Sheetlike structure in the proximity of compact DNA.

We determine the phase diagram of DNA with inter- and intrastrand native-pair interactions that mimic the compaction of DNA. We show that DNA takes an overall sheetlike structure in the region where an incipient transition to a compact phase would have occurred. The stability of this phase is due to the extra entropy from the folding of the sheet, which is absent in the remaining polymerlike states of the phase diagram.

Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions.

Replication Protein A (RPA) is asingle strandedDNA(ssDNA)binding protein that coordinates diverse DNA metabolic processes including DNA replication, repair, and recombination. RPA is a heterotrimeric protein with six functional oligosaccharide/oligonucleotide (OB) domains and flexible linkers. Flexibility enables RPA to adopt multiple configurations andis thought to modulate its function. Here, usingsingle moleculeconfocal fluorescencemicroscopy combinedwith optical tweezers and coarse-grained molecular dynamics simulations, we investigated the diffusional migration of single RPA molecules on ssDNA undertension.The diffusioncoefficientDis the highest (20,000nucleotides2/s) at 3pNtension and in 100 mMKCl and markedly decreases whentensionor salt concentrationincreases. We attribute the tension effect to intersegmental transfer which is hindered by DNA stretching and the salt effect to an increase in binding site size and interaction energy of RPA-ssDNA. Our integrative study allowed us to estimate the size and frequency of intersegmental transfer events that occur through transient bridging of distant sites on DNA by multiple binding sites on RPA. Interestingly, deletion of RPA trimeric core still allowed significant ssDNA binding although the reduced contact area made RPA 15-fold more mobile. Finally, we characterized the effect of RPA crowding on RPA migration. These findings reveal how the high affinity RPA-ssDNA interactions are remodeled to yield access, a key step in several DNA metabolic processes.

An improved Shorea robusta genomic DNA extraction protocol with high PCR fidelity.

Shorea robusta (Dipterocarpaceae), commonly known as Sal, is an economically and culturally important timber species, known to contain a wide spectrum of polyphenols, polysaccharides, and other secondary metabolites in the tissues, which can interfere with the extraction of high-quality genomic DNA. In order to screen simple sequence repeat (SSR) markers and carry out other DNA-based analyses for this species in our laboratory, a high-throughput DNA extraction methodology was needed. Hence, we have optimized a simple, rapid, safe, and reliable high-throughput protocol for DNA extraction suitable for both fresh and dry leaves. The standardized protocol delivered good DNA yield of ∼1500 µg from 1 g of leaf tissue, with purity indicated by a 260 nm/280 nm absorbance ratio ranging from 1.70 to 1.91, which validated the suitability of extracted DNA and revealed reduced levels of contaminants. Additionally, the protocol that we developed was found to be suitable for polymerase chain reaction (PCR) amplification using microsatellite markers. Genome-wide characterization with SSR markers has been established in S. robusta, which further validates the protocol and its usefulness in DNA-based studies across the genus and/or family.

Appearance of de Gennes length in force-induced transitions.

Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collapsed protein. Here, we find a phase diagram that shows these states depending on the size of the DNA handle and the protein. For a less stable protein, unfolding is solely governed by the size of the linker DNA, whereas if the protein's stability increases, complete unfolding becomes impossible because the rupture force for DNA has reached a saturation regime influenced by the de Gennes length. We show that unfolding occurs via a few intermediate states by monitoring the force-extension curve of the entire protein. We extend our study to a heterogeneous protein system, where similar intermediate states in two systems can lead to different protein unfolding paths.

Harnessing the potential of probiotics in the treatment of alcoholic liver disorders.

In the current scenario, prolonged consumption of alcohol across the globe is upsurging an appreciable number of patients with the risk of alcohol-associated liver diseases. According to the recent report, the gut-liver axis is crucial in the progression of alcohol-induced liver diseases, including steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. Despite several factors associated with alcoholic liver diseases, the complexity of the gut microflora and its great interaction with the liver have become a fascinating area for researchers due to the high exposure of the liver to free radicals, bacterial endotoxins, lipopolysaccharides, inflammatory markers, etc. Undoubtedly, alcohol-induced gut microbiota imbalance stimulates dysbiosis, disrupts the intestinal barrier function, and trigger immune as well as inflammatory responses which further aggravate hepatic injury. Since currently available drugs to mitigate liver disorders have significant side effects, hence, probiotics have been widely researched to alleviate alcohol-associated liver diseases and to improve liver health. A broad range of probiotic bacteria like Lactobacillus, Bifidobacteria, Escherichia coli, Sacchromyces, and Lactococcus are used to reduce or halt the progression of alcohol-associated liver diseases. Several underlying mechanisms, including alteration of the gut microbiome, modulation of intestinal barrier function and immune response, reduction in the level of endotoxins, and bacterial translocation, have been implicated through which probiotics can effectively suppress the occurrence of alcohol-induced liver disorders. This review addresses the therapeutic applications of probiotics in the treatment of alcohol-associated liver diseases. Novel insights into the mechanisms by which probiotics prevent alcohol-associated liver diseases have also been elaborated.

