Miracle-dz/UniFAR-FTUs huggingface dataset:
How does hybridization affect multiple metrics of fitness in fragmented populations of brook trout under moderate climate warming

As a population’s genetic makeup is often attributed to the combined fitness of its individuals, the adoption of deliberate hybridization practices is an area of interest for many hatchery and conservation programs. Using a common garden experimental design involving eight wild populations of Salvelinus fontinalis (brook trout), we studied how effective population size (Ne), divergence (QST, km), and environmental dissimilarity (pH, temperature) may influence hybridization outcomes for fitness related traits under moderate climate warming. Additionally, we looked at the ability of six of these populations to tolerate acute thermal warming, and whether or not this tolerance could be altered by hybridizing populations. Critical thermal maximum (CTmax) assays were conducted on juveniles from each population to assess thermal tolerance, and agitation temperature (a behavioural metric quantifying temperature at the onset of refugia-seeking behaviour) was recorded for assessing behavioural changes to elevated temperatures. Gametes were collected from different-sized, isolated populations of brook trout, and crossed in the lab. Fitness-related traits were compared between pure and F1 hybrid crosses via common garden experimental design. We had the unique opportunity to jointly investigate how these factors influence multiple metrics of hybrid fitness in wild, isolated, and varyingly-sized populations of a vertebrate species inhabiting a relatively undisturbed environment. Although population size and environmental dissimilarity were found to significantly affect hybrid fitness, these relationships were biologically weak. Although significant differences in CTmax were found between populations, this difference was at most 0.68 °C (29.11-29.79 °C), and no effect of hybridization was seen despite varying thermal regimes between these populations’ wild streams. These results will provide guidance to small population and captive-breeding conservation programs, as the lack of a strong relationship between hybridization and fitness encourages population-specific approach to genetic rescue projects. Additionally, this study highlights the level to which thermal tolerance is conserved between isolated populations of a vertebrate species, in the face of climate warming.
Spatial Distribution of Tick-Borne Pathogens as a Consequence of Vector-Host-Pathogen Interactions with Environment

Předkladana dizertacni prace se zabýva zakladnim výzkumem v oblasti ekologie klistěte (Ixodes ricinus) a jim přenasených patogenů (Borrelia burgdorferi sensu lato, virus klisťove encefalitidy). Konkretně se zaměřuje na analýzu, přiciny a důsledky jejich distribuce v prostoru a jejich interakce s přirozenými hostiteli klistěte.
Karakterisasi Ganoderma spp. di Kabupaten Banyumas dan Uji Peran Basidiospora dalam Siklus Penyakit Busuk Batang

Ganoderma sp. , one of fungi belonged to the family Ganodermataceae, order of Aphyllophorales, class of Basidiomycetes is very widely spread. This fungus is a soil-borne, and has parasitic and saprophytic features which are interesting because of their two contradictory roles namely harmful and beneficial effects. As a plant parasite, Ganoderma is able to cause root and stem rot of tropical perennial crop plantation and forest which cause serious losses. The fungus is well known as white rot fungus which is able to cause a wood rotten by lignin destruction. On the contrary, the fungus has some advantages such as medical potentials. In this study, some collections and characterization of Ganoderma spp. found in Banyumas has been conducted. The technique used for sampling Ganoderma spp. mushroom is a survey with Purposive Random Sampling method. Samples were taken from nature in the area of Banyumas Regency and its natural substrate were noted. Characterization based on the macromorphology and micromorphology was done for grouping and identification. Micromorphology observations were done by slicing and painting samples with plants microtechnique method. The result showed that there were 43 Ganoderma spp isolates, distributed from low to high lands of 100 - 500 m above sea level. The most fungi were found on the high lands, in Baturraden sub district, which included 16 isolates. The interesting finding is the discovery of Ganoderma spp. which attacked flamboyant plant ( Delonix regia ) in West Purwokerto sub district. Based on micromorphology observations, these fungi form a basidium and basidiospore inside and below as well as the surface of the fruit body. Some species were also found having such phenomenon so it needs further research on the role of basidiospora in the cycle of stem rot disease, especially basidiospora role in the initiation of diseases infection. As the soil infecting mushroom, study of the disease spreading is focused more on the role of the mycelium found in the remaining plants as infecting the material. Basidiopore role in the spread of the disease is rarely studied, but actually basidiospore is a potential source of genetic variation.
Ecobiology of Anaphothrips obscurus, a new dweller of citrus orchards brought in by more sustainable pest management practices

