A comprehensive workflow for optimizing RNA-seq data analysis.

BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge. RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz. CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.

Pb2(SeO3)(SiF6): the first selenite fluorosilicate with a wide bandgap and large birefringence achieved through perfluorinated group modification.

Birefringent crystals serve as the core elements of polarizing optical devices. However, the inherent challenge of balancing bandgap and birefringence poses a significant hurdle in designing crystals with excellent overall performance. In this study, we propose a novel approach, namely modification with perfluorinated groups, to achieve dual enhancement of the bandgap and birefringence of selenite materials. We have successfully synthesized the first selenite fluorosilicate, namely, Pb2(SeO3)(SiF6). This compound exhibits a three-dimensional structure composed of two-dimensional lead selenite layers bridged by SiF6 octahedrons. Notably, by introducing a perfluorinated SiF6 group, the bandgap of the lead selenite compound has been expanded to 4.4 eV. Furthermore, Pb2(SeO3)(SiF6) demonstrates a large birefringence (0.161 @ 546 nm), surpassing most of the selenite compounds with a bandgap larger than 4.2 eV. Theoretical calculations suggest that the large birefringence of Pb2(SeO3)(SiF6) can be attributed to the synergistic effects of SeO3, PbO4 and PbO3F4 polyhedrons. Our research not only pioneers a new system for selenite materials, enriching the diversity of selenite structures, but also provides a design methodology for obtaining wide bandgap birefringent selenite.

[(C5H6N2)2H](Sb4F13): a polyfluoroantimonite with a strong second harmonic generation effect.

It is of great difficulty to create a new antimonite with second-harmonic-generation (SHG) intensity larger than 6 times that of KDP. In this study, a polyfluoroantimonite strategy has been proposed to explore fluoroantimonites with large nonlinear optical (NLO) coefficients. Under the cooperation of chemical (highly asymmetric π-conjugated organic amine) and physical (viscous reaction medium ethylene glycol) methods, two novel polyfluoroantimonites, namely, (3PC)2(Sb4F14) and (3AP)2(Sb4F13), have been achieved. Interestingly, these two structures contain two new polyfluoroantimonite groups respectively, an isolated (Sb4F14)2- four-member polyhedral ring and an infinite [Sb4F13]∞- helical chain. More importantly, the polar (3AP)2(Sb4F13) displays a strong SHG intensity of 8.1 × KDP, a large birefringence of 0.258@546 nm and a high laser-induced damage threshold (LIDT) value of 149.7 MW cm-2. Theoretical calculations indicated that its strong SHG effect stems from the synergistic effect of the helical [Sb4F13]∞- polyfluoroantimonite chain and π-conjugated 3AP+ cation, with a contribution ratio of 48.93% and 50.77% respectively. This work provides a new approach for the design and synthesis of high-performance fluoroantimonites.

Assessing intracellular and extracellular distribution of antibiotic resistance genes in the commercial organic fertilizers.

Compost-based organic fertilizers often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Previous studies focused on quantification of total ARGs and MGEs. For a more accurate risk assessment of the dissemination risk of antibiotic resistance, it is necessary to quantify the intracellular and extracellular distribution of ARGs and MGEs. In the present study, extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) were separately analyzed in 51 commercial composts derived from different raw materials by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results showed that eARGs and eMGEs accounted for 11-56% and 4-45% of the total absolute abundance of ARGs and MGEs, respectively. Comparable diversity, host composition and association with MGEs were observed between eARGs and iARGs. Contents of high-risk ARGs were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7% and 8.2% of the total abundances, respectively. Twenty-four percent of the overall ARGs were present in plasmids, while 56.7% of potentially mobile ARGs were found to be associated with plasmids. Variation partitioning analysis, null model and neutral community model indicated that the compositions of both eARGs and iARGs were largely driven by deterministic mechanisms. These results provide important insights into the cellular distribution of ARGs in manure composts that should be paid with specific attention in risk assessment and management.

