Miracle-dz/UniFAR-FTUs huggingface dataset:
Methane Biogeochemistry and Methanogen Communities in Two Northern Peatland Ecosystems, New York State

Rates of methane (CH4) production vary considerably among northern peat-forming wetlands, and it is not clear whether variability is caused by environmental factors affecting CH4 production or differences in methanogen communities. We investigated CH4 production and emission dynamics concomitantly with 16S rRNA gene sequence-based community analysis of Archaea in two contrasting peat-forming northern wetlands, an ombrotrophic bog and a minerotrophic conifer swamp. Individual measurements of CH4 emissions to the atmosphere followed a lognormal distribution pattern in both sites, and mean rates were 30× greater in the bog site. Rates of CH4 production measured in vitro were initially 3× greater in the bog than in the conifer swamp; although, after 30 days of incubation, production rates were similar suggesting that in situ environmental conditions limited production in the conifer swamp. Amplified ribosomal DNA restriction analysis (ARDRA) and rarefaction techniques indicated that both sites had similar levels of archaeal richness, with 27 unique taxa in the bog and 23 taxa in the conifer swamp. However, the bog had more pronounced dominance of a few taxa, whereas the conifer swamp had more even distribution among taxa. A 16S rRNA gene sequence-based phylogenetic analysis indicated high levels of diversity with similarity to known methanogenic families Methanosarcinaceae, Methanosaetaceae, Methanobacteriaceae, and likely Methanomicrobiaceae as well as two additional lineages previously characterized as groups of yet uncultivated Euryarchaeota commonly occurring in flooded rice soils. Therefore, sites with low and high rates of CH4 production supported very diverse methanogenic communities.
The solenobiinae species of Finland (Lepidoptera: Psychidae), with a description of a new species

The Finnish Solenobiinae are revised. This subfamily is represented in Finland by two genera and seven species of which three are parthenogenetic: Solenobia triquetrella (Hubner) (also reported from Denmark, Norway and Sweden), Solenobia lichenella (Lin.) and Solenohia fennicella n. sp. , which is described here. Of the remaining species, Solenobia charlottae Meier (also recorded from S) and Siederia rupicolella Sauter (also recorded from S) are eartier known only from the mountains of Central Europe. Solenobia furnosella Heinemann (recorded also from D, N and S) and Siederia pineti (Zeller) (also from D and S) are bisexuals earlier known from Finland. – Notes for identifying each species and their distribution are given.
Concentration of anesthetic for long-term exposure and the effects of inter-suture distance in the goldfish Carassius auratus

This study aimed to determine the minimum concentration of 2-phenoxyethanol for long-term exposure and evaluate the effect of inter-suture distance on wound healing in the goldfish Carassius auratus . Twenty adult goldfish (standard length = 12.4 ± 1.1 cm; weight = 58.7 ± 17.2 g) were anesthetized in 2-phenoxiethanol at 1.2‰ and placed in an anesthesia delivery system at the following concentrations of 2-phenoxiethanol: 0.0 (control); 0.1; 0.2; 0.3 and 0.4‰, and the duration of sedation was measured. Fifteen days later, fishes were anesthetized using the same procedure, and a 36 mm incision was performed in the ventro-lateral region. The incision was sutured using a simple-interrupted pattern with 3, 6 or 9 mm as inter-suture distances. Results demonstrated that 2-phenoxiethanol at 0.4‰ maintain the sedation for surgical procedures up to 60 minutes, and 9 mm as inter-suture distance optimized the wound healing in goldfish.
Factors affecting habitat selection in a specialist fossorial skink

