Miracle-dz/UniFAR-FTUs huggingface dataset:
Dispersal, homing, and connectivity in the estuarine fish, Osmerus mordax.

Dispersal is one of the most ubiquitous components of life histories, determining rates of connectivity, stability and persistence of populations and species. Nonetheless, dispersal estimates for marine species remain elusive despite concerns about collapse in populations and large-scale alteration of marine communities. A review of different approaches and estimates from the published literature and a subsequent evaluation using indirect measures of dispersal indicate a significant bias in the literature towards low-latitude, low-dispersal taxa. One approach that uses genetic isolation by distance relationships appears particularly promising, especially in species with high gene flow in which assumptions of drift-dispersal equilibrium are met. Using a combination of approaches, I examined dispersal within populations of anadromous rainbow smelt (Osmerus mordax) and its ecological and evolutionary consequences for spatial structure. Across different smelt life history stages, significant behavioural contributions to dispersal were observed from hatch to estuarine larval transport to adult spawning site fidelity. Overall, patterns were consistent across life history stages in that dispersal was restricted to small spatial scales such as a single estuary. Consistent with these findings, analysis of nine microsatellite loci and otolith elemental composition indicated fine-scale structure indicative of limited movements and supporting estuarine dependence. In addition, I observed signatures indicative of historic isolation and contemporary hitch-hiking selection at a putatively non-neutral locus. Trends in gene flow suggest geography as the major determinant, though morphological variation was independent of geography and gene flow. My results suggest that rainbow smelt dramatically dampen dispersal potential through behavioural mechanisms present at each life history stage, resulting in fine-scale structure on a scale comparable to anadromous salmonids. Moreover, my results suggest that given low rates of gene flow, signatures of contemporary and historical isolating mechanisms may be visible. This work allows the identification of various behavioural contributions to dispersal trajectories and, considered in the context of historical forces, their implications for spatial structuring in marine populations. Moreover, these results suggest the potential for extremely fine-scale complexity in estuarine and marine species, even in the presence of high dispersal potential.
Disain Primer Aktin Spesifik Tuntun Angin (Elaeocarpus floribundus) (Actin Primer Design Specific of Tuntun Angin (Elaeocarpus floribundus))

Abstra k Aktin merupakan salah satu dari housekeeping gene yang dapat digunakan sebagai kontrol internal pada analisis ekspresi gen. Sampai saat ini, sekuen DNA dari gen penyandi aktin pada tanaman tuntun angin ( Elaeocarpus floribundus ) belum pernah dipublikasikan. Penelitian ini bertujuan merancang primer aktin spesifik untuk tanaman Elaeocarpus floribundus bedasarkan primer aktin degenerate. Pasangan primer degenerate rancangan yang digunakan adalah PlAc46S sebagai primer forward : 5’- ATGGTNGGNATGGGNCARAA-3’ dan PlAc245N sebagai primer reverse : 3’ - GTDATNACYTGNCCRTCNGG-5’ . Metode penelitian meliputi isolasi DNA dari daun segar, amplifikasi dengan teknik polymerase chain reaction (PCR), elektroforesis pada 1,2% gel agarose, perunutan nukleotida, dan analisis data menggunakan program BLASTn dan perangkat lunak MEGA versi 6.06. Fragmen DNA aktin telah berhasil diamplifikasi menggunakan primer aktin degenerate dan telah dirancang primer aktin spesifik untuk Elaeocarpus floribundus dengan urutan sebagai berikut:5’- CCAAATCATGTTTGAGACCT -3’ ( forward ) dan 5’- GAACACGTTAATTCCTGCTC -3’ (reverse). Primer tersebut selanjutnya dapat digunakan untuk mengamplifikasi gen aktin dari E. floribundus pada analisis ekspresi gen. K ata Kunci : aktin, Elaeocarpus floribundus, PCR, primer degenerate, tuntun angin. Abstra ct Actin is one of the housekeeping genes which commonly be used as an internal control in gene expression analysis. Until now, the DNA sequence of actin gene of tuntun angin ( Elaeocarpus floribundus ) has never been published. This study aimed to design the actin primer specific for E. floribundus based on degenerate actin primer. The pair of the degenerate actin primer s ( PlAc46S 5’- ATGGTNGGNATGGGNCARAA-3’ and PlAc245N 3’ - GTDATNACYTGNCCRTCNGG-5’ ) were used in this study. Methods included DNA isolation from fresh leaf, PCR, electrophoresis, sequencing, and data analysis using BLASTn program and MEGA software version 6.06. The actin DNA fragment has been successfully amplified using the degenerate actin primer and then the actin primer spe c ific for E. floribundus with the following sequences : 5’- CCAAATCATGTTTGAGACCT -3’ (forward) an d 5’- AACACGTTAATTCCTGCTC -3’ (reverse) have been designed . The primer pair s can be used to amplify the actin gene of E. floribundus . K eywords : actin, degenerate primer, Elaeocarpus floribundus , PCR, tuntun angin.
Nuclear Factor Erythroid 2 Activation Mediated by PRKCA in Increasing Ca2+ Intracellular in Diabetic Condition

Diabetes increases in the worldwide by prevalence and numbers of complications related to it. The most common risk factor for foot ulcers in diabetic is peripheral neuropathy. In diabetic condition, Ca concentration intracellular increases. NRF2 (Nuclear Factor Erythroid 2) acts as a bridging link in various inflammatory and apoptotic pathways impacting progress of diabetic neuropathy. The aim of this study is to predict the pathway of NRF2 activation that is mediated by the increased of intracellular Ca. Data interaction between Ca and NRF2 were retrieved from STITCH (Search Tool for Interacting Chemicals) which were experimentally and prediction, then were analyzed computationally. Pathway analysis used Cytoscape software. The functional analysis was evaluated using STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database. The consequence of increased intracellular Ca content is the increases of oxidative stress, ROS (Reactive Oxygen Species) and the translocation of the protein kinase Cα (PKRCA) to the plasma membrane as the initial step of their activations. This study reveals that activation NRF2 by Ca intracellular which increases in diabetic condition through PRKCA, PRKCA phosphorylate NRF2 in its Neh2 domain at Ser-40.
Biochemical Characterization of Plant Small CTD Phosphatases and Application of CTD Phosphatase Mutant in Hyperaccumulation of Flavonoids in Arabidopsis

Biochemical Characterization of Plant Small CTD Phosphatases and Application of CTD Phosphatase Mutant in Hyperaccumulation of Flavonoids in Arabidopsis. (August 2010) Yue Feng, B.S., China Agricultural University, China Chair of Advisory Committee: Dr. Hisashi Koiwa In addition to AtCPL1-4, the genome of Arabidopsis thaliana encodes a large number of putative acid phosphatases. The predicted Arabidopsis SCP1-like small phosphatases (SSP) are highly homologous to the catalytic domain of eukaryotic RNA polymerase II carboxyl terminal domain (pol II CTD) phosphatases. Among the family members, SSP4, SSP4b and SSP5 form a unique group characterized by long N-terminal extensions. These three SSPs showed similar and ubiquitous gene expression. SSP4 and SSP4b were localized exclusively in the nuclei, while SSP5 accumulated both in the nucleus and cytoplasm. In vitro observation revealed that SSP4 and SSP4b dephosphorylated the pol II CTD-PO4 at both Ser2 and Ser5 in the conserved heptad repeats; however, SSP5 dephosphorylated only Ser5 of CTD-PO4. These results indicate that Arabidopsis SSP family encodes active CTD phosphatases similarly to animal SCP1 family proteins and plant CPLs family proteins, but with distinct substrate specificities. ssp mutants did not exhibit phenotypic abnormalities under normal growth conditions. However, ssp5 single mutants and ssp4 ssp4b ssp5 triple mutants showed enhanced
Prespawn Mortality of Female Chinook Salmon Increases with Water Temperature and Percent Hatchery Origin

