Nuclear Targets Research Articles

Impact of vector meson polarization on its interaction with matter

The production of unstable particles on different nuclei provides the possibility to determine the total cross section of the interaction of vector mesons V=rho ,omega ,varphi , K^{*0}(892),J/psi etc. with nucleons. This interaction is defined by a set of amplitudes that correspond to the transverse (helicity lambda =pm 1) or longitudinal (lambda =0) polarization of the vector meson. The total cross section for the interaction of transversely polarized vector mesons with nucleon sigma _T=sigma (V_T N) has been extracted from the coherent photoproduction of vector mesons off nuclei, while the vector meson production in charge exchange reactions as pi ^pm (K^pm )+Arightarrow V^0(K^{*0})+A' provides the unique opportunity to obtain the not yet measured total cross section for longitudinally polarized vector meson interacting with nucleon sigma _L=sigma (V_L N). We shortly discuss the importance of the knowledge of sigma _L and possibility to extract its value from experiments on nuclear target.

Dampened Regulatory Circuitry of TEAD1/ITGA1/ITGA2 Promotes TGFβ1 Signaling to Orchestrate Prostate Cancer Progression.

The extracellular matrix (ECM) undergoes substantial changes during prostate cancer (PCa) progression, thereby regulating PCa growth and invasion. Herein, a meta-analysis of multiple PCa cohorts is performed which revealed that downregulation or genomic loss of ITGA1 and ITGA2 integrin genes is associated with tumor progression and worse prognosis. Genomic deletion of both ITGA1 and ITGA2 activated epithelial-to-mesenchymal transition (EMT) in benign prostate epithelial cells, thereby enhancing their invasive potential in vitro and converting them into tumorigenic cells in vivo. Mechanistically, EMT is induced by enhanced secretion and autocrine activation of TGFβ1 and nuclear targeting of YAP1. An unbiased genome-wide co-expression analysis of large PCa cohort datasets identified the transcription factor TEAD1 as a key regulator of ITGA1 and ITGA2 expression in PCa cells while TEAD1 loss phenocopied the dual loss of α1- and α2-integrins in vitro and in vivo. Remarkably, clinical data analysis revealed that TEAD1 downregulation or genomic loss is associated with aggressive PCa and together with low ITGA1 and ITGA2 expression synergistically impacted PCa prognosis and progression. This study thus demonstrated that loss of α1- and α2-integrins, either via deletion/inactivation of the ITGA1/ITGA2 locus or via loss of TEAD1, contributes to PCa progression by inducing TGFβ1-driven EMT.

Nuclear localization signal-tagged systems: relevant nuclear import principles in the context of current therapeutic design.

Nuclear targeting of therapeutics provides a strategy for enhancing efficacy of molecules active in the nucleus and minimizing off-target effects. 'Active' nuclear-directed transport and efficient translocations across nuclear pore complexes provide the most effective means of maximizing nuclear localization. Nuclear-targeting systems based on nuclear localization signal (NLS) motifs have progressed significantly since the beginning of the current millennium. Here, we offer a roadmap for understanding the basic mechanisms of nuclear import in the context of actionable therapeutic design for developing NLS-therapeutics with improved treatment efficacy.

Chapter 7 - Evolution of methods to detect paraneoplastic antibodies

An adaptive immune response in less than 1% of people who develop cancer produces antibodies against neuronal proteins. These antibodies can be associated with paraneoplastic syndromes, and their accurate detection should instigate a search for a specific cancer. Over the years, multiple systems, from indirect immunofluorescence to live cell-based assays, have been developed to identify these antibodies. As the specific antigens were identified, high throughput, multi-antigen substrates such as line blots and ELISAs were developed for clinical laboratories. However, the evolution of assays required to identify antibodies to membrane targets has shone a light on the importance of antigen conformation for antibody detection. This chapter discusses the early antibody assays used to detect antibodies to nuclear and cytosolic targets and how new approaches are required to detect antibodies to membrane targets. The chapter presents recent data that support international recommendations against the sole use of line blots for antibody detection and highlights a new antigen-specific approach that appears promising for the detection of submembrane targets.

