Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergent evolutionary processes driven by foraging opportunity in two sympatric morph pairs of Arctic charr with contrasting post-glacial origins

The expression of two or more discrete phenotypes amongst individuals within a species (morphs) provides multiple modes upon which selection can act semi-independently, and thus may be an important stage in speciation. In the present study, we compared two sympatric morph systems aiming to address hypotheses related to their evolutionary origin. Arctic charr in sympatry in Loch Tay, Scotland, exhibit one of two discrete, alternative body size phenotypes at maturity (large or small body size). Arctic charr in Loch Awe segregate into two temporally segregated spawning groups (breeding in either spring or autumn). Mitochondrial DNA restriction fragment length polymorphism analysis showed that the morph pairs in both lakes comprise separate gene pools, although segregation of the Loch Awe morphs is more subtle than that of Loch Tay. We conclude that the Loch Awe morphs diverged in situ (within the lake), whereas Loch Tay morphs most likely arose through multiple invasions by different ancestral groups that segregated before post-glacial invasion (i.e. in allopatry). Both morph pairs showed clear trophic segregation between planktonic and benthic resources (measured by stable isotope analysis) but this was significantly less distinct in Loch Tay than in Loch Awe. By contrast, both inter-morph morphological and life-history differences were more subtle in Loch Awe than in Loch Tay. The strong ecological but relatively weak morphological and life-history divergence of the in situ derived morphs compared to morphs with allopatric origins indicates a strong link between early ecological and subsequent genetic divergence of sympatric origin emerging species pairs. The emergence of parallel specialisms despite distinct genetic origins of these morph pairs suggests that the effect of available foraging opportunities may be at least as important as genetic origin in structuring sympatric divergence in post-glacial fishes with high levels of phenotypic plasticity. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.
Phylogenetic insights of Avena genus based on genomic analysis of 45S rDNA molecular organization

V Introduction . 1 Materials and Methods . 4 DNA extraction . 4 PCR experiments . 5 Sequence cloning . 6 Sequence and phylogenetic analysis . 8 Results . 9 45S rDNA genomic characterization . 9 Intergenic spacer polymorphisms evaluation . 9 5’ ETS partial sequences analysis . 10 5’ ETS complete sequences analysis . 12 Genome organization . 13 Evolution of the organizations A and C . 15 Phylogenetic analysis . 17 5’ETS sequences analysis . 17 Analysis through IRAP and REMAP . 18 IRAP/REMAP banding profiles vs 5’ETS sequences . 19 Discussion . 20 References . 26 Appendix . 30
Space competition between coral and algae — effect of two functional groups of algae on juvenile Acropora corals

Overharvesting of herbivorous fishes is assumed to be one of the causes for phase shift on coral reefs from coralto macroalgal-dominated communities by reducing inhibitor of algal growth. In order to reveal the effect of herbivorous fishes on algae and juvenile acroporid corals, field experiment was conducted in Okinawa, southern Japan. Grazer-exclusion cages were established where small (≈2 cm in length) coral branchlets of Acropora tenuis were transplanted both inside and outside the cages. During the exclusion experiment, algal biomass, survival and growth of the transplanted corals were monitored. The cages effectively excluded herbivorous fishes that resulted in significantly greater algal biomass inside the cages than outside. While algal biomass continued to increase within the cages, algal species composition has changed drastically at the middle of the experimental period. During the first half period (3 months) when encrusting turf algae covered substrate adjacent to coral branchlets inside the cages, coral branchlets could not expand their attachment area on the substrata. In contrast, during the second half period (3 months) corals started rapid growth after turf algae disappeared and frondose macroalgae dominated. We conclude that turf algae may prevent the growth of juvenile acroporid corals especially in the early stages of horizontal expansion prior to the vertical growth.
Laboratory Evaluation of Chlorpyrifos-Ethyl and Fipronil against Ancistrotermes cavithorax (Isoptera: Termitidae) in South Côte d’Ivoire

Ancistrotermes cavithorax, is an economically important species causing damage to wooden structures and agricultural crops in Côte d’Ivoire. Toxicities of two new chemical insecticides (Chlorpyrifos-ethyl and fipronil) were evaluated against this termite. The results showed that, Chlorpyrifos-ethyl was the highest toxicity than fipronil. The LT50 value of chlorpyrifos-ethyl at highest concentration (2000 ppm) was shorter (4±1.73 Mins.) than that of fipronil (97.3±1.32 Mins.). Chlorpyrifos-ethyl killed the termite workers faster than fipronil witch concentrations were slower than to kill the termites. The LD50 value of chlorpyrifos-ethyl was shorter (27.119) than that of fipronil (31.035). The study provides an opportunity to compare the toxicities of two new chemical insecticides and to use them effectively in the termite management programs.
The origin of snakes (Serpentes) as seen through eye anatomy

