4-Chloro-1,2-phenylenediamine induced structural perturbation and genotoxic aggregation in human serum albumin.

4-Chloro-1,2-phenylenediamine (4-Cl-OPD) is a halogenated aromatic diamine used as a precursor in permanent hair color production. Despite its well-documented mutagenic and carcinogenic effects in various in vitro and in vivo models, its role in fibrillar aggregate formation and their genotoxic effect in therapeutic proteins has received less attention. The significance of human serum albumin (HSA) arises from its involvement in bio-regulatory and transport processes. HSA misfolding and aggregation are responsible for some of the most frequent neurodegenerative disorders. We used various complementary approaches to track the formation of amyloid fibrils and their genotoxic effect. Molecular dynamics study demonstrated the complex stability. The impact of 4-Cl-OPD on the structural dynamics of HSA was confirmed by Raman spectroscopy, X-ray diffraction, HPLC and SDS-PAGE. Fibrilllar aggregates were investigated using Congo red assay, DLS, and SEM. The genotoxic nature of 4-Cl-OPD was confirmed using plasmid nicking assay and DAPI staining, which revealed DNA damage and cell apoptosis. 4-Cl-OPD provides a model system for studying fibrillar aggregation and their genotoxic potential in the current investigation. Future studies should investigate the inhibition of the aggregation/fibrillation process, which may yield valuable clinical insights.

Withania somnifera (L.) Dunal as Add-On Therapy for COPD Patients: A Randomized, Placebo-Controlled, Double-Blind Study.

Background: The current gold-standard therapies for chronic obstructive pulmonary disease (COPD) lack disease-modifying potential and exert adverse side effects. Moreover, COPD patients are at a higher risk of severe outcomes if they get infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the cause of the current epidemic. This is the first study to document clinical research on an adaptogenic and steroidal activity-containing herb as a complementary medicine for COPD treatment. Objective: We aimed to evaluate the efficacy of Withania somnifera (L.) Dunal [Solanaceae] (WS) as an add-on therapy for COPD patients. Methods: A randomized, placebo-controlled, and double-blind clinical study was conducted. A total of 150 patients were randomly assigned to three groups: control, placebo, and WS group. In addition to conventional medicines, WS root capsules or starch capsules were given twice a day to the WS group and the placebo group, respectively. Their lung functioning, quality of life, exercise tolerance, systemic oxidative stress (OS), and systemic inflammation were assessed before and after 12 weeks of intervention. WS root phytochemicals were identified by LC-ESI-MS. The inhibitory activity of these phytochemicals against angiotensin-converting enzyme 2 (ACE-2); the SARS-CoV-2 receptor; myeloperoxidase (MPO); and interleukin-6 (IL-6) was evaluated by in silico docking to investigate the mechanism of action of WS. Results: The pulmonary functioning, quality of life, and exercise tolerance improved, and inflammation reduced notably the most in the WS group. Systemic oxidative stress subsided significantly only in the WS group. Although a minor placebo effect was observed in the SGRQ test, but it was not present in other tests. Withanolides found in the WS roots demonstrated substantial inhibitory activity against the proteins ACE-2, MPO, and IL-6, compared to that of a standard drug or known inhibitor. Moreover, FEV1% predicted had significant correlation with systemic antioxidative status (positive correlation) and malondialdehyde (MDA, negative correlation), suggesting that the antioxidative potential of WS has significant contribution to improving lung functioning. Conclusion: Our study clinically demonstrated that WS root when given along with conventional drugs ameliorated COPD significantly more in comparison to the conventional drugs alone, in GOLD 2 and 3 categories of COPD patients. In silico, it has potent inhibitory activity against SARS-CoV-2 receptor, ACE-2, MPO, and IL-6.

An assembly and interaction of upconversion and plasmonic nanoparticles on organometallic nanofibers: enhanced multicolor upconversion, downshifting emission and the plasmonic effect.

