Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and genetic characterization of transgenic tomato expressing 3-hydroxy-3-methylglutaryl coenzyme A reductase

Mevalonic acid (MVA) pathway, in parallel with methylerythritol phosphate (MEP) pathway, produces precursor metabolites for isoprenoids, and affect fruit development in plants. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is supposed to be a key enzyme in the MVA pathway. To understand the role of HMGR in fruit development, we previously generated transgenic tomato (Solanum lycopersicum) expressing a melon HMGR gene (CmHMGR) and observed increased fruit size in these plants. To further examine this effect, we performed molecular and genetic characterization of the transgenic tomato line in the T4 generation. The line showed stable expression of CmHMGR mRNA and protein, an effect that could lead to the increase in fruit weight observed, which exceeded 20%. Interestingly, the CmHMGR mRNA was highly expressed during tomato fruit development, whereas expression of the endogenous HMGRs (SlHMGR1, SlHMGR2, and SlHMGR3) was lower than in the wild type, suggesting the presence of a regulatory mechanism at the transcriptional level, as in mammalian systems. A preliminary analysis using cDNA macroarray filters was performed, and genes showing more than 2.5-fold differences in expression between transgenic and wild-type plants were identified. Most of the genes involved in isoprenoid biosynthesis did not show significantly different transcription levels, but 121 annotated genes and 152 genes of unknown function were found to be differentially expressed. These results demonstrate that the transgenic tomato line expressing the HMGR gene is genetically stable and could be used as a comprehensive material to elucidate the roles of HMGRs in tomato fruit development.
A sperm competition model for the European bitterling (Rhodeus amarus)

Sperm competition occurs when the spermatozoa of one male coincide with those of another to fertilise the same eggs. In some taxa males perform multiple ejaculations, which may function in sperm competition or in maintaining a baseline density of spermatozoa in the female reproductive tract to ensure fertilisation, a process that has been termed ‘topping up’. We investigated multiple ejaculations in the European bitterling (Rhodeus amarus), a freshwater fish that oviposits in freshwater mussels. We quantified spermatozoa in the mussel mantle cavity following ejaculation, and measured sperm motility parameters of males adopting different mating tactics. Following ejaculation spermatozoa density in the mussel increased linearly, peaked after 30 s, and then declined exponentially. Spermatozoa motility parameters did not differ between male mating tactics. We parameterised a model of sperm competition for R. amarus, which accurately predicted male fertilisation probability. We discuss these results in the context of multiple ejaculations and male mating tactics.
Micropropagation of Six Rockrose (Cistus) Species

Micropropagation methods for six rockrose species ( Cistus albidus L., C. clusii Dunal, C. ladanifer L., C. laurifolius L., C. psilosepalus L., and C. salvifolius L.) were established. Cultures, initiated from nodal segments of seedlings, were grown on MS medium, alone, or supplemented with 0.88 μM BAP or 0.93 μM Kin. Multiple shoot formation was obtained after the first subculture (30 days) from which new nodal segments were taken and grown on the same culture medium to maintain proliferation. Shoots obtained at the third subculture were rooted alone or supplemented with different concentrations of IBA. The plantlets of the six species, thereby obtained, were successfully acclimatized to ex vitro conditions. Chemical names used: 6-benzylaminopurine (BAP), indole-3-butyric acid (IBA), 6-furfurylaminopurine (Kin).
Conservation genetics and ecology of two rare grevillea species