Snakes evolved from lizards but have dramatically different eyes. These differences are cited widely as compelling evidence that snakes had fossorial and nocturnal ancestors. Their eyes, however, also exhibit similarities to those of aquatic vertebrates. We used a comparative analysis of ophthalmic data among vertebrate taxa to evaluate alternative hypotheses concerning the ecological origin of the distinctive features of the eyes of snakes. In parsimony and phenetic analyses, eye and orbital characters retrieved groupings more consistent with ecological adaptation rather than accepted phylogenetic relationships. Fossorial lizards and mammals cluster together, whereas snakes are widely separated from these taxa and instead cluster with primitively aquatic vertebrates. This indicates that the eyes of snakes most closely resemble those of aquatic vertebrates, and suggests that the early evolution of snakes occurred in aquatic environments. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 469–482.
Changes in Antioxidant Activity of Miso by Variety, Cooking and Added Spices

味噌の種類，調理方法および併用する香辛料による抗酸化力の変化を調べた．味噌の抗酸化力は色度の明度，総イソフラボン量やアグリコン量に比例して増加し，豆味噌，米赤色辛味噌，麦味噌，米淡色辛味噌，米甘味噌の順に強かった．味噌を加熱すると，褐色度と抗酸化力は缶詰処理，焙る，炒める，煮るの順に強かったが，逆に，総イソフラボン量とアグリコン量は減少した．電子レンジで加熱した味噌は褐色度の増加やイソフラボンの分解が少なかった．香辛料を添加して加熱した味噌は，抗酸化力がポリフェノール量と相関しなかった．ショウガを添加して加熱した味噌はイソフラボンのアグリコン量は減少したが，抗酸化力とポリフェノール量が増加した．ニンニク，和芥子，唐辛子やゴマを添加して加熱した味噌ではイソフラボンアグリコン量は変化しなかったが，褐色度と抗酸化力が低下した．これらの結果は，味噌の抗酸化力は，味噌に含まれているイソフラボンや香辛料に含まれているポリフェノール化合物より加熱中に生成されるメラノイジンの影響を強く受けることを示唆していた．したがって，ショウガは固有の強力な抗酸化物質を付加して味噌の抗酸化力を増大させ，ニンニク，和芥子，唐辛子やゴマはメラノイジンの生成を抑制して味噌の抗酸化力を低下させたのだろう．香辛料を添加した味噌はいずれも単独味噌より有益な健康上の効果が期待できるであろう
Seed afterripening and germination photoinhibition in the genus Crocus (Iridaceae)

Abstract Mediterranean characteristics are attributed to the genus Crocus, which is inadequately studied in terms of seed germination. An afterripening requirement is very common in environments with warm and dry periods, and photoinhibition has been detected in many angiosperms inhabiting dry and open areas. The effects of afterripening and light on seed germination were investigated for the first time in 23 native Greek Crocus taxa, collected from various localities with either a Mediterranean or a temperate climate. Germination experiments were conducted in continuous darkness and in light at the optimal temperature for each taxon, with both freshly collected and afterripened seeds; warm stratification (20°C, darkness) was also examined in 22 taxa. A number of selected taxa were additionally investigated with respect to afterripening outdoors, afterripening and warm stratification at higher temperatures (35 and 25°C, respectively), stratification at 20/10°C, dry storage at low temperatures, response to gibberellic acid and phenology of embryo growth. It was postulated that an afterripening requirement is a characteristic of the genus Crocus, and we found that it can be fulfilled in nature during the Mediterranean dry summer. Also, for the vast majority of the taxa, warm stratification and stratification at 20/10°C can both meet the afterripening requirement. Embryos of the taxa studied are underdeveloped and have to grow prior to germination. Intrageneric differences of seed germination were observed only towards light, with photoinhibition being predominant in taxa from drier environments.
INTEGRACIÓN DE INDUCCIÓN DE RESISTENCIA CON BACTERIAS QUITINOLÍTICAS EN EL CONTROL DE LA SIGATOKA NEGRA (Mycosphaerella fijiensis Morelet) EN BANANO

