Miracle-dz/UniFAR-FTUs huggingface dataset:
Flow cytometric classification of oil palm cultivars.

Efficiencie in each nuclear lysis buffer on flow cytometric analysis (FCM) of oil palm were compared for cultivar classification. Embryos and unopened leaves of one to twelve months-old seedlings were used as initial materials with five nuclear lysis buffers, including LB01, WPB, Otto’s, Tris.MgCl 2 and Galbraith. Although these buffers showed distinct peaks of propidium idodide (PI) fluorescence for oil palm embryos, the buffers differed considerably in fluorescence intensity (FL), coefficient of variance (%CV), debris factor (%DF) and yield factor (YF) values when analyzed with their seedlings. The results show that LB01 was the most suitable buffer (lowest %CV and high FL value) for oil palm embryos resulting in 3.7 pg of 2C-DNA. For all the seedlings, only WPB gave the highest value of FL and lowest value of %CV resulting approximately in 3.8 pg of 2C-DNA, whereas the highest value of YF and lowest value of %DF were mostly found in LB01. Of interest is the fact that only WPB showed consistency position of PI fluorescence histograms when analyzed with all seedlings. WPB was therefore used to classify the cultivars of hybrid Tenera and its parents (Dura and Pisifera) by means of DNA contents. DNA contents of Dura and Pisifera ranged from 6.3 to 7.6 and 5.3 to 6.1 pg and their genome size (1C DNA contents) is therefore greater than 3,000 and 2,000 Mbp, respectively. The results confirmed that Dura, Pisifera and Tenera cultivars could be classified using FCM-derived DNA contents. Key words: 2C-DNA value, cultivars, flow cytometry, nuclear lysis buffers, oil palm.
Evolution of the Virulent Primary Isolate, SIV/DeltaB670, in vivo,Implications for Study Design and Antiviral Therapies

Antiretroviral drug treatments and vaccine strategies are hampered by the ability of the HIV to generate variants able to evade their protective effects. Understanding the effects of these interventions on virus evolution could aid in the design of targeted antiviral strategies. We addressed this in a cohort of SIV infected non-human primates given short-term antiviral drug treatment (ART) with and without DNA vaccinations. We hypothesized that the most potent therapies (e.g. those that suppress virus burden to the greatest degree) would limit virus evolution. Our results supported this hypothesis. There was no apparent vaccine effect however. These results could indicate that the immune response was not strong enough to induce changes in the global virus population, evolution must be monitored at the epitope level to be revealed, or the most informative time points were unavailable due to low virus burdens. We additionally hypothesized that infection of the gut associated lymphoid tissue may render this organ as a reservoir for expression of unique viral genotypes. We demonstrated that high plasma virus loads were associated with high tissue virus loads and wide dissemination of genotypes. In contrast, the lymphoid tissues on animlals that controlled their virus burden contained genotypes not expressed in other organs. Our results have important implications on studying virus evolution in vivo by demonstrating that large populations and potentially numerous virus genes need to be analyzed.
HYPOTHESIS ON FUNCTIONAL INADEQUACY OF THIOREDOXIN AND RELATED SYSTEMS IN PREECLAMPSIA

Objective: To outline a hypothesis suggesting that preeclampsia (preeclamptic toxemia, PET) arises because the thioredoxin-thioredoxin reductase (TRX-TDR) system and related reducing systems inadequately control the abnormal intracellular oxidizing conditions associated with the heightened metabolism of pregnancy.Background: PET has been regarded as a disease of oxidative stress. Thioredoxin is a widely present hormone-responsive antioxidant redox protein participating in diverse biological functions on the basis of sulfydryl-disulfide shuttle activity. Glutaredoxin (GRX) takes part with glutathione in a further similar system which also acts as a hydrogen donor.Hypothesis: The TRX-TDR system is at the crux of those processes which, when not functioning optimally in some pregnancies within the cells of the fetomaternal complex, lead to the phenomena of PET. The consequences are mediated particularly by the altered redox-based modulation of NF-kB activity in promoting TNF transcription. TNF and related cyt.
Immunité anti-tumorale et thérapies cellulaires du cancer

L’existence de lymphocytes T capables de reconnaitre des antigenes specifiques des tumeurs est maintenant completement admise. Ces cellules, ainsi que les cellules natural killer (NK), infiltrent le tissu tumoral et sont en mesure d’exercer une cytotoxicite a l’egard des cellules cancereuses. Cependant, au cours de l’histoire naturelle du developpement tumoral, la reponse immunitaire se revele inefficace. Ce constat est a l’origine de nombreux travaux de recherche dont l’objectif a terme est de concevoir de nouvelles approches therapeutiques du cancer. L’immunotherapie a fait la preuve de son efficacite sur des modeles experimentaux de tumeur chez l’animal. La therapie cellulaire du cancer par cellules immunocompetentes est actuellement en evaluation clinique. Dans ces strategies therapeutiques, deux approches sont en evaluation : stimuler in vivo le developpement d’une immunite protectrice, a l’aide de cellules presentatrices d’antigenes, ou encore apporter au patient des cellules effectrices eduquees in vitro.
The influence of the light environment and photosynthesis on oxidative signalling responses in plant-biotrophic pathogen interactions

Plants grow in a constantly fluctuating environment, which has driven the evolution of a highly flexible metabolism and development necessary for their sessile lifestyle. In contrast to the situation in the natural world, the detailed dissection of the regulatory networks that govern plants' responses to abiotic insults and their interaction with pathogens have been studied almost exclusively in controlled environments where a single challenge has been applied. However, the question arises of how such pathways operate when the plant is subjected to multiple stresses, especially where the expression of overlapping gene sets and common signalling molecules, such as reactive oxygen species (ROS), are implicated. This review will focus on the responsiveness of leaves to their light environment and how this might influence both basal and induced resistance to infection by biotrophic pathogens. While several signalling pathways operate in a complex network of defence responses, the functioning of the salicylic acid (SA) signalling pathway will receive specific consideration. This is because information is becoming available of its role in abiotic stress responses and it dependency on light. This article covers several topics, some of which formerly have received scant attention. These include the effects of infection on photosynthetic performance and carbohydrate metabolism, the parallels between the induction of acclimation to high light and immunity to pathogens, the role of light in the functioning of the SA signalling pathway and the light sensitivity of lesion formation and the use of lesion mimic mutants and transgenic plants. Finally, a model is proposed that attempts to extrapolate these controlled environment-based studies to the functioning of defences against pathogens in a field-grown crop.
Germination of fresh and frost-treated seeds from dry Central Asian steppes

We tested the germination of fresh and frost-treated seeds of 26 species of southern Mongolian mountain and desert steppes, covering the major growth forms of woody and herbaceous perennials and short-lived species in the region. In the field, germination depends on rains that are largely restricted to the summer months between June and August. Thus, germination tests were performed at alternating conditions of 10°C in darkness and 20°C in light (12 h/12 h), which correspond to temperatures at the study site in early and late summer. Seeds of both woody and herbaceous perennials germinated well under the chosen conditions and apparently did not require stratification or scarification. In contrast, germination of annual species was mostly below 30%, while seed viability was equally high in all three growth forms. Winter conditions, simulated by freezing dried seeds at −18°C, hardly changed seed germination in the perennial species, but several short-lived species responded with increased germination. Short-lived species are not abundant in the real vegetation, which is governed by perennials. Thus, we conclude that the important species in Mongolian mountain steppes germinate readily without a dormancy-breaking treatment. A review of the available literature revealed that a complete lack of dormancy, or presence of only conditional dormancy, is also widely described for other species of Central Asian deserts and steppes, which is in contrast to data from North American prairies.
TH1/TH2,3 Imbalance due to Cytokine‐Producing NK, γδ T and NK‐γδ T Cells in Murine Pregnancy Decidua in Success or Failure of Pregnancy

