Genomic constitution of <Emphasis Type="Italic">Festuca</Emphasis> × <Emphasis Type="Italic">Lolium</Emphasis> hybrids revealed by the DArTFest array

Complementary attributes of Festuca and Lolium grasses can be combined in hybrid cultivars called Festuloliums, which are becoming increasingly popular fodder crops and amenity plants. Genomic constitution of commercially available Festuloliums was reported to vary from almost equal representation of parental genomes to apparent lack of one of them based on molecular cytogenetic analyses and screening with a small set of DNA markers, both approaches with limited resolution. Here, we describe the use of the DArTFest array comprising 3,884 polymorphic DArT markers for characterization of genomes in five Festulolium cultivars. In any of the cultivars, the minimum number of informative markers, which discriminated the parental Lolium and Festuca genomes was 361 and 171, respectively. Using the DArTFest array, it was possible to determine hybrid genome constitution at resolution which has never been achieved before and the analysis of a set of randomly selected plants from each cultivar provided information on genetic structure of outcrossing Festulolium cultivars. In addition to a core set of markers typical for each hybrid cultivar, markers occurring at low frequency among the plants within each cultivar were identified. Biological significance of genomic loci associated with the rare markers is yet to be determined. Finally, with the aim to simplify the use of DArTFest arrays to characterize Festuca × Lolium hybrids, various bulking strategies were compared. While all bulks were suitable for identification of hybrids, only bulks of few plants have been found to reveal the rare markers.     

A case of adoption and allonursing in captive plains zebra (Equus burchellii)

Although allonursing (allowing non-filial offspring to suckle) can be a costly behaviour, it has been reported for many mammals including ungulate species. However, such behaviour is very rare in equids. This is the first report on adoption and allonursing in captive plains zebra (Equus burchellii), recorded in the Dv?r Králové Zoo, Czech Republic. We observed a case of adoption of an orphaned foal by a lactating mare, who then regularly nursed two foals (filial and non-filial). The allonursing mare rejected more suckling attempts, terminated suckling bouts more often, and had a shorter suckling bout duration than other mares. When nursing both foals at the same time, the suckling bout lasted for less time than when nursing a single foal, regardless of whether it was filial or non-filial. The allonursing mare apparently did not discriminate between the filial and non-filial foal.     

Factors Affecting Vocalization in Tengmalm’s Owl (Aegolius funereus) Fledglings during Post-Fledging Dependence Period: Scramble Competition or Honest Signalling of Need?

Begging behaviour of nestlings has been intensively studied for several decades as a key component of parent-offspring conflict. There are essentially two main theories to account for intensity of food solicitation among offspring: that intensity of begging is related to some form of scramble competition between nest mates or that it offers honest signalling of need to parents. The vast majority of studies which have addressed begging behaviour have been based on observations of, and experiments on, nestlings and have not considered begging behaviour, during the post-fledging period. Begging vocalizations in this post-fledging phase of dependence have rarely been studied, despite the importance of vocalizations as a communication method between offspring and parents, particularly for nocturnal species. We radiotracked 39 fledglings of the Tengmalm’s owl (Aegolius funereus) in two years with different availability of prey: 2010 (n = 29 fledglings) and 2011 (n = 10 fledglings) and made 1320 nightly localizations in which we recorded presence or absence of begging calls. Within years, the most important measures related to the probability of vocalization were body condition at fledging, time of night, number of surviving siblings, age and weather conditions. Begging intensity increased with age in both years; however, in the year with low prey availability fledglings vocalized significantly more often. The main factor causing these differences between years was probably the different availability of prey, affecting breeding success, post-fledging behaviour, and thus also both short- and long-term needs of offspring. We believe that our results suggest honest signalling of their fledgling’s need.     

