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Background: Thiopurine co‐therapy with anti‐tumour necrosis factor‐alpha (anti‐TNFα) agents is associated with higher anti‐TNFα drug levels and reduced immunogenicity in inflammatory bowel disease (IBD). Aims: We aimed to evaluate the association between 6‐thioguanine nucleotide (6‐TGN) and anti‐TNFα levels and the optimal 6‐TGN threshold level associated with higher anti‐TNFα levels in combination therapy. Methods: We performed a retrospective cross‐sectional multicentre study of patients with IBD on combination anti‐TNFα and thiopurine maintenance therapy between January 2015 and August 2021. Primary outcomes were infliximab and adalimumab levels. Secondary outcomes were antibodies to infliximab (ATI) or adalimumab (ATA). Univariable and multivariable linear regression were performed to identify variables associated with anti‐TNFα levels. Receiver operator characteristic curves were used to define the optimal 6‐TGN cut‐off levels associated with therapeutic anti‐TNFα levels. Results: The study included 743 paired 6‐TGN and anti‐TNFα levels (640 infliximab and 103 adalimumab). 6‐TGN levels were associated with infliximab levels, but not adalimumab levels, on univariable and multivariable regression. The optimal 6‐TGN cut‐off associated with therapeutic infliximab levels (≥5 mcg/mL) was 261 pmol/8 × 108 red blood cell (RBC) (area under the curve (AUC) = 0.57) for standard infliximab dosing and 227.5 pmol/8 × 108 RBC (AUC = 0.58) for escalated dosing. For therapeutic adalimumab levels (≥7.5 mcg/mL), the 6‐TGN cut‐off was 218.5 pmol/8 × 108 RBC (AUC = 0.59) for standard adalimumab dosing and 237.5 pmol/8 × 108 RBC (AUC = 0.63) for escalated dosing. Conclusion: 6‐TGN levels were weakly associated with infliximab but not adalimumab levels in combination therapy. 6‐TGN levels in the lower end of the therapeutic range (230–260 pmol/8 × 108 RBC) may be adequate to maintain higher infliximab levels, particularly with escalated infliximab dosing. [ABSTRACT FROM AUTHOR]

SUMMARY: Arabidopsis uracil phosphoribosyltransferase (UPP) is an essential enzyme and plants lacking this enzyme are strongly compromised in chloroplast function. Our analysis of UPP amiRNA mutants has confirmed that this vital function is crucial to establish a fully functional photosynthesis as the RIESKE iron sulfur protein (PetC) is almost absent, leading to a block in photosynthetic electron transport. Interestingly, this function appears to be unrelated to nucleotide homeostasis since nucleotide levels were not altered in the studied mutants. Transcriptomics and proteomic analysis showed that protein homeostasis but not gene expression is most likely responsible for this observation and high light provoked an upregulation of protease levels, including thylakoid filamentation temperature‐sensitive 1, 5 (FtsH), caseinolytic protease proteolytic subunit 1 (ClpP1), and processing peptidases, as well as components of the chloroplast protein import machinery in UPP amiRNA lines. Strongly reduced PetC amounts were not only detected by immunoblot from mature plants but in addition in a de‐etiolation experiment with young seedlings and are causing reduced high light‐induced non‐photochemical quenching Φ(NPQ) but increased unregulated energy dissipation Φ(NO). This impaired photosynthesis results in an inability to induce flavonoid biosynthesis. In addition, the levels of the osmoprotectants raffinose, proline, and fumarate were found to be reduced. In sum, our work suggests that UPP assists in stabilization PetC during import, processing or targeting to the thylakoid membrane, or protects it against proteolytic degradation. Significance Statement: The moonlighting enzyme uracil phosphoribosyltransferase from Arabidopsis is an essential protein. By in‐depth analysis of knockdown mutants, we observed disrupted chloroplast proteostasis, characterized by altered amounts of proteins in the categories protein import, processing, folding, and degradation, accompanied by massively reduced amounts of the PetC (Rieske) subunit of the cytochrome b6/f complex. [ABSTRACT FROM AUTHOR]

DNA lesions are linked to cancer, aging, and various diseases. The recognition and sequencing of special DNA lesions are of great interest but highly challenging. In this paper, an unnatural‐base‐pair‐promoting method for sequencing highly mutagenic ethenodeoxycytidine (εC) DNA lesions that occurred frequently is developed. First, a promising unnatural base pair of dεC–dNaM to recognize εC lesions is identified, and then a conversion PCR is developed to site‐precise transfer dεC–dNaM to dTPT3–dNaM for convenient Sanger sequencing. The low sequence dependence of this method and its capacity for the enrichment of dεC in the abundance of as low as 1.6 × 10–6 nucleotides is also validated. Importantly, the current method can be smoothly applied for recognition, amplification, enrichment, and sequencing of the real biological samples in which εC lesions are generated in vitro or in vivo, thus offering the first sequencing methodology of εC lesions at single‐base resolution. Owing to its simple operations and no destruction of inherent structures of DNA, the unnatural‐base‐pair strategy may provide a new platform to produce general tools for the sequencing of DNA lesions that are hardly sequenced by traditional strategies. [ABSTRACT FROM AUTHOR]

In 2015, the United States Food and Drug Administration (FDA) approved uridine triacetate to treat overdose and severe toxicity of the fluoropyrimidine chemotherapy agents 5‐fluorouracil (5‐FU) and its oral prodrug capecitabine. Uridine triacetate is as an oral prodrug of uridine that competes with cytotoxic fluoropyrimidine metabolites for incorporation into nucleotides. Two million people worldwide start fluoropyrimidine chemotherapy each year, with 20‐30% developing severe or life‐threatening adverse effects, often attributable to a genetic predisposition such as dihydropyrimidine dehydrogenase deficiency. Whilst genetic prescreening is recommended prior to starting fluoropyrimidine agents, this only prevents 20‐30% of early‐onset life‐threatening toxicity and so does not obviate the need for an antidote. Initial in‐human studies established that uridine triacetate more than doubles the maximum tolerated weekly 5‐FU bolus dose. A lack of clinical equipoise meant a placebo‐controlled phase III trial was not ethical and so the phase III trials used historical controls. These found that uridine triacetate improved survival in those with fluoropyrimidine overdose and severe toxicity from 16% to 94%, with 34% able to resume chemotherapy within 30 days. Five case reports of delayed fluoropyrimidine toxicity demonstrate improvement following uridine triacetate treatment 120‐504 h after last fluoropyrimidine administration, suggesting efficacy beyond the FDA licencing indications. Mechanistically uridine triacetate would be expected to be effective for overdose and severe toxicity of tegafur (a 5‐FU prodrug), but there are no published case reports describing this. Uridine triacetate is available internationally through an expanded access scheme and has been available in the UK since 2019 on a named patient basis. [ABSTRACT FROM AUTHOR]

Supramolecular recognition of nucleobases and short sequences is an emerging research field focusing on possible applications to treat many diseases. Controlling the affinity and selectivity of synthetic receptors to target desired nucleotides or short sequences is a highly challenging task. Herein, we elucidate the effect of substituents in the phenyl ring of the anthracene‐benzene azacyclophane on the recognition of nucleoside triphosphates (NTPs) and double‐stranded DNA. We show that introducing phenyl rings increases the affinity for NTPs 10‐fold and implements groove and intercalation binding modes with double‐stranded DNA. NMR studies and molecular modeling calculations support the ability of cyclophanes to encapsulate nucleobases as part of nucleotides. [ABSTRACT FROM AUTHOR]