PROBLEM: Recurrent spontaneous abortion in DBA/2‐mated CBA/J mice has been attributed to the production of Th1 cytokines (tumor necrosis factor [TNF]‐α and interferon [IFN]‐γ) by asialoGM1+ natural killer (NK) cells and Vγ1. 1δ6. 3+ T cells that infiltrate decidua by day 6.5, during the peri‐implantation period. Abortions can be prevented by a second population of Vγ1. 1δ6. 3 cells, which infiltrate on day 8.5 of gestation, and produce the Th2 cytokine interleukin (IL)‐10 and Th3 cytokine transforming growth factor (TGF)‐β2. In low abortion rate immunocompetent mice, most of the TGF‐β2 is derived from γδ T cells. However, TGF‐β2‐producing cells are present in the decidua of pregnant severe combined immune deficient (SCID) mice, which lack γδ T cells. METHODS: The cells in day 13.5 decidua of CBA×DBA/2 matings and SCID×SCID matings were identified using flow cytometry and combined surface staining for γδ and/or asialoGM1, and intracellular cytokine staining for TNF‐α, IFN‐γ, and TGF‐β2,3. RESULTS: TGF‐β2 and TNF‐α were found in asialoGM1+ NK cells in SCID mouse decidua. In CBA×DBA/2 mated mice, two major and one minor subsets of cytokine‐positive cells were identified: ‐γδ‐only T cells, double positive asialoGM1+γδ+ (NK‐γδ T) cells, and a small number of asialoGM1+γδ− NK‐only cells. The NK‐only and NK‐γδ T subsets showed a greater Th1/Th2,3 pattern of intracellular staining compared with the γδ‐only subset. In the CBA×DBA/2 and SCID×SCID systems, Th1/Th2,3 ratios could not predict actual observed abortion rates but did correlate with susceptibility to abortions (if exposed to an additional stimulus such as stress). The known effect of in vivo administration of anti‐asialoGM1 antibody on abortion rates within groups of mice exposed to such stresses could also be predicted. CONCLUSION: γδ+ cells in decidua (e.g. Vγ1+ cells which can recognize trophoblasts) differ based on the presence or absence of the NK marker‐asialo‐GM1. NK‐γδ T cells may be quite important in the Th1 response in early pregnancy that predisposes to abortions in CBA×DBA/2 matings, whereas γδ T‐only cells appear to be protective. In pregnant SCID mice, the TNF‐α+/TGF‐β2+ NK population is greatly expanded. An activating stimulus (such as stress or endotoxin) appears to be as important in triggering abortions, as is the Th1/Th2,3 ratio at the feto–maternal interface.
Relation of source and sink during grain filling period in wheat and some aspects of its regulation

The effects of changes in source-sink relation and of cytokinin applications were examined with regard to the development of flag leaves and grain growth in two contrasting spring wheats, Triticum aestivum L. , cv. Kolibri and Solo, grown in hydroculture at mean day/night temperatures of 21/19°C. Lowering temperatures during the phase of ear differentiation decreased the ratio of source and sink size (flag leaf area/grains per ear) but hardly affected maximum chlorophyll content of the flag leaf (source activity), maximum rates of grain growth (sink activity), or final grain weight. Nevertheless, considerable differences were produced with regard to the duration of grain filling, the development and coordination of source and sink activities after maxima had been attained. Changing the ratio of source and sink size during grain filling by spikelet removal affected final grain weight the less, the later the treatments began. Comparing, plants with identical source activities demonstrated that differences in grain weight were mainly due to different growth rates between day 16 and 40. Source activities were raised only temporarily (day 23) by spikelet removal done at day 2 or 14. From this it may be concluded that changing the ratio of source and sink size influenced grain weight by creating different intrinsic growth potentials in the grains. These potentials might be estimated 3 weeks after ear emergence by DNA and RNA content per grain. The effects of exogenous cytokinins were consistent with those due to spikelet removal suggesting that this hormone participates in a joint regulation of source and sink activity during grain filling.
Effect of Temperature on Growth and Survival in Juvenile Opossum Pipefish, Microphis brachyurus: First Observations on the Species in Culture Conditions

In Mexico, natural populations of the opossum pipefish, Microphys brachyurus, are under pressure by anthropogenic alteration of their habitat and unregulated fishing as this species is traded as an aquarium fish, where its survival is low due to inadequate culture practices. The development of culturing techniques has been a successful strategy to protect many exploited species through providing an alternative source to wild exploitation. The aim of this study was to examine the effect on growth, condition, and survival of pipefish cultured for 6 wk at temperatures of 26, 28, and 30 C. Pipefish were fed enriched Artemia nauplii maintaining a ration rate of 14% body weight per day (dry weight Artemia : wet weight fish). The pipefish cultured at 26 and 28 C were longer, heavier, grew faster, and presented better condition than those at 30 C. The survival of pipefish cultured at 26 C was greater (83%) than at 30 C (30%) but not different than at 28 C (50%). This study is the first to report the acceptance of Artemia nauplii by juveniles of the species and that a temperature of 30 C is not suitable for juvenile M . brachyurus culture.
Using ants as bioindicators in land management: simplifying assessment of ant community responses

Summary 1. The indicator qualities of terrestrial invertebrates are widely recognized in the context of detecting ecological change associated with human land-use. However, the use of terrestrial invertebrates as bioindicators remains more a topic of scientific discourse than a part of land-management practice, largely because their inordinate numbers, taxonomic challenges and general unfamiliarity make invertebrates too intimidating for most land-management agencies. Terrestrial invertebrates will not be widely adopted as bioindicators in land management until simple and efficient protocols have been developed that meet the needs of land managers. 2. In Australia, ants are one group of terrestrial insects that has been commonly adopted as bioindicators in land management, and this study examined the reliability of a simplified ant assessment protocol designed to be within the capacity of a wide range of land managers. 3. Ants had previously been surveyed intensively as part of a comprehensive assessment of biodiversity responses to SO 2 emissions from a large copper and lead smelter at Mt Isa in the Australian semi-arid tropics. This intensive ant survey yielded 174 species from 24 genera, and revealed seven key patterns of ant community structure and composition in relation to habitat and SO 2 levels. 4. We tested the extent to which a greatly simplified ant assessment was able to reproduce these results. Our simplified assessment was based on ant ‘bycatch’ from bucket-sized (20-litre) pitfall traps used to sample vertebrates as part of the broader biodiversity survey. We also greatly simplified the sorting of ant morphospecies by considering only large (using a threshold of 4 mm) species, and we reduced sorting time by considering only the presence or absence of species at each site. In this manner, the inclusion of ants in the assessment process required less than 10% of the effort demanded by the intensive ant survey. 5. Our simplified protocol reproduced virtually all the key findings of the intensive survey. This puts effective ant monitoring within the capacity of a wide range of land managers.
SPRUCE BUDWORM DEFOLIATION IN YOUNG BALSAM FIR: THE ‘GREEN’ TREE PHENOMENON

Abstract During a severe outbreak of spruce budworm, Choristoneura fumiferana (Clem.), some balsam fir trees, Abies balsamea (L.) Mill. , remain noticeably greener than others in the same stand. We show that this ‘green’ tree phenomenon is not caused by differential defoliation in which certain trees experience consistently low defoliation pressure throughout an outbreak. Rather, these trees remain ‘green’ because of their prolific, epicormic shoot production which is consistently high during an outbreak, giving them a ‘greener’ appearance than other trees that produce lower numbers of epicormic shoots. Résumé Au cours des épidémies graves de la Tordeuse des bourgeons de l’épinette, Choristoneura fumiferana (Clem.), certains sapins baumiers, Abies balsamea (L.) Mill. , restent beaucoup plus verts que d’autres sapins du même peuplement. Ce phénomène n’est pas causé par une défoliation différentielle par laquelle certains arbres subissent une moins grande pression de défoliation que d’autres durant une épidémie. Ces arbres demeurent plus verts surtout à cause de la production plus importante de pousses adventives durant une épidémie, ce qui les rends plus verts que les autres arbres qui produisent moins de pousses adventives. [Traduit par la Rédaction]
Is Succession-based Management of Coastal Dune Forest Restoration Valid?

Habitat restoration and the theory of ecological succession are linked intrinsically. However, restoration management does not always rely on successional principles. This separation between theory and practical application may stem from the failure of succession to achieve restoration targets. Here we test the predictions of succession in a restoration context to ascertain the validity of succession-based management. Specifically we answer the following 4 questions: 1) does the rate of species turnover decrease as coastal dune forest develops; 2) is there a sequence of changing species “types” from pioneer species adapted to harsh conditions to species adapted to high levels of competition; 3) is this sequence of types directional and the same across all sites with similar climatic conditions; and 4) does species diversity increase or decrease? Our study took place in 7 coastal dune forest sites of various ages regenerating after mining disturbance. We conducted tree surveys in 1999, 2001, 2005, and 2009 and herbaceous plant surveys in 1995, 1999, 2003, and 2005. We assessed trends in species turnover, composition, diversity, richness, and evenness to see if these were congruent with successional theories. Patterns in turnover for both taxa showed a decelerating decrease. Sites of a similar age shared similar species composition of coastal dune forest trees and herbaceous plants. As sites aged, they increased in the number and diversity of species. Succession-based management is a valid approach to dune forest rehabilitation as long as restoration managers recognize disturbance as an ecological reality.
EVALUATION OF ANTIMICROBIAL ACTIVITY OF ORGANIC FRACTIONS OF SIX MARINE ALGAE FROM TUNISIAN MEDITERRANEAN COASTS

