Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality and Conservation of Riparian Forest in a Mountain Subtropical Basin of Argentina

The aims of this work were to describe the conservation status of riparian forests located in a mountain subtropical basin of Tucuman province, Argentina, and assess how the quality of riparian forests is related with altitude, plant species richness, proportion of exotic species, and Total Suspended Solids (TSS) in adjacent rivers. Composition and species richness of riparian forests were studied at 16 sites located along an altitudinal gradient and TSS was determined from water samples collected in each site. In order to evaluate conservation status of riparian forests, we calculated an index of Quality of Yungas Riparian Forests (QBRy). We recorded 90 plant species at all sites, from which 77% were native. QBRy index was mainly associated with altitude and varied from riparian forests with good preservation or slightly disturbed to those with extreme degradation. At lower altitude, forests were more disturbed, more invaded by exotic plant species, and closer to urban and cropped areas. QBRy was not correlated with species richness or TSS. Like other riparian forests of Argentina, plant species invasion increased their degradation; therefore, future studies should focus on native riparian forests conservation and on the management of invasive plant species, which affect their quality.
PHYSICAL MAPPING OF GENOME AND GENES

Mapping genome of an organism is an important tool to provide a guide for the sequencing experiments by showing the exact positions of genes and other distinctive features in the chromosomal DNA. Whole genome sequencing of eukaryotic genomes is greatly facilitated by high- density genome maps. The highdensity maps serve as foundation during organizing and assembling the nucleotide sequences of genomes. Reference to the map ensures that regions containing repetitive DNA are assembled correctly. Distinctive features on the genome map are used as landmarks to aid assembly of master sequence from huge number of short sequences obtained from genomic library. First step for manipulation of genes for various applications is cloning that relies on mapping close to a convenient marker. A complete physical-genetic map of genome is necessary for comparative genomics studies with other genomes. High-resolution comparative physical maps will reveal regions of colinearity and rearrangement and will have important implications for phylogenetic studies and genome evolution.
Nutritional Composition of Iron, Zinc, Calcium, and Phosphorus in Wheat Grain Milling Fractions as Affected by Fertilizer Nitrogen Supply

Fe and Zn deficiencies are global nutritional problems. N supply could increase Fe and Zn concentrations in wheat grain. This study was conducted to determine the impacts of different N rates (0, 122, 174, and 300 kg/ha) on the distribution and speciation of Fe and Zn in wheat grain milling fractions under field conditions. Zn and protein concentrations were increased, whereas Fe was less affected in the flour fractions with increasing N rates. Further analysis with size-exclusion chromatography coupled with inductively coupled plasma mass spectrometry revealed that Fe and Zn bound to low-molecular-weight (LMW) compounds in the flour fractions (probably Fe-nicotianamine [NA], Fe-deoxymugineic acid, or Zn-NA) were less affected by increasing N supply, representing 3.5–10.9% of total Fe and 2.5–56.6% of total Zn. In the shorts fraction, LMW-Fe was absent, and LMW-Zn with higher N supply was over twice as high as that in control and 3–27 times as high as that in the other milling fractions. In the flour frac.
Preliminary analysis on the transcripts involved in resistance responses to eumusae leaf spot disease of banana caused by Mycosphaerella eumusae, a recent add-on of the sigatoka disease complex

Eumusae leaf spot disease, caused by Mycosphaerella eumusae, is widely distributed in different banana growing countries in Asia and Africa, causing severe losses in yield and quality of banana. The aim of this study was to identify the differentially expressed defense responsive genes through subtractive suppression hybridization (SSH) in the Musa-M. eumusae interaction system. In this method, leaf samples collected at different intervals between 0 and 72 h postinoculation (hpi) of M. eumusae from resistant (Manoranjitham- AAA) and susceptible (Grand Naine-AAA) cultivars were subjected to cDNA-SSH library construction. From the SSH library, 832 clones having the insert were selected and sequenced. All these sequences were assembled using CAP3, which resulted in 498 unigenes (59.85%), consisting of 78 contigs and 420 singletons. Furthermore, the BLAST2GO analysis performed showed that, out of the 498 unigenes, only 161 (32.32%) were involved in molecular functions, cellular component and biological processes. However, among these 161 unigenes, 57 were found to have top BLAST hits. Six genes were selected based on the function and subjected to validation through qPCR. Four genes, namely ethylene responsive factor, flavin containing monoxygenase, serine glyoxylate, and metallothionein, were found to have the highest-fold regulation in the resistant cultivar at 48 hpi, followed by lipoxygenase at 36 hpi. The main findings are that resistant plants deploy HR activity as a strategy to evade the fungus followed by the activation of various ROS scavengers to maintain homeostasis and the role of phytohormones may be induced as a part of plant defense against M. eumusae.
High-yield protein production from Pichia pastoris yeast : A protocol for benchtop fermentation