Improvement in Tol2 transposon for efficient large-cargo capacity transgene applications in cultured cells and zebrafish ( Danio rerio).

Most viruses and transposons serve as effective carriers for the introduction of foreign DNA up to 11 kb into vertebrate genomes. However, their activity markedly diminishes with payloads exceeding 11 kb. Expanding the payload capacity of transposons could facilitate more sophisticated cargo designs, improving the regulation of expression and minimizing mutagenic risks associated with molecular therapeutics, metabolic engineering, and transgenic animal production. In this study, we improved the Tol2 transposon by increasing protein expression levels using a translational enhancer ( QBI SP163, ST) and enhanced the nuclear targeting ability using the nuclear localization protein H2B (SHT). The modified Tol2 and ST transposon efficiently integrated large DNA cargos into human cell cultures (H1299), comparable to the well-established super PiggyBac system. Furthermore, mRNA from ST and SHT showed a significant increase in transgene delivery efficiency of large DNA payloads (8 kb, 14 kb, and 24 kb) into zebrafish ( Danio rerio). This study presents a modified Tol2 transposon as an enhanced nonviral vector for the delivery of large DNA payloads in transgenic applications.

Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.

XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of a human XIST-SPEN complex in vitro and identified novel sequence and structure determinants that may contribute to X chromosome silencing initiation. Binding of SPEN to XIST RNA requires RRM 4 of the protein, in contrast to the requirement of RRM 3 and RRM 4 for specific binding to SRA RNA. Measurements of SPEN binding to full-length, dimeric, trimeric, or other truncated versions of the A-repeat region revealed that high-affinity binding of XIST to SPEN in vitro requires a minimum of four A-repeat segments. SPEN binding to XIST A-repeat RNA changes the accessibility of the RNA at specific nucleotide sequences, as indicated by changes in RNA reactivity through chemical structure probing. Based on computational modeling, we found that inter-repeat duplexes formed by multiple A-repeats can present an unpaired adenosine in the context of a double-stranded region of RNA. The presence of this specific combination of sequence and structural motifs correlates with high-affinity SPEN binding in vitro. These data provide new information on the molecular basis of the XIST and SPEN interaction.

Arabidopsis BBX14 is involved in high light acclimation and seedling development.

The development of photosynthetically competent seedlings requires both light and retrograde biogenic signaling pathways. The transcription factor GLK1 functions at the interface between these pathways and receives input from the biogenic signal integrator GUN1. BBX14 was previously identified, together with GLK1, in a core module that mediates the response to high light (HL) levels and biogenic signals, which was studied by using inhibitors of chloroplast development. Our chromatin immunoprecipitation-Seq experiments revealed that BBX14 is a direct target of GLK1, and RNA-Seq analysis suggests that BBX14 may function as a regulator of the circadian clock. In addition, BBX14 plays a role in chlorophyll biosynthesis during early onset of light. Knockout of BBX14 results in a long hypocotyl phenotype dependent on a retrograde signal. Furthermore, the expression of BBX14 and BBX15 during biogenic signaling requires GUN1. Investigation of the role of BBX14 and BBX15 in GUN-type biogenic (gun) signaling showed that the overexpression of BBX14 or BBX15 caused de-repression of CA1 mRNA levels, when seedlings were grown on norflurazon. Notably, transcripts of the LHCB1.2 marker are not de-repressed. Furthermore, BBX14 is required to acclimate plants to HL stress. We propose that BBX14 is an integrator of biogenic signals and that BBX14 is a nuclear target of retrograde signals downstream of the GUN1/GLK1 module. However, we do not classify BBX14 or BBX15 overexpressors as gun mutants based on a critical evaluation of our results and those reported in the literature. Finally, we discuss a classification system necessary for the declaration of new gun mutants.

Biogeographic analysis based on phylogenomic data supports multiple ancient dispersals that facilitated the eastern Asia–North America–Mexico disjunction in the subfamily Linnaeoideae (Caprifoliaceae)

AbstractThe small subfamily Linnaeoideae of Caprifoliaceae exhibits a disjunct distribution in Eurasia and North America, including Mexico, with most taxa occurring in eastern Asia or Mexico and the monospecific Linnaea Gronov. ex L. having a circumboreal to north temperate distribution. We sampled 17 of the 20 species representing all Linnaeoideae genera and used nuclear (target enrichment) and complete plastome sequence data to reconstruct the phylogeny. Our results show strong topological conflicts between nuclear and plastid data, especially concerning Dipelta Maxim. and Diabelia Landrein, supporting hybridization events complicating the deep diversification. Nuclear data were used for divergence time estimation and ancestral area reconstruction. The divergence time between the Mexican Vesalea M. Martens & Galeotti and the Linnaea clade was dated to 39.5 Ma, with a 95% highest posterior density of 28.2 Ma (mid‐Oligocene) to 45.2 Ma (mid‐Eocene). Reconstructed ancestral areas support a widespread common ancestor of Linnaea plus Vesalea in Mexico and at least another area (eastern Asia, North America, or Europe). The biogeographic analysis, including fossils, supports the ancestral range of Linnaeoideae to be widespread in central and western China + Europe + Mexico, or eastern and northern Asia + central and western China + Mexico, or central and western China + North America + Mexico. The North Atlantic and/or the Bering land bridges may be important in the widespread distribution across continents in the Northern Hemisphere. Our study highlights the importance of utilizing fossils in biogeographic inferences andusing data from different genomes while reconstructing deep and shallow phylogenies of organisms.

Universality of Nucleon–Nucleon Correlations in Nuclei and Cumulative Pion Production

The structure of nuclear matter at short internucleon distances is one of the poorly studied aspects of nuclear physics. At distances of the order of the nucleon radius, nuclear matter is represented by the pairs of correlated nucleons with relative momenta exceeding the Fermi momenta that emerge for a short time. Such structures, whose local density is comparable to the density of neutron stars, arise from fluctuations in the average nuclear density. One of the important characteristics of nucleon–nucleon correlations is their universality implying the independence of their properties from the nuclear mass number. Therefore, the peculiarities of these objects of nuclear structure reflect the properties of nuclear matter rather than specific nuclei. Information about the short-distance physics is extracted from the analysis of processes with high energy–momentum transfers. Until now, the property of universality has been observed in electron–nucleus collisions only for the breakup of nucleon pairs. In this paper we analyze the data on the cumulative production of pions by protons on a set of nuclear targets and for the first time have established the existence of universality of two-nucleon correlations in the production of π+ and π– mesons. We have obtained evidence for the involvement of three-nucleon correlations in the production of pions beyond the kinematics of their production in interactions with two-nucleon objects.

Biallelic Landscape of DNMT3A Mutant Myeloid Neoplasia

The structure of DNMT3A comprises an N-terminal regulatory part promoting nuclear localization and targeting chromatin and a C-terminal domain, mainly involved in DNA binding and methylation catalysis. 1DNMT3A mutations in myeloid neoplasia (MN) and clonal hematopoiesis are mostly heterozygous. Homozygous null Dnmt3amice are born runted and Dnmt3a-/- cells express a hypomethylation phenotype. 2 An invariant detection of heterozygous mutations without homozygous, hemizygous, or biallelic configurations suggests absence of acquisition of more malignant phenotypes by progressive inactivation of DNMT3A. Moreover, residual DNMT3A function is essential for cell survival and potentially suggests that synthetic lethality might be a viable therapeutic strategy whereby cases with two intact alleles would be more resistant allowing a therapeutic window. Consequently, identification of biallelic DNMT3A mutant cases may be extremely instructive for the development of therapeutics targeting DNMT3A. We analyzed targeted NGS sequencing results of 4,895 cases with MN enrolled at our institution from 2002 to 2021 and retrospectively reviewed the clinical characteristics of all patients with deleterious DNMT3A mutations. DNMT3A mutations were identified in 461 patients, of whom 39 had double and 1 triple hits. Most of the mutants had AML (n=236) including biphenotypic AML (n=5), followed by MDS (n=142), MDS/MPN overlap (n=46) and MPN (n=37). In addition, mutations were identified in 9% of CHIP/CCUS (n=117) and 4% of aplastic anemia (n=68). Multiple DNMT3A hits were more often encountered in AML than MDS and MDS/MPN overlap (62.5% vs. 32.5% vs. 2.5%; P = .045). Single hits were represented by missense (73%) within the hotspot R882 (35%), frameshifts (10%), nonsense (9%), splice sites (6%) and in-frame ins/del (2%). Double hits configuration had a constellation of missense/missense (40%), missense/frameshifts (25%), missense/nonsense (13%), and missense/splice sites (10%) ( Fig1). R882 accounted for 10% of the multi hit carriers. Of note is that biallelic involvement was not confined to non-R882. Patients harboring multi hits carriedmore likely IDH2 (27.5% vs. 10.5%; OR 2.73; P = .011) and ETV6 (7.5% vs. 1.7%; OR 4.32 P = .043) mutations compared to patients with single hits DNMT3A by multivariate logistic regression analysis. Since deletion or UPD of DNMT3A locus has not been found, one can assume that all cases with one hit harbor monoallelic rather than biallelic subclones. For carriers of multiple mutations, one can stipulate that when the sum of VAFs exceeds the theoretical 60%, the presence of a biallelic subclone might be suspected. Indeed, 24 cases fulfilled this criterion. However, in 40% of patients with double hits, arithmetic VAF did not allow for unequivocal resolution of the mutational configuration, with either smaller biallelic subclones vs. subclonal mosaicism being possible. Next, we compared clinical features and outcomes of patients with mono vs. biallelic cases. In MDS, compared with single hits DNMT3A, biallelic cases showed significantly higher WBC (median 7.49 vs. 3.15 k/µL; P = .0052), ANC (4.88 vs. 1.52 k/µL; P = .0056), and platelet count (264 vs. 83 k/µL; P = .0036). In high-risk MDS and AML, with a median follow-up of 12.5 months (0.2-201), patients with biallelic DNMT3Ashowed significantly poorer 1-year OS rate than patients with single hits (42.8% vs. 65.8%; P = .0095). Longitudinal molecular analysis of 8 cases (2 MDS at onset and upon progression to sAML; 4 AML at diagnosis and following relapse after conventional intensive chemotherapy-induced remission; 1 AML at diagnosis and CR post SCT; 1 AML and donor-derived AML post SCT) demonstrated an early origin of biallelic hits with leukemogenic potential. Indeed, biallelic clones persisted or expanded in 6 transformed cases. Our study describes the likelihood that biallelic configuration of DNMT3A mutations, while rare, is indeed compatible with clonal expansion and thus questions the applicability of a synthetic lethality strategy. We are currently confirming that, indeed, truly biallelic cases vs. mosaicism are permissive using DNASeq of single sorted progenitor cells. The results of this analysis will be available at the time of ASH meeting.