Real‐time monitoring of molecular transformations is crucial for advancements in biotechnology. In this study, we introduce a novel self‐assembling 19F‐labeled nuclear magnetic resonance (NMR) probe that disassembles upon interaction with various nucleotides. This interaction not only activates the 19F signals but also produces distinct signatures for each specific component, thereby enabling precise identification and quantification of molecules in evolving samples. We demonstrate the capability of this probe for real‐time monitoring of adenosine triphosphate (ATP) hydrolysis and screening potential enzyme inhibitors. These applications highlight the probe's significant potential in enzyme analysis, drug development, and disease diagnostics. [ABSTRACT FROM AUTHOR]

Osteoclasts are bone resorbing cells that are essential to maintain skeletal integrity and function. While many of the growth factors and molecular signals that govern osteoclastogenesis are well studied, how the metabolome changes during osteoclastogenesis is unknown. Using a multifaceted approach, we identified a metabolomic signature of osteoclast differentiation consisting of increased amino acid and nucleotide metabolism. Maintenance of the osteoclast metabolic signature is governed by elevated glutaminolysis. Mechanistically, glutaminolysis provides amino acids and nucleotides which are essential for osteoclast differentiation and bone resorption in vitro. Genetic experiments in mice found that glutaminolysis is essential for osteoclastogenesis and bone resorption in vivo. Highlighting the therapeutic implications of these findings, inhibiting glutaminolysis using CB-839 prevented ovariectomy induced bone loss in mice. Collectively, our data provide strong genetic and pharmacological evidence that glutaminolysis is essential to regulate osteoclast metabolism, promote osteoclastogenesis and modulate bone resorption in mice. Synopsis: Metabolic rewiring is essential for osteoclast differentiation and bone resorption. This study shows that glutaminolysis regulates osteoclast differentiation and bone resorption by maintaining amino acid and nucleotide abundance. Amino acid and nucleotide abundance increases during osteoclastogenesis. Glutaminolysis and glutamate transamination reactions provide amino acids and nucleotides that are essential for osteoclast differentiation and function. GLS deficiency in myeloid cells leads to reduced osteoclastogenesis and increased bone mass. Increasing glutaminolysis in myeloid cells enhances osteoclastogenesis and reduces bone mass. Pharmacological inhibition of glutaminolysis prevents estrogen deficiency induced osteoclast expansion and bone loss. Metabolic rewiring is essential for osteoclast differentiation and bone resorption. This study shows that glutaminolysis regulates osteoclast differentiation and bone resorption by maintaining amino acid and nucleotide abundance. [ABSTRACT FROM AUTHOR]

DNA hydrogels, which hold potential for use in medicine, biosensors, and tissue engineering, can be produced through enzymatic rolling circle amplification (RCA) using phi29 DNA polymerase (DNAP). This paper introduces new DNAP variants designed for RCA‐based DNA hydrogel production, featuring enzymes with modified DNA binding, enhanced thermostability, reduced exonuclease activity, and protein tags for fluorescence detection or specific immobilization. We evaluated these enzymes by quantifying DNA output via quantitative PCR (qPCR) and assessing hydrogel mechanical properties through micromechanical indentation. The results showed that most variants generated similar DNA amounts and hydrogels with comparable mechanical properties. Additionally, all variants successfully incorporated non‐natural nucleotides, such as base‐modified dGTP derivatives and 2′fluoro‐dGTP, during RCA. This study's robust analytical approach offers a strong foundation for selecting new enzymes and producing DNA hydrogels with tailored material properties. [ABSTRACT FROM AUTHOR]

Precise regulation of sarcomeric contraction is essential for normal cardiac function. The heart must generate sufficient force to pump blood throughout the body, but either inadequate or excessive force can lead to dysregulation and disease. Myosin regulatory light chain (RLC) is a thick‐filament protein that binds to the neck of the myosin heavy chain. Post‐translational phosphorylation of RLC (RLC‐P) by myosin light chain kinase is known to influence acto‐myosin interactions, thereby increasing force production and Ca2+‐sensitivity of contraction. Here, we investigated the role of RLC‐P on cardiac structure and function as sarcomere length and [Ca2+] were altered. We found that at low, non‐activating levels of Ca2+, RLC‐P contributed to myosin head disorder, though there were no effects on isometric stress production and viscoelastic stiffness. With increases in sarcomere length and Ca2+‐activation, the structural changes due to RLC‐P become greater, which translates into greater force production, greater viscoelastic stiffness, slowed myosin detachment rates and altered nucleotide handling. Altogether, these data suggest that RLC‐P may alter thick‐filament structure by releasing ordered, off‐state myosin. These more disordered myosin heads are available to bind actin, which could result in greater force production as Ca2+ levels increase. However, prolonged cross‐bridge attachment duration due to slower ADP release could delay relaxation long enough to enable cross‐bridge rebinding. Together, this work further elucidates the effects of RLC‐P in regulating muscle function, thereby promoting a better understanding of thick‐filament regulatory contributions to cardiac function in health and disease. Key points: Myosin regulatory light chain (RLC) is a thick‐filament protein in the cardiac sarcomere that can be phosphorylated (RLC‐P), and changes in RLC‐P are associated with cardiac dysfunction and disease.This study assesses how RLC‐P alters cardiac muscle structure and function at different sarcomere lengths and calcium concentrations.At low, non‐activating levels of Ca2+, RLC‐P contributed to myofilament disorder, though there were no effects on isometric stress production and viscoelastic stiffness.With increases in sarcomere length and Ca2+‐activation, the structural changes due to RLC‐P become greater, which translates into greater force production, greater viscoelastic stiffness, slower myosin detachment rate and altered cross‐bridge nucleotide handling rates.This work elucidates the role of RLC‐P in regulating muscle function and facilitates understanding of thick‐filament regulatory protein contributions to cardiac function in health and disease. [ABSTRACT FROM AUTHOR]

Background: Metformin (Met) has been reported to play the key role in the pathogenesis of polycystic ovary syndrome (PCOS). However, the precise mechanisms underlying the actions of Met in PCOS remain incompletely understood. This study aimed to confirm the mechanism of Met interacting with a long non‐coding RNA LINC00548 in PCOS. Methods: Ovarian granulosa cells (OGCs) were incubated 500 nM dihydrotestosterone (DHT) to construct PCOS in vitro model and then were treated 20 μM Met. A series of cell experiments including Cell Counting Kit‐8, Terminal uridine nucleotide end labeling, and flow cytometry were performed to confirm the changes of OGC survival ability. Quantitative real‐time polymerase chain reaction was conducted to determine the levels of LINC00548, whereas Western blotting was applied to determine the levels of androgen receptor (AR) and klotho. Results: Met improved the cell viability and suppressed cell apoptosis in DHT‐treated OGCs. LINC00548 downregulated in DHT‐treated OGCs was upregulated by Met, and its overexpression further enhanced the positive effects of Met on the survival ability of DHT‐treated OGCs. In addition, Met could induce the upregulation of LINC00548 to suppress the activation of AR/klotho pathway in DHT‐treated OGCs. Conclusion: Overall, this study discovers that Met enhances the survival ability of OGCs in PCOS by elevating LINC00548 expression to suppress AR/klotho pathway. [ABSTRACT FROM AUTHOR]

Comprehensive Summary Enhancing the DNA toolbox with innovative photochemical reactions is pivotal for advancing nucleic acid‐based technologies. Aldehyde groups, versatile bioorthogonal handles for imine formation under acidic conditions, are particularly valuable due to their roles in nucleic acid epigenetics. Here, we present the first photocatalytic on‐DNA aldehyde allylation, enabling precise DNA functionalization under mild, neutral aqueous conditions. Our approach utilizes a photocatalytic polarity‐reversal reaction between DNA‐conjugated benzaldehydes and allyl sulfones. This reaction demonstrates exceptional chemoselectivity while preserving DNA integrity. By varying allyl sulfones, we achieve site‐specific labeling of non‐native DNA with the aldehyde group and cross‐linking with DNA‐bearing allyl sulfones. Furthermore, our method facilitates selective labeling and pull‐down enrichment of 5‐formylpyrimidine nucleotides among complex cellular DNA. This photocatalytic on‐DNA aldehyde transformation expands the limited bioorthogonal photochemical toolboxes, providing novel avenues for functionalizing both non‐native and native aldehyde modifications on DNA. [ABSTRACT FROM AUTHOR]

