Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of microsatellite markers for Dryobalanops aromatica (Dipterocarpaceae), a tropical emergent tree in Southeast Asia

Eight polymorphic microsatellite markers were developed in Dryobalanops aromatica, an emergent tree in tropical rain forests in Southeast Asia, using an enriched library method. For the assessment of microsatellite variation, 36 individuals from a natural population were analysed. The number of alleles per locus ranged from three to 16, with observed heterozygosity of 0.056–0.833 and expected heterozygosity of 0.054–0.882. These microsatellite markers will be useful for studies of population genetics, reproductive ecology and regeneration dynamics of D. aromatica.
Disease protection and growth promotion of potatoes (Solanum tuberosum L.) by Paenibacillus dendritiformis

One of the challenges in developing plant-beneficial bacterial agents for agricultural application is ensuring that an effective selection and screening procedure is in place. The sporadic success of using bacterial agents in the field is usually due to the inability of added bacteria to compete with the local microorganisms. In the present study, the effectiveness of Paenibacillus dendritiformis, a unique pattern-forming, Gram-positive, soil bacterium, to reduce disease indices and increase yield in potato crops was examined. This bacterium was chosen as a potential agent based on genome analysis carried out in previous studies. In vitro laboratory experiments, as well as three greenhouse and one field experiment, were conducted. The results show that, in agreement with the hypothesis, P. dendritiformis significantly reduced the maceration area of tuber slices infected by Pectobacterium carotovorum subsp. carotovorum, significantly reduced disease indices in greenhouse experiments and significantly increased tuber yield of infected plants in the field. This work demonstrates the potential of preliminary screening based on genome analysis to identify effective biocontrol agents.
Frost Rings Formed in 14-m Tall Red Pine

In codominant and suppressed trees in two red pine (Pinus resinosa Ait.) plantations in Simcoe County, Ontario, frost rings had formed at the start of most annual rings in the two internodes below the current leader until the trees were nearly 14-m tall. None occurred in the current shoot growth or below the sixth internode. They seldom formed when the stem radius (inside bark) exceeded 2 cm.
The genus Macbridella with notes on Calostilbe, Herpotrichia, Phaeonectria, and Letendraea

The brown coloration of ascospores is rejected as a generic character in the Hypocreales. The asci of the type species of Macbridella, M. chaetostroma (= Herpotrichia rhodosticta), are bitunicate. Macbridella olivacea (= M. cinnabarina), M. amazonensis, M. sansevierae, and M. striispora have unitunicate asci and are treated as species of Nectria. The asci of the type species of Letendraea, L. eurotioides, are bitunicate. Letendraea eurotioides is lectotypified. Phaeonectria is found to be synonymous with Calostilbe; Calostilbe is regarded as a synonym of Nectria.
A multivariate method for determining optimal subsample size in the analysis of macroinvertebrate samples

The depauperate macroinvertebrate communities of two disturbed urban streams were used to demonstrate a technique for determining optimal subsample size for the multivariate representation of community structure. Although multivariate analyses have commonly been applied to subsampled data, the effect of subsampling on multivariate patterns has not previously been investigated in detail. The minimum requirement for applying the method is eight fully processed community samples distributed across two treatments, with n = 4 (being a representative subset of a larger study to which subsampling will be applied). The data from each sample are subsampled repeatedly with the aid of a simulation program. Variation in community structure between treatments is tested by analysis of similarity for the complete data and for multiple sets of subsampled data. The optimal subsampling strategy is defined as the minimum effort required to achieve a median R-statistic no less than the value derived for the complete data. Subsampling to a fixed proportion is a less efficient strategy than subsampling to a fixed number of individuals. For the urban stream communities, subsampling to 300 individuals was adequate for four out of six comparisons and was adequate for all comparisons when a minimum proportion of 10% was applied. Several non-abundant taxa were found to be important contributors to differences between treatments. Subsamples need to be large enough to adequately estimate the abundance of such taxa. Further investigation is required to assess the relationship between optimal subsample size for multivariate analysis and the shape of cumulative species-abundance curves.
Hatch Timing Variations among Reservoir Gizzard Shad Populations: Implications for Stocked Sander spp. Fingerlings

