Miracle-dz/UniFAR-FTUs huggingface dataset:
Mito-nuclear discordance helps to reveal the phylogeographic patterns of Melitaea ornata (Lepidoptera: Nymphalidae)

Periodical changes of glacial and interglacial conditions have influenced the distribution of most living organisms and shape the separation of different genetic lineages significantly. We investigated the phylogeography of a nym-phalid butterfly Melitaea ornata . Our main aim was to explore the existence, the origin, and the variability of different genetic lineages based on a multilevel approach. M. ornata and its close relatives (with a focus on M. phoebe ) from the Palearctic were analysed based on five gene regions (COI, EF-1a, MDH, RPS5, and wingless) using Bayesian methods to infer the phylogeographic history. The DNA-based analyses have been complemented with species distribution modelling (SDM) and Wolbachia screening. The Bayesian inference analysis showed mito-nuclear discordance in M. ornata , which is split into an eastern and a western clade. Based on mitochondrial DNA , the western clade of M. ornata clusters together with M. phoebe , while the eastern clade is well-separated. In contrast to this, the combined nuDNA-based analysis revealed that M. ornata forms a monophyletic group which is clearly separated from M. phoebe . The timing of divergence analyses suggest that the split between M. ornata and M. phoebe is about 6 million years old based on both the COI and the concatenated nuclear genes. SDM predicted considerably larger area shifts for M. phoebe than for M. ornata . LGM refugia were predicted for both species to the Mediterranean peninsulas in Europe and several Middle-East and Asian localities. The prevalence of Wolbachia infection was 88.9% in M. phoebe and only 7% in M. ornata . Our results clearly indicate a lack of ongoing hybridization between M. phoebe and M. ornata , but argue for an ancient hybridization event in the Apennine Peninsula which strongly influenced the observed split between the two clades of M. ornata .
Assessing the influence of environmental parameters on aquatic plants of ponds in the hinterland of Long Beach in Montenegro

espanolLa distribucion y riqueza de plantas acuaticas en las 19 lagunas situadas en el interior de la Gran Playa y la Isla de Ada Bojana en el sur de Montenegro, en el periodo comprendido entre marzo 2014 y octubre 2014, han sido estudiadas en relacion a diversos factores ambientales. Se ha registrado presencia de 74 especies, de las cuales 10 eran sumergidas, 4 flotantes y 60 emergentes. La especie Phragmites australis fue la mas frecuente, se encuentra en 16 de las lagunas analizadas. Los resultados del Analisis de correspondencia canonica (CCA) han mostrado que los parametros fisicoquimicos estadisticamente significativos (concentracion de nitratos, distancia desde el mar y salinidad) representan un 28.3% de varianza en la distribucion de las plantas acuaticas. La riqueza de especies fue mas bien alta, 20 especies de media por laguna, y estaba moderadamente relacionada con los parametros fisicoquimicos, de acuerdo con el Modelo aditivo generalizado (GAM). EnglishThe distribution and richness of aquatic plants in 19 ponds in the hinterland of Long Beach and Ada Bojana Island in the southern part of Montenegro in the period from March 2014 to October 2014 have been studied in relation to some environmental factors. The presence of 74 species was recorded, 10 of which were submerged, 4 floating-leaved and 60 emergent plants. Phragmites australis was the most frequent species that is present in 16 of the analysed ponds. The results of Canonical Correspondence Analysis (CCA) have shown that statistically significant physicochemical parameters (concentration of nitrates, distance from the sea and salinity) accounted for 28.3% of variance in aquatic plant distribution. Species richness was rather high, 20 species per pond, on average, and was moderately related to the physicochemical parameters according to the Generalized Additive Models (GAM).
The Expression of Myogenin and Myostatin Genes in Baluchi Sheep

