Miracle-dz/UniFAR-FTUs huggingface dataset:
Consequences of Plasticity:How do Individual Conditions Affect Physiology, Survival and Copulatory Behaviours in Drosophila?

Drosophila melanogaster are a polygamous species: males and females repeat copulation with multiple mates. When more than one male’s sperm have to compete to fertilise the same female’s eggs, sperm competition occurs. This has driven individuals to develop physiological and behavioural plastic responses to enable them to outcompete others and increase their chances of siring successful offspring. But what effect do variable environmental conditions have on these responses? Plasticity comes with a cost, often causing reproductive-survival trade-offs to occur. Previous experiments have failed to show how stress impacts reproductive terminal investment, and other plastic responses, so this study aims to contribute knowledge to this field. The experiments were completed using a combination of stresses to weaken Drosophila: a two-day starvation period and either age (three, 14 and 28 days) or varying sperm competition levels (solitary males, pairs, groups of eight and solitary males in the presence of pheromones). Evidence of trade-offs and plastic reproductive terminal investment was investigated by monitoring behavioural responses (courtship behaviours, rejection responses and copulatory durations), physiological responses (spermatogenesis, egg production and fat reserve levels), as well as activity and starvation resistance as a proxy for longevity. Aged and starved flies, and flies that were not placed under sperm competition, were less active and had a shorter lifespan. These weaker males also tended to exert less energy into courtship behaviours; however they also copulated for longer. This suggests that they were investing in reproductive terminal investment. When males were placed with females that had been continuously fed, copulation lasted significantly longer. This could be to enable him to transfer more sperm, or as a method of mate guarding. In addition to this, older females spent less time rejecting males, suggesting that they were more willing to succumb to copulation. Despite efforts, both males and females produced significantly fewer offspring when placed in stressful environments.
The effect of remaining in water in estimation of time since death in skeletal remains

Determining the time since death of an individual from skeletal remains is a challenging stage. In determination of time since death, climate conditions, environmental factors, conditions such as whether the body was buried or not, and genetic and personal factors must be evaluated all together. With these factors changing and with the exposure duration growing longer, changes occur in the morphology of the bone might increase. In this study, as part of an investigation, bones which had been found in a water-well during an excavation work in Mardin was used. After 36 pieces of bone that belong to a human were analyzed, it was found that the bones had lost most of their weight and density, that they were considerably fragile, that their medulla was emptied, and that there were intense erosions on the surfaces of bony tissue. While under normal circumstances and under the condition that it was a buried body it would take at least 50 years for these changes to occur, considering that the bones remained in water for a very long time, the corrosion had to be much more than expected. With the DNA comparison, it was found that the bones belonged to people who were claimed to have been killed in the 90â€™s. In this study, it was aimed to determine the time of death of remains which were reported to have stayed in contact with water, and to study the effect of the environmental circumstances in which the bodies are found on the bones.
From lignocellulosic metagenomes to lignocellulolytic genes: trends, challenges and future prospects

Lignocellulose is the most abundant biomass on Earth with immense potential to act as a primary resource for the production of a range of compounds currently obtained from fossil fuel sources. However, lignocellulosic feedstocks remain largely underexploited due to the complex mixture of recalcitrant polymers present, whose structural features hinder access to the utilizable monosaccharide reservoir within cellulose. Various fungi and bacteria have been identified that can enzymatically decompose lignocellulose to its monomeric compounds for use as carbon sources. The investigation of such lignocellulolytic organisms has proven very useful in gaining primary insights into degradation processes and key microbial enzymes, but the established limitations of culture‐based approaches suggest that we have yet to understand the full range of lignocellulolytic mechanisms, likely expressed within natural systems. In this review, we focus on metagenomic approaches to study lignocellulose degradation from structural and functional perspectives, which may provide novel insights into this process in order to rationally design methods for the extraction of compounds from biomass that could enhance biorefinery efficiencies. © 2016 Society of Chemical Industry and John Wiley & Sons, Ltd
Comparaison de deux techniques d'identification des souches de levures de vinification basées sur le polymorphisme de l'ADN génomique: réaction de polymérisation en chaine (PCR) et analyse des caryotypes (électrophorèse en champ pulsé)

