Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of 101 novel SSR markers and construction of an SSR-based genetic linkage map in cucumber (Cucumis sativus L.)

Cucumber (Cucumis sativus L.) is an important vegetable crop grown worldwide, but the number of available and mapped simple-sequence repeat (SSR) markers is insufficient for construction of an SSR-based genetic linkage map. To improve this situation, we developed SSR markers from SSR-enriched genomic libraries for C. sativus. We sequenced 2304 clones, and obtained 101 primer pairs which showed clear amplification and polymorphism among genotypes in either C. sativus or Cucumis melo (melon). In C. sativus, all were amplified and 91 were polymorphic among the three genotypes that we analyzed. In C. melo, 41 were polymorphic among the three genotypes that we analyzed, but 32 were not amplified. In addition to the SSRs developed in this study, we used SSRs and sequence-characterized amplified regions (SCARs) reported previously in cucumber and melon to construct the first SSR-based linkage map of cucumber. The map now comprises 120 SSRs and 6 SCARs. It contains 22 markers from previous cucumber maps and 8 linkage groups, and spans a distance of 625.7 cM. The present map is the most comprehensive one in terms of the number of SSR markers and will therefore be highly useful in future cucumber genetic studies.
Coaggregation between Prevotella nigrescens and Prevotella intermedia with Actinomyces naeslundii strains

Using a visual coaggregation assay, 43% (6 of 14) of Prevotella nigrescens and 50% (4 of 8) of Prevotella intermedia strains coaggregated with Actinomyces naeslundii strains which represented the six Actinomyces coaggregation groups (A to F). For both species, coaggregation occurred most frequently with A. naeslundii strains from coaggregation groups C, D and E. No coaggregation was observed with Actinomyces israelii, Actinomyces odontolyticus or six oral Streptococcus species. Coaggregation was not inhibited by lactose, saliva or serum. Pretreatment of Prevotella strains with heat, SDS and proteinase K abolished coaggregation when the treated cells were added to untreated Actinomyces strains. The same pretreatment of the Actinomyces strains had no effect on their ability to coaggregate with untreated Prevotella strains. Pretreatment of all coaggregating P. nigrescens strains with trypsin abolished coaggregation, whereas the coaggregation ability of the P. intermedia and Actinomyces strains was resistant to trypsin pretreatment. Pretreatment of the strains of both Prevotella species and the Actinomyces with periodate abolished coaggregation in all cases. These results suggest that the Prevotella strains each possess a protein coaggregation adhesin, which for the P. intermedia strains is resistant to trypsin, that interacts with a non-protein receptor on the A. naeslundii strains.
The effect of external nutrient resources on the population dynamics of zooxanthellae in a reef coral

Experiments were done to determine if ammonium, phosphate and feeding on Artemia nauplii affected the population density of symbiotic algae (zooxanthellae) in the Red Sea coral Stylophora pistillata. Corals were incubated for 14 days under natural sunlight at reduced intensity in running seawater aquaria. The seawater was continuously spiked to give final concentrations of either 20 μM ammonium or 2 μM phosphate, or both. A second set of similarly treated corals was also fed Artemia nauplii daily. Population density of zooxanthellae in corals spiked with ammonium, or ammonium plus phosphate, approximately doubled, and the ratio of zooxanthellae carbon: nitrogen decreased. Phosphate supplementation alone had no effect. The increase in zooxanthellae numbers was linearly proportional to the increase in protein in zooxanthellae, suggesting that availability of inorganic nitrogen leads to increased protein synthesis in zooxanthellae. Feeding on Artemia alone or together with phosphate had no effect on the population density of zooxanthellae. Feeding on Artemia and ammonium produced a small increase in population density but it was not statistically significant. The small effect could be due to insufficient influx of ammonium in fed animals, or growth of both animal and algae resulting in little or no net change in the population density of zooxanthellae. The results are consistent with the hypothesis that the growth of zooxanthellae in S. pistillata from the Red Sea is nitrogen limited.
Check-list of the Skippers and Butterflies of Maryland

