Miracle-dz/UniFAR-FTUs huggingface dataset:
The resource ratio hypothesis and the meaning of competition

Since its appearance in the 1980 volume of American Naturalist, Tilman's resource ratio hypothesis has attracted much attention. In this issue of Functional Ecology we are publishing a critical appraisal of the hypothesis, with a reply from Professor Tilman. We hope this Special Forum will stimulate further discussion, and we look forward to publishing a selection of readers' views in future issues. Editors
Survival and avoidance response of the freshwater gastropod Melanoides tuberculatus (Muller) to different concentrations of tobacco waste

The Gastropod Melanoides tuberculatus plays a significant role in hampering fish larval production in earthen ponds. This study investigated use of tobacco waste to assess behavioural and survival responses of M. tuberculatus at different concentrations of tobacco waste solution of 0.25, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75 and 2 g L 1 . Mean escape time varied significantly among concentrations (P < 0.05). Escape time decreased in 1-, 2- and 3day-old solutions. Percentage survival decreased significantly with increasing concentrations of tobacco waste solution and exposure time (P < 0.05). Concentrations of 1.75 g L 1 and 2.0 g L 1 had high hazard ratios and low survival rates of gastropods and were the most effective in eradication of M. tuberculatus, hence recommended dose for preparing ponds for stocking. We conclude that tobacco waste solution can be used for control of M. tuberculatus.
Trichodina mutabilis (Protozoa: Ciliophora: Trichodinidae) from the characid fish Astyanax mexicanus in the Cuatro Ciénegas region, northern Mexico

As a part of a series of ongoing studies on trichodinids of freshwater fishes of Mexico, several species from diverse localities in the Cuatro Cienegas region, Coahuila, northern Mexico, were examined. Wet smears of gills and skin were made fresh and screened for the presence of trichodinids under light microscopy. Additional specimens were fixed for SEM. The only trichodinid species found was Trichodina mutabilis, a parasite of the characid fish Astyanax mexicanus. This ciliate protozoan has been introduced from Asia to many countries, including Mexico, with its original host, the Asian carps. The present record is the first for Mexico and the second in North America, being the first record of a Trichodina species for native wild freshwater fish in a natural environment in Mexico, since all previous records were from exotic cultured fishes.
Polimorfismo genético de beta-lactoglobulina y alphalactoalbúmina en el ganado criollo colombiano, mediante PCR-SSCP

The Colombian Creole Cattle has showed a disturbing decrease in population, from 23,415 individuals in 1999 to 20,102 in 2003. Despite that many efforts to recover the creole breeds have been done, its future conservation is unclear. Searching for economic desirable genes may contribute to its preservation and utilization as a genetic resource. Genes related with the improvement of milk proteins are considered as an economic important factor by the dairy industry. With the aim of characterizing beta-lactoglobulin (β-LG) and alpha-lactalbumin (α-LA) genes, 30 samples from each of the creole breeds (Blanco Orejinegro, Caqueteno, Casanareno, Costeno Con Cuernos, Chino Santandereano, Harton del Valle, Romosinuano and Sanmartinero), two Colombian breeds (Lucerna and Velasquez) and two introduced breeds (Holstein and Brahman) were analyzed. A DNA fragment of 262 bp for β-LG and 166 for α-LA using PCR-SSCP were amplified and analyzed. The average frequencies for β-LG (A) and β-LG (B) were 0.46 ± 0.020 and 0.53 ± 0.020, respectively, and 0.35 ± 0.019 for α-LA (A) and 0.64 ± 0.019 for α-LA (B). The genetic diversity (He) average for β-LG was 0.498 and 0.455 for α-LA. Creole breeds represent a valuable genetic base as an alternative for breeding and improvement programs in dairy production herds in order to produce milk with desirable characteristics for the dairy industry.
Improvement of the tube diffusion test with respect to detection of antibiotic residues and sulphonamides in raw milk

Improvements in detection of tetracycline, sulphonamide, macrolide, rifamycin, trimethoprim and aminoglycoside residues in milk were achieved by addition of either chloramphenicol or trimethoprim, and phenylbutazone to tube diffusion tests utilising Bacillus stearothermophilus var. calidolactis as bacterial test strain. If the modified tube diffusion tests are performed at pH 7 and 8.0 residues of beta-lactams, and of the forementioned groups can be detected below or near their maximum residue levels established for milk.
First Report of Black Leaf Spot Caused by Alternaria alternata on Ramie in China