Une nouvelle technique de la biologie moleculaire, la reaction de polymerisation en chaine (PCR) permet l'identification des souches de levures de vinification. Mise en oeuvre directement sur levures entieres, elle permet d'obtenir des profils variables selon les souches, par l'amplification de sequences d'ADN genomique. Utilisee sur lies, la PCR constitue un outil rapide et sensible pour le controle d'implantation des levains en vinification. Cependant le pouvoir discriminant de la PCR est inferieur a celui de l'electrophorese en champ pulse pour la caracterisation des souches de levures indigenes. Elle doit etre consideree comme une technique complementaire d'identification des souches de S. cerevisiae.
Enriched secondary subtropical forest through line-planting for sustainable timber production in Puerto Rico

Entre 1984 et 1990, des plantations lineaires de diverses essences nobles autochtones ou introduites, dont l'acajou, Swietenia macrophylla, ou le mahot bois-bleu, Talipariti elatum, ont ete installees sur une centaine d'hectares dans une zone de foret tropicale humide au Sud-Est du Puerto Rico. Compte tenu de l'accroissement annuel de la surface terriere (Ba) des meilleures tiges d'acajou (25 %), une duree de 176 ans serait necessaire apres la plantation pour obtenir une surface terriere moyenne par arbre de 0,20 m 2 , ce qui correspond a un diametre a hauteur de poitrine (Dbh) de 50 cm en moyenne. Pour le mahot bois-bleu, l'accroissement de la surface terriere s'avere trois fois plus rapide que pour l'acajou, ce qui donnerait une surface terriere moyenne de 0,20 m 2 en 57 ans. Actuellement, pour le quartile superieur des mahot bois-bleu, celle-ci depasse 0,10 m 2 par individu, ce qui permet desormais une recolte selective. Les essais sur des essences autochtones (Coccoloba pubescens, Calophyllum brasiliense et Cedrela odorata) ont donne les meilleurs resultats en termes de pourcentage d'accroissement en hauteur avec un bon taux de survie ; mais des etudes a plus long terme sont necessaires pour les confirmer. Les plantations lineaires dans les zones forestieres secondaires comme celles de Las Casas peuvent accroitre la valeur des forets secondaires en assurant a la fois une production durable de bois et la preservation de la biodiversite, ainsi que les autres avantages pour l'environnement qui decoulent de la preservation du couvert forestier. L'enrichissement et l'amenagement des forets secondaires devraient etre approfondis en tant qu'approche prometteuse pour une sylviculture durable.
The behaviour of Aphytis chrysomphali, a hymenopterus parasite of the coconut scale, Aspidiotus destructor, in Sri Lanka.

94 (a) Parasite egjs and newly hatched parasite larvae feeding on the body contents of the scale arc visible when the latter is slightly raised with a needle. (b) The larval meconia of the parasite whose number varies from 4 to 6 are visible through the transparent scale covering as black or brown coloured small shiny blantly pointed bodies. These get dislodged under the scale covering after the emergence of the parasite. (c) Thi ad lit parasite or its developins instars, the cast skins of the larvae and pupae or fragments of host integument are other indications. (d) Parasite exit holes on the surface of the scales could be used as a criterion to detect parasitism. However, it is not always possible to use this criterion since at times the parasites emerge beneath the edge of the scale covering withoat making an exit hole on the latter. ii. Sampling site and sampling method The studies on the parasitism of A. destructor by A. chrysomphali were carried out at Bandirippuwa Estate, Lunuwila in the North Western Province of Sri Lanka. The sampling site (Fig. 1) was a 0.8 ha block containing hybrid palms (Tall x Dwarf). There were about 15 infested palms in the plantation with an average of two infested fronds per palm. About four leaflets per frond were found to be affected by the scale. The study was based on samples from ten palms at the rate of one leaflet per palm collected approximately at 20 day interval commencing from March 1976. iii. Experiment The scales within 1 cm' leaf surface area were examined at five different points on the infested leaflet. The total number of scales and the number parasitised within the respec­ tive area were noted and the mean density per unit area was estimated from the values. The killing power or k value which is the difference between the logarithm of the density of A. destructor before and after the action of the parasite, A. chrysomphali, was plotted against the logarithm of the host density. RESULTS Table 1. Relationship between host density and parasitism Date of sampling Values Level of significance Fig. No. r= 5th March 0.180 0.68 < 0.001 2 a 25th MaTch 0.073 0.17 > 0.1 2 b 14th April 0.169 0.47 < 0.05 2 c 4th May 0.009 0.05 > 0.1 2 d 24th May 0.087 0.70 < 0.001 2 e 13th June -0.146 -0.19 > 0.1 2 f 2nd July 0.167 0.33 > 0.1 2 g * March July 0.081 0.24 < 0.05 2 h * Data of the seven samples combined
7. Cladistic Biogeography of Juglans ( Juglandaceae) Based on Chloroplast DNA Intergenic Spacer Sequences