Se evaluo en condiciones de campo en la zona bananera de Uraba-Colombia, el efecto de inductores de resistencia y bacterias quitinoliticas sobre el desarrollo de la Sigatoka Negra en plantas de banano del cultivar Gran Enano. Como inductores de resistencia se utilizaron acibenzolar-s-metil (ASM) (20 cm3 • ha-1 i.a.) y acido salicilico (AS) (20 cm3 • ha-1 i.a) cada uno en rotacion y en mezcla con fungicidas utilizados en el control convencional de la enfermedad; se evaluo tambien la mezcla de estos inductores con bacterias quitinoliticas aisladas de la filosfera de banano; asi como el efecto del fungicida biologico Biofun® (1,5 L • ha-1 de p.c. en rotacion con fungicidas y en mezcla con ASM. La aplicacion de ASM en rotacion y en mezcla con fungicidas convencionales presento un control de la enfermedad hasta un 50% mayor al obtenido con el control convencional, evidenciado esto en los valores mas bajos del area bajo la curva del indice de severidad de la enfermedad (IS) y mas altos de hojas sanas (HS) al momento de la floracion. Los tratamientos, que incluyeron AS en rotacion y mezcla con fungicidas convencionales, al igual que el producto Biofun® en rotacion y en mezcla con ASM, mostraron un control de la enfermedad estadisticamente igual al obtenido con el control convencional, lo cual revelo una reduccion de 46 - 100% de la cantidad de fungicidas convencionales usados en el control de la Sigatoka Negra.
In silico Spleen Tyrosine Kinase Inhibitor Screening by ChooseLD

Background: Spleen tyrosine kinase (SYK) is a protein related to various diseases. Aberrant SYK expression often causes the progression and initiation of several diseases including cancer and autoimmune diseases. Despite the importance of inhibiting SYK and identifying candidate inhibitors, no clinically effective inhibitors have been reported to date. Therefore, there is a need for novel SYK inhibitors. Results: Candidate compounds were investigated using in silico screening by chooseLD, which simulates ligand docking to proteins. Using this system, known inhibitors were correctly recognized as compounds with high affinity to SYK. Furthermore, many compounds in the DrugBank database were newly identified as having high affinity to the ATP-binding sites in the kinase domain with a similar affinity to previously reported inhibitors. Conclusions: Many drug candidate compounds from the DrugBank database were newly identified as inhibitors of SYK. Because compounds registered in the DrugBank are expected to have fewer side effects than currently available compounds, these newly identified compounds may be clinically useful inhibitors of SYK for the treatment of various diseases.
The “Pro” Sequence of the Sporulation-Specific ς Transcription Factor ςE Directs It to the Mother Cell Side of the Sporulation Septum

ABSTRACT ςE, a mother cell-specific transcription factor of sporulating Bacillus subtilis, is derived from an inactive precursor protein (pro-ςE). Activation of ςE occurs when a sporulation-specific protease (SpoIIGA) cleaves 27 amino acids from the pro-ςE amino terminus. This reaction is believed to take place at the mother cell-forespore septum. Using a chimera of pro-ςE and green fluorescent protein (GFP) to visualize the intracellular location of pro-ςE by fluorescence microscopy, and lysozyme treatment to separate the mother cell and forespore compartments, we determined that the pro-ςE::GFP signal, localized to the forespore septum prior to lysozyme treatment, is restricted to the mother cell compartment after treatment. Thus, pro-ςE::GFP had been sequestered to the mother cell side of the septum. This segregation of pro-ςE::GFP, and presumably pro-ςE, to the mother cell is likely to be the reason why ςE activity is restricted to that compartment.
Weed seed predation in a phenologically late crop

Seed predation of weed seeds in crops depends on the seasonal overlap between seed availability and the activity period of the predators. Published data show that the activity period of seed predators is directly related to canopy cover. In phenologically early crops, such as cereals, maturation of leaves results in a decreasing cover prior to weed seed shed, resulting in lower seed losses than maximally possible. We hypothesised that there would be better temporal overlap in sugar beet, a phenologically late crop. The pattern of predation of Chenopodium album L. seeds was consistent over fields and years, low in July and August and gradually increasing until harvest in September/November. The patterns of seed production and shed, measured using seed traps, differed among weed species. The proportion of annual seed losses by predators calculated from these measurements ranged from 0.26 to 0.83, depending on the duration of seed exposure on the soil surface. As expected, sugar beet had better temporal overlap between predator activity and weed seed production, which may cause higher seed losses than previously reported for any other annual crop.
Monitoring Abundance of Golden Eagles in the Western United States