Myogenin gene (MYoG) affects the synthesis of muscle myofibrillar growth and increase of meat production. The myostatin (MSTN) gene is identified as a specific negative regulator of skeletal muscle growth. Reduction of the expression level of MSTN throughmutation in the sequence of this gene leads to an increase of myogenesis and regeneration of muscle cells during the postnatal growing period of sheep. The Baluchi sheep are among the most popular breeds of sheep for breeding in Iran and have an important portion in meat production industry of the country. In present work the relative expression level of the two candidate genes have been studied at two age intervals (9 and 12 months) in male and female Baluchi sheep. In order to analyze the relative expression level of MYoG and MSTN gene in Baluchi sheep’s longissimus muscles, quantitative real-time polymerase chain reaction (qRT-PCR) reaction has been applied. Results of RT-PCR for sex effect showed MSTN and MYoG expression were not highly expressed in ram’ longissimus dorsi compared to ewe at the same age stages (P>0.05) and there were no significant differences between male 12 months comparing to female 12 months (P>0.05) and male 9 months with female 9 months (P>0.05). For the effect of age, relative expression of MYoG and MSTN genes on Baluchi sheep longissimus muscles did not show significant differences between males or females (P>0.05).
Complete mitochondrial genome of Whitmania laevis (Annelida, Hirudinea) and comparative analyses within Whitmania mitochondrial genomes

The complete mitochondrial genome of Whitmania laevis is 14,442 bp in length and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The almost-complete mitochondrial genome of Whitmania acranulata , consisting of 13,494 bp, contains 35 genes including 13 PCGs, 20 tRNA genes, and two rRNA genes. COI phylogenetic analyses showed that the samples reported in GenBank and analysed as Hirudo nipponia KC667144, Hirudinaria manillensis KC688268 and Erpobdella octoculata KC688270 are not the named species and they should belong to Whitmania . We compared and analyzed the characteristics of nucleotide composition, codon usage, and secondary structures of 22 tRNAs and two rRNAs from Whitmania taxa. Moreover, we analyzed phylogenetic relationships of Annelida using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 11 mitochondrial genes. Our results reveal that W. laevis has a close relationship with W. pigra .
Pharmacognostical studies of in vivo grown garden plant and in vitro generated plantlets from nodal explants of Justicia adhatoda L.

Justicia adhatoda L. (Family: Acanthaceae) has been exploited in India because of rich source of polyphenolic compounds which are used in stress related therapy. The Pharmacognostical study includes preliminary phytochemical screening of alkaloids, phenols, flavonoids and saponins which were confirmed in both in vivo grown garden plants as well as in vitro generated plantlets of J adhatoda . Explants inoculated on MS medium supplemented with different combination of auxins and cytokinins were successfully employed; combination of NAA (0.5µg/ml) and BA (2.0µg/ml) for nodal explants was found to be effective concentration to obtain plant regenerants from nodal explants. Rooting in the regenerants was also successfully initiated on transfer into half MS basal medium, supplemented with IBA (1.0 µg/ml). Addition of ADS (0.5µg/ml) in the above combinations of phytohormones induced multiple shoot from nodal explants. After hardening for 35 days in highly humidified acclimatized room, nearly 70 % of rooted plantlets survived in the field. Phytochemical screening revealed the presence of alkaloids, phenolic compounds, flavonoids and saponins in the methanol and aqueous extracts of both in vivo grown garden plants and in vitro genereated plantlet samples. Further analysis of the extracts on Thin Layer Chromatography and spectrophotometric estimation confirmed the presence of vasicine alkaloids in these extract samples with marked difference in quantity.
Global MEF2 Target Gene Analysis in Skeletal and Cardiac Muscle

ii ACKNOWLEDGEMENTS . iii TABLE OF CONTENTS . iv LIST OF TABLES . vi LIST OF FIGURES . vii LIST OF ABBREVIATIONS . ix CHAPTER I: Literature Review . 1 1. Development of striated muscle . 1 1.1 Early development of the mesodermal lineages . 1 1.2 Skeletal myogenesis . 2 1.3 Cardiogenesis . 7 1.4 Striated muscle contraction . 9 2. The role and regulation of MEF2 . 11 2.1 Overview of MEF2 . 11 2.2 Role of MEF2 during vertebrate development and adult tissue maintenance . 13 2.3 MEF2 protein:protein interactions . 15 2.4 MEF2 and chromatin remodelling . 17 2.5 Regulation of MEF2 by post-translational modifications . 22 2.6 MEF2 and miRNA gene silencing . 23 3. Therapeutic relevance of MEF2 in skeletal and cardiac muscle disease . 24 3.1 Metabolic disease . 24 3.1a: Diabetes . 25 3.1b: Pathways regulating muscle atrophy . 28 3.2 Role of MEF2 in skeletal muscle regeneration . 33 3.3 Role of MEF2 in cell death and muscle atrophy . 37 3.4 Cardiac hypertrophy . 39 4. Summary of Literature Review . 42
Prolonged exposure does not increase soil microbial community response to warming along geothermal gradients