Juglans L. is principally a New World genus within the tribe Juglandeae of the family Juglandaceae, comprising about 21 extant deciduous tree species occurring from North and South America, the West Indies, and southeastern Europe to eastern Asia and Japan (Manning, 1978). It is one of the approximately 65 genera that are known to exhibit a disjunct distributional pattern between eastern Asia and eastern North America (Manchester, 1987; Wen, 1999; Qian, 2002; fi gure 7.1). Four sections are commonly recognized within Juglans, based mainly on fruit morphology, wood anatomy, and leaf architecture (Dode, 1909a, 1909b; Manning, 1978). Section Rhysocaryon (black walnuts), which is endemic to the New World, comprises fi ve North American temperate taxa: J. californica S. Wats. , J. hindsii (Jeps.) Rehder, J. nigra L. , J. major (Torr. ex Sitgr.) Heller, and J. microcarpa Berl. ; three Central American subtropical taxa: J. mollis Engelm. , J. olanchana Stadl. & I. O. Williams, and J. guatemalensis Mann. ; and two South American tropical taxa, J. neotropica Diels and J. australis Griesb, mainly occurring in the highlands. They typically bear nuts that are four-chambered with thick nutshells and septa. Section Cardiocaryon (Asian butternuts) contains four taxa: J. hopeiensis Hu, J. ailantifolia Carr. , J. mandshurica Maxim. , and J. cathayensis Dode, all native to East Asia, and section Trachycaryon consists of the only North American butternut taxon, J. cinerea L. Both Asian and
Endosperm carotenoid concentrations in wheat are better correlated with PSY1 transcript levels than enzyme activities

Author(s): Qin, X; Fischer, K; Dubcovsky, J; Tian, L | Abstract: © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA. All rights reserved. Phytoene synthase (PSY) catalyzes a key reaction in the biosynthesis of carotenoids, which are major contributors of grain yellow pigment content (GYPC) in wheat (Triticum spp.). Although quantitative trait loci (QTL) for GYPC have been linked to PSY1 homoeologs in tetraploid and hexaploid wheat, the underlying molecular and biochemical mechanisms for such associations are not well understood. Functional characterization of wheat PSY1 homoeologs indicated that variations in PSY1 homoeolog enzyme activities did not correspond to different levels of GYPC in the wild-type tetraploid and hexaploid wheat genotypes analyzed. However, a correlation between PSY1 homoeolog expression and carotenoid accumulation in grain endosperm was evident, suggesting that GYPC is at least partially modulated by transcriptional regulation of PSY1 homoeologs in wheat grains. Further promoter analysis of PSY-A1 homoeologs with diverse expression profiles in three wheat genotypes revealed not only potential motifs for light and hormonal responses but also new candidate cis-regulatory elements. Overall, the knowledge on the association of PSY1 homoeolog expression and GYPC can be directly applied to breeding tetraploid and hexaploid wheat varieties with desirable carotenoid levels.
Historical allopatry and secondary contact or primary intergradation in the Puerto Rican crested anole, Anolis cristatellus, on Vieques Island in the Caribbean

