Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatiotemporal information is differentially conveyed by hippocampal projections to the anterior olfactory nucleus during episodic-like odour memory

The hippocampus is essential for representing spatiotemporal context and associating it with the sensory details of daily life to form episodic memories. However, the neural circuit underlying this process remains poorly understood. We selectively inhibited hippocampal projections to the anterior olfactory nucleus (AON) during behavioural tests of contextually-cued odour recall. We found that inhibition of intermediate HPC (iHPC)-lateral AON (lAON) pathway impaired spatial odour memory while inhibition of ventral HPC (vHPC)-medial AON (mAON) pathway disrupted both spatial and temporal odour memory. Our results indicate that the spatial and temporal information of episodic-like odour memory is conveyed by topographically distinct hippocampal-AON pathways.
Nutrient and salinity concentrations effects on quality and storability of cherry tomato fruits grown by hydroponic system

Bragantia, Campinas, v. 77, n. 2, p.385-393, 2018 ABSTRACT: This study was conducted to investigate the effects of nutrient and salinity concentrations on the quality of deepflow technique hydroponic system cultivated cherry tomatoes (Lycopersicon esculentum Mill ‘Unicorn’). The conditions were: (1) control (NS-1 × nutrient Solution, Electrical Conductivity – EC: 2.5 mS∙cm–1); (2) 2 × NS (2 × NS-Double NS, EC: 5 mS∙cm–1); (3) NS + 4.23 mM NaCl (NaCl-Sodium Chloride, EC: 5 mS∙cm–1); and (4) NS + 13.70 mM Sea Water – SW (EC: 7.5 mS∙cm–1). NS + 13.70 mM SW treatment showed the lowest fresh weight loss. Visual quality as well as shelf life was the longest in NS (1 × nutrient solution) treated tomato fruits. The longest POST HARVEST TECHNOLOGY Article
Wood anatomy of seed and basal bud originated downy birches (Betula pubescens Ehrh.) grown at four different sites

In trees, xylem must fulfil three important tasks: conducting water to leaves, storing nutrients and water, and supporting the trunk. The origin of the trunk, i.e., seed or basal bud that forms sprouts, and the growth site may affect xylem anatomy, differences of which can affect successful growth of trees. Both seedlings and sprouts of downy birch (Betula pubescens Ehrh.) from four different growth sites with two different soil media, peat and mineral soil, were studied. The diameter of fibres and vessels and the thickness of the double fibre wall were measured, and the number of vessels, rays and axial parenchyma cells was counted. The fibre wall:lumen ratio, vessel percentage area and vessel size:number ratio were calculated. Xylem from sprouts showed only occasionally more mature characteristics than that of seedlings. The number of rays was similar at all four sites, but differences were observed in all other studied characteristics between sites, particularly if soil type was different. The vessel size and number correlated with the number of axial parenchyma cells in juvenile wood, which emphasises the importance of their connections with storage cells particularly at this stage of growth. Good water conductivity was connected with weaker wood, particularly in maturing wood.
Timing of Avian Breeding in an Urbanised World

A large part of the world is urbanised, and the process of urbanisation is ongoing. This causes dramatic alterations of species' habitat such as increased night light, sound levels and temperature, along with direct disturbance by human activity. We used eight years of citizen science data from ten common bird species breeding in nest boxes throughout The Netherlands to study the relationship between urbanisation and a key life history trait, timing of breeding. We used nightly light levels in the form of sky brightness and light emission as a proxy for urbanisation as the dramatic change of the night-time environment is a prominent effect of urbanisation. We expected birds to lay earlier in areas with more light at night, i.e. in more urbanised areas. We found, however, no relationship between light levels and seasonal timing in the ten species studied. A limitation of our study is that there was only limited data for the areas that were urbanised most (e.g. inside cities). Most nest box study areas are located in areas with a limited level of urbanisation, and hence with relatively low light levels of light at night. The lack of data on breeding birds in more urbanised environments, which is a rapidly expanding habitat for an increasing number of species worldwide, should be the focus of attention and citizen science would be highly suitable to also provide data for such areas.
Preliminary report: one of the PD-1 gene variants may be a valuable marker for colorectal cancer

