Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen and phosphorus colimitation of phytoplankton in Lake Baikal: Insights from a spatial survey and nutrient enrichment experiments

Lake Baikal, Siberia, is the most biodiverse freshwater lake on Earth. However, despite decades of painstaking limnological research on Baikal, broad spatial data on nutrient (nitrogen (N), phosphorus (P), silica (Si)) concentrations and temperature are sparse, as is our understanding of the bottom‐up factors that limit phytoplankton in the lake. Earlier studies have suggested both N and P as limiting nutrients in Baikal, but the evidence, mostly based on elemental ratios, is limited and somewhat conflicting. We present experimental evidence that N and P co‐limit phytoplankton productivity in some areas of Baikal during summer, along with the results of a comprehensive spatial survey of surface temperature, nutrients and chlorophyll a (Chl a) in Lake Baikal that support the experimental finding of colimitation. Surface water incubations from two trophically contrasting locations revealed co‐limitation by N and P, as well as a positive effect of temperature (fluorescence after 5 d was ∼10% higher at 15°C than at 10°C). In a linear model of the survey data (26 sampling locations), N, P, and their interaction (N × P) were all significant predictors of Chl a concentration, indicating that either N or P (or both) may limit summer phytoplankton, depending on location. In contrast to the incubation experiments, temperature was not a significant predictor of Chl a concentration across the 26 sites we sampled. Lake Baikal is undergoing rapid warming and increased nutrient loading, which may boost phytoplankton productivity in the lake; however, the magnitude of this response will depend on ratios of soluble N and P inputs.
First Report of Botrytis Leaf Blight on Lily (Lilium longiflorum) Caused by Botrytis cinerea in Beijing, China

In China, winter brings selling season of cut flowers as it is customary to have living blooms for lunar New Year celebrations. Here, lily is one of the most popular new year flowers and captured over 19 percent of all flower sales. The flower market of Beijing is the largest in China and therefore many lily farms are present in the suburb of Beijing to reduce logistical cost. During winter of 2015, lily plants exhibited leaf blight symptoms in greenhouses of a lily farm at Changping District (116°12′E, 40°13′N), Beijing. The disease has resulted in serious loss of lily production in the farm, and approximately 10 to 15 percent of plants were destroyed due to the severe infection. The infection initially manifested as irregular lesions on the leaves, which gradually expanded into blight of grayish brown and frequently involve the entire leaf. Severely infected leaves were distorted, covered with grey mycelium and conidia. Flower buds had no lesions or sporulation. Conidia were hyaline, unicellular and ovo.
Effect of salt stress on photosynthesis and related physiological characteristics of Lycium ruthenicum Murr

ABSTRACT Halophytes could withstand the hyper-salinity soil and survive widely in areas where soil salt content is high because they can endure salt stress to a certain extent. Lycium ruthenicum Murr (LRM), with significant nutritional and medicinal values, is one of the most important native halophytes in the arid oasis-desert transition zone of northwestern China. In recent years, artificially planting LRM has been being popular since it can improve saline-alkalized soil and increase the income of local farmers as well. More efforts about the artificial planting of LRM are put in enhancing the productivity and quality, but survivorship of LRM seedling by appropriate saline irrigation is still unclear in arid areas. A field experiment was conducted to explore the responses of LRM to four levels of saline water irrigation (Ec of irrigation water: 2.00 μs cm−1 (T1), 4.51 μs cm−1 (T2), 6.89 μs cm−1 (T3), and 9.00 μs cm−1 (T4)) during the growing seasons in 2014 and 2015. The average soil electrical conductivity (Eca) in 0–60 cm depth increased while the biomass of LRM decreased with increasing Ec of irrigation water, and the differences of Eca among treatments decreased with increasing salinity level. In contrast to previous research findings, salt stress had more significant effect on photosynthesis and chlorophyll fluorescence of LRM, in which great changes were caused by a threshold following the increased salinity. Most of the light energy absorbed by LRM was used for photosynthesis and heat dissipation when soil salinity was low, what was used for chlorophyll fluorescence when soil salinity was high. The results of the experiment indicate that T2 was the most suitable irrigation method for artificially planting LRM in the field, and it’s the key to save freshwater resources in arid areas and improve the production of saline-alkali land.
Use of selenocysteine, the 21st amino acid, in the fungal kingdom

