Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

The Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high concentrations of reactive iron, methane, and ammonium in its sediments, enabling the activity and interactions of many microbial guilds. Here, we studied the microbial network in these sediments by analyzing geochemical and microbial community depth profiles at one offshore and two near coastal sites. Analysis of 16S rRNA gene amplicons revealed a distinct depth stratification of both archaeal and bacterial taxa. The microbial communities at the two near coastal sites were more similar to each other than the offshore site, which is likely due to differences in the quality and rate of organic matter degradation. The abundance of methanotrophic archaea of the ANME‐2a clade was shown to be related to the presence of methane and varied with sediment iron content. Metagenomic sequencing of sediment‐derived DNA from below the sulfate–methane transition zone revealed a broad potential for respiratory sulfur metabolism via partially reduced sulfur species. The potential for nitrogen cycling was dominated by reductive processes via a truncated denitrification pathway encoded exclusively by bacterial lineages. Gene‐centric fermentative metabolism analysis indicated a potential importance for acetate, formate, alcohol, and hydrogen metabolism. Methanogenic/‐trophic pathways were dominated by Methanosaetaceae, Methanosarcinaceae, Methanomassiliicoccaceae, Methanoregulaceae, and ANME‐2 archaea. Our results indicated flexible metabolic capabilities of core microbial community taxa, which could adapt to changing redox conditions, and with a spatial and depth distribution that is likely governed by the quality and input of available organic substrates and, for ANME‐2, of iron oxides.
Estudios histológicos del proceso de embriogénesis somática en palma Coco Cumbé (Parajubaea cocoides Burret) a partir de embriones cigóticos inmaduros

The aim of the present research was to determinate the type of tissue present in a sample obtained from an embryogenic callus of Coco Cumbe Palm, Parajubaea cocoides Burret and somatic embryos on globular stage. For this purpose, in order to the protocol established in the histotechnology analysis procedure manual of Patology Service from "Carlos Andrade Marin" Hospital (HCAM, according its acronyms in Spanish) was proceeded located in Quito, Pichincha, Ecuador. The results showed that the embryogenic calli are conformed by meristematic cells and although present cells with starch granules near to embryogenic cells, indicating embryos formation. In somatic embryos case, was verified that these were in globular stage, because of these showed a characteristic structure of the first development stage, named protoderm. Therefore was determined that calli present distinctive characteristics of embryogenic competence and viability of the somatic embryos.
The Contrasting Responses of Mycorrhizal Fungal Mycelium Associated with Woody Plants to Multiple Environmental Factors

Research Highlights: Extraradical mycorrhizal fungal mycelium (MFM) plays critical roles in nutrient absorption and carbon cycling in forest ecosystems. However, it is often ignored or treated as a root uptake apparatus in existing biogeochemical models. Methods: We conducted a meta-analysis to reveal how MFM responds to various, coinciding environmental factors and their interactions. Results: Nitrogen (N) addition and N-phosphorus (P)-potassium (K) combination significantly decreased MFM. However, elevated CO2, organic matter addition, P addition, and CO2-N combination significantly increased MFM. In contrast, warming, K addition, N-P combination, and P-K combination did not affect MFM. Mycorrhizal fungal levels (individual vs. community), mycorrhizal type (ectomycorrhizal fungi vs. arbuscular mycorrhizal fungi), treatment time (<1 year vs. >1 year), and mycelium estimation/sampling method (biomarker vs. non-biomarker; ingrowth mesh bag vs. soil core) significantly affected the responses of MFM to elevated CO2 and N addition. The effect sizes of N addition significantly increased with mean annual precipitation, but decreased with soil pH and host tree age. The effect sizes of P addition significantly increased with N concentration in host plant leaves. Conclusions: The differential responses revealed emphasize the importance of incorporating MFM in existing biogeochemical models to precisely assess and predict the impacts of global changes on forest ecosystem functions.
Effect of canola (Brassica napus) cultivar rotation on Plasmodiophora brassicae pathotype composition

Abstract: In Canada, clubroot (Plasmodiophora brassicae) disease is managed mainly by planting clubroot resistant (CR) canola (Brassica napus). New pathotypes of P. brassicae have emerged recently, however, which are virulent on most CR canola cultivars. To understand the impact of cultivar rotation on pathotype abundance, greenhouse experiments were conducted in which different canola cultivar rotations were grown in a soil mix containing equal amounts of pathotypes 5X and 3, which are virulent and avirulent, respectively, on CR canola. The rotation treatments included: T1, the same susceptible cultivar planted over four cycles; T2, the same CR cultivar planted over four cycles; and T3, different CR cultivars planted in each cycle. Clubroot severity increased from cycles one to four in all treatments, with the exception of one CR cultivar in T3 that may carry a different source of resistance. Pathogen populations were recovered with a susceptible bait crop and pathotyped on the differentials of Williams plus a CR host (B. napus ‘Mendel’). The percentage of galls classified as pathotype 5X in T1 declined from 50% to 6.7% over the course of the experiment, while galls classified as pathotype 5X increased from 50% to 66.7% in both T2 and T3. Quantitative PCR analysis of the soil with pathotype 5X-specific primers generally confirmed an increase in 5X DNA. The results suggest that continuous planting of CR canola favours a rapid proliferation of virulent pathotypes of P. brassicae, as indicated by the increases in pathotype 5X observed in this study.
BIOCHEMICAL EVALUATIONS OF QUINALPHOS EXPOSED ZEBRAFISH LIVER ORGANOTYPIC TISSUE CULTURE

As being a broad-spectrum, organophosphorus insecticide and acaricide, quinalphos is widely used against a range of pests and has a great threat to aquatic systems. Although the methods for detecting and predicting the harmful effects of chemicals on non-target organisms are traditionally perfected by in vivo experiments, cell culture methods that were used widely in recent decades are also an important tool for these kinds of research. In order to evaluate the effects of quinalphos on liver organotypic culture system of zebrafish, tissue cubes (1-2 mm3) were prepared by dissection and slicing of the liver tissues, embedded in agarose and cultured. The cubes were exposed to three different concentrations of quinalphos (2, 4 and 8 mg/L) for 24 and 96 hours. By performing the comet assay as an emerging tool for cytotoxicity, it was detected that quinalphos causes DNA damage. Increased levels of catalase, superoxide dismutase and glutathione-s-transferase were also measured. All of these parameters were noted as concentration- and time-dependent. Our data suggest that organotypic liver tissue culture of zebrafish is a practical alternative to the whole fish.
Quantitative and qualitative consequences of reduced pollen loads in a mixed‐mating plant

Abstract Greater pollination intensity can enhance maternal plant fitness by increasing seed set and seed quality as a result of more intense pollen competition or enhanced genetic sampling. We tested experimentally these effects by varying the pollen load from a single pollen donor on stigmas of female flowers of Dalechampia scandens (Euphorbiaceae) and measuring the effects on seed number and seed mass. Seed set increased rapidly with pollen number at low to moderate pollen loads, and a maximum set of three seeds occurred with a mean pollen load of 19 pollen grains. We did not detect a trade‐off between the number of seeds and seed mass within a fruit. Seed mass increased with increasing pollen load, supporting the hypothesis of enhanced seed quality via increased pollen‐competition intensity or genetic sampling. These results suggest that maternal fitness increases with larger pollen loads, even when the fertilization success is already high. Our results further highlight the importance of high rates of pollen arrival onto stigmas, as mediated by reliable pollinators. Comparing the pollen‐to‐seed response curve obtained in this experiment with those observed in natural populations suggests that pollen limitation may be more severe in natural populations than predicted from greenhouse studies. These results also indicate that declines in pollinator abundance may decrease plant fitness through lowered seed quality before an effect on seed set is detected.
Comparative study of spirometric parameters between active tobacco smokers and tobacco non-smokers

Aim of this study is to study effect of smoking on various spirometric parameters like forced vital capacity (FVC) , forced expiratory volume in 1 second (FEV1) and FEV1 / FVC ratio in apparently healthy tobacco smokers and nonsmokers and to compare the result of both the studies to assess the effects of smoking. The present study was carried out by computerized software of Pulmonary Function Test named ‘Spiro Excel’ on 50 non-smokers and 50 smokers. Smokers are divided in three gropus. Full series of test take 4 to 5 minutes. Tests were compared in the both smokers and non-smokers group by the ‘unpaired t test’. Statistical significance was indicated by ‘p’ value < 0.05. From the result it is found that actual value of spirometric parameters are significantly lower in all smokers group than non-smokers.
Altered motoneuron properties and spinal serotonin contribute to motor deficits in a rabbit hypoxia ischemia model of cerebral palsy

Cerebral palsy (CP) is caused by a variety of factors attributed to early brain damage, resulting in permanently impaired motor control, marked by muscle stiffness and spasticity. To find out if altered physiology of spinal motoneurons could contribute to movement deficits, we performed whole cell patch clamp in neonatal rabbit spinal cord slices after developmental injury at 79% gestation. After preterm hypoxia-ischemia (HI) rabbits are born with muscle stiffness, motor deficits, and increased levels of serotonin (5HT) in the spinal cord. There is a range in severity, thus kits are classified as severely affected, mildly affected, or unaffected based on modified Ashworth scores and other behavioral tests. At postnatal day 0-5, we recorded electrophysiological parameters of 40 motoneurons and a subset of 12 were tested for sensitivity to 5HT. Using a multivariate analysis of neuronal parameters, we found significant differences between severe, mild, unaffected and sham control motoneurons. Severe HI motoneurons showed more sustained firing patterns, depolarized resting membrane potential, and increased instantaneous firing frequency. Interestingly changes in persistent inward currents (PICs) and morphology in severe HI motoneurons do not appear to contribute to excitability. However, severe HI motoneurons were more responsive to αmethyl5HT than sham controls. Since there are higher levels of spinal serotonin in vivo, this would further increase excitability of severe motoneurons and promote muscle stiffness. In summary, changes we observed in spinal motoneuron physiology likely contribute to severity of the phenotype, and therapeutic strategies for CP could target excitability of spinal motoneurons.
Genetic and Heritability Estimation of Water Apple (Syzygiumaqueum (Burm.f.) Alston)

Nine different accessions of water apples were evaluated at Indonesian Tropical Fruit Research Institute(ITFRI), Solok, West Sumatera from January 2013 to December 2014. This present study was aimed to evaluate the variability, heritability, genetic advance and its characters in nine different accessions to provide useful information in the improvement program of water apples. The research used Randomized Complete Block Design (RCBD) with two replications. The ANOVA results exposed significant differences at 5% probability level for all characters. Genotypic variance on fruit weight, fruit length, fruit diameter, leaf length were broad. However, the genotypic variance on total soluble solids, leaf width were narrow. The phenotypic variation for all characters was broad. The heritability estimation was categorized as low, moderate, and high. High heritability estimation was recorded for fruit weight, fruit length, fruit diameter, and leaf diameter. Moderate heritability estimation was noticed for total soluble solids. Leaf width had low heritability estimation. High heritability and high genetic advance were observed on fruit weight.
Structural changes of the microplankton community following a pulse of inorganic nitrogen in a eutrophic river

Global change will increase the number and severity of extreme events resulting in strongly pulsed nutrient loading to rivers. Recent studies indicate the potential for rapid plankton shifts as short‐term response to storm events and highlight the need for high‐frequency methods to understand these complex processes. Here, we studied the effects of a strong short‐term pulse of ammonium nitrate in a eutrophic temperate river that elevated nitrate‐N concentrations from 3.1 to 10–55 mg L−1. An intense phytoplankton bloom increased chlorophyll a concentrations from below 10 μg L−1 to over 140 μg L−1 despite of high background N concentrations and followed the N‐pulse downstream. High‐throughput sequencing revealed the temporal dynamics of the bacterial (16S rRNA gene) and microeukaryotic (18S rRNA gene) community throughout the event. Bacterial and microeukaryotic community richness was reduced, and community composition changed significantly during the bloom. Few microeukaryote taxa (e.g., Cyclotella meneghiniana, Chlamydomonas) dominated the bloom and replaced the rich summer phytoplankton community. Long‐term monitoring data (2008–2016) using classical microscope analyses showed that seasonal shifts in phytoplankton community composition were linked to physical parameters and nutrient availability with P‐limitation observed in spring but not in summer. We conclude that a disturbance in abiotic and biotic control factors, such as caused by a nutrient pulse, can induce structural shifts in the microplankton community leading to a phytoplankton bloom, even in eutrophic waters.
Dispersal limitation relative to environmental filtering governs the vertical small‐scale assembly of soil microbiomes during restoration

1. Uncovering the plant-soil feedback mechanisms underlying the assembly of belowground microbial communities is essential for terrestrial biodiversity conservation. However, little is known about the small-scale spatial assembly processes of distinct soil microorganisms, especially during natural restoration of ex-arable ecosystems. 2. We examined the spatial structure of soil microbiomes in arable land and reforested soils to elucidate the underlying assembly processes at a small spatial scale. The analysis was based on a MiSeq sequencing database, detecting the diversity of archaeal, bacterial and fungal communities, simultaneously, from 300 soil samples along vertical and horizontal profiles during 30-year reforestation. 3. Compared with environmental filtering, dispersal limitation made crucial contributions to microbial community assembly. Archaeal and bacterial communities with a wider niche breadth were governed
The artificial substrate preference of invertebrates in Ogbe Creek, Lagos, Nigeria

The colonisation patterns of the invertebrates of Ogbe Creek on four different types of artificial substrates (Kakaban, gravel bucket, glass and wood) was investigated within the period of September and November, 2002. A total number of 100,700/cm invertebrates comprising of 33 species were harvested. The gravel bucket supported the highest number of invertebrates, 46,740/cm comprising 17 species, while the glass substrate had the lowest number of invertebrate’s 2,100 /cm comprising 11 species (p < 0.05). The Kakaban substrate had the highest species richness (5.55) while the wood had the lowest (2.78). The four artificial substrates showed selectivity with respects to the organism that colonised them. The ability of the invertebrates to colonise artificial substrates was found to be influenced by the nature and permanence of the substrate. [Life Science Journal. 2007; 4(3): 77 – 81] (ISSN: 1097 – 8135).
piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions

piRNA clusters are thought to repress transposable element activity in mammals and invertebrates. Here we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: the total size of the piRNA clusters of an organism ought to exceed 0.2% of a genome. Larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high and TE insertions recessive. If piRNA clusters are too small the load of deleterious TE insertions accumulating during a TE invasion may drive populations extinct before an effective piRNA based defence against the TE can be established. Our finding is solely based on three well supported assumptions: i) TEs multiply withing genomes, ii) TEs are mostly deleterious and iii) piRNA clusters act as transposons traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, piRNA clusters of some species meet our minimum size requirements while clusters of other species don’t. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.
Arc Regulates Transcription of Genes for Plasticity, Excitability and Alzheimer’s Disease

The immediate-early gene Arc is a master regulator of synaptic function and a critical determinant of memory consolidation. Arc protein is localized to excitatory synapses, where it controls AMPA receptor endocytosis, and to the nucleus, where it associates with Tip60, a subunit of a chromatin modifying complex. Here we show that Arc interacts with dynamic chromatin loops and associates with histone markers for active enhancers and transcription in cultured hippocampal neurons. When Arc induction by pharmacological network activation was prevented using a short hairpin RNA, the expression profile was altered for over 1900 genes. Many gene families were affected by the absence of Arc, most notably those associated with synaptic function, neuronal plasticity, intrinsic excitability (channels, receptors, transporters), and signaling pathways (transcription factors/regulators). Interestingly, about 100 genes whose activity-dependent expression level depends on Arc are associated with the pathophysiology of Alzheimer’s disease, suggesting a critical role for Arc in the development of neurodegenerative disorders. When endogenous Arc expression was induced in a non-neuronal cell line (HEK293T), the transcription of many neuronal genes was increased, suggesting Arc can control expression in the absence of activated signaling pathways. Taken together, these data establish Arc as a master regulator of neuronal activity-dependent gene expression and a significant factor underlying the pathophysiology Alzheimer’s disease.
Antinociceptive efficacy of preemptive intrathecal administration of CRH in rats

Objective To investigate whether preemptive intrathecal administration of CRH has an antinociceptive efficacy on inflammatory pain model rats. Methods The antinociceptive efficacy of preemptive intrathecal administration of CRH was evaluated by the flinch-licking time and the tail flicking latency in formalin-subjected pain model rats. The c-fos gene expression in spinal cord dorsal horn was analyzed by immunohistochemical technique and computer image technique. Results Comparing with NS control group, preemptive intrathecal administration of 0.5 μg CRH could markedly inhibit the phase Ⅱpain reaction and meanwhile decrease c-fos gene expression by 25.02% in the superficial lamella of spinal cord dorsal horn of the model rats. The antinociceptive efficacy could be counteracted by preemptive intraperitoneal injection of CP-154526 (the specific antibody of CRHR1, 10 mg/kg). Conclusion CRH could significantly inhibit pain reaction and spinal cord c-fos gene expression, and thereby preemptive intrathecal administration of CRH will contribute to the antinociceptive efficacy because of its potency of inhibiting hyperalgesia.
Embryogenic callus formation in Dioscorea rotundata Poir cv. `Blanco de Guinea'

Yam contributes to energy and nutritional requirements of most of the population of developing countries. However, their extensive culture is constrained by the limited availability of planting material with physiological and sanitary quality, and also part of the harvesting is used as seed in the next planting. For this reason, it is necessary to establish a methodology for plant regeneration and somatic embryogenesis could facilitate their micropropagation and genetic improvement. This study aimed to form embryogenic callus in Dioscorea rotundata Poir cv. ‘White Guinea’. The effect of the addition of 2,4-dichlorophenoxyacetic acid (2,4-D) (0, 1.0, 2.0 and 4.0 mg l-1) was determined, in combination with three types of explants from in vitro plants (leaves petiole, petiole segments and root sections). The highest percentage of embryogenic callus was obtained with 1.0 mg l-1 2,4-D and leaves with petiole as explants. These were characterized by the presence of compact whitish nodules.