UV-Transparent SHG Material Explored in an Alkali Metal Sulfate Selenite System.

The first examples of alkali metal selenite sulfates, namely, Na8(SeO3)(SO4)3 (1), Na2(H2SeO3)(SO4) (2), and K4(H2SeO3)(HSO4)2(SO4) (3), were successfully synthesized by hydrothermal reactions. Their structures display three different zero-dimensional configurations composed of isolated sulfate tetrahedra and selenite groups separated by alkali metals. Na8(SeO3)(SO4)3 (1) features a noncentrosymmetric structure, while Na2(H2SeO3)(SO4) (2) and K4(H2SeO3)(HSO4)2(SO4) (3) are centrosymmetric. Powder second-harmonic-generation measurements revealed that Na8(SeO3)(SO4)3 (1) shows a phase-matchable SHG intensity about 1.2 times that of KDP. UV-vis-NIR diffuse reflectance spectroscopic analysis indicated that Na8(SeO3)(SO4)3 (1) has a short UV cutoff edge and a large optical band gap, which makes it a possible UV nonlinear optical material. Theoretical calculations revealed that the birefringence of Na8(SeO3)(SO4)3 (1) is 0.041 at 532 nm, which is suitable for phase-matching condition. This work provides a good experimental foundation for the exploration of new UV nonlinear crystals in an alkali metal selenite sulfate system.

Hg4(Te2O5)(SO4): A Giant Birefringent Sulfate Crystal Triggered by a Highly Selective Cation.

Sulfate crystals are often criticized for their low birefringence. The small anisotropic SO4 group is becoming the biggest bottleneck hindering the application of sulfates in optical functional materials. In this study, we report a new method to significantly enhance the birefringence of sulfates. The title compound increases the birefringence recording of sulfates to 0.542@546 nm, which is significantly larger than that of the commercial birefringent crystal of TiO2 (0.306@546.1 nm). At the infrared wavelength, the birefringence of Hg4(Te2O5)(SO4) can be up to 0.400@1064 nm, which is also much larger than the infrared birefringent crystal of YVO4 (0.209@1064 nm). In addition, it also has a wide transparency range, high thermal stability, and excellent environmental stability, making it a potential birefringent material. Hg4(Te2O5)(SO4) features a novel two-dimensional layered structure composed of [Hg4(Te2O5)]2+ layers separated by isolated (SO4)2- tetrahedra. This compound was designed by introducing a highly selective cation in a tellurite sulfate system. The low valence low coordination cations connect with tellurite groups only, making the sulfate isolated in the structure. The steric repulsive action of the isolated SO4 tetrahedra may regulate the linear and lone pair groups arranged in a way that favors large birefringence. This method can be proven by theoretical calculations. PAWED studies showed that the large birefringence originated from the synergistic effect of (Hg2O2)2-, (Te2O5)2-, and (SO4)2- units, with a contribution ratio of 42.17, 37.92, and 19.88%, respectively. Our work breaks the limitation of low birefringence in sulfates and opens up new possibilities for their application as birefringent crystals.

Hg3Se(SeO3)(SO4): A Mixed-Valent Selenium Compound with Mid-Infrared Transmittance Obtained by In Situ Reaction.

Exploring new material systems is a highly significant task in the field of inorganic chemistry. A new mixed-valent selenium compound, Hg3Se(SeO3)(SO4), was successfully synthesized through in situ reactions. This compound exhibits a novel three-dimensional structure composed of Hg3Se(SO4) layers bridged by SeO3 trigonal pyramids. It is the first structure containing (SeO3)2-, (SO4)2-, and Se2- simultaneously. In addition, Hg3Se(SeO3)(SO4) possesses a wide bandgap (3.5 eV), moderate birefringence (Cal:0.064@546 nm, Exp:0.069@546 nm), a high laser-induced damage threshold (23.35 MW cm-2), and a wide transmittance window (0.28-6.6 µm). Our work demonstrates that mixed-valent (+4, -2) selenite selenide can be potential optical materials for the mid-infrared region.