Selenoproteins are a diverse class of proteins containing selenocysteine (Sec), the 21st amino acid, incorporated into proteins during translation through a unique recoding mechanism. Selenoproteins fulfil essential roles in several lineages, including vertebrates; yet, they are not ubiquitous across the tree of life. In particular, the fungal kingdom was thought to lack selenoproteins, a paradigm that we defy here. We show that the genetic machinery for Sec utilization is present in the genomes of five species belonging to diverse early-branching fungal phyla (Chytridiomycota, Zoopagomycota, and Mucoromycota). We identified several selenoprotein genes in each of these genomes, and we detected canonical Sec insertion RNA structures (SECIS elements) for some of them. The identified selenoproteins are known or predicted oxidoreductases, some of which are conserved in mammals. Phylogenetic analyses support a scenario of vertical inheritance of the Sec trait within eukaryotes and fungi. Sec was then lost in numerous independent events in various fungal lineages, even within Sec-containing phyla. Notably, Sec was lost at the base of Dikarya, resulting in the absence of this trait in Saccharomyces cerevisiae and other well studied fungi. Our results indicate that, despite scattered occurrence, selenoproteins are found in all kingdoms of life.
Dynamism and context dependency in the diversification of the megadiverse plant genus Solanum L. (Solanaceae)

Explosive radiations have been considered one of the most intriguing diversification patterns across the Tree of Life, but the subsequent change, movement and extinction of the constituent species makes radiations hard to discern or understand as geological time passes. We synthesised phylogenetic and distributional data for an ongoing radiation — the mega-diverse plant genus Solanum L. — to show how dispersal events and past climatic changes have interacted to shape diversification. We found that despite the vast diversity of Solanum lineages in the Neotropics, lineages in the Old World are diversifying more rapidly. This recent explosive diversification coincides with a long-distance dispersal event from the Neotropics, at the time when, and to places where, major climatic changes took place. Two different groups of Solanum have migrated and established in Australia, but only the arid-adapted lineages experienced significant increases in their diversification, which is consistent with adaptation to the continent’s long-term climatic trend and the diversification of other arid-adapted groups. Our findings provide a clear example of how successful colonisation of new areas and niches can – but do not always – drive explosive radiations.
Optimizing Growth, Seed Yield and Quality of Soybean (Glycine max L.) Plant Using Growth Substances

Aims: It is become necessary to reduce the gap between the demand and supply of edible oil and protein. So, the aim of the present investigation is to study the effect of foliar application with humic acid, salicylic acid and paclobutrazol on some morphological, anatomical and seed yield characteristics, as well as on some biochemical constituents of soybean (Glycine max L.) seed for maximizing its growth, yield and nutritional value. Methodology: A 2 year field trial was carried out during 2015 and 2016 at the Faculty of Agriculture Experiment Station, Benha University, Egypt . Soybean (Glycine max L.) cv. Giza 111 seeds were sown into plots (each plot unit about 3.5 m long and 3.0 m wide) in clay loam soil. A total of six treatments of humic acid, salyclic acid, and paclobutrazol were foliarly applied: humic acid at 2.5 and 5.0 gl -1 , salicylic acid at 50 and 100 mgl -1 , paclobutrazol at 10 and 20 mgl -1 and Control in a 3 randomized complete blocks. Results: All rates of humic acid, salicylic acid and paclobutrazol had a significant effect on soybean morphological characters during the 2 years. The treatment set of 10 mgl paclobutrazol, 5 gl humic acid, and 100 mgl salicylic acid resulted in relatively higher means for most vegetative Original Research Article Abd El-Aal and Eid; ARJA, 6(3): 1-19, 2017; Article no.ARJA. 36034 2 growth characters compared to both the other 3 and the Control treatments. Despite variations among the 6 rates effects, all enhanced chlorophyll and carotenoids contents. This positive response extended to include the contents of soybean shoot endogenous phytohormones. Soybean yield components and yield were significantly improved due to applying these 3 growth substances using these current rates, this in addition to their positive effect on N P K content, crude protein, total carbohydrates and percentage total lipids in soybean seed yield. Under the conditions of this trial, either of 10 mgl -1 paclobutrazol, 5 gl -1 humic acid, or 100 mgl -1 salicylic acid proved useful to improve soybean growth and yield, yet more further research deem necessary to include more expanded set of rates to be assessed under other perspectives.
A new species of Bryconamericus (Characidae: Stevardiinae: Diapomini) from the upper rio Paraná basin, Brazil

