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We employed all-atom molecular dynamics simulations to explore the mechanical response of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the bending and twisting deformations, as well as their stiffnesses, using the tilt, roll, and twist modes under stretching force. Findings indicate that the roll and twist angles vary linearly with the stretching force but show opposite trends. The tilt, roll, and twist elastic moduli are considered constants, while the coupling between roll and twist modes slightly decreases under stretching force. The effect of the stretching force on the roll and twist modes, including both their deformations and elasticities, exhibits sequence-dependence, with symmetry around the base pair step. Furthermore, we examined the overwinding path and mechanism of dsDNA from the perspective of the stiffness matrix, based on the tilt, roll, and twist modes. The correlations among tilt, roll, and twist angles imply an alternative overwinding pathway via twist–roll coupling when dsDNA is stretched, wherein entropic contribution prevails. [ABSTRACT FROM AUTHOR]

We evaluated the dissociation of isolated gas-phase nucleobase molecules induced by mega electron volt (MeV)-energy ions to gain fundamental insights into the reactions of nucleobases upon fast ion irradiation. We studied five nucleobase molecules—adenine, guanine, cytosine, thymine, and uracil—as gas-phase targets. We compared the fragmentation patterns obtained from carbon ion impacts with those obtained from proton impacts to clarify the effect of heavy ion irradiation. We also compared the results with electron impact and photoionization results. In addition, we identified several delayed fragmentation pathways by analyzing the correlation between fragment pairs generated from singly and doubly charged intermediate ions. To determine the lifetimes of delayed fragmentation from singly charged intermediate ions, we evaluated the detection efficiencies of the microchannel plate detector for the neutral fragment HCN as a function of kinetic energy using a new methodology. As the first demonstration of this method, we estimated the lifetimes of C5H5N5+ generated by 1.2-MeV C+ and 0.5-MeV H+ collisions to be 0.87 ± 0.43 and 0.67 ± 0.09 µs, respectively. These lifetimes were approximately one order of magnitude longer than those of the doubly charged intermediate ion C5H5N52+. [ABSTRACT FROM AUTHOR]

In recent years, magnetic skyrmion-based spin-torque nano-oscillators (STNOs) have attracted considerable interest for their prospect in future-generation communication and spintronic technologies. However, some critical issues, which hamper their practical applications, e.g., the long start-up time and variable skyrmion gyration orbit, remain to be resolved. Here, we numerically demonstrate the realization of a fixed-orbit STNO, which is based on an interlayer-coupled meron–skyrmion (MS) pair instead of a magnetic skyrmion. In this STNO, the MS pair possesses a structurally defined, fixed orbit within a broad range of driving currents, even in the presence of random defects. The output frequency range of the STNO based on an MS pair far exceeds that of the STNO typically featuring a single skyrmion. Moreover, the output frequency of this STNO can be further elevated if more MS pairs are incorporated. Our results reveal the nontrivial dynamics of the interlayer-coupled MS pair, opening perspectives for the design and optimization of fundamental spintronic devices. [ABSTRACT FROM AUTHOR]

Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs all-atom models using stiffness matrices in Fourier space (q-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version, cgDNA+. Our analysis shows that while cgDNA+ closely follows the q-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables, which are rather strong in the q → 0 (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated. [ABSTRACT FROM AUTHOR]

In this paper, we develop and analyze a number of perturbation series that target the coupled cluster singles and doubles (CCSD) ground state energy. We show how classical Møller–Plesset perturbation theory series can be restructured to target the CCSD energy based on a reference CCS calculation and how the corresponding cluster perturbation series differs from the classical Møller–Plesset perturbation series. Subsequently, we reformulate these series using the coupled cluster Lagrangian framework to obtain series, where fourth and fifth order energies are determined only using parameters through second order. To test the methods, we perform a series of test calculations on molecular photoswitches of both total energies and reaction energies. We find that the fifth order reaction energies are of CCSD quality and that they are of comparable accuracy to state-of-the-art approximations to the CCSD energy based on local pair natural orbitals. The advantage of the present approach over local correlation methods is the absence of user defined threshold parameters for neglecting or approximating contributions to the correlation energy. Fixed threshold parameters lead to discontinuous energy surfaces, although this effect is often small enough to be ignored, but the present approach has a differentiable energy that will facilitate derivation and implementation of gradients and higher derivatives. A further advantage is that the calculation of the perturbation correction is non-iterative and can, therefore, be calculated in parallel, leading to a short time-to-solution. [ABSTRACT FROM AUTHOR]

We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations. [ABSTRACT FROM AUTHOR]

Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA–DNA attraction, shifting the equilibrium away from the DNA condensed phase. [ABSTRACT FROM AUTHOR]

Torsional and bending deformations of DNA molecules often occur in vivo and are important for biological functions. DNA "under stress" is a conformational state, which is by far the most frequent state during DNA–protein and gene regulation. In DNA minicircles of length < 100 base pairs (bp), the combined effect of torsional and bending stresses can cause local unusual conformations, with certain base pair steps often absorbing most of the stress, leaving other steps close to their relaxed conformation. To better understand the superhelical dynamics of DNA under stress, molecular simulations of 94 bp minicircles with different torsional linking numbers were interpreted using Fourier analyses and principal component analyses. Sharp localized bends of nearly 90° in the helical axis were observed, which in turn decreased fluctuations of the rotational register and helped redistribute the torsional stress into writhe, i.e., superhelical turn up to 360°. In these kinked minicircles, only two-thirds of the DNA molecule bends and writhes and the remaining segment stays close to straight and preserves a conformational flexibility typical of canonical B-DNA (bending of 39° ± 17° distributed parsimoniously across 36 bp), which was confirmed and visualized by principal component analysis. These results confirm that stressed DNA molecules are highly heterogeneous along their sequence, with segments designed to locally store and release stress so that nearby segments can stay relaxed. [ABSTRACT FROM AUTHOR]

DNA deformability and differential hydration are crucial determinants of biological processes ranging from genetic material packaging to gene expression; their associative details, however, remain inadequately understood. Herein, we report investigations of the dynamic and thermodynamic responses of the local hydration of a variety of base pair sequences. Leveraging in silico sampling and our in-house analyses, we first report the local conformational propensity of sequences that are either predisposed toward the canonical A- or B-conformations or are restrained to potential transitory pathways. It is observed that the transition from the unrestrained A-form to the B-form leads to lengthwise structural deformation. The insertion of intermittent -(CG)- base pairs in otherwise homogeneous -(AT)- sequences bears dynamical consequences for the vicinal hydration layer. Calculation of the excess (pair) entropy suggests substantially higher values of hydration water surrounding A conformations over the B- conformations. Applying the Rosenfeld approximation, we project that the diffusivity of water molecules proximal to canonical B conformation is least for the minor groove of the canonical B-conformation. We determine that structure, composition, and conformation specific groove dimension together influence the local hydration characteristics and, therefore, are expected to be important determinants of biological processes. [ABSTRACT FROM AUTHOR]

