Gut microbiomes of free‐ranging and captive Namibian cheetahs: Diversity,putative functions and occurrence of potential pathogens

Although the significance of the gut microbiome for host health is well acknowledged, the impact of host traits and environmental factors on the interindividual variation of gut microbiomes of wildlife species is not well understood. Such information is essential; however, as changes in the composition of these microbial communities beyond the natural range might cause dysbiosis leading to increased susceptibility to infections. We examined the potential influence of sex, age, genetic relatedness, spatial tactics and the environment on the natural range of the gut microbiome diversity in free‐ranging Namibian cheetahs (Acinonyx jubatus). We further explored the impact of an altered diet and frequent contact with roaming dogs and cats on the occurrence of potential bacterial pathogens by comparing free‐ranging and captive individuals living under the same climatic conditions. Abundance patterns of particular bacterial genera differed between the sexes, and bacterial diversity and richness were higher in older (>3.5 years) than in younger individuals. In contrast, male spatial tactics, which probably influence host exposure to environmental bacteria, had no discernible effect on the gut microbiome. The profound resemblance of the gut microbiome of kin in contrast to nonkin suggests a predominant role of genetics in shaping bacterial community characteristics and functional similarities. We also detected various Operational Taxonomic Units (OTUs) assigned to potential pathogenic bacteria known to cause diseases in humans and wildlife species, such as Helicobacter spp., and Clostridium perfringens. Captive individuals did not differ in their microbial alpha diversity but exhibited higher abundances of OTUs related to potential pathogenic bacteria and shifts in disease‐associated functional pathways. Our study emphasizes the need to integrate ecological, genetic and pathogenic aspects to improve our comprehension of the main drivers of natural variation and shifts in gut microbial communities possibly affecting host health. This knowledge is essential for in situ and ex situ conservation management.     

Change of serum mitochondrial uncoupling protein 1 (UCP1) levels and daily rhythm of rectal and cutaneous temperatures in Equus caballus and Capra hyrcus

The aim of the present study was to monitor the daily rhythm of rectal and cutaneous temperatures together with the changes in the serum levels of mitochondrial uncoupling protein 1 (UCP1) in equine and goat species. On five gelding horses and five female goat rectal and cutaneous temperatures were recorded at 4 h intervals for a 48 h period. At the same time points blood samples were collected from each animal. Daily rhythms of rectal and cutaneous temperatures were observed in both species, in both day of monitoring. Mesor value of rectal temperature was statistically higher of about 4 °C than cutaneous temperature, and acrophase was postponed of about 2 h in both day of monitoring and in both species. UCP1 did not show daily rhythmicity in horses and goats. We can speculate that the thermogenesis due to thermal system is auxiliary to keeping the body temperature daily rhythm.     

Fine-tuning of the flavonoid and monolignol pathways during apple early fruit development

Planta - A coordinated regulation of different branches of the flavonoid pathway was highlighted that may contribute to elucidate the role of this important class of compounds during the early...     

Chronic Stress Causes Sex-Specific and Structure-Specific Alterations in Mitochondrial Respiratory Chain Activity in Rat Brain

Chronic restraint stress (CRS) induces a variety of changes in brain function, some of which are mediated by glucocorticoids. The response to stress occurs in a sex-specific way, and may include mitochondrial and synaptic alterations. The synapse is highly dependent on mitochondrial energy supply, and when mitochondria become dysfunctional, they orchestrate cell death. This study aimed to investigate the CRS effects on mitochondrial respiratory chain activity, as well as mitochondrial potential and mass in cell body and synapses using hippocampus, cortex and striatum of male and female rats. Rats were divided into non-stressed (control) and stressed group (CRS during 40 days). Results showed that CRS increased complex I–III activity in hippocampus. We also observed an interaction between CRS and sex in the striatal complex II activity, since CRS induced a reduction in complex II activity in males, while in females this activity was increased. Also an interaction was observed between stress and sex in cortical complex IV activity, since CRS induced increased activity in females, while it was reduced in males. Glucocorticoid receptor (GR) content in cortex and hippocampus was sexually dimorphic, with female rats presenting higher levels compared to males. No changes were observed in GR content, mitochondrial potential or mass of animals submitted to CRS. It was concluded that CRS induced changes in respiratory chain complex activities, and some of these changes are sex-dependent: these activities are increased in the striatal mitochondria by CRS protocol mainly in females, while in males it is decreased.

     

A validated antibody panel for the characterization of tau post-translational modifications

Background

Tau is a microtubule-binding protein, which is subject to various post-translational modifications (PTMs) including phosphorylation, methylation, acetylation, glycosylation, nitration, sumoylation and truncation. Aberrant PTMs such as hyperphosphorylation result in tau aggregation and the formation of neurofibrillary tangles, which are a hallmark of Alzheimer’s disease (AD). In order to study the importance of PTMs on tau function, antibodies raised against specific modification sites are widely used. However, quality control of these antibodies is lacking and their specificity for particular modifications is often unclear.

