Can we model the probability of presence of species without absence data?

In ecological studies, it is useful to estimate the probability that a species occurs at given locations. The probability of presence can be modeled by traditional statistical methods, if both presence and absence data are available. However, the challenge is that most species records contain only presence data, without reliable absence data. Previous presence‐only methods can estimate a relative index of habitat suitability, but cannot estimate the actual probability of presence. In this study, we develop a presence and background learning algorithm (PBL) that is successful in modeling the conditional probability of presence of a simulated species. The model is trained by two completely separate sets: observed presence and background data. Assuming that the probability of presence is one for ‘prototypical presence’ locations where the habitats are maximally suitable for a species, we can estimate a constant that can calibrate the trained model into the actual probability of presence. Experimental results show that the PBL method performs similarly to a presence‐absence method, and significantly better than the widely used maximum entropy method. The new algorithm enables us to model the probability that a species occurs conditional on environmental covariates without absence data. Hence, it has potential to improve modeling of the geographical distributions of species.     

Bunching up the background betters bias in species distribution models

Sets of presence records used to model species’ distributions typically consist of observations collected opportunistically rather than systematically. As a result, sampling probability is geographically uneven, which may confound the model's characterization of the species’ distribution. Modelers frequently address sampling bias by manipulating training data: either subsampling presence data or creating a similar spatial bias in non‐presence background data. We tested a new method, which we call ‘background thickening’, in the latter category. Background thickening entails concentrating background locations around presence locations in proportion to presence location density. We compared background thickening to two established sampling bias correction methods – target group background selection and presence thinning – using simulated data and data from a case study. In the case study, background thickening and presence thinning performed similarly well, both producing better model discrimination than target group background selection, and better model calibration than models without correction. In the simulation, background thickening performed better than presence thinning when the number of simulated presence locations was low, and vice versa. We discuss drawbacks to target group background selection, why background thickening and presence thinning are conservative but robust sampling bias correction methods, and why background thickening is better than presence thinning for small sample sizes. Particularly, background thickening is advantageous for treating sampling bias when data are scarce because it avoids discarding presence records.     

Reduction of trimethylamine N-oxide by Escherichia coli as anaerobic respiration.

E. coli was found to grow anaerobically on lactate in the presence of trimethylamine N-oxide (TMANO), reducing it to trimethylamine. Anaerobic growth on glucose was promoted in the presence of TMANO. When a culture grown in complex medium was transferred to defined medium, growth on glucose and ammonia took place in the presence of TMANO after consumption of complex nutrients introduced with the preculture, in contrast to growth in nitrate respiration. The amounts of ethanol, succinate, and lactate among the fermentation products were decreased and that of acetate was increased in the presence of TMANO. Formate generation was much reduced at pH 7.4, whereas stoichiometric formation of formate was observed in the absence of TMANO. Cells grown anaerobically in the presence of TMANO had a higher activity of amine N-oxide reductase than cells grown under other conditions. The content of cytochrome-558 was elevated in the presence of TMANO during growth in complex medium. Cytochrome c-552 found in cells grown in diluted complex medium or defined medium in the presence of TMANO was oxidized by TMANO in cell extracts. The molar growth yield on glucose was higher in the presence of TMANO than in its absence and lower than that in the presence of nitrate.     

Aminoacyl transfer RNA formation. VII. Lack of correlation between aminoacylation and PPi-ATP exchange catalyzed by isoleucyl-tRNA synthetase of Escherichia coli in the presence of various divalent cations.

Isoleucyl-tRNA formation and isoleucine-dependent PPi-ATP exchange catalyzed by purified isoleucyl-tRNA synthetase [EC 6.1.1.5] of Escherichia coli were studied in the presence of various amounts of either Mg2+, Ca2+, Fe2+, Ni2+, or Cu2+. In the presence of Mg2+, isoleucine-dependent PPi-ATP exchange was observed in parallel with isoleucyl-tRNA formation, while in the presence of Ca2+, isoleucyl-tRNA formation was observed without isoleucine-dependent PPi-ATP exchange. Moreover, isoleucine-dependent PPi-ATP exchange was much more in the presence of Fe2+ than in the presence of Mg2+, while little isoleucyl-tRNA was formed in the presence of Fe2+. In the presence of Ni2+ or Cu2+, neither reaction was observed. These data, indicating that formation of an isoleucyl-AMP-enzyme complex is not a necessary step in isoleucyl-tRNA formation, support the existence of a concerted mechanism of isoleucyl-tRNA formation in E. coli.     