Nucleotides are organic compounds consisting of a phosphate group, a nitrogenous base, namely adenine (A), thymine (T), cytosine (C), or guanine (G), and a sugar, here deoxyribose. The magnitude of the first hyperpolarizability β of these four DNA nucleotides was determined in aqueous solution with the nonlinear optical technique of hyper rayleigh scattering under non resonant conditions at a fundamental wavelength of 800 nm. The smallest value is found to be 1.67 ± 0.15 × 10−30 esu for thymidine-5′-monophosphate and the highest is 1.76 ± 0.16 × 10−30 esu for 2′-guanosine-5′-monophosphate. Polarization resolved studies were also performed to question the symmetry of the first hyperpolarizability tensor and access the ratio of some elements of the first hyperpolarizability tensor. These experimental results were then compared to the theoretical values of these first hyperpolarizabilities obtained with the density functional theory at the level of the PCM-B3LYP/6-31G+(d) basis and taking into account the solvent. [ABSTRACT FROM AUTHOR]

Background: The expansion of sequencing technologies as a result of the response to the COVID-19 pandemic enabled pathogen (meta)genomics to be deployed as a routine component of surveillance in many countries. Scaling genomic surveillance, however, comes with associated costs in both equipment and sequencing reagents, which should be optimized. Here, we evaluate the cost efficiency and performance of different read lengths in identifying pathogens in metagenomic samples. We carefully evaluated performance metrics, costs, and time requirements relative to choices of 75, 150 and 300 base pairs (bp) read lengths in pathogen identification. Results: Our findings revealed that moving from 75 bp to 150 bp read length approximately doubles both the cost and sequencing time. Opting for 300 bp reads leads to approximately two- and three-fold increases, respectively, in cost and sequencing time compared to 75 bp reads. For viral pathogen detection, the sensitivity median ranged from 99% with 75 bp reads to 100% with 150–300 bp reads. However, bacterial pathogens detection was less effective with shorter reads: 87% with 75 bp, 95% with 150 bp, and 97% with 300 bp reads. These findings were consistent across different levels of taxa abundance. The precision of pathogen detection using shorter reads was comparable to that of longer reads across most viral and bacterial taxa. Conclusions: During disease outbreak situations, when swift responses are required for pathogen identification, we suggest prioritizing 75 bp read lengths, especially if detection of viral pathogens is aimed. This practical approach allows better use of resources, enabling the sequencing of more samples using streamlined workflows, while maintaining a reliable response capability. [ABSTRACT FROM AUTHOR]

The nutritional quality improvement is among the most integral objective for any rice molecular breeding programs. The seed storage proteins (SSPs) have greater role to determine the nutritional quality of any cereal grains. Rice contains relatively balanced amino acid composition and the SSPs are fractioned into albumins (ALB), globulins (GLO), prolamins (PRO) and glutelins (GLU) according to differences in solubility. GLUs are further divided into subfamilies: GluA, GluB, GluC, and GluD depending on resemblance in amino acid. The GLU protein accounts for 60–80% of total protein contents, encoded by 15 genes located on different chromosomes of rice genome. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was employed to knockout Glu-B (LOC-Os02g15070) gene in non-basmati rice PK386 cultivar. The mutant displayed two base pair and three base pair mutation in the targeted regions. The homozygous mutant plant displayed reduction for both in total protein contents and GLU contents whereas, elevation in GLO, ALB and PRO. Moreover, the mutant plant also displayed reduction in physio-chemical properties e.g., total starch, amylose and gel consistency. The agronomic characteristics of both mutant and wild type displayed non-significant differences along with increase in higher percentage of chalkiness in mutant plants. The results obtained from scanning electron microscopy showed the loosely packed starch granules compared to wild type. The gene expression analysis displayed the lower expression of gene at 5 days after flowering (DAF), 10 DAF, 15 DAF and 20 DAF compared to wild type. GUS sub-cellular localization showed the staining in seed which further validated the results obtained from gene expression. Based on these findings it can be concluded Glu-B gene have significant role in controlling GLU contents and can be utilized in breeding programs to enhance the nutritional quality of rice, and may serve as healthy diet for patient allergic with high GLU contents. [ABSTRACT FROM AUTHOR]

Transient melting of the duplex‐DNA (B‐DNA) during DNA transactions allows repeated sequences to fold into non‐B‐DNA structures, including DNA junctions and G‐quadruplexes. These noncanonical structures can act as impediments to DNA polymerase progression along the duplex, thereby triggering DNA damage and ultimately jeopardizing genomic stability. Their stabilization by ad hoc ligands is currently being explored as a putative anticancer strategy since it might represent an efficient way to inflict toxic DNA damage specifically to rapidly dividing cancer cells. The relevance of this strategy is only emerging for three‐way DNA junctions (TWJs) and, to date, no molecule has been recognized as a reference TWJ ligand, featuring both high affinity and selectivity. Herein, we characterize such reference ligands through a combination of in vitro techniques comprising affinity and selectivity assays (competitive FRET‐melting and TWJ Screen assays), functional tests (qPCR and Taq stop assays) and structural analyses (molecular dynamics and NMR investigations). We identify novel azacryptands TrisNP‐amphi and TrisNP‐ana as the most promising ligands, interacting with TWJs with high affinity and selectivity. These ligands represent new molecular tools to investigate the cellular roles of TWJs and explore how they can be exploited in innovative anticancer therapies. [ABSTRACT FROM AUTHOR]

The creation of frustrated Lewis pairs on catalyst surface is an effective strategy for tuning CO2 activation. The critical step in the formation of frustrated Lewis pairs is the spatial effect of proximal Lewis acid‐Lewis base pairs. Here, we demonstrate a facile surface functionalization methodology that enables hydrogen bonding between N and H atoms to mediate the construction of frustrated Lewis pairs in poly(heptazine imide), thereby increasing the propensity to activate CO2 molecules. Experimental and theoretical results show that the construction of active hydrogen bonding regions can facilitate the bending of CO2 molecules. Furthermore, the delocalization of electron clouds induced by the hydrogen bonding‐mediated frustrated Lewis pairs can promote the heterolytic cleavage and photocatalytic conversion of CO2. This work highlights the potential of utilizing hydrogen bonding‐mediated strategy in heterogeneously photocatalytic activation of CO2 over polymer materials. [ABSTRACT FROM AUTHOR]

The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics. [ABSTRACT FROM AUTHOR]

The aim of this work was to the obtaining novel mixed-mode stationary phases with increased hydrophilicity and applying them in ion and hydrophilic interaction liquid chromatography. The resins were obtained by the sequential covalent attachment of branched polyethylenimine and polyelectrolytes synthesized from diepoxide and a secondary amine on the surface of epoxidized polystyrene–divinylbenzene. To increase the shielding degree of the polymer substrate, an additional polymerization of glycidol was carried out in the functional layer of the sorbent at an increased pH of the reaction medium. The synthesized phases possessed increased hydrophilicity compared to most resins based on a styrene–divinylbenzene copolymer with covalently attached layers. This was evidenced in the ion chromatography mode by a decrease in the relative retention of polarizable anions, weakly hydrated oxyhalides (up to a change in the elution order of the bromate), and haloacetic acids. In the hydrophilic interaction liquid chromatography mode, an increased hydrophilicity of the phases was confirmed by an increase in the retention factors of polar analytes, as well as by the reversal of the elution order of ascorbic and nicotinic acids as compared to the phases based on polystyrene–divinylbenzene presented in the literature. The low efficiency of the obtained stationary phases in the ion chromatography mode was noted, which is associated with slow mass transfer in the bulk polymer functional layer. The negative impact of the polymer layer on efficiency in hydrophilic interaction liquid chromatography is less pronounced due to the presumably smaller thickness of the part of the functional layer involved in this mode. The proposed method for the synthesis of resins ensures an increase in the efficiency, selectivity, and separation ability of sorbents in the hydrophilic interaction liquid chromatography mode as compared to phases based on a styrene–divinylbenzene copolymer described previously in the literature. The resulting highly hydrophilic resins makes it possible to separate a mixture of 9 nitrogenous bases and nucleosides in 18 min, 6 vitamins in 24 min, and 8 sugars in 11 min. Thus, the method of substrate hydrophilization proposed in this work is promising for improving the chromatographic characteristics of phases in the hydrophilic interaction liquid chromatography mode and can be used to create sorbents with increased selectivity and efficiency. [ABSTRACT FROM AUTHOR]