Habitat specialists maximize their fitness by using a subset of the habitats that are potentially available to them and fare poorly if they move elsewhere. The factors that constrain habitat use are diverse and often difficult to identify, but are important to distinguish if we are to understand the trade-offs that drive species to become specialists. In the present study, we investigated habitat use in a fossorial skink, Lerista labialis, and explore the factors that confine it to the crests of sand dunes in the Simpson Desert, central Australia. Models positing that L. labialis selects dune crests because of their sparse cover of vegetation, more favourable temperatures, and greater abundance of preferred prey, received no support. Instead, a model positing that dune crests provide soft and less compacted sand that facilitates movement by L. labialis, was strongly supported. Sand on the crests was consistently softer that that on the sides and swales of the dunes; the skinks preferred soft rather than hard sand for movement in captivity, and were captured more often on experimentally softened sand than on compacted sand in the field. There was no evidence that L. labialis responds to attributes of the substrate other than softness because captive animals used loose sand from the dune crests, sides, and swales equally. We suggest that the dune crest environment allows L. labialis to reduce the energetic costs of locomotion, provides priority of access to the subterranean galleries of its termite prey, and also a secure refuge from surface-active predators and extreme surface temperatures. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 531–544.
How robust are Palearctic migrants to habitat loss and degradation in the Sahel

The Sahel region of West Africa is an important wintering ground for Palearctic migrants. It is, however, undergoing significant anthropogenic degradation that is likely to reduce its value in this regard. Despite there being evidence that the populations of several Palearctic species may be determined by conditions on their Sahelian wintering grounds, there are almost no baseline data on their habitat use there and so the effects that habitat change might have on their future density and distribution cannot be determined. This study measured which habitat variables were associated with the presence of Common Whitethroat Sylvia communis, Lesser Whitethroat S. curruca and Subalpine Warbler S. cantillans by carrying out point counts and habitat measurements at 1861 points at 16 sites in northern Nigeria during the winters of 2001 and 2002. Common Whitethroats were most common at intermediate tree heights and densities of Salvadora persica (with this effect strongest in the pre-migratory period), and increased as Balanites aegyptiaca density increased initially, although this effect levelled off at higher Balanites densities. Subalpine Warblers were most common at intermediate tree heights and Balanites densities, increased as Acacia and Salvadora density increased, decreased with tree density and were least common at intermediate shrub densities. Lesser Whitethroats were most common at intermediate tree heights, Acacia and Salvadora densities, increased with Balanites density, and decreased with tree density and diversity. The shallow slopes of the significant relationships found between Palearctic warbler species and habitat parameters suggest that the group may be robust to habitat degradation, with densities remaining relatively constant across a wide range of habitat types. Common Whitethroats, in particular, appear to be able to survive in extremely degraded habitats, yet may be vulnerable to the disappearance of Salvadora, the fruit of which may allow pre-migratory fattening.
Reproductive features and gonad development cycle of the soft bottom-gravel gorgonian Leptogorgia sarmentosa (Esper, 1791) in the NW Mediterranean Sea

Abstract Leptogorgia sarmentosa (Cnidaria: Octocorallia) is a common soft bottom-gravel gorgonian in the northwestern Mediterranean Sea. This study examined the annual reproductive cycle of a L. sarmentosa. population at a depth of 30 m, and further determined the sex ratio, the intra-colonial gonadal output variability and the age at first reproduction. L. sarmentosa was gonochoric and the population studied was characterized by a sex ratio slightly biased towards female colonies (1 male:1.6 female). Secondary branches had higher polyp fertility (number of gonads per polyp) compared to primary branches, but because of the number of polyps on the former, most of the sexual effort was actually contributed by the primary branches, as in other gorgonian species. Male colonies became fertile above a height of 21 cm, but female colonies had gonads even in the 1–10 cm height class. Spawning occurred between late August and early September, although there was no direct observation of broadcast spawning or surface brooder strategy. The maximum gonad size was 550 μm in males and 500 μm in females, with a mean diameter of 270 μm for spermaries, and 190 μm for eggs. The number of gonads per polyp prior to spawning reached 4–5 spermaries polyp! 1 in male colonies, and 3–4 eggs polyp! 1 in female colonies. Spawning did not appear to be synchronized with the full moon. L. sarmentosa appeared to have a different reproductive strategy to other Mediterranean gorgonians (living on hard bottom substrata), probably because of its different habitat preferences and biological (morphology, diet, prey capture rates, growth, biochemical levels) features.
The typification of Colletotrichum gloeosporioides

The anamorphic species Colletotrichum gloeosporioides has never been adequately typified according to modern nomenclatural practice, resulting in uncertainty as to application of the named A lectotype specimen is therefore designated to preserve current usage, with an epitype also chosen as eligible lectotype material is not preserved in a living state. The epitype strain is described and characterized using morphological and molecular methods. There are three distinct rDNA ITS sequences of the epitype strain in GENBANK, so it has been re-sequenced to confirm the true base-pair structure.
Progressive supranuclear palsy pathology caused by a novel silent mutation in exon 10 of the tau gene

Genetic mutations in the tau gene on chromosome 17 are known to cause frontotemporal dementias. We have identified a novel silent mutation (S305S) in the tau gene in a subject without significant atrophy or cellular degeneration of the frontal and temporal cortices. Rather the cellular pathology was characteristic of progressive supranuclear palsy, with neurofibrillary tangles concentrating within the subcortical regions of the basal ganglia. Two affected family members presented with symptoms of dementia and later developed neurological deficits including abnormality of vertical gaze and extrapyramidal signs. The third presented with dystonia of the left arm and dysarthria, and later developed a supranuclear gaze palsy and falls. The mutation is located in exon 10 of the tau gene and forms part of a stem-loop structure at the 5' splice donor site. Although the mutation does not give rise to an amino acid change in the tau protein, functional exon-trapping experiments show that it results in a significant 4.8-fold increase in the splicing of exon 10, resulting in the presence of tau containing four microtubule-binding repeats. This study provides direct molecular evidence for a functional mutation that causes progressive supranuclear palsy pathology and demonstrates that mutations in the tau gene are pleiotropic.
To defend or not to defend? Size, residence, and conditional mating in male variegated pupfish, Cyprinodon variegatus

In both the field and laboratory, we investigated the competitive strategies of different-sized residents and intruders in a species with multiple male mating tactics (i.e. territorial defense and sneak spawning), the variegated pupfish, Cyprinodon variegatus. Medium and large males were observed defending territories in the wild, and these two sizes of residents dominated all intruders in the laboratory in both the presence and absence of a female. Under laboratory conditions, some small males defended territories, but a relatively high proportion of small residents were defeated by intruders. When a female was present, intruders of all sizes frequently interrupted the spawning attempts of residents. Although no size of intruder in the laboratory interrupted more than the others, the tactics used by the different intruders to interrupt were different. Medium and large intruders were disruptive to the spawning pair, eliciting aggression from the resident, while small intruders sidled with a spawning pair, often without response from the resident, allowing the female to deposit an egg before leaving. These results suggest that medium and large males use overt aggressive behaviors to interrupt spawns; in contrast, small males devalue territory possession and rely on more surreptitious tactics to spawn.
Avaliação preliminar da qualidade das águas da Floresta Nacional de São Francisco de Paula, RS, Brasil

Preliminary evaluation of the water quality in the National Forest of Sao Francisco de Paula, RS, Brazil) - A preliminary analysis of the water quality of Rolante River and Lajeado Stream microbasins was accomplished with the purpose of verifying the impact of human activities on these water bodies. Both microbasins cross the area of the National Forest of Sao Francisco de Paula (FLONA-SFP), a national conservation unit located in Rio Grande do Sul State, Brazil. Physical and chemical variables were analyzed, as well as the composition and abundance of benthic macroinvertebrates. In a general way, the water quality was considered good, although it was detected some contamination for the variables phosphorus, nitrate, nitrite, fecal coliform and total dissolved solids in the point PT5, copper (Cu) and zinc (Zn) in the point PT6 (Lajeado stream) and fecal coliform in the points PT1 and PT2 (Rolante river). The contamination is originated probably from the use of pesticides, animal keeping and from agricultural and domestic sewage.
Effects of lactic acid bacteria and Saccharomyces cerevisiae on growth of Aspergillus westerdijkiae and ochratoxin A production and toxicity