Small and isolated plant populations have a higher probability of extinction – they are more susceptible to a range of environmental, demographic and genetic processes that may reduce population viability. In recent times, the number of populations and species that are susceptible to these processes has increased as a result of world-wide, human-induced habitat fragmentation. Habitat fragmentation typically reduces the formerly more continuous natural distribution of a species to a series of smaller and more isolated populations that occur in smaller and more isolated habitat patches. Such populations are often exposed to a range of additional processes that may threaten their viability, such as changes to disturbance regimes, environmental conditions and interactions with other species. However, our current understanding of the complex effects and interactions of these processes is poor. Species responses vary widely, studies are biased towards trees, herbs and self-incompatible species, and most studies investigate only one or two processes that may affect viability. Consequently, we are unable to make accurate predictions about the likely impacts of habitat fragmentation on population and species viability. I tested several hypotheses about the impact of habitat fragmentation, small population size, and population isolation on populations of two Grevillea species (Proteaceae) that occur in the Sydney region of New South Wales, Australia. These species provided an opportunity to investigate some of the ecological and genetic consequences of small population size and isolation, and to contrast them between a species for which the small size and isolation of its populations is the natural state ( G. longifolia ) and one for which it arose recently due to severe habitat fragmentation ( G. caleyi ). This comparative approach is important in identifying the processes involved in reducing population and species viability. The species share many aspects of their biology and ecology. Both are large, perennial shrubs that are self-compatible and naturally bird-pollinated. They are fire-sensitive and regenerate post-fire by mass germination from a long-lived, soil-stored seed bank. Both species consist of populations that vary dramatically in size and degree of isolation. I used microsatellite and AFLP markers to investigate genetics and mating these species, G. caleyi . Both species showed a surprisingly large amount of genetic structuring among populations, although G. caleyi populations showed more structuring ( F ST than
ONTOGENY AND EVOLUTION OF THE EARLY CAMBRIAN TRILOBITE GENUS NEPHROLENELLUS (OLENELLOIDEA)

Abstract The cephalon of Nephrolenellus multinodus and its stratigraphically higher sister-taxon N. geniculatus passed through the same four successive phases of development: entry into phase 2 is defined by a change from a decrease to an increase in the dynamic pattern of distance between the intergenal spine bases relative to cephalic length; entry into phase 3 is defined by the appearance of genal spines; and entry into phase 4 is defined by the effective isolation of glabellar furrow S3 from the axial furrow. Phase transitions were associated with significant changes in allometric growth patterns of the cephalon. Five instars are identified within the early development (phases 1 and 2) of N. multinodus. Despite the general similarity in cephalic ontogeny, significant interspecific differences in patterns of shape change are documented throughout phases 1, 2, and 3 of cephalic development which, with differences in rates of glabellar shape change relative to size (higher in N. multinodus) and ontogenetic loss of glabellar axial nodes (higher in N. geniculatus), demonstrate that evolutionary modification to ontogeny was mosaic and complex. Stratigraphic occurrences and a temporal trend towards increased rate of glabellar axial node loss relative to size in N. geniculatus are consistent with a hypothesis that N. geniculatus was a direct descendant of N. multinodus. However, ontogenetic data are needed for immediate outgroups of Nephrolenellus to determine whether two potential autapomorphies of N. multinodus, which refute such a hypothesis, are indeed unique to this taxon. Nephrolenellus jasperensis is recognized as a junior synonym of N. multinodus.
Nutrient uptake and partitioning by zucchini squash, head lettuce and potato in response to nitrogen

The effect of N application level on uptake and partitioning of nutrients by zucchini squash (Cucurbita pepo L.) cv. Blackjack, head lettuce (Lactuca sativa L.) cv. Monte110 and potato (Solanum tuberosum L.) cv. Sebago was investigated in sand culture experiments with a stable nutrient supply. Plants were grown during 14 (zucchini squash), 8 (lettuce) and 12 weeks (potato). Five nitrate N levels ranging from 2-36 mol m-3 for lettuce and 2-43 mol m-3 for zucchini squash and potato were applied in a complete nutrient solution. Gamma x quadratic response surface models fitted actual nutrient uptake data (R2> 0 . 9 5 ) . From these models, predicted nutrient uptake, partitioning of nutrients between plant parts and nutrient uptake rates were derived. Nitrogen had a pronounced effect on nutrient uptake of all species. The maximum predicted whole plant (excluding roots) uptake of N and K (parenthesis) was calculated (mol m-3 N) for zucchini squash (19.3, 17.7), lettuce (16.5, 12.1) and potato (12.7, 11.2) respectively. An N deficiency (2 mol m-3)did not result in remobilization of nutrients from vegetative to reproductive growth for zucchini squash and potato. Remobilization of N and K from outer leaves to head occurred for lettuce over the last week of the growth period at all N levels. An N deficiency increased partitioning of N and K by 36 and 54% respectively to reproductive growth for zucchini squash compared with adequate N for fresh yield (14 mol m-3), whereas an N deficiency had a negligible effect on partitioning to reproductive growth for potato. Partitioning, as measured by the ratio of nutrients in fruit, head or tuber to whole plant increased over the growth period, and at final harvest, partitioning was lowest for Ca (0.22-0.24 zucchini squash, 0.21-0.32 lettuce and 0.03-0.09 potato) and highest for K (0.39-0.60 zucchini squash, 0.59-0.68 lettuce and 0.63-0.86 potato). Potato tubers and lettuce head, in contrast to zucchini squash fruit, were dominant sinks for N, K and P.
Repeated probing of hosts: an important component of superparasitism