The abundance and frequency of Anaphothrips obscurus (Thysanoptera: Thripidae) increased in a cover of Festuca arundinacea (Poaceae) when this plant was used to improve the biological control of the clementine key pest Tetranychus urticae (Acari: Tetranychidae). To unveil the ecological role of A. obscurus in this system, we re‐explored field data and performed laboratory studies aiming to determine its demographic parameters and feeding habits, as well as its role as a prey of predatory mites (Acari: Phytoseiidae) occurring in the Spanish citrus agreoecosystem. Field studies indicate that T. urticae populations decreased, whereas those of A. obscurus and phytoseiids, as a whole, increased. Reproductive and demographic parameters of macropterous and brachypterous morphs of A. obscurus were different and confirmed the host status of F. arundinacea. Anaphothrips obscurus could compete with T. urticae as a result of its higher intrinsic rate of increase in F. arundinacea. However, A. obscurus zoophagy on T. urticae eggs and the host status of citrus can be discarded. Anaphothrips obscurus can be a prey for Euseius stipulatus, Neoseiulus barkeri and Neoseiulus californicus (three phytoseiids preying on T. urticae), suggesting that apparent competition between A. obscurus and T. urticae could occur in citrus orchards.
Differences in acquired knowledge and attitudes achieved with traditional, computer-supported and virtual laboratory biology laboratory exercises

Abstract This paper reports on the contribution to biological knowledge of three different laboratory technologies and also endeavours to discover which technology students prefer the most. To examine differences in knowledge gained and learners’ preferences for different technologies in biology laboratory work, we prepared three variants (triplets) of three laboratory exercises. Each laboratory variant in a triplet was prepared as a classical laboratory work, a computer-supported laboratory and an interactive virtual simulation. A group of 670 learners at a school for all genders, aged between 11 and 15 (6th to 9th grade) of lower secondary Slovenia schools performed three well-known and easy to perform laboratory exercises that are included in their curriculum (‘Gas Exchange’, ‘Activity of Yeast’ and ‘Heart Rate’) as a traditional, computer-supported laboratory and computer simulation. The data indicated that there were no statistical differences pertaining to students’ knowledge gain between these laboratory technologies with regard to grade, gender or school score. In this study, students preferred a computer-supported laboratory mostly followed by a classic laboratory with a computer simulation in last place, regardless of students’ grade, gender or academic scores.
Iron Redox Transformation by the Thermo-Acidophilic Archaea from the Genus Sulfolobus

Abstract Iron redox transformations by five representative Sulfolobus strains (S. metallicus Kra23, S. tokodaii 7, S. acidocaldarius 98-3, S. solfataricus P1, S. shibatae B12) were studied to clarify the general trend of Fe metabolism across different species of the genus Sulfolobus. Negligible to major Fe(II) oxidation was detected in cell suspensions of the strains. Fe(III)-reducing ability was differently expressed in each strain with dependence on the oxygen level and growth status; growth-uncoupled cell suspensions of all strains reduced Fe(III) under either anaerobic or microaerobic conditions, or under both conditions. A linear correlation between cell growth and Fe(III) reduction was also found in S. tokodaii 7, S. solfataricus P1, and S. shibatae B12. In addition to Fe redox behaviors, the strains were also tested for reduction of highly toxic Cr(VI) to less toxic and soluble Cr(III), as an application possibility; the trend in degree of Cr(V) reduction did not necessarily correspond to that of Fe(III) reduction, suggesting the involvement of different reduction mechanisms.
Ecology of the rare but irruptive Pilliga mouse, Pseudomys pilligaensis. V. Relationships with yellow-footed antechinus, Antechinus flavipes, and house mouse, Mus domesticus

