Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat shock protein 70 (Hsp70) is involved in the Zika virus cellular infection process

Zika virus (ZIKV) is a historically neglected flavivirus that has recently caused epidemics in the western hemisphere. ZIKV has been associated with severe symptoms including infant microcephaly and Guillain Barré syndrome, stimulating interest in understanding factors governing ZIKV infection. Heat shock protein 70 (Hsp70) has been shown to be an infection factor for multiple viruses. We investigated the role of Hsp70 in the ZIKV infection process. We localized Hsp70 protein to the Vero cell membrane surface by confocal microscopy and demonstrated that, inside the cell, there is significant co-localization between Hsp70 and ZIKV E protein. Inducing and suppressing Hsp70 expression increased and decreased ZIKV production, respectively. Antibody blocking cell surface-localized Hsp70 decreased ZIKV cell infection rates and production of infectious virus particles, as did competition with recombinant Hsp70 protein. Our data suggest that Hsp70 is an important factor in the ZIKV infection process. Understanding the interactions between Hsp70 and ZIKV may lead to novel therapeutics for ZIKV infection, particularly for pregnant women and fetuses.
Protein from Jawla prawn (Acetes spp.) and Squilla (Orato squilla nepa)

A simple method of isolation of protein from jawla prawn and squilla, which does not involve any chemical treatment, is reported. The method consists in blending the jawla prawn/squilla with equal quantity of water, removal of chitinous matter, heating the pulp at 112°C for 15-20 minutes and drying the precipitated protein after filtration.
Controls on the distribution and resilience of Quercus garryana: ecophysiological evidence of oak's water‐limitation tolerance

The composition of forests in Western North America is changing. The decline in the shadeintolerant Oregon white oak (Quercus garryana var. garryana) is attributed to increased competition with the tall-growing Douglas fir (Pseudotsuga menziesii var. menziesii) as a result of widespread fire exclusion. In a warmer, drier future, both species will experience increased water stress, and their distribution will depend on ecophysiological adaptations to water limitation, of which little is known for Q. garryana. Here, we report a suite of new ecophysiological observations to better understand the oak’s water-limitation tolerance, in order to predict its fate in a changing climate. Our study site in the Central Belt of the Franciscan Formation in the Northern California Coast Ranges receives almost no rain in the leaf-on growing season and has limited subsurface water storage capacity. In spite of low pre-dawn water potentials (Ψ; to below 3.0 MPa), mature trees maintained high rates of sapflow. Sapflow continued due to a high Ψ gradient ( 1.6 MPa on average) at mid-day between shoots and the subsurface (inferred from pre-dawn measurements) throughout the dry season. Depletion and recharge of stored water in stem tissue and leaves helped to sustain transpiration. Leaves experienced low Ψ (below 4 MPa), and declining hydraulic conductance yet remained functional. Pressure–volume curve analyses revealed that the maintenance of positive turgor pressures in leaves at low Ψ may be attributable to dynamic adjustment due to changes in cell wall elasticity. The turgor loss point may be of limited use in delineating ecophysiological limits to growth and reproduction, as transpiration and apparently normal physiological behavior continued after pre-dawn water potentials declined below turgor loss limits inferred from rehydrated leaves. These findings indicate that Q. garryana is a water-limitation-tolerant tree species that maintains hydraulic function as subsurface water supply and atmospheric demand conditions exceed the ranges at which P. menziesii can operate. These observations can be used to explain Q. garryana’s extant species range and anticipate its likely resilience in
The Goldilocks effect: female geladas in mid-sized groups have higher fitness

The cost-to-benefit ratio of group-living is thought to vary with group size: individuals in “optimal” groups should have higher fitness than individuals in groups that are too large or small. However, the relationship between group size and individual fitness has been difficult to establish, a gap we address here in the gelada. We demonstrate group size effects on the production of surviving offspring and on female mortality rates, which are largely explained by group-size variation in infanticide risk and foraging competition. We also identify a mechanism by which females may alter group size: in large groups, females groomed with less than half of their group, increasing the likelihood of fissions. Our findings provide insight into how and why group size shapes fitness in long-lived species.
Agreement in Tree Marking: What Is the Uncertainty of Human Tree Selection in Selective Forest Management?

