Miracle-dz/UniFAR-FTUs huggingface dataset:
Implications of Stisa2 catalytic residue restoration through site directed mutagenesis

Abstract Objective Restoration of catalytic activity of Isa2 from Solanum tuberosum (Stisa2) through restoration of conserved catalytic residues by site directed mutagenesis. Methods The six conserved amino acid residues absent in the Stisa2 gene were restored by mutation using the overlap extension PCR and the asymmetrical overlap extension PCR methods. Next, mutant Stisa2 with restored catalytic residues was expressed in E. coli Rosetta 2 under optimized conditions. Evaluation of debranching activity on starch, amylopectin and β-limit dextrin was carried out by measuring the amount of glucose equivalents released using the bicinchoninic acid assay. Results Both qualitative and quantitative analysis showed that the restoration of the conserved residues in the catalytic site did not restore starch debranching activity. Molecular modeling showed greater than expected distances between the catalytic triad in mutant Stisa2. These additional distances are likely to prevent hydrogen bonding which stabilizes the reaction intermediate, and are critical for catalytic activity. Conclusions These results suggest that during evolution, mutations in other highly conserved regions have caused significant changes to the structure and function of the catalytic network. Catalytically inactive Isa2, which is conserved in starch-producing plants, has evolved important non-catalytic roles such as in substrate binding and in regulating isoamylase activity.
HIGH RESOLUTION MELTING ASSAY FOR SCREENING OFY-CHROMOSOME SNPS IN BULLS

High-resolution melting (HRM) assay is a novel tool for polymorphism analysis. We describe here the application of HRM analysis for screening of two polymorphic sites on the ZFY gene (ZFY-9 and ZFY-10) present at male specific region of bull Y-chromosome which are generally being used to identify Y-chromosome haplotypes (Y1, Y2 and Y3) in many cattle breeds/population world wide.The Y-chromosome haplotypes are important for the understanding of effective male contribution, Y-chromosome diversity and male lineages.Wetested 20bulls with known genotypes for two sites(ZFY -intron 9, 120> C/T; and ZFY- intron 10, 655> C/T)that were previously genotyped by Allele Specific PCR (AS-PCR) and validated through direct sequencing (two representative samples from each region) and then examined the sensitivity of mutati on detection using quantitative PCR (qPCR) followed by HRM curve analysis. Absolute concordance was observed among AS-PCR, direct sequencing and HRM analysis. Known Y- chromosomevariants were readily detectable using HRM assay. Thus, the qPCR-HRM assay is a sensitive in-tube methodology that allowed the rapid and sensitive identification of Y-chromosome variations.The results demonstrate that qPCR-HRM method is a fast, simple and reliable assay for detection of Y-chromosome variations.
Fertility variation among individuals in natural stands of Acacia leucophloea

Abstract Growth characteristics and fertility variations were evaluated at four natural stands of tropical arid zone species, A. leucophloea in southern India. Three stands (TNL 1, TNL 2 and PDM) were situated in dry upland regions while one stand (RKP) was at waterlogged site. The tree height and girth at breast height did not vary between stands in two years. Fertility variation (sibling coefficient, ψ) was estimated based on flowering abundance and fruit set collected for two consecutive years. Fruit production per tree was generally lower in the RKP stand than the other three stands. No year-to-year variation was observed on fruit set in all stands. Growth and flower production showed a weak-positive correlation in both years (R2 = 0.39 to 0.1). The correlation to check if the larger inflorescence size, the higher number of fruit production was also failed. Male fertility variation did not vary much among stands (ψm = 1.28 ~ 1.62). Female fertility variation was low (ψf = 1.71 ~ 2.02) in the three stands situated in dry upland regions than the RKP stand (ψf = 4.09 ~ 4.16). The cumulative contribution of trees to the overall fertility was deviated from the ideal situation (equal contribution) in all stands, especially the RKP stand showed a skewed distribution (R2 ≤ 6.5). The effective population size was low in the RKP predicting a high genetic drift when compared with other sites. Similarly high group coancestry and low gene diversity were observed in the stand RKP. The implications of fertility variation on gene diversity of the species and future management of the natural stands were also discussed.
First description of the nest of the ruddy treerunner (Margarornis rubiginosus)

