Structural and Energetic Features of Base-Base Stacking Contacts in RNA.

Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.

Practical Guide to Measuring Wetland Carbon Pools and Fluxes.

Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions. Supplementary Information: The online version contains supplementary material available at 10.1007/s13157-023-01722-2.

Comparative ejaculatory response, fresh and frozen semen quality and fertility to artificial vagina vs electroejaculation method of semen collection in mithun (Bos frontalis) bulls.

The study aimed to describe a comparative ejaculatory response, fresh and frozen-thawed semen quality and fertility of semen collected by artificial vagina and electroejaculation in mithun. Experimental bulls were divided into two groups, G-I: young bulls (n = 4; 4-5 years of age) and G-II: older bulls (n = 4; 8-10 years of age). Sixteen ejaculates were collected from each group G-I (AV1 ) and G-II (AV2 ) by artificial vagina method (control). Thirty-six ejaculates were collected from the same bulls from each group G-I (EE1 ) and G-II (EE2 ) by electroejaculation method (treatment). The study did not reveal any significant (p > 0.05) difference in the ejaculatory responses between EE1 and EE2 . Mann-Whitney U test indicated that salivation discomfort sign score was significantly (p < 0.05) higher in EE1 . Fresh and frozen-thawed semen quality parameters, and motility and velocity profiles recorded by computer-assisted sperm analyser were significantly (p < 0.05) lower in electroejaculation than the artificial vagina. The conception rates (AV1 vs EE1 & AV2 vs EE2 ) at day 35-45 post insemination were nonsignificantly higher (p > 0.05) in the artificial vagina group. It concluded that, although artificial vagina method has better semen quality, nevertheless, electroejaculation has the potential for semen collection from free-range mithun bulls to incorporate in assisted reproductive technology procedures.

Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies.

In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that 67 out of 80 pairs exhibit stable geometries and optimal deviations from their macromolecular crystal occurrences. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. QM calculated interaction energies of base:ligand pairs reveal a rich hydrogen bonding landscape, ranging from weak interactions (base:other, -3 kcal/mol) to strong (base:phosphate, -48 kcal/mol) contacts. The analysis was further extended to study the biological importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in the context of RNA:ligand recognition. This can, in turn, contribute toward current efforts to develop antimicrobials that target RNAs.

Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.

Identification and characterization of base-multiplets, which are essentially mediated by base-pairing interactions, can provide insights into the diversity in the structure and dynamics of complex functional RNAs, and thus facilitate hypothesis driven biological research. The necessary nomenclature scheme, an extension of the geometric classification scheme for base-pairs by Leontis and Westhof, is however available only for base-triplets. In the absence of information on topology, this scheme is not applicable to quartets and higher order multiplets. Here we propose a topology-based classification scheme which, in conjunction with a graph-based algorithm, can be used for the automated identification and characterization of higher order base-multiplets in RNA structures. Here, the RNA structure is represented as a graph, where nodes represent nucleotides and edges represent base-pairing connectivity. Sets of connected components (of n nodes) within these graphs constitute subgraphs representing multiplets of "n" nucleotides. The different topological variants of the RNA multiplets thus correspond to different nonisomorphic forms of these subgraphs. To annotate RNA base-multiplets unambiguously, we propose a set of topology-based nomenclature rules for quartets, which are extendable to higher multiplets. We also demonstrate the utility of our approach toward the identification and annotation of higher order RNA multiplets, by investigating the occurrence contexts of selected examples in order to gain insights regarding their probable functional roles.

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions.

The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. A systematic and comprehensive classification and annotation of these interactions is necessary for a molecular-level understanding of their roles. However, unlike in the case of base pairing, where a widely accepted nomenclature and classification scheme exists in the public domain, currently available classification schemes for base-base stacking need major enhancements to comprehensively capture the necessary features underlying the rich stacking diversity in RNA. Here, we extend the previous stacking classification based on nucleobase interacting faces by introducing a structurally intuitive geometry-cum topology-based scheme. Specifically, a stack is first classified in terms of the geometry described by the relative orientation of the glycosidic bonds, which generates eight basic stacking geometric families for heterodimeric stacks and six of those for homodimeric stacks. Further annotation in terms of the identity of the bases and the region of involvement of purines (five-membered, six-membered, or both rings) leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we present an algorithm for automated identification of stacks in RNA crystal structures and analyze the stacking context in selected RNA structures. Overall, the work described here is expected to greatly facilitate the structure-based RNA research.

Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis).

BACKGROUND: Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun. RESULTS: We generated ≈300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. Repeat sequences constitute around 43.66% of the assembly. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle. CONCLUSION: Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations.

Structural landscape of base pairs containing post-transcriptional modifications in RNA.

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA.

Cyathea gigantea (Cyatheaceae) as an antimicrobial agent against multidrug resistant organisms.

BACKGROUND: Rapid emergence of multidrug resistant (MDR) organisms in hospital and community settings often result into treatment failure, thus leading the clinicians with fewer treatment options. Cyathea gigantea, an ethnomedicinally important fern used in cuts and wound infections. So, if this medicinal plant is used in treating the MDR infections then it might bring certain relief in future treatment options. METHODS: Antibacterial activity of C. gigantea against MDR bacteria was assed using well diffusion and broth microdilution methods to determine the diameters of growth inhibition zones, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). Synergistic activity was also determined with the conventional antibiotics by disc diffusion method followed by FIC index of each of the tested antibiotic was calculated. The active extract was then subjected to fractionation by column chromatography and antibacterial activity was done with each of the collected fractions. RESULTS: Crude extract of C. gigantea was found to be active against all the tested organisms. The MIC was 200 µg/ml against Gram-positive i.e., Staphylococcus aureus ATCC 25923 and 400 µg/ml against Gram-negative i.e., Escherichia coli ATCC 25922 and Pseudomonas aeruginosa PAO1, while the MBC was 400 µg/ml in case of Gram-positive and 800 µg/ml for Gram-negative. The synergistic activity revealed that the plant extract increased the antibacterial property of the studied antibiotics and the FIC index showed that significant synergistic activity was shown by ciprofloxacin followed by tetracycline, ampicillin and oxacillin. Antibacterial activity with the fractionated extract showed that the FR II, FR III and FR IV were active against both Gram-positive and Gram-negative bacteria, whereas FR I, FR V and FR VI did not show antibacterial property against any of the tested bacteria. CONCLUSIONS: Extracts of C. gigantea was found active against both selected Gram-positive and Gram-negative organisms and thus offers the scientific basis for the traditional use of the fern. The present study also provides the basis for future study to validate the possible use against multidrug resistant organisms.

Identification of sperm motility markers in bovine transition protein genes.

Transition proteins (TNPs) are essential in chromatin condensation during spermiogenesis, and hence, they are the candidate genes for identifying sperm motility markers. Coding and in silico predicted promoter regions of these genes were investigated in crossbred and purebred cattle, and also, their mRNA quantification was done to explore its use as a diagnostic tool of infertility. PCR-SSCP analysis revealed two band patterns in fragment III of TNP1 and fragment II of TNP2 gene. Sequence analysis revealed a deletion of "G" nucleotide in 3'UTR region of TNP1 and C>T SNP in intronic region of TNP2 gene. Least square analysis of variance did not reveal any significant influence of nucleotide deletion on any sperm motility parameters in both crossbred and purebred cattle. However, C>T SNP had a significant effect on initial progressive motility (p < 0.05) in purebred cattle and post-thaw motility in overall cattle population. RT-qPCR analysis did not reveal any significant variation in TNP1 and TNP2 gene expression among poorly motile and good quality spermatozoa of Vrindavani bulls.

Consequences of Mg2+ binding on the geometry and stability of RNA base pairs.

Metal ions are crucial for folding and function of noncoding RNAs. The fact that RNAs have very specific metal ion binding motifs further implies that contribution of metal ions (like Mg2+) in RNA's folding is not limited to simple compensation of electrostatic repulsions. Rather, their binding to RNA is driven by very specific contextual requirements. Elucidation of such factors is necessary for a comprehensive understanding of the sequence-structure-function paradigm in RNA. In this work, we have studied the consequences of Mg2+ binding on the geometry and stability of different noncanonical base pairs that shape up the complex structural landscape of RNA. Our results show that majority of the Mg2+ bound nucleobases are also part of a base pair. Interestingly, such base pairs belong only to a specific set of base pairing geometries. Out of them, we are able to identify 14 unique cases for which the native base pairing geometries are unstable under gas phase geometry optimization carried out in the absence of Mg2+ binding. Our density functional theory based calculations, performed using dispersion corrected M05-2X functional, suggest that, depending on its mode of binding, Mg2+ can stabilize and even fine tune a number of such base pairing geometries. These findings not only provide insights into how metal ions modulate the structure and dynamics of RNA molecules, they also provide a basis for improving the RNA structure prediction algorithms.

Short-hairpin Mediated Myostatin Knockdown Resulted in Altered Expression of Myogenic Regulatory Factors with Enhanced Myoblast Proliferation in Fetal Myoblast Cells of Goats.

Myostatin (MSTN) is a well-known negative regulator of skeletal muscle development. Reduced expression due to natural mutations in the coding region and knockout as well as knockdown of MSTN results in an increase in the muscle mass. In the present study, we demonstrated as high as 60 and 52% downregulation (p < 0.01) of MSTN mRNA and protein in the primary fetal myoblast cells of goats using synthetic shRNAs (n = 3), without any interferon response. We, for the first time, evaluated the effect of MSTN knockdown on the expression of MRFs (namely, MyoD, Myf5), follistatin (FST), and IGFs (IGF-1 & IGF-2) in goat myoblast cells. MSTN knockdown caused an upregulation (p < 0.05) of MyoD and downregulation (p < 0.01) of MYf5 and FST expression. Moreover, we report up to ∼four fold (p < 0.001) enhanced proliferation in myoblasts after four days of culture. The anti-MSTN shRNA demonstrated in the present study could be used for the production of transgenic goats to increase the muscle mass.

How Does Mg2+ Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair.

Reverse Watson-Crick G:C basepairs (G:C W:W Trans) occur frequently in different functional RNAs. This is one of the few basepairs whose gas-phase-optimized isolated geometry is inconsistent with the corresponding experimental geometry. Several earlier studies indicate that through post-transcriptional modification, direct protonation, or coordination with Mg2+, accumulation of positive charge near N7 of guanine can stabilize the experimental geometry. Interestingly, recent studies reveal significant variation in the position of putatively bound Mg2+. This, in conjunction with recently raised doubts regarding some of the Mg2+ assignments near the imino nitrogen of guanine, is suggestive of the existence of multiple Mg2+ binding modes for this basepair. Our detailed investigation of Mg2+-bound G:C W:W Trans pairs occurring in high-resolution RNA crystal structures shows that they are found in 14 different contexts, eight of which display Mg2+ binding at the Hoogsteen edge of guanine. Further examination of occurrences in these eight contexts led to the characterization of three different Mg2+ binding modes: 1) direct binding via N7 coordination, 2) direct binding via O6 coordination, and 3) binding via hydrogen-bonding interaction with the first-shell water molecules. In the crystal structures, the latter two modes are associated with a buckled and propeller-twisted geometry of the basepair. Interestingly, respective optimized geometries of these different Mg2+ binding modes (optimized using six different DFT functionals) are consistent with their corresponding experimental geometries. Subsequent interaction energy calculations at the MP2 level, and decomposition of its components, suggest that for G:C W:W Trans , Mg2+ binding can fine tune the basepair geometries without compromising with their stability. Our results, therefore, underline the importance of the mode of binding of Mg2+ ions in shaping RNA structure, folding and function.

Prediction of Anti-Alzheimer's Activity of Flavonoids Targeting Acetylcholinesterase in silico.

INTRODUCTION: Prenylated and pyrano-flavonoids of the genus Artocarpus J. R. Forster & G. Forster are well known for their acetylcholinesterase (AChE) inhibitory, anti-cholinergic, anti-inflammatory, anti-microbial, anti-oxidant, anti-proliferative and tyrosinase inhibitory activities. Some of these compounds have also been shown to be effective against Alzheimer's disease. OBJECTIVE: The aim of the in silico study was to establish protocols to predict the most effective flavonoid from prenylated and pyrano-flavonoid classes for AChE inhibition linking to the potential treatment of Alzheimer's disease. METHODOLOGY: Three flavonoids isolated from Artocarpus anisophyllus Miq. were selected for the study. With these compounds, Lipinski filter, ADME/Tox screening, molecular docking and quantitative structure-activity relationship (QSAR) were performed in silico. In vitro activity was evaluated by bioactivity staining based on the Ellman's method. RESULTS: In the Lipinski filter and ADME/Tox screening, all test compounds produced positive results, but in the target fishing, only one flavonoid could successfully target AChE. Molecular docking was performed on this flavonoid, and this compound gained the score as -13.5762. From the QSAR analysis the IC50 was found to be 1659.59 nM. Again, 100 derivatives were generated from the parent compound and docking was performed. The derivative compound 20 was the best scorer, i.e. -31.6392 and IC50 was predicted as 6.025 nM. CONCLUSION: Results indicated that flavonoids could be efficient inhibitors of AChE and thus, could be useful in the management of Alzheimer's disease. Copyright © 2017 John Wiley & Sons, Ltd.

Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity.

Molecular level understanding of mutational effects on stability and activity of enzymes is challenging particularly when several point mutations are incorporated during the directed evolution experiments. In our earlier study, we have suggested the lack of consistency in the effect of point mutations incorporated during the initial generations of directed evolution experiments, towards conformational stabilization of B. subtilis lipase mutants of later generations. Here, we report that the cumulative point mutations incorporated in mutants 2M (with two point mutations) to 6M (with six point mutations) possibly do not retain their original stabilizing nature in the most thermostable 12M mutant (with 12 point mutations). We have carried out MD simulations using structures incorporating reversal of different sets of point mutations to assess their effect on the conformational stability and activity of 12M. Our analysis has revealed that reversal of certain point mutations in 12M had little effect on its conformational stability, suggesting that these mutations were probably inconsequential towards the thermostability of the 12M mutant. Interestingly these mutations involved evolutionarily conserved residues. On the other hand, some of the other point mutations incorporated in nonconserved regions, appeared to contribute significantly towards the conformational stability and/or activity of 12M. Based on the analysis of dynamics of in silico mutants generated using the consensus sequence, we identified experimentally verifiable residue positions to further increase the conformational stability and activity of the 12M mutant.

The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs.

The roles of protonated nucleobases in stabilizing different structural motifs and in facilitating catalytic functions of RNA are well known. Among different polar sites of all the nucleobases, N7 of guanine has the highest protonation propensity at physiological pH. However, unlike other easily protonable sites such as N1 and N3 of adenine or N3 of cytosine, N7 protonation of guanine does not lead to the stabilization of base pairs involving its protonated Hoogsteen edge. It also does not facilitate its participation in any acid-base catalysis process. To explore the possible roles of N7 protonated guanine, we have studied its base pairing potentials involving WatsonCrick and sugar edges, which undergo major charge redistribution upon N7 protonation. We have carried out quantum chemical geometry optimization at the M05-2X/6-311G+(2d,2p) level, followed by interaction energy calculation at the MP2/aug-cc-pVDZ level, along with the analysis of the context of occurrence for selected base pairs involving the sugar edge or the WatsonCrick edge of guanine within a non-redundant set of 167 RNA crystal structures. Our results suggest that, four base pairs - G:C W:W trans, G:rC W:S cis, G:G W:H cis and G:G S:H trans may involve N7 protonated guanine. These base pairs deviate significantly from their respective experimental geometries upon QM optimization, but they retain their experimental geometries if guanine N7 protonation is considered during optimization. Our study also reveals the role of guanine N7 protonation (i) in stabilizing important RNA structural motifs, (ii) in providing a framework for designing pH driven molecular motors and (iii) in providing an alternative strategy to mimic the effect of post-transcriptional changes.

Lipopolysaccharide and Concanavalin A Differentially Induce the Expression of Immune Response Genes in Caprine Monocyte Derived Macrophages.

Monocyte derived macrophages (MDMs), as an in vitro model in pathogen challenge studies, are generally induced with lipopolysaccharide (LPS) and concanavalin A (ConA) to assay cellular immunity. General immune responses to LPS and ConA have been studied in a wide range of species, but similar studies are limited to goats. In the present study, caprine MDMs were induced with LPS and ConA and the expression profile of immune response (IR) genes, namely, Tumor Necrosis Factor Alpha (TNFA), Interferon Gamma (IFNG), Interleukin 2 (IL2), Granulocyte Macrophage Colony Stimulating Factor (GMCSF), Interleukin 10 (IL10), Transforming Growth Factor Beta (TGFB), Natural Resistance-Associated Macrophage Protein-1 (NRAMP1), inducible nitric oxide synthase (NOS2), and caspase1 (CASP1) were studied to compare the potential of LPS and ConA in initiating immune responses in goat macrophages. Real Time quantitative PCR (RT-qPCR) analysis revealed that both LPS and ConA caused an upregulation (p < 0.05) of GMCSF, TGFB1, IL10, and IFNG and down-regulation of NRAMP1. TNFA and IL2, and NOS2 were upregulated (p < 0.05) by ConA and LPS, respectively. Whereas, the expression of CASP1 remain unaltered. Comparatively, the effect of ConA was more pronounced (p < 0.05) in regulating the expression of IR genes suggesting its suitability for studying the general immune responses in caprine MDM.