Abstract Growth and survival of stocked Sander spp. fingerlings can be influenced by timing of stocking in relation to the peak in density of larval gizzard shad Dorosoma cepedianum. However, coordinating stockings to coincide with peaks in gizzard shad density is difficult due to temporal variation in spawn timing among reservoirs. We used weekly estimates of larval gizzard shad density and length distributions to identify dates of peak hatching and peak total density in Ohio reservoirs and to explore the influence of spring water temperature regimes on timing of peak larval density. Gizzard shad density peaked over 21–32 d among reservoirs but generally varied by 12 d or less among years for any given population. Density peaks were driven by hatching, as larvae smaller than 10 mm accounted for a majority of the gizzard shad collected on the peak date. Peaks in gizzard shad density corresponded to water temperatures of 17–22°C and occurred most frequently when water temperatures had been stable or rising.
A weighted—averaging regression and calibration model for inferring total phosphorus concentration from diatoms in British Columbia (Canada) lakes

SUMMARY 1. The relationship between surficial sediment diatom taxa (Bacillariophyceae) and measured limnological variables in forty-six British Columbia lakes was explored using canonical correspondence analysis (CCA). Lake-water total phosphorus concentration (TP), maximum lake depth, conductivity, and calcium concentration each accounted for independent and statistically significant directions of variation in the distribution of diatom taxa. 2. Weighted-averaging (WA) models were developed to infer lake-water TP from the relative abundances of 131 diatom taxa in the surficial sediments of thirty-seven lakes. WA regression and calibration with classical deshrinking provided the best model for TP reconstructions. 3. Our quantitative inference model has two major advantages over existing multiple linear-regression models: (i) inferences are based on the responses of individual taxa to TP, and do not involve grouping the taxa into a small number of ecological categories; and (ii) the model assumes that diatoms respond to TP in a unimodal, rather than a linear, fashion. 4. The WA model can now be used to infer past lake-water TP, within the range 5–28νgr1−1, from diatoms preserved in the sediments of British Columbia lakes. The model can provide quantitative estimates of the onset, rate, and magnitude of lake eutrophication in response to natural processes and human disturbances.
An environmental assessment of an impacted, urbanized watershed: the Mona Lake Watershed, Michigan

The ecological health and integrity of watersheds throughout the world are being threatened by a variety of stressors. Often, restoration practices focus on single problems whereas comprehensive, multidisciplinary approaches are needed to address both the symptoms and underlying causes of impairment. A comprehensive assess- ment of a small, urbanized watershed in west Michigan, USA was conducted to evalu- ate the major stressors in the system. This assessment approach for the Mona Lake wa- tershed included analyses of land use/land cover change, water quality in both the major surface inflows and the receiving water body, and toxic inputs into a major in- flow. Because these issues are common to many watersheds, we developed a concep- tual model that spatially links these stressors and predicted impacts, allowing us to as- sess them in a comprehensive manner. Based on our results, we generated a set of re- commendations targeted for specific source or problem areas. This approach can be applied to other watersheds.
Increment and decay in Norway spruce and Scots pine after artificial logging damage

The effects of depth, size, location, and season of artificial logging damage on increment and decay of Norway spruce (Picea abies (L.) Karst. ) and Scots pine (Pinus sylvestris L.) trees were studied in long-term experiments in central Finland. Damage types applied were root damage, root collar damage, increment borer hole, and stem damage. In root collar and stem damages, two sizes (100 or 400 cm2) and depths (shallow or deep) were applied. Five to 20 years after damaging, the damages did not result in a decrease in radial, height, or volume increment. In Norway spruce, the frequency of decay in the root collar and stem damages was high. From large and deep damages, decay spread faster than from smaller and shallow ones. In Scots pine, a lower proportion of trees were decayed compared with Norway spruce. Increment coring resulted in decay in most of the trees, but the decay spread slowly. The effect of compass direction or the month of damaging was negligible. The most common decay fungus in Norway spruc.
Preferred males acquire mates of higher phenotypic quality

Several field studies have shown that ornamented males of both polygynous and monogamous animals gain an advantage in terms of mate acquisition. Male reproductive success is strongly positively related to the number of mates acquired, but differential quality of female mates may also play an important role. Darwin (The descent of man, and selection in relation to sex (1871)) and Fisher (The genetical theory of natural selection (1958)) suggested that preferred males of monogamous species should experience a reproductive advantage because of differences in female phenotypic quality. Good condition is supposed to allow females to breed early and to grant them high fecundity. Preferred males should acquire early-breeding females in good condition and for that reason have greater reproductive success. Several genetic models confirm the possible significance of this sexual selection mechanism. Alternatively, preferred males may acquire mates that invest more in reproduction because they have acquired males of higher quality. Field data on birds suggest that preferred males do acquire early-breeding mates, but it has never been shown that such mates are of a higher phenotypic quality in terms of condition. Long-tailed males of the monogamous swallow, Hirundo rustica, are preferred by females. In this study, observations using males with naturally varying and experimentally manipulated tails show that females mated to long-tailed males were heavier, bred earlier, produced more offspring per season and were much more likely to survive to the next breeding season that were females mated to short-tailed male swallows. This is the first demonstration that preferred males actually obtain mates of high phenotypic quality. Preferred males had a direct reproductive benefit of mating with long-lived females, because pairs consisting of mate-faithful individuals reproduced earlier and produced more offspring than did pairs without previous common experience.
Defining leaving no one behind: what’s new?

The commitment to leave no one behind is at the heart of the 2030 Agenda and one of its most distinctive features, compared to the Millennium Development Goals (MDGs). While the MDGs made significant progress in reducing overall poverty – defined both in terms of income and more widely in relation to health, education and living standards – often the poorest and most marginalised groups did not benefit at all or enough (Bhatkal, et al., 2015; Ravallion, 2016). The commitment to leave no one behind addresses this issue.
Genetic Diversity in Three Forms of Anabas testudineus Bloch

Summary Karyotype and RAPD analysis were studied in 3 forms of climbing perch, Anabas testudineus viz. wild (native, non-spotted), Thai (introduced from Thailand, spotted) and Thai (a spot-ted-released form from local hatcheries). 2 n =46 chromosomes were found in the spotted-released form. The total length of 2 n chromosome complement was 89.96 μ m with a chromosomal length ranging from 0.92 and 2.96 μ m. The centromeric formula of this spotted-released form was 15m+9sm+22t. This form did not show any CMA-bands. The karyotypic features of this spotted-re-leased form were totally different from those given by previous reports on spotted forms. Four primers, namely OPA-2, OPA-4, OPA-7 and OPA-8, were tested on these 3 forms. The wild form showed unique bands in the OPA-2 (1300, 550, 350 bp) and OPA-7 (280 bp) primers. The spotted and spotted-released form showed different RAPD banding patterns in primers OPA-4, OPA-7 and OPA-8. The wild form was found to be separate from the other 2 forms at 13.5 linkage distance. The 2 Thai forms have 11.0 linkage distances indicating that these 2 forms are not genetically very close. The karyotype and RAPD results indicate that either the Thai spotted-released form is not developed exactly from the same stock as the Thai spotted form or that due to the application of physical stress or chemical treatment this spotted-released form has been modi ﬁ ed.
ULTRACYTOCHEMICAL DEMONSTRATION OF FUNCTIONAL GROUPS IN THE LUMENAL PLASMA MEMBRANE OF RABBIT TRANSITIONAL EPITHELIUM

The ultrathin sectioning, freeze-etching, negative staining, ruthenium red staining, ultracytochemical demonstration of sulfhydryl (SH) groups and performic acid-phosphotungustic acid (PFP) reaction were performed on intact and isolated lumenal plasma membranes of the normal rabbit urinary bladder. The lumenal membrane was characterized by a scalloped configuration with the concave plaque and crest-like interplaque regions. The concave plaque regions showed an asymmetric unit membrane of 12nm in width, having a thicker outer leaflet of 6nm which is composed of periodic dots. The plaque regions consisted of the hexagonal particle array (HPA) in the EF face and the interplaque regions smooth in the freeze-replica images. HPA, 13nm in diameter, was shown to be composed of 12 subparticles of 2.5nm in diameter in the negatively stained isolated membranes. The surface coat, 5-10nm in width, was demonstrated on the lumenal surface by a ruthenium red staining.The PFP reaction revealed the trilaminar structure in the interplaque regions, whereas the density (2nm in width) spanning membrane, resembling a ladder-like structure, was observed in the plaque regions. Hexagonally arranged electron lucent areas were also recognized in tangential sections. The substances stained with the PFP reaction may represent phospholipids and glycolipids in the lumenal plasma membrane. Reaction products for SH groups in the form of particles of 3-9nm in diameter were observed in and around the membrane in both the plaque and the interplaque regions and were often deposited directly on the lumenal membrane. It is suggested that the SH groups demonstrated here are derived from the surface proteins, perhaps enzyme proteins in the lumenal plasma membrane.
Maturity Effects on Colony-Forming Units of Macrophomina phaseolina Infection as Measured using Near-Isogenic Lines of Soybeans

Charcoal rot (Macrophomina phaseolina) causes significant yield losses in soybean [Glycine max (L.) Merr. ]. The actual effect of maturity on disease severity can be confounded by genotypic background. We evaluated disease severity using two sets of near-isogenic lines (NIL) differing in maturity genes. Field experiments were established on two soil types (sandy loam and clay) and evaluated over two years (2008 and 2009). Disease severity, expressed as colony-forming units (CFU), was evaluated for each line at physiological maturity. Within a year, similar levels of disease severity were observed on both soil types. Regression analysis indicated no significant (P < 0.05) relationship between maturity and CFU for either set of NIL on either soil type in either year. Adding selected environmental variables (rainfall, temperature, etc.) to the equation allowed the detection of a significant relationship in only one environment (P = 0.0306, F = 6.00). Results demonstrated little evidence of a relationship between maturity and disease severity.
Endotherm Energetics: from a Scalable Individual-based Model to Ecological Applications

We outline a computer model of heat and mass transfer through flesh, fat and porous fur for endotherms of any dimensions. We then validate it with a series of laboratory studies. Finally, we explore applications of the model to Bergmann's rule, predicting the mouse-to-elephant curve, climate-disease-toxicant interactions, animal 'design' via genetic engineering and energetic constraints on community structure. As a first test of the model we present calculations and metabolic chamber measurements for mammals ranging in size from mice to Holstein calves. We then compare simultaneous measurements on deer mice, Peromyscus maniculatus, of oxygen consumption, doubly labelled water turnover and food consumption with calculations of metabolic rate using body temperature radio-telemetry as input to the endotherm model. The endotherm model derived in the Appendix requires data on allometry (body dimensions, surface area), fur properties, core temperature, air and radiant temperatures and wind speed. The model is useful for calculating energetic expenditure in different microclimates without the need for extensive physiological measurements in the laboratory. Model predictions of metabolic rate at 12-degrees-C and at 22-degrees-C were well correlated with each of the three empirical estimates. The model shows that the posture an animal assumes can influence measurements of metabolic rate. Model calculations of metabolic rate using postures ranging from a curled-up ball-like geometry to a sprawled-out, cylinder or ellipsoid geometry bracket all three sets of simultaneous empirical data taken on the same animals. Applications of the model show that it can be applied in a wide variety of circumstances to gain insight into physiological and ecological problems.
A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae)

A new picoplanktonic alga, Ostreococcus tauri Courties et Chretiennot-Dinet, gen. et sp. nov. (Chlorophyta, Prasinophyceae) is described from the Thau Lagoon on the Mediterranean coast, France. Alm.
Olive cake dietary supplementation in rabbit: immune and oxidative status

Abstract The aim of the present study was to study the effect of three different types of dehydrated olive cakes on immunitary and oxidative status of growing rabbits. One hundred and sixty New Zealand White weaned rabbits, 30 day old, were divided into four homogeneous groups. To experimental groups was administered a similar diet integrated with 5% of three types of olive cake (A, B, C) obtained from local olive oil mills. The olive cakes A and C were both of high quality (C better than A), while the by-product B had the lowest level of total polyphenols, o-diphenols and oleic acid and the highest peroxide number. The aspecific immunitary and oxidative status was improved in animals fed olive cakes richer in antioxidant components.
Genome-wide identification of R genes and exploitation of candidate RGA markers in rice

By scanning the whole genomic sequence of japonica rice using 45 known plant disease resistance (R) genes, we identified 2119 resistance gene homologs or analogs (RGAs) and verified that RGAs are not randomly distributed but tend to cluster in the rice genome. The RGAs were classified into 21 families according to their functional domain based on Hidden Markov model (HMM). By comparing the RGAs of japonica rice with the whole genomic sequence of indica rice, we found 702 RGAs allelic between the two subspecies and revealed that 671 (95.6%) of them have length difference (InDels) in their genomic sequences (including coding and non-coding regions) between the two subspecies, suggesting that RGAs are highly polymorphic between the two subspecies in rice. We also exploited 402 PCR-based and co-dominant candidate RGA markers by designing primer pairs on the regions flanking the InDels and validating them via e-PCR. The length differences of the candidate RGA markers between the two subspecies are from 1 to 742 bp, with an average of 10.26 bp. All related information of the RGAs is available from our web site (http://ibi.zju.edu.cn/RGAs/index.html).
In vitro assessment of fungicidal activity of Ageratum conyzoides and Cybopogon flexuosus weed extracts against some phytopathogenic fungi associated with fruit rot of water melon (Citrullus lunatus (Thunb.))

The ethanolic extracts of Cybopogon flexuosus and Ageratum conyzoides were tested at concentrations of 20, 40, 60, 80, 100 and 120 mg/ml for their in vitro fungicidal activities against five phytopathogenic fungi isolated from diseased watermelon fruits. The pathogens were Fusarium verticillioides, Aspergillus flavus, Botryodiplodia theobromae, Curvularia lunata and Alternaria cucumeria – Amans as confirmed by pathogenicity tests. All isolated pathogenic fungi were significantly (p ≥ 0.05) highly pathogenic with the exception of A. cucumeria which had the least significant (p ≥ 0.05) pathogenicity. The inhibitory effects of the extracts increased significantly (p ≥ 0.05) with increase in concentrations. Some of the concentrations reduced the mycelial growth of the pathogens to a significant (p ≥ 0.05) level. Very strong fungicidal activity was produced by extracts of A. conyzoides at 100 mg/ml against all the fungi. The inhibitory effects of C. flexuosus extracts at 20, 40 and 60 mg/ml were greater than those of C. flexuosus on A. flavus, F. verticillioides and A. cucumeria. The results of the investigation indicated that plant extracts possess antifungal activity that can be exploited as an ideal treatment for future plant disease management in the control of rot of water melon.
Analysis and Improvement of Seed Storage Proteins

イネ，コムギ，トウモロコシなどのイネ科種子には10－12％，ダイズなどマメ科種子には20－40％のタンパク質が含まれるが，その多くを貯蔵タンパク質と呼ばれるタンパク質が占めている（Shewryら 2002）．種子貯蔵タンパク質とは，登熟期の種子に組織特異的・時期特異的に大量に蓄積し，種子が発芽する際に必要な栄養素を貯蔵するタンパク質のことである（井出・藤原 2009）．食料における穀物への依存度が高い発展途上国の人々にとって，種子貯蔵タンパク質は特に貴重なタンパク源であることから，その栄養性の改善は重要な課題である．また一部の種子貯蔵タンパク質は，優れた食品加工特性や生理機能性を有することから，それらを原材料として作られる食品の嗜好性や健康維持増進性が先進国において注目されている．一方，その遺伝子発現の特異性ゆえに，遺伝子発現調節機構（Furtadoら 2008）やタンパク質・mRNAの細胞内輸送・集積機構（Fujiら 2007，Wang ら 2008）に関する研究材料，あるいは医薬品等の有用組換えタンパク質を生産するための基盤（Takaiwaら 2007）としても研究が進められている．本稿では，このように穀物種子の品質に大きく影響を及ぼす貯蔵タンパク質に関して，著者がこれまで取り組んできたイネ種子の主要な貯蔵タンパク質であるグルテリンを例に，タンパク質の基礎的な分析方法について解説するとともに，タンパク質組成の変動をもたらす植物栄養生理に関する最近の知見を紹介する．