Under the Bald and Golden Eagle Protection Act, the United States Fish and Wildlife Service (Service) can authorize take of golden eagles (Aquila chrysaetos), such as nest removal, disturbance, and lethal take, if the take is compatible with the preservation of the golden eagle. The Service needs baseline information on the current abundance and trend of subpopulations of the golden eagle to properly manage take of the species. Annually during late summer of 2006–2012, we used distance sampling on approximately 17,500 km of aerial line transects to estimate golden eagle abundance in 4 Bird Conservation Regions (BCRs; North American Bird Conservation Initiative Monitoring Subcommitte 2007) that collectively cover about 80% of the species' range in the coterminous western United States. We estimated study area abundances of 24,509 (90% CI: 19,406–31,947) in 2006 and 21,715 (90% CI: 18,165–27,624) in 2012, including all breeding and non-breeding individuals. We used a Bayesian hierarchical model to estimate trends in individual BCRs and the entire study area based on numbers of golden eagles counted along surveyed transects. We detected declines (90% credible intervals [CRIs] for trend coefficients <0.0) in numbers of golden eagles classified as juveniles in BCR 10 (Northern Rockies) and BCR 16 (Southern Rockies and Colorado Plateau) during 2006–2012. However, our results indicate the total abundance of golden eagles has not declined 2006–2012 in much of the western United States. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.
A mammoth mouthful? A test of the idea that larger animals ingest larger seeds

Aim It has been widely assumed that large seeds generally require large animals to ingest and disperse them. However, this relationship has only been quantified in single animal groups (e.g. birds) and in a few communities. Our goal was to provide the first broad-scale study of the relationship between animal body mass and ingested seed size. Location Global. Methods We compiled a dataset of 13,135 unique animal × seed interactions, animal body masses and seed sizes in these interactions, across all vertebrate groups (fish, amphibians, reptiles, birds and mammals). Results Contrary to expectations, ingested seed size was negatively related to animal body mass. This negative relationship was largely driven by large ungulates ingesting small and dry seeds, and analyses excluding either ungulates or seeds with non-fleshy fruit types showed a positive relationship between animal body mass and ingested seed size. Large animals ingested both seeds with a larger maximum size (the 95th quantile had a positive slope) and a smaller minimum size (the 5th quantile had a negative slope). Larger animals ingest larger seeds from fleshy fruits but smaller seeds from non-fleshy fruits. A significant positive relationship was found between animal size and the number of seed species ingested. Main conclusions Our data show that one of the assumptions that has underpinned the study of animal–seed interactions does not hold true across the full range of animal taxa and fruit types. These findings shed new light on theories about which types of plant species might be at risk if large animals go extinct, and cast doubt on the generality of a few theories (e.g. optimal diet theory, fruit-size hypothesis) about the relationship between frugivores and seeds.
Additive trees in the analysis of community data

The paper advocates a more extensive use of additive trees in community ecology. When the distance/dissimilarity coefficient is selected carefully, these trees can illuminate structural aspects that are not obvious otherwise. In particular, starting from squared distances based on presence/absence data, the resulting trees approximate relationships in species richness, a feature not available through other graphical techniques. The construction of additive trees is illustrated by three actual examples, representing different circumstances in the analysis of grassland community data.
Antioxidant and ACE inhibitory activities of soybean hydrolysates: Effect of enzyme and degree of hydrolysis

Native soy protein isolate (SPI) was hydrolyzed with 4 different proteolytic enzymes, including bromelain, papain, Neutrase, and Flavourzyme. SPI hydrolysates with the degree of hydrolysis (DH) in range of 6 to 15% were prepared by each enzyme. The angiotensin I converting enzyme (ACE) inhibitory and the antioxidant activities of the SPI hydrolysates, such as superoxide dismutase-like activity and inhibition of the linoleic acid autoxidation, were evaluated. Overall, as the DH increased, all evaluated bioactivities of the SPI hydrolysates significantly increased. The significantly highest ACE inhibitory and antioxidant activities were found in hydrolysates made with papain and bromelain, respectively. SPI hydrolysates by Flavourzyme showed the significantly lowest activity in all tested bioactivities. The results suggested that ACE inhibitory and antioxidant activities of SPI hydrolysates were determined by the DH and by the enzyme used.
Cell type‐specific regulation of the TGF‐β‐responsive α2(I) collagen gene by CpG methylation

