Miracle-dz/UniFAR-FTUs huggingface dataset:
The ecological integrity of the Lower Olifants River, Limpopo province, South Africa: 2009–2015 – Part A: Olifants River main stem

The major rivers of the South African ‘Lowveld’ (low-latitude savanna) suffer numerous impacts from upstream economic activities. Whereas monitoring these rivers is required to detect biodiversity losses, record pollution events and devise mitigation strategies, current monitoring programmes are inadequate. In 2009, the South African Earth Observation Network initiated an intensive long-term research programme on the Lowveld reaches of the Olifants River. Physico-chemical parameters, aquatic macroinvertebrates and fish abundances were recorded at four Lowveld sites in the Olifants River. We review six years of this programme. The results suggest deterioration in the ecological condition of the Olifants River with no discernible improvement through protected areas. Trends could not be detected. The parameters measured, sampling methods and/or sampling frequency might be responsible for the limited trends observed, or alternatively the results simply reflect stable conditions despite on-going pollution. Real time monitoring and an expansion in the parameters monitored would add value to the monitoring programme.
The effect of cold stress on resistance in Cavendish bananas to Fusarium wilt

69 INTRODUCTION . 70 MATERIALS AND METHODS. 72 Fungal isolates and culture conditions . 72 RNA extraction . 72 cDNA-AFLP analysis . 73 Isolation of polymorphic fragments and sequence data analysis . 73 Quantitative analysis of transcript abundance. 74 RESULTS . 75 cDNA-AFLP analysis . 75 Quantitative verification of cDNA-AFLP . 76 © University of Pretoria
Sleep in birds: lying on the continuum of activity and rest

Abstract Sleep is highly organized activity which is associated with decreased muscular activity and reduced response to environmental stimuli. The sleep is regulated by both, circadian and homeostatic mechanisms. Sleep patterns can be studied by behavioral assays by observing different sleep behaviors or by neuronal activity such as EEG (electroencephalogram), EOG (electro-oculogram), and EMG (electromyogram). Sleep is organized into non-rapid eye movement (NREM) and rapid eye movement. The sleep pattern in birds are similar to that in mammals, however, few differences such as existence of unihemispheric sleep (UHS) in almost all birds compared to few marine mammals do exist. The UHS results in asymmetry of the brain function measured as slow wave activity (SWA). Several migrants exhibit sleeplessness and they compensate it by NREM. They employ UHS during their migratory flight to remain alert while sleeping and maintain the balance while flying which is advantageous for these birds. Thus, sleep is of fundamental significance for the animal as it lies on the continuum of activity and rest. The present review focuses on some of above mentioned facts about sleep in higher vertebrates particularly in birds.
THE BIOPHYSICAL CHARACTERISTICS AND STRUCTURAL EXPLORATION OF PROGRAMMED CELL DEATH REGULATOR B-CELL LYMPHOMA 2-ASSOCIATED X PROTEIN OF CHINESE LIVER FLUKE (CLONORCHIS SINENSIS)

Objective: The balance between deaths and cellular life is regulated by B-cell lymphoma 2 (BCL-2)-associated X protein (BAX) an important pro-apoptotic components of BCL-2 family. With this initial point, the aim of this study was to determine a comparative composite based structure of BAX of Chinese liver fluke and different structural analysis. Methods: Protein amino acid of BAX of Chinese liver fluke mined from National Centre for Biotechnology Information (http://ncbi.nlm.nih.gov). Molecular model of BAX of Chinese liver fluke protein was generated by the comparative composite modeling tool Iterative Threading ASSEmbly Refinement suite. Afterward, I-TASSER generated molecular model was subjected to further structural improvements by energy minimization step. Distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of bioinformatical tools. Results: Analysis of Ramachandran plot created by PROCHECK tool is a consensus standard for validation purpose of protein structural modeling. Altogether 97.8% of the residues were detected in allowed and favored regions, which in turn validate the quality of generated protein structural model. Total negatively and positively charged residues within the BAX of Chinese liver fluke were 23 and 20, respectively. Chimera package-guided hydrophobicity molecular surface analysis illustrates that molecule specific hydrophobicity surface is exclusive to BAX protein molecule. Conclusion: Within the scope of this scientific investigation, we have successfully utilized molecular modeling approach to suggest the first molecular three-dimensional model structure of BAX of Chinese liver fluke. The synchronous balance between cellular deaths and cellular life is keeping up by BAX, an important pro-apoptotic family member of BCL-2 family. Consequently, it would be an exciting approach to resolve its structural characterization and molecular structure to propose mode of mechanism action.
HRS1/HHOs GARP transcription factors and reactive oxygen species are regulators of Arabidopsis nitrogen starvation response