Although numerous papers have been published on skippers and butterflies of Maryland during the last 100 years, a statewide list has never appeared as was mentioned by Field et al. (34). Clark (13) published a list which covered the District of Columbia and nearby Maryland and Virginia. Thus, this detailed manual served well as a guide for those studying Maryland Rhopalocera, especially those species occurring in the central part of the state. Members of the Natural History Society of Maryland and the Maryland Academy of Sciences published many articles between 1926 and 1939. More recently R. S. Simmons, W. A. Anderson and others published many records. This author has made a life-time study of Maryland Rhopalocera and presents here a check-list to establish a base-line for future studies. The physiographic zones of Maryland have been discussed by Vokes (91). The biotic areas were given by Stewart and Robbins (89) and Paradiso (74). More recently the vegetative zones were discussed by Brown and Brown (8). For the purposes of this paper the biotic areas of Stewart and Robbins are followed except for the elimination of the Upper Chesapeake section. The Western
Isolation and characterization of six polymorphic microsatellite loci for the Malagasy spider tortoise, Pyxis arachnoides and cross-amplification in Pyxis planicauda

Pyxis arachnoides is a Critically Endangered Malagasy tortoise for which little data about its natural history and genetic variation are available. This lack of knowledge complicates undertaking conservation measures considering Pyxis genetic diversity. Here, we describe six new microsatellites for Pyxis arachnoides from wild specimens and several localities, and the cross amplification of two Astrochelys radiata microsatellites. Of these microsatellites, two are monomorphic among the three distinct subspecies and a closely related species, while the remaining six are polymorphic. Microsatellite data are needed for this species to study the inter- and intra-subspecies genetic diversity, especially for the highly endangered subspecies P. a. brygooi, which currently occurs only in remote localities. The availability of polymorphic microsatellites will allow identifying the population of origin of individuals and will aid in justifying their management as separate evolutionary lineages for conservation purposes. The rationale is to preserve both evolutionary processes and adaptive potential.
The Morphology of Maxillary Sinus in Modern Japanese with the Use of CT Image

本研究は頭蓋のX線CT（Computed Tomography）画像から上顎洞の形態やサイズを計測し，分析を行なったものである。 近代日本人女性乾燥頭蓋42体84側（平均年齢38. 9歳）を資料として，CT装置による撮影を行ない，得られた画像から画像解析ソフトによる上顎洞の前後径，高径，幅径，体積の計測を行ない，本研究と同様の機器・手法で行われた同時代の日本人男性乾燥頭蓋に関する計測結果（野木・金澤，2001; 野木，2002）との比較を行なったところ，前後径，高径，体積の各項目において，男性の上顎洞よりも女性の上顎洞のほうがサイズは小さかった。 主成分分析を行ったところ，上顎洞の大きさの変異は第1主成分のサイズファクターで説明されることがわかった。 頭蓋の直接計測値との相関については，体積が顔長，頭蓋最大幅，上顔高との正の有意な相関があり，前後径と頭蓋最大長，高径と顔長に有意の相関がみられた。 上顎洞底部の形態を大きく3つのタイプ，「ラウンド型」「フラット型」「イレギュラー型」に分類したところ，ラウンド型は他のタイプと比較して全体の体積が小さく，イレギュラー型は大きかった。 年齢や歯の残存状態と上顎洞のサイズとの関係をみていくと，20歳代，完全歯列の上顎洞はサイズが最大で，50歳以上，無歯顎へと移行していくにしたがってサイズは減少していった。
Antimicrobial Activity of Tetradenia riparia (Hochst.) Lamiaceae, a Medicinal Plant from Tanzania

Aims: To evaluate the antibacterial activity of Tetradenia ripariacrude extracts against Escherichia coli,Staphylococcus aureusand Enterococcuss faecalis.The phytochemicals that are responsible for the bioactivity were also screened. Study Design:In vitroassay of antibacterial properties. Place and Duration of Study:Samples were collected from Njari village at Uru North in Moshi district located in north eastern Tanzania. Extraction and phytochemical analyses
Infection, recovery from infection and resistance of apricot trees to Verticillium albo-atrum

Summary In infection studies of apricot with the microsclerotial form of Verticillium albo-atrum R. & B. , otherwise described as V. dahliae Kleb. , more apricot plants became infected and disease symptoms became more pronounced as concentration of inoculum increased. V. albo-atrum does not persist indefinitely in an infected tree but some factor causes the fungus to become ‘inactivated’, in which condition V. albo-atrum cannot be isolated from tissues previously known to have been infected. However, it is not known for certain whether inactivated fungus is dormant or dead. One selection ‘Zailisky Altai’, obtained from a wild population of Prunus armeniaca, was resistant to V. albo-atrum and is of potential value as a root-stock in soil infected with this fungus.
Seasonal and individual variation in selection by feral cats for areas with widespread primary prey and localised alternative prey

Abstract Context. Seasonal and individual variation in predator selection for primary and alternative prey can affect predator–prey dynamics, which can further influence invasive-predator impacts on rare prey. Aims. We evaluated individual and seasonal variation in resource selection by feral cats (Felis silvestris catus) for areas with European rabbits (Oryctolagus cuniculus) around a breeding colony of endangered black-fronted terns (Chlidonias albostriatus) in the Upper Ohau River, within the Mackenzie Basin of New Zealand. Methods. Within a feral cat population subject to localised control (within a 1-km area surrounding the tern colony), we mapped the movements of 17 individuals using GPS collars, and evaluated individual and seasonal variation in third-order resource selection (i.e. within home ranges) by using resource-selection functions with mixed effects. The year was divided into breeding and non-breeding seasons for terns. Key results. Three of the eight feral cats monitored during the breeding season used the colony in proportion to availability and one selected it. These four individuals therefore pose a threat to the tern colony despite ongoing predator control. Selection by feral cats for areas with high relative rabbit abundance was not ubiquitous year-round, despite previous research showing that rabbits are their primary prey in the Mackenzie Basin. Conclusions. Results suggest that rabbit control around the colony should reduce use by feral cats that select areas with high relative rabbit abundance (less than half the individuals monitored), but is unlikely to alleviate the impacts of those that select areas with low relative rabbit abundance. Hence, predator control is also required to target these individuals. Results thus support the current coupled-control of feral cats and rabbits within a 1-km buffer surrounding the tern colony. Future research should determine what scale of coupled-control yields the greatest benefits to localised prey, such as the tern colony, and whether rabbits aid hyperpredation of terns by feral cats via landscape supplementation. Implications. The present study has highlighted the importance of considering seasonal and individual effects in resource selection by predators, and the role of primary prey, when designing management programs to protect rare prey.
Vegetation recovery following pollution control at Trail, British Columbia. --

Sulphur dioxide emissions from the heavy metal smelter at Trail, British Columbia, reached a peak in the late 1920's. By this date serious destruction of the natural vegetation had occurred. The recommendations of a tribunal set up to investigate the problem of air pollution were implemented in 1941. Hence air qualities suitable for the reestablishment of the vegetation have prevailed for some 30 years. Apart from a decrease in precipitation as one moves south through the study area, environmental conditions appear to be of minor importance in controlling recovery patterns with regrowth being limited principally by a shortage of viable propagules. The degree of destruction of the former vegetation cover is considered to be the major factor underlying the patterns of vegetation recovery. Much of the birch and aspen cover appears to have developed initially from remnant rootstocks, with coniferous regrowth restricted to areas where seed is available from mature trees which survived the fumigations.
Morphology of Lungs of the Porcupine (Hystrix cristata)

Abstract Ozdemir, D. , Ozudogru, Z. , Yilmaz, S. , Atalar, O. , Karan, M. and Dinc, G. 2006. Morphology of lungs of the porcupine (Hystrix cristata). J. Appl. Anim. Res., 29: 157–159. This study was carried out to investigate the structure of lungs of the porcupines. It was found that pulmo dexter and sinister consisted of five and three lobes, respectively and lobus caudalis was the largest part of both the pulmones. The upper air-conducting airways of the lung were lined by an epithelium characterized by ciliated cells among which were dispersed goblet cells. The alveolar surface was lined by squamous type I pneumocytes and cuboidal type II granular pneumocytes.
The Use of Allelopathic Legume Cover and Mulch Species for Weed Control in Cropping Systems

Traditional weed control practices in Mexico use legumes as cover crops or manures. Legumes used in these practices play a dual role in agroecosystems by protecting the soil from erosion and by enriching it with organic matter and N through Rhizobium symbiosis. Farmers in the tropical regions of Mexico use Mucuna spp. , Canavalia spp. and other legumes to control weeds in their fields. We conducted in vitro bioassays and greenhouse experiments to evaluate the toxic effect of four legumes velvetbean [Mucuna deeringiana (Bort) Merr. ], jackbean [Canavalia ensiformis (L.) DC. ], jumbiebean [Leucaena leucocephala (Lam.) de Wit], and wild tamarind [Lysiloma latisiliquum (L.) Benth. ] on weed growth, and on the survival of insects and nematodes. The aqueous leachates (1%) of the four legumes were tested on three test plants by seed germination and radicle growth bioassays in petri dishes. The aqueous leachates of all four legumes exhibited strong phytotoxic effect on the radicle growth of the test plants. The effects of velvetbean and jackbean leachates were also evaluated on the survival of phytopathogenic nematodes. Both leachates had nematotoxic effects. Greenhouse experiments were conducted to evaluate the effect of the four legumes dried leaves incorporated as mulches to potting soil, on the number and biomass of weeds, and on the biomass of tomato (Lycopersicon esculentum L.) plants. The decomposition of velvetbean and jackbean leaves in potting soil significantly reduced (>50%) the development of phytopathogenic nematodes in the roots of tomato. A 5-yr field experiment conducted at the University of Yucatan (UADY) evaluated the effect of velvetbean and jackbean used as living cover crops, and jumbiebean and wild tamarind used as dead mulches incorporated on soil surface, on weed growth, and corn (Zea mays L.) yield. The experimental field was treated with the traditional slash and burn system in February 1994. In July 1994 the experiment was performed using the local agricultural practices in a complete randomized block design with three repetitions. The treatments were: corn+velvetbean, corn+jackbean, corn+jumbiebean, corn+wild tamarind, corn+Paraquat (1,1'-dimethyl-4,4'-bipyridinium ion) herbicide, corn weeded by hand, and plots without corn weeded by hand. The number, biomass, diversity, and relative importance of weeds, as well as corn yield, were evaluated. In addition, taxonomic composition of weeds was determined. All legumes reduced weed growth with velvetbean (as living cover crop) producing the largest weed biomass reduction (68%). These legumes also improved the yield of corn during the first 2 yr of the experiment. For better management of natural resources, the use of legumes as biological tools in agriculture to control weeds and improve soil conditions should be encouraged through coordinated efforts between farmers, academic, and governmental institutions.
Uptake of Radionuclides by Some Fungi

Abstract Mycobiota including Alternaria alternata, Fusarium verticillioides and Aspergillus pulvérulents were tested for their ability to uptake radiocobalt (Co-60) and radiocesium (Cs-137) from radionuclide containing medium. A. alternata was the most efficient fungal species for uptake of radioisotopes, followed by A. pulverulents, whereas F. verticilliodies came in the last rank. The conditions of radioisotope uptake were optimized such as the form of the fungal organism either spores or mycelium, inoculum age and pH of growing medium. Furthermore the total pigments of the tested fungi were extracted and tested for their ability to bind with radioisotope, where melanin of A. alternata produced about 60% for radioisotope uptake out of total added radioisotope radioactivity. Moreover, transmission electron microscopic examination of radioisotope exposed spores showed high precipitation of melanin granules in the spore wall and within the cell as comparing to untreated spores.
Original article Prevalence and characterisation of Bacillus cereus in vacuum packed potato puree

Summary Refrigerated processed foods of extended durability (REPFED) potato puree was analysed for Bacillus cereus contamination along the production line and during the product shelf-life. Isolated B. cereus strains were tested for their psychrotrophic character and the ability to produce enterotoxins. Bacillus cereus contamination during four subsequent productions was in the range of 2.3–4.0 log cfu g )1 . Productions five and six were significantly less contaminated with B. cereus (£1 log cfu g )1 ). All B. cereus isolates from the first four productions were able to grow at 7 � and 10 � C, whereas the majority of the isolates from productions five and six did not. No B. cereus isolates grew at 4 � C. randomly amplified polymorphic DNA (RAPD) fingerprinting showed that the most of B. cereus contamination originated from one source. In total, 30.4% of isolates expressed enterotoxic character. The present study points out the necessity to prevent an ‘in house’ colonisation and contamination during food processing in order to accomplish the safety of REPFED throughout the shelf-life. It also indicates the most critical steps in the production line of ready-toeat potato puree and impact of failures regarding the food safety. The data provided can be used for risk assessment studies regarding B. cereus in REPFED.
Itaconic acid production by Aspergillus terreus on raw starchy materials

Starchy materials such as corn starch, soft wheat flour, potato flour, cassava flour, sorghum starch, sweet potato and industrial potato flours, either acid or enzymatically hydrolysed, were used as substrates for itaconic acid production by Aspergillus terreus NRRL 1960. Both production and yield were highest on corn starch (18·4 g l−1 and 34·0%, respectively). The degree of hydrolysis had a great influence on acid production which was highest when corn starch was saccharified at 85 DE (dextrose equivalent). In a 3 litre benchtop fermenter, itaconic acid production and productivity were 19·8 g l−1 and 0·13 g l−1 h−1, respectively.
Acute effects of low-dose cypermethrin on male rat cells

Effects of synthetic pyrethroid insecticide α-cypermethrin were investigated following intradermal dose (5–50 mM) of cypermethrin to male albino Wistar rats. Glucose, protein, cholesterol, triglycerides, urea, uric acid, creatinine, hemoglobin, blood RBC, and WBC content were determined 6 h after pesticide administration. Biochemical parameters and blood cell count changed significantly in treated rats at all doses. Low-dose cypermethrin affected early biochemical changes in rats.
Gut Adaptation to Healthy Starch Assimilation in Dairy Ruminants: A Lifetime Development

By an evolutionary definition, due to high dependence on natural resources especially on pastures, ruminants have long developed extensive rumen fermentation. This exceptionality enables utilization of resistant plant cell wall fibres using microbial enzymes symbiotically [1,2]. Accordingly, only so much starch could have been supplied to the rumen and post-rumen. Owing to such a limited starch nutrition in nature, ruminants have not required extensive amylolytic capacity particularly post-ruminally [3]. However, due to modernization of the dairy industry especially over the last few decades, nutritional and health demands for effective starch fermentation in rumen and capacious starch assimilation and glucose absorption in small intestine have increased. Collecting all of these optimums together has, thus, become a serious challenge on-farm [3,4]. Consequently, unhealthy and inefficient rumen fermentation, ineffective post-rumen starch assimilation, and metabolic disorders (e.g., subacute rumen acidosis, rumenitis, liver steatosis, laminitis, and immune malfunction) frequently occur in today’s dairy farming [4,5]. The drama requires feasible and pragmatic actions to overcome the challenges and improve economics and food safety globally [6,7].
Models of Cell Tetrads and Clones in Meristematic Cell Layers

Regular repetitions of new wall orientation with respect to the orientation of older walls were analyzed. Wall patterns in four-cell groups (tetrads) in meristematic cell layers appear to be most suitable for such an analysis. The distribution of the five main tetrad types was studied in epidermal layers of Aponogeton crispus leaves, Selaginella kraussiana rhizophores, Tropaeolum peregrinum leaf primordia, and Angiopteris lygodiifolia shoot apices. Relationships were found between the growth directions of the organs and the lineages giving rise to different tetrad types, which point to mechanisms that regulate cell division orientation, possibly by positioning of microtubule-organizing sites. Our analysis of tetrads and larger cell groups (clones) is based on mathematical formalization in terms of double-wall map OL-systems. We use these systems to express and test biological hypotheses concerning similarities in cell division orientations and their effects on tissue growth. In histological studies, only the most recent division wall orientations have been analyzed until now, and there have been few attempts to identify lineages in cell groups with several wall generations. Even if consecutive division structures can be observed, it has proved to be too difficult to recognize unambiguous organizing principles for them. The recognition of such principles has become manageable since we can now perform iterative computations on cell wall networks.