The singular BRCA1/2 mutational landscape of Asturias is updated 10 years after the first study. We analyzed BRCA1 and BRCA2 pathogenic variants in 1653 index cases. In total, 238 families were identified to carry a pathogenic variant, 163 families in BRCA1 and 75 families in BRCA2. This yielded a prevalence rate of 14.4%. Seven recurrent variants were found accounting for 55% of the cases. Among them, three are widely distributed (BRCA1 c.211A>G, c.470_471del and c.3331_3334del) and four had been reported as novel in Asturias: two in BRCA1 (c.1674del and c.2901_2902dup) and two in BRCA2 (c.2095C>T and c.4040_4035delinsC). A common haplotype was established for all recurrent variants indicating a shared ancestral origin. Three splicing analyses are shown: BRCA1:c.5152+3A>C and BRCA1:c.5333‐3T>G that lead to skipping of exon 18, and 22 respectively, and BRCA1:c.5278‐1G>T giving rise to two transcripts, one lacking exon 21 (p.Ille1760Glyfs*60) and one lacking the first 8 nucleotides of exon 21 (p.Phe1761Asnfs*14), supporting pathogenicity for these variants. [ABSTRACT FROM AUTHOR]

Precise regulation of sarcomeric contraction is essential for normal cardiac function. The heart must generate sufficient force to pump blood throughout the body, but either inadequate or excessive force can lead to dysregulation and disease. Myosin regulatory light chain (RLC) is a thick‐filament protein that binds to the neck of the myosin heavy chain. Post‐translational phosphorylation of RLC (RLC‐P) by myosin light chain kinase is known to influence acto‐myosin interactions, thereby increasing force production and Ca2+‐sensitivity of contraction. Here, we investigated the role of RLC‐P on cardiac structure and function as sarcomere length and [Ca2+] were altered. We found that at low, non‐activating levels of Ca2+, RLC‐P contributed to myosin head disorder, though there were no effects on isometric stress production and viscoelastic stiffness. With increases in sarcomere length and Ca2+‐activation, the structural changes due to RLC‐P become greater, which translates into greater force production, greater viscoelastic stiffness, slowed myosin detachment rates and altered nucleotide handling. Altogether, these data suggest that RLC‐P may alter thick‐filament structure by releasing ordered, off‐state myosin. These more disordered myosin heads are available to bind actin, which could result in greater force production as Ca2+ levels increase. However, prolonged cross‐bridge attachment duration due to slower ADP release could delay relaxation long enough to enable cross‐bridge rebinding. Together, this work further elucidates the effects of RLC‐P in regulating muscle function, thereby promoting a better understanding of thick‐filament regulatory contributions to cardiac function in health and disease. Key points: Myosin regulatory light chain (RLC) is a thick‐filament protein in the cardiac sarcomere that can be phosphorylated (RLC‐P), and changes in RLC‐P are associated with cardiac dysfunction and disease.This study assesses how RLC‐P alters cardiac muscle structure and function at different sarcomere lengths and calcium concentrations.At low, non‐activating levels of Ca2+, RLC‐P contributed to myofilament disorder, though there were no effects on isometric stress production and viscoelastic stiffness.With increases in sarcomere length and Ca2+‐activation, the structural changes due to RLC‐P become greater, which translates into greater force production, greater viscoelastic stiffness, slower myosin detachment rate and altered cross‐bridge nucleotide handling rates.This work elucidates the role of RLC‐P in regulating muscle function and facilitates understanding of thick‐filament regulatory protein contributions to cardiac function in health and disease. [ABSTRACT FROM AUTHOR]

The 5’ cap structure is crucial to mRNA function, with its diverse methylation patterns depending on the cellular state. Sensitive analytical methods are sought after to quantify this cap variety also referred to as cap epitranscriptome. To address a bottleneck for accurate and precise quantitation, we report a facile and fast access to high‐quality synthetic standards via a new route, involving P(III)‐amidite chemistry. A range of cap nucleotides and their stable heavy isotopic labeled analogues were derived from nucleoside diphosphates, which themselves were directly prepared in a one‐step reaction sequence starting from unprotected nucleosides using a triphosphorylating reagent in combination with ethylenediamine. Considering a wider scope, the route also enables direct access to magic spot nucleotides and diphosphates of isoprenyl‐alcohols. Stable‐isotope labeled cap nucleotides derived from this route paved the way for the development of a highly sensitive LC–MS/MS method, applied to the characterization of mouse brain cap epitranscriptomes, which turned out to be very different from those of cultured cell lines of widespread use in the life sciences. [ABSTRACT FROM AUTHOR]

ABSTRACT Cottonseed oil is a high‐quality edible oil. A comprehensive analysis of the genetic basis of cottonseed oil formation at the molecular level will greatly promote the molecular improvement of this trait. This study performed a genome‐wide association study involving three modules integrated into the 3VmrMLM framework for cottonseed oil content (COC). In total, 49,533 single‐nucleotide polymorphisms were screened across 152 upland cotton accessions. Twenty‐six, 10 and 26 quantitative trait nucleotides (QTNs) for COC were respectively detected by the three modules: Single_env, Multi_env and Epistasis. Eight QTNs were simultaneously detected in at least two datasets or by at least two modules, and four genes associated with the stable QTNs were simultaneously enriched in GO and KEGG analyses. Using Multi_env, five QTN‐by‐environment interactions were detected, and six genes were simultaneously enriched in GO and KEGG analyses. Using Epistasis, 10 QTN‐by‐QTN interactions (QQIs) were detected, and eight protein–protein interactions involving six QQIs and eight gene pairs were predicted by a protein–protein interaction analysis. These findings provide novel insights into the genetic basis of COC. [ABSTRACT FROM AUTHOR]

We report a systematic study on controlling the enzyme activity of a terminal uridylyl transferase (TUTase) called SpCID1, which provides methods to effect site‐specific incorporation of a single modified nucleotide analog at the 3′‐end of an RNA oligonucleotide (ON). Responsive heterocycle‐modified fluorescent UTP probes that are useful in analyzing non‐canonical nucleic acid structures and azide‐ and alkyne‐modified UTP analogs that are compatible for chemoenzymatic functionalization were used as study systems. In the first strategy, we balanced the concentration of essential metal ion cofactors (Mg2+ and Mn2+ ions) to restrict the processivity of the enzyme, which gave a very good control on the incorporation of clickable nucleotide analogs. In the second approach, borate that complexes with 2′ and 3′ oxygen atoms of a ribose sugar was used as a reversibly binding chelator to block repeated addition of nucleotide analogs. Notably, in the presence of heterocycle‐modified fluorescent UTPs, we obtained single‐nucleotide incorporated RNA products in reasonable yields, while with clickable nucleotides yields were very good. Further, 3′‐end azide‐ and alkyne‐labeled RNA ONs were post‐enzymatically functionalized by CuAAC and SPAAC reactions with fluorescent probes. These strategies broaden the scope of TUTase in site‐specifically installing modifications of different types onto RNA for various applications. [ABSTRACT FROM AUTHOR]