In 2012 and 2013, black leaf spot disease was observed on ramie plants in Hunan and Hubei Provinces, China. In the field, the symptoms of this disease included dark green to black big spots on leaves, often resulting in upwardly curled leaf margins. The pathogen isolates were identified as Alternaria alternata (Fr.) Keissler on the basis of morphology and sequence similarity of 99–100% to the published data for internal transcribed spacer (ITS), and glyceraldehyde-3-phosphate dehydrogenase (gdp). To our knowledge, this is the first report of Alternaria leaf spot of ramie in China.
Molecular cloning and characterization of a putative OGG_N domain from the camel, Camelus dromedarius

Reactive oxygen species (ROS) oxidize the guanine base in the DNA to 8-oxoguanine (8-oxoG). This lesion, if left unrepaired, causes the transversion of G:C pair to T:A following replication. 8-oxoG is targeted by one of the DNA glycosylases, namely OGG1. Arabian camel (one humped camel, Camelus dromedarius ) is adapted to live in desert climate conditions under direct exposure to endogenous and exogenous ROS-producing conditions, among of them the sunlight. In the recent study, partial sequence of camel OGG-1 gene was cloned and analyzed for the first time. A DNA fragment of 567 bases was amplified by reverse transcription PCR. It is equivalent to about 55% from the coding region of the known transcript of many organisms. The level of expression of OGG-1 in different camel tissues (liver, kidney, spleen, lung and testis) was examined using real time-PCR. The highest level of OGG-1 transcript was found in the camel liver (represented as 100%) followed by testis (85%), spleen (78%), kidney (37%) and lung (3%) using 18S ribosomal subunit as endogenous control. The obtained cDNA sequence of OGG-1 showed high similarity with Ailuropoda melanoleuca (86%), Sus scrofa (86%), Canis familiaris (85%), Bos taurus (85%), Macaca mulatta (85%), Homo sapiens (84%), Pan troglodytes (84%) and Pongo abelii (82%). Keywords: Camelus dromedarius , cloning, OGG1, gene expression, DNA glycosylase
Turf transplants for restoration of alpine vegetation: does size matter?

Summary 1. Turfs transplanted from native vegetation can be used to restore diverse plant communities on disturbed sites. There is, however, limited understanding of optimal turf size and the tolerance of different plant communities and species to transplanting. 2. The effects of turf size in restoration of alpine plant communities were studied in SW-Iceland. Treatments tested in 2-m2 plots were as follows: planting of sixteen 5 × 5 cm turfs, four 10 × 10 cm turfs, one 20 × 20 cm turf or one 30 × 30 cm turf; a 20 × 20 cm turf shredded and spread over the plot and controls without turfs. The 10-cm thick turfs were extracted from nearby heath and grassland vegetation and planted in mineral soil and road verges at 260–410 m elevation. Species composition, cover and colonization were monitored for three growing seasons. 3. Grassland vegetation tolerated division into small turfs better than heath vegetation, but responses varied by functional groups. Cover of dwarf-shrubs decreased with decreasing turf size; grass cover was highest in plots with 5 × 5 cm turfs and lowest in plots with shredded turfs, while moss cover increased most rapidly in plots with shredded turfs. 4. Synthesis and applications. Optimum turf size for the restoration of native species varied among functional groups of plants and decreased as follows: evergreen dwarf-shrubs > deciduous dwarf-shrubs > sedges > grasses > mosses. Turfs that are at least 20–30 cm in diameter may be needed for the transplantation of dwarf-shrubs, while turfs as small as 5 cm in diameter can be used to establish many grass species. Even smaller units can be used to facilitate moss colonization. Turfs that are salvaged from development projects can be a valuable source of native species for use in restoration schemes. Turf size for transplanting should be selected with regard to donor vegetation, growth form and abundance of the target species.
Histidine-Containing Dipeptide Concentration and Antioxidant Effects of Meat Extracts from Silky Fowl: Comparison with Meat-Type Chicken Breast and Thigh Meats

This study investigated functional dipeptide (anserine and carnosine) concentrations and antioxidant activities of Silky Fowl. Fresh meat from Silky Fowl contained 1.6to 2.3-fold higher carnosine content compared with other chickens ( p < 0.05). The carnosine content of fresh meat from Silky Fowl was higher than the anserine content, in contrast to that of common chicken. Our study showed that the meat extract of Silky Fowl is a good scavenger of the hydroxyl radical. Significant correlations between the total dipeptide content of meat extracts and hydroxyl radical scavenging (IC50 values) activity were additionally revealed by multiple regression analysis (breast: R = 0.684, p < 0.001; thigh: R = 0.729, p < 0.001). Since Silky Fowl is especially rich in carnosine, these findings make this breed potentially useful as a rich dietary source of antioxidant dipeptides.
Function of bromodomain and extra-terminal motif proteins (BETs) in GATA1-mediated transcription

Bromodomain and Extra-Terminal motif proteins (BETs) associate with acetylated histones and transcription factors. While pharmacologic inhibition of this ubiquitous protein family is an emerging therapeutic approach for neoplastic and inflammatory disease, the mechanisms through which BETs act remain largely uncharacterized. Here we explore the role of BETs in the physiologically relevant context of erythropoiesis driven by the transcription factor GATA1. First, we characterize functions of the BET family as a whole using a pharmacologic approach. We find that BETs are broadly required for GATA1-mediated transcriptional activation, but that repression is largely BET-independent. BETs support activation by facilitating both GATA1 occupancy and transcription downstream of its binding. Second, we test the specific roles of BETs BRD2, BRD3, and BRD4 in GATA1-activated transcription. BRD2 and BRD4 are required for efficient transcriptional activation by GATA1. Despite co-localizing with the great majority of GATA1 binding sites, we find that BRD3 is not required for GATA1-mediated transcriptional activation. However, exogenous BRD3 efficiently compensates for BRD2 loss, suggesting that BRD2 and BRD3 function redundantly. Third, we tested the role of BETs in mitotic bookmarking. We present evidence that mitotic binding by BRD4, the BET most strongly implicated in preserving transcriptional state during mitosis, is extensively remodeled during this phase of the cell cycle. Additionally, disruption of mitotic BET occupancy has no measurable impact on post-mitotic gene reactivation, calling into question the role of BETs in mitotic bookmarking. These results elucidate new factors critical for GATA1-mediated erythropoiesis. In addition to furthering understanding of the mechanisms underlying BET function, these findings have important consequences for the rational development of BET inhibitors. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Pharmacology First Advisor Gerd A. Blobel
Phenology, irradiance and temperature characteristics of a freshwater red alga, Nemalionopsis tortuosa (Thoreales), from Kagoshima, southern Japan

Phenology, irradiance and temperature characteristics of a freshwater benthic red alga, Nemalionopsis tortuosa Yoneda et Yagi (Thoreales), were examined from Kagoshima Prefecture, southern Japan for the conservation of this endemic and endangered species. Field surveys confirmed that algae occurred in shaded habitats from winter to early summer, and disappeared during August through November. A net photosynthesis–irradiance (P–E) model revealed that net photosynthetic rate quickly increased and saturated at low irradiances, where the saturating irradiance (Ek) and compensation irradiance (Ec) were 10 (8–12, 95% credible interval (CRI)) and 8 (6–10, 95% CRI) μmol photon m−2 s−1, respectively. Gross photosynthesis and dark respiration was determined over a range of temperatures (8–36°C) by dissolved oxygen measurements, and revealed that the maximum gross photosynthetic rate was highest at 29.5 (27.4–32.0, 95%CRI) °C. Dark respiration also increased linearly when temperature increased from 8°C to 36°C, indicating that the increase in dark respiration at higher temperature most likely caused decreases in net photosynthesis. The maximum quantum yield (Fv/Fm) that was determined using a pulse amplitude modulated‐chlorophyll fluorometer (Imaging‐PAM) was estimated to be 0.51 (0.50–0.52, 95%CRI) and occurred at an optimal temperature of 21.7 (20.1–23.4, 95%CRI) °C. This species can be considered well‐adapted to the relatively low natural irradiance and temperature conditions of the shaded habitat examined in this study. Our findings can be applied to aid in the creation of a nature‐reserve to protect this species.
Living cells in wood. 1. Absence, scarcity and histology of axial parenchyma as keys to function

The diversity of expression in axial parenchyma (or lack of it) in woods is reviewed and synthesized with recent work in wood physiology, and questions and hypotheses relative to axial parenchyma anatomy are offered. Cell shape, location, abundance, size, wall characteristics and contents are all characteristics for the assessment of the physiological functions of axial parenchyma, a tissue that has been neglected in the consideration of how wood histology has evolved. Axial parenchyma occurrence should be considered with respect to mechanisms for the prevention and reversal of embolisms in tracheary elements. This mechanism complements cohesion–tension-based water movement and root pressure as a way of maintaining ﬂow in xylem. Septate ﬁbres can substitute for axial parenchyma (‘axial parenchyma absent’) and account for water movement in xylem and for the supply of carbohydrate abundance underlying massive and sudden events of foliation, ﬂowering and fruiting, as can ﬁbre dimorphism and the co-occurrence of septate ﬁbres and axial parenchyma. Rayless woods may or may not contain axial parenchyma and are informative when analysing parenchyma function. Interconnections between ray and axial parenchyma are common, and so axial and radial parenchyma must be considered as complementary parts of a network, with distinctive but interactive functions. Upright ray cells and more numerous rays per millimetre enhance interconnection and are more often found in woods that contain tracheids. Vesselless woods in both gymnosperms and angiosperms have axial parenchyma, the distribution of which suggests a function in osmotic water shifting. Water and photosynthate storage in axial parenchyma may be associated with seasonal changes and with succulent or subsucculent modes of construction. Apotracheal axial parenchyma distribution often demon-strates storage functions that can be read independently of osmotic water shifting capabilities. Axial parenchyma may serve to both enhance mechanical strength or, when parenchyma is thin-walled, as a tissue that adapts to volume change with a change in water content. Other functions of axial parenchyma (contributing resistance to pathogens; a site for the recovery of physical damage) are considered. The diagnostic features of axial parenchyma and septate ﬁbres are reviewed in order to clarify distinctions and to aid in cell type identiﬁcation. Systematic listings are given for particular axial parenchyma conditions (e.g. axial parenchyma ‘absent’ with septate ﬁbres substituting). A knowledge of the axial parenchyma information presented here is desirable for a full understanding of xylem function. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society , 2015, 177 , 291–321. that regulate sugar water membrane transport, activity. droplets with high
New and little known Palearctic species of the genus Ochthebius (Subgen. Hymenodes) (Coleoptera: Hydraenidae)

Ochthebius (Hymenodes) subdifficilis sp. n. , O. (H.) wewalkai sp. n. , and O. (H.) orchymonti sp. n. are described. O. (H.) difficilis Mulsant is compared. O. (H.) schneideri Kuwert is redescribed from syntypes and a lectotype is designated. All species mentioned are similar to O. difficilis and probably closely related to it.
A new species of Gypsophila and a new name for Silene (Caryophyllaceae) from Turkey

Gypsophila turcica Hamzaoglu is described as a new species. The specimen was collected from gypsaceous hills, at an altitude between 1755 and 1835 m from Zara District (Sivas Province). The new species is similar to Gypsophila festucifolia Hub. -Mor. The differences between these 2 taxa are discussed. Moreover, Silene choruhensis Hamzaoglu nom. nova should replace S. ispirensis A.P.Khokhr. 1997, which is an illegitimate name as a younger homonym of S. ispirensis Boiss. 1856.
Identification, sequence characterization and expression analysis of the arginine kinase gene in response to laminarin challenge from the Oriental land snail, Nesiohelix samarangae

Arginine kinase (ArK) is known to play an important role in most invertebrates the level of ATP by phosphorylation of phosphagens in cell and immuninty in living organisms. ArK has been identified in many kinds of organisms ranging from invertebrate to vertebrate. However, no ArK gene has been cloned and investigated from N. samarangae. This leads us to identify ArK cDNA (NsArK) from the expressed sequence tag (EST) sequencing of N. samarangae. Sequence analysis indicated that the coding region of 1,065 bp contains 355 amino acid residues. Molecular phylogenetic analysis shows that NsArK had very high similarities with mollusca and arthropoda. In an attempt to investigate a potential role of NsArK in the digestive gland of N. samarangae, expression patterns were analyzed. RT-PCR analsysis shows that NsArK mRNA is induced in the rane of 1.2 fold at 6 hr by laminarin when compared with the control. The immunnologial and physiological role of NsArK remains to be further investigated in N. samarangae.
Studies on the electrical properties of the dorsal cochlear nucleus cartwheel neurons