Plants need to cope with strong variations in the nitrogen content of the soil solution. Although many molecular actors are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of Nitrogen. Indeed, following N removal plants activate their Nitrogen Starvation Response (NSR) being characterized in particular by the activation of very high affinity nitrate transport systems (NRT2.4, NRT2.5) and other sentinel genes such as GDH3. Here we show using a combination of functional genomics (via TF perturbation) and molecular physiology studies, that the GARP Transcription Factors (TFs) belonging the HHO sub-family are important regulators of the NSR through two potential mechanisms. First, HHOs directly repress NRT2.4 and NRT2.5 high-affinity nitrate transporters. Genotypes affected in HHO genes (mutants and overexpressors) display modified high-affinity nitrate transport activities opening interesting perspectives in biotechnology applications. Second, we show that Reactive Oxygen Species (ROS) are important to control NSR in wild type plants and that HRS1 and HHO1 overexpressors are affected in their ROS content, defining a potential feedforward branch of the signaling pathway. Taken together our results define two new classes of molecular actors in the control of NSR including ROS and the first transcription factors to date. This work (i) opens perspectives on a poorly understood nutrient related signaling pathway, and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.
Wnt/Yes-Associated Protein Interactions During Neural Tissue Patterning of Human Induced Pluripotent Stem Cells

Human induced pluripotent stem cells (hiPSCs) have special ability to self-assemble into neural spheroids or mini-brain-like structures. During the self-assembly process, Wnt signaling plays an important role in regional patterning and establishing positional identity of hiPSC-derived neural progenitors. Recently, the role of Wnt signaling in regulating Yes-associated protein (YAP) expression (nuclear or cytoplasmic), the pivotal regulator during organ growth and tissue generation, has attracted increasing interests. However, the interactions between Wnt and YAP expression for neural lineage commitment of hiPSCs remain poorly explored. The objective of this study is to investigate the effects of Wnt signaling and YAP expression on the cellular population in three-dimensional (3D) neural spheroids derived from hiPSCs. In this study, Wnt signaling was activated using CHIR99021 for 3D neural spheroids derived from human iPSK3 cells through embryoid body formation. Our results indicate that Wnt activation ind.
The complete mitochondrial genome of Enallagma cyathigerum (Odonata: Coenagrionidae) and phylogenetic analysis

Abstract To better understand the diversity and evolution of Odonata, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Enallagma cyathigerum. This mitogenome was 16,661 bp in size and encoded the typical 37 genes, i.e. 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes. The nucleotide composition of the E. cyathigerum mitogenome was significantly biased toward A and T, with an A + T content of 74.2%. Eleven PCGs started with a typical ATN codon, whereas the remaining two PCGs (nad1 and nad3) used TTG as the initial codon. All the 22 tRNAs had a typical secondary cloverleaf structure. The Bayesian phylogenetic analysis based on the concatenated nucleotide sequences of 13 PCGs strongly supported the sister relationship of E. cyathigerum and two Ischnura species from the same family Coenagrionidae. The phylogenetic tree strongly supported the monophyly of each of the two suborders (Zygoptera and Anisoptera) and recovered a phylogeny of Zygoptera + (Anisoptera + Anisozygoptera).
Individual level reliability of PAS-induced neural plasticity

Objective We assessed the individual level reliability of neural plasticity changes induced by paired associative stimulation (PAS), which combines peripheral nerve stimulation with transcranial magnetic stimulation to induce short-term plastic changes in the brain. Methods For 5 consecutive weeks, motor evoked potentials (MEPs) of 8 healthy subjects were acquired every 10 minutes post-PAS intervention for a period of 60 minutes. The post-PAS MEPs were evaluated against base-line MEPs using permutation and Kolmogorov-Smirnov tests to determine whether the MEP magnitudes changed after PAS. Moreover, various sample sizes of the MEP data were used to deduce the minimum number of MEPs needed to reliably detect individual propensity to neural plasticity. Results Group analysis exhibited significant increase in post-PAS MEPs, confirming previous results. While high between-sessions variability was observed at individual level, data show that between 40 to 50 MEPs can reliably assess each subject’s responsiveness to PAS. Subjects exhibited three different plasticity patterns: in the modulated hemisphere only, both hemispheres, or neither hemisphere. Conclusions PAS can reliably assess individual differences in neural plasticity. Significance A marker of individual plasticity may be useful to predict the effects of a motor rehabilitation, drug or other intervention to increase recovery of function after brain injury. Highlights Paired associative stimulation (PAS) assesses neural plasticity non invasively. The study shows how PAS can reliably determine individual differences in plasticity. PAS may be used to predict intervention outcome or individualize treatment dose.
Are ranger patrols effective in reducing poaching‐related threats within protected areas?

Poaching is one of the greatest threats to wildlife conservation world-wide. However, the spatial and temporal patterns of poaching activities within protected areas, and the effectiveness of ranger patrols and ranger posts in mitigating these threats, are relatively unknown. We used 10 years (2006–2015) of ranger-based monitoring data and dynamic multi-season occupancy models to quantify poaching-related threats, to examine factors influencing the spatio-temporal dynamics of these threats and to test the efficiency of management actions to combat poaching in Nyungwe National Park (NNP), Rwanda. The probability of occurrence of poaching-related threats was highest at lower elevations (1,801–2,200 m), especially in areas that were close to roads and tourist trails; conversely, occurrence probability was lowest at high elevation sites (2,601–3,000 m), and near the park boundary and ranger posts. The number of ranger patrols substantially increased the probability that poaching-related threats disappear at a site if threats were originally present (i.e. probability of extinction of threats). Without ranger visits, the annual probability of extinction of poaching-related threats was an estimated 7%; this probability would increase to 20% and 57% with 20 and 50 ranger visits per year, respectively. Our results suggest that poaching-related threats can be effectively reduced in NNP by adding ranger posts in areas where they do not currently exist, and by increasing the number of patrols to sites where the probability of poaching activities is high. Synthesis and applications. Our application of dynamic occupancy models to predict the probability of presence of poaching-related threats is novel, and explicitly considers imperfect detection of illegal activities. Based on the modelled relationships, we identify areas that are most vulnerable to poaching, and offer insights regarding how ranger patrols can be optimally deployed to reduce poaching-related threats and other illegal activites, while taking into account potential sampling biases. We show that poaching can be effectively reduced by increasing ranger patrols to areas under high risk of poaching activities, and by adding ranger patrols near these sites. These findings are broadly applicable to national parks and protected areas experiencing a high degree of poaching and other illegal activities.
Quantitative and qualitative analysis of sea bream, Sparus aurata (L.), humoral immune response, vaccinated with commercial and experimental vaccines against vibriosis and photobacteriosis

The specific humoral immune response of sea bream, Sparus aurata (L.), against Vibrio anguillarum O1 and Photobacterium damselae subsp. piscicida (Phdp) after immunization with commercial and experimental bacterins was analysed quantitatively and qualitatively. Specific anti-V. anguillarum O1 and anti-Phdp levels provoked by the adjuvanted commercial vaccine reached higher levels in comparison to the aqueous commercial and experimental bacterins. Infection of vaccinated fish with V. anguillarum O1 bacterial cells acted as a boost of the humoral immune response, except for the sera of the group vaccinated with the adjuvanted vaccine. Infection with Phdp acted as a boost of the humoral immune response mainly for the group vaccinated with a monovalent Phdp bacterin and to a lesser degree for the group vaccinated with the aqueous commercial vaccine. Western blot analysis of the sera against V. anguillarum O1 whole cell antigens revealed strong reactions to only a few antigens below 54 kD and above 15 kD and weak reactions to other antigens. Similar reactions were observed from the sera isolated from the controls. Western blot analysis of the sera against Phdp whole cell antigens revealed strong reactions to only a handful of antigens below 20.7 and below 6.4 kD. Sera from the control group, as in the case of V. anguillarum O1, reacted with Phdp whole cell antigens. No differences regarding antigen reactions between monovalent and bivalent formulations were noted, in contrast to the adjuvanted and aqueous bacterins.
Occurrence of Newcastle disease in poultry population of Mizoram, India

