Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome profiling of lentil in response to Ascochyta lentis infection

Aim of study: The purpose was to identify some general and genotypic-specific defense responses, in order to obtain a set of candidate genes presumably involved in the resistance. Area of study: The experiment was carried out in Leon, Spain. Material and methods: We have analyzed the response of three lentil genotypes to Ascochyta lentis (isolate AL 84) at transcriptomic level using the Massive Analysis of cDNA Ends (MACE) technique: the susceptible cultivar 'Lupa', the moderately resistant 'ILL5588' and the resistant wild accession 'BG 16880' ( L. culinaris subsp. orientalis ). Main results: MACE results yielded a total of 50,935 contigs. The average number of detected contigs in each of the six samples was approximately of 40,000. In response to Ascochyta infection, the jasmonic acid pathway and the lignin biosynthesis were up-regulated in resistant genotypes, while they were down-regulated in the susceptible one. The response to chitin, the salicylic pathway and the auxin response were activated only in the resistant L. c. culinaris genotype, while the giberellin synthesis was only induced in the susceptible L. c. culinaris cv. 'Lupa'. A set of 18 lentil gene sequences putatively involved in the response to the pathogen were validated by RT-qPCR. Research highlights: It can be concluded that in response to the infection by Ascochyta , the lignin biosynthesis and the JA pathway were critical for the resistance, while the giberellin synthesis seems to be related with susceptibility to the pathogen.
An assessment of environmental metabarcoding protocols aiming at favouring contemporary biodiversity in inventories of deep-sea communities

The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly under target of resource-extraction industries although being drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased towards describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on DNA metabarcoding biodiversity inventories targeting prokaryotes (16S-V4V5), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed towards small fragments, we evaluated the effect of removing short DNA fragments via size-selection and ethanol reconcentration using DNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by DNA and RNA co-extracted from 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using environmental RNA (eRNA). With ribosomal loci, RNA, while resolving similar spatial patterns than co-extracted DNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to over-abundance of rRNA and RNA release. With the mitochondrial locus, RNA detected lower metazoan richness and resolved less spatial patterns than co-extracted DNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (≥10 g) for accurately surveying eukaryotic diversity. We conclude that DNA should be favoured over RNA for logistically realistic, repeatable, and reliable surveys, and confirm that large sediment samples (≥10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.
Biofilm rupture by laser-induced stress waves increases with loading amplitude, independent of location

Integral to the production of safe and biocompatible medical devices is to determine the interfacial properties that affect or control strong biofilm adhesion. The laser spallation technique has recently emerged as an advantageous method to quantify biofilm adhesion across candidate biomedical surfaces. However, there is a possibility that membrane tension is a factor that contributes to the stress required to separate biofilm and substrate. In that case, the stress amplitude, controlled by laser fluence, that initiates biofilm rupture would vary systematically with location on the biofilm. Film rupture, also known as spallation, occurs when film material is ejected during stress wave loading. In order to determine effects of membrane tension, we present a protocol that measures spall size with increasing laser fluence (variable fluence) and with respect to distance from the biofilm centroid (iso-fluence). Streptococcus mutans biofilms on titanium substrates serves as our model system. A total of 185 biofilm loading locations are analyzed in this study. We demonstrate that biofilm spall size increases monotonically with laser fluence and apply our procedure to failure of non-biological films. In iso-fluence experiments, no correlation is found between biofilm spall size and loading location, thus providing evidence that membrane tension does not play a dominant role in biofilm adhesion measurements. We recommend our procedure as a straightforward method to determine membrane effects in the measurement of adhesion of biological films on substrate surfaces via the laser spallation technique. Graphical Abstract
Birth Weight and Body Measurements of Purebred and Crossbred Belgian Blue Calves

The Belgian Blue (BB) is a breed of cattle characterized by double muscling. Introduction of Belgian Blue cattle to Indonesian is to increase beef production. A preliminary study was done to compare birth weight and body measurements of purebred BB calves to F1 BB x Friesian Holstein (FH) calves. A total of 10 purebred BB calves and 20 F-1 BB x FH calves were used in this study. Results showed that birth weight and chest girth were significantly affected by genotype of calves (P<0.05). The purebreds had higher birth weight and chest girth (P<0.05). The birth weight were 54.82 kg and 42.86 kg for purebreds and crossbreds, respectively. The body height were 75.30 cm and 76.35 cm for purebreds and crossbreds, respectively. The body length were 66.96 cm and 66.33 cm for purebreds and crossbreds, respectively. The chest girth were 88.46 cm and 81.15 cm for purebreds and crossbreds, respectively. This study was a preliminary information used for recommendation in developing BB cattle.
Simultaneous assessment of P50, MMN, ERN and P300 event-related potentials among patients with Schizophrenia – an exploratory study

Purpose P50 suppression (sensory gating or inhibition), MMN (mismatch negativity; bottom-up detection of change), ERN (error related negativity; conflict monitoring) and P300 (attention allocation and memory updating for salient events) are event related potentials (ERPs) widely reported to show abnormal cognitive functioning among patients with schizophrenia. In real-life scenarios the brain processing underlying these ERPs occur simultaneously, and yet prior ERP studies have evaluated them in isolation. The current study uses a novel paradigm that can examine these multiple ERPs simultaneously, and explore if the reported ERP deficits would hold true during a more realistic setting. Method Data from 21 patients with schizophrenia and 25 age- and gender-matched healthy controls were used, who underwent ERP recordings during the Assessing Neurocognition via Gamified Experimental Logic (ANGEL) paradigm. This is a gamified visual odd-ball paradigm that generates P300, the error responses generate ERN, and paired-tone audio distractors generate P50 and MMN. Peak-peak amplitude, mean amplitude and area-under-curve measures of ERP were measured at electrodes reflecting best morphology. Results Though patients showed apparent ERP morphology differences relative to the controls, the standard ERP measures were comparable between groups, except for reduced ERN among patients. Interestingly, significant group differences were seen in N1-P2 complex suppression, despite comparable P50 suppression. Contribution of the research The current study is the first to report multiple ERP component measures simultaneously evoked among patients with schizophrenia, and shows greater signs for impaired prediction mechanism. The findings of the study would provide a more ecologically valid evaluation of ERP-based cognitive functioning, and need to be replicated in a larger sample as well as other mental disorders.
Standing room only: faculty intervention increases voluntary lecture attendance and performance for disadvantaged year 1 Bioscience students

Abstract Literature shows that attendance is an important bidirectional link in engaging students in learning. However, metacognitive awareness eludes many first-year students – particularly the disadvantaged, including those with low admission scores, English as a second language or coming from low socio-economic status (SES), migrant, or first-in-family backgrounds. Our intention was to encourage punctual lecture attendance, but without making it compulsory, in a year 1 Anatomy unit. We compared lecture attendance without and with updatings which informed students of their own accumulated attendance. Thus, the lecturer encouraged student time management. Compared with the other cohort, for students who were informed of their accumulated attendance, lecture attendance (56.5 vs. 77.5%) and performance (54.2 vs. 58.9%) were higher, the failure rate was about one-third lower (31.7 vs. 22.1%), the percentage of students scoring over 80% was 2.5 times higher, and the performance advantage of students’ admission score was removed. Furthermore, updating on attendance resulted in low SES students attending to the level of high SES students. These findings suggest that simply updating students on their accumulated lecture attendance has a surprisingly strong effect on their performance, particularly if they are underachievers or from low SES backgrounds.
Increasing Yield Components of Several Promising Lines of Red Rice through Application of Mycorrhiza Bio-Fertilizer and Additive Intercropping with Soybean in Aerobic Irrigation System

This study aimed to examine the effect of application of a bio-fertilizer containing arbuscular mycorrhizal fungi (AMF) and additive intercropping with soybean relay-planted between double rows of rice on growth and yield components of various promising lines of red rice grown in aerobic irrigation systems on permanent raised-beds. The field experiment, carried out on farmers' riceland in Beleke village of Gerung district in West Lombok, Indonesia, from May to September 2018, was designed according to Split Split-Plot design with three blocks and three treatment factors, i.e. intercropping (T0= without; T1= with soybean) as the main plot factor, red rice promising lines with 4 genotypes (G1= MG4, G2= MG10, G3= AM4, G4= AM10) as the sub-plot factor, and AMF bio-fertilizer (M0= without; M1= with AMF) as the sub-sub-plot factor. The pre-germinated red rice seeds were planted on permanent raised-beds, with a base spacing of 25x20 cm, which was then modified into a double-row pattern of 20x20 cm within the double-row and 30 cm between double-rows. The results indicated that application of the bio-fertilizer “Technofert” containing AMF significantly increased growth and yield components of various promising lines of red rice, especially in relation to filled grain number and grain yield per clump, but significantly reduced percentage of unfilled grain number. Additive intercropping with soybean that was relay planted between double-rows of rice (one week after seeding rice) also significantly increased grain yield of the red rice genotypes. Among the four selected genotypes, grain yield of AM10 was the highest, especially when bio-fertilized with AMF and intercropped with soybean.
Enhancing the Performance of Basmati Rice (Oryza sativa L.) through Fly Ash and Nitrogen Management

Fly ash is produced as a result of coal combustion in thermal power station and discharged in ash ponds. In India and most countries major source of electrical energy is coal based thermal power plants, which produces 175 million tonnes. Disposal of high amount of fly ash from thermal power plants absorbs huge amount of water, energy and land area by ash ponds. The fly ash utilization in the country is estimated to be about 59% only (Kanungo, 2013) Therefore fly ash management would remain a great concern of the century. However, several studies purposed that fly ash can be used as a soil ameliorant that may improve physical, chemical, biological properties of the soil and is a source of readily available plant micro and International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 10 (2019) Journal homepage: http://www.ijcmas. com
Infraspecific molecular trees are associated with serial macroevolution in Pottiaceae (Bryophyta)

Zander R.H. 2019. Infraspecific molecular trees are associated with serial macroevolution in Pottiaceae (Bryophyta). Ukrainian Botanical Journal, 76(5): 390–405. Abstract. The analytic orientation of this paper is intended as a replacement for the antiquated but still prevalent phylogenetic inferential models and techniques of the late 20 сentury that are focused entirely on shared descent. Serial descent, that is, progenitor to descendant, may occur at the species or infraspecies level. In molecular systematics, species level paraphyly occurs when two examples of the same species are separated on a cladogram by a second species. This implies linear macroevolution of the second species from the first. Molecular cladograms often show cladistic structure (branching) among examples of the same species. If well-supported, such indicates a potential for evolution. A range of infraspecific and intraspecific cladistic structure in species of Pottiaceae (Bryophyta) was demonstrated in previously published molecular cladograms and data sets of other authors. This includes well-supported cladistic structure of molecular strains, and well-supported paraphyly involving other species. Large numbers of base pair changes among strains are considered here evidence of evolvability and increasing age of a species. Infraspecific strains are apparently lost in older species through speciation and extinction. Cluster analysis using DNA metadata of Oxystegus species matched published molecular cladograms to a large extent. The fact that apparent molecular strains are present in both nonparaphyletic and paraphyletic species, about half the species studied, shore up the theory that internal racial differentiation at the molecular level leads to or signals serial descent of multiple extant morphotaxa. It is because much infraspecific molecular cladistic structure exists that newly speciated taxa are already strongly cladistically dichotomized. Thus, the ultimate source of molecular paraphyly is internal to each species, and does not imply polyphyly by convergent species or cryptic taxa. Molecular systematics cannot effectively model progenitor-descendant radiation. Species with many strains are potential sources of future biological diversity. Recognition of differential evolvability may allow facilitation of complex, interactive, diverse ecosystems successfully tracking climate change.
Increased Absorption and Translocation Contribute to Improved Efficacy of Dicamba to Control Early Growth Stage Palmer Amaranth (Amaranthus palmeri)

Abstract Rapid growth of Palmer amaranth (Amaranthus palmeri S. Watson) poses a challenge for timely management of this weed. Dose–response studies were conducted in 2017 and 2018 under field and greenhouse conditions near Garden City and Manhattan, KS, respectively, to evaluate the efficacy of dicamba to control ≤10-, 15-cm, and 30-cm-tall A. palmeri, which mimics three herbicide application timings: on-time application (Day 0) and 1- (Day 1) and 4-d (Day 4) delays. Visual injury rating and reduction in shoot biomass (% of nontreated), and mortality were assessed at 4 wk after treatment using a three- and four-parameter log-logistic model in R. Increasing dicamba doses increased A. palmeri control regardless of plant height in both the field and greenhouse studies. The results suggest that delaying application 1 (15 cm) and 4 d (30 cm) resulted in 2- and 27-fold increases in the effective dose of dicamba on A. palmeri, respectively, under field conditions. However, in the greenhouse, for the same level of A. palmeri control, more than 1- and 2-fold increases in dicamba dose, respectively, were required. Similarly, the effective dose of dicamba required for 50% reduction in A. palmeri shoot biomass (GR50) increased more than 4- and 8-fold or more than 1- and 2-fold when dicamba application was delayed by 1 (15 cm) and 4 d (30 cm), in the field or in the greenhouse, respectively. To understand the basis of increased efficacy of dicamba in controlling early growth stages of A. palmeri, dicamba absorption and translocation studies were conducted. Results indicate a significant reduction in dicamba absorption (7%) and translocation (15%) with increase in A. palmeri height. Therefore, increased absorption and translocation of dicamba results in increased efficacy in improving A. palmeri control at early growth stages.
mTOR-coordinated Post-Transcriptional Gene Regulations: from Fundamental to Pathogenic Insights

Post-transcriptional regulations of mRNA transcripts such as alternative splicing and alternative polyadenylation can affect the expression of genes without changing the transcript levels. Recent studies have demonstrated that these post-transcriptional events can have significant physiological impacts on various biological systems and play important roles in the pathogenesis of a number of diseases, including cancers. Nevertheless, how cellular signaling pathways control these post-transcriptional processes in cells are not very well explored in the field yet. The mammalian target of rapamycin complex 1 (mTORC1) pathway plays a key role in sensing cellular nutrient and energy status and regulating the proliferation and growth of cells by controlling various anabolic and catabolic processes. Dysregulation of mTORC1 pathway can tip the metabolic balance of cells and is associated with a number of pathological conditions, including various types of cancers, diabetes, and cardiovascular diseases. Numerous reports have shown that mTORC1 controls its downstream pathways through translational and/or transcriptional regulation of the expression of key downstream effectors. And, recent studies have also shown that mTORC1 can control downstream pathways via post-transcriptional regulations. In this review, we will discuss the roles of post-transcriptional processes in gene expression regulations and how mTORC1-mediated post-transcriptional regulations contribute to cellular physiological changes. We highlight post-transcriptional regulation as an additional layer of gene expression control by mTORC1 to steer cellular biology. These emphasize the importance of studying post-transcriptional events in transcriptome datasets for gaining a fuller understanding of gene expression regulations in the biological systems of interest.
Trading mental effort for confidence in the metacognitive control of value-based decision-making

Why do we sometimes opt for actions or items that we do not value the most? Under current neurocomputational theories, such preference reversals are typically interpreted in terms of errors that arise from the unreliable signaling of value to brain decision systems. But, an alternative explanation is that people may change their mind because they are reassessing the value of alternative options while pondering the decision. So, why do we carefully ponder some decisions, but not others? In this work, we derive a computational model of the metacognitive control of decisions or MCD. In brief, we assume that fast and automatic processes first provide an initial (and largely uncertain) representation of options’ values, yielding prior estimates of decision difficulty. This uncertain value representation is then refined by deploying cognitive (e.g., attentional, mnesic) resources, the allocation of which is controlled by an effort-confidence tradeoff. Importantly, the anticipated benefit of allocating resources varies in a decision-by-decision manner according to the prior estimate of decision difficulty. The ensuing MCD model predicts choices, response time, subjective feeling of effort, choice confidence, and choice-induced preference change. We test these predictions in a systematic manner, using a dedicated behavioral paradigm. Our results provide a quantitative link between mental effort, choice confidence, and preference reversals, which could inform interpretations of related neuroimaging findings.
Effects of fibrolytic enzymes and lactic acid bacteria on fermentation quality and in vitro digestibility of Napier grass silage

Abstract An experiment was conducted to evaluate the effect of xylanase and cellulase derived from dried tomato pomace treated with Aspergillus niger and fermented juice of epiphytic of lactic acid bacteria (FJLB) on fermentative quality and in vitro digestibility of Napier grass silages. Thus, we treated Napier grass silage with or without fibrolytic enzymes (ENZ) in combination with or without FJLB. The pH values of silages treated with FJLB, but not ENZ, were found to be lower than the other silages during the ensiling process. The content of water soluble carbohydrates (WSC) of all silages was likely to decrease during fermentation in all silages. However, after 30 days of ensiling, the addition of ENZ resulted in higher WSC content when compared to the other treatments. At 30 day of ensiling, the crude protein of silage was higher in silage treated with FJLB. The gas production related to the soluble fraction was higher in silage treated with ENZ but total gas production was similar between treatments. The latter is in line the observation that the degradability of organic matter also was not different between treatments. It is concluded that neither the fermentation quality nor the in vitro digestibility of organic matter is improved when Napier grass is ensiled with both FJLB and fibrolytic enzymes compared with FJLB alone. Highlights Ensiling Napier grass, which contains high water soluble carbohydrates, without additives results in an acceptable fermentation quality. A combination of fermented juice of epiphytic lactic acid bacteria (FJLB) and fibrolytic enzymes has no effect on quality of Napier grass silage.