We present novel inorganic-organic hybrid nanoparticles (HNPs) constituting inorganic NPs, NaY0.78Er0.02Yb0.2F4, and organometallic nanofiber, Tb(ASA)3Phen (TAP). X-ray diffraction, Fourier transform infrared absorption and transmission electron microscopy analyses reveal that prepared ultrafine upconversion NPs (UCNPs (5-8 nm)) are dispersed on the surface of the TAP nanofibers. We observe that the addition of TAP in UCNPs effectively limits the surface quenching to boost the upconversion (UC) intensity and enables tuning of UC emission from the green to the red region by controlling the phonon frequency around the Er3+ ion. On the other hand, TAP is an excellent source of green emission under ultraviolet exposure. Therefore prepared HNPs not only give enhanced and tunable UC but also emit a strong green color in the downshifting (DS) process. To further enhance the dual-mode emission of HNPs, silver NPs (AgNPs) are introduced. The emission intensity of UC as well as DS emission is found to be strongly modulated in the presence of AgNPs. It is found that AgNPs enhance red UC emission. The possible mechanism involved in enhanced emission intensity and color output is investigated in detail. The important optical properties of these nano-hybrid materials provide a great opportunity in the fields of biological imaging, drug delivery and energy devices.

Lanthanide doped ultrafine hybrid nanostructures: multicolour luminescence, upconversion based energy transfer and luminescent solar collector applications.

We herein demonstrate novel inorganic-organic hybrid nanoparticles (HNPs) composed of inorganic NPs, NaY0.78Er0.02Yb0.2F4, and an organic ß-diketonate complex, Eu(TTA)3Phen, for energy harvesting applications. Both the systems maintain their core integrity and remain entangled through weak interacting forces. HNPs incorporate the characteristic optical behaviour of both the systems i.e. they give an intense red emission under UV excitation, due to Eu3+ in organic complexes, and efficient green upconversion emission of Er3+ in inorganic NPs for NIR (980 nm) excitation. However, (i) an energy transfer from Er3+ (inorganic NPs) to Eu3+ (organic complex) under NIR excitation, and (ii) an increase in the decay time of 5D0 → 7F2 transition of Eu3+ for HNPs as compared to the Eu(TTA)3Phen complex, under different excitation wavelengths, are added optical characteristics which point to an important role of the interface between both the systems. Herein, the ultra-small size (6-9 nm) and spherical shape of the inorganic NPs offer a large surface area, which improves the weak interaction force between both the systems. Furthermore, the HNPs dispersed in the PMMA polymer have been successfully utilized for luminescent solar collector (LSC) applications.

A strategy to achieve efficient dual-mode luminescence in lanthanide-based magnetic hybrid nanostructure and its demonstration for the detection of latent fingerprints.

We have synthesized a novel inorganic-organic hybrid nanostructure (IOHN) composed of fluoride nanophosphor (NaGd0.78Er0.02Yb0.2F4) and ß-diketones complex (Eu(DBM)3Phen). The Le Bail fitting of X-ray diffraction data suggests that the nanophoshor crystallizes in a hexagonal structure (P63/m space group). The TEM studies reveal that the nanophosphor and the IOHN both have average particle size of 6-8nm. The Eu(DBM)3Phen and NaGd0.78Er0.02Yb0.2F4 show characteristic down-shifting (DS) and up-conversion (UC) emission, under UV and NIR excitation, respectively. The IOHN comprises an excellent dual-mode optical features (DS and UC) of both the phases. Energy transfer from Er3+ (doped in inorganic phase) to Eu3+ (coordinated in organic phase) clearly demonstrates for a viable coupling between both the phases. IOHN material was found to be unique for the visualization of latent fingermarks. Because of ultrafine particle size the surface to volume ratio is relatively higher which improves the attachment of particles with the fingermarks. On the other hand, the strong paramagnetic property helps to remove excess material with magnetic wand easily. These properties provide an opportunity to probe even very weak fingermarks. Notwithstanding this, the dual-mode emission is useful for the visualization of latent fingermarks on multi-color surfaces as well.

Host-Sensitized NIR Quantum Cutting Emission in Nd(3+) Doped GdNbO4 Phosphors and Effect of Bi(3+) Ion Codoping.