Introduction: Programmed death-1 (PD-1) is an immunosuppressive molecule, which has importance for tumor-cell-mediated immune escape. We investigated the role of PD-1.5 C/T gene polymorphisms in the susceptibility and progression of colorectal cancer (CRC). Material and methods: In this study, the PD-1.5 C/T polymorphism was investigated in 99 CRC patients and 150 healthy controls by the nested polymerase chain reaction-restriction fragment length polymorphism method. Results: The distributions of PD-1.5 C/T genotypes and alleles were in agreement with Hardy-Weinberg equilibrium in controls (p > 0.05) but not in CRC patients (p = 0.02). We found a statistically significant difference between CRC patients and controls for the genotypic distribution of PD-1.5 C/T genotypes (p = 0.003) and also for alleles (p = 0.004). The T allele frequency was higher in patients than controls (p = 0.001). The patients who had a C allele with distance metastasis had higher frequency of heterozygous CT genotype of PD-1.5 C/T polymorphism than those with no metastasis (p < 0.001). We also detected higher frequency of CC genotype in patients who had angiolymphatic invasion (p = 0.043). The patients who had a mucinous component had higher frequency of the T allele than those with absence of the mucinous component (p = 0.023). Conclusions: Our results showed significant associations between PD-1 genotypes and CRC susceptibility and progression of the disease.
Rapid and sensitive virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

Newcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND. However, these diagnostics are hindered by the genetic diversity and rapid evolution of NDVs. A highly sensitive amplicon sequencing (AmpSeq) workflow for virulence and genotype prediction of NDV samples using a third-generation, real-time DNA sequencing platform is described using both egg-propagated virus and clinical samples. 1D MinION sequencing of barcoded NDV amplicons was performed on 33 egg-grown isolates, (23 unique lineages, including 15 different NDV genotypes), and from 15 clinical swab samples from field outbreaks. Assembly-based data analysis was performed in a customized, Galaxy-based AmpSeq workflow. For all egg-grown samples, NDV was detected and virulence and genotype were predicted. For clinical samples, NDV was detected in ten of eleven NDV samples. Six of the clinical samples contained two mixed genotypes, of which the MinION method detected both genotypes in four of those samples. Additionally, testing a dilution series of one NDV sample resulted in detection of NDV with a 50% egg infectious dose (EID50) as low as 101 EID50/ml. This was accomplished in as little as 7 minutes of sequencing time, with a 98.37% sequence identity compared to the expected consensus. The high sensitivity, fast sequencing capabilities, accuracy of the consensus sequences, and the low cost of multiplexing allowed for identification of NDV of different genotypes circulating worldwide. This general method will likely be applicable to other infections agents.
Artemisia capillaris Thunb. inhibits melanin synthesis activity via ERK-dependent MITF pathway in B16/F10 melanoma cells

Genus Artemisia occurs as a hardy plant and has a wide range of culinary and medicinal features. In this study, we aimed to describe the melanin inhibitory activity of one Artemisia species, i.e., Artemisia capillaris Thunb. Ethanol extracts of fermented Artemisia capillaris (Art.EtOH.FT) and non-fermented Artemisia capillaris (Art.EtOH.CT) were tested for their ability to inhibit tyrosinase activity and melanin pigmentation. Both extracts showed dose-dependent inhibition against α-melanocyte stimulating hormone-stimulated melanin formation and tyrosinase activity, without cytotoxicity. At 100 μg/mL, both extracts showed greater inhibition than kojic acid, the positive control. Protein expressions of microphthalmia-associated transcription factor (MITF), tyrosinase (TYR), tyrosinase-related protein 1 (TRP-1), and tyrosinase-related protein 2 (TRP-2) at the transcriptional level were determined by using real-time and semi-quantitative polymerase chain reaction. To complete the mechanistic study, presences of upstream elements of MITF, the phosphorylated-extracellular signal-regulated kinase (p-ERK), and phosphorylated-mitogen-activated protein kinase kinase (p-MEK) were confirmed by using western blot analysis. Expressions of p-TYR, p-TRP-1 and p-TRP- 2, downstream factors for p-ERK and p-MITF, were translationally inhibited by both extracts. Art.EtOH. FT induced more potent effects than Art.EtOH. CT, especially signal transduction effects. In summary, Artemisia capillaris extracts appear to act as potent hypopigmentation agents.
Molecular dynamics simulation and docking studies on novel mutants (T11V, T12P and D364S) of the nucleotide-binding domain of human heat shock 70 kDa protein

Abstract The aim of investigating protein interaction between Homo sapiens adenovirus and heat shock 70 kDa protein (Hsp70) is to study a potentially synergistic interaction that would enhance the anti-apoptotic mechanisms, hence increasing the virus replication rate and improve the killing efficiency of tumour cells in cancer therapy. Currently, the protein interaction between Hsp70 and E1A 32 kDa of human adenovirus C serotype 5 (Ad5) is still unknown. Mutant models (T11V, T12P and D364S) were built, simulated and their interactions with Ad5 were studied. The E1A 32 kDa of human Ad5 motif (PNLVP) showed the lowest binding energy and intermolecular energy values with the novel T11V mutant at -8.26 kcal/mol and -11.21 kcal/mol. The protein-ligand complex models revealed that the T11V mutant had the strongest and most stable interaction with the PNLVP motif among all the four protein-ligand complex structures. This knowledge would assist future in vivo investigations of this protein-ligand complex structure in cancer treatment research.
Some Physicochemical Properties of the Whole Fruit Mandarin Jam