We discovered a nest of a Ruddy Treerunner Margarornis rubiginosus at Monteverde Cloud Forest Preserve, Puntarenas province, Costa Rica (1,530 m) on 25 April 2004. The nest of this species has not been described previously1–3. It was sited at c.25 m in the crown of a tree adjacent to a suspension bridge along a regularly used trail within mature cloud forest. The nest was on the underside of a thick branch (diameter: 45 cm), which projected from the main trunk at an angle of 20o from vertical. The nest was an oval mass of moss, well camouflaged on an epiphytecovered branch (Fig. 1), and was c.30 cm tall and 20 cm wide. The nest entrance, which oriented downwards from the bottom of the nest, had a diameter of c.10 cm, and the entrance tunnel appeared to narrow considerably within. The lip of the nest entrance appeared to be woven of brown and green plant fibres, whereas the remainder of the exterior was of shaggy moss. Moss hung down around the entrance, making it difficult to view into the nest from any angle except directly below. The branch to which the nest was attached, and the nest's structure, protected the interior of the nest from rain. The nest was sited underneath a large, leafy bromeliad and may have been attached to the root structure of this epiphyte. Nests of Neotropical ovenbirds (Furnariidae) are variable and often highly cryptic3. The nest of only one other species of Margarornis has been described; that of the Pearled Treerunner M. squamiger, which is a ball of moss with a side entrance, placed below a limb or rock2. Hanging nests of moss may prove to be a common feature amongst the four species in this genus. We observed one or two adults feeding nestlings. During two hours of observation, we witnessed 20 feeding visits, but only one adult was seen per visit, making it impossible to
The monothiol glutaredoxin Grx4 interacts with the Cryptococcus iron regulator Cirl and regulates iron homeostasis and virulence in the Cryptococcus neoformans

The acquisition of iron and the maintenance of iron homeostasis are important aspects of the virulence in the pathogenic fungus Cryptococcus neoformans. In this study, we identified the monothiol glutaredoxin Grx4 as a binding partner of Cir1, a master regulator of iron-responsive genes and virulence factor elaboration in C. neoformans. Monothiol glutaredoxins are important regulators of iron homeostasis because of their conserved roles in [2Fe-2S] cluster sensing and trafficking. We confirmed that Grx4 binds Cir1 and demonstrated that iron repletion promotes the relocalization of Grx4 from the nucleus to the cytoplasm. Nuclear retention is partially dependent on Cir1 and also influenced by treatment with the proteasome inhibitor bortezomib. Cir1 remains in the nucleus in both iron replete and iron limiting conditions. We also found that a grx4Δ mutant displayed iron-related phenotypes similar to those of a cir1Δ mutant, including poor growth upon iron deprivation. Importantly, a grx4Δ mutant was avirulent in mice, a phenotype consistent with observed defects in the key virulence determinants, capsule and melanin, and poor growth at 37°C. A comparative transcriptome analysis of a grx4Δ mutant and the WT strain in low iron and iron-replete conditions confirmed a central role for Grx4 in iron homeostasis. Dysregulation of iron-related metabolism was consistent with grx4Δ mutant phenotypes related to oxidative stress, mitochondrial function, and DNA repair. Overall, the phenotypes of the grx4Δ mutant and the RNA-Seq analysis support the hypothesis that Grx4 functions as a sensor of iron levels, in part through an interaction with Cir1, to extensively regulate iron homeostasis and contribute to virulence.
Characterisation of Staphylococcus aureus isolated from meat processing plants – a preliminary study