Bryconamericus is the most diverse genus within Stevardiinae, comprising 61 valid species distributed in Cisand TransAndean basins from Panama in Central America to northern Argentina in South America. Three species are known from the upper rio Paraná basin: B. exodon, B. iheringii, and B. turiuba. Herein we describe a new species of Bryconamericus from the upper rio Paraná basin inhabiting tributaries of Ivaí, Piquiri, and Tibagi basins, Paraná State, Brazil. The new species differs from its congeners by the presence of unaligned teeth in the outer tooth row of the premaxilla; a single, vertical, dorsally expanded and rounded humeral spot; 36-39 pored scales in the longitudinal series; body depth 31.6-37.9% SL; anal-fin base length 24.8-30.1% SL; number of branched anal-fin rays 19-22, and bony hooks on pelvicand anal-fin rays of sexually dimorphic males. The new species is syntopic with other Stervadiinae in the upper rio Paraná basin such as B. iheringii, B. turiuba, Piabarchus stramineus, and Piabina argentea.
Landscape context and farm uptake limit effects of bird conservation in the Swedish Volunteer & Farmer Alliance

In Europe, agri-environmental schemes (AES) have been unsuccessful in halting biodiversity declines to any great extent. Two particular shortcomings of AES include the low farm uptake and the modest efficacy of many AES options. Partly in response to these shortcomings, initiatives encouraging farmers to take an active role in biodiversity conservation have gained in popularity. However, almost no evaluations of such initiatives exist. 2. We evaluated uptake of conservation advice on farms in the Swedish Volunteer & Farmer Alliance, a BirdLife Sweden-coordinated project aimed at farmland bird conservation, and the response of farmland birds to those actions using farm-level survey data, in a before-after implementation assessment. 3. Uptake was higher for unsubsidised (i.e. non-AES) measures than for AES options, and depended on farmers’ interest in nature, farm size (higher uptake on larger farms) and production type (higher on organic farms). 4. In general, abundances of non-crop nesting and field-nesting bird species declined between inventory years (median interval 3 years). Decreases were more marked in agriculturally marginal regions than in more arable-dominated regions, and declines were stronger on organic than conventional farms. 5. Negative abundance trends among non-crop nesting species were reduced by an increasing number of conservation measures at the farm, but only in the more arable-dominated landscapes. Changes in other non-crop species and in field-nesting species did not significantly relate to implemented measures, but the power to detect such effects was generally small due to the small sample size of high-uptake farms as well as high inter-farm variability. 6. Implications: Our results suggest that Volunteer Farmer Alliances and the addition of unsubsidised measures may be successful in changing the local number of non-crop nesting farmland birds at the farm level, and especially so in intensively managed agricultural landscapes. Thus, unsubsidised measures can be a useful addition to the set of agri-environment tools, although their effects on breeding bird numbers are (as with AES) dependent on landscape context, as well as on ensuring high on-farm uptake of different interventions.
Effects of functional diversity and functional dominance on complementary light use depend on evenness