A study was undertaken to survey the prevalence of viral diseases of poultry in Mizoram during March, 2013 to February, 2014. Out of 476 poultry carcasses examined, 208(43.69%) cases were diagnosed as viral diseases. Forty cases of Newcastle disease (8.40%) could be diagnosed based on the clinical history, signs, gross and histopathology, and confirmed by HA and HI tests with detection of the viral antigen. All age groups of birds were affected with morbidity and mortality rates of 35–50% and 25–35%, respectively and the highest incidence during the winter season followed by rainy and summer seasons. Most common signs were depression, emaciation, greenish or white diarrhea and edema of the head, face and wattles, while some birds developed respiratory signs like sneezing, gasping, nasal discharge and coughing. Post-mortem findings included pin-point haemorrhages at the tips of the proventriculus glands, hemorrhagic ulcers in intestinal wall and caecal tonsils, hemorrhagic tracheitis with congestion and catarrhal exudates. The spleen was enlarged, friable and appeared dark red or mottled, while the kidneys were enlarged, congested and swollen with urate deposition.Significant microscopic changes were haemorrhages and necrosis of the proventriculus mucosa with mononuclear cell infiltration. Caecal tonsil revealed haemorrhages, infiltration of heterophils in the lamina propria, lymphoid depletion and formation of germinal centres. There were sloughing of tracheal mucosa with loss of cilia and congestion, while brain sections revealed non-suppurative encephalitis, neuronal degeneration, gliosis and perivascular cuffing.
Assessment of Verticillium dahliae Kleb. And Soil Fungal Communities Associated with Strawberry Fields

Background: Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique. Methods: The study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided. Results: A total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed. Conclusions: From a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.
The RS Domain of Human CFIm68 Plays a Key Role in Selection Between Alternative Sites of Pre-mRNA Cleavage and Polyadenylation

Many eukaryotic protein-coding genes give rise to alternative mRNA isoforms with identical protein-coding capacities but which differ in the extents of their 3´ untranslated regions (3´UTRs), due to the usage of alternative sites of pre-mRNA cleavage and polyadenylation. By governing the presence of regulatory 3´UTR sequences, this type of alternative polyadenylation (APA) can significantly influence the stability, localisation and translation efficiency of mRNA. Though a variety of molecular mechanisms for APA have been proposed, previous studies have identified a pivotal role for the multi-subunit cleavage factor I (CFIm) in this process in mammals. Here we show that, in line with previous reports, depletion of the CFIm 68 kDa subunit (CFIm68) by CRISPR/Cas9-mediated gene disruption in HEK293 cells leads to a shift towards the use of promoter-proximal poly(A) sites. Using these cells as the basis for a complementation assay, we show that CFIm68 lacking its arginine/serine-rich (RS) domain retains the ability to form a nuclear complex with other CFIm subunits, but selectively lacks the capacity to restore polyadenylation at promoter-distal sites. In addition, nanoparticle-mediated analysis indicates that the RS domain is extensively phosphorylated in vivo. Overall, these results suggest that the CFIm68 RS domain makes a key regulatory contribution to APA.
Paleo-Oscillomics: Reconstructing Language-Relevant Computational Capacities in Neanderthals from the Molecular Basis of Neural Oscillations

Language seemingly evolved from changes in brain anatomy and wiring. We argue that language evolution can be better understood if particular changes in phasal and cross-frequency coupling properties of neural oscillations, resulting in core features of language, are considered. Because we cannot track the oscillatory activity of the brain from extinct hominins, we used our current understanding of the language oscillogenome (that is, the set of genes responsible for basic aspects of the oscillatory activity relevant for language) to infer some properties of the Neanderthal oscillome. We have found that several candidates for the language oscillogenome show differences in their methylation patterns between Neanderthals and humans. We argue that differences in their expression levels could be informative of differences in cognitive functions important for language.
High impact journals in ecology cover proportionally more statistically significant findings

Unbiased scientific reporting is crucial for data and research synthesis. Previous studies suggest that statistically significant results are more likely to be published and more likely to be submitted to high impact journals. However, the most recent research on statistical significance in relation to journal impact factors in ecological research was published more than two decades ago or addressed a small subset of the literature. Here, we extract p-values from all articles published in 11 journals in 2012 and 2014 across a wide range of impact factors with six journals sampled in both years. Our results indicate that the proportion of statistically significant results increases with rising impact factor. Such a trend can have important consequences for syntheses of ecological data and it highlights the importance of covering a wide range of impact factors when identifying published studies for data syntheses. This trend can also lead to a biased understanding of the probability of true effects in ecology and conservation. We caution against the possible downplaying of non-significant results by either journals or authors.