Acetylated tau exacerbates apoptosis by disturbing mitochondrial dynamics in HEK293 cells.

An increase in tau acetylation at K274 and K281 and abnormal mitochondrial dynamics have been observed in the brains of Alzheimer's disease (AD) patients. Here, we constructed three types of tau plasmids, TauKQ (acetylated tau mutant, by mutating its K274/K281 into glutamine to mimic disease-associated lysine acetylation), TauKR (non-acetylated tau mutant, by mutating its K274/K281 into arginine), and TauWT (wild-type human full-length tau). By transfecting these tau plasmids in HEK293 cells, we found that TauWT and TauKR induced mitochondrial fusion by increasing the level of mitochondrial fusion proteins. Conversely, TauKQ induced mitochondrial fission by reducing mitochondrial fusion proteins, exacerbating mitochondrial dysfunction and apoptosis. BGP-15 ameliorated TauKQ-induced mitochondrial dysfunction and apoptosis by improving mitochondrial dynamics. Our findings suggest that acetylation of K274/281 represents an important post-translational modification site regulating mitochondrial dynamics, and that BGP-15 holds potential as a therapeutic agent for mitochondria-associated diseases such as AD.

A UV non-hydrogen pure selenite nonlinear optical material for achieving balanced properties through framework-optimized structural transformation.

For non-centrosymmetric (NCS) oxides intended for ultraviolet (UV) nonlinear optical (NLO) applications, achieving a wide band gap, large second harmonic generation (SHG) intensity, and sufficient birefringence to satisfy phase matching is a significant challenge due to their inherent incompatibility. To address this issue, this study proposes a strategy called framework-optimized structural transformation. Building upon centrosymmetric (CS) NaGa(SeO3)2 as a foundation, an original UV selenite NLO material, NaLu(SeO3)2, was successfully synthesized. The derived NaLu(SeO3)2 exhibits a balanced comprehensive performance, including a band gap (5.3 eV), an SHG response (2.7 × KDP), a UV cut-off edge (210 nm), a laser-induced damage threshold (LIDT) (151.69 MW cm-2), birefringence (Cal: 0.138@546 nm, Exp: 0.153@546 nm), thermal stability (∼575 °C) and environmental stability. Notably, its SHG effect, band gap, LIDT, and birefringence are all the largest among UV non-hydrogen pure selenite materials. Such progress can be attributed to the successful arrangement of the SeO3 groups by optimizing the cations on the framework of the parent compound.

Ca2 Ln(BS3 )(SiS4 ) (Ln = La, Ce, and Gd): Mixed Metal Thioborate-Thiosilicates as Well-Performed Infrared Nonlinear Optical Materials.

The first examples of thioborate-thiosilicates, namely Ca2 Ln(BS3 )(SiS4 ) (Ln = La, Ce, and Gd), are synthesized by rationally designed high-temperature solid-state reactions. They crystalize in the polar space group P63 mc and feature a novel three-dimensional crystal structure in which the discrete [BS3 ]3- and [SiS4 ]4- anionic groups are linked by Ca2+ and Ln3+ cations occupying the same atomic site. Remarkably, all three compounds show comprehensive properties required as promising infrared nonlinear optical materials, including phase-matchable strong second harmonic generation (SHG) responses at 2.05 µm (1.1-1.2 times that of AgGaS2 ), high laser-induced damage thresholds (7-10 times that of AgGaS2 ), wide light transmission range (0.45-11 µm), high thermal stabilities (>800 °C), and large calculated birefringence (0.126-0.149 @1064 nm), which justify the material design strategy of combining [BS3 ]3- and [SiS4 ]4- active units. Theoretical calculations suggest that their large SHG effects originate mainly from the synergy effects of the LnS6 , BS3 , and SiS4 groups. This work not only broadens the scope of research on metal chalcogenides but also provides a new synthetic route for mixed anionic thioborates.

Ba4B14O25: A Deep Ultraviolet Transparent Nonlinear Optical Crystal with Strong Second Harmonic Generation Response Achieved by a Boron-Rich Closed-Loop Strategy.

Discovering new deep ultraviolet (DUV) nonlinear optical (NLO) materials is the current research hotspot. However, how to perfectly integrate several stringent performances into a crystal is a great challenge because of the natural incompatibility among them, particularly wide band gap and large NLO coefficient. To tackle the challenge, a boron-rich closed-loop strategy is supposed, based on which a new barium borate, Ba4B14O25, is designed and synthesized successfully via the high-temperature solid-state melting method. It features a highly polymeric 3D geometry with the closed-loop anionic framework [B14O25]8- constructed by the fundamental building blocks [B14O33]24-. The high-density π-conjugated [BO3]3- groups and the fully closed-loop B-O-B connections make Ba4B14O25 possess excellent NLO properties, including short UV cutoff edge (<200 nm), large second harmonic generation response (3.0 × KDP) and phase-matching capability, being a promising DUV-transparent NLO candidate material. The work provides a creative design strategy for the exploration of DUV NLO crystals.

(C5H6.16N2Cl0.84)(IO2Cl2): a birefringent crystal featuring unprecedented (IO2Cl2)- anions and π-conjugated organic cations.

Birefringent crystals can manipulate the polarization state of lasers and have vital application in polarizers, optical isolators, phase compensators, etc. The design and synthesis of crystals with large birefringence remains a challenging task. To design crystals with large birefringence, we combine an unprecedented chloroiodate(v) group (IO2Cl2)- featuring large polarizability anisotropy and a strong stereochemically active lone pair (SCALP) with the π-conjugated 2-amino-5-chloropyridine group. The superior synergy effect of (IO2Cl2)- and 2-amino-5-chloropyridine groups produces a new birefringent crystal, namely (C5H6.16N2Cl0.84)(IO2Cl2). It exhibits remarkably large birefringence of 0.67 at 546 nm, far exceeding those of most visible birefringent materials reported. This work discovers the first chloroiodate(v) group and provides a new synthetic route for birefringent materials.

Highly Birefringent d0 Transition Metal Fluoroantimonite in the Mid Infrared Band: Order-Disorder Regulation by Cationic Size.

An unusual O/F ordered d0 transition metal fluoroantimonite, namely, K2SbMoO2F7, has been created by the cationic size effect of alkali metals. It features the largest birefringence of 0.220@550 nm among inorganic antimonites with a halogen element, which is an order of magnitude larger than the disordered A2SbMoO2F7 (A = Rb, Cs). These three new compounds exhibit two different structures, although all of the structures were made of [SbMoO2F7]2- chains formed by SbF5 square pyramids and MoO2F4 octahedrons. A transparent single crystal of K2SbMoO2F7 with dimensions of 7.0 × 5.0 × 1.0 mm3 has been successfully grown by the aqueous solution volatilization method. The UV-vis-MIR transmission spectrum showed that K2SbMoO2F7 can display excellent transmittance in the range of 0.5-5.0 µm and 6.0-9.8 µm, indicating its application potential as a birefringent material in the mid infrared band. This work offers a fresh approach to the design and synthesis of mid infrared birefringent materials.

Ln2 F2 (OH2 )(MoO3 )2 (SeO3 )2 : Promising Multifunctional Nonlinear Optical Materials Created by Partial Fluorination Strategy under Corrosion Resistant Supercritical Reactions.

