Miracle-dz/UniFAR-FTUs huggingface dataset:
Biased extinction and evolutionary trends

The directionality of long-term trends can be strongly biased by forces intrinsic to a clade. Trends in body size and skeletal shape may be dictated more by variations in survivorship that reflect differences in ecology than by long-term directional changes in the environment. Hence, mass extinctions can help drive evolutionary trends by selectively eliminating some morphologies and permitting the survivors to found the next radiation. Examples include repeated trends toward larger maximum body size and the evolution of keeled species from those with globose tests in planktonic foraminifera. Both the trends in size and shape develop because small species with globose tests are significantly more resistant to extinction than species that are large or have peripheral keels. Hence, the survivors of both the Cretaceous-Tertiary and Eocene-Oligocene extinction episodes are small, unkeeled taxa. Large species and species with keels evolved convergently after both mass extinctions as the founders radiated anew. Comparison of three radiations of planktonic foraminifera suggest that the convergent evolution of similar test shapes and sizes is not due to synchronous changes in oceanography that track evolutionary trends. Instead, the reestablishment of habitat heterogeneity is needed to permit the ensuing radiation to unfold rather than to closely guide its progress. Similar evolutionary trends will develop in each radiation as long as the founders have similar morphology and the evolution of variants present in the previous radiation is not precluded by the environment.
Sequence features explain most of the mRNA stability variation across genes in yeast

The stability of messenger RNA (mRNA) is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to half-life are unknown. Here, we built a quantitative model for Saccharomyces cerevisiae explaining 60% of the half-life variation between genes based on mRNA sequence features alone, and predicts half-life at a median relative error of 30%. The model integrates known cis-regulatory elements, identifies novel ones, and quantifies their contributions at single-nucleotide resolution. We show quantitatively that codon usage is the major determinant of mRNA stability. Nonetheless, single-nucleotide variations have the largest effect when occurring on 3’UTR motifs or upstream AUGs. Application of the approach to Schizosaccharomyces pombe supports the generality of these findings. Analyzing the effect of these sequence elements on mRNA half-life data of 34 knockout strains showed that the effect of codon usage not only requires functional decapping and deadenylation, but also the 5’-to-3’ exonuclease Xrn1, the non-sense mediated decay genes, but not no-go decay. Altogether, this study quantitatively delineates the contributions of mRNA sequence features on stability in yeast, reveals their functional dependencies on degradation pathways, and allows accurate prediction of half-life from mRNA sequence.
Factors Affecting Female Incubation Behavior in the Bull-Headed Shrike

Abstract In most avian species, parents incubate their eggs until they hatch, paying an energetic cost in the process. Incubating individuals are expected to efficiently adjust their investment in incubation according to the thermal demands of their eggs and their partner's contribution to the process. In this study, the effects of ambient temperature, incubation stage, clutch size, and food provisioning by males on the incubation behavior of females, were investigated in the Bull-headed Shrike Lanius bucephalus. We video recorded behavior at 16 nests throughout the 15-day incubation period and established that only females incubate. During the early stage of incubation (5–7 days after completion of the clutch) female shrikes spent more time incubating, with longer periods on the nest (on-bout duration) and shorter periods off the nest (off-bout duration), than during the late stage (9–11 days after clutch completion). Females with larger clutches spent more time incubating than those with smaller clutches. Ambient temperature did not strongly affect female incubation behavior. Male provisioning was positively correlated with the length of time females spent incubating and their on-bout duration. Male provisioning plays an important role in the greater involvement of females in incubation, thereby ensuring normal embryonic development.
Numerical taxonomy of Galium (Rubiaceae) in Egypt

On the basis of fifty morphological characters, including vegetative parts, flowers, fruits, seeds, pollen grains, and anatomical structure, a systematic study of 13 taxa belonging to genus Galium (Rubiaceae) from Egypt was conducted by means of numerical analysis. Four branches and clusters were distinguished. Representatives of these groups were clustered together according to characters with high factor loading in the principal coordinates analysis. The results showed congruence between the UPGMA clustering and principal coordinates analysis in suggesting four groups. There was some degree of similarity among the species of sect. Aparine (Kolgyda). The results indicated also that the sect. Leiogalium (G. mollugo) was a separate group, while Aparine (Kolgyda) was the most heterogeneous one.
Efficient Synthesis of OpticallyPure Nω-Alkylated l-Arginines