Crystallization of salt-free chymotrypsinogen and chymotrypsin from solution in dilute ethyl alcohol

Chymotrypsinogen and chymotrypsin crystallize readily from dilute solutions of ethyl alcohol in the absence of salts. The crystals formed in the presence of alcohol differ in appearance from those formed in the presence of ammonium sulfate. Chymotrypsinogen yields well formed polyhedrons instead of fine needles usually produced in ammonium sulfate solution. Chymotrypsin yields fine needles in the presence of alcohol and rhombohedrons in the presence of ammonium sulfate. The enzymatic properties of the crystals formed in the presence of alcohol are identical with those of the crystals isolated in the presence of ammonium sulfate.     

Regulation of growth and polyamine biosynthesis of the ciliated protozoan Tetrahymena thermophila. Effects of L-arginine metabolites and polyamines

Growth of Tetrahymena thermophila in a synthetic nutrient medium with or without the essential amino acid L-arginine was studied in the presence or absence of the arginine metabolites L-citrulline and L-ornithine and the polyamines putrescine, spermidine, and spermine. The effects of the growth conditions on the stimulations of the enzymes of the arginine metabolic and polyamine biosynthetic pathway, arginine deiminase (ADI), citrulline hydrolase (CH), ornithine decarboxylase (ODC), and ornithine-oxo-acid aminotransferase were determined. Tetrahymena cells were unable to grow in the absence of L-arginine and the amino-acid utilization was greatly impaired. None of the metabolites or polyamines was able to substitute for arginine. In the presence of arginine, Tetrahymena cultures grew well and citrulline and ornithine did not alter the growth behaviour in any way. In the presence of putrescine, the lag period was decreased from 3 h to 2 h. Spermidine and spermine acted similar to putrescine but less pronounced. The stimulation of the activity of ADI, the key enzyme of arginine degradation, was absolutely dependent upon the presence of arginine in the medium: in the absence of arginine, the low ADI activity which was present in the cells before inoculation was decreased to zero levels within 30 min. In the presence of arginine, the stimulation of ADI was not altered by citrulline and ornithine but putrescine, spermidine, and spermine decreased ADI-stimulation to half of the control values. The stimulation of CH activity in the presence of arginine was not altered by any added metabolite or polyamine. In the media without arginine, stimulation of CH was greatly reduced, in the presence of ornithine more than in its absence, and even more in the presence of putrescine and spermidine. Stimulation of ODC activity in the presence of arginine was not affected by citrulline and ornithine but in the presence of polyamines it was rapidly decreased to unstimulated levels after an initial ca. 10-fold increase. The "hyperstimulation" of ODC in the absence of free arginine was reduced to normal in the presence of citrulline, the stimulation was decreased even below normal levels in the presence of ornithine and polyamines decreased ODC activity to zero levels. O delta T activity was stimulated more in the presence of arginine than in its absence. In both cases the stimulation was enhanced in the presence of polyamines and only in the absence of arginine--by ornithine.(ABSTRACT TRUNCATED AT 400 WORDS)     

Determinants of DNA quadruplex structural type: sequence and potassium binding

There are DNA sequences which adopt the same quadruplex structural type in the presence of sodium as in the presence of sodium and potassium. There are also sequences that appear to have a requirement for the presence of potassium for the adoption of a particular quadruplex structural type. Information about the basis for these potassium effects has been obtained by examining the structures of a set of DNAs with differing numbers of loop residues and different lengths of runs of dG residues in the presence of sodium alone and in the presence of potassium and sodium. On the basis of the results, obtained primarily via solution-state NMR, it appears that very small loops favor parallel stranded quartet structures which do not require the presence of potassium. DNAs with loops of two to four residues and runs of two dG residues can form quadruplex structures of the "edge" or "chair" type in the presence of potassium but not in the presence of sodium alone. When all of the loops contain four residues, a "crossover" or "basket" type structure can be formed in the presence of sodium as well as in the presence of sodium and potassium. Structures with runs of three or four dG residues and with loops from two to four residues can form basket or crossover type structures in the absence of potassium. The presence of a purine in a loop can block both potassium binding and formation of chair type structures. Modeling of the interactions of cations with these quadruplex structures indicates that the potassium ions required for chair type structures interact with a terminal quartet and residues in the adjacent loop.     

Phylogenetic and functional diversity of bacterioplankton during Alexandrium spp. blooms

The phylogenetic and functional diversity of the bacterioplankton assemblage associated with blooms of toxic Alexandrium spp. was studied in three harbours of the NW Mediterranean. Denaturing gradient gel electrophoresis and DNA sequence analysis revealed the presence of a bacterium within the Roseobacter clade related to the presence of Alexandrium cells. Phylogenetic diversity was affected by the presence of Alexandrium spp., geographic situation and seasonality. In contrast, functional diversity, assessed with Biolog plates, was clearly affected by seasonality, but not by the presence of Alexandrium, indicating that the presence of the bacterium associated with the blooms was not enough to modify the metabolic pattern of the bacterioplankton assemblage.     

Evidence of brain-warming in the mobulid rays, Mobula tarapacana and Manta birostris (Chondrichthyes: Elasmobranchii: Batoidea: Myliobatiformes)

The presence of cranial retia mirabilia in rays of the genus Mobula is well established. Although previously regarded as consisting exclusively of arteries, the presence of veins has now been established in gross dissections of the rete in the mobulid, Manta birostris. Histological examination of the retia in Manta birostris and Mobula tarapacana confirms the presence of veins. These findings suggest the presence of a counter-current heat-exchanger that warms the brain.     

Stability differences of muscle F-actin in formamide in the presence of Mg2+ and Ca2+

Muscle G-actin was polymerized by addition of 2 mM Mg²⁺ or 2 mM Ca²⁺. Subsequent addition of formamide reduced the specific viscosity of the polymer solution. However, kinetic analysis of this reduction in the presence or absence of 0.1 M KCl revealed differences between F-actin formed in the presence of Mg²⁺ and F-actin formed in the presence of Ca²⁺. In the presence of Mg²⁺ the viscosity dropped instantaneously, reaching within minutes a steady-state level that was constant for many hours. In contrast, in the presence of Ca²⁺ the high-shear viscosity continued to decrease slowly after an initial drop, and it could take hours until a quasi-equilibrium was obtained. The time was dependent on both formamide and protein concentration. Addition of formamide increased the critical actin concentration in the presence of Ca²⁺, but not in the presence of Mg²⁺. This is taken as evidence that in the presence of Ca²⁺, but not in the presence of Mg²⁺, formamide causes partial depolymerization of F-actin.     

Binding of Chlorpromazine to S-100 Protein

Chlorpromazine (CPZ) induces in S-100 conformational changes resulting in the exposure of titratable SH groups of the protein to the solvent. This effect is even greater in the presence of Mg2+ +/- Ca2+. S-100 possesses binding sites for CPZ. The binding of CPZ to 3 microM S-100 is half-saturated by 0.18 microM CPZ in the presence of Mg2+ plus Ca2+ and by 0.24 microM CPZ in the presence of Mg2+ plus EGTA. The extent of the binding is greater in the presence of Ca2+ than in the presence of EGTA, especially at low CPZ concentrations.     

Adherence ofStreptococcus gordonii HG 222 in the presence of saliva

The influence of the presence of saliva from different salivary glands on the adherence ofStreptococcus gordonii strain HG 222 to saliva-coated polystyrene surfaces was tested. In the presence of undiluted parotid saliva or diluted whole, submandibular and sublingual saliva the adherence of HG 222 was enhanced by the formation of small aggregates on the attachment surface. In the presence of undiluted whole, submandibular and sublingual saliva large aggregates were formed and the adherence to saliva-coated polystyrene surfaces was inhibited.Adherence in the presence of whole saliva compared to adherence in buffer was decreased when lower densities of bacterial suspension were used, although in this case in the presence of whole saliva smaller bacterial aggregates were formed.In conclusion, these results suggest that the presence of saliva in solution may both enhance and decrease the adherence ofS. gordonii HG 222 to saliva-coated polystyrene surfaces, partly depending on the size of bacterial aggregates that are formed in the presence of saliva.Abbreviations CHW saliva clarified human whole saliva - PAR saliva parotid saliva - SM saliva submandibular saliva - SL saliva sublingual saliva     

Impacts of male and food density on female performance in the brackish cladoceran Daphniopsis australis

The roles of male and food density in regulating female performance were investigated in the brackish cladoceran, Daphniopsis australis. Parthenogenetic females and ephippial females were tested using a 2 × 4 factorial experiment involving the presence and the absence of a male cross-classified with nil, low, medium and high food densities. For parthenogenetic females, the male presence and food density failed to trigger the switch from asexual to sexual reproduction, but the presence of male negatively affected parthenogenesis through egg abortion. Food density affected the animal longevity but depended on the male presence. The reproductive output was favoured by increasing food densities, but the male presence increased egg abortion, suggesting male being an added stress factor to parthenogenetic females. For ephippial females, food densities affected the frequency of switch from sexual to asexual modes in the absence and the presence of a male. However, the male enhanced switch frequency under low and high food densities. Longevity was increased with the male presence but was unaffected by food density. The ephippial females successfully produced diapausing eggs with the male presence. Although, ephippial females could switch to parthenogenesis but the reproductive output of switched ephippial females was inferior to that of parthenogenetic females since birth. The results reveal that the male presence and food density can impact the performance of female D. australis. Hence, this study provides an insight into the understanding of the reproductive biology of cladocerans and a possible alternative explanation for population dynamic of this species and other cladocerans in the field.     

ACTIVITY OF AMINOACYL-TRANSFER RNA SYNTHETASES IN BRAIN MITOCHONDRIA 1

Abstract— The binding capacity for amino acids of low molecular wt. RNAs isolated from mitochondrial and cytoplasmic fractions from brain was studied in the presence of partially purified aminoacyl-tRNA synthetases obtained from both subcellular fractions. The ability of mitochondrial tRNAs to bind amino acids was greater by about three times in the presence of mitochondrial aminoacyl-tRNA synthetases than in the presence of cytoplasmic enzymes. In contrast, the amino acid-binding ability of cytoplasmic tRNA was the same in the presence of mitochondrial enzymes as in the presence of those from the cytoplasm. When homologous (rabbit) and heterologous (calf) tRNAs were tested in the presence of mitochondrial or cytoplasmic enzymes obtained from rabbit brain and a mixture of amino acids, a significant species specificity was seen: in both heterologous systems the highest amount of tRNA binding was only 44-66 per cent of that obtained with the homologous enzyme system.     

Spectroscopic studies on the protective effect of a specific sugar on concanavalin A at acidic, neutral and alkaline pH

A Systematic investigation of the effect of pH on concanavalin A in the presence of specific and non-specific sugars is made using CD (circular dichroism) and fluorescence. The specific and non-specific sugars for concanavalin A were methyl alpha-D-glucopyranoside and methyl alpha-D-galactopyranoside respectively. Far-UV CD showed changes in the MRE value at 217 nm in the presence of the above-mentioned sugars. At pH 7, the CD and fluorescence spectra obtained in the presence of methyl alpha-D-glucopyranoside were slightly different from those for the native state and a significant difference was obtained in the presence of methyl alpha-D-galactopyranoside. Near-UV CD spectra showed the retention of a native-like tertiary structure in the presence of the specific sugar upon pH denaturation. Tryptophan fluorescence studies indicated a change in the tryptophan enviornment. The results obtained from our CD data are consistent with those obtained from fluorescence studies. Upon pH exposure of concanavalin A in the presence of methyl alpha-D-glucopyranoside and methyl alpha-D-galactopyranoside, the former acted as a protector preventing conformational alteration at different pH while the presence of latter induced a different stable conformational state and this state persists over the pH range from 2 to 10.     

Early diagnosis of crepitant gangrene caused by Bacteroides melaninogenicus.

A rapid non-invasive test for the presence of B. melaninogenicus in the wounds of crepitant non-clostridial gangrene is described. The wounds are viewed under an ultraviolet light, and the presence of bright red fluorescene indicates the probable presence of B. melaninogenicus.     

Strategic mate‐guarding behaviour in ladybirds

Mate‐guarding behaviour is regarded as a means of increasing paternity share by reducing sperm competition. It is known to be a plastic response which varies with operational sex ratios and competitor presence in the vicinity. In a recent study, prolonged mating duration in Menochilus sexmaculatus (Fabricius) (Coleoptera: Coccinellidae) has been found to incorporate mate‐guarding behaviour. The present investigation was conducted to assess its plasticity in the presence of competitors. The physical and chemical presence of competitors of both sexes at varying densities was provided to a pair of ladybirds, and their time to commence mating, latent period and mate‐guarding duration was observed. These were compared to a control treatment where other partners were absent. All treatments were conducted with sibling as well as non‐sibling competitors. It was our hypothesis that mate guarding would be increased in the presence of male competitors and would be reduced by female presence. The results revealed that while mate‐guarding duration was increased by the chemical presence of males it was decreased by their physical presence. The latter result was attributed to interference by other males who dislodge the mating male in order to access the female. Female chemical presence had no effect on mate guarding, while physical presence increased the duration of mate guarding. The reasons for the latter behaviour require further investigation. Responses were not significantly affected by the relationship between the focal pair and the competitor. The authenticity of the mate guarding in this ladybird is strongly affirmed by our results.     

Relationships between NADPH diaphorase staining and neuronal, endothelial, and inducible nitric oxide synthase and cytochrome P450 reductase immunoreactivities in guinea-pig tissues

 The presence of NADPH diaphorase staining was compared with the immunohistochemical localization of four NADPH-dependent enzymes – neuronal (type I), inducible (type II), and endothelial (type III) nitric oxide synthase (NOS) and cytochrome P450 reductase. Cell types that were immunoreactive for the NADPH-dependent enzymes were also stained for NADPH diaphorase, suggesting that endothelial and neuronal NOS and cytochrome P450 reductase all show NADPH diaphorase activity in formaldehyde-fixed tissue. However, in some tissues, the presence of NADPH diaphorase staining did not coincide with the presence of any of the NADPH-dependent enzymes we examined. In vascular endothelial cells, the punctate pattern of staining observed with NADPH diaphorase histochemistry was identical to that seen following immunohistochemistry using antibodies to endothelial NOS. In enteric and pancreatic neurons and in skeletal muscle, the presence of NADPH diaphorase staining correlated with the presence of neuronal NOS. In the liver, sebaceous glands of the skin, ciliated epithelium, and a subpopulation of the cells in the subserosal glands of the trachea, zona glomerulosa of the adrenal cortex, and epithelial cells of the lacrimal and salivary glands, the presence of NADPH diaphorase staining coincided with the presence of cytochrome P450 reductase immunoreactivity. In epithelial cells of the renal tubules and zona fasciculata and zona reticularis of the adrenal cortex, NADPH diaphorase staining was observed that did not coincide with the presence of any of the enzymes. Inducible NOS was not observed in any tissue. Thus, while tissues that demonstrate immunoreactivity for neuronal and endothelial NOS also stain positively for NADPH diaphorase activity, the presence of NADPH diaphorase staining does not reliably or specifically indicate the presence of one or more NOS isoforms. Accepted: 2 September 1996     

Asymmetrical costs of sexual conflict in the seaweed fly, Coelopa frigida

Abstract.  1. Sexual conflict can play an important role in the evolution of animal life-history characteristics, including lifespan. Seaweed flies show an increase in mortality rates when exposed to brown algae. The seaweed stimulates females to oviposit and males to mount females. Females typically respond to male mounts by performing a violent rejection response.
2. Here the contribution of sexual conflict to the increase in mortality seen in the presence of seaweed was determined. The survival of single and mixed sex pairs of flies was followed in the presence and absence of seaweed.
3. The two sexes showed differential survival rates, with females living longer in the absence of seaweed. The presence of seaweed reduced survival in both sexes. In the presence of seaweed, female survival was lower when paired with a male. Over 40% of the reduction in survival in females in the presence of seaweed appears to be attributable to sexual conflict.
4. The presence of a female did not significantly affect male survival. Thus the mortality cost of being in the presence of the opposite sex and seaweed appears highly asymmetric.
5. In the presence of seaweed, female survival was lower when females were paired with small males. Small males exhibit higher levels of harassment of females, thus it is argued that pre-copulatory sexual conflict is the probable cause of the increased mortality cost to females of being in the presence of both males and seaweed.