Posttranslational modifications (PTMs) greatly enhance the functional diversity of proteins, surpassing the number of gene‐encoded variations. One intriguing PTM is ADP‐ribosylation, which utilizes nicotinamide adenine dinucleotide (NAD+) as a substrate and is essential in cell signaling pathways regulating cellular responses. Here, we report the first cell‐permeable NAD+ analogs and demonstrate their utility for investigating cellular ADP‐ribosylation. Using a desthiobiotin‐labelled analog for affinity enrichment of proteins that are ADP‐ribosylated in living cells under oxidative stress, we identified protein targets associated with host‐virus interactions, DNA damage and repair, protein biosynthesis, and ribosome biogenesis. Most of these targets have been noted in various literature sources, highlighting the potential of our probes for cellular ADP‐ribosylome studies. [ABSTRACT FROM AUTHOR]

Reactive N‐hydroxy‐9‐azabicyclo[3.3.1]nonane (ABNOH) linked 2′‐deoxyuridine 5′‐O‐mono‐ and triphosphates were synthesized through a CuAAC reaction of ABNOH‐PEG4‐N3 with 5‐ethynyl‐dUMP or ‐dUTP. The modified triphosphate was used as substrate for enzymatic synthesis of modified DNA probes with KOD XL DNA polymerase. The keto‐ABNO radical reacted with tryptophan (Trp) and Trp‐containing peptides to form a stable tricyclic fused hexahydropyrrolo‐indole conjugates. Similarly modified ABNOH‐linked nucleotides reacted with Trp‐containing peptides to form a stable conjugate in the presence but surprisingly even in the absence of NaNO2 (presumably through activation by O2). The reactive ABNOH‐modified DNA probe was used for bioconjugations and crosslinking with Trp‐containing peptides or proteins. [ABSTRACT FROM AUTHOR]

The occurrence of black pepper virus F (BPVF) was identified for the first time from India, and its complete genome sequence was determined using overlapping fragments obtained through reverse transcription polymerase chain reaction (RT‐PCR). The RNA 1 and RNA 2 of the Indian isolate of BPVF (BPVF‐IND) contained 6376 and 3340 nucleotides potentially coding for proteins of 230.7 kDa and 114 kDa respectively. Comparison of the RNA 1 sequence of BPVF‐IND with that of BPVF from Brazil (BPVF‐ BR‐PA) and China (BPVF‐ ZYP‐1) revealed an identity of 95% and 90%, respectively, while RNA 2 showed an identity of 96% and 90%. The phylogenetic analysis of the Pro‐Pol region of RNA 1 and coat protein region of RNA 2 revealed close clustering of all three BPVF isolates well separated from other species of the genus, Fabavirus. Diagnostics assays based on the RT‐PCR and RT‐recombinase polymerase amplification (RT‐RPA) were developed for the sensitive detection of the virus that will help in the identification and propagation of virus‐free black pepper plants. [ABSTRACT FROM AUTHOR]

Summary: Objective: Children with overweight/obesity (OW/OB) exhibit poor cardiometabolic health, yet mechanisms influencing brain health remain unclear. We examined the differences in neurological‐related circulating proteins in plasma among children with metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO) and the association with metabolic syndrome markers. Methods: In this cross‐sectional study, we included 84 Caucasian children (39% girls), aged 10.1 ± 1.1 years, from the ActiveBrains project (NCT02295072). A ninety‐two‐protein targeted approach using Olink's® technology was used. Results: We identified distinct concentrations of CD38, LAIR2, MANF and NRP2 proteins in MHO compared with MUO. Moreover, individual metabolic syndrome (MS) markers were linked to nine proteins (CD38, CPM, EDA2R, IL12, JAMB, KYNU, LAYN, MSR1 and SMOC2) in children with OW/OB. These proteins play crucial roles in diverse biological processes (e.g., angiogenesis, cholesterol transport, nicotinamide adenine dinucleotide (NAD+) catalysis and maintenance of blood–brain barrier) related to brain health. Conclusion: Our proteomics study suggests that cardiometabolic health (represented by MHO/MUO or individual MS markers) is associated with the concentration in plasma of several proteins involved in brain health. Larger‐scale studies are needed to contrast/confirm these findings, with CD38 standing out as a particularly noteworthy and robust discovery. [ABSTRACT FROM AUTHOR]

BACKGROUND: The taste of fish is highly dependent on the composition of free amino acids (FAAs) and nucleotides. The present study aimed to investigate the effect of long‐term frozen storage periods (−18 °C, up to 6 months) and thawing methods [water thawing (WT, 25 °C), air thawing (AT, 25 °C), and chilled air thawing (CAT, 4 °C)] on the taste quality of tilapia (Oreochromis niloticus) fillets. RESULTS: The results showed that increase in bitter FAAs of CAT samples was 150.57% at 6 months of storage, which was lower than that of AT and WT. Glycine was the most abundant FAA and CAT maintained the highest sweet FAAs (249.90 mg/100 g). Additionally, the inosine monophosphate (IMP) of CAT samples were 1.18 and 1.09 times higher than that of WT and AT, respectively, at a frozen period of 6 months. In particular, the increase in equivalent umami concentration (EUC) values ranged from 24.25% to 103.16% in the three groups during the first 2 months. Data from principal component analysis (PCA) and orthogonal partial least‐squares discrimination analysis (OPLS‐DA) indicated that the taste quality was highly correlated with high levels of FAAs, hypoxanthine inosine (HxR) and hypoxanthine (Hx) as the storage time progressed. CONCLUSION: In general, CAT is beneficial in maintaining the taste quality of tilapia fillets during frozen storage, and frozen durations for 2 months enhances the umami flavor. This study provides useful information for the preservation of frozen aquatic products during the storage and thawing, and enrich the theoretical knowledge of the flavor chemistry of fish products. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

A portfolio of six modified 2′‐deoxyribonucleoside triphosphate (dNTP) derivatives derived from 5‐substituted pyrimidine or 7‐substituted 7‐deazapurine bearing different carbohydrate units (d‐glucose, d‐galactose, d‐mannose, l‐fucose, sialic acid and N−Ac‐d‐galactosamine) tethered through propargyl‐glycoside linker was designed and synthesized via the Sonogashira reactions of halogenated dNTPs with the corresponding propargyl‐glycosides. The nucleotides were found to be good substrates for DNA polymerases in enzymatic primer extension and PCR synthesis of modified and hypermodified DNA displaying up to four different sugars. Proof of concept binding study of sugar‐modified oligonucleotides with concanavalin A showed positive effect of avidity and sugar units count. [ABSTRACT FROM AUTHOR]

Composite DNA letters, by merging all four DNA nucleotides in specified ratios, offer a pathway to substantially increase the logical density of DNA digital storage (DDS) systems. However, these letters are susceptible to nucleotide errors and sampling bias, leading to a high letter error rate, which complicates precise data retrieval and augments reading expenses. To address this, Derrick‐cp is introduced as an innovative soft‐decision decoding algorithm tailored for DDS utilizing composite letters. Derrick‐cp capitalizes on the distinctive error sensitivities among letters to accurately predict and rectify letter errors, thus enhancing the error‐correcting performance of Reed‐Solomon codes beyond traditional hard‐decision decoding limits. Through comparative analyses in the existing dataset and simulated experiments, Derrick‐cp's superiority is validated, notably halving the sequencing depth requirement and slashing costs by up to 22% against conventional hard‐decision strategies. This advancement signals Derrick‐cp's significant role in elevating both the precision and cost‐efficiency of composite letter‐based DDS. [ABSTRACT FROM AUTHOR]