It has historically been exceedingly challenging to create physically and chemically stable lanthanide compounds with strong second harmonic generation (SHG) due to their strong preference to central symmetry. In this work, five new non-centrosymmetric lanthanide selenites, namely, Ln2 F2 (OH2 )(MoO3 )2 (SeO3 )2 (Ln = Sm, Eu, Gd, Tb and Dy), are achieved by partial fluorination of the lanthanide oxygen polyhedron. An HF corrosion resistant supercritical hydrothermal method is developed, which is a facile and universal method for HF corrosion and high-temperature high-pressure environment. The title compounds displayed a novel 3D framework composed of 1D molybdenum selenite chains bridged by Ln2 F2 O12 (OH2 ) dimers. Their powder SHG responses showed a large difference, ranging from 1.0 to 9.0 × KH2 PO4 (KDP) at 1064 nm. The half-filled Gd compound exhibited very strong SHG efficiency of up to 1.2 × KTP (KTiOPO4 ) at 2050 nm. Compounds Tb and Gd are the first lanthanide selenites with SHG intensity reaching KTP level, which is very rare in this system. Furthermore, these compounds can also possess excellent physicochemical stability and strong luminescence emission, indicating that they are promising multifunctional nonlinear optical materials. This work offered an effective way for design and synthesis of multifunctional and high-performant nonlinear optical materials.

Ce(IO3)3F and Ce(IO3)2(NO3): Two Mixed-Anion Cerium Iodates with Good Nonlinear Optical and Birefringent Properties.

Two new mixed-anion cerium iodates, namely, Ce(IO3)3F and Ce(IO3)2(NO3), have been rationally designed through the integration of hybrid anionic functional building blocks (FBBs). The structure of Ce(IO3)3F features a novel [Ce(IO3)3F] bilayer, and the material exhibits large birefringence (0.225 @546 nm). The structure of Ce(IO3)2(NO3) features [Ce3(IO3)6]3+ triple layers that are further linked by planar NO3- units. Ce(IO3)2(NO3) shows a moderate SHG response (1 × KDP) and a high laser-induced damage threshold value (22 × AgGaS2). This work demonstrates that the rich coordination geometries of cerium cations facilitate tuning of the structures of related compounds through modulating anionic FBBs.

α- and ß-(C4H5N2O)(IO3)·HIO3: Two SHG Materials Based on Organic-Inorganic Hybrid Iodates.

Organic-inorganic hybrid nonlinear optical (NLO) materials are highly anticipated because of the integration of both merits of the organic and inorganic moieties. Herein, the 2-pyrimidinone cation (C4H5N2O)+ has been incorporated into the iodate system to form two polymorphic organic-inorganic hybrid iodates, namely, α- and ß-(C4H5N2O)(IO3)·HIO3. They crystallize in different polar space groups (Ia and Pca21), and their structures feature one-dimensional (1D) chain structures composed of (C4H5N2O)+ cations, IO3- anions, and HIO3 molecules interconnected via hydrogen bonds. α- and ß-(C4H5N2O) (IO3)·HIO3 exhibit strong and moderate second-harmonic-generation (SHG) responses of 6.4 and 0.9 × KH2PO4 (KDP), respectively, the same band gaps of 3.65 eV, and high powder laser-induced damage threshold (LIDT) values [51 and 57 × AgGaS2 (AGS)]. The results of theoretical calculations revealed that the large SHG effect of α-(C4H5N2O)(IO3)·HIO3 originated from the IO3 and HIO3 groups. This work indicates that (C4H5N2O)+ is a potential group for designing new NLO materials with brilliant optical performances.

(NH4 )2 (I5 O12 )(IO3 ) and K1.03 (NH4 )0.97 (I5 O12 )(IO3 ): Mixed-Valent Polyiodates with Unprecedented I5 O12 - Unit Exhibiting Strong Second-Harmonic Generation Responses and Giant Birefringence.