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta.

Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta. Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae.

First synthetic report and antioxidant potential of natural product (±)-5,7-dihydroxy-8-methyl-3-(2',4'-dihydroxybenzyl)chroman-4-one from Chinese medicine Gan Luo Xin pill.

The first synthetic route of naturally occurring (±)-5,7-dihydroxy-8-methyl-3-(2',4'-dihydroxybenzyl)chroman-4-one (1) from Gan Luo Xin pill was successfully accomplished. The synthetic route has been developed retro-synthetically in 9 simple steps with a high yield of ∼80%. The synthetic protocol was developed using readily available starting material phloroglucinol. The key intermediate 2,4,6-trihydroxy-3-methyl acetophenone (4) was synthesized via Vilsmeier-Haack reaction, followed by reduction using sodium cyanoborohydride and acylation reaction. LC-MS, IR, 1H NMR, 13C NMR of 1 have been analyzed to confirm the structure of (±)-5,7-dihydroxy-8-methyl-3-(2',4'-dihydroxybenzyl)chroman-4-one (1) and found in agreement with the natural molecule. The target compound showed 97% and 87% antioxidant activity in DPPH and ABTS assay at 1 mg/ml concentration, respectively. The compound (1) also showed ferric ion reducing activity with the absorbance of 0.18 at 700 nm. The present study could be useful in developing synthetic routes of other potential naturally occurring homoisoflavonoid.

Molecular characterization of rare D--/D-- variants in individuals of Indian origin.

BACKGROUND: Rh antigens are critical in haemolytic disease of the foetus and newborn (HDFN). The D-- phenotype is a rare blood group characterised by the lack of expression of C, c, E and e antigens at the surface of red blood cells because of mutations in both RHCE alleles inactivating the expression of a "normal" protein. The aim of the study was to determine the molecular basis of D-- individuals of Indian origin. MATERIALS AND METHODS: Ten Rh D-positive postnatal women who had produced antibodies against all Rh antigens, except D, leading to HDFN and foetal loss, were investigated. Extensive serological and molecular (polymerase chain reaction [PCR] using sequence-specific primers), quantitative multiplex PCR of short fluorescent fragments (QMPSF), and Sanger sequencing analyses were carried out. RESULTS: Serological testing with anti-C, anti-c, anti-E, and anti-e reagents showed absence of the four antigens in all ten index cases, as well as in three siblings. Flow cytometry indicated absence of these antigens with a typical exalted expression of the D antigen, thus confirming the rare D-- phenotype. Molecular analysis by QMPSF suggested homozygous CE-D hybrid alleles causing the D-- phenotype: RHCE-D(3-9)-CE (n = 11), RHCE-D(3-8)-CE (n=1), and RHCE-D(2-6)-CE (n=1). DISCUSSION: For the first time, we report the molecular basis of the D-- phenotype in the Indian population. Identification and characterisation of RHCE-null variants by molecular methods can help resolve transfusion-related problems in these individuals. Family studies of index cases helped to identify rare blood donors and offer counselling to females of child-bearing age on the complications involved in such pregnancies.

D--phenotype due to RHD-RHCE hybrid transcript in a case of severe haemolytic disease of newborn with anti-Rh 17(Hrₒ) antibodies.

BACKGROUND: D antigen is one among the most immunogenic antigens and is the most common cause of Haemolytic Disease of Fetus and Newborn (HDFN). The D-phenotype is a rare Rh variant in which none of the RhCE antigens are expressed on the red cell surface. Individuals having D-phenotype are capable of producing a rare alloantibody named as anti-Rh17(Hr° ) in response to pregnancy or transfusion and has the potential to react with C/c and E/e antigens causing severe haemolytic transfusion reaction (HTR) and haemolytic disease of fetus and newborn (HDFN). CASE REPORT: We have encountered a case of severe HDFN with an accidental discovery of D- phenotype of the mother with anti-Rh-17 antibodies. D- phenotype has been confirmed with molecular typing along with genotyping of all family members. CONCLUSION: Rare phenotypes like D- individuals especially if allo-immunised are of great concern at times of transfusion requirements. Hence, proper identification of these individuals are important to contribute them to the rare donor pool and to adopt adequate patient blood management strategies.