The citrus fruits have a high nutritive value and are also beneficial effects for human health due to their high flavonoid content. Mandarin (Citrus unshiu March.) a kind of citrus fruits are consumed as fresh and processed juice and/or juice concentrate. The aim of this work was to produce jam and evaluate its physical, chemical and sensory qualities from satsuma mandarins that are inconsumable or low quality small fruits. The jam was produced with 1:1 fruits: sugar ratios in an open vessel by traditional technique. Produced whole fruit mandarin jam had reasonable favour score from applied hedonic scale. The mean values of total soluble solid, titratable acidity as citric acid, dry matter, ash percent and pH of jam samples on wet basis were found as 70.38, 0.098, 74.77, 0.28 and 2.87 respectively. Hunter L, a and b values of tangerin jam were measured as 45.34, 11.48, and 21.16 respectively. Total phenolic content, antioxidant capacity and vitamine C of sample were measured 201.60 mg/100g as gallic acid equivalent and 102,24 mg FeSO4.7H2O/100g, 0.07 mg/100 g respectively.
How the cheetahs' specialized palate accommodates its abnormally large teeth

The term focal palatine erosion was introduced into the literature to describe infection of a palatal depression palatal to the 4th maxillary premolar in cheetahs, previously hypothesized to be of pathological nature or to possibly accommodate the large mandibular molar teeth. Currently, there exists no literature that describes the normal anatomy of the palate of a cheetah (Acinonyx jubatus) with specific reference to these structures. The palates of six adult cheetahs, three young cheetah cubs and dry skulls of 27 cheetah, 25 lion (Panthera leo) and 18 leopards (Panthera pardus) were used in this macroscopic and microscopic study which proves the cheetah palate to have not only one but also up to three sets of palatal depressions corresponding to the cusps of the opposing mandibular cheek teeth. The largest depression caudo-palatal to the maxillary fourth premolar tooth was always associated with a bone depression extending into the zygomatic arch bone, never described before. Through statistical analysis it is proven, for the first time, that cheetah in fact have relative macrodontia as determined by its tooth indices and comparing it to those of other African big cats namely lion and leopard. Up to eight palatal depressions are present on the palates of adult cheetahs and these are described as functional anatomical structures present to accommodate not only one but also all three opposing mandibular cheek teeth cusps. Palatal depressions are formed as the mandibular cheek teeth erupt into final occlusion and are filled up with bone and/or soft tissue after loss of the opposing mandibular teeth or its cusps, further supporting the above hypothesis. Apart from the above, the structural anatomy of the cheetah palate and vomeronasal organ was compared with that of the domestic cat.
Determining The Critical Weight Of The Rocky Mountain Wood Ticks Dermacentor andersoni Stiles (Acari: Ixodidae)

The feeding cycle of female ixodid ticks is divided into preparatory, slow and rapid feeding phases. Female ticks, virgin or mated, reach a ‘critical weight’ (CW; 10-13X the unfed weight) at the transition between the slow and rapid feeding phases, which is characterized by several physiological and behavioural changes. To date, the CW has been determined for Amblyomma hebraeum only. This study established that, in both mated and virgin Dermacentor Andersoni, salivary gland degeneration and ovarian development are triggered when the tick exceeds 10-13X the unfed weight. However, mated ticks undergo these changes 4 days earlier than virgin ticks. Unlike A. hebraeum, virgin D. andersoni regularly fed well beyond their CW, and occasionally fed up to 100X their unfed weight.
Landscape‐scale effects of single‐ and multiple small wind turbines on bat activity

While the effects of wind farms on bats are widely studied, effects of small wind turbines (SWTs, here <25 m hub height) remain understudied. SWTs are installed in a wider range of habitats compared to wind farms and their effect on wildlife can therefore be different. While single SWTs can adversely affect bat activity in their immediate vicinity, they are often installed in clusters, and to date, no data are available on whether installation of more than one turbine increases the likelihood of adverse effects on bats. Here, we test whether (1) SWT installations affect the activity of two species of bat (the common pipistrelle Pipistrellus pipistrellus and soprano pipistrelle P. pygmaeus) on a landscape scale (here defined as up to 500 m from SWTs) and (2) such an effect is stronger when multiple (2–4) SWTs are installed. We show that, after accounting for potentially confounding effects (e.g. variation in habitat and weather), (1) mean P. pipistrellus activity is lower at 0–100 m compared to 200–500 m from SWTs and (2) the effect on P. pygmaeus activity tends to be similar and stronger in multiple SWT sites, although evidence for the latter is limited. We conclude that in some cases, adverse effects of SWTs on bat activity may be measurable over longer spatial scales (within 100 m) than previously thought. However, combined with earlier findings, it is likely that the bulk of such effects operate within relative close proximity of SWTs (<25 m). Moreover, although these effects may be species‐specific, with, for example, P. pygmaeus potentially more strongly affected by multiple SWT sites, this requires further data. These findings are highly relevant to decision‐making aimed at minimizing any adverse effects of wind turbines, specifically single‐ versus multiple SWT developments, on wildlife.
FRET primers for quantitative real-time PCR: Optimization for genomic and cDNA templates