Second-harmonic generation (SHG) response and birefringence are crucial properties for linear and nonlinear optical (NLO) materials, while it is difficult to further optimize these two key properties by using a single traditional functional building block (FBB) in one compound. Herein, a novel IO4 5- unit is identified, which possesses a square-planar configuration and two stereochemically active lone-pairs (SCALPs). By combining IO4 5- and IO3 - units, the first examples of mixed-valent polyiodates featuring an unprecedented bowl-shaped I5 O12 - polymerized unit, namely (NH4 )2 (I5 O12 )(IO3 ) and K1.03 (NH4 )0.97 (I5 O12 )(IO3 ), are successfully synthesized. Excitingly, both crystals exhibit strong SHG responses (16 × KDP and 19.5 × KDP @1064 nm) as well as giant birefringence (∆nexp  = 0.431 and 0.405 @546 nm). Detailed structure-property analyses reveal that the parallel aligned planar IO4 5- units induce the properly aligned high-density SCALPs, leading to strong SHG response and giant birefringence for both materials. This work not only provides two new potential NLO and birefringent crystals, but also discovers a novel promising FBB (IO4 5- ) for developing high-performance linear and nonlinear optical materials.

Single-Crystalline Li2Sn(IO3)6 Microwires: Combining Optical-Waveguiding and Frequency-Doubling Functions.

High-quality single-crystalline Li2Sn(IO3)6 microwires (MWs) have been successfully prepared by using a facile hydrothermal method. The as-synthesized Li2Sn(IO3)6 MWs exhibit regular hexagonal prism morphology, excellent surface smoothness, and remarkable diameter uniformity. The optical propagation loss has been determined to be as low as 0.026 dB µm-1 at 785 nm wavelength, implying the low-loss optical waveguiding capability of the Li2Sn(IO3)6 MWs. The effective frequency-doubling conversions of the fundamental frequency light source in the wavelength range from 916 to 1560 nm have been observed, and the second-harmonic generation (SHG) conversion efficiency has been measured to be 2.1% with a 1560 nm fundamental pump source (pulse duration of 10 ns, and average power of 9.06 nW) transmitted through a 1.32-µm-diameter and 300-µm-length Li2Sn(IO3)6 MW. These intriguing optical waveguiding and strong SHG conversion capabilities of the Li2Sn(IO3)6 MWs suggest its potential applications for photonic devices in micrometer scale.

AAl(Te4O10) (A = Na, Ag) and K2Ga2(HTe6O16)(HTeO3): Three Aluminum/Gallium Tellurites with Large Birefringence and Wide Band Gap.

The exploration of novel inorganic tellurites is significant because of their promising applications in nonlinear-optical materials and birefringent materials. Herein, three new aluminum/gallium tellurites, namely, NaAl(Te4O10) (1), AgAl(Te4O10) (2), and K2Ga2(HTe6O16)(HTeO3) (3), have been successfully obtained by mild hydrothermal reactions. The isostructural compounds 1 and 2 contain the Te3O8 trimer, while compound 3 contains an unprecedented Te6O16 hexamer. Notably, all three compounds exhibit large birefringence values of over 0.1 at 532 nm, which are currently the largest reported birefringence values among tellurium(IV) oxides without additional anionic groups.

AKTeO2(CO3) (A = Li, Na): The First Carbonatotellurites Featuring a Zero-Dimensional [Te2C2O10]4- Cluster and a Wide Band Gap.

The first carbonatotellurites, AKTeO2(CO3) (A = Li, Na), have been successfully synthesized by using boric acid as the mineralizer. AKTeO2(CO3) (A = Li, Na) crystallize in the monoclinic space group P21/n (no. 14), and their structures exhibit the novel zero-dimensional (0D) [Te2C2O10]4- clusters, in which two [TeO4]4- groups form a [Te2O6]4- dimer via edge-sharing, with each side of the dimer attached by a [CO3]2- group via a Te-O-C bridge. The alkali metal cations occupy the voids between the 0D clusters and maintain the charge balance. The ultraviolet-visible-near-infrared diffuse reflectance spectra show that the short absorption cut-off edges of LiKTeO2(CO3) (LKTC) and NaKTeO2(CO3) (NKTC) are 248 and 240 nm, respectively, and LKTC exhibits the largest experimental band gap (4.58 eV) among all of the tellurites containing the π-conjugated anionic groups reported. Theoretical calculations revealed that they exhibit moderate birefringences of 0.029 and 0.040@1064 nm, respectively.