The aim of this study was to examine three strains of the yeast Saccharomyces cerevisiae and three strains of lactic acid bacteria belonging to the genus Lactobacillus for their antifungal activity against the ochratoxin A producer Aspergillus westerdijkiae, as well as for their effect on OTA genotoxicity and cytotoxicity. When inoculated simultaneously, fungal growth was completely inhibited by S. cerevisiae. In the case of lactic acid bacteria, growth inhibition also occurred but to a less extent. A significant decrease in toxin production in co-culture with the yeast strains and LAB was observed. The supernatant of 24-h-old cultures of yeast strains in medium with OTA did not influence significantly the viability of porcine kidney epithelial LLC-PK1 cell line, whereas the supernatant from the LAB increased the viability compared to the control. Regarding genotoxicity, a decreased fragmentation of DNA was observed in the presence of the supernatant from wine and brewing yeasts, and Lactobacillus brevis .
THE HYPOXIC TOLERANCE OF THE PROTOBRANCH BIVALVE NUCULA SULCATA BRONN

Abstract Examination of the hypoxic tolerance of Nucula sulcata determined that the mean survival time under hypoxia was 9.57 d with a maximum longevity of 30 d. Comparison between the three species, N. sulcata, N. nitidosa, and N. nucleus reveals that N. sulcata is the most tolerant of hypoxia followed by N. nucleus and N. nitidosa. It is suggested that the hypoxic tolerance of the species is a reflection of the normal habitat they occupy.
Electric crows: powerlines, climate change and the emergence of a native invader

Climate change and other anthropogenic global change drivers act in complex, mutually exacerbating ways to alter the abundance and distribution of species. In South Africa, pied crows Corvus albus have increased in numbers and range in recent decades. Popular opinion links these changes to urbanisation and infrastructure development, but there has been no empirical test of this idea. We aimed to clarify the drivers of pied crow population changes in South Africa.
An Empirically Based Typology of Private Forest Owners in Denmark: Improving Communication Between Authorities and Owners

For policy instruments to be effective, they should motivate forest owners to adjust behaviour in agreement with forest policy objectives. It may therefore be beneficial to know the motivations of private forest owners. Often, forest owners are assumed to constitute an entity, although statistics and structural changes indicate increasing heterogeneity. Instead, forest owners can be divided into types, i.e. groups that include forest owners with similar attitudes, and where attitudes of each group differ from those of other groups. Based on a survey among private forest owners in Denmark, three types of owners were identified: (1) the classic forest owner to whom the forest has economic importance; (2) the hobby owner who enjoys work and recreation in the forest; and (3) the indifferent farmer to whom the different values provided by the forest are equally (un)important. Implications of this typology for forest policy formulation and implementation are discussed.
Distribution and partial properties of three viruses infecting cucumber in West Iran and their reservoir weed hosts

Field surveys during 2013–2014 indicated the distribution of Cucumber mosaic virus (CMV), Watermelon mosaic virus-2 (WMV-2) and Zucchini yellow mosaic virus (ZYMV) in the major cucumber-growing areas of Lorestan province, West Iran. A total of 249 (48.2%) of 516 symptomatic cucumber samples were found to be infected. According to the ELISA, viruses in decreasing order were WMV-2 (24.2%), CMV (14.7%) and ZYMV (10%). Moreover, among the 29 positive weed samples with above-mentioned viruses, Sonchus oleraceous and Malva sp. for CMV and Bryonia dioica for ZYMV were found as new natural hosts in Iran. Some weed isolates were more analysed using biological and molecular assays. Using recombination analysis, a tentative breakpoint was found in N-terminal of coat protein of ZYMV-Bd isolate. This isolate is more distinct from the other Iranian ZYMV isolates and fall into group II. However, all Iranian isolates belonged to group I which was divided into two subgroups, IA and IB.
Diagnosis and genetics of Marfan syndrome

Introduction: Marfan syndrome (MFS) is a connective tissue disorder with highly variable features in cardiovascular, ocular and skeletal systems. MFS is generally caused by one of the 2900-plus described different genetic mutations in the fibrillin-1 gene (FBN1). Areas covered: By revising the Ghent criteria in 2010, more weight has been given to genetic testing in the diagnosis of MFS. We provide an overview of correlations between different mutation types and clinical MFS features by using the Universal Mutation Database (UMD). Expert opinion: In this paper, we classified FBN1 mutations based on their action on DNA level and we found the following genotype–phenotype correlations: i) cysteine mutations are associated with ectopia lentis; ii) introduction of a cysteine leads to less severe involvement of cardiovascular and skeletal system; iii) whole gene deletions and premature termination codon (PTC) mutations are associated with increased skeletal and cardiovascular involvement, but lower prevalence of ectopia lentis and iv) intronic mutations lead to MFS by exon skipping, small insertions/deletions and PTC mutations. Classification based on mutation effect at protein level (reduced vs truncated/deformed fibrillin-1) may partly explain genotype–phenotype association and warrants further investigation for individualized prognosis and treatment.
Male Body Size and Fitness in the Web‐building Spider Nephila clavipes

