Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning

At present, there is much variability between MALDI-TOF MS methodology for the characterization of bacteria through differences in e.g., sample preparation methods, matrix solutions, organic solvents, acquisition methods and data analysis methods. After evaluation of the existing methods, a standard protocol was developed to generate MALDI-TOF mass spectra obtained from a collection of reference strains belonging to the genera Leuconostoc, Fructobacillus and Lactococcus. Bacterial cells were harvested after 24 h of growth at 28 °C on the media MRS or TSA. Mass spectra were generated, using the CHCA matrix combined with a 50:48:2 acetonitrile:water:trifluoroacetic acid matrix solution, and analyzed by the cell smear method and the cell extract method. After a data preprocessing step, the resulting high quality data set was used for PCA, distance calculation and multi-dimensional scaling. Using these analyses, species-specific information in the MALDI-TOF mass spectra could be demonstrated. As a next step, the spectra, as well as the binary character set derived from these spectra, were successfully used for species identification within the genera Leuconostoc, Fructobacillus, and Lactococcus. Using MALDI-TOF MS identification libraries for Leuconostoc and Fructobacillus strains, 84% of the MALDI-TOF mass spectra were correctly identified at the species level. Similarly, the same analysis strategy within the genus Lactococcus resulted in 94% correct identifications, taking species and subspecies levels into consideration. Finally, two machine learning techniques were evaluated as alternative species identification tools. The two techniques, support vector machines and random forests, resulted in accuracies between 94% and 98% for the identification of Leuconostoc and Fructobacillus species, respectively.     

In sacco degradation kinetics of fresh and field-cured peanut (Arachis hypogaea L.) forage harvested at different maturities

There is interest in growing peanut (Arachis hypogaea L.) for forage, but little is known about the nutritive value and forage quality of modern cultivars. The objective of this study was to compare the chemical composition and in sacco degradation kinetics of three cultivars of peanuts (cv. ‘C99-R’, ‘Georgia-01R’, and ‘York’) at either stage 2 or 8 maturities when fresh and field-cured. Herbage yield was at least 3000 kg DM/ha for all cultivars at both maturities. Crude protein (CP) was greater (P < 0.0001) at R2 stage than at R8 stage; whereas, neutral detergent fiber (aNDF), acid detergent fiber, and Lignin (sa) were greater (P < 0.01) at R8 than R2 maturity stages. Water soluble carbohydrate and acid detergent insoluble nitrogen was not different (P > 0.07) among cultivars, maturity stage, or harvest forms. In vitro true digestibility was greatest (P < 0.02) for C99-R and least for York. Undegradable intake protein concentration was greatest (P < 0.04) in York and least for C99-R. Maturity had a greater effect on the degradation kinetics than harvest form or cultivar. The dry matter (DM) and CP in the soluble wash fraction (A) and insoluble but degradable fraction (B) and the effective ruminal degradability were greater among all cultivars and both harvest forms of the R2 maturity stage than the R8. The undegradable DM, aNDF, and CP in the undegradable fraction were greatest (P < 0.002) for all three cultivars at R8 maturity. The rate of degradation of DM and CP in the B fraction was faster (P < 0.001) at R2 stage than at R8 stage; whereas, rate of aNDF degradation was not different (P > 0.09) among treatments. Lag of DM, aNDF, or CP degradation was not different (P > 0.1) among treatments. The cultivars C99-R and Georgia-01R are recommended for further feeding trials.     

Multiple mating in the traumatically inseminating Warehouse pirate bug, Xylocoris flavipes: effects on fecundity and longevity

Optimal mating frequencies differ between sexes as a consequence of the sexual differentiation of reproductive costs per mating, where mating is normally more costly to females than males. In mating systems where sexual reproduction is costly to females, sexual conflict may cause both direct (i.e. by reducing female fecundity or causing mortality) and indirect (i.e. increased risk of mortality, reduced offspring viability) reductions in lifetime reproductive success of females, which have individual and population consequences. We investigated the direct and indirect costs of multiple mating in a traumatically inseminating (TI) predatory Warehouse pirate bug, Xylocoris flavipes (Reuter) (Hemiptera: Anthocoridae), where the male penetrates the female's abdomen during copulation. This study aimed to quantify the effects of TI on female fecundity, egg viability, the lifetime fecundity schedule, longevity and prey consumption in this cosmopolitan biocontrol agent. We found no difference in the total reproductive output between mating treatments in terms of total eggs laid or offspring viability, but there were significant differences found in daily fecundity schedules and adult longevity. In terms of lifetime reproduction, female Warehouse pirate bugs appear to be adapted to compensate for the costs of TI mating to their longevity.     

Is parental care behavior in Belostoma species an evolutionary cause for their common sexual size dimorphism pattern?

Current evidence suggests that sexual size dimorphism (SSD) reflects the male and female adaptation to their different reproductive roles. Belostoma and Lethocerus species, included in Belostomatidae, present different kinds of paternal care. Females of Belostoma Latreille species lay their eggs on the back of males. Males carry, aerate and protect the clutch until hatching, which is critical for offspring survival. Males of Lethocerus Mayr species exhibit some parental care behavior but do not carry the eggs. The genera are nearly related. We studied and compared the SSD patterns of B. oxyurum (Dufour), B. micantulum (Stål), B. elegans (Mayr), B. bifoveolatum Spinola, B. gestroi Montandon and Lethocerus annulipes (Herrich‐Schäffer) by means of a multivariate approach to distinguish selection targets in different components of size. Morphometric analysis revealed that SSD patterns vary among traits and that the arrangements are similar in Belostoma species, showing a common trend under resembling selective mechanisms. The widespread SSD trend in insects is that all components of body size are biased towards females, generally related to a fecundity advantage, a pattern now also detected in L. annulipes. We found in Belostoma species that the male has relatively longer middle and hind legs. We propose that SSD in hind legs biased towards males is a selective response for paternal care; they denote a brood‐adapted morphology. The middle leg enlargement may be an associated response to maintain effective locomotion.     