AbstractHigh rates of prespawn mortality, when adult salmon die after completing migration but prior to spawning, can lead to population declines and can impede recovery of threatened stocks. In this study, annual prespawn mortality of female Chinook Salmon Oncorhynchus tshawytscha ranged from 1% to 100% over 14 years in seven study reaches located throughout the upper Willamette River Basin, Oregon. Prespawn mortality rates were positively correlated with the annual maximum seven-day average maximum stream temperature and the percentage of spawning fish of hatchery origin. Observed prespawn mortality rates varied considerably, but where maximum temperatures exceeded 20°C and the composition of spawning fish was >80% hatchery origin, annual female prespawn mortality rates were consistently >80%. In several spawning tributaries, prespawn mortality rates generally decreased at higher elevations. The proximate cause of prespawn death was not evaluated here and observed patterns likely reflect additional fact.
Survival of White Spot Syndrome Virus–Infected Litopenaeus vannamei Fed with Ethanol Extract of Uncaria Tomentosa

With the present project, the phytochemical composition of Uncaria tomentosa cultivated in Chapecó (Brazil) was analyzed and then the potential of using this local plant extract to protect by oral feeding virus-infected Litopenaeus vannamei shrimp was also investigated. For this study, five treatments were tested: uninfected shrimp fed with pelleted feed (TC), WSSV-infected shrimp fed with pelleted feed (T1), infected shrimp fed with pelleted feed with 1% ethanol extract of U. tomentosa (EEUT) (T2), infected shrimp fed with pelleted feed with 2% EEUT (T3), and infected shrimp fed pelleted feed with 4% EEUT (T4). The chemical analysis of EEUT showed the presence of alkaloids, flavonoids, sterols, terpenes, coumarins, and tannins and also a high in vitro free radical-scavenging activity as well as high total phenolic content. Shrimp fed with 2 and 4% EEUT (T3 and T4) showed a survival probability significantly higher than T1 and T2 treatments and no clinical symptoms of WSSV infection. Immunological assay also showed a positive phenoloxidase activity effect on shrimp fed with EEUT.
Interaction of Rickettsiae and Phagocytic Host Cells

Infection of human subjects with virulent or attenuated (Strain E) Rickettsia prowazekii was followed within 2 weeks by the appearance of antibodies which would enhance phagocytosis of homologous rickettsiae by mouse peritoneal leukocytes. Although an injection of conventional killed epidemic typhus vaccine appeared to cause more rapid appearance of antibodies (by the end of 1 week), the titers attained at this time were low and, on the average, did not increase significantly in later specimens. Serum from all groups also enhanced phagocytosis of R. mooseri but for the most part these antibodies occurred in lower titers than the antibodies involved in the opsonization of R. prowazekii. The cross-reactions observed with the murine typhus antigen tended to be lower relative to the homologous reaction in the group which received the living attenuated (E strain) vaccine than in the other groups studied.
The Role of Polyamines in Osmotic Stress Tolerance in Gulf Killifish Fundulus grandis

Polyamines are a family of low molecular weight organic cations produced in part by the coordinated actions of arginase II (Arg II) and ornithine decarboxylase (Odc). Although little is known of their functions in fish, polyamines have been implicated in diverse physiological processes. We describe a possible role of polyamines in hypoosmotic tolerance in the gulf killifish, Fundulus grandis, a species known to tolerate acute fluctuations in wide salinity range. Adult fish were reared in 5 ppt water for at least 1 month, and acutely transferred to 0.1, 0.5, 1, 2, and 5 ppt. Fish were randomly sampled from each salinity at 6 h, 1 d, 3 d, and 7 d post‐transfer. We have shown that relative Arg II and Odc mRNA levels, and Odc protein activity are highly up‐regulated in the gills. Hypoosmotic exposure also increases the concentration of the polyamines, putrescene, spermidine, and spermine. Although gill putrescine levels remain elevated throughout the first 7 days post ‐ transfer to freshwater, the concentrations of spermidine and spermine decrease with time suggesting a catabolic regulation of compounds. We are investigating the role of polyamine catabolism in apoptosis during salinity‐induced gill remodeling.
Phenological phases of the host plant shape plant–treehopper interaction networks