Abstract Introduction: Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) belonging to the clonal complex 398 (CC398) emerged recently in livestock as a new type of MRSA, which may cause zoonotic infections. This study presents data on the characterisation of S. aureus isolated from the meat processing plants. Material and Methods: S. aureus was isolated from 90 samples collected in the raw meat warehouse, from devices and surfaces of meat processing plants, and from finished meat products. The isolates were subjected to molecular analysis in order to investigate the presence of enterotoxin genes, the mecA gene, and to verify whether they belong to the clonal complex 398. The genetic relatedness of the isolates was determined using pulsed-field electrophoresis. Likewise, antimicrobial susceptibility was tested. Results: From 21 S. aureus strains isolated, five belonged to the CC398, two of which were recognised as MRSA and three as methicillin-sensitive Staphylococcus aureus (MSSA). The most prevalent enterotoxin genes were seg and sei. Two MRSA CC398 isolates, three MSSA CC398, and one MSSA were classified as multidrug-resistant. Conclusion: The first isolation of MSSA CC398 from beef in Poland indicates contamination of beef by strains belonging to this clonal complex. The occurrence of multidrug-resistant enterotoxigenic S. aureus isolates in the finished meat products constitutes a potential risk for the consumers.
Colour patterning in the skin of the reed-frog

A collec1ion 01 37 Natal reed·frogs, HyperoJius marmoratus, from a single locality was studied for their dorsal colour pattems. Data were assembled on the spectrophotometry, the structure and distribution of ttie chromato· phores by means of light and electron microscopy, and the features of colour patterning. An attempt was made to regard colour patterns as the end result of a definable process of differentiation. A number of possible rules was set out according to which the patterns Observed might be generated. S. Afr. J. Zool . 1987, 22(2)
Vertical Distribution of Juvenile Skipjack Tuna Katsuwonus pelamis in The Tropical Western Pacific Ocean

The vertical distribution of juvenile skipjack tuna Katsuwonus pelamis was investigated in the tropical western Pacific (0-25°N and 130-160°E) based on midwater trawl sampling from October to December in 1992 to 1996. Most juveniles were sampled between depths of 40 and 120 m, that is, at depths ranging immediately above and below the thermocline, and at temperatures between 20 and 30°C. Relatively lower temperatures were observed in the pelagic zone of the research area from 1992 to 1994 (period of a shallow thermocline), in contrast to relatively higher temperatures from 1995 to 1996 (with a deep thermocline). The vertical distribution of skipjack juveniles became shallower from 1992 to 1993, whereas it became deeper in 1995 and 1996. These findings suggest that the vertical distribution of skipjack tuna during the juvenile period changed annually relative to the vertical temperature profile. Moreover, fluctuations in vertical temperature are believed to affect the expansion or contraction of the vertical habitat of skipjack juveniles in the pelagic zone. The mean standard length of juveniles collected in 1994 at a depth of 80-100 m in the North Equatorial Counter Current area was significantly larger than that of juveniles collected at 40-60 m. These findings suggest that the vertical distribution of juvenile skipjack tuna becomes deeper in line with their growth. Discipline: Fisheries Additional key words: annual change, habitat, North Equatorial Current, North Equatorial Counter Current, thermocline Present address: 5 Fisheries Management and Oceanography Division, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency (Nagasaki, Nagasaki 851-2213, Japan) *Corresponding author: e-mail katsuwo@affrc.go. jp Received 22 February 2016; accepted 29 June 2016. Introduction The pelagic zone of the tropical Pacific Ocean is known as the main spawning ground of skipjack tuna Katsuwonus pelamis (Matsumoto et al. 1984). The region also ranks as the world’s largest fishing ground of skipjack stock (FAO 2014). Distribution patterns and recruitment levels of skipjack tuna in the region fluctuate with large environmental changes, such as El Niño and La Niña (Bertignac et al. 1998, Lehodey 2001, Lehodey et al. 1997, Lehodey et al. 1998, Lehodey et al. 2003). To explore this phenomenon, research must be conducted on the early life ecology of this species. Previous studies have reported that tuna larvae no longer than 10 mm (and less than 10 days old after hatching) are mainly distributed in the epipelagic zone of the depth above 60 m, where the sea surface temperature is higher than 24°C (Strasburg 1960, Ueyanagi 1969). However, very little is known about the vertical and
Multiple anti-predator mechanisms in the red-spotted Argentina Frog (Amphibia: Hylidae)