A number of N ω -substituted L-arginineshave been described to date, particularly with regard to nitricoxide synthase (NOS) modulators. Elaborate multistep syntheses andlow yields limit the scope of preparing these modified L-arginines. We describe a synthetic methodologythat delivers N ω -alkylated L-argininederivatives from protected L-ornithinein a three-step sequence with excellent overall yields (81-90%)and in high purity. Analysis of the synthesized amino acids on aCrownpak Cr(+) column revealed no significant racemization,that is, >99.9% ee for all final compounds.
A genomic approach reinforces a hypothesis of mitochondrial capture in eastern Australian rosellas

ABSTRACT Recently, there have been contradictory results regarding relationships among 3 Australian parrot species known commonly as the Northern (Platycercus venustus), Pale-headed (P. adscitus), and Eastern rosella (P. eximius). An early phylogenetic analysis of the rosella genus Platycercus found that P. adscitus and P. eximius, 2 species putatively forming a hybrid zone, were sister taxa, while the geographically isolated P. venustus was in turn their sister taxon. However, a recent reexamination using multilocus sequence data found that evolutionary relationships differed depending on marker choice. Mitochondrial DNA (mtDNA) supported the earlier finding, but nuclear sequence data reflected an alternative relationship aligning P. adscitus and P. venustus as sister taxa. Two hypotheses were proposed to reconcile the discordance: (1) incomplete lineage sorting, and (2) mtDNA introgression from P. adscitus into populations of P. eximius. To clarify the relationships among these 3 species and to distinguish between the proposed hypotheses, restriction site-associated DNA (RAD) sequencing data from 23 individuals (∼4 individuals per subspecies) were examined. Species trees were generated based on datasets either excluding loci with missing data (393 loci) or including them (5 nonoverlapping subsets of 1,000 loci). Findings strongly supported a sister relationship between P. adscitus and P. venustus (posterior probabilities of 1 at all nodes), suggesting that the discordant patterns previously identified may have been the result of mitochondrial introgression and/or capture. This and other potential explanations are discussed.
Risk of biological invasions is concentrated in biodiversity hotspots

Understanding the locations of potential invasion hotspots and the extent to which they overlap with biodiversity hotspots is crucial for prioritizing efforts to reduce the impacts of alien species on global biodiversity. Using ensembles of species distribution models based on climate, anthropogenic predictors, vegetation, and water resources, we predict global potential invasion hotspots for alien herpetofauna (reptiles and amphibians). On average, when subjected to current and future climate scenarios, potential richness of alien herpetofauna per grid cell (the minimum unit of our spatial variables for modeling and projecting) in biodiversity hotspots is nearly 1.4 times higher than in other regions. Furthermore, potential invasion hotspots are projected to occupy a large proportion of the total area within biodiversity hotspots. These results suggest that biodiversity hotspots are at greater risk from alien herpetofaunal invasions than are other regions. Our results provide key information for globally targeting early detection and rapid-response programs to help prevent or mitigate future impacts of alien herpetofauna on biodiversity.
Genetic variation in Irish Whitebeam, Sorbus hibernica E. F. Warb. (Rosaceae) and its relationship to a Sorbus from the Menai Strait, North Wales

Genetic variation within the Irish endemic Sorbus hibernica, Irish Whitebeam, and its relationships to S. aria, S. eminens, S. porrigentiformis and a taxon from the Menai Strait have been assessed using AFLPs and morphology. Sorbus hibernica is genetically distinct from S. aria, S. eminens and S. porrigentiformis but is close to the Menai Strait taxon. Sorbus hibernica cannot be separated from the Menai Strait taxon using leaf or fruit characters, but they differ in ploidy.
RAPD polymorphism in Tetragonisca angustula (Hymenoptera; Meliponinae, Trigonini) Populations