Several studies have recently focused on the structural pattern of plant–insect interaction networks. However, insects and plants have dynamic cycles and differ in their level of specialisation over time, space, and scales. Thus, it is expected that sap‐sucking insects, such as treehoppers, and plants will not share similar patterns of interactions in all phenological stages of the plants. It was postulated that phenological stages of the host plant could change the structure of plant–treehopper networks, which will be more specialised during the reproductive stage than during the vegetative stage, mainly because of high concentrations of toxic compounds in the flowers. Here, quantitative metrics derived from graph theory were used to describe, for the first time, the changes in the structure of plant–treehopper interactions during the phenological stages of the host plants in Brazilian Atlantic Forest. The results revealed high temporal turnover of plant–treehopper interactions, and high similarity in the treehopper composition between the phenological stages. In both phenological stages, plant–treehopper networks exhibited a modular and non‐nested pattern. However, during the reproductive stage, the results showed lower species richness of plants and treehoppers, and higher levels of network specialisation compared with the vegetative phase. These findings demonstrate that the organisation of the same ecological interaction can change throughout plant phenology. In short, it was shown that the phenological phases of the host plants can constitute a remarkable mechanism that shapes plant–treehopper interaction networks in a tropical rainforest.
Pengaruh kitosan terhadap produksi saponin kultur kalus daun ginseng jawa (Talinum paniculatum (Jacq.) Gaertn.)

Ginseng jawa ( Talinum paniculatum ) potensial untuk dikembangkan sebagai bahan obat karena mengandung saponin ginsenosida yang mirip dengan ginseng korea ( Panax ginseng ). Penerapan elisitasi pada kultur in vitro merupakan salah satu teknologi yang mumpuni untuk meningkatkan produktivitas saponin T . paniculatum secara efisien. Kitosan merupakan elisitor biotik yang sering digunakan dalam elisitasi karena mampu meningkatkan produksi metabolit sekunder langsung pada enzim kunci terkait. Penelitian ini bertujuan untuk mengetahui pengaruh konsentrasi kitosan dan waktu inkubasi terhadap biomassa kalus dan produksi saponin kultur kalus T . paniculatum . Produksi kalus T . paniculatum dilakukan pada media MS dengan kombinasi 2,4-D 2 mg/L dan kinetin 3 mg/L. Elisitasi dilakukan pada kalus yang telah memasuki fase stasioner dengan variasi interkasi perlakuan konsentrasi kitosan 0, 50, 100, dan 150 mg/L dan waktu inkubasi 0, 3, 5, dan 7 hari (n = 3). Kalus kering hasil elisitasi diekstraksi dengan etanol 96% dan diuji secara semi-kuantitatif menggunakan kromatografi lapis tipis (KLT). Biomassa kalus terelisitasi pada berbagai variasi konsentrasi kitosan dan waktu inkubasi (0,056-0,072) tidak berbeda signifikan dibandingkan kontrol (0,054). Luas noda saponin KLT terbesar (0,495 cm 2 ) dihasilkan pada perlakuan konsentrasi kitosan 50 dan 100 mg/L selama 7 hari. Melalui penelitian ini, diketahui bahwa perlakuan elisitasi kitosan dan waktu inkubasi tidak mempengaruhi pertumbuhan kalus daun T. paniculatum . Produksi saponin tertinggi dihasilkan pada perlakuan elisitasi kitosan 100 mg/L selama 7 hari. Penelitian ini diharapkan berkontribusi dalam peningkatan produksi saponin T. paniculatum
Prevalence of parasitic infection in farmed Nile tilapia and factors associated with transmission in Kiambu County, Kenya

The current study was undertaken between October 2016 and March 2017 to determine the prevalence of fish parasites infesting farmed Tilapia and the associated risk factors in Kiambu County, Kenya. A total of 148 questionnaires supplemented with direct observations were administered to fish farmers to assess the status of fish farming and management practices that could influence the occurrence of fish parasites in the farms. A total of 260 fish were purchased from farmers and examined for ecto-and endo-parasites. Most of the farmers were males, over 50 years of age, had been in fish farming for more than five years and were involved in farming of fish, crops and livestock as their main occupation. In majority (60.8%) of the farms, Tilapia (Oreochromis niloticus) was the main species farmed under semi intensive farming system in earthen ponds. Farm owners (66.7%) were responsible for day to day management of the farms and most had attained secondary school education. The management practices identified as possible risk factors for occurrence of fish parasites included: use of rivers as sources of fish pond water, earthen ponds with overgrown vegetation in and around them, stocking with fingerlings from noncertified sources, failure to change water within a production cycle, lack of pond draining, cleaning and treatment after harvesting and lack of or infrequent fertilization of ponds. Others were: use of poor quality feeds and lack of feeding or improper feeding, sharing of fishing nets among farmers and between ponds in the same farm, failure to clean and disinfect fishing nets, lack of knowledge on signs of fish diseases in general and parasitism in particular and presence of predators especially, predatory birds. The mean weight, total length and standard length of the
An All Low-Voltage Devices Level Shifter with Stress Protection for Powering Events

Modern system-on-chip (SoC) applications commonly comprise multiple voltage domains to save power consumption according to the required circuit performance. Level shifter (LS) blocks usually interface these power domains to guarantee fitting voltage levels for the control signals among low supply and high supply voltage domains. Using only thin-oxide transistors for LS implementations enables their subsequent integration into the digital domain of an SoC and enhances circuit speed performance. Nevertheless, thin devices entail overvoltage issues when the voltage difference between the supply domains to be communicated is large, e.g. during the SoC's power-up sequence. Here we propose an LS architecture along with a three-devices protection scheme to avoid powering-up overvoltage issues, which have been neglected by reported LS works, validated through simulations. The results disclose a maximum operating frequency of 400MHz and an average energy-per-transition of 470fJ.
FORECASTING ABILITIES OF INDIVIDUAL PETROLEUM EXPLORERS: PRELIMINARY FINDINGS FROM CROWDSOURCED PROSPECT ASSESSMENTS

Petroleum explorers regularly make numerous forecasts for prospects and wells, but the quality of their predictions has inadequate documentation. Here I discuss the forecasting abilities of individual explorers inferred from a survey about future exploration wells, some of which were drilled in late 2018 and 2019. A total of 104 petroleum explorers provided 7,068 answers about eleven wells and about themselves, and subsets from this dataset were used to study their predictions. The survey participants were diverse, and most had M.Sc. or Ph.D. degrees with >16 years of industry experience working as individual contributors and/or middle managers for oil companies. Assessments of the geological probability of success (PoS) by different explorers for the same well were highly variable, and average assessments poorly discriminated between future discoveries and dry holes. Point (binary or multiple choice) forecasts by explorers participating in the survey were, on average, only slightly better than random guessing. The participants' highest academic degree had little apparent influence on the quality of the point forecasts. Years of experience resulted in only slightly better correlation with increasing quality of forecasts. Survey participants more familiar with the prospects (those who generated them or evaluated proprietary company data) made, on average, worse exploration forecasts than those who studied only the limited publicly available information provided with the survey. The duration of time spent on the survey did not affect the quality of forecasts. The aggregated opinion of all explorers (wisdom of the crowd) may be beneficial in assessments of the geological PoS, but perhaps not so when forecasted outcomes have binary or multiple possibilities. The generally poor forecasting abilities of individual petroleum explorers may surprise some decision‐makers and investors. However, many of the study results are based on relatively small datasets and should be treated as preliminary. Further research with larger datasets is necessary to replicate, validate and explain the findings of this study.
Characterization of calmodulin in the clam Anodonta woodiana: differential expressions in response to environmental Ca2+ and Cd2+

Abstract Aims To explore effect of Ca2+ and Cd2+ on the calmodulin (CaM), one complete cDNA sequence (AwCaM1) was cloned and characterized from the freshwater mussel Anodonta woodiana and its expressions were analyzed. Materials and methods The AwCaM1 was cloned from the A. woodiana using the rapid amplification of cDNA ends methods and its expression was determined by real-time PCR. Results In the hepatopancreas, AwCaM1 expression was up-regulated with a time and dose dependent pattern in the Ca2+ treated groups (0.01, 0.02, 0.04 and 0.08 mg/L) during experiment observed, and increased more than 56.15% (p<0.05) compared with that of control group. AwCaM1 mRNA level increased more 65.04% (p<0.05) in the Cd2+ treated groups (8 and 16 mg/L). In the gill, AwCaM1 expression increased more than 79.41% (p<0.05) compared with that of control group in all the Ca2+ treated groups, and more than 88.23% (p<0.05) in all the Cd2+ treated groups. Conclusion These results indicated that up-regulations of AwCaM1 expression in bivalve A. woodiana are associated with Ca2+ absorb and environmental adaption derived from Ca2+ and Cd2+ treatment.