Molecular characterization of RhD variant phenotypes among blood donors: A study from the coastal region of India.

BACKGROUND: RhD expression varies with population and ethnicity. Accurate typing of RhD antigen among blood donors is important to prevent development of anti-D among recipients of blood transfusion. We aimed to screen blood donors for variant D phenotypes and accurately characterize them by genotyping. MATERIAL AND METHODS: We have done prospective study on blood donors by performing RhD typing using three different commercial monoclonal anti-D reagents by both column agglutination and conventional tube techniques. Samples that showed ambiguous results were further screened with the Bio-Rad Partial RhD typing kit. Minor phenotyping for C, c, E, e antigens was performed. Multiplex PCR and Sequencing of all RHD exons with Sanger's sequencing was performed for molecular characterization of variant D. RESULTS: A total of 16,974 blood donors were screened during the study period. Among them, 31 (0.18 %) donors were found to have a RhD variant phenotype. The male to female ratio was 10:1. The presence of 'C' antigen was noted among all RhD variant samples. Serological typing identified two samples as DV phenotype and the rest could not be characterized. Molecular genotyping characterized 90.3 % of the samples as Indian specific weak D type 150 variants. Three samples were subjected to Sangers sequencing and showed wild type pattern. CONCLUSION: The present study showed that the most common variant in this population was Weak D type 150. This study highlights that serological methods may serve as a screening tool, however, molecular techniques are essential for characterization of RhD variants.

Molecular characterization of a rare Rh phenotype Dc-from the Indian subcontinent.

Unusual Rh phenotypes such as Rhnull, D-- and Dc- etc. are rarely encountered in routine blood bank testing. The Rhnull phenotype is characterized by the absence of all Rh antigens, D-- phenotype does not express any RhCcEe antigens whereas Dc- phenotype individual lacks expression of antithetical E /e antigens. These individuals may produce multiple Rh antibodies against missing antigens. An old woman (B RhD positive) from Bangladesh with end-stage renal disease developed severe anaemia. Cross-matching with ABO and RhD compatible blood units showed +3 agglutination reaction. Detailed immunohaematological investigations showed a lack of C, E and e antigens, thus identifying the rare Rh variant as Dc-. Antibodies against C and e antigens were also detected in the patient's serum. PCR-SSP confirmed the absence of the molecular region defining the C, E and e antigens. Copy number analysis by QMPSF revealed the homozygous state of (RHCE-D(4-9)-CE) allele at the RHCE gene locus. This is the first report of the rare Dc- variant individual from the Indian subcontinent.

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures.

To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.

Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis.

Lyotropic cholesteric liquid crystal phases are ubiquitously observed in biological and synthetic polymer solutions, characterized by a complex interplay between thermal fluctuations and entropic and enthalpic forces. The elucidation of the link between microscopic features and macroscopic chiral structure, and of the relative roles of these competing contributions on phase organization, remains a topical issue. Here, we provide theoretical evidence of a previously unidentified mechanism of chirality amplification in lyotropic liquid crystals, whereby phase chirality is governed by fluctuation-stabilized helical deformations in the conformations of their constituent molecules. Our results compare favorably to recent experimental studies of DNA origami assemblies and demonstrate the influence of intramolecular mechanics on chiral supramolecular order, with potential implications for a broad class of experimentally relevant colloidal systems.

ssDNA diffuses along replication protein A via a reptation mechanism.

Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA-RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1-7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.

RHD-Positive Alleles among D- C/E+ Individuals from India.

BACKGROUND: Molecular bases of blood group systems, including Rh blood group, have been poorly studied in the Indian population so far, while specificities of Europeans, East Asians and Africans have been well known for years. In order to gain insights into the molecular bases of this population, we sought to characterize the RHD allele in D- Indian donors expressing C and/or E antigen(s). METHODS: RHD gene was analyzed in 171 serologically D-, C/E+ samples by standard molecular methods such as quantitative, multiplex PCR of short fluorescent fragments (QMPSF) and direct sequencing when necessary. RESULTS: RHD whole gene deletion at the homozygous state was found to be the most common genotype associated with D- phenotype (118/171, 69.0%). Nonfunctional, negative hybrid genes with reported molecular backgrounds were observed in approximately one-third of the samples, while only four samples carry single-nucleotide variations, including one novel nonsense (RHD(Y243X)), one novel frameshift (RHD(c.701delG)), and two missense (RHD(T148R) and RHD(T148R, T195M)) alleles. CONCLUSION: Overall we report for the first time the molecular bases of D antigen negativity in the D-, C/E+ Indian population, which appears to be qualitatively similar to other populations, but with a population-specific, quantitative distribution of D-- alleles.