Molecular evolution, characterization and expression profiling of uterine aldoketoreductase 1B5 gene in endometrium of goat (Capra hircus).

Aldoketoreductase 1B5 (AKR1B5), a member of the Aldoketoreductase family, is involved in the production of Prostaglandin F2α (PGF2α) as one of vital prostaglandin F synthase (PGFS). PGs (Prostaglandins) play a crucial role in female reproductive system. In the present study, we cloned and characterized the full-length open reading frame of AKR1B5 gene in Black Bengal (BB) goat. The complete coding sequence of AKR1B5 comprises an entire open reading frame of 951 bp, encoding 316 amino acid (AA) residues. BB AKR1B5 showed >82.9% identity with that of cattle, rabbit, human, and rat at nucleotide and amino acid levels, respectively. Further, a systematic study of AKR1B5 sequence evolution was also conducted using Phylogenetic Analysis by Maximum Likelihood (PAML), entropy plot, and Blossum 62 in a phylogenetic context. Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (Ka/Ks) revealed that negative selection may have been operating on this gene during evolution in goat, cattle, rabbit, human, and rat, which showed its conservation across species. Further, expression of AKR1B5 was determined by quantitative real-time PCR in goat endometrial tissues at different stages of the estrous cycle and early pregnancy. Our results indicated its high expression at luteolytic phase (stage III; day 16-21) during the estrous cycle. However, during early (day ∼30-40) pregnancy the expression was highest as compared to estrous cycle.

Effect of link margin and frequency granularity on the performance of a flexgrid optical network.

We show how dynamically adjustable modulation formats can be used to reduce link margins in flexgrid networks, reverting to lower order QAM due to reduced OSNR, if ageing occurs. Spectral savings amount to as much as 63% gain in capacity across a network using 64QAM with a fine frequency granularity of 6.25 GHz, with variable baud rate transponder. Further, a fixed baud rate, demand multiplexed transponder with adaptive modulation has been suggested. These transponders provide twice as much network capacity as compared to widely used fixed baud rate transponders operating at fixed grid of 50 GHz.

Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study.

Protonated nucleobases have significant roles in facilitating catalytic functions of RNA, and in stabilizing different structural motifs. Reported pKa values of nucleobase protonation suggest that the population of neutral nucleobases is 10(3)-10(4) times higher than that of protonated nucleobases under physiological conditions (pH ∼ 7.4). Therefore, a molecular level understanding of various putative roles of protonated nucleobases cannot be achieved without addressing the question of how their occurrence propensities and stabilities are related to the free energy costs associated with the process of protonation under physiological conditions. With water as the proton donor, we use advanced QM methods to evaluate the site specific protonation propensities of nucleobases in terms of their associated free energy changes (ΔGprot). Quantitative follow up on the energetics of base pair formation and database search for evaluating their occurrence frequencies, reveal a lack of correlation between base pair stability and occurrence propensities on the one hand, and ease of protonation on the other. For example, although N7 protonated adenine (ΔGprot = 40.0 kcal mol(-1)) is found to participate in stable base pairing, base pairs involving N7 protonated guanine (ΔGprot = 36.8 kcal mol(-1)), on geometry optimization, converge to a minima where guanine transfers its extra proton to its partner base. Such observations, along with examples of weak base pairs involving N3 protonation of cytosine (ΔGprot = 37.0 kcal mol(-1)) are rationalized by analysing the protonation induced charge redistributions which are found to significantly influence, both positively and negatively, the hydrogen bonding potentials of different functional sites of individual nucleobases. Protonation induced charge redistribution is also found to strongly influence (i) the aromatic character of the rings of the participating bases and (ii) hydrogen bonding potential of the free edges of the protonated base pair. Comprehensive analysis of a non-redundant RNA crystal structure dataset further reveals that, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities.