Miracle-dz/UniFAR-FTUs huggingface dataset:
Taxonomy and molecular systematic position of freshwater genus Racekiela (Porifera: Spongillida) with the description of a new species from North-west Mexico

Racekiela montemflumina sp. nov. is the first species of the genus Racekiela found in freshwater habitats from Mexico. The species is abundant in small creeks at the northern side of State of Durango, located between 2500 and 2700 m altitude. The new species description is provided together with in situ photographs of specimens, and SEM photographs of the spicules and gemmular structure. Two distinct classes of gemmuloscleres differing in size and shape (birotules and pseudobirotules) are present. The rotule of the birotula is discoidal, flat or slightly umbonate, with serrated margins and small crenulate teeth, or spines. The proportion of the diameter of the rotule vs. length of the shaft is the lowest of all the Racekiela species. Rotule of pseudobirotule is small, umbonate or with a prominent spike, and with hooks curved toward the shaft or almost straight. The birotules are embedded in the theca, but pseudobirotules protrude from the outer gemmular membrane. Fragments of cytochrome oxidase subunit I (COI) mtDNA, and internal transcribed spacers 1 and 2 (ITS1-5.8S-ITS2) rDNA were sequenced in order to establish the molecular identity and systematic position of genus Racekiela and the new species. COI showed an identical nucleotide composition with at least 11 spongillid-specimens from six previously sequenced species (GenBank). Phylogenetic analysis using the ribosomal region was concordant with previous information, which showed the monophyly of family Lubomirskiidae, and the non-monophyly of the families Spongillidae and Malawispongiidae. Specifically, Racekiela montemflumina sp. nov. erected as a sister clade of several species from the genera Ephydatia and Cortispongilla. Our species constitutes the first representative of genus Racekiela sequenced. This is also the first record of a freshwater sponge in Mexico in decades. www.zoobank.org/urn:lsid:zoobank.org:pub:71E826B6-59DC-475B-9391-27A7DED66E7A
Horizon symmetries of black holes with supertranslation field

Near-horizon symmetries are studied for black hole solutions to Einstein equations containing supertranslation field constructed by Compere and Long. The metric is transformed to variables in which the horizon is located at the surface $r=2M$, where $M$ is the mass of black hole. We consider general diffeomorphisms which preserve the gauge and the near-horizon structure of the metric and find the corresponding transformations of metric components. We review the action of the generators of supertranslations preserving the static gauge of the metric and determine a subgroup of supertranslations preserving the gauge and near-horizon structure of the metric. Variation of the surface charge corresponding to the Killing vectors of asymptotic horizon symmetries is calculated. Sufficient conditions of integrability of the variation of the surface charge to a closed integral form are found and an example of metrics with integrable charge variation is discussed.
Green Gold: Avocado price shocks and violence in Mexico

The role of economic incentives in political armed conflict is well documented, but there is very little evidence on a growing and increasingly globalized form of violence: organized crime. Most existing research focuses on the impact of price shocks on wages and how this affects an individual’s opportunity cost to join an armed group or political movement. However, unlike other violent groups, organized criminal groups do not compete for political power, but profits in illegal markets. In Mexico, these groups have more than doubled in the past two decades, leading to an explosion of violence and record high 35,000 people being murdered in 2019. Mexican cartels engage in rent-seeking behavior in both licit and illicit markets, especially in rural areas where illicit crop cultivation supports the drug trade. In this paper I use a differences-in-differences strategy exploiting variation in avocado and illicit drug prices from 2003-2018 to understand how price shocks to both legal and illegal commodities impact cartel competition in different markets. I find rising avocado prices have a significant effect on violent crime in avocado-growing municipalities at the monthly level. Cartels also are more likely to enter an avocado-growing municipalities as prices increase, and less likely to leave them. Avocados may also be complementary to illicit crop cultivation. ∗I am grateful to my advisor Jesse Anttila-Hughes for his supervision and suggestions for this paper, and to Fernanda Sobrino for her input and sharing her novel dataset Maping Criminal Organizations (joint with Marco Alcocer, Cecilia Farafan, Projects Brian Phillips, Victor Manuel Sanchez and Patrick Signorent) used in this paper. Special thanks to the U.S. Dept. of Agriculture and Katy Looft for her assistance and sharing monthly avocado
Perlite Affects Some Plant Indicators and Reduces Water Deficit in Tomato

ABSTRACT Water deficit in semi-arid areas is a limiting factor affecting crop production and quality. Suitable water regimes, and use of perlite to store moisture, may help overcome drought. The experiment was conducted from March to July 2016 in a field in Diyala, Iraq. The objective was to determine effects of tomato (Solanum lycopersicum L.) genotypes ‘Bobcat,’ ‘Finenss,’ and ‘Hadeer’; irrigation levels of 50% and 100% based on field capacity, and addition of perlite, at 0%, 5%, and 10% as a volumetric percent of soil, on plant growth and development, and water management. Combinations of factors resulted in 18 treatments. The ‘Finenss’+50% irrigation+10% perlite produced the least proline in leaves. Treatment ‘Bobcat’+50% irrigation+10% perlite produced the longest roots and least root dry weight. Treatment ‘Bobcat’+100% irrigation+5% perlite had the highest water use efficiency and can likely be recommended as an irrigation management strategy for tomato production under deficit irrigation. By using this strategy, approximately 50% of irrigation water can be conserved without reduction in yield. Perlite decreases adverse effects of water deficit and improves growth and production at normal and deficit conditions.
Tautog (Tautoga onitis) life history and habitat requirements

v Introduction . 1 Nomenclature and Taxonomy. 1 Distribution and Habitat . 2 Reproduction . 6 Development . 7 Age and Growth . 8 Feeding and Diet . 9 Behavior . 11 Population Structure . 13 Natural and Human-Induced Environmental Factors . 13 Ecological Roles . 16 Research Needs . 17 Endnotes . 18 Acknowledgments . 18 References Cited . 18
Targeted delivery of etoposide to osteosarcoma cells using poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) nanoparticles

Folic acid (FA)-functionalized poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) nanoparticles were prepared to enhance the delivery efficiency of the anticancer drug etoposide for the clinical treatment of osteosarcoma. PHBV nanoparticles were synthesized by emulsification/solvent evaporation technique and obtained in the size range of 200-250 nm and zeta potential range of -21 and -27 mV. Encapsulation efficiency and in vitro drug release were studied. The cytotoxic, apoptotic, and necrotic effects of PHBV nanoparticles were also investigated using Saos-2 osteosarcoma cells. The results obtained in this study demonstrate that etoposide-loaded and FA-functionalized PHBV nanoparticles can be successfully used for targeted treatment of osteosarcoma.
Characterization Of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) From Vibrio Vulnificus

iii List of Tables . v List of Figures . vi List of Abbreviations . vii Chapter 1: Introduction . 1 Chapter 2: Results and Discussion . 5 2.1: VvDxr Sequence Analysis . 6 2.2: Structural Analysis . 6 2.3: VvDxr Overall Analysis . 7 2.4: Active Site . 8 2.5: VvDxr in Complex with Metals . 9 Chapter 3: Materials and Methods . 38 References . 44 Appendix A: DSF Ligand Screening Conditions . 49 Appendix B: Optimized Index Conditions . 55
Phylogenetic relationships of turfgrasses as revealed by fragment analysis of chloroplast DNA

Chloroplast DNAs (cpDNAs) were analyzed in order to clarify the phylogenetic relationships among tur- fgrasses. Physical maps of cpDNAs from Agrostis stolonifera and Zoysia japonica, which are representative species of cool (C3 type) and warm (C4 type) season turfgrasses, respectively, were constructed with four re- striction enzymes, i.e., PsfI, SalI, SacI, and XhoI. The genome structures of these cpDNAs were found to be similar to each other in terms of genome size and gene orders, showing thereby a similarity to other grass cpDNAs. CpDNAs of 5 species of cool season turfgrass- es and 6 species of warm season turfgrasses as well as four species of cereals, distributed among 14 genera of Gramineae, were digested with PstI, XhoI, and BamHI, and their restriction fragment patterns were compared. Their genome sizes were estimated to be 135-140 kbp. Each species showed characteristic RFLP patterns. On the basis of the frequency of commonly shared frag- ments, a dendrogram showing the phylogenetic relation- ships among their cpDNAs was constructed. This den- drogram shows that turfgrasses can be divided into three major groups; these correspond to the subfamilies. Cool and warm season turfgrasses are clearly distinguishable from each other, and the latter can be further classified into two subgroups that correspond to Eragrostoideae and Panicoideae. Our classification of turfgrasses and cereals by RFLP analysis of cpDNA agreed in principal with their conventional taxonomy, except for the loca- tion of Festuca and Lolium.
Impact of Eastern oyster Crassostrea virginica biodeposit resuspension on the seston, nutrient, phytoplankton, and zooplankton dynamics: a mesocosm experiment

: To test the effect of Crassostrea virginica biodeposit resuspension on nutrient and plankton dynamics, a 4 wk experiment was performed in six 1000 l shear-turbulence- resuspension-mesocosms (STURM) without a sediment bottom (R). Three tanks (R_BD) received daily additions of oyster biodeposits (5.77 ± 3.33 mg total suspended solids). Simulated tidal resuspension of bio - deposits in the R_BD tanks resulted in concentrations of 90 mg l –1 total suspended solids when mixing was on, decreasing to ca. 20 mg l –1 when mixing was off. However, bulk settling speeds of particles in the R_BD tanks increased 3-fold over the experiment. Particulate nitrogen, phosphorus, and carbon concentrations as well as dissolved inorganic nitrogen, nitrate + nitrite, dissolved organic phosphorus, and total dissolved phosphorus levels were significantly higher in the R_BD tanks. In the R_BD tanks the greatest part (72%) of the nitrogen was partitioned in the total dissolved nitrogen, but in the R tanks the greatest part (51.5%) was partitioned in microphytobenthos. While chlorophyll a concentrations were higher in the R_BD tanks than in the R tanks (despite tuni-cates being found in the R_BD tanks), phytoplankton biomass (carbon) as estimated using direct cell counts was not significantly different and there was little difference in phytoplankton composition. However, the ratio of chl a :C was higher in the R_BD tanks, suggesting phytoplankton adjusted to low light in the R_BD tanks by increasing chl a in their cells. Acartia sp. abundance was also raised in the R_BD tanks. Addition and regular tidal resuspension of oyster biodeposits profoundly
Mapping the Dark Side: Visual Selectivity of Default Network Deactivations

The default network (DN) activates for internally referenced mental states, whereas it deactivates in response to sensory stimulation. We show that BOLD signal decreases in the DN are tuned to the spatial location of visual stimuli, allowing us to decode the location of a visual stimulus from DN regions. Our results indicate that the DN represents sensory information, and suggest it may utilize this reference frame for higher-level cognition.
Current molecular methods for the detection of GB virus C

&NA; The GB virus C (GBV-C), also referred to as hepatitis G virus, is a RNA hepatitis virus, which infects humans naturally and can cause high levels of viremia, which, however, in most cases, does not lead to serious illness. It is not usually routinely screened in clinical laboratories, though its presence in patients infected with other viruses such as hepatitis C virus and HIV has been commonly reported. The virus can be detected in the blood of infected individuals using reverse-transcription polymerase chain reaction (RT-PCR) mainly. It is a technique that is commonly used for different RNA material detection and other screening such as gene expression and testing. The method includes several steps, that is, transcription of the RNA into complementary DNA (cDNA) by reverse transcriptase, amplification of the cDNA by PCR using well defined primers that target a particular region of the gene, and detection of the PCR products by various means such as agarose gel electrophoresis or hybridization and immunoassay using, for example, automated detection systems. Several primers targeting different regions of the genome, that is, NS3, NS5, and 5’ NTR, have been developed for the amplification of the specific region and the detection of the virus. Moreover, variants of the RT-PCR have been designed to maximize the identification potential. These include, for example, RT-PCR-ELISA, RT digital-PCR, and SYBR green real-time multiplex RT-PCR. Another type of method used to screen the virus is the detection of the presence of antibodies E2 (anti-E2) produced against the viral glycoprotein E2 in individuals who have been infected with the virus and have recovered or are in the process of recovering. The anti-E2s are detected by radio-immunoprecipitation assay and ELISA. Use of both antibody and RNA detection methods is necessary for a better epidemiological investigation of the prevalence of GBV-C.
IN VİTRO DİRECT WHOLE PLANT REGENERATİON OF WATER LETTUCE (Pistia stratiotes L) USİNG THİDİAZURON

Water lettuce (Pistia stratiotes L.) belongs to Araceae family is an important stoloniferous floating plant of aquatic environment. The most common places where water lettuce plants can be easşly found are likes lakes, streams or stagnat water ponds. The plant shows wide distribution in tropical and subtropical regions of Africa, Asia, and America (Tripathi et al., 2010). The plant is perennial monocotoledenous with relatively soft leaves that are arranged in rosette formation. Hot season is important for flowering whereas, fruit bearings ocur after rainfall (Chadha, 1998). It considered to be the most reproductive plant of fresh water environments due to its properties and uses. Alkaloids, glycosides, flavonoids, and steroids are the essentially important biological compounds it contains. The plant leaves are rich in vitamin A, B and C which are used to cure diseases like eczema, leprosy, ulcers, piles, and syphilis. Besides thta, curing of chronic skin diseases is also done by using leaf extracts alongwith coconut oil (Kirtikar and Basu, 2001). Furthermore, it has diuretic, antidiabetic, antidermatophytic, antifungal, and antimicrobial properties (Prem Kumar and Shyamsundar, 2005), antiseptic, antitubercular, and antidysentric activities. Use of water lettuce for phytoremediation of Cd (Maine and Duarte, 2001), nitrate and ammonium (Nelson and Smith, 1981), and other heavy metals (Mishra and Tripathi, 2008) highlights the importance of this fresh water plant. Water lettuce make heavy foliage in water which inhibits the algae growth and keep water bodies clean. Water lettuce can be multiplicate by vegetative means in water bodies (Aasim et al., 2013) or by in vitro regeneration means (Zhang et al., 2008; Aasim et al., 2013). There is still need to develope efficient, reliable and reproduceable in vitro regeneration ptotocol fort his highly economic plant. Keeping in view, this study was designed to produce whole plants using thidiazuron under in vitro conditions. This regeneration protocol will be beneficial for the application of biotechnological tools like genetic transformation, secondary metabolites isolation or phytoremediation studies against heavy metals from water bodies.
Genetic Characterization of Portunid Crabs Scylla serrata and Scylla tranquebarica from the West Coast of India Using Random Amplified Polymorphic DNA Markers

Crabs of the genus Scylla (Decapoda: Portunidae) are commercially important and widely distributed throughout the Indian and Pacific Oceans. These crabs have an extended planktonic larval phase in their life cycle which suggests high dispersal potential and the possibility of extensive gene flow between conspecific populations on a geographic mesoscale (tens to hundreds of kilometers). Hence, genetic differentiation studies were carried out for Scylla serrata and S. tranquebarica along the west coast of India using RAPD markers. Twenty five wild specimens of each species were collected from a mangrove area of Ratnagiri district on the west coast of India. Three primers OPE-1, OPE-3 and OPE-4 produced clear and reproducible profiles and were selected for analyzing 20 individuals, each of S. serrata and S. tranquebarica . Primer OPE-4 gave a maximum percentage of 95.23% of polymorphic bands in S. serrata and OPE-3 showed 91% polymorphic bands in S. tranquebarica . Using primers OPE-1 and OPE-3, the two species were clearly clustered into separate groups. The average genetic similarity at the intra-specific level was calculated as 0.64 and 0.73 in S. serrata and S. tranquebarica , respectively, while the interspecies similarity was 0.56. The average
PHYLOGENETIC RELATIONSHIPS OF LEPTOBRACHIUM HASSELTII TSCHUDI, 1838 (AMPHIBIA, ANURA, MEGOPHRYIDAE) - DETECTION OF A POSSIBLE CRYPTIC SPECIES

By examining mitochondrial DNA phylogeny using 2424bp of sequence data 12S rRNA, tRNAval, and 16S rRNA genes, we evaluated the taxonomic relationships among Javan litter frogs Leptobrachium hasseltii from southern Sumatra, Java, and Bali. Leptobrachium hasseltii formed a well-supported monophyletic group, which comprised two major clades. One major clade represented the southern Sumatran and Javan populations and the other consisted of the population from Bali. The Javan and southern Sumatran clade included two subclades: the West Javan-southern Sumatran group and the Central Javan group. The genetic divergence between the two major clades (Bali vs. Java-Sumatra) suggested their separation happen at species level. Further studies using morphological and acoustic data are needed to determine the taxonomic status of Bali population.
Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers

Abstract The aim of this study was to characterise the genetic diversity, genetic relationship and population structure within local Turkish Denizli chicken subpopulations in rural areas using 19 microsatellite markers. To assess the uniqueness and relations of the Denizli subpopulations we used six local Italian chicken breeds’ samples, which were genotyped in the same laboratory with the same molecular markers. In total, 105 alleles were found across 19 microsatellite loci with a mean number of 5.53 alleles per locus. Considering all subpopulations and loci, genetic differentiation based on global FST was 0.030 (p < .01). Global FIS values (0.200) indicated that non-random mating occurred in all subpopulations of Denizli fowl and all subpopulations deviated significantly (p < .01) from HWE. Over all subpopulations, the mean observed heterozygosity was 0.473, ranging from 0.399 to 0.562. Genetic differentiations between pairs of subpopulations based on the proportion of shared alleles ranged 0.140–0.297. The neighbour-net tree, based on marker estimated kinship distances, separated Denizli subpopulations and Italian breeds into two main clusters. The most likely number of different populations was estimated using the clustering procedure implemented in STRUCTURE. Structure analysis showed a clear separation of the Denizli fowl subpopulations from the Italian populations. A second step sub-clustering allowed discriminating among the six subpopulations of Denizli breed. The results of this study can be used as baseline genetic information to place breeders’ flocks in conservation programmes, controlling inbreeding and safeguarding the genetic variability of the populations.
The energetics of the brackish water serpulid polychaete Mercierella enigmatica Fauvel

Investigations of the distribution of Mercierella enigmatica and the physical environment in the Thames estuary form the basis for a detailed laboratory study of the energy relations of this fouling organism. It was found that Mercierella*s intertidal distribution is positively correlated with that of the surface water at Greenhithe, which effectively buffers the animal against extremes in oxygen tension, salinity, and tenperature, whilst allowing unlimited feeding• The following components of the energy budget under winter and summer conditions were investigated: particulate feeding; the integumentary uptake of dissolved organic compounds; egestion; respiration; nitrogenous excretion; somatic growth; reproduction; tube production; and mucus production. The flow of energy through the various channels was quantified using microbomb calorimetry, biochemical techniques, respirometry (a volumetric micro-respirometer was designed specifically for this purpose), and radioactive tracers. A comprehensive investigation of the uptake kinetics, effects of endogenous and exogenous factors, and the fate of absorbed organic molecules, shows that these are apparently of little value as a supplementary nutritional source. An alternative hypothesis is ft proposed for the role of exogenous DOM in Mercierella*s energy budget. The oxygenational properties of the blood pigment were investigated, and the relative significance of the potential respiratory surfaces during the different phases of activity are
Biocontrol of Macrophomina phaseolina (Tassi) Goid: differential production of H2O2 and in the relationship pathogen – PGPR in soybean seedling

ABSTRACT We examined the biocontrol and the differential production of H2O2 and in the relationship Macrophomina phaseolina – PGPR in soybean seedling. Fungal colonisation was efficiently prevented by inoculation with Pseudomonas fluorescens 9. Its ability to improve ROS production and gene expression of antioxidant enzymes could be related to its capacity to control the disease.
Genetic diversity in Vernonia amygdalina Delile accessions revealed by random amplified polymorphic DNAs (RAPDs)

The bitter leaf plant (Vernonia amygdalina Delile) is an indigenous shrub tree species highly cultivated in West and Central Africa for its nutritional and medicinal values. We used 10 random amplified polymorphic DNA (RAPD) markers to assay 30 accessions of V. amygdalina Delile ecotypes (bitter and less bitter leaves, respectively) collected from the southern states of Nigeria (Cross River, Edo, and Oyo). The results obtained showed that RAPD markers were highly polymorphic (98.0%) and generated a total of 29 PCR bands – ranging from two for OPH-03 to 10 for OPB-01 primers. The polymorphic information content was highest for the OPB-01 primer (0.768). Moreover, gene diversity (He = 0.800) was high, and cluster analysis delineated the accessions into seven groups, which indicated that a significant genetic diversity was present among the accessions studied. The geographical distinctness observed among the accessions indicated a possible effect of plant isolation by distance and a restricted gene flow. The results obtained in this study showed a genetic variability that could be exploited for varietal delineation and used to improve this indigenous species in Nigeria. This is the first report on the molecular study of genetic diversity in V. amygdalina.