Aim: This study investigated the adjunctive effect of polydeoxyribonucleotide (PDRN) on bone formation in alveolar ridge preservation (ARP) sockets. Materials and Methods: Both mandibular second, third and fourth premolars of eight beagle dogs were randomly divided into ARP and ARP/PDRN groups. Following tooth extraction, ARP procedures were conducted using collagenized alloplastic graft material and bilayer collagen membrane soaked with normal saline (ARP group) or PDRN (ARP/PDRN group) for 10 min before application. Both groups were also randomly allocated to 2‐, 4‐ or 12‐week healing subgroups. The primary endpoint of this study was to compare histomorphometric differences between ARP and ARP/PDRN. The secondary endpoints of this study were to compare micro‐CT analysis and three‐dimensional volumetric measurement between the two groups. Results: In the histomorphometric analysis, the ARP/PDRN group exhibited greater new bone formation at coronal, middle and total position compared with the ARP group at 2‐week healing. The number of newly formed blood vessels was higher in the ARP/PDRN group than in the ARP group at 2‐ and 4‐week healing. In micro‐CT analysis, the mean new bone volume/total bone volume between ARP and ARP/PDRN was statistically significant at 2‐week healing. Ridge volume alterations were significantly decreased in the ARP/PDRN group during entire healing time compared with the ARP group, especially on the buccal side. Conclusions: The application of PDRN in ARP might provide additional benefits for early bone regeneration and maintenance of buccal ridge volume. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: ZnO nanoparticles (nps) among metal oxide (MOs) are proven to be essential electron transporting layers (ETLs) applied in organic solar cells (OSCs). However, intrinsic defects, interfacial charge recombination, and catalytic behavior towards the active layer restrict the applications of ZnO nps for efficient and long‐term stable OSCs. The commonly available biomolecule cytidine 5'‐monophosphate (CMP‐OH) with phosphonic acid, its salt cytidine 5'‐monophosphate disodium salt (CMP‐ONa) with a phosphate group as an anchoring group and conjugated terminal functional in both analogous molecules provide carrier transfer bridge at bottom interface of the active layer. Systematized theoretical investigations and characterizations have discovered the multi‐site coordination of CMP‐OH towards acceptor molecules and ZnO nps. The dual‐side alignment of CMP analogous molecules hinders interfacial charge recombination and enhances charge transfer potential at once. Inevitably, PM6:L8‐BO‐based OSCs with modified ETL obtain 18.13% efficiency, 12% higher than that of unmodified nps. Besides higher efficiency, CMP‐OH‐based OSC devices illustrate remarkably improved thermal stability for 500 h at 85 °C with 72% of initial PCE and operation stability for 2000 h with 90.1% of initial PCE. This work reveals the passivation mechanism of multi‐anchoring groups towards MOs and single‐functional groups towards the active layer to optimize the interface for efficient and highly stable OSCs. [ABSTRACT FROM AUTHOR]

Peptide−oligonucleotide conjugates (POCs) are covalent architectures composed of a DNA or RNA molecules linked to a peptide. These constructs have found widespread applications ranging from hybrid nanomaterials to gene‐targeted therapies. Considering the important role of POCs, a new catalytic approach for their preparation is reported here, that could be applied either on solid support in anhydrous media, or post‐synthetically in aqueous buffer. Single amino acids, peptides and cell penetrating peptides (CPPs) were conjugated to various oligo(ribo)nucleotides with high conversions and good isolated yields. The applicability of the method was demonstrated on more than 35 examples including an analogue of a commercial therapeutic oligonucleotide. Other conjugation partners, such as deoxycholic acid and biotin were also successfully conjugated to oligonucleotides. To highlight the potential of this catalytic approach, these conditions have been applied to iterative processes, which is of high interest for the development of DNA‐Encoded Libraries. [ABSTRACT FROM AUTHOR]

Background: This study aimed to investigate mutations associated with, the causes of, and the conditions that contribute to HIV drug resistance (DR). This research provides crucial insights into the mechanisms through which HIV evades antiretroviral drugs and suggests strategies to counter this phenomenon. Our objective was to assess the prevalence and structure of DR in HIV‐1 across various regions in Russia and identify the primary factors influencing the development of HIV DR. Methods: The study used nucleotide sequences from the HIV‐1 pol gene obtained from 1369 patients with a history of therapy and virological failure between 2005 and 2019 to analyze the frequency and structure of DR and the factors associated with it. Results: The analysed HIV‐1 genotypes included viruses resistant to nucleoside reverse transcriptase inhibitors (NRTIs; 11.8%), non‐nucleoside reverse transcriptase inhibitors (NNRTIs; 6.4%), and NRTIs + NNRTIs (31.7%). The mutations M184V/I and G190A/S/E were the most prevalent, accounting for 54.5% and 26.6%, respectively. The dominance of multiple DR persisted throughout the entire observation period. The likelihood of encountering drug‐resistant variants was increased among men, patients in the late stage of infection, and those with a viral load <30 000 RNA copies/mL. Injection drug use was not associated with DR. Conclusion: This study has yielded new insights into HIV DR in Russia, offering valuable information to identify clinical or programmatic events warranting closer attention and support. [ABSTRACT FROM AUTHOR]

In order to increase the content of flavoring components and nutrients in the stock, effects of microwave (MW) combined with ultrasonic pretreatment on water‐soluble proteins, flavor nucleotides, volatile gas constituents and sensory evaluation in the stewed stock were explored. The results showed that, compared with the control group (CK), MW, and ultrasonic (US) pretreatment could significantly promote the degradation of nucleotides and form a large number of 5′‐flavor nucleotides. The combined treatment of MW and US promoted protein hydrolysis and increased the content of water‐soluble protein. The microwave combined ultrasonication pretreated stew stock had the brightest color and the overall sensory score was better than that of the CK. In addition, GC–MS analysis showed that a total of 49 volatile substances were detected in the stock samples. After microwave combined ultrasonication pretreatment, the relative contents of aldehydes and alcohols in the stock increased significantly. The sensor response value of the electronic nose was the highest, indicating that the intensity of flavor characteristics increased. Therefore, MW combined with ultrasonic pretreatment can effectively promote the formation and dissolution of nutrients, and increase the content of flavorful nucleotides and volatile gases. Practical application: This study provides a novel processing method for traditional stewed stock. Ultrasonic combined with MW treatment can quickly degrade the protein in the raw material and dissolve it into the stock. At the same time, it promotes the formation of flavor nucleotides and accelerates the Maillard reaction to produce more flavor substances. The technology has the advantages of short processing time, environmental protection and safety. It can be used as a potential pretreatment technology to regulate the flavor of stock‐soup. [ABSTRACT FROM AUTHOR]

Nicotinamide adenine dinucleotide (NAD+) is a redox active molecule that is universally found in biology. Despite the importance and simplicity of this molecule, few reports exist that investigate which molecular features are important for the activity of this ribodinucleotide. By exploiting the nonenzymatic reduction and oxidation of NAD+ by pyruvate and methylene blue, respectively, we were able to identify key molecular features necessary for the intrinsic activity of NAD+ through kinetic analysis. Such features may explain how NAD+ could have been selected early during the emergence of life. Simpler molecules, such as nicotinamide, that lack an anomeric carbon are incapable of accepting electrons from pyruvate. The phosphate moiety inhibits activity in the absence of metal ions but facilitates activity at physiological pH and model prebiotic conditions by recruiting catalytic Mg2+. Reduction proceeds through consecutive single electron transfer events. Of the derivatives tested, including nicotinamide mononucleotide, nicotinamide riboside, 3‐(aminocarbonyl)‐1‐(2,3‐dihydroxypropyl)pyridinium, 1‐methylnicotinamide, and nicotinamide, only NAD+ and nicotinamide mononucleotide would be capable of efficiently accepting and donating electrons within a nonenzymatic electron transport chain. The data are consistent with early metabolic chemistry exploiting NAD+ or nicotinamide mononucleotide and not simpler molecules. [ABSTRACT FROM AUTHOR]