Host-sensitized near-infrared quantum cutting (QC) emission has been demonstrated in Nd(3+) doped Gd(1-x)Nd(x)NbO4 phosphors for various x values. Further, the effect of Bi(3+) ion addition as a sensitizer on near-infrared QC is studied in detail. X-ray diffraction confirms a monoclinic structure for pure and Nd(3+) doped phosphors. Pulsed laser excitation at 266 nm of Gd(1-x)Nd(x)NbO4 and Gd(0.99-x)Nd(x)Bi(0.01)NbO4 causes efficient room-temperature energy transfer from the NbO4(3-) to the Nd(3+) ions and the NbO4(3-) and Bi(3+) ions to the Nd(3+) ions, respectively, which emits more than one near-infrared photon for single impinging ultraviolet photon. The emission band of Nd(3+) shows unusual character where the intensity of the (4)F(3/2)-(4)I(9/2) transition at 888 nm is higher than the intensity of the transition (4)F(3/2)-(4)I(11/2) at 1064 nm, due to energy transfer from GdNbO4 host to Nd(3+) ion. Using photoluminescence lifetime studies, the quantum cutting efficiencies are found to be the maximum 166% and 172% for Gd(0.95)Nd(0.05)NbO4 and Gd(0.94)Nd(0.05)Bi(0.01)NbO4, respectively. The present study could establish Nd(3+) ion as an alternative of Yb(3+) ion for near-infrared quantum cutting. This work facilitates the probing of Nd(3+) ions doped phosphor materials for next generation Si-solar cells.

Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration.

Liver regeneration after partial hepatectomy (PHx) is a complex and well-orchestrated biological process in which synchronized cell proliferation is induced in response to the loss of liver mass. To define long noncoding RNAs (lncRNAs) that participate in the regulation of liver regeneration, we performed microarray analysis and identified more than 400 lncRNAs exhibiting significantly altered expression. Of these, one lncRNA, LncPHx2 (Long noncoding RNA induced by PHx 2), was highly upregulated during liver regeneration. Depletion of LncPHx2 during liver regeneration using antisense oligonucleotides led to a transient increase in hepatocyte proliferation and more rapid liver regeneration. Gene expression analysis showed that LncPHx2 depletion resulted in upregulation of mRNAs encoding proteins known to promote cell proliferation, including MCM components, DNA polymerases, histone proteins, and transcription factors. LncPHx2 interacts with the mRNAs of MCM components, making it a candidate to regulate the expression of MCMs and other genes post-transcriptionally. Collectively, our data demonstrate that LncPHx2 is a key lncRNA that participates in a negative feedback loop modulating hepatocyte proliferation through RNA-RNA interactions.

Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes.

Molecular cancer diagnostics are an important clinical advance in cancer management, but new methods are still needed. In this context, gene expression signatures obtained by microarray represent a useful molecular diagnostic. Here, we describe novel probe-level microarray analyses that reveal connections between mRNA processing and neoplasia in multiple tumor types, with diagnostic potential. We now show that characteristic differences in mRNA processing, primarily in the 3'-untranslated region, define molecular signatures that can distinguish similar tumor subtypes with different survival characteristics, with at least 74% accuracy. Using a mouse model of B-cell leukemia/lymphoma, we find that differences in transcript isoform abundance are likely due to both alternative polyadenylation (APA) and differential degradation. While truncation of the 3'-UTR is the most common observed pattern, genes with elongated transcripts were also observed, and distinct groups of affected genes are found in related but distinct tumor types. Genes with elongated transcripts are overrepresented in ontology categories related to cell-cell adhesion and morphology. Analysis of microarray data from human primary tumor samples revealed similar phenomena. Western blot analysis of selected proteins confirms that changes in the 3'-UTR can correlate with changes in protein expression. Our work suggests that alternative mRNA processing, particularly APA, can be a powerful molecular biomarker with prognostic potential. Finally, these findings provide insights into the molecular mechanisms of gene deregulation in tumorigenesis.

Position-dependent motif characterization using non-negative matrix factorization.

