictyostelium discoideum is a widely used model organism for studying basic functions of protozoan and metazoan cells, such as osmoregulation and cell motility. There is evidence from other species that cellular water channels, aquaporins (AQP), are central to both processes. Yet, data on D. discoideum AQPs is almost absent. Despite cloning of two putative D. discoideum AQPs, WacA, and AqpA, water permeability has not been shown. Further, WacA and AqpA are expressed at the late multicellular stage and in spores but not in amoebae. We cloned a novel AQP, AqpB, from amoeboidal D. discoideum cells. Wild-type AqpB was impermeable to water, glycerol, and urea when expressed in Xenopus laevis oocytes. Neither stepwise truncation of the N terminus nor selected point mutations activated the water channel. However, mutational truncation by 12 amino acids of an extraordinary long intracellular loop induced water permeability of AqpB, hinting at a novel gating mechanism. This AqpB mutant was inhibited by mercuric chloride, confirming the presence of a cysteine residue in the selectivity filter as predicted by our structure model. We detected AqpB by Western blot analysis in a glycosylated and a non-glycosylated form throughout all developmental stages. When expressed in D. discoideum amoebae, AqpB-GFP fusion constructs localized to vacuolar structures, to the plasma membrane, and to lamellipodia-like membrane protrusions. We conclude that the localization pattern in conjunction with channel gating may be indicative of AqpB functions in osmoregulation as well as cell motility of D. discoideum.