Variants in the 5′ UTR of ANKRD26 are a common cause of inherited thrombocytopenia (ANKRD26‐RT), and are associated with sustained ANKRD26 expression, which inhibits megakaryocyte maturation and proplatelet formation. ANKRD26 expression is controlled by the binding of a RUNX1/FLI1 complex to the 5′ UTR. To date, all reported ANKRD26‐RD associated variants have been within the RUNX1 binding site and a 22 base pair flanking region. Here, we report a novel variant in the 5′ UTR of ANKRD26, c.‐107C>T. This variant is in the FLI1 binding site, and is predicted to disrupt FLI1 binding due to loss of a hydrogen bond with FLI1. Differentiated PBMCs from affected family members showed impaired megakaryocyte maturation and proplatelet formation and sustained expression of ANKRD26, and platelets from affected family members had higher ANKRD26 expression than control platelets. The variant increased activity of the ANKRD26 promotor in a reporter assay. We also provide evidence that the previously reported c.‐140C>G ANKRD26 5′ UTR variant is benign and not associated with thrombocytopenia. Identification of the c.‐107C>T variant extends the range of the regulatory region in the 5′ UTR of ANKRD26 that is associated with ANKRD26‐RT. [ABSTRACT FROM AUTHOR]

• Nodal explants can be used to micropropagate P. longum for ex-situ conservation. • Thidiazuron was the most efficient hormone for regenerating shoots. • Indole-3-butyric acid was the most efficient hormone for regenerating roots. • First report on genetic fidelity of mother and in vitro -raised P. longum plants. • No polymorphisms found between mother and in vitro plants for all tested markers. Piper longum L. has been widely used to treat digestive disorders, insomnia, diabetes, bronchitis, and cough since ancient times, which has caused a decline in its population in natural habitat. This study aims to develop a protocol for micropropagation in P. longum using direct organogenesis using nodal explant as well as to compare genetic uniformity between the mother plant and in vitro -grown plants using Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeats (ISSR), and Start Codon Targeted (SCoT) markers. Nodal explants were cultured on Murashige & Skoog (MS) medium added with α-naphthaleneacetic acid (NAA), Kinetin (KN), Thidiazuron (TDZ), 6-Benzylaminopurine (BAP), and 10 % coconut water. The highest number of shoots (5.33±1.15) and longest shoot length (6.16±0.65 cm) were found in MS media added with 1.0 mg/L TDZ, while the highest number of roots (7.0 ± 1.0) and the longest root length (5.53±0.35 cm) were found in MS media added with 1.0 mg/L Indole-3-butyric acid (IBA) in nodal explants. The evaluation of genetic homogeneity using 12 specific RAPD, ISSR, and SCoT markers revealed that the in vitro -raised plants are genetically very similar, or even identical, to the wild mother plants, and there is no polymorphism between the mother plant and in vitro -raised plants for the specific markers tested. Twelve of twenty-four RAPD, ISSR, and SCoT primers amplified a total of 39 loci varying in size from 150 to 1400 base pairs. This study showed that an effective protocol developed for the in vitro propagation of P. longum by direct organogenesis can be used to produce true-to-type plants, which may aid in homozygous breeding programs and ex-situ conservation and could be used for commercial propagation. [ABSTRACT FROM AUTHOR]

• Four methods with different cooling rates were applied to the tilapia freezing. • Volatile bases (TBV-N), thiobarbituric acid (TBARS), microstructure were analyzed. • TBV-N, colors parameters and TBARS were statistically significant in all treatments. • Air blast and combined method altered less the texture of fillets after storage time. • Cryogenic freezing showed thermal stress, cracking and tissue quality damaged. The Nile tilapia (Oreochromis niloticus) fillets were frozen with static air (SA) at -20 °C, air blast freezing (AF) at -25 °C, combined method (CM - immersion in liquid nitrogen followed by AF) and cryogenic freezing (CF - immersion in liquid nitrogen). The effects of different freezing methods and of storage time at -18 °C (0, 30, 60 and 90 days) on fillet quality were evaluated. The temperature records were obtained, and the freezing times were determined by monitoring the temperatures of the geometric centers of the fillets. For CF, CM, AF and SA, the freezing times were 5.32, 127, 146 and 268 min, respectively. The quality of the frozen fillets was evaluated by measuring pH, volatile nitrogenous bases (TBV-N), thiobarbituric acid reactive substances (TBARS), and fatty acids and by obtaining a texture profile and performing scanning electron microscopy (SEM). The samples frozen by CF, after storage, had the highest levels of TBV-N because the high freezing rate produced superficial cracks that negatively affected the quality of the fillets. Freezing the samples with SA produced the worst quality indices and the microstructure was visibly damaged, with greater spaces between the fibers left by ice crystals. For all parameters evaluated, freezing with AF and CM resulted in fast freezing rates and better-quality tilapia fillets for 90 days of storage. [Display omitted] [ABSTRACT FROM AUTHOR]

Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis (Mtb), the tuberculosis-causing agent, exhibits diverse genetic lineages, with known links to virulence. While genomic and transcriptomic variations between modern and ancient Mtb lineages have been explored, the role of small non-coding RNA (sRNA) in post-translational gene regulation remains largely uncharted. In this study, Mtb Lineage 1 (L1) Sabahan strains (n = 3) underwent sRNA sequencing, revealing 351 sRNAs, including 23 known sRNAs and 328 novel ones identified using ANNOgesic. Thirteen sRNAs were selected based on the best average cut-off value of 300, with RT-qPCR revealing significant expression differences for sRNA 1 (p = 0.0132) and sRNA 29 (p = 0.0012) between Mtb L1 and other lineages (L2 and L4, n = 3) (p > 0.05). Further characterization using RACE (rapid amplification of cDNA ends), followed by target prediction with TargetRNA3 unveils that sRNA 1 (55 base pairs) targets Rv0506, Rv0697, and Rv3590c, and sRNA 29 (86 base pairs) targets Rv33859c, Rv3345c, Rv0755c, Rv0107c, Rv1817, Rv2950c, Rv1181, Rv3610c, and Rv3296. Functional characterization with Mycobrowser reveals these targets involved in regulating intermediary metabolism and respiration, cell wall and cell processes, lipid metabolism, information pathways, and PE/PPE. In summary, two novel sRNAs, sRNA 1 and sRNA 29, exhibited differential expression between L1 and other lineages, with predicted roles in essential Mtb functions. These findings offer insights into Mtb regulatory mechanisms, holding promise for the development of improved tuberculosis treatment strategies in the future. [ABSTRACT FROM AUTHOR]

A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases. [ABSTRACT FROM AUTHOR]