MOTIVATION: Cis-acting regulatory elements are frequently constrained by both sequence content and positioning relative to a functional site, such as a splice or polyadenylation site. We describe an approach to regulatory motif analysis based on non-negative matrix factorization (NMF). Whereas existing pattern recognition algorithms commonly focus primarily on sequence content, our method simultaneously characterizes both positioning and sequence content of putative motifs. RESULTS: Tests on artificially generated sequences show that NMF can faithfully reproduce both positioning and content of test motifs. We show how the variation of the residual sum of squares can be used to give a robust estimate of the number of motifs or patterns in a sequence set. Our analysis distinguishes multiple motifs with significant overlap in sequence content and/or positioning. Finally, we demonstrate the use of the NMF approach through characterization of biologically interesting datasets. Specifically, an analysis of mRNA 3'-processing (cleavage and polyadenylation) sites from a broad range of higher eukaryotes reveals a conserved core pattern of three elements.

Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis.

Gene expression and processing during mouse male germ cell maturation (spermatogenesis) is highly specialized. Previous reports have suggested that there is a high incidence of alternative 3'-processing in male germ cell mRNAs, including reduced usage of the canonical polyadenylation signal, AAUAAA. We used EST libraries generated from mouse testicular cells to identify 3'-processing sites used at various stages of spermatogenesis (spermatogonia, spermatocytes and round spermatids) and testicular somatic Sertoli cells. We assessed differences in 3'-processing characteristics in the testicular samples, compared to control sets of widely used 3'-processing sites. Using a new method for comparison of degenerate regulatory elements between sequence samples, we identified significant changes in the use of putative 3'-processing regulatory sequence elements in all spermatogenic cell types. In addition, we observed a trend towards truncated 3'-untranslated regions (3'-UTRs), with the most significant differences apparent in round spermatids. In contrast, Sertoli cells displayed a much smaller trend towards 3'-UTR truncation and no significant difference in 3'-processing regulatory sequences. Finally, we identified a number of genes encoding mRNAs that were specifically subject to alternative 3'-processing during meiosis and postmeiotic development. Our results highlight developmental differences in polyadenylation site choice and in the elements that likely control them during spermatogenesis.

Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo.

Fully grown oocytes (FGOs) contain all the necessary transcripts to activate molecular pathways underlying the oocyte-to-embryo transition (OET). To elucidate this critical period of development, an extensive survey of the FGO transcriptome was performed by analyzing 19,000 expressed sequence tags of the Mus musculus FGO cDNA library. Expression of 5400 genes and transposable elements is reported. For a majority of genes expressed in mouse FGOs, homologs transcribed in eggs of Xenopus laevis or Ciona intestinalis were found, pinpointing evolutionary conservation of most regulatory cascades underlying the OET in chordates. A large proportion of identified genes belongs to several gene families with oocyte-restricted expression, a likely result of lineage-specific genomic duplications. Gene loss by mutation and expression in female germline of retrotransposed genes specific to M. musculus is documented. These findings indicate rapid diversification of genes involved in female reproduction. Comparison of the FGO and two-cell embryo transcriptomes demarcated the processes important for oogenesis from those involved in OET and identified novel motifs in maternal mRNAs associated with transcript stability. Discovery of oocyte-specific eukaryotic translation initiation factor 4E distinguishes a novel system of translational regulation. These results implicate conserved pathways underlying transition from oogenesis to initiation of development and illustrate how genes acquire and lose reproductive functions during evolution, a potential mechanism for reproductive isolation.

PACdb: PolyA Cleavage Site and 3'-UTR Database.

UNLABELLED: The PolyA Cleavage Site and 3'-UTR Database (PACdb) is a web-accessible database that catalogs putative 3'-processing sites and 3'-UTR sequences for multiple organisms. Sites have been identified primarily via expressed sequence tag-genome alignments, enabling delineation of both the specificities and heterogeneity of 3'-processing events. AVAILABILITY: By web browser or CGI: PACdb: http://harlequin.jax.org/pacdb/; AtPACdb: http://harlequin.jax.org/atpacdb/. SUPPLEMENTARY INFORMATION: Available online at http://harlequin.jax.org/pacdb/supplemental.php.