Twenty four organic extracts obtained from six marine algae: Cystoseira compressa, Cystoseira crinita, Cystoseira sedoides, Gelidium latifolium, Dictyopteris membranaceae and Halurus equisetifolius collected from Tunisian Mediterranean coasts, were evaluated for their antibacterial and antifungal activities against eight human pathogenic bacteria and five human pathogenic yeast using the agar disk diffusion assay. The results showed that all marine algae extracts exhibited a moderate activity against four bacteria strains, Staphylococus aureus, Echerichia coli, Staphylococcus epidermis and Micrococcus luteus. No activity was observed against Staphylococcus thyphymerium, Pseudomonas aeruginosa, Enterococcus feacium and Listeria monocytogenes. However, the chloroformic and the ethyl acetate extract obtained from Cystoseira crinita and Cystoseira sedoides showed a higher antifungal activity against four Candida strains. These finding suggest that the chloroformic and ethyl acetate extracts of the brown algae could be contained a new antifungal compound(s). The purification and the determination of chemical structure of compound(s) of these active extracts are under investigation.
LINKING PLANKTONIC BIOMASS AND METABOLISM TO NET GAS FLUXES IN NORTHERN TEMPERATE LAKES

Plankton communities in oligotrophic waters are characteristically dominated by the biomass of heterotrophs, including bacteria, micro-, and macrozooplankton. It has been generally assumed that these inverted biomass pyramids are the direct result of high specific production rates of phytoplankton and a tight coupling between producers and consumers. There are, however, at least two alternative hypotheses: (1) heterotrophic biomass turnover is much slower in oligotrophic than eutrophic systems; and (2) oligotrophic planktonic communities are significantly subsidized by allochthonous organic matter. In this study we assessed these hypotheses by establishing the relationship between plankton biomass structure (partition between auto- and heterotrophs), plankton function (plankton primary production and respiration) and whole-lake gas (O2 and CO2) fluxes in 20 temperate lakes that span a large range in primary production. We show that the balance of phytoplankton production and community respiration (P/R rat.
Splenectomy impairs aerobic swim performance in trout

Critical swim speed (Ucrit) measurements show that trout (Oncorhynchus mykiss) with an intact spleen perform aerobic exercise better than those without (control: Ucrit = 2.19 body lengths/s; splenectomized: Ucrit = 1.84 body lengths/s). Their better performance is correlated with higher blood haemoglobin concentration at exhaustion (control: 9.92 g/dL; splenectomized: 7.96 g/dL), derived from release of red cells from the spleen.
Stomatal, mesophyll conductance and biochemical limitations to photosynthesis as affected by drought and leaf ontogeny in ash and oak trees

Gas exchange measurements were carried out on ash and oak trees in a forest plantation during three whole growing seasons characterized by different water availability (2001, 2002 and 2003). A quantitative limitation analysis was applied to estimate the effects of drought and leaf ontogeny on stomatal ( S L ) and non-stomatal limitations ( NS L ) to light-saturated net photosynthesis ( A max ), relative to the seasonal maximum rates obtained under conditions of optimal soil water content. Furthermore, based on combined gas exchange and chlorophyll fluorescence measurements, NS L was partitioned into a diffusive (due to a decrease in mesophyll conductance, MC L ) and a biochemical component (due to a decrease in carboxylation capacity, B L ). During the wettest year (2002), the seasonal pattern of both A max and stomatal conductance ( g sw ) was characterized in both species by a rapid increase during spring and a slight decline over the summer. However, with a moderate (year 2001) or a severe (year 2003) water stress, the summer decline of A max and g sw was more pronounced and increased with drought intensity (30‐40% in 2001, 60‐75% in 2003). The limitation analysis showed that during the spring and the autumn periods S L , MC L and B L were of similar magnitude. By contrast, from the summer data it emerged that all the limitations increased with drought intensity, but their relative contribution changed. At mild to moderate water stress (corresponding to values of g sw > 100 mmol H 2 O m