Hydrolyzed proteins have gained significant importance in the food industry due to their potential antioxidant and antimicrobial properties. They have been recognized for their ability to improve the shelf life and safety of food products. In this study, the researchers focused on incorporating hydrolyzed protein from sesame meal (SMPH) into a composite coating along with chitosan-cress seed gum (CH-CG). The aim was to investigate the effect of this composite coating, in both free and nanoparticle forms, on the shelf life of ostrich fillets during a 12-day refrigerated storage period. Initially, SMPH was produced using microbial alcalase protease enzymes, and its degree of hydrolysis and antioxidant properties were evaluated. Then, SMPH was encapsulated using liposomes. Six treatments were evaluated to examine the effect of CH-CG coating and SMPH, in both free and nanoparticle forms, on the extension of the shelf life of ostrich fillets: control, CH-CG, CH-CG + 0.5% SMPH, CH-CG + 1% SMPH, CH-CG + 0.5% nano SMPH (NSMPH), and CH-CG + 1% NSMPH. Chemical parameters (peroxide value, thiobarbituric acid, and nitrogenous volatile bases) and microbial parameters (total bacterial count and psychrotrophic bacteria count) were periodically analyzed. The results showed that SMPH with a hydrolysis time of 90 min and a molecular weight of 3 kD exhibited the highest protein content, degree of hydrolysis, and DPPH free radical scavenging activity (P < 0.05). The particle size of NSMPH was found to be 56.3 nm, the zeta potential was 38.1 mV, and the encapsulation efficiency was 75.95%. The chemical and microbial analyses indicated that the composite coating with SMPH led to a slower increase in oxidative and microbial indices compared to the control treatment, and NSMPH enhanced its antimicrobial and antioxidant properties. Among all the treatments, the CH-CG + 1% NSMPH treatment demonstrated the most favorable results among all the tested treatments. Therefore, this treatment has the potential to serve as a natural preservative option in the meat industry, offering improved preservation, reduced spoilage, and enhanced product quality and safety. [ABSTRACT FROM AUTHOR]

Photodynamic therapy (PDT) combines a light source, oxygen, and a photosensitizer (PS) to generate reactive oxygen species (ROS) for treating diseases. In this study, we evaluated two meso‐tetra‐pyridyl porphyrins with [Pd(bpy)Cl]+, namely 3‐PdTPyP and 4‐PdTPyP, as PS for PDT application. DNA interaction was assessed by spectroscopic measurements (UV–Vis and fluorescence emission), viscosity analysis, and molecular docking simulations. The results indicate that Pd(II)‐porphyrins do not intercalate into DNA, suggesting that the minor groove is the primary interaction site, mainly through van der Waals forces. These metalloporphyrins effectively induced nitrogenous bases oxidation, particularly in purines, after white light irradiation. The induced DNA lesions were able to inactivate plasmid DNA metabolism (DNA replication and transcription) in a bacterial model. 3‐PdTPyP and 4‐PdTPyP significantly decreased the viability of treated melanoma cell lines (A375 and B16‐F10), demonstrating that melanoma cell lines were more sensitive to these Pd(II)‐porphyrins than the fibroblast cell line (L929). Moreover, 3‐PdTPyP was more photototoxic to A375 cells (IC50 = 0.43 μM), whereas 4‐PdTPyP was more photototoxic to B16‐F10 cells (IC50 = 0.51 μM). These findings suggest that these porphyrins are promising PS for future PDT research focused on skin cancer. [ABSTRACT FROM AUTHOR]

Finding the optimal beam pair and update time in 5G systems operating at mmWave frequencies is time-intensive and resource-demanding. This intricate procedure calls for the proposal of more intelligent approaches. Therefore, this work proposes a machine learning-based method for optimizing beam pair selection and its update time. The method is structured around three main modules: spatial characterization of beam pair service areas, training of a machine learning model using collected beam pair data, and an algorithm that uses the decision function of the trained model to compute the optimal update time for beam pairs based on the spatial position and velocity of user equipment. When the machine learning model is deployed in a network with a single gNB equipped with a 8 × 8 UPA and one UE equipped with a 1 × 2 UPA in an mmWave scenario simulated in NS3, improvements in SINR and throughput up to 407 % , were observed. Improvements are gathered because of a reduction of 85.7 % in beam pair selections because of an increase of approximately 1543 % in the effective time between successive beam pair searches. This method could offer real-time optimization of the beam pair procedures in 5G networks and beyond. [ABSTRACT FROM AUTHOR]

Organic molecule‐mediated noncanonical DNA self‐assembly expands the standard DNA base‐pairing alphabets. However, only a very limited number of small molecules have been recognized as mediators because of the tedious and complicated experiments like crystallization and microscopy imaging. Here we present an integrative screening protocol incorporating molecular dynamics (MD) for fast theoretical simulation and native polyacrylamide gel electrophoresis for convenient experimental validation. Melamine, the molecule that was confirmed mediating noncanonical DNA base‐pairing, and 38 other candidate molecules were applied to demonstrate the feasibility of this protocol. We successfully identified seven stable noncanonical DNA duplex structures, and another eight novel structures with sub‐stability. In addition, we discovered that hairpins at both ends can significantly stabilize the noncanonical DNA structures, providing a guideline to design small organic molecule‐incorporated DNA structures. Such an efficient screening protocol will accelerate the design of alternative DNA‐molecule architectures beyond Watson–Crick pairs. Considering the wide range of potential mediators, it will also facilitate applications such as noncovalent, highly dense loading of drug molecules in DNA‐based delivery system and probe design for sensitive detection of certain molecules. [ABSTRACT FROM AUTHOR]

The inherent chiral structures of DNA serve as attractive scaffolds to construct DNA hybrid catalysts for valuable enantioselective transformations. Duplex and G‐quadruplex DNA‐based enantioselective catalysis has made great progress, yet novel design strategies of DNA hybrid catalysts are highly demanding and atomistic analysis of active centers is still challenging. DNA i‐motif structures could be finely tuned by different cytosine‐cytosine base pairs, providing a new platform to design DNA catalysts. Herein, we found that a human telomeric i‐motif DNA containing cytosine‐silver(I)‐cytosine (C‐Ag+‐C) base pairs interacting with Cu(II) ions (i‐motif DNA(Ag+)/Cu2+) could catalyze Diels–Alder reactions with full conversions and up to 95 % enantiomeric excess. As characterized by various physicochemical techniques, the presence of Ag+ is proved to replace the protons in hemiprotonated cytosine‐cytosine (C : C+) base pairs and stabilize the DNA i‐motif to allow the acceptance of Cu(II) ions. The i‐motif DNA(Ag+)/Cu2+ catalyst shows about 8‐fold rate acceleration compared with DNA and Cu2+. Based on DNA mutation experiments, thermodynamic studies and density function theory calculations, the catalytic center of Cu(II) ion is proposed to be located in a specific loop region via binding to one nitrogen‐7 atom of an unpaired adenine and two phosphate‐oxygen atoms from nearby deoxythymidine monophosphate and deoxyadenosine monophosphate, respectively. [ABSTRACT FROM AUTHOR]

RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick RNA hairpins, the most basic secondary structure elements, undergo a glass-like transition below TG ~ 20 °C where the heat capacity abruptly changes and the RNA folds into a diversity of misfolded structures. We hypothesize that an altered RNA biochemistry, determined by sequence-independent ribose-water interactions, outweighs sequencedependent base pairing. The ubiquitous ribose-water interactions lead to universal RNA phase transitions below TG, such as maximum stability at TS ~ 5 °C where water density is maximum, and cold denaturation at TC ~ 50 °C. RNA cold biochemistry may have a profound impact on RNA function and evolution. [ABSTRACT FROM AUTHOR]