Co-ordinating Editor: Hans Henrik Bruun Abstract Questions: Does functional diversity play a more important role than species richness in complementary resource use? Is the effect of functional diversity on complementarity greater when species evenness is higher? Does functional dominance play an important role in resource use when species evenness is low? Location: An arable field in Linhai City, Zhejiang Province, China. Methods: We assembled experimental plant communities with different species richness (one, two, four, eight and 12 species) and evenness (low and high). In each community, we quantified light interception efficiency (LIE) and light complementarity index (LC) to reflect light use. We measured four functional traits related to light capture to quantify functional diversity and functional dominance. We then tested effects of observed species richness, functional diversity and functional dominance on LIE, LC and aboveground biomass in the low and high evenness communities. Results: Functional diversity was positively related to LIE, LC and aboveground biomass in the high evenness communities, but not in the low evenness communities. In contrast, functional dominance was positively related to LIE and negatively related to LC in the low evenness communities, but not in the high evenness communities. Moreover, functional dominance had a larger promotion to aboveground biomass in the low evenness communities. Observed species richness and evenness had a significant interactive effect on LIE and LC. LIE of a species mixture of the low evenness communities was positively correlated with LIE of the monoculture consisting of the species with the highest initial abundance in the species mixture, while LC of a species mixture of the low evenness communities was negatively correlated with it. Conclusions: Functional diversity and functional dominance play a crucial role in light complementary use of plant communities, and their effects on light complementarity are mediated by species evenness. Thus, interactions of functional traits and evenness may greatly affect ecosystem functioning.
A re‐evaluation of hemispheric asymmetries in herbivory: a response to Kozlov & Klemola 2017

Kozlov & Klemola (Journal of Ecology, 105, 2017: 000‐000) argued that our conclusion about hemispheric asymmetries in herbivory is not supported after the replacement of data points extracted from Moles & Westoby (Oikos, 90, 2000: 517–524.). To re‐evaluate the asymmetries in herbivory, we analysed the revised dataset according to Kozlov & Klemola's (2017) suggestion, as well as the dataset used in Kozlov et al. (Global Ecology and Biogeography, 24, 2015: 1126–1135.). All the analyses showed that herbivory decreased with latitude only in the Northern hemisphere, but in the Southern hemisphere, herbivory showed no relation to latitude. Model selection showed that in both datasets, hemisphere is a key determinant of herbivory, with Southern hemisphere having higher levels of herbivory than the Northern hemisphere. Synthesis. Based on currently available data collected from publications, we found evidence for hemispheric asymmetries in herbivory. This conclusion is unlikely to change even when the controversial data points are replaced.
The Human Impact

Earth in Human Hands: Shaping Our Planet's Future . By David Grinspoon. 2016. Grand Central Publishing. (ISBN 9781455589128). 522 pages. Hardcover. $28.00. Dr. Grinspoon's massive review of Earth's past, present, and future begins with a nod to the Anthropocene and the idea that humans, with regard to the state of the planet, are “at the controls, but we're not in control” (p. ix). Influenced by a host of planetary scientists like his “uncle” Carl Sagan, the author approaches the state of the earth in a truly evolutionary way. Grinspoon provides the reader with a detailed review of the natural history of our planet and other similar planets. He emphasizes that our understanding of how our planet has been shaped will give us the knowledge needed to better control the planet that humanity has impacted so significantly. His Darwinian approach to planetary change, coupled with his excellent writing style, make this massive text an enjoyable read. With eight …
Genetic Variability and Divergence Studies for Yield Component Traits in Grain Amaranth (Amaranthus spp.)

Grain amaranth is fast growing, dicotyledonous, belonging to genus Amaranthus and family Amaranthaceae. Grain amaranth is a nutritionally potential photo-synthetically efficient C4 plant which is highly adaptable to various climatic conditions. In addition, these crops are well adapted to harsh environmental conditions and are therefore suitable for cultivation on marginal soils. The amaranth grain is one of the valuable foods as it has high protein content and well balanced amino acid profile (Gamel, et al., 2004). Chemical composition and nutritional value of grain amaranth (Dodok et al., 1994) confirms its high potential for use as human and animal nutrition as well as medicine (Teutenico and Knorr, 1985). With the increasing need of exploring alternate sources of food, it is necessary to accelerate and expand the production of amaranthus.
Isolation and Characterization of Microsatellite Markers for Stenotaphrum Trin. Using 454 Sequencing Technology