Anurans employ a wide variety of anti-predator mechanisms to defend themselves. In casque-headed hylids, defence is thought to be a complex combination of several anti-predator mechanisms. However, the defence traits of only a few species are known; some hypotheses have yet to be addressed, whereas others, already tested in some species, need to be tested in additional taxa. The anti-predator mechanism of the casque-headed frog, Argenteohyla siemersi, is described here. It is a complex mechanism consisting of (1) behavioural and ecological traits, including secretive and semi-phragmotic habits and posture; (2) morphological features, including cryptic and aposematic colourations, a skull covered with bony dermal spines and protuberances that are associated with two types of granular venom glands; and (3) physiological and chemical traits, such as a highly lethal skin secretion. Our results are compared with those of previous studies of defence mechanisms in casque-headed frogs in an effort to understand the mechanisms and evaluate their potential phylogenetic signal in this group of anurans.
Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem

Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats.
Trace element concentration and its risk assessment in common kilka (Clupeonella cultriventris caspia Bordin, 1904) from southern basin of Caspian Sea

Abstract This study evaluated the extent of metal levels of zinc (Zn), copper (Cu), manganese (Mn), chromium (Cr), nickel (Ni), lead (Pb), cadmium (Cd), and mercury (Hg) in edible muscles of common kilka at Babolsar and Amirabad coastal regions from the southern basin of Caspian Sea. These values were compared with the WHO and the UNFAO safety standards regarding the amount of the abovementioned heavy metals in fish tissues (mg/kg w.w.). Results showed that Zn concentrations were highest among the trace elements examined, while concentrations of Hg were generally the lowest in the analyzed tissues. In the other hand, the accumulation of these elements was not significantly different between coastal regions (p > 0.05). While accumulation of Cu and Mn at edible muscles of Clupeonella cultriventris were significant difference between two coastal regions (p < 0.05). The distribution patterns of trace element concentration follows the order: Zn > Cu > Cr > Cd > Ni > Mn > Pb > Hg. Furthermore, Pearson correlation revealed that Zn, Cu, Mn, Ni, Cr, Pb, Cd and Hg in edible muscles of C. cultriventris were not significantly correlated in length (R2 < 0.50; p > 0.05), but it was significantly correlated in weight (p < 0.05). The calculated target hazard quotients (THQ) of all trace elements were less than 1. Consequently, there was no obvious public risk from the intake of these trace elements through C. cultriventris consumption.
Biodiversity, feeding habits and reproductive strategies of benthic macrofauna in a protected area of the northern Adriatic Sea: a three-year study

The macrozoobenthic community at a sublittoral station located in the Marine Protected Area of Miramare, Gulf of Trieste (Italy) was investigated monthly from June 2002 to July 2005. Community variables were studied and related to food sources (particulate, total and biopolymeric carbon contents, benthic microalgae and meiofauna). In addition, the macrofaunal response to a heatwave that occurred in summer 2003 in the area was also explored. Univariate and multivariate analyses highlighted that the macrozoobenthic community structure shifted towards the end of the study. Diversity remained fairly stable throughout the study, despite the high turnover values. From a dominance of short-lived invertebrates related to irregular fresh organic matter inputs, the community shifted toward long-lived taxa, principally related to an increase of biopolymeric C and microalgal biomass. Semelparous invertebrates seem to be less resistant to high temperatures compared to iteroparous ones. The latter proved to be capable competitors since they prevailed over the semelparous species towards the end of the study. The community exhibited a certain degree of resistance to high temperature, due to the adaptation of the macrofaunal invertebrates to this particular stress, induced by the wide natural fluctuations in temperature that occur on a seasonal basis in the Gulf of Trieste. This study highlights the importance of long datasets to assess the state and ecological processes of the macrofaunal communities.
Response of rocket salad germplasm (Eruca and Diplotaxis spp.) to major pathogens causing damping-off, wilting and leaf spot diseases