Parasitoids that encounter a previously parasitized host inspect it externally and internally, sometimes eventually laying additional eggs (superparasitism). The fitness effects of increased clutch sizes generated through superparasitism are widely studied, whereas the consequences of multiple host probings during the inspection received less attention. To address this issue, we offered a host to 1–5 females of the encyrtid wasp Copidosoma koehleri consecutively, or presented it 1–5 times to a single female. We noted whether the hosts died before pupation of either host or wasp, produced parasitoid pupae, or developed into moth pupae. Additional hosts were dissected after varying numbers of probings to determine their parasitoid egg loads. Host rejection rates prior to ovipositor insertion did not differ between treatments. Host rejections after ovipositor insertion, characterized by brief (<10 s) probing durations, were more common in the single- than in the multiple-female treatment. This could reflect avoidance of self-superparasitism, or increased selectivity by host-experienced females. Egg number per host increased with the number of prolonged probings in both treatments. Some hosts that received 1–2 probings (brief or prolonged) yielded moth pupae, while no hosts with five probings survived to pupation. Hosts probed three times (corresponding to <1 and 2.2 eggs in the single- and multiple-female treatments, respectively) produced the largest proportion of parasitoid pupae. The parasitoids’ success is thus strongly affected by the number of host probings. Overcoming host defenses through repeated probings is a previously overlooked potential benefit of superparasitism. [Behav Ecol]
Species overlap, speciation and the evolution of aggregation pheromones in bark beetles

Theoretical predictions suggest that species-specific signals used in the attraction of mates should evolve to reduce the risk of mismating and hybridization. These predictions lead to the hypothesis that the signals of spatially overlapping (i.e. sympatric or syntopic) species should differ more substantially than those of non-overlapping species. Earlier studies have tested this prediction for auditory and visual signals. Here we test the hypothesis using olfactory signals, specifically the aggregation pheromones of species from two genera of bark beetles, Dendroctonus and Ips. We found no direct evidence from within these genera regarding the fact that the chemical blends that make up these pheromones differ more substantially in species that overlap in their geographical ranges and/or host-tree use than in allopatric taxa. However, when comparing between genera, the pheromones of overlapping species appear to be more similar than non-overlapping species. We hypothesize that the species of host tree utilized by the beetles may have some influence on their pheromone blends. Additionally, within genera, species that overlap in host use tend to be more closely related than species that use different hosts. These results may provide indirect evidence for an effect of species overlap on the evolution of bark beetle pheromones.
Effect of corn and beet pulp based concentrate on ruminal parameters in wethers fed with fresh forage