Antidiabetic activity of ethanolic extract of Cyperus rotundus rhizomes in streptozotocin-induced diabetic mice.

OBJECTIVE: In the present investigation, ethanolic extract of Cyperus rotundus (EECR) rhizomes was evaluated for antidiabetic activity in streptozotocin (STZ)-induced diabetic swiss mice. MATERIALS AND METHODS: After administration of EECR extract for 3 weeks, the body weight, blood glucose, biomarker enzymes (serum glutamic pyruvic transaminase [SGPT] and serum glutamic oxaloacetic transaminase [SGOT]), and plasma lipid levels were measured in STZ-induced diabetic mice. RESULTS: The ethanolic extract at dose levels of 250 and 500 mg/kg body weight revealed significant antidiabetic activity, improvement in body weight, and reduction in elevated biochemical parameters such as SGPT, SGOT, cholesterol, and triglyceride levels. CONCLUSION: These experimental findings seemed to indicate the use of this plant in traditional Indian medicine for the treatment of diabetes.

Pharmacognostical evaluation of aerial parts of Graptophyllum pictum (L.) Griff. (Syn: Justicia picta Linn.): A well-known folklore medicinal plant.

OBJECTIVE: Graptophyllum pictum (L.) Griff. (Family-Acanthaceae) occupies a key role in traditional system of medicine. Since an extensive literature survey did not provide any information about studies on its standardization. Therefore, we designed the current study to establish the quality control parameters of G. pictum aerial parts. MATERIALS AND METHODS: The investigation included determination of various standardization parameters such as macroscopic and microscopic studies, physicochemical parameters as well as phytochemical analysis of the crude drug. RESULTS: The microscopy study of aerial parts revealed that stem shows typical dicotyledonous characters with prismatic crystals of calcium oxalate in the cortical region and dorsiventral leaf. Physicochemical constants such as moisture content, ash values, fluorescence analysis, and extractive values were established. Preliminary phytochemical analysis confirmed the presence of alkaloids, flavonoids, saponins, tannins, etc. CONCLUSION: The present study suggests establishing the parameters for pharmacopoeial standardization of G. pictum.

Molecular determinants of the interactions between proteins and ssDNA.

ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB-ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6-65 nt. In addition to charge-charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB-ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.

Hepatoprotective potential of ethanolic extract of Pandanus odoratissimus root against paracetamol-induced hepatotoxicity in rats.

BACKGROUND: Pandanus odoratissimus (Pandanaceae) is popular in the indigenous system of medicines like Ayurveda, Siddha, Unani and Homoeopathy. In the traditional system of medicine various plant parts such as leaves, root, flowers, and oils are used as anthelmintic, tonic, stomachic, digestive and in the treatment of jaundice and various liver disorders. OBJECTIVE: The aim was to investigate the hepatoprotective activity of ethanolic extract of the root of P. odoratissimus against paracetamol (PCM) induced hepatotoxicity in rats. MATERIALS AND METHODS: Hepatotoxicity was induced in male Wistar rat by PCM (2 g/kg b.w. p.o. for 7 days). The ethanolic extract of P. odoratissimus root was administered at the dose level of 200 mg/kg and 400 mg/kg b.w. orally for 7 days and silymarin (100 mg/kg b.w. p.o.) as standard drug was administered once daily for a week. The hepatoprotective effect of ethanolic extract was evaluated by assessment of biochemical parameters such as serum glutamic oxaloacetic transaminase, serum glutamic-pyruvic transaminase, serum alkaline phosphatase, total and direct bilirubin and triglycerides. Histopathological study of rat liver was also done. RESULTS: Experimental findings revealed that the extract at dose level of 200 mg/kg and 400 mg/kg of b.w. showed dose dependant hepatoprotective effect against PCM induced hepatotoxicity by significantly restoring the levels of serum enzymes to normal that was comparable to that of silymarin, but the extract at dose level of 400 mg/kg was found to be more potent when compared to that of 200 mg/kg. Besides, the results obtained from histopathological study also support the study. CONCLUSION: From the results, it can be concluded that ethanolic extract of the root of P. odoratissimus afforded significant protection against PCM induced hepatotoxicity in rats.