The chemistry of FRET (fluorescence resonance energy transfer) primers real-time thermal cycling technique depends on internally labeled primers with FRET dyes. Fluorescent dyes are linked internally close to the 3` end of both primers. FRET primers technique was tested and optimized on PCR products as an amplification template. It showed high efficiency, correlation coefficient and wide dynamic range in short amplification time. FRET primers technique was not tested on real sample materials such as genomic and cDNA. The main objective of this study was to test and optimize FRET primers on genomic and cDNA as an amplification templates to be used in research and diagnosis. Two steps amplification protocol (denaturation step and annealing-elongation step) showed higher efficiency, correlation coefficient and wider dynamic range compared to three steps protocol in case of genomic and cDNA templates. Moreover, shorter amplification time is needed for two steps protocol that makes FRET primers suitable and alternative choice for research and diagnostic purposes.
Holmes-ITS2: Consolidated ITS2 resources and search engines for plant DNA-based marker analyses

Plants are valuable resources for a variety of products in modern societies. Plant species identification is an integral part of research and practical application on plants. In parallel with high-throughput sequencing technology, the high-throughput screening of species is in high demand. Highly accurate and efficient DNA-based marker identification is essential for the effective analysis of plant species or biological constituents of a mixture of plants as well. Therefore, it is of general interests and significance to generate a comprehensive and accurate DNA-based marker sequence resource, as well as to build efficient sequence search engines, for the accurate and fast identification of plant species. In this work, we have firstly established a high-quality ITS2 sequence database of plant species containing more than 150,000 entries, through the systematical collection and manually collation of the published ITS2 sequencing data of plant species, data quality control, as well as representative sequence refinement based on clustering method. Secondly, an accurate and efficient plant species identification system based on ITS2 sequence was constructed, which is the proper combination of sequence search algorithms including BLAST and Kraken. Through the deployment of high-performance and frequently updated web service, it’s expected to serve for a wide range of researchers involving the taxonomy classification of plant species, as well as for deciphering of plant mixed systems including herbal materials in TCM preparations. The Holmes-ITS2 web service is freely accessible at: http://its2.tcm. microbioinformatics.org/. The input of this web service could be multiple sequences in a single fasta format, to search for matching ITS2 biomarker sequences already annotated in the database. This sequence-based search is based on two engines: BLAST, and k-mer based Kraken. Alternatively, users can directly search for species name for the corresponding ITS2 biomarker sequences. The web service has been put to the test by more than 50 experts from China, Denmark and US, and the average running time for the search ranges from 3-30 seconds for up to 100 sequences as a batch query.
Dispersal of Goeppertia marantifolia clonal offspring increases with greater canopy openness and larger plant size

Abstract: Many plants within the neotropical understorey produce both seeds and clonal offspring. Plant attributes (i.e. size) and variability in light can influence seed dispersal but it is not known if these factors influence the dispersal of clonal offspring. Our goal was to determine if canopy openness and plant size influence clonal-offspring dispersal of the herb Goeppertia marantifolia, which produces clonal bulbils on above-ground shoots. We monitored plants in permanent plots with varying levels of canopy openness in Corcovado National Park, Costa Rica. We recorded canopy openness, leaf area and the distance clonal offspring travelled from their parent plant (N = 283). Our path analysis model demonstrated that canopy openness had a strong positive effect on dispersal distance, while the association between clonal-offspring dispersal distance and parent plant leaf area was only weakly positive. On average, plants experiencing high canopy openness dispersed their clonal offspring further than plants under low canopy openness (124 cm vs. 79 cm, respectively). Contrary to studies on species that utilize rhizomes and stolons for clonal reproduction, we found that in this bulbil-producing species light availability is positively associated with clonal dispersal distance. Therefore, the influence of resource availability on spatial population dynamics of clonal species may be influenced by the species’ growth-form.
Genomics using the Assembly of the Mink Genome

The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH. Other parts were in ROH in up to about 1/6 of the individuals. Some haplotypes must have achieved high frequencies during the relatively short time since domestication of the American mink. However, there was no evidence of haplotypes nearing fixation. Selection is therefore likely to be ongoing. The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly.