Miracle-dz/UniFAR-FTUs huggingface dataset:
Farmland carabid beetle communities at multiple levels of spatial scale

Carabid beetle communities were studied at three levels of spatial scale, i.e. within fields (three sets of traps, mean distance 15 m), between fields (five fields within 1 km from each other) and between patches of farmland (four study areas 4-8 km from each other). We compared carabid assemblages sampled on five crop types in each study area, i.e. ley, set-aside, spring cereal, potato, and sugar beet. Because of small sample sizes, only the community composition was studied within fields with a DCA ordination, but the differences were small. Analyses of species richness, activity density, community composition as revealed by DCA ordinations, dominance structure, diversity, and evenness showed that carabid communities varied significantly among patches of farmland but not between fields with different crops within the patches. Only the communities of potato fields were found to resemble each other. Only five carabid beetle species showed a preference for crops, and twelve species favoured some study areas. We conclude that the effect of spatial scale should be emphasised in further studies as it seems that carabid beetles may be very localised even in agricultural habitats.
Identification of B-cell Epitope Regions in Cell Surface Proteins of Streptococcus pneumoniae Serotype 19F Using Bioinformatic Tools

Pneumococcal conjugate vaccines (PCVs) were developed through chemical coupling of polysaccharide capsules of pneumococci to immunogenic carrier proteins and World Health Organization recommends inclusion of these vaccines in national immunization programs for children. However, the PCVs implementation in developing countries is prevented by the high vaccine manufacturing costs. This issue can be resolved by construction of protein based vaccines against pneumococci. We already identified three pneumococcal surface proteins including autolysin, zinc binding lipoprotein (ZBL), and plasmid stabilization protein (PSP) as appropriate protein candidates for eliciting protection against S. pneumoniae serotype 19F. The protein protective antigenicity and the absence of autoimmunity induction were used as selection criteria. However, regarding the necessity of the antibody response for protection against pneumococci, analysis of protective B-cell epitopes of these proteins is required to elucidate their usefulness in new vaccine formulations. In the present study, therefore, we aim to identify protective B-cell epitope regions of these proteins via widely used bioinformatic tools. Both of the Bepipred and BCPreds programs were used for identification of linear B-cell epitopes. The conformational B-cell epitopes were predicted using the CBTope program. The immunoprotective abilities of epitopes were evaluated using VaxiJen. We determined the linear B-cell epitope regions, which were predicted by both Bepipred and BCPreds and have common amino acids with conformational B-cell epitopes. Our results showed that all of the three studied proteins included such protective overlapped linear B-cell epitope regions. However, a truncated form of PSP had the greatest number of the protective overlapped B-cell epitope regions. Moreover, the most probable protective epitope region resides in this protein and this epitope region is completely conserved in PSPs of serotype 19F pneumococcal strains. Therefore, the truncated PSP was an appropriate candidate for development of protein based vaccines against S. pneumoniae serotype 19F.
Feed intake and efficiency in beef cattle: overview of recent Australian research and challenges for the future

In the last 10 years, there have been 3 major research and development projects in Australia on the efficiency of feed utilisation by beef cattle. The primary objective of these projects has been to examine individual animal variation in feed efficiency and its exploitation for genetic improvement in beef cattle. The results of these projects indicate that genetic variation in feed efficiency exists in Australian beef herds, that feed efficiency is moderately heritable and that the potential exists to reduce the cost of beef production through selection for efficient cattle. These results have been further developed for industry application through the generation of BREEDPLAN estimated breeding values for net (or residual) feed intake (a feed efficiency trait) for Angus and Hereford–Polled Hereford breeds. Although economic analyses have indicated substantial benefit from selection for feed efficiency, the high initial cost of identifying animals which are superior for feed efficiency is a barrier to rapid adoption of the technology. Developing cost-effective methods of implementing the feed efficiency technology is thus an on-going research activity. Challenges for the future include: the development and use of more sophisticated statistical analyses procedures (such as random regression) for feed intake and efficiency evaluation; development of accurate methods of assessing individual animal feed intake at pasture; the adoption of a whole-production system approach to feed utilisation; and better integration of the disciplines of genetics and nutrition. The outcomes from research in the efficiency of feed utilisation in beef cattle have wider applications, not only in other livestock species, but also in human energetics, such as the control of obesity.
An empirical assessment of the consistency of taxonomic identifications

Abstract Plankton counting and analysis is essential in ecological study, yet scant literature exists as to the reliability of those counts and the consistency of the experts who make the counts. To assess how variable expert taxonomic identifications are, a set of six archived mesozooplankton samples from a series of Longhurst Hardy Plankton Recorder net hauls were counted by expert zooplankton analysts located at six marine laboratories. Sample identifications were repeated on two separate days with over 700 target specimens counted and identified on each day across the samples. Twenty percent of the analysts returned counts that varied by more than 10%. Thirty-three percent of analysts exhibited low identification consistencies, returning Intraclass Correlation Coefficient scores of less than 0.80. Statistical analyses of these data suggest that over 83% of the observed categorical count variance can be attributed to inconsistencies within analysts. We suggest this is the root cause of variation in expert specimen labelling consistency.
Assessing Effectiveness of a Field-Trip Based Course in Professional Education

Abstract Field trips are important opportunities for students to learn and exercise integrative, interdisciplinary problem-solving skills for real-world situations. This paper examines the extent to which a field trip-based course in natural resource management contributes to the preparation of practitioners to solve complex environmental problems. It describes a field trip-based course at the Yale School of Forestry and Environmental Studies, the individuals involved in the course, and a field trip to the La Amistad Biosphere Reserve, Costa Rica to carry out a rapid assessment of AMISCONDE, an integrated conservation and development project in southern Costa Rica. This paper also evaluates the success of the course in terms of how well it prepares students to deal with real-life natural resource management problems and in terms of the opportunity it provides to students to assess a natural resource management issue. The paper concludes that the course is to a large extent successful in the former and less so in the latter. It recommends the following for the planning and implementation of field trip based courses. During the period prior to the field trip, (1) instructors need to clarify course goals and how students are expected to meet those goals; (2) the majority of class time should be spent discussing the management problem that is the focus of the field trip; (3) instructors and students need to discuss and operationalize the policy sciences framework; and (4) the course should provide sessions on rapid assessment techniques and team building exercises. During the field trip, (1) time spent on the project should be maximized; (2) instructors should ensure that hosts understand that students will want to meet with stakeholders independently; and (3) group meetings among students and instructors should focus more on discussing events of the day instead of individual research projects.
The basis of reproductive seasonally in Mastomys rats (Rodentia: Muridae) in Tanzania

ABSTRACT Reproduction of the African murid genus Mastomys, multimammate rats, is seasonal, starting after the rains and extending well into the dry season. During a two-year study in Tanzania, we tested three hypotheses to investigate the proximal causes of this seasonality. Food availability was no limiting factor since food supply could not induce continuous breeding. Temperature was always high and thus not a restrictive climatic factor. Diet was probably always sufficiently varied and protein-rich to allow reproduction. This contradicts earlier hypotheses that consider Mastomys as an opportunistic breeder in which reproduction is seasonally limited by poor conditions; environmental predictors were believed not to be involved since the animals live in an unpredictably unstable environment. However, although the occurrence of rain may be unpredictable, it is highly predictable that heavy rainfall will be followed by good conditions. Laboratory experiments show that sprouting grass has a stimulatory effect on reproduction, suggesting that breeding is triggered by new vegetation.
Two new species of the genus Sinella Brook, 1882 (Collembola: Entomobryidae) from East China

Two new species, Sinella hexaseta sp. nov. and Sinella pauciseta sp. nov., collected from East China, Anhui and Zhejiang provinces, respectively, were described. Both are easily discriminated from each other and all known Sinella species by their unique dorsocentral chaetotaxic patterns on Abd. IV. In S. pauciseta sp. nov., postlabial setae H1–4 are ciliate, which are smooth in all other known species of the genus.
Spike density, speltoidy, and compactoidy in hexaploid wheat.

F2 progeny from F1 plants monosomic for chromosome IX of Hymar obtained from the cross of chromosome IX deficient Chinese Spring × Hymar, a variety of club wheat, were studied for spike type segregation and chromosomal constitution. Spikes from plants with two members of chromosome IX from Hymar were club, intermediate, or common-type. Spikes from plants monosomic for chromosome IX were likewise club, intermediate, or common type but all had typical speltoid characteristics. When the spike type segregates were combined, there resulted an almost perfect fit to a 1:2:1 ratio of club, intermediate, and common spike type plants, respectively, indicating that chromosome IX was not associated with inheritance of spike type. It is suggested that subcompactoidy and compactoidy resulting from an increase in the dosage of chromosome IX is caused by an increase in the dosage of the gene for square-headedness carried by this chromosome. The shortening of plants having higher dosages of chromosome IX is probably cause.
Water‐soluble arsenic residues from several arsenolipids occurring in the tissues of the starspotted shark Musterus manazo

Alkali-labile and alkali-stable arsenolipid fractions were prepared from 12 tissues of the starspotted shark Musterus manazo and analyzed by high-performance liquid chromatography-inductively coupled mass spectrometry. At least six arsenolipids were found in the shark. Two major alkali-labile arsenolipids (a dimethylated arsenic-containing lipid and an arsenocholine-containing lipid) were shown in ordinary muscle, dark muscle, heart, bone, skin and stomach, whereas a single major arsenolipid, the dimethylated arsenic-containing lipid, was shown in the intestine, liver, kidney, spleen and brain. Besides these lipids, four other minor alkali-labile arsenolipids were present. On the other hand, as for the alkali-stable arsenolipids, a dimethylated arsenic-containing lipid and an arsenocholine-containing lipid were also found in dark muscle, skin, stomach and intestine, whereas only dimethylated arsenic-containing lipid was found in the liver.
Changes in Fumitory Achenes During Low Temperature After-Ripening

Fumitory (Fumaria officinalis L.) achenes were after-ripened in moist sand at 4 C for 0, 15, 30, 45, and 60 days. Embryo size in longitudinal section increased 14 times during after-ripening. The percentage of ether soluble lipids and their fatty acids remained constant during the entire after-ripening period. Soluble carbohydrates were the highest at the 45-day period of after-ripening when embryo growth was rapid. The concentration of 70% ethyl alcohol soluble amino acids increased gradually over the first 45 days of after-ripening and decreased over the last 15 days as embryo growth became more rapid.
Endophytic actinomycetes from Pinus thunbergii and their antifungal activity against Cylindrocladium sp.

The inside of Pinus thunbergii could be a reliable screening source for a useful agent in controlling plant disease. Isolation of endophytic actinomycetes from P. thunbergii and their potential as biocontrol agents against the plant pathogen Cylindrocladium sp. were investigated. Two endophytic actinomycetes, Streptomyces sp. and Microbispora sp. , were isolated from surface-sterilised root tissues of P. thunbergii seedlings. The recovery test of these two endophytic actinomycetes from pine seedling showed that Streptomyces sp. was isolated from only roots, but Microbispora sp. was isolated from both roots and leaves. Thus, Microbispora sp. is able to move to leaves from roots. Moreover, we evaluated the potential of both strains as biocontrol agents against Cylindrocladium sp. Two weeks after inoculation of Cylindrocladium sp. alone, pine seedlings showed a 50% mortality rate. Co-inoculation of Cylindrocladium sp. and Microbispora sp. did not affect seedling mortality rate. However, inoculation with both Cylindrocladium sp. and Streptomyces sp. reduced seedling mortality to 12%. Streptomyces sp. could be a useful agent in controlling pine disease caused by Cylindrocladium sp. Thus, it seems that Streptomyces sp. may induce a local host defence reaction and Microbispora sp. systemically spreads to aerial parts through the transpiration stream.
Influência do gene cnm de Streptococcus mutans na formação de biofilme e na interação do microrganismo às células endoteliais.

Siriani LK. Influence of cnm gene of Streptococcus mutans in biofilm formation and interaction to endothelial cells. [Ph. D. thesis (Microbiology)]. São Paulo: Instituto de Ciências Biomédicas, Universidade de São Paulo; 2012. Streptococcus mutans is considered a primary etiological agent of dental caries and an important etiological agent of infectious endocarditis. It can be classified into four serotypes (c, e, f and k), which serotype c is the most prevalent in the population. S. mutans may also have access to the bloodstream, which they may infect the endothelial cells of the coronary arteries by binding to and subsequently invading them. The recent breakthrough of cnm gene, which encodes a collagen binding protein found in some S. mutans strains, has set off new studies on this species, such as biofilm formation and bacteria-cell interactions. This study aims investigating the role of the cnm gene in the abilities of S. mutans: (1) biofilm formation on collagen-treated surfaces and the expression of biofilm formation key genes spaP and brpA; (2) adhesion (30 min and 2 h), invasion (5 h) and persistence (24 h) in endothelial cells and (3) dentin demineralization. Experiments on collagen-dependent biofilm formation, and adhesion, invasion and persistence in primary Human Coronary Artery Endothelial Cells (HCAEC) were performed using S. mutans strains UA159 (serotype c), B14 (serotype e), OM50E (serotype e), LM7 (serotype e), OMZ175 (serotype f), NCTC 11060 (serotype f) and the clinical isolates of this study 7.1 (serotype c), C2A4 (serotype e) and 61 (serotype k). Mutants cnm were constructed in all strains presenting the gene, except for C2A4. Strains OMZ175 and 61 and their respective mutants were also employed to evaluate both the expression of spaP and brpA genes by PCR Real Time and the dentin demineralization through Optical Coherence Tomography (OCT). One hundred forty four clinical isolates of S. mutans were collected from 47 patients. Of the clinical isolates, 138 out of 144 were identified as serotype c, 1/144 was identified
Factors affecting nest-site selection and nest success of translocated greater sage grouse

Translocations have been used for decades to restore or augment wildlife populations, yet more often than not, little to no data and/or arbitrary means are used for determining translocation success. The objectives of our study were to describe nesting habitat utilised by the greater sage grouse translocated into an extant population and to identify factors related to nest success, thereby demonstrating the adaptability of the birds to their new environment and producing one measure of long-term translocation success. We trapped female grouse individuals during the spring on and near leks of source populations, fitted them with radio-transmitters, and released them in the morning onto an active lek in an extant population in Strawberry Valley, Utah. We monitored translocated females for nesting activity and documented nesting attempts, nest success, clutch size and embryo viability. Data were recorded on habitat variables associated with nest sites and paired-random sites, including factors known to be important for resident females that nested successfully. We used logistic regression and an a priori information-theoretic approach for modelling nest v. paired-random sites and successful v. unsuccessful nest sites. Our analyses suggested that crown area of the nest shrub and percentage grass cover were the two variables that discriminated between nest and paired-random sites. Females that nested successfully selected sites with more total shrub canopy cover, intermediate size-shrub crown area, aspects other than NW and SE, and steeper slopes than for unsuccessful nests. After being translocated from distant sites with differing habitat characteristics, these birds were able to initiate a nest, nest successfully, and select micro-habitat features similar to those selected by resident sage grouse across the species range. Our results demonstrate the adaptability of the translocated female sage grouse individuals and produce one tangible measure of long-term translocation success.
A re-interpretation of the Fabroniaceae, III: Anacamptodon and Fabronidium revisited, Mamillariella, Helicodontiadelphus and Bryobartlettia gen. nov.

Anacamptodon is shown by SEM to have a typically formed diplolepideous exostome.Fabronidium is transferred to the Leskeaceae nearSchwetschkea, with a single species,F. guatemaliensis (C. Müll.) comb. nov.Mamillariella is redescribed and illustrated from authentic material and is placed in the Leskeaceae nearLindbergia. The monotypicHelicodontiadelphus is described and illustrated from the type and only known collection.Helicodontiadelphus australiensis Dix. is synonymized withEriodon cylindritheca (Dix.) Dix. & Sainsb. of the Brachytheciaceae.Bryobartlettia costata gen. et sp. nov. is described from New Zealand and is placed in the Leskeaceae nearIwatsukiella. A summary of the generic changes in the Fabroniaceae is provided in chart form.
Identification of a novel HMW glutenin subunit and comparison of its amino acid sequence with those of homologous subunits

Aegilops tauschii is the donor of the D genome of common wheat (Triticum aestivum). Genetic variation of HMW glutenin subunits encoded by the Glu-1Dtlocus of Ae. tauschii has been found to be higher than that specified by the Glu-1D locus in common wheat. In the present note, we report the identification of a novel HMW glutenin subunit, Dy13t, from Ae. tauschii. The newly identified subunit possessed an electrophoretic mobility that was faster than that of the Dyl2 subunit of common wheat. The complete ORF of encoding the Dy13t subunit contained 624 codons (excluding the stop codons). The amino acid sequence deduced from the Dy13tgene ORF was the shortest among those of the previously reported subunits derived by the D genome. A further comparison of Dy13t amino acid sequence with those of the subunits characterized from the A, B, D, R genomes of Triticeae showed that the smaller size of the Dy13t subunit was associated with a reduction in the size of its repetitive domain.
Two blue tit Parus caeruleus populations from Corsica differ in social dominance

Although the causes and consequences of social dominance have been examined extensively, avian studies have rarely focused on between-population differences in social dominance. On the island of Corsica, two resident blue tit Parus caeruleus populations 25 km apart differ significantly in body size measures, timing and effort of reproduction, and song structure, and some of these population differences have a genetic basis. Because earlier avian studies have shown that social dominance is influenced by body size or mass, we predicted that individuals from these two blue tit populations would also differ in their ability to dominate other individuals. Consistent with this prediction, we found that male blue tits of these two populations differ in social dominance, and that heavier or larger individuals dominate lighter or smaller ones in aviary experiments. We propose that social dominance may serve to maintain phenotypic population differentiation at a micro-geographic scale by acting as a barrier to dispersal.
Physiological change in an insular lizard population confirms the reversed island syndrome

Unpredictable environmental conditions and highly fluctuating population densities are believed to have produced a ‘reversed island syndrome’ (RIS) in an insular population of the Wall lizard on Licosa Islet, Italy. Several of the physiological, behavioural, and life-history changes that constitute the RIS could result from positive selection on increased activity of melanocortins. For example, increased levels of α-melanocyte-stimulating hormone (MSH) should lead to increased investment in reproduction and increased immunocompetence in the island population. We tested the crucial assumption of this idea that plasma levels of α-MSH in Licosa Islet lizards are elevated compared to those of the mainland relatives. We also tested for differences in reproductive effort between populations, by measuring plasma levels of 5-α-dihydrotestosterone in males and clutch mass in females. In addition, we assessed ectoparasite load as an indicator for the lizards’ resistance to environmental stress. In agreement with the RIS, we found that insular lizards exhibit higher α-MSH levels, allocate more energy to reproduction, and have a reduced ectoparasite load compared to the nearest mainland population. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●●, ●●–●●.