A Mouse Model of Zhu-Tokita-Takenouchi-Kim Syndrome Reveals Indispensable Son Functions in Myeloid-Lymphoid Lineage Balance and Terminal Differentiation

SON is a DNA- and RNA-binding protein mainly localized in nuclear speckles. Compromised SON function leads to aberrant and alternative RNA splicing, particularly for transcripts bearing weak splice sites. SON also binds to DNA and suppresses H3K4me3 modifications at transcription start sites by inhibiting the MLL1/2 methyltransferase complex. More recent studies suggest that SON serves as the core of nuclear speckles, and SON is required for the association between nuclear speckles and p53 target genes to boost RNA expression. Therefore, SON governs the expression of a myriad of target genes by regulating transcription and RNA splicing as well as nuclear speckle assembly, yet exerts its effects on specific sets of genes. However, the role of SON in organ development and hematopoiesis remains poorly understood. Recently, we identified that heterozygous loss-of-function (LoF) mutations in the SON gene cause a neurodevelopmental disorder with multi-organ anomalies in human patients. This syndrome has been designated as a novel rare disease named Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome. The ZTTK SON-Shine Foundation, a family-initiated non-profit organization, was launched, and through this foundation, we work with families to characterize clinical symptoms associated with SON LoF. Among the clinical symptoms observed in individuals with ZTTK syndrome, a noticeable feature is a wide range of hematological abnormalities, including bone marrow failure, high mean corpuscular volume (MCV), polycythemia, severe anemia, and thrombosis. Furthermore, immunoglobulin deficiency, poor responses to vaccines, and frequent infections were reported, implicating SON LoF in various hematopoietic abnormalities. To study how heterozygous LoF of SON affects organ development and causes clinical features associated with ZTTK syndrome, we created a mouse model of Son haploinsufficiency ( Son +/-). While complete knockout of Son ( Son -/-) led to embryonic lethality, Son +/- mice were viable and recapitulated many clinical features of human ZTTK syndrome patients. The Son +/- mice showed severe growth retardation, signs of cognitive impairment, skeletal abnormalities, kidney agenesis/hypoplasia, and, importantly, hematopoietic abnormalities, such as high MCV, low lymphocyte counts, and immunoglobulin deficiency. To examine the hematopoietic features found in ZTTK syndrome patients are due to SON LoF, we further examined hematopoiesis of our Son +/- mice. We found that Son +/- fetal liver as well as adult mouse bone marrow contain a reduced size of the early-stage hematopoietic stem and progenitor cell (HSPC) pool (marked as Lin-Sca1+cKit+: LSK). Analysis of LSK subpopulations revealed that Son +/- mice have myeloid-lymphoid lineage imbalance at the stage of multipotent progenitor (MPP), with increased megakaryocyte/erythroid lineage-biased MPPs (MPP2) while lymphoid lineage-biased MPPs (MPP4) are decreased. In addition, erythroid terminal differentiation and B cell maturation were impaired in Son +/- mice. Single-cell RNA-sequencing of mouse bone marrow Lin-cKit+ cells and transcriptome-based clustering also revealed that Son haploinsufficiency leads to a reduction in lymphoid lineage-committed progenitor cells and decreased expression of lymphoid lineage/B cell development genes, while erythroid lineage-promoting genes were aberrantly activated in myeloid lineage progenitors. Deep bulk RNA-sequencing and alternative splicing analysis identified that that Son haploinsufficiency caused alternative splicing of chromatin modifiers genes and epigenetic regulator genes. Furthermore, from our ATAC-sequencing analysis, we found that Son haploinsufficiency causes decreased chromatin accessibility in the gene loci critical for lymphoid lineage specification. Taken together, our Son +/- mouse model revealed that the normal level of Son is required to achieve the sufficient expression levels of the genes directing lymphoid lineage specification, B cell lineage development, and erythroid terminal differentiation. Our study demonstrates the indispensable roles of SON in multiple stages of hematopoiesis and provides valuable insight into the clinical significance of abnormal SON levels in hematopoietic diseases.

Probing the hidden-bottom pentaquark resonances in photonuclear bottomonium production near threshold: Differential observables

We study the near-threshold ϒ(1S) meson photoproduction from protons and nuclei by considering incoherent direct non-resonant (γp→ϒ(1S)p, γn→ϒ(1S)n) and two-step resonant (γp→Pbi+→ϒ(1S)p, γn→Pbi0→ϒ(1S)n, i=1, 2, 3; Pb1+,0=Pb+,0(11080), Pb2+,0=Pb+,0(11125), Pb3+,0=Pb+,0(11130)) bottomonium production processes with the main goal of clarifying the possibility to observe the non-strange hidden-bottom pentaquark states Pbi+,0 in this production via differential observables. We calculate the absolute excitation functions, energy and momentum distributions for the non-resonant, resonant and for the combined (non-resonant plus resonant) production of ϒ(1S) mesons on protons, on carbon and tungsten target nuclei at near-threshold incident photon beam energies by assuming the spin-parity assignments of the hypothetical hidden-bottom resonances Pb+,0(11080), Pb+,0(11125) and Pb+,0(11130) as JP=(1/2)−, JP=(1/2)− and JP=(3/2)− within four different realistic choices for the branching ratios of their decays to the ϒ(1S)p and ϒ(1S)n modes (0.125, 0.25, 0.5 and 1%) as well as for two options for the background contribution. We demonstrate that the measurements of these combined observables on proton and nuclear targets in the near-threshold energy region in future experiments at the planned high-luminosity electron-ion colliders EIC and EicC in the US and China should provide evidence for the existence of the above hidden-bottom pentaquark resonances as well as clarify their decay rates.

Single-Spin Asymmetry of Neutrons in Polarized pA Collisions

Absorptive corrections, which are known to suppress proton-neutron transitions with a large fractional momentum z→1 in pp collisions, become dramatically strong on a nuclear target, and they push the partial cross sections of leading neutron production to the very periphery of the nucleus. The mechanism of the pion π and axial vector meson a1 interference, which successfully explains the observed single-spin asymmetry in a polarized pp→nX, is extended to the collisions of polarized protons with nuclei. When corrected for nuclear effects, it explains the observed single-spin azimuthal asymmetry of neutrons that is produced in inelastic events, which is where the nucleus violently breaks up. This single-spin asymmetry is found to be negative and nearly atomic mass number A-independent.

Halo-independent bounds on Inelastic Dark Matter

We discuss halo-independent constraints on the Inelastic Dark Matter (IDM) scenario, in which a Weakly Interaction Massive Particle (WIMP) state χ with mass m χ interacts with nuclear targets by upscattering to a heavier state χ′ with mass m χ + δ.In order to do so we adopt the single-stream method, that exploits the complementarity of Direct Detection (DD) and Capture in the Sun to extend the experimental sensitivity to the full range of incoming WIMP speeds.We show that a non-vanishing mass splitting δ modifies such range, and that for particular combinations of m χ and δ the complementarity between the two detection techniques required by the method is lost. In such cases a specific choice of the WIMP speed distribution in our Galaxy is required to obtain a constraint on the WIMP-nucleus cross section or coupling. Specifically, assuming for the escape velocity in our Galaxy u esc the reference value u esc ref = 560 km/s a halo-independent bound is possible when δ ≲ 510 keV for a Spin-Independent interaction and when δ ≲ 245 keV for a Spin-Dependent interaction (with the Spin-Independent value slightly reduced to δ ≲ 490 keV when u esc > u esc ref). In the low WIMP mass regime the bound from capture in the Sun is always more constraining than that for DD and is sufficient alone to provide a halo-independent constraint, while for large WIMP masses the halo-independent bound is given by a combination of capture in the Sun and DD. In this latter case the reduction in sensitivity due to the mass splitting δ is more pronounced for DD than for capture, and capture plays a more important role to determine the halo-independent bound compared to the elastic case. In particular we find that, for u esc = u esc ref, unless the mass of the target used in DD is larger than about four times that of the target driving capture in the Sun, DD does not play any role in the determination of the maximal value of δ for which a halo-independent bound is possible. We also discuss the issue of thermalization of IDM within the Sun and show that its impact on our results is mild.

Dual agonistic and antagonistic roles of ZC3H18 provide for co-activation of distinct nuclear RNA decay pathways

The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the nuclear exosome targeting (NEXT) complex and the poly(A) exosome targeting (PAXT) connection. Via its association with the ARS2 and ZC3H18 proteins, NEXT/exosome is recruited to capped and short unadenylated transcripts. Conversely, PAXT/exosome is considered to target longer and adenylated substrates via their poly(A) tails. Here, mutational analysis of the core PAXT component ZFC3H1 uncovers a separate branch of the PAXT pathway, which targets short adenylated RNAs and relies on a direct ARS2-ZFC3H1 interaction. We further demonstrate that similar acidic-rich short linear motifs of ZFC3H1 and ZC3H18 compete for a common ARS2 epitope. Consequently, while promoting NEXT function, ZC3H18 antagonizes PAXT activity. We suggest that this organization of RNA decay complexes provides co-activation of NEXT and PAXT at loci with abundant production of short exosome substrates.

The Gerasimov-Drell-Hearn sum rule with nuclear targets

Hadron properties are modified when the hadron is embedded in a nuclear medium. Here we discuss the Gerasimov-Drell-Hearn, GDH, sum rule for polarised photoproduction from a polarised nucleon within a polarised nuclear target. Strong enhancement is expected with the suppression of the proton and nucleon resonance masses and enhancement of the proton’s anomalous magnetic moment in medium. This could be tested in polarised photoproduction experiments with interesting targets being polarised deuterons, ^3He, ^6Li and ^7Li. The largest contribution to the GDH sum rule comes from the Delta resonance excitation. In existing data with polarised deuterons and ^3He the Delta excitation is shifted to slightly lower energy when compared to model predictions where the Delta is treated with its free mass.

Bioimaging based on Poly(ethylenimine)-Coated Carbon Dots and Gold Nanoparticles for pH Sensing and Metal Enhanced Fluorescence.

When exposed to specific light wavelengths, carbon dots (CDs), which tend to be fluorescent, can emit colorful light. It provides them with a lot of adaptability for different applications including bioimaging, optoelectronics, and even environmental sensing. Poly(ethylenimine) (PEI) coated carbon dots (PEI-CDs) with a long emission wavelength were synthesized via the hydrothermal method. The resultant CDs show strong fluorescence with quantum yield up to 20.2%. The PEI-CDs exist with distinct pH-sensitive features with pH values in the range of 2-14. The optical characteristics of CDs are pH-responsive due to the presence of different amine groups on PEI, which is a functional polycationic polymer. One of the most widely employed nanoparticles for improving the fluorescence plasmonic characteristics of a nanocomposite is gold. Gold nanoparticles were coupled with PEI-CDs in this assay by using the EDC-NHS coupling to increase the photoluminescence property of the PEI-CDs by using the metal-enhanced fluorescence approach. In the presence of gold nanoparticles, the fluorescence is enhanced 5-6 times. The likely mechanism in our investigation was primarily derived from enhancement of the intrinsic radiative decay rate rather than the local electric field impact. Moreover, PEI-CDs can be used as a bioimaging agent, as these molecules are nontoxic to the cells, and the positively charged PEI-CDs have the potential for nuclear targeting, allowing for electrostatic contact with DNA in the nucleus. This finding will expand the application that the PEI-CDs can be used in the future for targeted imaging applications.

Development of Seven New dPCR Animal Species Assays and a Reference Material to Support Quantitative Ratio Measurements of Food and Feed Products.

Laboratory testing methods to confirm the identity of meat products and eliminate food fraud regularly rely on PCR amplification of extracted DNA, with most published assays detecting mitochondrial sequences, providing sensitive presence/absence results. By targeting single-copy nuclear targets instead, relative quantification measurements are achievable, providing additional information on the proportions of meat species detected. In this Methods paper, new assays for horse, donkey, duck, kangaroo, camel, water buffalo and crocodile have been developed to expand the range of species that can be quantified, and a previously published reference assay targeting the myostatin gene has been modified to include marsupials and reptiles. The accuracy of this ratio measurement approach was demonstrated using dPCR with mixtures of meat DNA down to 0.1%. However, the limit of detection (LOD) of this approach is not just determined by the assay targets, but by the samples themselves, with food or feed ingredients and processing impacting the DNA yield and integrity. In routine testing settings, the myostatin assay can provide multiple quality control roles, including monitoring the yield and purity of extracted DNA, identifying the presence of additional meats not detected by the suite of species-specific assays and potentially estimating a sample-specific LOD based on measured copy numbers of the myostatin target. In addition to the myostatin positive control assay, a synthetic DNA reference material (RM) has been designed, containing PCR targets for beef, pork, sheep, chicken, goat, kangaroo, horse, water buffalo and myostatin, to be used as a positive template control. The availability of standardised measurement methods and associated RMs significantly improves the reliability, comparability and transparency of laboratory testing, leading to greater confidence in results.

Exploring the pharmacokinetic properties and inhibitory potentials of plant-derived alkaloids against nuclear protein targets in triple-negative breast cancer: An In Silico approach

Triple-negative breast cancer (TNBC) overexpresses poly-ADP ribose-polymerase (PARP), and histone deacetylase (HDAC) specific isoforms, PARP2 and HDAC7 respectively. There is a paucity of research assessing plant-based alkaloids for the development of HDAC7- and PARP2-isoform specific inhibitor compounds. This study evaluated the pharmacokinetic properties and inhibitory potentials of plant-derived alkaloids, including chelidonine and oxymatrine on PARP2 and HDAC7 using in silico protocols. ADME/T analysis revealed that chelidonine and oxymatrine had high human intestinal absorption and blood-brain barrier permeability, low CYP promiscuity, and no Ames mutagenicity or carcinogenicity. Moreso, chelidonine and oxymatrine had zero violations of the Lipinski rule of five. Chelidonine displayed the greatest PARP2 binding affinity (-9.6 Kcal/mol), when compared to oxymatrine (-8.4 Kcal/mol), co-crystalized ligand (-7.9 Kcal/mol) and the reference veliparib drug (-8.8 Kcal/mol). However, the co-crystalized HDAC-IN-5 had the most favorable binding interaction with HDAC7 (-9.8 Kcal/mol). The binding impact of chelidonine on HDAC7 (-8.6 Kcal/mol) was also greater than that of oxymatrine (-7.3 Kcal/mol) and romidepsin (-7.7 Kcal/mol). Chelidonine exhibited propitious drug-like properties and stronger inhibitory effects on PARP2 and HDAC7 than the reference drugs. This indicates its suitability for progression into pre-clinical and clinical trials for the development of PARP2- and HDAC7-isoform specific inhibitors that could be used for targeted TNBC treatment.

Trypanosoma cruzi Fibrillarins: Two paralogous proteins with non-identical signals for nuclear transport

Trypanosoma cruzi is a parasitic protozoa causative of Chagas disease. As part of our interest in studying the basic biology of this microorganism, this work reports our observations related to the characterization of motifs and structural domains present in two fibrillarin isoforms (TcFib1 and TcFib2) that were found to be necessary for the nuclear targeting of these nucleolar proteins. Previous characterization of these proteins indicated that they share 68.67% of identical amino acids and are both expressed as nucleolar proteins in T. cruzi epimastigotes. Using an approach based on the transfection of recombinant genes encoding fluorescent fibrillarin-EGFP fusion proteins, this study found evidence for the presence of 4 motifs or protein domains that help target these proteins to the nucleus: The GAR domain and carboxyl terminus in both TcFibs, as well as two lysines and a computationally predicted cNLS in TcFib1. As a distinctive feature, the GAR domain of TcFib2 proved to be essential for the nuclear localization of this protein paralog. Such a difference between TcFib1 and Tcfib2 nuclear localization signals can be explained as the presence of two partially related nuclear import pathways for the two fibrillarin homologues in this organism.