DNA origami nanostructures (DONs) are able to scavenge reactive oxygen species (ROS) and their scavenging efficiency toward ROS radicals was shown to be comparable to that of genomic DNA. Herein, we demonstrate that DONs are highly efficient singlet oxygen quenchers outperforming double‐stranded (ds) DNA by several orders of magnitude. To this end, a ROS mixture rich in singlet oxygen is generated by light irradiation of the photosensitizer methylene blue and its cytotoxic effect on Escherichia coli cells is quantified in the presence and absence of DONs. DONs are found to be vastly superior to dsDNA in protecting the bacteria from ROS‐induced damage and even surpass established ROS scavengers. At a concentration of 15 nM, DONs are about 50 000 times more efficient ROS scavengers than dsDNA at an equivalent concentration. This is attributed to the dominant role of singlet oxygen, which has a long diffusion length and reacts specifically with guanine. The dense packing of the available guanines into the small volume of the DON increases the overall quenching probability compared to a linear dsDNA with the same number of base pairs. DONs thus have great potential to alleviate oxidative stress caused by singlet oxygen in diverse therapeutic settings. [ABSTRACT FROM AUTHOR]

This paper is an attempt to generalize the nitrogen isotope information of the molecules that make up the cell from our point of view. Nitrogen in the cell exists as 20 proteinaceous amino acids, nucleobases, hemes, chlorophylls, and others, and their composition is similar among organisms. Based on a physiologically simple autonomous system that maintains a balance between inputs and outputs, it is theoretically predicted that 15N is distributed to each cellular compound with a certain regularity, and thus a specific relationship in nitrogen isotopic ratios among compounds. Previous studies essentially confirm this. The nitrogen isotopic ratio of compound i constituting the cell can be generalized as δ15Ni = δ15Nplant + Δi (TP − 1) + γi, where TP represents the trophic position, and Δi and γi are the trophic discrimination factor and the intracellular 15N distribution of compound i, respectively. Knowing reliable values of Δi and γi will help us to better understand nitrogen dynamics in the biosphere and advance our understanding of the picture of the Earth's environment through biogeochemistry. [ABSTRACT FROM AUTHOR]

The detection of enhancer-promoter interactions (EPIs) is crucial for understanding gene expression regulation, disease mechanisms, and more. In this study, we developed TF-EPI, a deep learning model based on Transformer designed to detect these interactions solely from DNA sequences. The performance of TF-EPI surpassed that of other state-of-the-art methods on multiple benchmark datasets. Importantly, by utilizing the attention mechanism of the Transformer, we identified distinct cell type-specific motifs and sequences in enhancers and promoters, which were validated against databases such as JASPAR and UniBind, highlighting the potential of our method in discovering new biological insights. Moreover, our analysis of the transcription factors (TFs) corresponding to these motifs and short sequence pairs revealed the heterogeneity and commonality of gene regulatory mechanisms and demonstrated the ability to identify TFs relevant to the source information of the cell line. Finally, the introduction of transfer learning can mitigate the challenges posed by cell type-specific gene regulation, yielding enhanced accuracy in cross-cell line EPI detection. Overall, our work unveils important sequence information for the investigation of enhancer-promoter pairs based on the attention mechanism of the Transformer, providing an important milestone in the investigation of cis-regulatory grammar. [ABSTRACT FROM AUTHOR]

Background: β-Aminobutyric acid (BABA) has been successfully used to prime stress resistance in numerous plant species; however, its effectiveness in forest trees has been poorly explored thus far. This study aimed to investigate the influence of BABA on morphological, physiological, and epigenetic parameters in field elms under various growth conditions. Epigenetic changes were assessed in both DNA and RNA through the use of reversed-phase ultra-performance liquid chromatography (UPLC) coupled with sensitive mass spectrometry. Results: The presented results confirm the influence of BABA on the development, physiology, and stress tolerance in field elms. However, the most important findings are related to the broad epigenetic changes promoted by this amino acid, which involve both DNA and RNA. Our findings confirm, for the first time, that BABA influences not only well-known epigenetic markers in plants, such as 5-methylcytosine, but also several other non-canonical nucleobases, such as 5-hydroxymethyluracil, 5-formylcytosine, 5-hydroxymethylcytosine, N6-methyladenine, uracil (in DNA) and thymine (in RNA). The significant effect on the levels of N6-methyladenine, the main bacterial epigenetic marker, is particularly noteworthy. In this case, the question arises as to whether this effect is due to epigenetic changes in the microbiome, the plant genome, or both. Conclusions: The plant phenotype is the result of complex interactions between the plant's DNA, the microbiome, and the environment. We propose that different types of epigenetic changes in the plant and microbiome may play important roles in the largely unknown memory process that enables plants to adapt faster to changing environmental conditions. [ABSTRACT FROM AUTHOR]

DNA is continuously exposed to a variety of harmful factors, which, on the one hand, can force undesirable processes such as ageing, carcinogenesis and mutagenesis, while on the other hand, can accelerate evolutionary changes. Of all the canonical nucleosides, 2′-deoxyguanosine (dG) exhibits the lowest ionization potential, making it particularly prone to the one-electron oxidizing process. The most abundant type of nucleobase damage is constituted by 7,8-dihydro-8-oxo-2′-deoxyguanosine (OXOdG), with an oxidation potential that is 0.56 V lower than that of canonical dG. All this has led to OXOdG, as an isolated lesion, being perceived as a sink for radical cations in the genome. In this paper, a comparative analysis of the electronic properties of an OXOGC base pair within the context of a clustered DNA lesion (CDL) has been conducted. It is based on previous DFT studies that were carried out at the M06-2x/6-31++G** level of theory in non-equilibrated and equilibrated condensed phases. The results of the comparative analysis presented here reveal the following: (A) The ionization potentials of OXOG4C2 were largely unaffected by a second lesion. (B) The positive charge and spin were found predominantly on the OXOG4C2 moiety. (C) The electron-hole transfers A3T3→G4C2 and G4C2←A5T1 were found in the Marcus inverted region and were resistant to the presence of a second DNA lesion in close proximity. It can therefore be reasonably postulated that OXOGC becomes the sink for a radical cation migrating through the double helix, irrespective of the presence of other 2′-deoxyguanosine lesions in the CDL structure. [ABSTRACT FROM AUTHOR]

Simple Summary: Pig production has environmental impacts such as global warming and eutrophication. This is closely linked to the feed efficiency of production, i.e., how much feed is required to produce a given quantity of pig meat; this depends on traits such as growth rate, feed intake, and litter size. Commercial pig breeding creates genetic improvement in those traits, and this should reduce the environmental impact. We applied two life cycle assessment (LCA) studies to quantify this reduction. In the first LCA, we compared the environmental impact of pigs in 2021 to the predicted impact for 2030, and we found a 7–9% improvement over those 9 years. In the second LCA, we compared the impact of pigs from a particular breeding company to the North American pig industry average, and we found that those pigs have a 7–8% lower impact. We conclude that commercial pig breeding delivers positive environmental outcomes as a result of its selection for production and reproduction traits. Lifecycle assessment (LCA) quantified changes in environmental impact categories (global warming, eutrophication, etc.) from 2021 to 2030 due to genetic trends in (re)production traits in pig lines of the breeding company Genus-PIC. The 2030 levels were projected with selection index theory based on weightings of traits in the breeding goals and genetic covariances among them. The projected improvement was 0.9% annually for most impact categories. Another LCA compared the impacts of 2021 North American pig production based on PIC genetics versus the industry average. Software openLCA converted material and energy flows to impact categories of frameworks ReCiPe-2016, PEF-3.1, and IPCC-2021. Flows came from data recorded by customers (1.1/4.7 million sows/finishing pigs) and by subscribers to a third-party data aggregator (1.3/9.1 million). PIC genetics have a 7–8% better impact than industry average for 13/18 categories of ReCiPe-2016, 19/25 of PEF-3.1, and all categories of IPCC-2001. Pig breeding delivers positive environmental outcomes as correlated responses to selection for profitability-oriented breeding goals. This trend is additive; technology development will increase it. Different investment levels in breeding population structure and technology and different operational efficiencies of breeding companies cause substantial differences in the environmental impact of pig production. [ABSTRACT FROM AUTHOR]