Tetragonisca angustula is one of the commonest Neotropical stingless bees and an important pollinator agent. For this study, RAPD markers were used in order to estimate the genetic structure and quantify the genetic variability in five populations (14 colonies) of T. angustula. 12 primers were used that reproduced 171 fragments ofwhich 150 were polymorphic (87.72%). The estimate of gene diversity with the Shannon's index was 0.3929 (± 0.2329). The gene flow (Nm) was 1.4474 and the G ST value was 0.2568. Isolation was verified along with the values of the genetic distance among the populations from the Northwest of Parana state (Maringa and Cianorte) and from Sao Paulo state (Junqueiropolis). Six markers that differentiated T. angustula from Sao Paulo state and Parana state populations, were identified; however those markers were not able to separate the subspecies T. a. angustula and T. a. fiebrigi. This study shows a high polymorphism degree among those populations and higher biological potential to maintenance in domestic bee hives.
Chloroplast inheritance in the sea daffodil (Pancratium maritimum, Amaryllidaceae) through controlled crosses, seed germination and molecular analyses

Abstract Chloroplast inheritance is a very important information to obtain when cpDNA is used to study phylogeography or reconstruct phylogenies. A procedure used for the analyses of chloroplast inheritance in the sea daffodil (Pancratium maritimum) is described using multi-facet approach (artificial cross, germination and end-point PCR amplification).
Detection of genetically modified BT-maize in cooked food products by PCR

A comparison was made of eight known and published PCR primer sets to detect zein, cryIA(b), bla and bar genes and the 35S cauliflower mosaic virus promoter of transgenic Bt Maximizer maize event 176 (Novartis) in cooked food products. Transgenic pop corn, polenta and cookies were used as models. The polenta and cookies were made with different percentages (100, 1, 0.1% w/w) of transgenic maize flour. The DNA extracted from samples taken at different times of cooking revealed a progressive decrease in the average DNA fragment length, which was, however, still amplifiable by PCR. Of the primer sets tested, Cry 03/04 showed the best performance and led to the detection of transgenic DNA in final cooked products containing amounts of Bt-maize DNA as low as 0.1%. Cette etude evalue plusieurs methodes PCR pour la detection d'ADN transgenique dans des produits alimentaires cuits a base de mais. Du pop corn, de la polenta et des cookies, contenant differents pourcentages (100, 1, 0,1%) de farine de mais transgenique sont analyses. Les amorces PCR Cry 03/04 montrent les meilleures performances et conduisent a la detection d'ADN transgenique dans des produits cuits contenant des teneurs en mais-Bt de 0,1%.
Foxtail millet WRKY genes and drought stress

SUMMARY Foxtail millet (Setaria italica (L.) P. Beauv. ) is a naturally stress-tolerant plant, a major reserve crop and a model for panicoid grasses. The recent completion of the S. italica genome facilitates identification and characterization of WRKY transcription factor family proteins that are important regulators of major plant processes, including growth, development and stress response. The present study identified 103 WRKY transcription factor-encoding genes in the S. italica genome. The genes were named SiWRKY1–SiWRKY103 according to their order on the chromosomes. A comprehensive expression analysis of SiWRKY genes among four different tissues was performed using publicly available RNA sequencing data. Eighty-four SiWRKY genes were more highly expressed in root tissue than in other tissues and nine genes were only expressed in roots. Additionally, real-time quantitative polymerase chain reaction was performed to comprehensively analyse the expression of all SiWRKY genes in response to dehydration. Results indicated that most SiWRKY genes (over 0.8) were up-regulated by drought stress. In conclusion, genome-wide identification and expression profiling of SiWRKY genes provided a set of candidates for cloning and functional analyses in plants’ response to drought stress.
0025 Effects of organic or inorganic Co, Cu, Mn, and Zn supplementation to late-gestating beef cows on productive and physiological responses of the offspring.