Abstract. We investigated relationships between Pseudomys pilligaensis and other small mammal species in terms of their population fluctuations and habitat selection during a population irruption of P. pilligaensis. Antechinus flavipes showed only seasonal fluctuations in numbers, suggesting that it did not respond to the same environmental factors as P. pilligaensis. A. flavipes consistently selected areas with less sand in all phases of the irruption of P. pilligaensis, resulting in a clear separation from P. pilligaensis except in the Peak phase of the latter’s irruption. Numbers of Mus domesticus fluctuated similarly to P. pilligaensis until the latter’s irruption peak in April 2000. However, M. domesticus disappeared after July 2000 from our sites. M. domesticus seemed to occupy the area only temporarily when seeds were abundant. In the Increase and Peak phases of the irruption of P. pilligaensis, M. domesticus occupied core habitats characterised by more sand and shrub, and less litter, while in the Low phase P. pilligaensis occupied the core habitats that M. domesticus used to occupy. This may suggest that M. domesticus was excluded from core habitats through competition with P. pilligaensis in the Low phase of the latter’s irruption. However, since increased anthropogenic disturbance might create conditions that M. domesticus prefers, it is important to assess carefully any impacts of such disturbance on P. pilligaensis.
CLARIFYING THE ROLE OF MICROGLIA VERSUS MACROPHAGES IN FACILITATING NEUROINFLAMMATION SURROUNDING INTRACORTICAL MICROELECTRODES

Microelectrode technology holds enormous potential in both basic neuroscience and functional rehabilitation applications. For example, recorded signals can be used to develop our understanding of neuronal circuits or as control signals for various rehabilitation applications. Unfortunately, widespread implementation of intracortical microelectrodes is limited in both research and clinical settings due to loss in signal quality over time. Several mechanical, material and biological factors have been suggested to impact recording quality, and it is likely that multiple factors simultaneously affect recording performance. Increasing evidence suggests a dominant role of microglia/macrophages and infiltrating myeloid cells in mediating neurodegeneration and impacting microelectrode performance. To overcome challenges associated with microelectrode failure, the field has actively sought to investigate neuroprotective strategies to improve recording quality. However, the immune-privileged cortical tissue introduces an added level of complexity that has yet to be fully elucidated. The overall goal of this dissertation was to identify a key mechanistic pathway that facilitates
Synthesis of N‐Methylated Pseudodesmin A Analogues: on the Structural Importance of N‐H Hydrogen Bonds

The structural importance of backbone amide protons in the bacterial cyclic lipopeptide pseudodesmin A, a viscosin group member, is studied by selective introduction of N-methylated amino acids. Site-selective N-methylation was conveniently achieved by introduction of N-Me-L-Leu at positions 1 and 7 during solid phase peptide synthesis. The impact of this modification on conformation, antibiotic activity and supramolecular behaviour allowed to establish the significance of intra- and intermolecular hydrogen bonds.
Antiviral and antimicrobial activities of three sesquiterpene lactones from Centaurea solstitialis L. ssp. solstitialis

Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Gazi University, Etiler 06330 Ankara, Turkey Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Etiler 06330 Ankara, Turkey Department of Virology, Faculty of Veterinary Medicine, University of Ankara, Dis-kapi 06100 Ankara, Turkey Department of Pharmacognosy, Faculty of Pharmacy, Yeditepe University, Kadikoy 34755 Istanbul, Turkey
Commensal Nesting of Scincella lateralis (Little Brown Skinks) in Alligator mississippiensis (American Alligator) Nests and Ondatra zibethicus (Muskrat) Houses in Southwestern Louisiana

Abstract Scincella lateralis (Little Brown Skink, hereafter Skink) are ubiquitous throughout the southeastern US and primarily nest in leaf litter on the forest floor. However, their presence in coastal marsh settings necessitates their use of alternate nesting habitats. We investigated Skink nesting ecology in Alligator mississippiensis (American Alligator) nests and Ondatra zibethicus (Muskrat) houses in an intermediate/brackish coastal marsh habitat at Rockefeller Wildlife Refuge in southwestern Louisiana. For our field studies, we found and collected Skink eggs from 16 June through 5 October, and hatched eggshells from 6 July through 5 October. We found Skink eggs/eggshells in 36 of 109 active American Alligator nests (33.0%), 19 of 36 inactive Alligator nests (52.8%), and 13 of 51 Muskrat houses (25.5%). Clutch size ranged from 1 to 5 eggs (average = 3.0). The mean depth of Skink eggs was 24.6 cm in American Alligator nests and 17.1 cm in Muskrat houses. Multiple clutches commonly occurred in a structure, indicating repeated use by a single female Skink or communal nesting. In one extreme case of communal nesting, we collected at least 932 Skink eggs and hatched eggshells from a single Alligator nest. Skink eggs that we measured weekly during a 30-day incubation period increased in length and width. Earliest hatch dates for laboratory-incubated Skink eggs occurred from 28 June through 3 July; the last Skink hatched on 14 October. We documented a hatch rate of 87.6%. Hatchlings (n = 806) had a mean total length of 5.01 cm (n = 23) and a mean snout—vent length of 2.02 cm (n = 18). Our study indicated that Skinks readily nest commensally and communally within coastal marsh Alligator nests and Muskrat houses.
Establishment of Agrobacterium tumefaciensmediated transformation system for Phomopsis asparagi, the pathogen of asparagus stem blight / Asparagus (Kuşkonmaz) pas hastalığına neden olan Phomopsis asparagi için Agrobacterium tumefaciens’e dayalı transformasyon sistemi geliştirilmesi

Abstract Objective: The transformation system for the asparagus stem blight pathogen Phomopsis asparagi (Sacc.) Bubak has not yet been reported. In the present study, we intend to achieve and optimize the genetic transformation of P. asparagi. This study aims at establishing the foundation for understanding the pathogenic mechanism of P. asparagi, which will be of great theoretical and practical significance. Methods: The Agrobacterium tumefaciens-mediated transformation (ATMT) system for P. asparagi was constructed at three aspects, i.e. condition optimization, insertion verification and transformant stability. Results: The optimal conditions for this ATMT system were as follows: 8 h of pre-induction, 48 h of co-culture, 200 μmol/L AS in ISM, co-culture at 25-28°C and pH 5.6-5.8 of ISM at the co-culture phase. The PCR result of the hph gene revealed that an expected band of about 500 bp was amplified from all the 10 transformants selected at random, and the PCR result of the Vir gene revealed that an expected band of about 730 bp was amplified from the four strains of A. tumefacien as positive controls, whereas no corresponding DNA band could be amplified from the 10 transformants. The results of the two PCR amplifications clearly showed that T-DNA was indeed inserted into the genome of target isolate FJ2. The stability result revealed that transformants still displayed high resistance to hygromycin B and could grow normally after subculture for five generations. Conclusion: A stable and efficient ATMT transformation system for P. asparagus was constructed systematically, in which a high transformation rate was achieved. For improving this system, the trasformation conditions were optimized through gradient experiments, T-DNA insertion was verified through dual PCR and the insertion segment containing hph gene in the transformant was proved hereditary stable through subculture. This system layed a foundation for the research on pathogenic mechanism and pathogenicity-related genes of P. asparagi.
Molecular Cloning and Characterization of Two Key Enzymes involved inthe Diterpenoid Biosynthesis Pathway of Isodon rubescens

Isodon rubescens, an important medical plant, contains various terpenoids. This plant’s active compounds are primarily oridonin with antitumor properties. As the precursor for oridonin biosynthesis, are synthesized by MEP pathway. On the basis of our earlier studies, we isolated and cloned two important genes catalyzing diterpenoid biosynthesis in the MEP pathway. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase and 4-hydroxy-3- methylbut-2-enyl diphosphate reductase are the fifth enzymes and the last step key enzyme for the methylerythritol phosphate (MEP) pathway, respectively, which is important for the regulation of isoprenoid biosynthesis. Sequence analysis revealed that DcIspF (accession no. KT948057) was 966 bp, contains a gene open reading frame (ORF) of 708 bp belonging to the MECDP-synthase superfamily and DcIspH (accession no KT948058) contains a 1389 bp ORF encoding a predicted 462 amino acid polypeptides as a member of the lytB_ispH superfamily. The deduced DcIspF and DcIspH amino acid sequences shared high similarity with DcIspF and DcIspH of other plant respectively, each of them exhibiting an N-terminal transit peptide and conserved amino acid sites. Quantitative real-time PCR analysis showed that the expression of DcIspF was considerably higher in leaves, the lowest in callus. These results indicate that we have identified functional DcIspF and DcIspH enzymes, which may play a pivotal role in the biosynthesis of diterpenoid in I. rubescens.
The use of field and artificial freezing studies to assess frost tolerance in natural populations of Pinus oocarpa

The susceptibility of Pinus oocarpa to freezing temperatures limits the commercial deployment of the highly productive Pinus patula × P. oocarpa hybrid in South Africa. Identifying P. oocarpa germplasm with increased frost tolerance is important. Twenty-three P. oocarpa provenances, originating from Mexico, Honduras, Guatemala and Nicaragua, were therefore assessed for their tolerance to freezing conditions by analysing field survival after frost events, subjecting needles to freezing temperatures and assessing damage using the electrolyte leakage test, and exposing young plants to freezing temperatures in a semi-controlled environment and scoring tissue damage based on a visual assessment. The performance of many of the provenances represented in the field and artificial freezing studies were similar and there was a strong correlation between provenance ranking in the whole plant freezing and electrolyte leakage test. We therefore support the use of these techniques as a means to assess cold tolerance in P. oocarpa at the provenance level. Provenances from north-western Mexico demonstrated more frost tolerance than those from southern Mexico. Provenances representing Honduras and Guatemala appear to be highly susceptible to frost.
Growth and mortality rates of Pseudupeneus grandisquamis and Urobatis halleri bycatch species in the shrimp fishery Crecimiento y tasas de mortalidad de Pseudupeneus grandisquamis y Urobatis halleri, especies de fauna acompañante en la pesquería de camarón

Population dynamics of the goatfish Pseudupeneus grandisquamis and the round ray Urobatis halleri were assessed as dominant shrimp trawl bycatch species in the Gulf of California. Samplings were collected during the 2004-2005 shrimp season onboard 13 shrimp vessels. A total of 3,586 organisms were analyzed (n = 2,463 of P. grandisquamis and n = 1,123 of U. halleri); size frequencies were obtained by the von Bertalanffy model; growth, natural mortality (M), mortality by fishing (F), total mortality (Z), and exploitation rate (E) were determined by Pauly, Jensen, Ricker, and Taylor equations and the catch curve method. Size of P. grandisquamis ranged from 20-210 mm in total length (TL); growth parameters (L∞ 213 mm; K/year 0.9; t0/year −0.19) indicated moderate growth, longevity (3.3 years), and high mortality rates (Mp = 1.73/ year; Mj = 1.35/year). Size of U. halleri ranged from 90-450 mm in TL; growth parameters (L∞ 472 mm; K/year 0.27; t0/year −0.54) indicated slow growth, moderate to high longevity (11.1 years), and moderate mortality rates (Mp = 0.6; Mj = 0.4 year −1 ). Exploitation rate was <0.5 for P. grandisquamis and 0.8 for U. halleri, which was greater than the value suggested for a healthy stock (E ≤ 0.5). According to the high mortality and exploitation rates estimated, it is conclude that shrimp trawl fishery represents a risk for U. halleri but not for P. grandisquamis.