Simple Summary: Activin is a dimeric growth factor with diverse biological activities in vertebrates. This study aimed to investigate the regulatory role of the activin signaling pathway in the ovary of cultured Acipenser sinensis. One activinβA subunit with a full-length cDNA sequence of 1572 base pairs was identified. Multiple sequence alignment and phylogenetic analyses indicated the conserved evolution of ActivinβA from mammals to fish species. Transcripts of activinβA were distributed ubiquitously in ovary and non-ovarian tissues. The in vitro human recombinant Activin A incubation stimulated not only the activin system-related gene transcriptions of activinβA, follistatin, its receptors activinRIIA and activinRIIB, and smad2, smad3, and smad4, but also the ovary development-related genes cyp19a1a, erα, and erβ. Gonadotropin activated activin signaling by recruiting activinβA, follistatin, activinRIIA, and smad2. These results were helpful for not only the molecular exploration of activin signaling in fish species, but also the ovarian maturation regulation of A. sinensis. Activin is a dimeric growth factor with diverse biological activities in vertebrates. This study aimed to investigate the regulatory role of the activin signaling pathway in the ovary of the endangered, cultured sturgeon species Acipenser sinensis. One activinβA subunit was identified, with a full-length complementary DNA (cDNA) sequence of 1572 base pairs. Multiple sequence alignment suggested that ActivinβA shared high sequence identities with its counterparts in four other sturgeon species. Phylogenetic analysis indicated the conserved evolution of ActivinβA among vertebrates from mammals to fish species. Transcripts of activinβA were distributed ubiquitously in the liver, kidney, intestine, ovary, midbrain, hypothalamus, and pituitary, with the highest transcription found in the pituitary. In Chinese sturgeon ovarian cells, in vitro human recombinant Activin A incubation stimulated the activin system-related gene transcriptions of activinβA, follistatin, its receptors -activinRIIA and activinRIIB, and drosophila mothers against decapentaplegic proteins (smads) smad2, smad3, and smad4. Ovary development-related mRNA levels of cyp19a1a and aromatase receptors of erα and erβ were enhanced by Activin A or human chorionic gonadotropin (hCG) incubation. Furthermore, 15 IU/mL hCG treatment increased the transcription levels of activinβA, follistatin, activinRIIA, and smad2. This suggested that the activin system was functional for the regulation of ovary development in Chinese sturgeon, possibly under the regulation of gonadotropin, by recruiting activinβA, follistatin, activinRIIA, and smad2. These results were helpful for the molecular exploration of activin signaling in fish species, as well as the ovarian maturation regulation of A. sinensis. [ABSTRACT FROM AUTHOR]

Rationale and Objectives: To evaluate the targeting accuracy of a novel robot-assisted guidance technique relying on one pair of 2D C-arm images. Material and Methods: In total, 160 punctures were carried out semi-automatically by using a novel robotic device. The needle's paths were planned based on one pair of 2D fluoroscopic images from different angles. Conically shaped aluminum tips inside a gelatin-filled plexiglass phantom served as targets. The accuracy of the needle placement was assessed by taking control CTs and measuring the Euclidean distance (ED) and normal distance (ND) between the needle and the target point. In addition, the procedural time per needle placement was evaluated. Results: The accomplished mean NDs at the target for the 45°, 60°, 75° and 90° angles were 1.86 mm (SD ± 0.19), 2.68 mm (SD ± 0.18), 2.19 mm (SD ± 0.18) and 1.86 mm (SD ± 0.18), respectively. The corresponding mean EDs were 2.32 mm (SD ± 0.16), 2.68 mm (SD ± 0.18), 2.65 mm (SD ± 0.16) and 2.44 mm (SD ± 0.15). The mean duration of the total procedure, including image acquisition, trajectory planning and placement of four needles sequentially, was 12.7 min. Conclusions: Robotic guidance based on two 2D fluoroscopy images allows for the precise placement of needle-like instruments at the first attempt without the need for using an invasive dynamic reference frame. This novel approach seems to be a valuable tool for the precise targeting of various anatomical structures that can be identified in fluoroscopic images. [ABSTRACT FROM AUTHOR]

HIV-1 transcript function is controlled in part by twinned transcriptional start site usage, where 5' capped RNAs beginning with a single guanosine (1G) are preferentially packaged into progeny virions as genomic RNA (gRNA) whereas those beginning with three sequential guanosines (3G) are retained in cells as mRNAs. In 3G transcripts, one of the additional guanosines base pairs with a cytosine located within a conserved 5' polyA element, resulting in formation of an extended 5' polyA structure as opposed to the hairpin structure formed in 1G RNAs. To understand how this remodeling influences overall transcript function, we applied in vitro biophysical studies with in-cell genome packaging and competitive translation assays to native and 5' polyA mutant transcripts generated with promoters that differentially produce 1G or 3G RNAs. We identified mutations that stabilize the 5' polyA hairpin structure in 3G RNAs, which promote RNA dimerization and Gag binding without sequestering the 5' cap. None of these 3G transcripts were competitively packaged, confirming that cap exposure is a dominant negative determinant of viral genome packaging. For all RNAs examined, conformations that favored 5' cap exposure were both poorly packaged and more efficiently translated than those that favored 5' cap sequestration. We propose that structural plasticity of 5' polyA and other conserved RNA elements place the 5' leader on a thermodynamic tipping point for low-energetic (~3 kcal/mol) control of global transcript structure and function. [ABSTRACT FROM AUTHOR]

Fludarabine (FA) is still considered as a first-line chemotherapy drug for hematological tumors related to B lymphocytes. However, it is worth noting that the non-specific distribution and non-different cytotoxicity of FA may lead to irreversible consequences such as central nervous system damage such as blindness, coma, and even death. Therefore, it is very important to develop a system to targeting delivery FA. In preliminary studies, it was found that B lymphoma cells would specific highly expressing the sialic acid-binding immunoglobulin-like lectin 2 (known as CD22). Inspired by the specific recognition of sialic acid residues and CD22, we have developed a supramolecular prodrug based on polysialic acid, an endogenous biomacromolecule, achieving targeted-therapy of B-cell non-Hodgkin's lymphoma (B-NHL). Specifically, the prepared hydrophobic reactive oxygen species-responsive FA dimeric prodrug (F2A) interacts with the TPSA, which polysialic acid were modified by the thymidine derivatives, through non-covalent intermolecular interactions similar to "Watson–Crick" base pairing, resulting in the formation of nanoscale supramolecular prodrug (F@TPSA). Cell experiments have confirmed that F@TPSA can be endocytosed by CD22+ B lymphoma cells including Raji and Ramos cells, and there is a significant difference of endocytosis in other leukocytes. Furthermore, in B-NHL mouse model, compared with FA, F@TPSA is determined to have a stronger tumor targeting and inhibitory effect. More importantly, the distribution of F@TPSA in vivo tends to be enriched in lymphoma tissue rather than nonspecific, thus reducing the leukopenia of FA. The targeted delivery system based on PSA provides a new prodrug modification strategy for targeted treatment of B-NHL. [ABSTRACT FROM AUTHOR]

The genus Ainsliaea DC. is one of the major groups within the tribe Pertyeae (Asteraceae). It comprises several important Chinese medicinal species. However, the phylogenetic position has undergone a long process of exploration. The complete chloroplast (cp) genome sequences data has not been employed in species identification and phylogeny of Ainsliaea. In this study, the complete cp genomes of two Ainsliaea species (A. gracilis and A. henryi) were reported, followed by structural, comparative, and phylogenetic analyses within the tribe Peryteae. Both cp genomes displayed a typical quadripartite circular structure, with the LSC and SSC regions separated by the IR regions. The genomes were 152,959 (A. gracilis) and 152,805 (A. henryi) base pairs (bp) long, with a GC content of 37.6%. They were highly conserved, containing 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1). Moreover, thirteen highly polymorphic regions (e.g., trnK-UUU, trnG-UCC, trnT-GGU, accD-psaI, and rpl22-rps19) were identified, indicating their potential as DNA barcodes. The phylogenetic analysis confirmed the placement of Ainsliaea in the tribe Pertyeae, revealing close relationships with the genera Myripnois and Pertya. In comparison with Ainsliaea, Myripnois was more closely related to Pertya. This study lays a theoretical foundation for future research on species identification, population genetics, resource conservation, and sustainable utilization within Ainsliaea and Pertyeae. [ABSTRACT FROM AUTHOR]

Summary Deep mutational scanning (DMS) experiments provide a powerful method to measure the functional effects of genetic mutations at massive scales. However, the data generated from these experiments can be difficult to analyze, with significant variation between experimental replicates. To overcome this challenge, we developed popDMS, a computational method based on population genetics theory, to infer the functional effects of mutations from DMS data. Through extensive tests, we found that the functional effects of single mutations and epistasis inferred by popDMS are highly consistent across replicates, comparing favorably with existing methods. Our approach is flexible and can be widely applied to DMS data that includes multiple time points, multiple replicates, and different experimental conditions. Availability and implementation popDMS is implemented in Python and Julia, and is freely available on GitHub at https://github.com/bartonlab/popDMS. [ABSTRACT FROM AUTHOR]

Simultaneous determination of a tandem of drugs like perindopril and rosuvastatin with differences in water and organic solvent solubilities, hydrophobicity, polarities, and UV‐absorbing possibilities between them necessitates careful selection of chromatographic conditions. The four specified and different bonded reversed‐phase columns were tested with running mobile phases containing various composition contents concepts; the concept of using diluted trifluoroacetic acid in mobile phase composition with acetonitrile enabled simultaneous acidification and weak ion‐pairing with protonized molecules of analytes, yielding appropriate, short, reasonable run times and resolutions of analytes, satisfying UV‐transparency, and good peak symmetries. These facts especially stand for the peak of perindopril, as a member of the group of proline‐containing moiety in its structure, often and easily prone to peak‐tailing, skewing, or splitting on the high‐performance liquid chromatography chromatograms, which is usually solved by using alkyl‐sulfonate base and ion pairs on higher concentrations of buffering salts with low pH values and with column temperatures increasing by 50°C–60°C. Linearity range was 0.002/004–0.5 mg/mL. The score for method AGREE was 0.73–0.77. The method development approaches, with all columns employing our concepts in mobile phases and experimental conditions, can cover the complete needs and demands of quality control departments and laboratories as simple high‐throughput analysis methods. [ABSTRACT FROM AUTHOR]

The efficient preparation of single-stranded DNA (ssDNA) rings, as a macromolecular construction approach with topological features, has aroused much interest due to the ssDNA rings' numerous applications in biotechnology and DNA nanotechnology. However, an extra splint is essential for enzymatic circularization, and by-products of multimers are usually present at high concentrations. Here, we proposed a simple and robust strategy using permuted precursor (linear ssDNA) for circularization by forming an intramolecular dynamic nick using a part of the linear ssDNA substrate itself as the template. After the simulation of the secondary structure for desired circular ssDNA, the linear ssDNA substrate is designed to have its ends on the duplex part (≥5 bp). By using this permuted substrate with 5′-phosphate, the splint-free circularization is simply carried out by T4 DNA ligase. Very interestingly, formation of only several base pairs (2–4) flanking the nick is enough for ligation, although they form only instantaneously under ligation conditions. More significantly, the 5-bp intramolecular duplex part commonly exists in genomes or functional DNA, demonstrating the high generality of our approach. Our findings are also helpful for understanding the mechanism of enzymatic DNA ligation from the viewpoint of substrate binding. [ABSTRACT FROM AUTHOR]

Human terminal deoxynucleotidyl transferase (TdT) can catalyze template-independent DNA synthesis during the V(D)J recombination and DNA repair through nonhomologous end joining. The capacity for template-independent random addition of nucleotides to single-stranded DNA makes this polymerase useful in various molecular biological applications involving sequential stepwise synthesis of oligonucleotides using modified dNTP. Nonetheless, a serious limitation to the applications of this enzyme is strong selectivity of human TdT toward dNTPs in the order dGTP > dTTP ≈ dATP > dCTP. This study involved molecular dynamics to simulate a potential impact of amino acid substitutions on the enzyme's selectivity toward dNTPs. It was found that the formation of stable hydrogen bonds between a nitrogenous base and amino acid residues at positions 395 and 456 is crucial for the preferences for dNTPs. A set of single-substitution and double-substitution mutants at these positions was analyzed by molecular dynamics simulations. The data revealed two TdT mutants—containing either substitution D395N or substitutions D395N+E456N—that possess substantially equalized selectivity toward various dNTPs as compared to the wild-type enzyme. These results will enable rational design of TdT-like enzymes with equalized dNTP selectivity for biotechnological applications. [ABSTRACT FROM AUTHOR]

Quantum mechanical calculations are used to explore the thermodynamics of possible prebiotic synthesis of the building blocks of nucleic acids. Different combinations of D-ribofuranose (Ribf) and N-(2-aminoethyl)-glycine (AEG) (trifunctional connectors (TCs)); the nature of the Ribf, its anomeric form, and its ring puckering (conformation); and the nature of the nucleobases (recognition units (RUs)) are considered. The combinatorial explosion of possible nucleosides has been drastically reduced on physicochemical grounds followed by a detailed thermodynamic evaluation of alternative synthetic pathways. The synthesis of nucleosides containing N-(2-aminoethyl)-glycine (AEG) is predicted to be thermodynamically favored suggesting a possible role of AEG as a component of an ancestral proto-RNA that may have preceded today's nucleic acids. A new pathway for the building of free nucleotides (exemplified by 5'-uridine monophosphate (UMP)) and of AEG dipeptides is proposed. This new pathway leads to a spontaneous formation of free UMP assisted by an AEG nucleoside in an aqueous environment. This appears to be a workaround to the "water problem" that prohibits the synthesis of nucleotides in water. [ABSTRACT FROM AUTHOR]

Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism. [ABSTRACT FROM AUTHOR]

Researchers at the Arc Institute, led by Patrick Hsu, have discovered a new RNA-guided system that allows for modular and programmable DNA insertions, excisions, and inversions. This system, called bridge RNAs, retains the programmability of RNA interference (RNAi) and CRISPR while enabling large-scale genome design. Hsu believes that this discovery could lead to advancements in genome engineering, allowing for long-range insertions, deletions, and genome translocations. The bridge RNA system provides a unified and modular mechanism for fundamental DNA rearrangements required for genome design. [Extracted from the article]

The current arterial signal coordination models only target through traffic or critical traffic, resulting in fairness issues for traffic in other directions. Moreover, these models fail to achieve system optimality between intersections along the arterial. To address these problems, this paper establishes an arterial signal coordination optimization model based on all-direction pairs of adjacent intersections. The model takes the minimum weighted green wave band center offset of all-direction pairs at the intersections as the objective function. The optimization variables are the cycle length, offset, and phase sequence. The phase sequence structure adopts the ring-and-barrier structure, and the phase sequence optimization includes not only the main road but also the minor road intersecting with it. The model is an integer linear programming model, and it optimizes all-direction pairs of the upstream and downstream intersections. By analyzing the spatiotemporal diagram of the intersections, constraints are established for the phase sequence of the main road and intersecting roads. Through optimization of the offset and phase sequence, the coordination of flow direction pairs between upstream and downstream intersections can be optimized to improve the overall traffic fairness of the arterial. [ABSTRACT FROM AUTHOR]

We compared the Institute for Clinical and Economic Review's (ICER) ratings of comparative clinical effectiveness with the German Federal Joint Committee's (G-BA) added benefit ratings, and explored what factors may explain the disagreement between the 2 organizations. We included drugs if they were assessed by ICER under its 2020 to 2023 Value Assessment Framework and had a corresponding assessment by G-BA as of January 2024 for the same indication, patient population, and comparator drug. To compare assessments, we modified ICER's proposed crosswalk between G-BA and ICER benefit ratings to account for G-BA's certainty ratings. We also determined whether each pair was based on similar evidence. Assessment pairs exhibiting disagreement based on the modified crosswalk despite a similar evidence base were qualitatively analyzed to identify reasons for disagreement. Out of 15 drug assessment pairs matched on indication, patient subgroup, and comparator, none showed agreement in their assessments when based on similar evidence. Disagreement was attributed to differences in evidence evaluation, including evaluations of safety, generalizability, and study design, as well as G-BA's rejection of the available evidence in 4 cases as unsuitable. The findings demonstrate that even under conditions where populations and comparators are identical and the evidence base is consistent, different assessors may arrive at divergent conclusions about comparative effectiveness, thus underscoring the presence of value judgments within assessments of clinical effectiveness. To support initiatives that seek to facilitate the exchange of value assessments between countries, these value judgments should always be transparently presented and justified in assessment summaries. • Several studies have documented disagreement in the comparative effectiveness assessments of the same drugs by different national health technology assessment (HTA) bodies. However, we are not aware of any studies that compare Institute for Clinical and Economic Review's (ICER) comparative effectiveness assessments with those of other HTA bodies. Furthermore, existing studies have matched and compared comparative effectiveness assessments at the drug level or the indication and patient subgroup level only. • We identified 15 drug assessment pairs matched on indication, patient subgroup, and comparator treatment. Seven assessment pairs were based on similar evidence. Using a novel crosswalk to translate G-BA ratings into ICER ratings that accounts for G-BA's assessment of certainty, G-BA and ICER did not agree in their assessment for any of these 7 drugs. • The findings demonstrate that even when populations and comparators are identical and the evidence base is similar, different assessors may arrive at divergent conclusions about comparative effectiveness, thus underscoring the role of value judgments. To support initiatives seeking to facilitate exchange of value assessments between jurisdictions, value judgments should be transparently presented and justified in assessment summaries. A recently published framework is 1 tool HTA bodies could use to organize and justify value judgments. [ABSTRACT FROM AUTHOR]

The global prevalence of RNA virus infections has presented significant challenges to public health in recent years, necessitating the expansion of its alternative therapeutic library. Due to its evolutional conservation, RNA‐dependent RNA polymerase (RdRp) has emerged as a potential target for broad‐spectrum antiviral nucleoside analogues. However, after over half a century of structural modification, exploring unclaimed chemical space using frequently‐used structural substitution methods to design new nucleoside analogues is challenging. In this study, we explore the use of the "ring‐opening" strategy to design new base mimics, thereby using these base mimics to design new nucleoside analogues with broad‐spectrum antiviral activities. A total of 29 compounds were synthesized. Their activity against viral RdRp was initially screened using an influenza A virus RdRp high‐throughput screening model. Then, the antiviral activity of 38a was verified against influenza virus strain A/PR/8/34 (H1N1), demonstrating a 50% inhibitory concentration (IC50) value of 9.95 μM, which was superior to that of ribavirin (the positive control, IC50 = 11.43 μM). Moreover, 38a also has inhibitory activity against coronavirus 229E with an IC50 of 30.82 μM. In addition, compounds 42 and 46f exhibit an 82% inhibition rate against vesicular stomatitis virus at a concentration of 20 μM and hardly induce cytotoxicity in host cells. This work demonstrates the feasibility of designing nucleoside analogues with "ring‐opening" bases and suggests the "ring‐opening" nucleosides may have greater polarity, and designing prodrugs is an important aspect of optimizing their antiviral activity. Future research should focus on enhancing the conformational restriction of open‐loop bases to mimic Watson‐Crick base pairing better and improve antiviral activity. [ABSTRACT FROM AUTHOR]

Objective: The introduction of fluorescently labeled nucleotides in the process of DNA amplification in molecular genetic analysis is a very attractive alternative to post-labeling or the use of labeled primers in the reaction (RCA). Methods: To study the substrate efficiency, the kinetic index (amplification efficiency) was studied, which allowed us to evaluate the inhibitory effect of modified substrates; as well as the yield of the isothermal amplification reaction product and the density of embedding the label into the growing DNA chain. Results and Discussion: Two pairs of Cy5-labeled dU and dC triphosphates with similar electroneutral fluorophore structures, differing in the length of the hydrocarbon linker between the fluorophore and the nitrogenous base were synthesized. A comparative analysis of their substrate behavior in the rolling circle amplification (RCA) reaction using Bst 3.0 DNA polymerase was carried out. It was found that nucleotides with a long linker between the fluorophore and the pyrimidine base are more efficiently incorporated into the growing DNA chain, while the nucleotides with a short linker cause lesser inhibition of RCA. In each of the pairs consisting of dU and dC with similar fluorophores and linkers, the fluorescently labeled uridine derivatives demonstrated a higher incorporation density. It was revealed that, under simultaneous incorporation of the labeled dU and dC, the inhibitory effects do not sum up. This gives grounds for a more careful study of different Cy5-dC variants with a view to increasing the sensitivity of the analysis under simultaneous introduction of the labeled dU and dC. Conclusions: The work presents the results of comparative study of the substrate properties of fluorescently labeled deoxynucleoside triphosphates in RCA. The influence of the chemical nature of the nucleotide (dU or dC) and the structure of the fluorophore on the substrate properties of modified deoxynucleoside triphosphates has been studied. Deoxyuridines with a long linker between the fluorophore and the nitrogenous base were found to be the most effective substrates. In addition, the possibility of simultaneous use of labeled dU and dC in the process of isothermal amplification has been shown, which is potentially capable of increasing the sensitivity of the analysis method. [ABSTRACT FROM AUTHOR]