Hippocampal Spatial Position Evaluation on MRI for Research and Clinical Practice

In clinical practice as well as in many volumetric studies we use different reorientations of the brain position towards x and y axis on the magnetic resonance imaging (MRI) scans. In order to find out whether it has an overall effect on the resulting 2D data, manual hippocampal area measurements and rotation variability of the brain (in two reoriented axes) and the skull were performed in 23 Alzheimer''s disease patients and 31 healthy controls. After the MRI scanning, native brain scans (nat) were reoriented into the two different artificial planes (anterior commissure – posterior commissure axis (AC-PC) and hippocampal horizontal long axis (hipp)). Hippocampal area and temporal horn of the lateral ventricle was measured manually using freeware Image J program. We found that 1) hippocampal area of nat images is larger compared to hipp images, area of the nat images is equal to the AC-PC images and area of the hipp images is smaller compared to AC-PC images, 2) hippocampal area together with the area of the temporal horn for nat images is larger compared to hipp images, area of the hipp images is smaller compared to the AC-PC images and area of the nat images is smaller compared to the AC-PC images. The conclusion is that the measured area of the hippocampus in the native MRI is almost the same as the area of MRI reoriented only into the AC-PC axis. Therefore, when performing 2D area studies of the hippocampus or in the clinical practice we recommend usage of not-reoriented MRI images or to reorient them into the AC-PC axis. Surprising finding was that rotation of both AC-PC and hipp line towards x-axis among patients varies up to 35° and the same is true for the skull rotation so that it is not only a matter of the brain position.     

Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS

Background

Brucella abortus is the etiological agent of a worldwide zoonosis called brucellosis. This alpha-proteobacterium is dividing asymmetrically, and PdhS, an essential histidine kinase, was reported to be an old pole marker.

Results

We were interested to identify functions that could be recruited to bacterial poles. The Brucella ORFeome, a collection of cloned predicted coding sequences, was placed in fusion with yellow fluorescent protein (YFP) coding sequence and screened for polar localizations in B. abortus. We report that AidB-YFP was systematically localized to the new poles and at constrictions sites in B. abortus, either in culture or inside infected HeLa cells or RAW264.7 macrophages. AidB is an acyl-CoA dehydrogenase (ACAD) homolog, similar to E. coli AidB, an enzyme putatively involved in destroying alkylating agents. Accordingly, a B. abortus aidB mutant is more sensitive than the wild-type strain to the lethality induced by methanesulphonic acid ethyl ester (EMS). The exposure to EMS led to a very low frequency of constriction events, suggesting that cell cycle is blocked during alkylation damage. The localization of AidB-YFP at the new poles and at constriction sites seems to be specific for this ACAD homolog since two other ACAD homologs fused to YFP did not show specific localization. The overexpression of aidB, but not the two other ACAD coding sequences, leads to multiple morphological defects.

Conclusions

Data reported here suggest that AidB is a marker of new poles and constriction sites, that could be considered as sites of preparation of new poles in the sibling cells originating from cell division. The possible role of AidB in the generation or the function of new poles needs further investigation.     

Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi

Background

Lignocellulosic materials have been moved towards the forefront of the biofuel industry as a sustainable resource. However, saccharification and the production of bioproducts derived from plant cell wall biomass are complex and lengthy processes. The understanding of termite gut biology and feeding strategies may improve the current state of biomass conversion technology and bioproduct production.

Results

The study herein shows comprehensive functional characterization of crude body extracts from Coptotermes gestroi along with global proteomic analysis of the termite's digestome, targeting the identification of glycoside hydrolases and accessory proteins responsible for plant biomass conversion. The crude protein extract from C. gestroi was enzymatically efficient over a broad pH range on a series of natural polysaccharides, formed by glucose-, xylose-, mannan- and/or arabinose-containing polymers, linked by various types of glycosidic bonds, as well as ramification types. Our proteomic approach successfully identified a large number of relevant polypeptides in the C. gestroi digestome. A total of 55 different proteins were identified and classified into 29 CAZy families. Based on the total number of peptides identified, the majority of components found in the C. gestroi digestome were cellulose-degrading enzymes. Xylanolytic enzymes, mannan- hydrolytic enzymes, pectinases and starch-degrading and debranching enzymes were also identified. Our strategy enabled validation of liquid chromatography with tandem mass spectrometry recognized proteins, by enzymatic functional assays and by following the degradation products of specific 8-amino-1,3,6-pyrenetrisulfonic acid labeled oligosaccharides through capillary zone electrophoresis.

Conclusions

Here we describe the first global study on the enzymatic repertoire involved in plant polysaccharide degradation by the lower termite C. gestroi. The biochemical characterization of whole body termite extracts evidenced their ability to cleave all types of glycosidic bonds present in plant polysaccharides. The comprehensive proteomic analysis, revealed a complete collection of hydrolytic enzymes including cellulases (GH1, GH3, GH5, GH7, GH9 and CBM 6), hemicellulases (GH2, GH10, GH11, GH16, GH43 and CBM 27) and pectinases (GH28 and GH29).     