Adult firefly abundance is linked to weather during the larval stage in the previous year

1. Much is known about the brief adult phase of fireflies. However, fireflies spend a relatively long developmental period under the soil surface. Climatic and soil conditions may directly affect the eggs, larvae, and pupae, and also affect them indirectly through predators, competitors, and prey items. Climatic conditions during the early life stages of this iconic species are therefore relevant to their hypothesised decline within the context of global warming. 2. Data on the abundance of fireflies were extracted from the publicly available citizen dataset across North America over a period of 9 years. The effects of weather in the 24 months before the observations of firefly abundance were documented based on 6761 observations. 3. Climatic conditions during both the larval and adult phases have a non‐linear effect on adult firefly abundance. Maximum winter and spring temperatures and mean precipitation in the 20‐month period before the observations had the greatest impact on the abundance of firefly adults. Low maximum soil moisture during the 5–19 months preceding the observations affected the adult abundance negatively, and high maximum soil moisture affected it positively. 4. After correcting the firefly abundance for these weather effects, it is estimated that the abundance of fireflies increased over the time period of this study. 5. This study suggests that early life climatic conditions have a small but significant impact on adult firefly abundance with a total R² of 0.017.     

The three criteria for resistance by plant carrion‐provisioning: insect entrapment and predator enrichment on Mimulus bolanderi

1. Many sticky plants provision mutualistic scavenging arthropod predators with carrion, which in turn protect the plant from insect herbivores. While insect entrapment is a common trait across plants, which plants attract these predators and may derive protection is still largely unknown. 2. Three conditions were proposed that must be satisfied for observational data to suggest this defensive strategy: (i) the consistent presence of scavenging predators, (ii) positive correlation between predator numbers and carrion, and (iii) suitability of these predators for controlling known herbivores. 3. As a case study, we examined the fire‐following annual, Mimulus [Diplacus] bolanderi (Phyrmaceae), which is part of a well‐studied radiation of California monkeyflowers. Many monkeyflowers entrap insects, though attraction to predators has not been quantified in this genus. 4. A guild of scavenging arthropod predators on M. bolanderi (condition #1) was found, which correlated positively with carrion abundance (#2) and could consume the primary herbivore (#3), suggesting a carrion‐mediated defensive strategy. Lastly, as M. bolanderi is variable in time and space, these interactions are facultative, and these predators are quick to adopt ephemeral carrion resources on novel host plants.     

猎蝽的伪装现象

从具有伪装现象的猎蝽类群、伪装所用的材料、类型、载物能力、伪装行为、去伪装对猎蝽的影响及伪装的生物学意义 7方面综述了猎蝽的伪装现象及其研究动态 ;特别对猎蝽的载物能力进行了讨论 ,提出了绝对载物能力和平均载物能力的概念与计算方法     

Seasonal variations in the chemical composition and dry matter degradability of exclosure forages in the semi-arid region of northern Ethiopia

The present study was conduced at two sites (Tembien and Wukro) in the semi-arid region of Tigray in northern Ethiopia to investigate the seasonal dynamics in the chemical composition and dry matter digestibility of grass and browse species of exclosures. The browse species studied in Tembien and Wukro had a mean crude protein (CP) value of 166 and 117 g/kg dry matter (DM), respectively. The mean in vitro dry matter digestibility (IVDMD) coefficient and predicted metabolizable energy (ME) density of the browse species were 0.72 and 9.83 MJ/kg DM, respectively at Tembien, 0.62 and 8.38 MJ/kg DM, respectively, at Wukro. Neutral detergent fibre (NDF) and acid detergent fibre (ADF) values of the browse species varied from 192 to 437 and 127 to 391 g/kg DM, respectively. Acid detergent lignin (ADL) values ranged from 36 to 190 g/kg DM. The mean CP of the grass species in Tembien and Wukro during the long rainy season was 76 and 73 g/kg DM, respectively and values declined below a critical maintenance level during the dry and short rain seasons. Mean IVDMD and ME values for the two sites were 0.41 and 0.47, and 5.38 and 6.11 MJ/kg DM, respectively. The NDF, ADF, and lignin values of the grass species were generally above 700, 400, and 70 g/kg DM, respectively. The CP, IVDMD and ME values of the mixed grass samples differed (P<0.05) among harvesting months and values ranged from 20 to 103 g/kg DM, 0.47 to 0.72 MJ/kg DM, and 6.16 to 9.91 MJ/kg DM, respectively. The browse species could be used as useful dry season protein supplements to the N deficient native grass species. Especial emphasis should be given to propagate Maerua angolensis and Cadaba farinosa at community nursery sites. Harvesting in September, rather than the current extended harvest period that took place in October and November, can considerably improve the feeding value of native grass hay for smallholder ruminant production systems.