text: Eighty-four pregnant Angus × Hereford cows were ranked by BW and BCS, and allocated to 21 drylot pens at the end of their 2 trimester of gestation (d 0). Pens were assigned to receive: 1) diet supplemented with sulfate sources of Cu, Co, Mn, and Zn (INR), 2) diet supplemented with an organic source of Cu, Mn, Co, and Zn (ORG), and 3) no Cu, Co, Mn, and Zn supplementation (CON). From d 0 until calving, cows were offered a foragebased diet formulated to meet requirements for energy, protein, macrominerals, Se, I, and vitamins. The INR and ORG diets were formulated to provide the same daily amount of Cu, Co, Mn, and Zn. Cow BCS was recorded, and liver samples were collected on d -10 and 2 wk (d 75) before the calving season. Within 3h after calving, calf BW was recorded, liver samples were collected, and the placenta was retrieved for cotyledon collection. All liver and cotyledon samples were analyzed for Cu, Co, Mn, and Zn. After calving, cow-calf pairs were assigned to the general management of the herd that included inorganic mineral supplementation. Calves were weaned a 6 mo of age and preconditioned for 45 d. Cows receiving CON had less (P≤0.05) BCS gain during the last trimester of gestation compared with INR and ORG cows, although cows from all treatments had similar (P=0.61) and adequate pre-calving BCS. On d 75, liver concentrations of Co, Cu, and Zn were greater (P≤0.05) for INR and ORG compared with CON, whereas INR cows had reduced (P=0.04) liver Co but greater (P=0.03) liver Cu compared with ORG cows. In the cotyledons, Co concentrations were greater (P≤0.05) in ORG and INR compared with CON cows, whereas Cu concentrations were increased (P=0.05) in ORG compared with CON cows. Calves from INR and ORG cows had greater (P<0.01) liver Co concentrations compared with calves from CON cows. Liver Cu and Zn concentrations were also greater (P≤0.05) for calves from ORG cows compared with cohorts from CON cows. Calf BW and value at weaning and upon preconditioning were greater (P≤0.04) for calves from ORG cows compared with calves from CON cows, and similar (P≥0.18) between calves from INR cows compared with the other treatments. Therefore, supplementing late-gestating beef cows with organic Co, Cu, Zn, and Mn is an alternative to enhance offspring productivity and economic returns in cow-calf systems.
Studies on the effect of age and caecectomy on amino acid excretion and digestibility in laying hens Untersuchungen mit Legehennen zum Einfluss von Alter und Caecectomie auf die Ausscheidung und Verdaulichkeit von Aminosäuren

The digestibility of amino acids (AA) is considered a suitable measure of feed protein quality in order to formulate economically feasible poultry diets that improve the overall efficiency of protein utilisation and reduce the emission of nitrogenous gases from farms. For growing birds, the determination of AA digestibility after collecting ileal digesta from slaughtered birds is a widely practised procedure. PAYNE et al., (1968; quoted by RAVINDRAN et al., 1999) were the first to suggest that the analysis of ileal contents rather than excreta may be a reliable method for assessing protein and AA digestibility in poultry. However, to obtain a sufficient amount of ileal digesta, many birds need to be slaughtered, which is disadvantageous especially when laying hens are the subject of interest. Another limitation to precaecal digestibility studies is that they neither allow consideration of the effects that may arise from discontinuous digesta flow during the day, nor do they allow repeated measures. Collecting excreta quantitatively may be an alternative because the contribution of urine to AA excretion is negligibly low (PARSONS, 1986; WHITTOW, 2000). However, the postileal microflora might change the profile of AA in the digesta when flowing through this part of the gastrointestinal tract. Because the caeca are the main sites of postileal microflora activity, caecectomy (surgical caeca removal) has been proposed as a method for reducing the microbial influence on digestibility (PARSONS, 1984; JOHNS et al., 1986; PARSONS, 1986; GREEN et al., 1987; GREEN, 1988). There are some experiments with broilers and turkeys that show an effect of age on AA digestibility determined with excreta of non-caecectomised poultry (BATAL and PARSONS, 2002a; BATAL and PARSONS, 2002b; PALANDER et al., 2004). As mentioned before though, these results are not easy to interpret because of microflora effects on digestibility. However, to the knowledge of the authors, the effects of birds’ age on AA digestibility in caecectomised hens have not yet been studied. The objectives of this experiment were therefore to study the AA digestibility of a diet in caecectomised laying hens that were 27, 40, and 57 weeks (wk) old, and to compare 27 wk old caecectomised and non-caecectomised hens. Energy was also of interest.
Power Output of Two Sizes of Atlantic Salmon (Salmo Salar) at their Maximum Sustained Swimming Speeds