Introduction Over the last several decades, geneticists have learned how to manipulate DNA to identify, excise, move and place genes into a variety of organisms that are quite different genetically from the source organism. A major use for many of these recombinant organisms is to produce proteins. Since many proteins are of immense commercial value, numerous studies have focused on finding ways to produce them inexpensively, easily and in a fully functional form.
Autumn dormancy regulates the expression of cas18, vsp and corF genes during cold acclimation of lucerne (Medicago sativa L.)

Abstract. As a global forage legume, lucerne (alfalfa, Medicago sativa L.) is valuable for studying the evolutionary and ecological mechanisms of plant adaptation to freezing, owing to the characteristic of contrasting winter hardiness induced by autumn dormancy. Autumn-dormant lucerne plants often exhibit greater cold tolerance than non-dormant plants under natural field conditions. The study examined the autumn shoot growth of four diverse lucerne cultivars, and the influence of two sampling dates in late autumn, three sampling positions and four autumn-dormancy categories on cas18, vsp and corF gene transcripts during the first year of lucerne establishment. Results showed that in field-grown lucerne, non-dormant and highly non-dormant cultivars had greater shoot growth than a dormant cultivar in autumn. The level of transcripts of cas18 (which encodes a dehydrin-like protein) was highest in dormant cultivars and lowest in semi-dormant cultivars in both November and December; in particular, the cas18 transcripts in the crown remained highest in both November and December. The level of transcripts of vsp (which encodes vegetative storage protein) in all dormant cultivar tissues was highest in both November and December. In semi-dormant cultivars, the expression of vsp in the taproot increased compared with the lateral root and crown in November. The corF transcript in the dormant cultivar was markedly higher than in the semi-dormant cultivar and almost zero in the non-dormant and highly non-dormant cultivars. These results indicate that the significant impact of autumn dormancy and plant position on gene expression of cas18, vsp and corF occurring during autumn hardening, and continuing low temperatures, are likely to have significant consequences on lucerne productivity and its long-term persistence.
Potential of thidiazuron in improved micropropagation of Picrorhiza kurroa– an endangered medicinal herb of alpine Himalaya

Abstract The potential of thidiazuron (1-phenyl-3-(1, 2, 3-thiadiazol-5-yl) urea (TDZ) in the micropropagation of Picrorhiza kurroa, a western Himalayan herb was studied. The roots and rhizomes of this plant are rich in medicinally important glycosides i.e., picroside I, picroside II and kutkoside. Nodal segments (2.0–2.5 cm) from plants were pretreated with 0, 0.25, 0.50, 0.75, 1.0 μM TDZ for 7, 15 and 30 days. Maximum shoot multiplication was recorded after 60 days, provided, the nodal segments pretreated with 0.5 μM TDZ for 15 days were transferred to 0.8% agar gelled MS medium containing 3.0% sucrose. The shoots also showed profuse rooting having maximum length. When these plantlets were incubated at 15°C for 10 days and transferred to sand under polyhouse conditions, 100% survival was recorded after one month. In contrast, when the plantlets were not incubated at 15°C, only 86% survival was recorded. While the stomata and chlorophyll content of the tissue culture-raised plantlets treated at 15°C were comparable to that of plants growing in the field, the ones that were not treated at 15°C showed lower number of stomata and chlorophyll content.
Assay of the Carboxylase Activity of Rubisco from Chlamydomonas reinhardtii

[Abstract] The performance of the carbon-fixing enzyme, ribulose 1, 5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39, Rubisco), controls biomass accumulation in green plants, algae and most autotrophic bacteria. In particular, the carboxylase activity of Rubisco incorporates carbon from CO2 to ribulose 1, 5-bisphosphate (RuBP) producing two molecules of 3-phosphoglycerate. Here a detailed protocol is given for the assay of the carboxylase activity of Rubisco from Chlamydomonas reinhardtii, a model organism for chloroplast studies and a fitting host for biotechnologically oriented genetic manipulation of the enzyme. Rubisco has to be pre-incubated with Mg2+ ions and bicarbonate to induce the catalytically competent active center (Laing and Christeller, 1976). Once Rubisco is activated, the assay of its carboxylase activity described here is based on the fixation of 14C-carbon dioxide/bicarbonate into acid-resistant radioactivity (Lorimer et al., 1977). Although a spectrophotometric assay is also available (Lilley and Walker, 1974), the method based on fixation of a radioactive substrate is irreplaceable when processing a large number of samples, and it is still the technique most often used for the determination of Rubisco activity.
Aplicação foliar de fungicidas e incidência de grãos ardidos e fumonisinas totais em milho

The objective of this work was to evaluate fungicide leaf application on the reduction of fungal pathogen incidence, kernel rot, and total fumonisins in corn ( Zea mays ) kernels. Three experiments were performed: one in the municipality of Luis Eduardo Magalhaes, in the state of Bahia, and two in the municipality of Sete Lagoas, in the state of Minas Gerais, Brazil, during the 2010/2011 and 2011/2012 crop seasons, with planting of different commercial hybrids. The following fungicides were applied zero, one, and two times: picoxystrobin + cyproconazole, pyraclostrobin + epoxiconazole, trifloxystrobin + tebuconazole, azoxystrobin + cyproconazole, and thiophanate‑methyl. For all trials, the quantification of kernel rot incidence, the grain pathology test, and the quantification of total fumonisins were performed. No significant difference was observed for the factors fungicide and number of applications, except for grain yield, in all trials. These results show the ineffectiveness of fungicide applications in reducing fungi incidence, kernel rot, and levels of total fumonisins in corn kernels.
Wave hindcast statistics in the seasonally ice-covered Baltic Sea

We used six years of wave hindcasts, calculated by the wave model WAM, to compile wave statistics for the Baltic Sea. The wave model was implemented taking into account the special features of the Baltic Sea: irregular coastline, archipelago and ice. To our knowledge, there is no single way to present annual statistics in seasonally ice-covered seas. We discuss five different possibilities to calculate the statistics, and the differences between them. According to verification against wave buoy and satellite altimeter measurements, the quality of the hindcast significant wave height is sufficient for presenting reliable wave statistics. The mean values of the significant wave height are smaller than 1.5 m. According to the mean values and exceedance probabilities, the severest wave climate is in the Baltic Proper. The wave climate in the other basins is considerably less severe. The maximum hindcast significant wave height is over 9 m, whereas the measured maximum is 8.2 m.
Expression and purification of recombinant Shiga toxin 2B from Escherichia coli O157:H7