New methods for sustainable forest management are being introduced in Ireland and other countries worldwide. These require different approaches to thinnings. This study explored how different levels of expertise in managing forest ecosystems affect the way individuals approach the task of selecting trees before and after training. Both experts and novices responded differently when provided with the same task. Before training, when presented with the task to carry out a thinning without specific instructions, experts applied the method of thinning they were most familiar with. When trained in one of these alternative thinning methods, novices successfully applied this method, whereas the experts did not. The level of agreement as to the choice of trees for removal was generally surprisingly low and among experts it was highest before training and declined most after training. Prior knowledge in managing forest environments affected how participants approached the task; the longer an expert applies a task in a particular way, the harder it is to change this strategy. This is crucial information, suggesting that if new approaches to selective forest management are to be successfully implemented, more effort should be made to convince experts and/or training should focus on individuals who have yet to become familiar with using a specific approach. The results of this study also suggest that the success rate of applying new methods should be monitored. This will ensure the application of forest management most suited to a given environment.
Genetic Diversity and Population Structure of Pinus yunnanensis by Simple Sequence Repeat Markers

Pinus yunnanensis is the main species used for reforestation in Yunnan province, China. To manage the genetic resources of this economically and ecologically important species efficiently, greater knowledge of the distribution of its genetic diversity is needed. In this study, the genetic diversity of 20 natural populations representing most of the P. yunnanensis range was examined using seven simple sequence repeats. No loci showed significant departure from Hardy-Weinberg equilibrium. Most genetic diversity was found within populations, and overall genetic differentiation was low (FST = 0.045). There was no sign of isolation by distance. Clustering of populations using both neighbor joining pair groups and principal coordinates analysis based on Nei's genetic distance showed the presence of two major clusters. This result was reinforced using the Bayesian software STRUCTURE, which identified two southern populations as clearly separate from the others. There were no signs of genetic erosion, but some populations should be a focus of conservation efforts because of their higher level of genetic diversity and the presence of private alleles. These results will inform conservation and management of P. yunnanensis and will guide future studies of population genetics and breeding programs.
Culture-Independent Analysis of Microbial Communities Associated with Hydroponically Grown "Living Lettuce"

The bacteria associated on and within a plant make up that plant’s microbiome. Given recent interest in how microbes can affect human health, as well as developments in DNA sequencing that allow us to examine microbial communities without culture techniques, a number of recent studies have investigated the composition of the microbial communities on edible plants. Leafy green salad vegetables pose an added interest, since they are consumed without sterilization or cooking. This study investigated the bacterial composition of endophytic and epiphytic communities of hydroponically grown green leaf lettuce that is sold with the roots intact and referred to as “living lettuce. ” In addition to examining the composition of the bacterial communities associated with living lettuce, comparisons were made to conventionally grown and packaged lettuce, both at the time of purchase and following refrigerator storage to reflect the time of consumption. The structure of bacterial communities was determined using next generation sequencing of the 16S rRNA gene. Bacterial communities on living lettuce were significantly different from those observed on conventional lettuce. While differences between the dominant phyla and subphyla of communities of the two types of lettuce were observed on the day of purchase, community composition became more similar following two weeks of refrigeration. As expected, community diversity decreased across both types of lettuce following refrigerator storage. Major taxa observed were consistent with results from previous studies of the bacterial communities of salad greens, and there were no significant populations of known human pathogens such as Salmonella spp. and Escherichia coli. This study demonstrates that the bacteria associated with hydroponically grown living lettuce, while different than that of traditionally grown and packaged lettuce, presents no apparent risk to the consumer in terms of its associated bacteria.
QTL analysis of soybean oil content under 17 environments