St. augustinegrass ( Stenotaphrum sp.) is a warm-season perennial turfgrass that grows widely in tropical regions around the world. St. augustinegrass is valued for both its turf performance and high levels of resistance to biotic and abiotic stresses. The current study was aimed at developing nuclear microsatellite markers for st. augustinegrass. Pyrosequenc- ing of an enriched microsatellite library on the Roche FLX platform using a 454 Titanium kit produced 57,306 sequence reads; 2614 of which contained short tandem repeats. One hundred primer pairs were tested with 18 accessions from the U.S. Department of Agriculture National Plant Germplasm System st. augustinegrass collection grown in Grifﬁn, GA. This collection contains both Stenotaphrum dimidiatum and Stenotaphrum secundatum accessions. Among revealed 100 primer pairs, 33 were polymorphic. A total of 175 alleles were ampliﬁed. The number of observed alleles per primer pair ranged from two to 10, with an averageof5.3. Shannon’s information index and Nei’s genetic diversity values were 0.4403 and 0.2873, respectively. This set of microsatellite markers is useful for assessment of genetic diversity and construction of molecular genetic linkage maps in st. augustinegrass. St. augustinegrass
Genetic Variation and Differentiation in Wild and Selected Manila Clam Inferred from Microsatellite Loci

ABSTRACT Manila clam is widely distributed and cultured along the coasts of China. To assess genetic variation in selected strains cultured in China, four selected strains or populations, zebra (Z), white (W), orange (O), and white zebra (WZ), along with one wild population from Lvshun were analyzed with 10 microsatellite loci. The observed heterozygosity ranged from 0.335–0.538 across populations. The highest expected heterozygosity value was detected in the Z strain (0.716), whereas the lowest value was found in the WZ strain (0.578). FST revealed significant differentiation between all pairs of populations. The differentiation between the W strain and the O strain is the lowest (FST = 0.086). whereas the differentiation between Z and WZ strains was the highest (FST = 0.337). There was no significant reduction in heterozygosity in all four selected strains; however, the number of alleles per locus was considerably lower in the selected strains than in the wild population. These results provide valuable genetic information for the preservation, management, and further selective breeding of the Manila clam.
Effects of Genetic Background on Susceptibility and the Acceleration of Hearing Loss in Mice

Acquired hearing loss, which includes age-related hearing loss and noise-induced hear- ing loss, is a common hearing impairment and shows phenotypic variability. One reason for phenotypic variability is influence of genetic background. The modifiers underlying genetic background are modulated and advance the hearing phenotypes through gene-gene interactions with other etiological genetic factors. Moreover, the modifiers play a role in the susceptibility of environmental hearing risk factors, namely, the strength and weakness of environmental susceptibility often modulate and advance hearing phenotypes via gene-environment interactions. The complicated gene-gene and gene-environment interactions make genetic analysis of acquired hearing loss difficult. In par - ticular, the effects of environmental factors cannot be completely excluded or controlled. Although genome-wide approaches to identify genetic modifiers have proven challeng - ing in humans, the responsible genes and mutations are widely unknown. In this chap -ter, we suggest that mouse models are useful for studying genetic background effects for acquired hearing loss. The genetic analysis of mouse models identified the genetic modifiers. We review the genetic research in mouse models for acquired hearing loss to identify and confirm the modifiers by both forward and reverse genetics approaches.
Synaptobrevin-2 C-terminal Flexible Region Regulates the Discharge of Catecholamine through the Fusion Pore

The discharge of neurotransmitters from vesicles is a regulated process. Synaptobrevin-2 a SNARE protein, participates in this process through its interaction with other SNARE and associate proteins. Synaptobrevin-2 transmembrane domain is embedded into the vesicle lipid bilayer except for its last three residues. These residues are hydrophilic and constitute synaptobrevin-2 C-terminal flexible region. This region interacts with the intravesicular lipid bilayer phosphate head groups to initiate the fusion pore formation. Here it is shown that, this region also modulates the intravesicular membrane potential thereby the discharged of catecholamine. Synapotobrevin-2 Y113 residue was mutated to lysine or glutamate. The effects of these mutations on the exocytotic process in chromaffin cells were assessed using capacitance measurements, combined with amperometry and stimulation by flash photolysis of caged Ca2+. Both Y113E and Y113K mutations reduced the amplitudes of vesicle fusions and reduced the rates of release of catecholamine molecules in quanta release events. Further investigation revealed that the proximity of these charged residues near the vesicle lipid bilayer most likely changed the intravesicular potential, thereby slowing the flux of ions through the fusion pore, hence reducing the rate of catecholamine secretion. These results suggest that catecholamine efflux is couple with the intravesicular membrane potential.