The α2(I) collagen gene shows cell type‐specific expression, however, the mechanism behind this specificity remains to be determined. We demonstrate here that transforming growth factor‐beta (TGF‐β)‐mediated induction of α2(I) collagen gene is regulated by DNA methylation in a cell type‐specific manner. Human α2(I) collagen mRNA and type I collagen protein were expressed in normal human fibroblasts (NHF), and also strongly enhanced by TGF‐β; they were not detected in HaCaT, HeLa, or HepG2 cells (termed “collagen‐induction resistant (CIR) cells”) even following stimulation with TGF‐β. On the other hand, the transcriptional activity of exogenously transfected α2(I) collagen promoter was clearly up‐regulated by TGF‐β in the CIR cells as well as in NHF. In the CIR cells, CpG clusters around the transcription start site of the α2(I) collagen gene were heavily methylated, whereas no methylation was detected in NHF. Moreover, α2(I) collagen gene was reactivated in the CIR cells by 5‐Aza‐2‐deoxycytidine (5‐AdC) treatment to some extent. However, demethylation by 5‐AdC was limited and it was unable to recover the TGF‐β responsiveness. In NHF, the α2(I) collagen gene has a Smad3‐accessible chromatin structure and acetylated histones in the promoter regions. By contrast, in the CIR cells, Smad3 failed to bind to the chromatin and histones were not acetylated in this area. Furthermore, in vitro methylation of the reporter gene containing the α2(I) collagen promoter significantly reduced both basal and TGF‐β‐induced enhancement of the transcriptional activity in NHF. Thus, we propose that α2(I) collagen gene provides the first example of the TGF‐β responsive gene whose cell type‐specificity is regulated by CpG methylation. © 2004 Wiley‐Liss, Inc.
Identification of differentially expressed genes in Sulfobacillus sp. TPY grown on either elemental sulphur or Fe2

Sulfobacillus sp. TPY is a moderately thermophilic and acidophilic bacterium found in hydrothermal vents in the Pacific Ocean. This bacterium can oxidize ferrous sulfate (Fe 2+ ) and elemental sulfur (S 0 ) under separate conditions. We used random arbitrarily primed polymerase chain reaction (RAP-PCR) to screen and identify differentially expressed genes from bacteria grown on Fe 2+ or S 0 as the energy source. Fifty-five differential cDNA fragments were isolated and subjected to single-pass sequencing. Thirty-five fragments were identified as orthologs of known genes in the GenBank databases, of which 19 were confirmed to be differentially expressed at the transcriptional level by Northern blot analysis. Among these 19 genes, 14 genes, including isocitrate dehydrogenase, formyltetrahydrofolate deformylase, 3-hydroxybutyryl-CoA dehydrogenase, and GTP-binding protein, were upregulated in TPY grown on Fe 2+ or downregulated in TPY grown on S 0 , while five genes such as the outer membrane adhesion-like protein, phosphomannomutase, and cysteine desulfurase sufS were upregulated in TPY strain grown on S 0 or downregulated in TPY grown on Fe 2+ . These altered genes are involved in metabolism, osmotic stress, cell membrane alterations, oxidative stress, and the regulatory adaptive response. These results will aid our understanding of the molecular basis of Fe 2+ or S 0 oxidation by the moderately thermophilic and acidophilic bacteria.
Investigation of Post-Translational Modifications in Staphylococcus aureus

High temperature requirement enzymes are commonly referred to as “proteasechaperones” because of their ability to mediate both protein degradation and folding. These housekeeping proteases are conserved amongst prokaryotes and eukaryotes and are involved in repairing a wealth of cellular damage in response to stress. Staphylococcus aureus encodes two such enzymes, named HtrA1 and HtrA2, which have previously been implicated in the regulation of pathogenesis, seemingly though modulation of Agr activity. Work presented herein, however, demonstrates that single and double htrA mutants of S. aureus do not exhibit alterations in agr expression, or virulence determinant production, suggesting that previous observations were a consequence of unintended mutations acquired during strain construction. To understand the role of these proteases in S. aureus physiology we first determined that, while transcription of the htrA genes is moderate under standard conditions, it is increased in response to extracellular stressors that induce protein, DNA, and cell envelope damage. Furthermore, we found that htrA mutant strains are more sensitive to elevated temperatures, alterations in pH, ferrous-ion mediated oxidative stress, DNA damage, and LL-37 exposure,. Given that the role of proteases is best understood by determining their substrates, we also performed a yeast-2 hybrid screen to identify proteins that interact with HtrA1 and HtrA2. We identified several cellular components that are involved in the response to pH alterations (general stress protein SAUSA300_1685 and