Qi, Z. , Han, X. , Hou, M. , Xin, D. , Wang, Z. , Zhu, R. , Hu, Z. , Jiang, H. , Li, C. , Liu, C. , Hu, G. and Chen, Q. 2014. QTL analysis of soybean oil content under 17 environments. Can. J. Plant Sci. 94: 245-261. Soybean oil content is a key trait driver of successful soybean quality. Due to its complex nature, less stable quantitative trait loci (QTL) are known. The goal of this study was to identify important and stable QTL affecting soybean oil content using recombination inbred lines (RILs) derived from a cross between Charleston and Dongnong594. The plant materials were planted in three environments across 9 yr in China. The genetic effects were then partitioned into additive main effects (A), epistatic main effects (AA) and their environment interaction effects (AE and AAE) by using composite interval mapping, multiple interval mapping and composite interval mapping in a mixed linear model. Fifty-six QTL were identified on 15 of 20 soybean chromosomes excluding LG C1, D2, E, M and O by composite interval mapping and multiple interval mapping methods. Seven oil content QTL detected on LG A1, 1 on LG A2, 5 on LG B1, 4 on LG B2, 8 on LG C2, 11 on LG D1a, 2 on LG D1b, 4 on LG F, 5 on LG G, 2 on LG H, 1 on LG I, 1 on LG J, 1 on LG K, 2 on LG L and 2 on LG N. Eight QTL showed a good stability across 17 environments. The additive main-effect QTL contributed more phenotypic variation than the epistasis and environmental interaction. This indicated that it is feasible to improve soybean oil content by marker-assisted selection.
Karyotype characteristics and polymorphism peculiarities of Chironomus luridus (Diptera: Chironomidae) from Central and Northwest Caucasus

Abstract The study presents data on the karyotype characteristics and features of chromosomal polymorphism of Chironomus luridus Strenzke, 1959 (Diptera: Chironomidae) from several Caucasian populations (Central and Northwest Caucasus). Eight banding sequences were found in the Caucasian populations. Inversion polymorphism was observed only in arm C. The genetic distances between all the studied populations of C. luridus were calculated using Nei criteria. The studied Caucasian populations are generally closest to Asian populations. However, most of the Caucasian populations (Northwest Caucasus) form their own separate cluster. The principal component analysis (PCA) shows a similar picture. Two of the Caucasian populations do not follow Hardy-Weinberg expectation, bearing a marked deficiency of lur C1.2 heterozygotes, arguably, due to negative selection of heterozygotes. All the obtained data are indicative of relative remoteness of the Northwest Caucasian populations from the previously studied ones and total complexity of the entire Caucasus from the microevolution standpoint.
The translational landscape of Zika virus during infection of mammalian and insect cells

Zika virus is a single-stranded, positive-sense RNA virus of the family Flaviviridae, which has recently undergone a rapid expansion among humans in the Western Hemisphere. Here, we report a high-resolution map of ribosomal occupancy of the Zika virus genome during infection of mammalian and insect cells, obtained by ribosome profiling. In contrast to some other flaviviruses such as West Nile, we find no evidence for substantial frameshift-induced ribosomal drop-off during translation of the viral polyprotein, indicating that Zika virus must use alternative mechanisms to downregulate levels of catalytically active viral polymerase. We also show that high levels of ribosome-protected fragments map in-frame to two previously overlooked upstream open reading frames (uORFs) initiating at CUG and UUG codons, with likely consequences for the efficiency of polyprotein expression. Curiously, in African isolates of Zika virus, the two uORFs are fused in-frame into a single uORF. A parallel RNA-Seq analysis reveals the 5′ end position of the subgenomic flavivirus RNA in mammalian and insect cells. Together, these provide the first analysis of flavivirus gene expression by ribosome profiling. Recent Zika virus outbreaks have been associated with congenital diseases and neurological complications. An enhanced understanding of the molecular biology of this pathogen may contribute towards the development of improved treatment and control methods. We present a single-codon resolution analysis of Zika virus translation in mammalian and mosquito cells using ribosome profiling. The analysis revealed two hitherto uncharacterized uORFs in the 5′ leader of Zika virus Brazilian isolate PE243, both of which are occupied by ribosomes during infection. In contrast, these two uORFs are fused into a single uORF in African isolates. This observation provides a new avenue for further investigations into potential factors involved in the emergence of Zika virus from a rarely detected pathogen into a major epidemic.
Edible Giblets and Bone Mineral Characteristics of Two Slow-Growing Chicken Genotypes Reared in an Organic System

