Extracting abundance information from DNA-based data

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet reconstruction and quantitative food webs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, capture bias, capture noise, species pipeline biases, and pipeline noise all combine to inject error into DNA-based datasets. We focus on methods for correcting the latter two error sources, as the first two are addressed extensively in the ecological literature. To extract abundance information, it is useful to distinguish two concepts. (1) Across-species quantification describes relative species abundances within one sample. (2) In contrast, within-species quantification describes how the abundance of each individual species varies from sample to sample, as in a time series, an environmental gradient, or different experimental treatments. Firstly, we review methods to remove species pipeline biases and pipeline noise. Secondly, we demonstrate experimentally (with a detailed protocol) how to use a 'DNA spike-in' to remove pipeline noise and recover within-species abundance information. We also introduce a statistical estimator that can partially remove pipeline noise from datasets that lack a physical DNA spike-in.

Effect of Nitrogen Rate and Application Ratio on Late Sown Sunflower in Wet Soil under Zero Tillage in the Coastal Zone of Southwestern Bangladesh

Background: The cropping pattern of southwestern (SW) coastal Bangladesh has been improving from Fallow-Fallow-Transplanted aman paddy to Sunflower-Fallow-Transplanted aman paddy. The emerging cropping pattern of SW Bangladesh from single transplanted aman paddy to double cropping, sunflower in winter after transplanted aman paddy needs new crop husbandry including nutrient management particularly nitrogen (N). Hence, the present study aimed to evaluate the yield response of late sown sunflower to rates and application ratio (basal:top dressed) of N in the coastal soil of SW Bangladesh. Methods: The field experiment was conducted during winter season (2018-19) in a randomized complete block design and replicated thrice. The experimental treatments consisted of seven N rates (0, 60, 90, 120, 150, 180 and 210 kg ha-1) and three application ratio (50%:50%, 25%:75% and 0%:100%). Result: Results revealed that with the increased of N rates, dry matter, seed yield, yield attributes and net income were substantially increased: the highest values of these parameters were found at 150 and 180 kg N ha-1 when applied @ ratio of 25%:75% (basal: top dressed) despite non-significant interaction while the agronomic efficiency was higher at 60 kg ha-1 next decreased. The findings of the study suggested that N @ 150 kg ha-1 with 25%:75% application ratio is suitable for late sown sunflower in the coastal soil of SW Bangladesh.

Productivity of switchgrass (Panicum virgatum L.) agrophytocenoses for long-term use

Purpose. To determene the productivity of switchgrass (Panicum virgatum L.) agrophytocenoses under the long-term use. Methods. Field, statistical, calculation and comparative. Results. During long-term switchgrass cultivation, the lowest yield was obtained in the first vegetation year: 19.7 t/ha in the control treatment, 25.3 and 17.5 t/ha in the experimental treatments. The average raw biomass yield was as following: 30.3 t/ha in the control (variety ‘Cave-in-Rock’), 32.6 t/ha and 26.5 t/ha in the experimental treatments (varieties ‘Kanlow’ and ‘Morozko’, respectively). The yield of solid biofuel (17.3 t/ha) indicates the advantage of ‘Kanlow’ over the control (11.7 t/ha). The lowest yield (15.7 t/ha) was obtained from ‘Morozko’ variety. The energy yield over the treatments: 312.8 GJ/ha in the control, 397.5 and 367.2 GJ/ha in the experimental treatments, respectively. The cost of the grown production was as following: 416.03 UAH/t in the control (‘Cave-in-Rock’), 312.01 UAH/t in ‘Kanlow’, and 366.42 UAH/t in ‘Morozko’. The profitability of the control (‘Cave-in-Rock’) was 69.5%, ‘Kanlow’ – 101.4%, ‘Morozko’ – 66.8%. Economic evaluation of the productivity of switchgrass agrophytocenoses resulted in the following ranking: ‘Kanlow’, ‘Cave-in-Rock’, ‘Morozko’. When analyzing the energy equivalent of switchgrass biomass production and energy consumption, it was found that ‘Kanlow’ yielded 588.8 GJ/ha and the control – 468.3 GJ/ha, which is lower by 120.5 GJ/ha. Conclusions. The yield of switchgrass agrophytocenoses on average over the years of research (2014–2019) was 30.3 t/ha in ‘Cave-in-Rock’ (the control), 32.6 t/ha in ‘Kanlow’, and 26.5 t/ha in ‘Morozko’. The energy equivalent of the obtained yield was 468.3 GJ/ha in ‘Cave-in-Rock’ and 588.8 GJ/ha in ‘Kanlow’, which is by 120.5 GJ/ha higher than in the control.

Neonatal and fetal therapy of congenital diaphragmatic hernia-related pulmonary hypertension

Congenital diaphragmatic hernia (CDH) is a complex malformation characterised by a triad of pulmonary hypoplasia, pulmonary hypertension (PH) and cardiac ventricular dysfunction. Much of the mortality and morbidity in CDH is largely accounted for by PH, especially when persistent beyond the neonatal period and refractory to available treatment. Gentle ventilation, haemodynamic optimisation and pulmonary vasodilation constitute the foundations of neonatal treatment of CDH-related PH (CDH-PH). Moreover, early prenatal diagnosis, the ability to assess severity and the developmental nature of the condition generate the perfect rationale for fetal therapy. Shortcomings of currently available clinical therapies in combination with increased understanding of CDH pathophysiology have spurred experimental drug trials, exploring new therapeutic mechanisms to tackle CDH-PH. We herein discuss clinically available neonatal and fetal therapies specifically targeting CDH-PH and review the most promising experimental treatments and future research avenues.

Diallyl-n-Sulfide of Garlic Inhibits Glycogenolysis in Heat-Stressed Laying Sentul Chicken

Heat stress causes a decrease in metabolic function and immunity, which results in a decrease in production. The provision of natural extracts such as the active compound dyally n-suldifa (Dn-S) is one strategy to overcome the adverse effects of heat stress. One hundred and twenty-five female laying native chickens, with an average body weight of 1213.83±15.52 g, 40 weeks old, were used in this experiment, to study the impact of Dn-S administration from garlic on the metabolite profile of the glycogenolysis pathway. laying. Laying hens were distributed into five treatment groups, each with 25 samples. Dn-S isolation from garlic isolated by distillation technique. The study was carried out with five types of experimental treatments, as follows the group with a comfort zone temperature (24°C) and without the administration of Diallyl n-Sulfide (Dn-S), heat stress (38°C) and without Dn-S, heat stress (38°C) and 100 µL Dn-S, heat stress (38°C) and 125 µL Dn-S, heat stress (38°C) and 150 µL Dn-S/head. Based on the results of the study, it was shown that heat stress causes an increase in the rate of glycogenolysis and intermediate metabolites and their catalyzing enzymes. It appears that the administration of 150 µL Dn-S, effectively reduces the rate of glycogenolysis. It was concluded that heat stress on laying hens could be avoid by administering garlic Dn-S.

Evaluating the Role of Breathing Guidance on Game-Based Interventions for Relaxation Training

Working in a fast-paced environment can lead to shallow breathing, which can exacerbate stress and anxiety. To address this issue, this study aimed to develop micro-interventions that can promote deep breathing in the presence of stressors. First, we examined two types of breathing guides to help individuals learn deep breathing: providing their breathing rate as a biofeedback signal, and providing a pacing signal to which they can synchronize their breathing. Second, we examined the extent to which these two breathing guides can be integrated into a casual game, to increase enjoyment and skill transfer. We used a 2 × 2 factorial design, with breathing guide (biofeedback vs. pacing) and gaming (game vs. no game) as independent factors. This led to four experimental groups: biofeedback alone, biofeedback integrated into a game, pacing alone, and pacing integrated into a game. In a first experiment, we evaluated the four experimental treatments in a laboratory setting, where 30 healthy participants completed a stressful task before and after performing one of the four treatments (or a control condition) while wearing a chest strap that measured their breathing rate. Two-way ANOVA of breathing rates, with treatment (5 groups) and time (pre-test, post-test) as independent factors shows a significant effect for time [F(4, 50) = 18.49, p &lt; 0.001, ηtime2=0.27] and treatment [F(4, 50) = 2.54, p = 0.05, η2 = 0.17], but no interaction effects. Post-hoc t-tests between pre and post-test breathing rates shows statistical significance for the game with biofeedback group [t(5) = 5.94, p = 0.001, d = 2.68], but not for the other four groups, indicating that only game with biofeedback led to skill transfer at post-test. Further, two-way ANOVA of self-reported enjoyment scores on the four experimental treatments, with breathing guide and game as independent factors, found a main effect for game [F(1,20)=24.49,p<0.001, ηgame2=0.55], indicating that the game-based interventions were more enjoyable than the non-game interventions. In a second experiment, conducted in an ambulatory setting, 36 healthy participants practiced one of the four experimental treatments as they saw fit over the course of a day. We found that the game-based interventions were practiced more often than the non-game interventions [t (34) = 1.99, p = 0.027, d = 0.67]. However, we also found that participants in the game-based interventions could only achieve deep breathing 50% of the times, whereas participants in the non-game groups succeeded 85% of the times, which indicated that the former need adequate training time to be effective. Finally, participant feedback indicated that the non-game interventions were better at promoting in-the-moment relaxation, whereas the game-based interventions were more successful at promoting deep breathing during stressful tasks.

L-Arginine Supplementation for Nulliparous Sows during the Last Third of Gestation

We evaluated the effects of L-arginine supplementation during the last third of gestation on molecular mechanisms related to skeletal muscle development of piglets and litter traits at birth. Twenty-three nulliparous sows averaging 205.37 ± 11.50 kg of body weight were randomly assigned to the following experimental treatments: control (CON), where pregnant sows were fed diets to meet their nutritional requirements; arginine (ARG), where sows where fed CON + 1.0% L-arginine. Skeletal muscle from piglets born from sows from ARG group had greater mRNA expression of MYOD (p = 0.043) and MYOG (p ≤ 0.01), and tended to present greater mRNA expression (p = 0.06) of IGF-2 gene compared to those born from CON sows. However, there were no differences (p > 0.05) in the histomorphometric variables of fetuses’ skeletal muscle. The total weight of born piglets, total weight of born alive piglets, piglet weight at birth, coefficient of variation of birth weight, and the incidence of intrauterine growth restriction (IUGR) piglets did not differ between groups. No stillborn piglets (p < 0.01) were verified in the ARG sows compared to CON group. The blood levels of estradiol (p = 0.035) and urea (p = 0.03) were higher in ARG sows compared to those from the CON group. In summary, our data show that arginine supplementation of nulliparous sows at late gestation enhance mRNA expression of key myogenic regulatory factors, which likely contribute to improve animal growth rates in later stages of development.

Herbal Plants as Feed Additives in Broiler Chicken Diets

This study evaluated the effect of some herbal plants as natural feed additives on broiler production parameters, carcass parts, and breast meat quality. A total of 150 broiler chicks, Cobb 500 hybrid, were allocated to five treatments with 30 broilers /group, for 42 days. The experimental treatments were: Control (C); a diet containing 5% alfalfa meal (A); a diet containing 5% alfalfa meal and 1% basil (AB); a diet containing 5% alfalfa and 1% thyme (AT) and a diet containing 5% alfalfa and 1% sage (AS). Bodyweight was significantly (P<0.05) affected in AS group compared with C and A groups. Feed conversion ratio was significantly higher only in A and AB groups. Experimental groups had significantly greater (P<0.05) gizzard weight. The total polyphenols content and the antioxidant capacity were significantly (P<0.05) higher in AB, AT, and AS groups versus the C group. The cholesterol concentration was significantly (P<0.05) decreased in AB, AT, and AS meat samples compared with C and A samples. Instrumental colour measurements indicated significant alterations (P<0.05) among the groups regarding the values of L*, a*, b*, H°, C*, and ΔE*. The texture analysis showed that hardness, gumminess, and chewiness were significantly (P<0.05) higher in AB, AT, and AS groups than in C and A groups.

INTERNAL QUALITIES OF EGG(S) OF LAYING BIRDS FED DIETS CONTAINING VERNONIAAMYGDALINALEAF (BITTER LEAF) MEAL AT DIFFERENT GROWING PHASES

One hundred and twenty eight Isa-Brown pullet chicks were used for this study to determine the internal qualities of egg(s) from birds fed diets containing Vernoniaamygdalina leaf meals at different growing phases. The leaves used were air-dried, crushed and milled, and was then incorporated into the experimental treatments (T2, T3, and T4) at 2% inclusion each. The birds were randomly allotted into four dietary treatments (T1, T2, T3 and T4) and each treatment was replicated four times with each replicate having 8 birds from the chick phase to the growing phase, thereafter 6 birds per replicate were randomly picked at the laying phase (point of cage), with T1 serving as the control treatment throughout the experimental period of 39weeks. The parameters measured include egg weight, shell weight, shell thickness, shell height, yolk weight, yolk height, yolk width, albumin length, albumin height, albumin weight, while yolk index and Haugh unit were calculated. The result of the experiment showed that T3 with 2% inclusion of Vernoniaamygdalinafrom the growing phase had the best shell thickness, yolk color and acceptable value for Haugh unit. Other parameters measured showed that yolk weight, and Haugh unit were significant at (p<0.05) with 2% inclusion of Vernoniaamygdalina. Every other parameter measured showed no significant difference across the treatments at (p>0.05). The result showed that 2% inclusion of Vernoniaamygdalinaleaf meal at the growing phase of the experiment improved the internal qualities of eggs.

Micropropagation of Raspberries (Rubus idaeus L.) in Liquid Media by Temporary Immersion Bioreactor in Comparison with Gelled Media

Temporary Immersion Bioreactor (TIB) is a suitable technique for large scale micropropagation of plant species. The aim of this work was to test the capacity of in vitro proliferation of the primocane-fruiting red raspberry cv Maravilla and floricane-fruiting red raspberry cv Willamette on gelled media compared to liquid media. The two varieties were cultured in vitro on two media, Murashige and Skoog 1962 (MS) and Driver and Kuniyuki walnut medium, 1984 (DKW), both supplemented with 0.5 mg/l 6-benzyladenine (BA). In the control cultures on gelled media the media were gelled with 5g/l Plant Agar, whereas for the cultures in liquid media Plantform bioreactors were used. After six weeks of in vitro culture we recorded the proliferation rates and lengths of the axillary shoots obtained in all the experimental treatments. The highest proliferation rate was 16 ± 2.03, obtained in cv. Willamette on gelled MS medium with 0.5 mg/l BA. The longest shoots (3.17 ± 0.32 cm) were obtained at cv. Maravilla on the DKW medium with 0.5 mg / l BA in the bioreactor. Our research highlighted that Rubus idaeus L. Maravilla and Willamette can be TIB propagated, although further research is needed to improve the efficiency of this method.