Methods

In this study, we first designed an online tool called ‘TauPTM’, which enables the visualization of PTMs and their interactions on human tau. Using TauPTM, we next searched for commercially available antibodies against tau PTMs and characterized their specificity by peptide array, immunoblotting, electrochemiluminescence ELISA and immunofluorescence technologies.

Results

We demonstrate that commercially available antibodies can show a significant lack of specificity, and PTM-specific antibodies in particular often recognize non-modified versions of the protein. In addition, detection may be hindered by other PTMs in close vicinity, complicating the interpretation of results. Finally, we compiled a panel of specific antibodies and show that they are useful to detect PTM-modified endogenous tau in hiPSC-derived neurons and mouse brains.

Conclusion

This study has created a platform to reliably and robustly detect changes in localization and abundance of post-translationally modified tau in health and disease. A web-based version of TauPTM is fully available at http://www.tauptm.org.

     

Complexity and algorithms for copy-number evolution problems

Background

Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome’s copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis.

Results

We model the evolution of a tumor by segmental deletions and amplifications, and gauge distance from profile \(\mathbf {a}\) to \(\mathbf {b}\) by the minimum number of events needed to transform \(\mathbf {a}\) into \(\mathbf {b}\). Given two profiles, our first problem aims to find a parental profile that minimizes the sum of distances to its children. Given k profiles, the second, more general problem, seeks a phylogenetic tree, whose k leaves are labeled by the k given profiles and whose internal vertices are labeled by ancestral profiles such that the sum of edge distances is minimum.

Conclusions

For the former problem we give a pseudo-polynomial dynamic programming algorithm that is linear in the profile length, and an integer linear program formulation. For the latter problem we show it is NP-hard and give an integer linear program formulation that scales to practical problem instance sizes. We assess the efficiency and quality of our algorithms on simulated instances.

Availability

https://github.com/raphael-group/CNT-ILP

     

Evolution of Hot Polaron States with a Nanosecond Lifetime in a Manganite Perovskite

Understanding and controlling the relaxation process of optically excited charge carriers in solids with strong correlations is of great interest in the quest for new strategies to exploit solar energy. Usually, optically excited electrons in a solid thermalize rapidly on a femtosecond to picosecond timescale due to interactions with other electrons and phonons. New mechanisms to slow down thermalization will thus be of great significance for efficient light energy conversion, e.g., in photovoltaic devices. Ultrafast optical pump–probe experiments in the manganite Pr_0.65Ca_0.35MnO_3, a photovoltaic, thermoelectric, and electrocatalytic material with strong polaronic correlations, reveal an ultraslow recombination dynamics on a nanosecond‐time scale. The nature of long living excitations is further elucidated by photovoltaic measurements, showing the presence of photodiffusion of excited electron–hole polaron pairs. Theoretical considerations suggest that the excited charge carriers are trapped in a hot polaron state. Escape from this state is possible via a slow dipole‐forbidden recombination process or via rare thermal fluctuations toward a conical intersection followed by a radiation‐less decay. The strong correlation between the excited polaron and the octahedral dynamics of its environment appears to be substantial for stabilizing the hot polaron.     

Quantification and identification of lightning damage in tropical forests

Accurate estimates of tree mortality are essential for the development of mechanistic forest dynamics models, and for estimating carbon storage and cycling. However, identifying agents of tree mortality is difficult and imprecise. Although lightning kills thousands of trees each year and is an important agent of mortality in some forests, the frequency and distribution of lightning‐caused tree death remain unknown for most forests. Moreover, because all evidence regarding the effects of lightning on trees is necessarily anecdotal and post hoc, rigorous tests of hypotheses regarding the ecological effects of lightning are impossible. We developed a combined electronic sensor/camera‐based system for the location and characterization of lightning strikes to the forest canopy in near real time and tested the system in the forest of Barro Colorado Island, Panama. Cameras mounted on towers provided continuous video recordings of the forest canopy that were analyzed to determine the locations of lightning strikes. We used a preliminary version of this system to record and locate 18 lightning strikes to the forest over a 3‐year period. Data from field surveys of known lightning strike locations (obtained from the camera system) enabled us to develop a protocol for reliable, ground‐based identification of suspected lightning damage to tropical trees. In all cases, lightning damage was relatively inconspicuous; it would have been overlooked by ground‐based observers having no knowledge of the event. We identified three types of evidence that can be used to consistently identify lightning strike damage in tropical forests: (1) localized and directionally biased branch mortality associated with flashover among tree and sapling crowns, (2) mortality of lianas or saplings near lianas, and (3) scorched or wilting epiphytic and hemiepiphytic plants. The longitudinal trunk scars that are typical of lightning‐damaged temperate trees were never observed in this study. Given the prevalence of communications towers worldwide, the lightning detection system described here could be implemented in diverse forest types. Data from multiple systems would provide an outstanding opportunity for comparative research on the ecological effects of lightning. Such comparative data are increasingly important given expected increases in lightning frequency with climatic change.