Cartwheel cells in the dorsal cochlear nucleus (DCN) are glycinergic inhibitory interneurons which form synapses on principal neurons and among themselves. Their activity is characterized by the presence of the complex spike, a brief burst of highfrequency spikes riding on a slow depolarization. The feedforward inhibition mediated by cartwheel cells prominently shapes the response of DCN principal cells to somatosensory input. Therefore, knowledge on how activity of cartwheel cells is regulated is important for input processing in the DCN. I examined two aspects of cartwheel cells, the ionic mechanism of complex spike generation and the glycine reversal potential, using gramicidin perforated-patch recording in a mouse brain slice preparation. Complex spikes require both Ca and Na currents. I monitored the change in spike waveforms elicited by subtype-specific blockers Ca channels and Caactivated K channels. T/Rand L-type Cachannels contributed to the slow depolarization of complex spikes, whereas the P/Q-type Ca channels reduced the duration of the slow depolarization by coupling to SK channels. Single action potentials repolarized to more negative potential due to the presence of BK channels, which lowered the tendency to fire complex spikes. Thus, the balance between the depolarizing influence of a variety of Ca channels and the repolarizing effect of Ca-activated K channels shaped the complex spike and controlled its occurrence. In a second set of experiments, I examined the factors controlling the activitydependence of glycine responses in cartwheel cells. Glycine reversal potential (Egly) determines whether the glycine response of the cell is hyperpolarizing or depolarizing. Egly shifted negative, increasing inhibition, after complex spiking or Ca spiking, and
Conditional modelling of ring‐recovery data

1. Ring‐recovery data can be used to obtain estimates of survival probability which is a key demographic parameter of interest for wild animal populations. Conditional modelling of ring‐recovery data is needed when cohort numbers are unavailable or unreliable. It is often necessary to include in such analysis a recovery probability that is declining as a function of time, and failure to do this can result in biased estimates of annual survival.
Characterization of Micrococcus luteus and Bacillus marisflavi Recovered from Common Dentex (Dentex dentex) Larviculture System

In this manuscript, thirty yellow-pigmented Gram-positive bacteria were isolated from natural intestine microflora and from sea water around the marine cage of a rearing tank of common dentex ( Dentex dentex ), in the Aegean Sea on the Turkish coast and were characterized. Eighteen isolates were assigned to the species Micrococcus luteus , the other twelve to the species Bacillus marisflavi . Eight representative strains, six from B. marisflavi and two from M. luteus , were chosen for further 16S rDNA analyses. A pathogenicity assay for the isolated bacterial strains was carried out in rainbow trout and it evidenced absence of pathogenicity in the tested strains. The isolated strains were tested for in vitro antagonistic activity against Listonella anguillarum , a pathogen bacterium diffused in Mediterranean aquaculture and affecting various fish species. The isolated bacterial strains showed antagonistic activity against the pathogenic bacterium, suggesting a possible role of isolates as probiotics. In this study, for the first time, bacterial strains of the species B. marisflavi , known as an environmental species, were recovered in the gut microbiota of a healthy fish. The use of the isolates characterized in this study, mainly the yellow-pigmented bacterium, is suggested as possible probiotics to improve fish health, along with alternative methods of maintaining a healthy environment.
Nitrogen fixation by Baltic cyanobacteria is adapted to the prevailing photon flux density

N-2 fixation, measured as acetylene reduction, was studied in laboratory cultures and in natural assemblages (both as a mixed population and as individually picked colonies) of the heterocystous cyanobacteria Aphanizomenon sp. and Nodularia spp. from the Baltic Sea. During a diurnal cycle of alternating light and darkness, these organisms reduced acetylene predominantly during the period of illumination, although considerable activity was also observed during the dark period. In both laboratory cultures and natural populations N-2 fixation was saturated below photon flux density of 600 mu m(- 2) s(-1). In cyanobacterial blooms in the Baltic Sea, nitrogenase activity was mostly confined to the surface layers. Samples collected from greater depths did not possess the same capacity for acetylene reduction as samples from the surface itself, even when incubated at the photon flux density prevailing in surface waters. This suggests that, with respect to N-2 fixation, Baltic cyanobacteria are adapted to the intensity of illumination that they are currently experiencing. [KEYWORDS: Baltic cyanobacteria; N-2 fixation; Aphanizomenon; Nodularia Fe-protein; planktonic cyanobacteria; anabaena-variabilis; nodularia-spumigena; gloeothece nageli; alternating light; n-2 fixation; gas vesicles; sea; blooms]