Recent work has revealed surprisingly deep mitochondrial genetic divergence in the lizard Anolis cristatellus among samples obtained from the small Caribbean island of Vieques. Here we sought to determine whether this had resulted from natural or anthropogenic causes, and (if the former) whether divergence occurred in a biogeographical context of allopatry followed by secondary contact, or via isolation-by-distance across the species’ historical range. We first estimated a mitochondrial gene tree for 379 samples and then genotyped 3407 single nucleotide polymorphic sites from 48 individuals using a modified genotyping-by-sequencing approach. We found that A. cristatellus samples from Vieques belong to two highly divergent mitochondrial subclades, but the geographical distribution of these haplogroups indicates that this pattern is probably natural in origin. Analysis of our single nucleotide polymorphic dataset revealed differentiation that is consistent with isolation-by-distance between the western and eastern ends of Vieques, suggesting that the overall pattern of divergence probably reflects primary intergradation with a mitochondrial break on the historical Puerto Rico Bank palaeo-island that happened to coincide with the present-day location of Vieques. Our findings help to underline the growing consensus that results from a single genetic marker can prove highly misleading in studies of historical population genetic structure.
Immobilization of arctic foxes with tiletamine hydrochloride and zolazepam hydrochloride (Zoletil

We used Zoletil® (also known as Telazol®) to immobilize 19 adult arctic foxes (Alopex lagopus) under field conditions at Karrak Lake, Nunavut, Canada. A single dose of 15 mg provided safe handling for approximately 15 min regardless of sex and body mass. Mean induction time was 2.4 min, and foxes showed first awakening behavior, first stand-up attempt, and complete recovery at mean intervals of 13.5, 22.8, and 39.3 min after injection, respectively. Anesthetic depth was suitable for safe handling and minor clinical procedures such as ear-tagging and venipuncture. All breeding females immobilized with Zoletil (n=3) weaned litters. Immobilization was characterized by quick induction, safe handling, and predictable recovery; therefore, we recommend Zoletil (or Telazol) for immobilizing adult arctic foxes in the field.
STANDARDIZATION OF DNA EXTRACTION PROTOCOL IN GREENGRAM (Vigna radiata (L.) Wilczek)

Green gram is a widely cultivated pulse crop rich in protein, high in vitamin-B content and essential aminoacids. It is easily digestable and low flatulence produced crop. The quality and quantity of DNA used for amplification by PCR is the key to reproducible results and success of genotyping. Especially, DNA purity is extremely crucial for obtaining clear and discriminate patterns. DNA extraction from Green gram is difficult due to presence of contaminants such as phenols. Therefore, the present study was under taken to obtain high quality and pure DNA in Green gram. With few modifications four different DNA extraction protocols were tried in the present study to obtain high quality and pure DNA viz., (i) Doyle and Doyle (1987), (ii) Method of Murray and Thompson (1980), (iii) Porebski et al.(1997), and (iv) Lin et al. (2001). Out of the four methods tried for DNA extraction, the method of Lin et al. (2001) was found most efficient, as the DNA obtained through this protocol was relatively pure which gave amplifying products in the PCR. The genotype used for the standardization was MGG -361
Tissue culture and rapid propagation of water-chestnut(Eleocharis tuberosa)

The shoot tips of Chinese water chestnut ( Eleocharis tuberosa Roem.et Schult) cultivars Fanglin were used as explants in the test of tissue culture and rapid propagation. The results showed that the proliferated coefficient of the plumules was 3~4 on MS medium containing 1.0~1.5mg/L 6[CD2]BA, 4.0g/L agar and 30 g/L sugar. But the coefficient reached 6~8 on liquid medium with the same components except agar. The culture with the liquid medium was not only getting higher proliferated coefficient than the solid one, but also getting the seedling that grew orderly and vigorously with fresh green leaves and higher leaf like stems.
The Synthesis of N-Ribosyl Transferase Inhibitors Based on a Transition State Blueprint

A quarter of a century ago transition state analysis and transition state analogue design promised the prospect of extraordinarily potent enzyme inhibitors. The present overview describes the transition state analysis of a variety of N-ribosyl transferases, the design and synthesis of extremely powerful transition state analogue inhibitors of these nucleoside processing enzymes, and their current therapeutic uses and potentials.
A defensive body plan was pre-adaptive for termitophily in the rove beetle tribe Termitohospitini (Staphylinidae: Aleocharinae)