The maximum sustained swimming speeds ( U ms) for large (0.45 m long) and small (0.15 m) Atlantic salmon were respectively 0.91ms−1 and 0.54ms−1. Video and cin6 films of fish swimming close to U ms were analysed to obtain variables required for the application of two hydrodynamic models, those of Lighthill and Yates, to determine the mean thrust ( T ) and mean power output ( P ) at these swimming speeds ( U ) close to U ms. A large fish (‘Salmon’) and a small fish (‘Smolt’) were selected for analysis. For salmon using Lighthill's model, T =0.30N and P =0.26W, and using Yates' model, T =0.28N and P =0.25W ( U /=0.87ms−1=0.96 U ms). For smolt using Lighthill's model, T =0.0052N and P =0.0019W, and using Yates' model, T =0.0065 N and P =0.0024W ( U =0.37ms−1=0.69 U ms). The power output for smolt swimming at 0.69 U ms was corrected to that required to swim at U ms, giving P =0.0059W (Lighthill's model) and P =0.0074W (Yates' model). At U ms it was assumed that all the red muscle was used. Two fish were selected from each size group and cross-sectioned to estimate their red muscle masses. Using a maximum mass-specific power output of 5–8 W kg− for slow red muscle fibres allowed us to calculate that the large and small fish have a power output capacity of 0.125–0.3 W and 0.007–0.019 W, respectively. The power output values at U ms derived from the different approaches for the large (0.25–0.26 W) and small (0.0059–0.0074 W) salmon agree closely. Effects of scaling are discussed.
Chromosomal inversions facilitate chromosome-scale evolution in Anopheles funestus

Understanding the neutral and selective forces that shape the genetic diversity along chromosomes is one of the central goals of evolutionary genomics. Contrary to expectations, combined actions of recombination and selection can result in reduced diversity along an entire chromosome, but this hypothesis still lacks strong empirical supports. Here we show that nucleotide diversity is specific to chromosome arms in the African malaria mosquito Anopheles funestus. We analysed the population history and genetic diversity in 132 wild-caught individuals representing two diverging ecotypes using RADseq markers. Genome scans revealed that genetic differentiation between ecotypes is accumulated within segregating polymorphic chromosomal inversions. Importantly, the presence of multiple overlapping inversions is associated with strong reductions in diversity throughout entire chromosome arms. The depression in genetic diversity is correlated to the frequency of inversions, being stronger in forest populations that are fixed for several adaptive inversions. Our results emphasize the role of polymorphic inversions in the genome architecture of adaptive speciation in An. funestus and provide a case of chromosome-scale evolution associated with the interplay between population demography, selection and recombination.
Effect of different active ingredients of fungicides on Alternaria spp. growth in vitro

The impact of different active ingredients of fungicides on the development of Alternaria species in vitro was estimated by using Amistar 250 SC (azoxystrobin), Signum 334 WG (boscalid, pyraclostrobin), Zato 50 WG (trifloxystrobin) and Folicur 250 EW (tebuconazol). The growth colonies of micromycetes Alternaria alternata (isolated from Thymus vulgaris, Levisticum officinale), Alternaria alternata, Alternaria brassicae (isolated from Brassica oleracea convar. capitata var. alba) and Alternaria dauci (isolated from Daucus carota) were tested on the potato dextrose agar medium with additions of fungicides. All tested fungicides showed sufficient inhibitory activity on the growth Alternaria spp. colonies,, which decreased on average from 94-25% Aver 21 days in comparison with the control.