Small male size in relation to female size in many web spiders has led to considerable speculation as to its selective advantages. In some species the males compete for females and fights are generally won by the larger competitor. Even in these species small male size persists; Nephila clavipes is an example. A study is presented focussing on the costs and benefits of male size. Zusammenfassung Die Okologie und Populationsdynamik von Nephila clavipes in Panama werden umrissen. Im Jahr gibt es zwei Fortpflanzungsperioden. Zu Beginn jeder Fortpflanzungsperiode ist die Konkurrenz der Mannchen um die Weib-chen stark. Das groste Mannchen in einem Netz erobert und verteidigt die Nabe, an der das Weibchen sich aufhalt, hier findet auch die Paarung statt. Die Mannchen variieren in ihrer Korpergrose, sind jedoch kleiner als die Weibchen. Die Grosenklassen-Verteilungen sind unterschiedlich, nicht nur zwi-schen den zwei Fortpflanzungsperioden, sondern auch zwischen verschiedenen Standorten. Es wird angenommen, das die Mannchengrose durch das Nah-rungsangebot beeinflust wird. Grosere Mannchen schienen die Suche nach Weibchen besser zu uberleben als kleinere Mannchen, kleinere Mannchen hiel-ten sich langer als grosere in den Netzen von subadulten Weibchen auf. Ver-suche mit sterilisierten Mannchen erlauben Ruckschlusse auf den Befruchtungs-erfolg verschieden groser Mannchen und sukzessiver Paarungen.
Denaturing gradient gel electrophoresis analysis of gut bacterial community for the Japanese earthworms

The gut bacterial community structure for Pheretima hilgendorfi and P. heteropoda (Family Megascolecidae), and Allolobophora japonica (Family Lumbricidae) collected from agricultural grasslands in Japan was analyzed by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16S rRNA gene fragments (PCR-DGGE) and compared with those in the surrounding soils. Denaturing gradient gel electrophoresis (DGGE) profiles indicated that each earthworm species had their own specific bacterial communities, and multidimentional scaling analysis grouped the DGGE profiles into three groups: gut samples from P. hilgendorfi and P. heteropoda, gut samples from A. japonica and samples from the surrounding soils. Nine dominant bands were identified by their direct sequencing and cloning. Major three bands from P. hilgendorfi and P. heteropoda were closely related to Bacillus species belonging to the phylum Firmicutes. Major four and two bands from A. japonica were closely related to the phyla Proteobacteria and Bacteroidetes, respectively.
Low-molecular-mass carbohydrates and soluble polysaccharides of green and red morphs of Gracilaria domingensis (Gracilariales, Rhodophyta)

Abstract We studied the chemical structure and yield of low-molecular-mass carbohydrates (LMMC) and soluble polysaccharides produced by green and red morphs of Gracilaria domingensis. Red plants had higher amounts of the LMMC floridoside than green morphs (324.4±8.1 and 220.1±6.0 μmol g-1 dry biomass, respectively). The yield of polysaccharides was similar between morphs (46.3±5.8% for the red and 41.4±8.3% for the green) as was the monosaccharide composition. The same agaran (6-O-methylated and sulphated) was isolated from both morphs, as determined by 13C NMR spectroscopy analysis. The floridean starch content (mg g-1 dry biomass) for the green morphs (116.2±1.7) was lower than that of the red morphs (143.9±1.8). This study showed that green and red morphs of G. domingensis are similar in their polysaccharide composition, but differ in the short-term storage compounds, starch and floridoside. These differences may be related to light and shade photosynthetic strategies, which lead to different storage accumulation.