This study was conducted to compare edible giblets weight, tibial bone mineral density (BMD), and bone mineral content (BMC) of two slow-growing broiler genotypes (Hubbard S757; S757 and Hubbard Grey Barred JA; GB-JA) reared with outdoor access, and to determine the relationship between these variables. Day-old chicks (straight-run) of the genotypes S757 (n=120) and GB-JA (n=120) were housed for 98 days. Each genotype was assigned to six pens of 20 birds each. Birds were reared in indoor floor pens and moving shelters with outdoor access (during daylight hours). Absolute body (BW), heart (HW), spleen (SW), liver (LW), gizzard (GW), and abdominal fat pad (AFW) weights of the genotype S757 and male birds were statistically higher than that of the genotype GB-JA and female birds. Genotype statistically affected relative HW, whereas sex affected relative GW. Although BMD values were not influenced by genotype or sex, S757 birds and males presented statistically higher tibial BMC, lean, lean+BMC, total mass values (g) and area (cm2) compared with GB-JA birds and females. BW, HW, SW, LW, GW and AFW were positively correlated with BMC obtained by DXA. In conclusion, the measured traits influenced by genetic strain and sex. The use of the Hubbard S757 genotype in organic production systems with outdoor access is recommend.
Isolasi dan karakterisasi enzim β-1,3-endoglukanase dari tanaman kubis (Brassica oleracea CV. Capitata L.)

Isolation and characterization of β-1,3-endoglucanase from cabbage (Brassica oleracea var. capitata L.) have been done. It showed 40oC of optimum temperature, and optimum pH is 7. After the purification with hydrophobic interaction chromatography and ion exchange chromatography, it’s activity was increased. Based on SDS-PAGE analysis, β-1,3-endoglucanase have molecular weight around 48 kD. Antifungal activity of β-1,3-endoglukanase show that it has best inhibition zone on Fusarium solanii at extract from ion exchange chromatography.
FRONTIERS IN PALAEONTOLOGY VIBRATIONAL SPECTROSCOPY OF FOSSILS

Over the last two decades, there has an been increasing interest in applying vibrational spectroscopy in palaeontological research. For example, this chemical analyt- ical technique has been used to elucidate the chemical composition of a wide variety of fossils, including Archaean putative microfossils, stromatolites, chitinozoans, acritarchs, fossil algae, fossil plant cuticles, putative fossil arthropods, conodonts, scolecodonts and dinosaur bones. The insights provided by these data have been equally far ranging: to taxonomically identify a fossil, to determine biogenicity of a putative fossil, to identify preserved biologically synthe- sized compounds and to elucidate the preservational mech- anisms of fossil material. Vibrational spectroscopy has clearly been a useful tool for investigating various palaeon- tological problems. However, it is also a tool that has been misapplied and misinterpreted, and thus, this review is ded- icated to providing a palaeontologist who is new to vibra- tional spectroscopy with a basic understanding of these techniques, and the types of chemical information that can be obtained. Two example applications of these techniques are discussed in detail, one looking into fossil palynomorph taxonomy and other into the enigmatic Burgess Shale-type preservation.
Avaliação da atividade antimicrobiana in vitro do extrato aquoso e do óleo essencial do alecrim (Rosmarinus officinalis L.) e do cravo-da-índia (Caryophyllus aromaticus L.) frente a cepas de Staphylococcus aureus e Escherichia coli

Staphylococcus aureus e Escherichia coli apresentam fatores de virulencia que lhes permitem grande capacidade de adaptacao, culminando no crescente aumento de sua resistencia antimicrobiana, o que e agravado pelo uso indiscriminado e incorreto dos antibioticos.
Phylogenetic analyses of Chaetopteridae (Annelida)