Concurrent lactation and pregnancy: pregnant domestic horse mares do not increase mother-offspring conflict during intensive lactation

Lactation is the most energy demanding part of parental care in mammals, so parent-offspring conflict arises over milk provided by the mother. In some species females commonly become pregnant shortly after parturition of previous young. This further intensifies mother-offspring conflict due to concurrent pregnancy and lactation. In equids it has been well established that pregnant females wean their foals earlier than non-pregnant ones. Intensified mother-offspring conflict was presumed to associate with pregnancy also during the period of intensive lactation, i.e., before the weaning process starts. We investigated the effect of pregnancy on suckling behaviour characteristics as indicators of mother-offspring conflict in domestic horses. Contrary to expectation, here we provide evidence of a decreased mother-offspring conflict related to pregnancy in lactating females during first two trimesters of pregnancy. Pregnant mares provided longer suckling bouts and did not reject or terminate suckling of their foals more often than non-pregnant mares. Our results suggest that pregnant mares cope with parallel investment into a nursed foal and a foetus through enhancing nursing behaviour in early stages of pregnancy before the initially low requirements of the foetus increase. They compensate their suckling foal with the perspective of its early weaning due to ongoing pregnancy.     

Seed germination temperatures of eight Mexican Agave species with economic importance

The genetic diversity of Agave plants is threatened by clonal commercial reproduction and climatic change. Sexual reproduction is uncommon and research on seed germination is scarce. The present study evaluated the seed germination of Agave lechuguilla, Agave striata, Agave americana var. marginata, Agave asperrima, Agave cupreata, Agave duranguesis, Agave angustifolia ssp. tequilana and Agave salmiana at constant temperatures (10, 15, 20, 25, 30, 35 and 40°C). Initial imbibition (after the first 12 h) was significantly variable among species, positively correlated with seed weight (r = 0.6560, P < 0.001) and increased with temperature (from 35% at 10°C to 66% at 40°C). Temperature affected maximum imbibition (83–150%) for A. asperrima, A. lechuguilla, A. salmiana and A. striata; other species averaged 110%. Most germination kinetics best fitted a logistic model, whereas only a few treatments fit a Weibull model. The time to germination onset diminished (P < 0.05) from 125–173 h at 15°C to 68–84 h at 25°C, and then ascended to 84–196 h at 35°C. The mean germination rate and seed germination percentage after 312 h peaked at 25°C (0.50–0.95% seeds/h and 85–99%, respectively) and fell (P < 0.05) to near zero at 10 and 40°C. Temperatures of 10, 35 and 40°C were partially lethal to A. asperrima, A. duranguensis and A. salmiana seeds. The time to germination onset, seed germination percentage after 312 h and mean germination rate are best described by a Gaussian distribution, with its optimum at approximately 25°C. Thus, optimum temperatures are related to the ecological characteristics of each species area.     

Dissemination biases in ecology: effect sizes matter more than quality

Publication and citation decisions in ecology are likely influenced by many factors, potentially including journal impact factors, direction and magnitude of reported effects, and year of publication. Dissemination bias exists when publication or citation of a study depends on any of these factors. We defined several dissemination biases and determined their prevalence across many sub‐disciplines in ecology, then determined whether or not data quality also affected these biases. We identified dissemination biases in ecology by conducting a meta‐analysis of citation trends for 3867 studies included in 52 meta‐analyses. We correlated effect size, year of publication, impact factor and citation rate within each meta‐analysis. In addition, we explored how data quality as defined in meta‐analyses (sample size or variance) influenced each form of bias. We also explored how the direction of the predicted or observed effect, and the research field, influenced any biases. Year of publication did not influence citation rates. The first papers published in an area reported the strongest effects, and high impact factor journals published the most extreme effects. Effect size was more important than data quality for many publication and citation trends. Dissemination biases appear common in ecology, and although their magnitude was generally small many were associated with theory tenacity, evidenced as tendencies to cite papers that most strongly support our ideas. The consequences of this behavior are amplified by the fact that papers reporting strong effects were often of lower data quality than papers reporting much weaker effects. Furthermore, high impact factor journals published the strongest effects, generally in the absence of any correlation with data quality. Increasing awareness of the prevalence of theory tenacity, confirmation bias, and the inattention to data quality among ecologists is a first step towards reducing the impact of these biases on research in our field.