Maternal nutrition contributes to gene–environment interactions that influence susceptibility to common congenital anomalies such as neural tube defects (NTDs). Supplemental myo‐inositol (MI) can prevent NTDs in some mouse models and shows potential for prevention of human NTDs. We investigated effects of maternal MI intake on embryonic MI status and metabolism in curly tail mice, which are genetically predisposed to NTDs that are inositol‐responsive but folic acid resistant. Dietary MI deficiency caused diminished MI in maternal plasma and embryos, showing that de novo synthesis is insufficient to maintain MI levels in either adult or embryonic mice. Under normal maternal dietary conditions, curly tail embryos that developed cranial NTDs had significantly lower MI content than unaffected embryos, revealing an association between diminished MI status and failure of cranial neurulation. Expression of inositol‐3‐phosphate synthase 1, required for inositol biosynthesis, was less abundant in the cranial neural tube than at other axial levels. Supplemental MI or d‐chiro‐inositol (DCI) have previously been found to prevent NTDs in curly tail embryos. Here, we investigated the metabolic effects of MI and DCI treatments by mass spectrometry‐based metabolome analysis. Among inositol‐responsive metabolites, we noted a disproportionate effect on nucleotides, especially purines. We also found altered proportions of 5‐methyltetrahydrolate and tetrahydrofolate in MI‐treated embryos suggesting altered folate metabolism. Treatment with nucleotides or the one‐carbon donor formate has also been found to prevent NTDs in curly tail embryos. Together, these findings suggest that the protective effect of inositol may be mediated through the enhanced supply of nucleotides during neural tube closure. [ABSTRACT FROM AUTHOR]

The 3,3′‐linked cyclic dinucleotides (CDNs) of adenosine monophosphate (AMP) and guanosine monophosphate (GMP), cyclic di‐AMP (c‐di‐AMP), cyclic di‐GMP (c‐di‐GMP), and c‐GMP–AMP (cGAMP) are second messenger molecules in bacteria that regulate processes, such as biofilm formation, motility, virulence, stress response, and cell wall homeostasis. To analyze the profiles of the three CDNs together with their breakdown and precursor molecules, 5′‐phosphoadenylyl‐(3′ → 5′)adenine (pApA), 5′‐guanylyl‐(3′ → 5′)guanine (pGpG), 5′‐AMP, 3′‐ and 5′‐GMP, adenosine triphosphate (ATP), and GTP, we established an LC–MS/MS‐based approach for semi‐quantification and profiling. Weak anion exchange solid‐phase extraction was employed to improve selectivity and instrumental signal/noise of CDNs as well as pApA and pGpG. CDNs were analyzed using reverse‐phase UHPLC–MS/MS, whereas all other nucleotides were analyzed using hydrophilic interaction chromatography (HILIC)–MS/MS. The instrument limit of quantification ranged from 0.72 (c‐di‐AMP) to 60 nM (ATP and GTP). We applied this method to the analysis of the nine nucleotides in eight bacterial strains and found that the profiles varied widely in terms of both absolute and relative concentrations. Thus, CDN concentrations were generally <1 pmol/mg biomass, and the hydrolysis products, pApA and pGpG, were detected at lower pmol/mg concentrations. The presented method is a relatively simple and straightforward approach to profiling nucleotides with the rationale of comparing their relative levels between populations of bacterial strains. [ABSTRACT FROM AUTHOR]

Background: Caused by duplications of the gene encoding peripheral myelin protein 22 (PMP22), Charcot–Marie–Tooth disease type 1A (CMT1A) is the most common hereditary neuropathy. Despite this shared genetic origin, there is considerable variability in clinical severity. It is hypothesized that genetic modifiers contribute to this heterogeneity, the identification of which may reveal novel therapeutic targets. In this study, we present a comprehensive analysis of clinical examination results from 1564 CMT1A patients sourced from a prospective natural history study conducted by the RDCRN‐INC (Inherited Neuropathy Consortium). Our primary objective is to delineate extreme phenotype profiles (mild and severe) within this patient cohort, thereby enhancing our ability to detect genetic modifiers with large effects. Methods: We have conducted large‐scale statistical analyses of the RDCRN‐INC database to characterize CMT1A severity across multiple metrics. Results: We defined patients below the 10th (mild) and above the 90th (severe) percentiles of age‐normalized disease severity based on the CMT Examination Score V2 and foot dorsiflexion strength (MRC scale). Based on extreme phenotype categories, we defined a statistically justified recruitment strategy, which we propose to use in future modifier studies. Interpretation: Leveraging whole genome sequencing with base pair resolution, a future genetic modifier evaluation will include single nucleotide association, gene burden tests, and structural variant analysis. The present work not only provides insight into the severity and course of CMT1A, but also elucidates the statistical foundation and practical considerations for a cost‐efficient and straightforward patient enrollment strategy that we intend to conduct on additional patients recruited globally. [ABSTRACT FROM AUTHOR]

The development of in vitro transcribed mRNA (IVT mRNA)‐based therapeutics/vaccines depends on the management of IVT mRNA immunogenicity. IVT mRNA, which is used for intracellular protein translation, often triggers unwanted immune responses, interfering with protein expression and leading to reduced therapeutic efficacy. Currently, the predominant approach for mitigating immune responses involves the incorporation of costly chemically modified nucleotides like pseudouridine (Ψ) or N1‐methylpseudouridine (m1Ψ) into IVT mRNA, raising concerns about expense and the potential misincorporation of amino acids into chemically modified codon sequences. Here, an Additional Chimeric Element incorporated mRNA (ACE mRNA), a novel approach incorporating two segments within a single IVT mRNA structure, is introduced. The first segment retains conventional IVT mRNA components prepared with unmodified nucleotides, while the second, comprised of RNA/DNA chimeric elements, aims to modulate immunogenicity. Notably, ACE mRNA demonstrates a noteworthy reduction in immunogenicity of unmodified IVT mRNA, concurrently demonstrating enhanced protein expression efficiency. The reduced immune responses are based on the ability of RNA/DNA chimeric elements to restrict retinoic acid‐inducible gene I (RIG‐I) and stimulator of interferon genes (STING)‐mediated immune activation. The developed ACE mRNA shows great potential in modulating the immunogenicity of IVT mRNA without the need for chemically modified nucleotides, thereby advancing the safety and efficacy of mRNA‐based therapeutics/vaccines. [ABSTRACT FROM AUTHOR]

Die Welt, in der wir leben, ist homochiral. Die Riboseeinheiten, die das Rückgrat von DNA und RNA bilden, sind alle D‐konfiguriert, und die kodierten Aminosäuren, aus denen die Proteine aller lebenden Arten bestehen, weisen an den α‐Kohlenstoffatomen eine L‐Konfiguration auf. Die Homochiralität der α‐Aminosäuren ist unerlässlich für die Faltung der Peptide in wohldefinierte und funktionelle 3D‐Strukturen und die Homochiralität der D‐Ribose ist entscheidend für die Ausbildung einer Helix und die Basenpaarung. Die Frage, warum die Natur nur kodierte L‐α‐Aminosäuren verwendet, ist nicht geklärt. Wir zeigen hier, dass eine RNA‐Peptid‐Welt, in der Peptide an aus D‐Ribose aufgebauten RNAs wachsen, zur Selbstselektion von homo‐L‐Peptiden führt, was eine mögliche Erklärung für die in der Natur beobachtete Kombination von homo‐D‐Ribose und homo‐L‐Aminosäuren liefert. [ABSTRACT FROM AUTHOR]

Spontaneous interactions between nucleotides and lipid membranes are likely to have played a prominent role in the emergence of life on Earth. However, the effect of nucleotides on the physicochemical properties of model protocellular membranes is relatively less understood. To this end, we aimed to discern the effect of canonical nucleotides on the properties of single‐chain amphiphile membranes under prebiotically relevant conditions of multiple wet‐dry cycles. Furthermore, the change in the critical aggregation concentration of the membranes and their stability in the presence of nucleotides was also investigated in astrobiologically relevant analogue environments. We report that different nucleotides, lipid headgroups, and the ionic makeup of the system affect lipid‐nucleotide interactions, and these, in turn, modulate the effect of nucleotides on the membrane properties. Specifically, the presence of AMP, UMP, and CMP promoted self‐assembly of oleic acid membranes and increased their stability against certain prebiotically relevant selection pressures. This study takes us a step towards an appreciable understanding of how nucleotides might have shaped the protocellular landscape of the prebiotic Earth. [ABSTRACT FROM AUTHOR]

Objectives: ACE2, known as a host receptor involved with SARS‐CoV‐2 infection, binds to viral spike proteins for host cell entry. However, details regarding its induction and function in oral mucosal cells remain unknown. Materials and Methods: We examined ACE2 expression and its induction by transfected mimic nucleotides and pro‐inflammatory cytokines in oral keratinocytes (RT7) and fibroblasts (GT1). Subsequently, the effects of viral spike S1 protein via ACE2 on CXCL10 expression induced by pro‐inflammatory cytokines in both cells were examined. Results: ACE2 was constitutively expressed in RT7 and GT1. Transfected Poly(I:C) and Poly(dA:dT) increased ACE2 expression in those cells, while knockdown of RIG‐I decreased ACE2 expression induced by those transfected ds nucleotides. IFN‐γ and TNF‐α enhanced transfected ds nucleotides‐induced ACE2 expression in RT7 but not GT1. S1 protein alone did not affect CXCL10 expression in either cell type, whereas it enhanced IFN‐β‐induced CXCL10 in both, while immune responses of IFN‐γ‐ and TNF‐α‐induced CXCL10 enhanced by S1 protein were different between RT7 and GT1. Finally, knockdown of ACE2 decreased cytokines and S1 protein mediated‐CXCL10 levels in both cells. Conclusions: ACE2 in oral mucosal cells may contribute to development of infection and inflammation in cooperation with pro‐inflammatory cytokines following SARS‐CoV‐2 invasion. [ABSTRACT FROM AUTHOR]

Besides being a key player in numerous fundamental biological processes, RNA also represents a versatile platform for the creation of therapeutic agents and efficient vaccines. The production of RNA oligonucleotides, especially those decorated with chemical modifications, cannot meet the exponential demand. Due to the inherent limits of solid‐phase synthesis and in vitro transcription, alternative, biocatalytic approaches are in dire need to facilitate the production of RNA oligonucleotides. Here, we present a first step towards the controlled enzymatic synthesis of RNA oligonucleotides. We have explored the possibility of a simple protection step of the vicinal cis‐diol moiety to temporarily block ribonucleotides. We demonstrate that pyrimidine nucleotides protected with acetals, particularly 2′,3′‐O‐isopropylidene, are well‐tolerated by the template‐independent RNA polymerase PUP (polyU polymerase) and highly efficient coupling reactions can be achieved within minutes – an important feature for the development of enzymatic de novo synthesis protocols. Even though purines are not equally well‐tolerated, these findings clearly demonstrate the possibility of using cis‐diol‐protected ribonucleotides combined with template‐independent polymerases for the stepwise construction of RNA oligonucleotides. [ABSTRACT FROM AUTHOR]

Nucleoside monophosphates (NMPs) are the subunits of RNA. They are incorporated into growing complementary strands when sequences are copied in enzyme‐free reactions using organic leaving groups at the phosphates. Amino acids are rarely considered as leaving groups, but proline can act as a leaving group when N‐linked to NMPs, so that prolinyl NMPs hydrolyze in aqueous buffer at 37 °C, with half‐life times as short as 2.4 h, and they act as monomers in enzyme‐free primer extension. Still, their level of reactivity is insufficient for practical purposes, requiring months for some extensions. Herein we report the synthesis of eight substituted prolinyl AMPs together with seven related compounds and the results of a study of their reactivity. A δ‐carboxy prolinyl NMP was found to be converted with a half‐life time of just 11 min in magnesium‐free buffer, and a δ‐isopropyl prolinyl NMP was shown to react sevenfold faster than its prolinyl counterpart in enzyme‐free genetic copying of RNA. Our results indicate that both anchimeric and steric effects can be employed to increase the reactivity of aminoacidyl nucleotides, i.e. compounds that combine two fundamental classes of biomolecules in one functional entity. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) are a category of noncoding RNAs characterized by their length, often exceeding 200 nucleotides. There is a growing body of data that indicate the significant involvement of lncRNAs in a wide range of disorders, including cancer. lncRNA H19 was among the initial lncRNAs to be identified and is transcribed from the H19 gene. The H19 lncRNA exhibits significant upregulation in a diverse range of human malignancies, such as breast, colorectal, pancreatic, glioma, and gastric cancer. Moreover, the overexpression of H19 is frequently associated with a worse prognosis among individuals diagnosed with cancer. H19 has been shown to have a role in facilitating several cellular processes, including cell proliferation, invasion, migration, epithelial–mesenchymal transition, metastasis, and apoptosis. This article summarizes the aberrant upregulation of H19 in human malignancies, indicating promising avenues for future investigations on cancer diagnostics and therapeutic interventions. Significance statement: LncRNA H19 has strongly influenced the development of human cancers and carcinogenesis.Through interactions with proteins and microRNAs, lncRNA H19 modifies significant signaling pathways.Proliferation, migration, invasion, apoptosis, angiogenesis, stemness, drug resistance, and other essential features of cancer biology are all impacted by lncRNA H19.Complex networks involving posttranscriptional, epigenetic, and genetic regulatory processes are correlated with lncRNA H19.lncRNA H19 has been brought to light as a possible target for therapeutic measures or as a marker for cancer diagnosis. [ABSTRACT FROM AUTHOR]

Here we present a systematic analysis of the synthesis of unsymmetrical disulphides employing 6‐thioguanosine and its mono‐ and dinucleotides by three of the most common strategies: a nucleophilic substitution of the thiol, a thiol exchange reaction with another disulphide and oxidative dehydrogenation coupling reactions of S−H bonds. The exchange reaction was found to be the most efficient approach and could be used not only for nucleosides but also for nucleotides. [ABSTRACT FROM AUTHOR]

Aging shows biologically complex features with high individual variability, which reflects the exposure to several stimuli and the adaptation to them. Among them, metabolic changes are well observed as consequences or possible causes of aging. Calorie restriction extends organismal life span in experimental models. Several metabolites; for example, resveratrol or nicotinamide mononucleotide, are reported to mimic calorie restriction effects in vivo. Metabolomic research would be useful to evaluate metabolites as biomarkers in aging‐relevant events and to identify metabolic regulation of aging. We recently developed the metabolomic approach for whole blood analysis, which functions as strong tool for this purpose. We review the update findings in aging‐relevant metabolites detected by this method. Geriatr Gerontol Int 2024; 24: 44–48. [ABSTRACT FROM AUTHOR]

Sequencing for RNA modifications with the nanopore direct RNA sequencing platform provides ionic current levels, helicase dwell times, and base call data that differentiate the modifications from the canonical form. Herein, model RNAs were synthesized with site‐specific uridine (U) base modifications that enable the study of increasing an alkyl group size, halogen identity, or a change in base acidity to impact the nanopore data. The analysis concluded that increases in alkyl size trend with greater current blockage but a similar change in base‐call error was not found. The addition of a halogen series to C5 of U revealed that the current levels recorded a trend with the water‐octanol partition coefficient of the base, as well as the base call error. Studies with U modifications that are deprotonated (i. e., anionic) under the sequencing conditions gave broad current levels that influenced the base call error. Some modifications led to helicase dwell time changes. These insights provide design parameters for modification‐specific chemical reagents that can shift nanopore signatures to minimize false positive reads, a known issue with this sequencing approach. [ABSTRACT FROM AUTHOR]

The GTPase FlhF, a signal recognition particle (SRP)‐type enzyme, is pivotal for spatial–numerical control and bacterial flagella assembly across diverse species, including pathogens. This study presents the X‐ray structure of FlhF in its GDP‐bound state at a resolution of 2.28 Å. The structure exhibits the classical N‐ and G‐domain fold, consistent with related SRP GTPases such as Ffh and FtsY. Comparative analysis with GTP‐loaded FlhF elucidates the conformational changes associated with GTP hydrolysis. These topological reconfigurations are similarly evident in Ffh and FtsY, and play a pivotal role in regulating the functions of these hydrolases. [ABSTRACT FROM AUTHOR]

Colorectal cancer is a common malignant digestive tract tumour with high morbidity and mortality. Early detection, treatment and diagnosis are crucial for preventing and treating colorectal cancer, which develops through multi‐stage accumulation and gene participation, affecting tumour marker levels. Chronic wounds can lead to the development of certain cancers, such as colorectal cancer. The prolonged inflammation and tissue repair caused by chronic wounds can trigger cellular changes, potentially promoting cancerous cell growth in the colon. The formation and progression of colorectal cancer involve changes in tumour markers, such as carcinoembryonic antigen (CEA), sugar chain antigen 19–9 (CA199) and CA125. This study explores the clinical application value of a stool routine combined with serum tumour marker detection in diagnosing colorectal cancer. The experiment team examined the clinical information of 56 colorectal cancer patients alongside a control group of 56 healthy patients. Distinct stool characteristics and heightened occult blood rates were evident in colorectal cancer cases. The combined approach integrating stool routine and serum tumour markers improved diagnostic accuracy, displaying enhanced sensitivity and specificity compared with individual markers or stool routines alone. Bioinformatics analysis indicated increased CEA and CA125 levels in colorectal cancer tissues versus normal tissues, hinting at potential prognostic implications. Exploring wound‐healing genes like Vascular Endothelial Growth Factor A (VEGFA), Tumour Protein 53 (TP53) and Transforming Growth Factor Alpha (TGFA) revealed heightened expression in colorectal cancer, suggesting their potential role in disease progression. These markers showed associations with various immune cell types, suggesting their impact within the tumour microenvironment (p < 0.05). Single‐cell RNA sequencing data highlighted varying CEA expressions across different cell populations in colorectal cancer. The findings indicated that integrating clinical assessments with accurate biomarkers may provide valuable insights into prognostic implications. [ABSTRACT FROM AUTHOR]

The novel HLA‐A*02:1144 allele differs from HLA‐A*02:03:01:01 by 3 nucleotides in exon 7. [ABSTRACT FROM AUTHOR]

By using the thin‐film transistor (TFT) technology, the oligo nucleotides array has been proved to be achieved in‐situ on a throughput matrix backplane of 16*16, with oligonucleotide lengths reaching 150mers, and the yield of each oligo has surpassed tens of fmol per pixel. This TFT‐based methods effectively balance the synthesis throughput with the loading capacity and offer a significantly lower cost for higher quality DNA for various applications in molecular biology. [ABSTRACT FROM AUTHOR]

Background and Purpose: Platelet function during inflammation is dependent on activation by endogenous nucleotides. Non‐canonical signalling via the P2Y1 receptor is important for these non‐thrombotic functions of platelets. However, apart from ADP, the role of other endogenous nucleotides acting as agonists at P2Y1 receptors is unknown. This study compared the effects of ADP, Ap3A, NAD+, ADP‐ribose, and Up4A on platelet functions contributing to inflammation or haemostasis. Experimental Approach: Platelets obtained from healthy human volunteers were incubated with ADP, Ap3A, NAD+, ADP‐ribose, or Up4A, with aggregation and fibrinogen binding measured (examples of function during haemostasis) or before exposure to fMLP to measure platelet chemotaxis (an inflammatory function). In silico molecular docking of these nucleotides to the binding pocket of P2Y1 receptors was then assessed. Key Results: Platelet aggregation and binding to fibrinogen induced by ADP was not mimicked by NAD+, ADP‐ribose, and Up4A. However, these endogenous nucleotides induced P2Y1‐dependent platelet chemotaxis, an effect that required RhoA and Rac‐1 activity, but not canonical PLC activity. Analysis of molecular docking of the P2Y1 receptor revealed distinct differences of amino acid interactions and depth of fit within the binding pocket for Ap3A, NAD+, ADP‐ribose, or Up4A compared with ADP. Conclusion and Implications: Platelet function (aggregation vs motility) can be differentially modulated by biased‐agonist activation of P2Y1 receptors. This may be due to the character of the ligand‐binding pocket interaction. This has implications for future therapeutic strategies aimed to suppress platelet activation during inflammation without affecting haemostasis as is the requirement of current ant‐platelet drugs. LINKED ARTICLES: This article is part of a themed issue on Platelet purinergic receptor and non‐thrombotic disease. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.4/issuetoc [ABSTRACT FROM AUTHOR]

Chronic wounds have been a major factor of serious harm to global public health. At present, it is known that almost all chronic wounds contain biofilms, which seriously hinder the healing process. Removal of biofilms can effectively promote the healing of chronic wounds. As the study of wound biofilms deepens, many new treatment methods have emerged, thus bringing revolutionary means for the treatment of chronic wound biofilm. This review summarizes various methods for the treatment of chronic wound biofilm worldwide to provide a theoretical summary and practical basis for the selection of suitable wound biofilm treatment methods in clinical practice. [ABSTRACT FROM AUTHOR]

Nucleoside monophosphates perform various essential functions and serve as second messengers in living systems. Despite the success of nucleotide‐selective probes based on proteins, the creation of synthetic receptors for nucleoside monophosphates remains a challenging task. In this paper, we explore the design of synthetic receptors based on a combination of three recognition motifs. We show that each binding motif contributes to the formation of the host‐guest complexes. The core macrocycle provides recognition of the phosphate residue of the nucleotide, while naphthalimide and the attached cytosine residue participate in the coordination of the nucleobase via π‐π and hydrogen bonding interactions. The presence of cytosine in the receptor structure substantially increases the overall affinity of receptors for nucleotides. A considerable increase (100‐fold) in binding affinities is observed for the tetranucleotide DNA sequences 5′‐GGGG ‐3′ and 5′‐CCCC‐3′, as compared to the previously reported system without the attached cytosine. [ABSTRACT FROM AUTHOR]

Trimming of sequencing reads is a pre‐processing step that aims to discard sequence segments such as primers, adapters and low quality nucleotides that will interfere with clustering and classification steps. We evaluated the impact of trimming length of paired‐end 16S and 18S rRNA amplicon reads on the ability to reconstruct the taxonomic composition and relative abundances of communities with a known composition in both even and uneven proportions. We found that maximizing read retention maximizes recall but reduces precision by increasing false positives. The presence of expected taxa was accurately predicted across broad trim length ranges but recovering original relative proportions remains a difficult challenge. We show that parameters that maximize taxonomic recovery do not simultaneously maximize relative abundance accuracy. Trim length represents one of several experimental parameters that have non‐uniform impact across microbial clades, making it a difficult parameter to optimize. This study offers insights, guidelines, and helps researchers assess the significance of their decisions when trimming raw reads in a microbiome analysis based on overlapping or non‐overlapping paired‐end amplicons. [ABSTRACT FROM AUTHOR]