Predicting effects of climate change on ecosystem functioning requires knowledge of soil microbial community responses to warming. We used natural geothermal gradients (from +1°C to +19°C above ambient) in two subarctic grasslands to test the hypothesis that long-term exposure (>50 years) intensifies microbial community responses to warming compared to short-term exposure (5-7 years). Community profiles from amplicon sequencing of bacterial and fungal rRNA genes did not support this hypothesis: significant changes relative to ambient were observed from +9°C and upwards in the long-term and from 7°C to 11°C / +3°C to +5°C and upwards in the short-term, for bacteria and fungi, respectively. Our results suggest that bacterial communities in high-latitude grasslands will not undergo lasting shifts in community composition under the warming predicted for the coming 100 years. Fungal communities do appear to be temperature sensitive to the warming within this range, but only for short-term exposures.
A study of the original material of Lithothamnion engelhartii Foslie (Corallinales, Rhodophyta)

Abstract Eight collections of the type material of Lithothamnion engelhartii from Cape Jaffa and Kingston (South Australia) were re-examined and two disparate entities were shown to be included. Some specimens exhibit embedded conceptacles in the thallus where the perithallium dominates. The other specimens lack embedded conceptacles and the thallus is formed by unattached-superimposed lamellae where the hypothallium prevails. The lectotype selected here fits the second description and is in agreement with most other type specimens and recent material collected at Eyre Peninsula (South Australia). The lectotype specimen displays dorsiventral organization lacking perithallial protuberances. The hypothallium is polystromatic with coaxial to non-coaxial regions and forms a relatively thin ascending perithallium. Subepithallial cells are elongate and support single flattened epithallial cells. Multiporate conceptacles are bisporangial, develop in dense aggregations, and do not become embedded in the thallus (except via superimposition of new lamellae). Pore canals are conical to pyriform and develop differentiated cells lining the canals along the base. Syntype material exhibits simple spermatangia, and this character, together with the presence of elongate basal pore cells and the lack of a predominantly coaxial hypothallium, suggests an affiliation with the temperate species of Leptophytum from the NE Pacific.
Nucleic amplification testing: Individual verses Minipool, what to choose?

Dear Sir, The commonly used NAT testing technologies include Polymerase Chain reaction (PCR) and transcription mediated amplification[1]. TMA is a transcriptionamplification process, using two enzymesReverse transcriptase & RNA polymerase to produce millions of copy of targeted RNA sequences. It comprises of three stepstarget capture, amplification & detection. TMA allows for simultaneous testing of multiple viruses in a single test tube. [2] Today there are two NAT tests availableCOBAS Ampliscreen HBV test/ COBAS Taq screen MPXa multiplex assay for HBV, HCV & HIVboth of these are manufactured by Roche Molecular system Inc and Procleix Ultrio assay a multiplex assay for HBV, HCV & HIV manufactured by Gen Probe Inc. (Novartis) (Chiron in US) [3]
Encapsulation of somatic embryoids of Curculigo orchioides Gaertn. and its germination