Phylogenetic relationships within Chaetopteridae were assessed using parsimony cladistic analysis of 43 external morphological characters and molecular phylogenetic analysis of three genes: mitochondrial cytochrome oxidase subunit I DNA (COI) and nuclear 28S and 18S ribosomal DNA. The group currently comprises four accepted genera: Chaetopterus Cuvier, Spiochaetopterus Sars, Phyllochaetopterus Grube and Mesochaetopterus Potts, with 97 available species names. We selected 79 species and one subspecies with adequately detailed data for morphological comparison. Sixteen additional unidentified chaetopterid species were included to enhance representation of the morphological and genetic diversity of the family. The morphological matrix was coded chiefly from the original descriptions, as well as revisions, type specimens and newly collected specimens. Chaetopteridae was monophyletic in the molecular phylogeny, and united by a number of morphological features, including a single pair of grooved peristomial palps, three morphologically distinct tagmata (A, B, C) and the presence of stout, modified cutting chaetae on anterior chaetiger 4 (A4). Chaetopterus and Mesochaetopterus formed well‐supported sister clades based on sequence data; however, the reciprocal monophyly of these genera was not supported by morphological data. Spiochaetopterus and Phyllochaetopterus were paraphyletic/polyphyletic as currently defined, and the status of these and other available generic names is discussed.
Hair Cortisol Measurement and Relationships with Growth Among Amazonian Shuar Children

 Optimize hair cortisol extraction protocol  Establish reference levels of hair cortisol in Shuar children  Examine relationships between cortisol and growth parameters Cortisol is a hormone secreted by the adrenal gland in response to stress. It is a widely-used biomarker of stress. Cortisol can be analyzed from saliva, blood, urine, and hair. However, collecting saliva, urine, and blood only provide "point samples" (reflecting acute/short-term cortisol level), making it challenging to examine chronic physiological stress Advantages of hair collection:  Non-invasive  Hair grows at a rate of 1 cm/month, allowing assessment of cumulative concentrations of cortisol, and therefore stress, over a period of months corresponding to the length of hair used
Generation of a spatiotemporally inducible reporter mouse model for in vivo imaging of pancreatic cancer therapy

A conditional, Cre-loxP based mouse model for non-invasive real time in vivo monitoring of pancreatic cancer cell proliferation has been characterized as drug validation platform via chemotherapeutic intervention studies and in vivo bioluminescence imaging of therapeutic response. Furthermore, a new spatiotemporally inducible reporter mouse model has been generated and validated for in vivo and ex vivo imaging of Cre and Flp recombinase mediated recombination events, respectively, which is based on a combination of different bioluminescent and fluorescent reporter proteins.
Study on angiotensin I-Converting enzyme inhibitory activity and antioxidative activity of peptides derived from some Thai traditional fermented fishery products

Some of Thai traditional fermented fishery products were found to be a source of angiotensin I-converting enzyme (ACE) inhibitory and antioxidative peptides which could be used for the hypertension control. The highest ACE inhibitory activity was found in the extract from Pla-som. For antioxidative activities, the extracts from Bu-du, Kung-chom and Kem-buk-nud exhibited the highest 2,2-diphenyl-1-picryl hydrazyl (DPPH) radical scavenging activity, 2,2-azino-bis (3-ethylbenzothiazoline-6sulfonic acid) (ABTS) radical scavenging activity and ferric reducing antioxidant power (FRAP) (p<0.05), respectively. Based on principal component analysis (PCA), peptides with high ACE inhibitory activity were more likely present in products with low pH and low salt content. The presence of these peptides was probably governed by the use of garlic and raw material used but not affected by the ratio of free and total free α -amino acids (F/T ratio). For antioxidative activities, peptides with high FRAP were more likely found in products with high F/T ratio. Products with high DPPH radical scavenging activity more likely had high ABTS radical scavenging activity but both activities showed no correlation to pH, salt content and F/T ratio. In addition, ACE inhibitory activity exhibited no correlation to antioxidative activities. Since ACE inhibition is the main effect on blood pressure lowering, Pla-som produced from Puntius gonionotus which showed the highest ACE inhibitory activity was further studied. Inoculation of Pediococcus acidilactici BCC 9545 and Staphylococcus xylosus BCC3710 in Pla-som produced from Puntius gonionotus resulted in a reduction of fermentation time but could not increase the release of ACE inhibitory