Enterohemorrhagic Escherichia coli are important human food-borne pathogens. Recently, Shiga toxinproducing E. coli (STEC) causes life-threatening hemolytic-uremic syndrome (HUS). In this study, Stx2B gene, a subunit of Shiga toxin, was amplified via polymerase chain reaction (PCR) from the chromosomal DNA of clinical fecal sample using appropriate primers. The PCR product was cloned to commercially available plasmid pH6HTN His6HaloTag® T7 containing two purification tags, namely, six histadine tag and Halo tag. The integrity of the constructed plasmid was confirmed using restriction enzyme mapping and sequencing. Then, Stx2B protein expressed after induction with isopropyl β-D-1-thiogalactopyranoside (IPTG) in E. coli JM109 (DE3) under the control of the T7 promotor. The two step purification trains were used to purify native Stx2B. First step purification was Ni-immobilized metal ion affinity chromatography (IMAC) column, followed by second step using HaloLink resin. The native Stx2B was obtained after column cleavage of halo-tag using HaloTEV protease. Maximum protein expression of Stx2B economically was obtained using 1 mM IPTG for 4 h at 37°C. Protein identity was confirmed by a band at ~11.4 kDa using 15% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and StxB2 yield was 450 μg ml -1 confirmed by Bradford assay. Recombinant Stx2B protein was produced in highly pure yield using HaloTag technology. Key words : Escherichia coli O157:H7, StxB gene, expression, HaloTag technology, purification.
Genetic and demographic consequences of human-driven landscape changes on bird populations: The case of Aphrastura spinicauda (Furnariidae) in the temperate rainforest of South America

Habitat fragmentation can disrupt dispersal of organisms and therefore it can also influence genetic processes at the population level. Time since isolation, however, can be a limiting factor to detect the full extent of genetic consequences on populations, especially when fragmentation occurs at small spatiotemporal scales as in many human-modified landscapes. Naturally fragmented systems that have been isolated for long periods of time (i.e. thousands of years), such as relict cloud-forests in north-central Chile provide a good opportunity to study large-scale and long-term effects of forest fragmentation. The goals of this study were (1) to contrast the genetic structure of Aphrastura spinicauda (Furnariidae) populations inhabiting naturally fragmented relict-forests with those found in human-caused fragments and (2) to determine if forest replacement by open habitat reduces landscape connectivity and therefore influences the genetic structure of populations by comparing populations in fragmented and continuous forests. Six populations were sampled at a regional scale (distance range: 100-1000 km) with two of those (one continuous forest and one anthropogenic fragmented landscape) further divided into several subpopulations to investigate genetic spatial patterns at a short and small time-space scale (distance range: 2-30 km). Individuals were genotyped at five microsatellite loci. Genetic consequences of isolation were observed at both small and large time-space scales although patterns in human-caused fragments were less pronounced. Relict forests were inhabited by two genetically distinct populations, but two continuous-forest Cintia Cornelius, 2006, Ph.D. Dissertation, p. 4 populations separated by the same distance were not differentiated, indicating that large distances are a barrier for A. spinicauda dispersal only if habitat separating populations is not forest. A similar pattern was observed at the small scale. The comparison of genetic differentiation among four sites in the continuous forest revealed that these subpopulations were not genetically differentiated. In contrast, subpopulations in forest fragments that were similarly distributed across space (but not connected by forest) were significantly differentiated suggesting reduced dispersal among fragments. There was a significant isolation by distance pattern at the large spatial scale. At the small scale, however, it was significant only after controlling for the landscape context of individual fragments (i.e. number and size of fragments within the neighborhood of a focal patch). In this study, I showed that time-space scales are important in revealing the genetic consequences of habitat fragmentation and that forest replacement by open habitat, geographic distance among populations, and size of forest fragments are important in determining genetic differentiation of populations.
An overview of the progress and challenges of peatland restoration in Western Europe

Peatlands are the most efficient terrestrial carbon store on Earth, and deliver multiple other ecosystem services including climate regulation, water purification, preservation of ecological and archaeological records, etc. Disturbed and degraded peatlands do not provide the same ecological services and thus bear a significant cost to society. Because this cost may be alleviated by appropriate restoration measures, money is being invested in peatland restoration projects around the world. Here, we review over 25 years of restoration in Western Europe. First, we provide an overview of techniques used in different contexts and evaluate the status of the evidence base for restoration outcomes. Between 1993 and 2015, the EU‐LIFE nature programme alone invested 167.6M € in 80 projects, which aim to restore over 913 km2 of peatland habitats in Western European countries, mostly in protected sites part of the Natura 2000 EU network. This represents less than 2% of the total remaining area of peatlands in these countries, most of which have been impacted to some degree by anthropogenic disturbances. Potential for restoration should be considered in nondesignated sites. We reviewed a number of case studies covering a range of restoration approaches used in different parts of Western Europe. We found that published evidence of restoration progress was limited to specific sites/areas, and in many cases lacked baseline measurements and clear goals, that is, measurable target or contemporary reference(s). We discuss barriers and opportunities to turn the tide for peatland restoration in Western Europe and promote the establishment of robust, standardized monitoring schemes.
Tubulin Conformation and Anaesthetic Interaction - An Experimental Study