Abstract In the present study, 26 accessions of rocket salad belonging to four species (Eruca sativa Mill., Diplotaxis tenuifolia (L.) DC. , Diplotaxis muralis (L.) DC. and Erucastrum spp. ) were tested for resistance to damping-off, wilting and leaf spot disease causal agents. High susceptibility to Rhizoctonia solani was detected in all accessions while variability in rocket seedling susceptibility for Sclerotinia assays was observed. Susceptibility to wilting caused by the fungus Fusarium oxysporum f. sp. raphani was tested. E. sativa varieties exhibited a lower severity degree associated to yellowing-related symptoms compared to D. tenuifolia. Resistance assay using the bacterium Xanthomonas campestris pv. campestris was also performed. Five E. sativa varieties showed a disease incidence lower than 60% while all the D. tenuifolia accessions, showed a susceptibility of 100%. The present study represents a step towards the identification of genetic resources useful in breeding for the selections of novel resistant varieties.
Identification of novel targets in prostate cancer progression

We have developed novel fluorescence bio-imaging based automated models to screen for novel candidate targets involved in prostate cancer metastasis. Utilizing these models and adopting a functional genomics based approach; we identified SYK as a novel regulator of prostate cancer progression. We also identified functional involvement of MST1R in regulating the progression of prostate cancer. For both of these targets, there is supporting human clinical data to validate our results in prostate cancer.
Semiaquilegia guangxiensis (Ranunculaceae), a new species from the limestone areas of Guangxi, China, based on morphological and molecular evidence

A new species of Ranunculaceae, Semiaquilegia guangxiensis , is described and illustrated. The plant is morphologically similar to S. adoxoides , but it obviously differs from the latter by the following characteristics: stamens 20–30 (vs. 8–14 in S. adoxoides ); staminodes ca. 10, half the length of the filaments (vs. ca. 2, as long as filaments in S. adoxoides ); follicles ca. 1 cm long, ca. 3 mm wide (vs. 6–7 mm long, ca. 2 mm wide in S. adoxoides ); seeds 1.5–2.5 mm long (vs. ca. 1 mm long in S. adoxoides ). Its affinity to S. adoxoides and placement in Semiaquilegia are confirmed by phylogenetic analyses based on nuclear ITS and chloroplast trn L-F sequences.
Estimates of observer expertise improve species distributions from citizen science data

Citizen science data are increasingly making valuable contributions to ecological studies. However, many citizen science surveys are also designed to encourage wide participation and therefore the participants have a range of natural history expertise, leading to variation and potentially bias in the data. We assessed a recently proposed measure of observer expertise, calculated based on the average numbers of species recorded by observers. We investigated if this observer expertise score is associated with how often an observer reports any individual species. Species reporting rates increased monotonically with the observer's expertise score for 197 of 200 species, suggesting that this expertise score describes inter‐observer variation in the detectability of individual species. Expertise scores were incorporated into single‐species occupancy models as a covariate, to explain inter‐observer variation in detectability. Including expertise as a detectability covariate led to improved model fit and improved predictive performance on validation data. The expertise score had a large effect on the estimated detectability, comparable in magnitude to the effect of the duration of the observation period. Expertise scores were also included into single‐species occupancy models that estimated seasonal patterns in species occupancy and seasonal expertise effects. The addition of a seasonal effect of expertise led to improved model fit and increased predictive performance on validation data. The seasonal expertise accounted for bias that may be introduced by seasonal differences in the effect of expertise, caused by changes in the environment or species behaviour. Measures of observer expertise included in models as a covariate can account for heterogeneity and bias introduced by variable expertise, although in this example the differences in estimated occupancy were small. This method of incorporating observer expertise can be used in any regression model of species occurrence, occupancy, abundance, or density to produce more reliable ecological inference and may be most important where citizen science schemes encourage wide participation. Overall, the results highlight the value of recording observer identity and other detectability covariates, to control for sources of bias associated with the observation process.