Curculigo orchioides Gaertn is an endangered medicinal plant with antioxidant and anticancer properties. The rhizome and tuberous roots of the plant have been used extensively in India in indigenous medicine. Due to its multiple uses, the demand for Curculigo orchioides is constantly on the rise; however, the supply is rather erratic and inadequate. Destructive harvesting, combined with habitat destruction in the form of deforestation has aggravated the problem. The plant is now considered ‘endangered’ in its natural habitat. Therefore, the need for conservation of this plant is crucial. Here we described an efficient protocol for germination of sodium alginate encapsulated embryoids of Curculigo orchioides. Morphogenic callus was induced on Murashige and Skoog (1962) [16] basal medium (MS) containing 0.5 3 mg/1 of 2, 4-dichlorophenoxyacetic acid (2, 4-D) and 0.5 mg/1 N6 –benzylaminopurine (BAP) from rhizome explants. Transfer of morphogenic calli to MS medium with 1-4 mg/1 BAP resulted in somatic embryogenesis, at high frequencies with an average of 23 ± 0.8 somatic embryos per gram of morphogenic callus on MS medium with BAP (1 mg/l). Further, germination of sodium alginate encapsulated somatic embryoids of Curculigo orchioides were tested on half-strength Murashige and Skoog (MS) basal medium fortified with coconut water (10% v/v). The frequencies of regeneration from encapsulated somatic embryoids were affected significantly by concentration of sodium alginate and the duration of exposure to calcium chloride. Somatic embryoids encapsulated with 2.5% sodium alginate dissolved in MS basal salts solution recorded significantly higher germination than other treatments. A relatively short (5 min) incubation with calcium chloride solution provided uniform encapsulation of somatic embryoids that gave the highest percentage (80%) of germination. Germinated synthetic seeds produced normal plantlets. Based on the present observations an improved protocol may be developed for ex-situ conservation of the endangered species – C. orchioides.
Identification and Characterization of Glutathione S-Transferase Genes in the Antennae of Codling Moth (Lepidoptera: Tortricidae)

Abstract In insects, glutathione S-transferases (GSTs) are multifunctional enzymes playing an important role in metabolizing a wide range of endogenous and exogenous compounds, including plant secondary compounds, insecticides, and odorant molecules. In this study, we identified 14 GSTs from codling moth Cydia pomonella (L.), which is a worldwide internal pest of tree fruit. The cytosolic GSTs contain the conserved glutathione (GSH)binding domain and substrate-binding domain. The microsomal GSTs are transmembrane proteins containing a conserved motif consisting of 16 amino acids. Real-time polymerase chain reaction (RT-PCR) revealed that 10 CpomGSTs were expressed in the antennae. Among them, a novel signal peptide containing GST (CpomGSTd2) was restrictedly expressed in the antennae and the expression levels were significantly higher in male than in female. Phylogenetic analysis shows that CpomGSTd2 shares close relationships with olfactory GSTs of other insects. We prepared the recombinant CpomGSTd2 and determined its GST catalytic property using 1-chloro-2, 4-dinitrobenzene (CDNB) and reduced GSH as substrates. This protein exhibited high GST catalytic activity within the temperature ranged from 25 to 50 ° C and the optimal pH was 7.0. Our results suggest that antenna is important site for GST-mediated biotransformation and CpomGSTd2 may play a role in the odorant degradation for chemosensory perception.
Why is the giant panda black and white?

Lay Summary We use comparative information on carnivores and bear subspecies to investigate coloration of the giant panda. We find that white fur on the body is for matching white snowy backgrounds, black fur on legs is for camouflage in shade, but that markings on the face are for communication to other pandas or to would-be predators. The giant panda’s extrordinary pelage coloration has several different functions.
Mechanical Properties of Maturing Dystrophic Skeletal Muscle

The main goal for my research was to challenge the long held belief that the mechanical properties of maturing dystrophic compared to control skeletal muscle membranes are weaker, leading to onset of Duchenne muscular dystrophy (DMD). We built on a previous report from our lab that suggested sarcolemmal membranes from dystrophic mice are not more susceptible to damage early in maturation (i.e., age 9-12 days) and determined if and when muscle mechanical properties change as the mice mature. Across four studies, I have helped define the role of dystrophin-deficient skeletal muscle membranes in the onset of DMD. A linear viscoelastic muscle model was used to determine passive stiffness and damping in control and dystrophic muscles from maturing mice aged 14-35 days. Results confirmed my hypothesis that there are no differences in passive mechanical properties between normal and dystrophic mice. Recognizing the limitations of the linear model, a nonlinear model was developed to determine the stiffness and damping of active and passive dystrophic muscles from maturing mice aged 21 and 35 days. The nonlinear model achieved a significantly better fit to experimental data than the linear model when muscles were stretched to 15% strain beyond resting length. Active and passive mechanical properties of dystrophic mice were not different than control at 14 and 28 days of age. The previously developed nonlinear model was used to determine a more complete timecourse (14-100 days of age) of dystrophic muscle mechanical properties. There was no difference in passive stiffness between mdx and control muscles at each age. However, the mdx:utrn muscles showed increased stiffness compared to control and mdx muscles at 21 and 28 days, suggesting a temporary change within the muscle that only occurs with a lack of both utrophin and dystrophin. Fast-twitch and slow-twitch muscle mechanical properties were compared in control and dystrophic mice aged 3, 5, and 9 weeks of age. Dystrophic and control slow-twitch muscles did not have different mechanical properties, suggesting that a lack of dystrophin does not affect slow-twitch muscles during maturation (3-5 weeks) or well after maturation (9 weeks).
Report of the Director.

It gives me great pleasure to present the annual report of the National Aerospace Laboratories for the year 2007-08. HIGHLIGHTS The year 2007-08 was an eventful one for NAL. While two Tenth Five Year Plan(FYP) Network Projects(with a total of 65 modules) with NAL as the nodal laboratory and 5 projects where the laboratory was a participant were completed successfully, the third network project related to civil aircraft (with 4 major modules) was proposed to be extended by an year in the Eleventh plan period to meet the modified scope and objectives. The Eleventh FYP projects are at various stages of approval and initiation. The most important and welcome development for NAL and CSIR for the year is that the Indian Air Force has come forward to make a firm commitment to procure fifteen SARAS aircrafts designed and developed by NAL for its operational use, with an indication that it may need thirty more in the next plan period. This is a dream-come-true for NAL. It is the culmination of several years of hard work put in by all those who have been closely associated with this programme. It is a great boost to the Laboratorys civil aviation programme, but at the same time it places a heavy onerous responsibility on our shoulders. We are thankful to the IAF for their confidence and faith in NAL. With the unstinted support and cooperation of CSIR, motivation and commitment of our scientists and staff and the good wishes and support from our close associates, we are confident that we will succeed in meeting the IAFs expectations. The coming year is a particularly special one for us at NAL, as 2008 marks the beginning of our Golden Jubilee Year. It is indeed a proud moment for all of us (when I say us I also include our predecessors) when NAL completes five decades of dedicated service to the nation. NAL has come to be recognized as a leader in the country in aerospace sciences and technologies, thanks to the single minded efforts and invaluable contributions of its scientists, ably supported by its officers and staff, both technical and administrative. NAL today is recognized internationally for its excellent facilities and the skill and competence of its human resources. We have made significant and valuable contributions to all the major national aerospace programmes, at the same time building within NAL technological excellence. Today our sister …
Path analysis and genetic diversity of Euterpe edulis Martius for vegetative and fruit traits.

Euterpe edulis (juçara) is a species in risk of extinction caused by its indiscriminate exploration. With the fragmentation of E. edulis natural populations, an increase on inter-population genetic variability may be occurring due to the reduction on the population size and an increase of mating of related individuals. For this reason, the objective of this work was to quantify the inter-population genetic diversity of juçara based on characters related to fruit production as a way to generate information to be used in the improvement programs of the species. The experiment was carried out in 20 forestry fragments in the South region and in Caparaó in the state of Espírito Santo. Ten characters were evaluated on the plants, which were analyzed by mixed models with the procedure RELM/BLUP for genetic value prediction. With the genetic correlations, the multi-co-linearity diagnosis was carried out and techniques for the path analysis, correspondence analysis and principal component analysis were applied to verify the relations and interrelations among the characters and the genetic diversity among populations. It was found that the populations GU3, AL4, JM1, MI1 and MQ1 derived from different municipalities are the ones which present higher inter-population genetic divergence among the 20 studied populations.
Spatiotemporal index standardization improves the stock assessment of northern shrimp in the Gulf of Maine

Estimated trends in relative stock abundance are a primary input to fish stock assessments. Accurate and precise estimates are essential for successful conservation and management. Scientifically designed data collection ensures that estimates of relative abundance are unbiased. However, the statistical efficiency of a design-based estimator may be low under certain circumstances. We apply a recently developed spatiotemporal model that incorporates habitat variables to estimate a model-based abundance index for northern shrimp (Pandalus borealis) in the Gulf of Maine. We contrast this spatiotemporal index with a classical design-based index and evaluate the impacts of differences between the two abundance indices on the stock assessment. We show that using the spatiotemporal index in the assessment model greatly alters the estimates of recruitment and spawning stock biomass and the determination of stock status. Also, incorporating the spatiotemporal index leads to less retrospective bias and outperforms .