Termitophily—the symbiosis of organisms with termite societies—has evolved a disproportionate number of times within the rove beetle subfamily Aleocharinae (Staphylinidae). Among aleocharine termitophiles, defensive (limuloid) and mimetic (physogastric & physothoracic) body forms have evolved convergently, but due to lack of a comprehensive aleocharine phylogeny, the context in which termitophily and associated adaptations evolve is unknown. We present the first example of a robust, morphology-based phylogenetic placement of an exclusively termitophilous tribe, the Termitohospitini. Termitohospitini is recovered to be nested within Myllaenini sensu nov, and sister to Myllaena (new synonymy). Furthermore, we also recovered the small tribe Masuriini nested within Myllaenini sensu nov (new status). Reconstructing ecological transitions within this clade, we present evidence that the stem lineage of Myllaenini sensu nov invaded intertidal marine habitats, the common ancestor for Myllaena + Termitohospitini then transitioned to freshwater riparian habitats, with Termitohospitini alone subsequently shifting to termitophily. We conclude that: (1) Termitohospitini was ancestrally a limuloid-bodied riparian inhabitant; (2) a limuloid form may have been pre-adaptive for defense against host attack during the evolution of termitophily; (3) the strongly tapered abdomen of an ancestral limuloid body was a constraint on the evolution of physogastry, leading to the emergence of the unusual physothoracic body form observed in termitohospitines that likely integrates these obligate termitophiles to life inside termite colonies. “one of the most astonishing spectacles in all natural history. ” — Richard Dawkins
Defining the substrate specificity of an unusual acyltransferase: a step towards the production of an advanced biofuel

The direct use of vegetable oils as a biofuel suffers from problems such as high viscosity, low volatility and poor cold temperature properties. 3-acetyl-1,2-diacyl-sn-glycerols (acetyl-TAGs) have lower viscosity and freezing temperature than regular vegetable oils. However, by modifying their fatty acid composition, further improvement in their fuel properties is possible. Our goal was to develop plants that synthesize seed oils with further improved fuel properties. Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) synthesizes acetyl-TAGs by the acetyl-CoA dependent acylation of diacylglycerol (DAG). Knowledge of the substrate specificity of EaDAcT for its acetyl-CoA donor and DAG acceptor substrates is important to generate the required acetyl-TAG composition in seed oil. A rapid method to quantify acetyl-TAGs was developed based on electrospray ionization mass spectrometry to gain information about the substrate specificity of EaDAcT. This method is as accurate and more rapid than the traditional radiolabeled substrate based assay and additionally provides information on acetyl-TAG molecular species present. Using this assay, EaDAcT specificity for different chain length acylCoA and DAGs was tested. It was found that although EaDAcT can use other short chain length acyl-CoAs as acyl donors, it has high preference for acetyl-CoA. Further, EaDAcT can acetylate a variety of DAGs with short, medium and long chain length fatty acids with high preference for DAGs containing unsaturated fatty acids. To generate acetyl-TAGs with lower molecular mass, EaDAcT was transformed into transgenic Camelina sativa lines producing high amounts of medium chain fatty acids (MCFAs). EaDAcT expression was also combined with the knockdown of DGAT1 and PDAT enzymes, which compete with EaDAcT for their common DAG substrate. High acetyl-TAG yielding homozygous T3 transgenic lines were generated but the incorporation of MCFAs into acetyl-TAGs was inefficient. A small increase in the viscosity of acetyl-TAGs from these lines was observed compared to acetyl-TAGs produced in wild type Camelina plant. The combined effect of insufficient lowering of molecular mass and increased fatty acid saturation levels of acetyl-TAGs might be responsible for this increased viscosity. Overall, it was concluded that the molecular mass and the saturation levels of fatty acids of acetyl-TAGs need to be considered at the same time in future attempts to further decrease their viscosity. DEFINING THE SUBSTRATE SPECIFICITY OF AN UNUSUAL ACYLTRANSFERASE: A STEP TOWARDS THE PRODUCTION OF AN ADVANCED BIOFUEL