The current endeavour of neuroscience and philosophy is to discover the code of consciousness or rather how the material brain produces our in Material sense of awareness. Some scientists believe that consciousness is something distinct from the physical brain and body, as consciousness continues to exist even when the brain is not functioning. But from a scientific viewpoint, consciousness is a function of the brain. Since the brain is a material entity, consciousness is subject to the study of science. The human brain is a complex mass of tissue endowed with extraordinary capabilities. Microtubules turn out to be a common target of neurotransmitter action and play a significant role in learning and memory. Memory and consciousness are interrelated, thus, microtubules could be the link between these two phenomena. Microtubules are cylindrical hexagonal lattice polymers of the protein tubulin, comprising 15% of total brain protein. Microtubules regulate synapses and are suggested to process information via interactive bit-like states of tubulin. Microtubules are very dynamic polymers whose assembly and disassembly is determined by whether their heterodimer tubulin subunits are in a straight or curved conformation. Curvature is introduced by bending at the interfaces between monomers. This is because GTP hydrolysis promotes bends in protofilaments. However, while GDPbound protofilaments are still associated together as a microtubule or 2-D sheet, the contacts between neighbouring subunits constrain them to remain in a straight form. The resulting tension is proposed to store conformational energy that is released during depolymerisation. Also, the mechanism by which anaesthetics prevent consciousness remains largely unknown because the mechanism by which brain physiology produces consciousness is unexplained. Tubulins have other smaller non-polar regions that contain pi electron-rich indole rings separated by only about 2 nm. Penrose- Hameroff Orchestrated Objective Reduction (Orch-OR) Theory proposes that these electrons are close enough to become quantum entangled. They suppose that quantum-superposed states develop in tubulins, remain coherent and recruit more superposed tubulins until a mass-time-energy threshold, related to quantum gravity, is reached called as the 'bing' moment. This paper characterizes the conformation of tubulin in presence of anesthetics.
Population and individual effects of non-coding variants inform genetic risk factors

Identifying functional non-coding variants can enhance genome interpretation and inform novel genetic risk factors. We used whole genomes and peripheral white blood cell transcriptomes from 624 Sardinian individuals to identify non-coding variants that contribute to population, family, and individual differences in transcript abundance. We identified 21,183 independent expression quantitative trait loci (eQTLs) and 6,768 independent splicing quantitative trait loci (sQTLs) influencing 73 and 41% of all tested genes. When we compared Sardinian eQTLs to those previously identified in Europe, we identified differentiated eQTLs at genes involved in malarial resistance and multiple sclerosis, reflecting the long-term epidemiological history of the island’s population. Taking advantage of pedigree data for the population sample, we identify segregating patterns of outlier gene expression and allelic imbalance in 61 Sardinian trios. We identified 809 expression outliers (median z-score of 2.97) averaging 13.3 genes with outlier expression per individual. We then connected these outlier expression events to rare non-coding variants. Our results provide new insight into the effects of non-coding variants and their relationship to population history, traits and individual genetic risk.
Anaticola crassicornis (Phthiraptera: Ischnocera: Philopteridae) on wild geese from Pakistan.

Twenty-eight geese (Anser anser, A. albifrons and A. indicus) from different localities around Karachi, Pakistan, were examined for lice. One species of chewing louse, Anaticola crassicornis (Scopoli), was found on every bird examined. This is the first record of this louse species from members of Anser. In the light of past confusion, the authors redescribe A. crassicornis in detail, with special reference to its genitalia, and compare it with A. anseris. Despite the louse not appearing on ducks sampled at the same time as the geese, we hypothesize that A. crassicornis is likely to have passed to the geese as a result of recent host switching from an unidentified anatid host.