Abstract Four wethers housed in individual pens and fitted with ruminal cannulae were grouped (two wethers per group) and fed fresh forage (Italian ryegrass, Lolium multiflorum) with either beet pulp (BP) or corn based concentrate (C) as supplements, using a crossover experimental design. The experiment was carried out during two experimental periods: the growing phase (early spring, G) and the reproductive phase (late spring, R) of the ryegrass. The diet of each animal was changed as the grass moved from the vegetative phase to the reproductive phase. The intake, the chemical composition of the diet and ruminal parameters such as pH, ammonia and volatile fatty acid were determined. Total dry matter intake (DMI) decreased from early to late spring (1081 vs 767 g/d; P<0.0001). Herbage DMI in particular decreased more (811 vs 543 g/d; P<0.05) than concentrate DMI (271 vs 224 g/d; P<0.054). There were marked differences in the chemical composition of the diet in wethers fed with the forage from early or late spring. This was because of changes in the characteristics of the forage. In detail, DM, NDF and ADF increased from early to late spring while CP, and EE decreased (P<0.05). Ruminal pH was lower in G than in R (6.24 vs 6.57, P<0.05). The concentrate used had no effect on the pH value. The ammonia concentration in the rumen fluid decreased from early to late spring (10.79 vs 6.68 mg/100 ml, P<0.05) and it was not influenced by the source of carbohydrates from the concentrate. VFA rumen fluid concentration increased (P<0.05) after feeding and decreased before the second meal. In the rumen fluid, the maximum total VFA concentration and the lowest pH were observed 2 h after the morning meal. Acetate and butyrate concentrations in the rumen fluid were influenced by the period (P<0.05) but not by the concentrate source. By contrast, the concentrate source significantly influenced the rumen fermentation patterns of propionate and VFA ratios, with higher propionic acid and lower acetate to propionate ratios in C than BP. This highlights the importance of the carbohydrate source in supplements for pasture based rations which varied according to the proportion of beet pulp and corn in the ingested diet.
Study of PD-L2 Gene Expression in Patients with NSCLC-type Subclasses of Lung Cancer Using Real-Time PCR

Introduction: Lung cancer is one of the biggest health problems in the world. Non-small cell lung cancers (NSCLCs), which account for approximately 85% of lung cancer cases, are the leading cause of deaths due to cancer worldwide. The type 1planned death molecule (PD-I, CD279) and its PD-L1 ligands (B7-H1, CD274) and PD-L2 (B7-DC, CD273) are the key molecules inhibiting the immune regulation. The aim of this study was to investigate the expression of PD-L2 gene and the evaluation of cancerous stages of NSCLC and its subclasses in lung cancer patients in Tehran hospitals using Real-Time PCR. Materials and Methods: A total of 35 clinical samples were collected from patients with NSCLCderived lung cancer from three hospitals in Tehran (Khatam, Athiyah and Masih Hospitals). Of the 35 samples obtained in 2017, 20% of them were women and 80% were men. The age range of patients varied from 37 to 80 years. The disease grade gradients among the patients in this investigation varied and 22 different grades were observed. To investigate the PDL-2 gene Original Research Article Jafarikia et al.; AJMPCP, 2(2): 1-8, 2019; Article no.AJMPCP. 46130 2 expression, after extraction of total RNA and cDNA synthesis using Real-Time PCR, the expression of the gene was investigated. Results: 74% of adenocarcinoma cases were in T-categories of lung cancer and 25% of patients were in grade IIIa. Patients with T3 stage had four samples, 2 of which were adenocarcinoma and other 2 samples being SCC and their age ranged from 55 to 62 years old. Three patients were in the T1 category, of which 100% had adenocarcinoma. The results showed that expression of PDL2 gene was increased 5.45 fold among patients with NSCLC-type lung cancer compared to those with normal condition. Conclusion: PD-L2 expression detection methods, including the detection of mRNA expression by using Real-Time PCR and the use of multiple systems for detecting PD-L2 expression with cell type and in association with other immune markers, can make a deeper understanding of PD-L2 as a biomarker and help to diagnose lung tumors of the NSCLC type. In our studies, it was found that expression of PD-L2 gene in cancer patients is higher than normal conditions.
VEGF-Dependent Mechanisms Controlling Osteoblast Differentiation and Bone Formation During Bone Repair

Osteoblast-derived vascular endothelial growth factor (VEGF) is important for bone development and postnatal bone homeostasis. Several studies have demonstrated that VEGF affects bone repair and regeneration; however, the cellular mechanisms by which it works are not fully understood. In this study, we investigated the functions of osteoblast-derived VEGF in healing of a cortical bone defect. In addition, how VEGF signaling modulates BMP2 functions during bone healing was also examined. To define the roles of osteoblast-derived VEGF in bone repair, a mouse tibial monocortical defect model was used. The effects of deleting Vegfa or Vefgr2 in osteoblast precursors and their descendants on the bone repair process were analyzed at various time points after surgery. To study how VEGF modulates the osteogenic activity of BMP2, BMP2, with or without the soluble VEGFR (sFlt1, VEGF decoy receptor), was delivered to the cortical defects in VE-cadherin-cre;tdTomato mice. The results indicate that osteoblast-derived VEGF is important at various stages during healing of the cortical defect. In the inflammation phase, osteoblast-derived VEGF controls neutrophil release into the circulation and macrophage-related angiogenic responses. VEGF is required, at optimal levels, for angiogenesis-osteogenesis coupling in
A viability model to assess the sustainability of mixed herds under climatic uncertainty

On the Bolivian arid highlands, breeders' strategies combining herd diversification (llamas and sheep) and the control of breeding rate were assessed under unpredictable environmental conditions. A survey of 14 farms made it possible to characterise practices in llama flocks (controlled and uncontrolled breeding practices) and in sheep flocks (high care and low care practices). The efficiency of these practices was evaluated using annual numerical productivity indexes. To assess the effectiveness of these practices, a dynamic model of mixed herds, based on the mathematical framework of the viability theory, was developed. The model made it possible to analyse the long-term interactions between management practices and climatic uncertainty on livestock system sustainability. Numerical productivity at weaning was found to be significantly lower in llama flocks managed with controlled breeding compared to uncontrolled breeding (44% and 70% respectively). For sheep, numerical productivity at weaning of high-care flocks was not significantly higher than that of low-care ones (83% and 69%, respectively). It was not possible to conclude whether high-care practices were more efficient in increasing numbers than low-care ones. On a long-term perspective, the dynamic analysis showed that the control of the llama flock breeding rate stabilises the evolution of the mixed herd only when a low offtake rate can satisfy a minimum income. Thus, foregoing short-term yield can be a sound strategy to insure mixed herd viability in an extremely harsh and unpredictable environment. However, the effectiveness of this practice is closely related to wealth (herd size). The model is discussed in terms of its heuristic value for assessing management practices and sustainability of pastoral systems.
Four new Penicillium species having Thysanophora -like melanized conidiophores

Five fungal isolates, tentatively identified as belonging to Thysanophora, were re-examined to confirm their generic placement. DNA sequences from multiple loci were determined and compared to homologous sequences from other fungi. The Thysanophora-like isolates belong in the genus Penicillium on the basis of phylogenetic analysis of their gene sequences. Because these isolates have unique phylogenetic positions within Penicillium and have unique phenotypes we describe them as the new species P. boreae, P. subarcticum and P. canariense spp. nov. In addition, P. pullum sp. nov. is described for NRRL 721, which served as the typical isolate of P. fuscum in the monographic studies of Raper & Thom and Ramirez; however, the name P. fuscum has been applied and neotypified using a different specimen and NRRL 721 is markedly different phylogenetically from the neotype of P. fuscum.
Body composition in lambs and young sheep and its prediction in vivo from tritiated water space and body weight

SUMMARY Tritiated water (TOH) space was determined in sixty-one sheep of known age (3 days to 18 months). Representative samples of the minced carcass were subsequently analysed to determine body composition (water, fat, protein, ash and energy). The regressions of the weight of the various body components on TOH space and body weight reported here gave equations suitable for prediction. These were similar to equations derived from published results for adults. Combining data on young sheep and adults gave broadly based equations that could be used to predict the body composition of healthy sheep of all ages from 3 days to adults.
Behaviour of the maize transposable element Ac in Arabidopsis thaliana

Summary The somatic and germinal activity of the maize transposable element, Ac, has been analysed in progeny of 43 transformants of A. thaliana using a streptomycin resistance assay to monitor Ac excision. The ability to assay somatic activity enabled, for the first time, a detailed analysis of Ac activity in individual A. thaliana seedlings to be made. The effects of T-DNA copy number, generation, dosage at each locus, flanking sequences and orientation of the element were compared. The most striking observation was the variability in Acactivity in genotypically identical individuals and the poor penetrance of the variegated phenotype. In general, increasing Ac dosage increased both somatic and germinal excision frequencies. The majority of families from individuals selected as inheriting an excision event carried transposed Ac elements re-integrated in different positions in the genome.