Multimodal analysis of metals in copper–zinc superoxide dismutase isoforms separated on electrophoresis gels

It has been suggested that copper–zinc superoxide dismutase (CuZnSOD) isoforms of distinct isoelectric point (pI) could result from differences in their metallation state. Our aim was then to develop and validate analytical methods for the determination and understanding of metallation states in human CuZnSOD isoforms. To avoid metal losses during sample preparation steps, CuZnSOD isoforms were separated according to their pI using non-denaturing isoelectric focusing (IEF) gel electrophoresis. Metal quantification was directly performed in-gel. Cu/Zn ratios of CuZnSOD isoforms were quantified by Particle-Induced X-ray Emission (PIXE) and Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS). Cu/Zn ratios were measured close to the value of 1 as expected from the known stoichiometry of CuZnSOD with slight, but statistically significant, differences between acidic and basic isoforms. Overall, this study demonstrates that metal quantification can be performed directly on metalloproteins separated on electrophoresis gels.     

Modulation of the intrinsic chromatin binding property of HIV-1 integrase by LEDGF/p75

The stable insertion of the retroviral genome into the host chromosomes requires the association between integration complexes and cellular chromatin via the interaction between retroviral integrase and the nucleosomal target DNA. This final association may involve the chromatin-binding properties of both the retroviral integrase and its cellular cofactor LEDGF/p75. To investigate this and better understand the LEDGF/p75-mediated chromatin tethering of HIV-1 integrase, we used a combination of biochemical and chromosome-binding assays. Our study revealed that retroviral integrase has an intrinsic ability to bind and recognize specific chromatin regions in metaphase even in the absence of its cofactor. Furthermore, this integrase chromatin-binding property was modulated by the interaction with its cofactor LEDGF/p75, which redirected the enzyme to alternative chromosome regions. We also better determined the chromatin features recognized by each partner alone or within the functional intasome, as well as the chronology of efficient LEDGF/p75-mediated targeting of HIV-1 integrase to chromatin. Our data support a new chromatin-binding function of integrase acting in concert with LEDGF/p75 for the optimal association with the nucleosomal substrate. This work also provides additional information about the behavior of retroviral integration complexes in metaphase chromatin and the mechanism of action of LEDGF/p75 in this specific context.     

Hierarchy of factors affecting behavioural signs used for oestrus detection of Holstein and Normande dairy cows in a seasonal calving system

As oestrous expression of dairy cows has decreased over the last decades oestrus detection has become more difficult. The objective of this study is to identify the main factors that affect oestrus detection in seasonal calving dairy cows, and to establish their relative importance. In each of 5 years 36 Normande and 36 Holstein cows were assigned to a Low or High winter-feeding level group. Half of each group was then assigned to a Low or High pasture-feeding group. The Low-Low strategy resulted in the lowest milk yield and the greatest body condition (BC) loss from calving to nadir BC score (6302 kg; -0.98 unit). The High-High strategy had the converse effect (7549 kg; -0.75 units). Low-High and High-Low strategies had intermediate values. The Normande cows had lower milk yield and BC loss than Holstein cows (6153 kg versus 7620 kg; -0.82 unit versus -1.20 unit). A database of 415 observed spontaneous oestruses was created. Oestruses were classified according to detection signs: (1) standing to be mounted, (2) mounting without standing, (3) other signs without standing or mounting (slight signs). Presence of another cow in oestrus, access to pasture, Normande breed and Low-Low strategy increased standing detection. In the Normande breed, 97% of oestruses were detected by standing while combining the presence of a herdmate in oestrus and access to pasture with a milk production of less than 6550 kg. Holstein cows had a higher frequency of slight signs oestruses than Normande ones, which was associated with a decreased subsequent calving rate (P<0.05). In multiparous Holstein cows, the odds of slight signs detection was multiplied by 7.8 for the High-High group in comparison with the Low-Low group (P<0.05). In our study milk yield had an effect on oestrus detection which was not explained by BC loss. As High-High cows produced more milk than others, we logically found that an increase in milk yield increased slight signs detection. Conversely, as they lost less BC than others, BC loss improved the chance of standing or mounting detection. These two results show that an increase in milk yield may reduce oestrous behaviour even if BC loss is moderate. Oestrus detection is crucial in seasonal compact calving systems. High phenotypic milk yields appear unsuitable with such systems in regard to depressed oestrous behaviour.     

Capture–recapture models with heterogeneity to study survival senescence in the wild

Detecting senescence in wild populations and estimating its strength raise three challenges. First, in the presence of individual heterogeneity in survival probability, the proportion of high‐survival individuals increases with age. This increase can mask a senescence‐related decrease in survival probability when the probability is estimated at the population level. To accommodate individual heterogeneity we use a mixture model structure (discrete classes of individuals). Second, the study individuals can elude the observers in the field, and their detection rate can be heterogeneous. To account for detectability issues we use capture–mark–recapture (CMR) methodology, mixture models and data that provide information on individuals’ detectability. Last, emigration to non‐monitored sites can bias survival estimates, because it can occur at the end of the individuals’ histories and mimic earlier death. To model emigration we use Markovian transitions to and from an unobservable state. These different model structures are merged together using hidden Markov chain CMR models, or multievent models. Simulation studies illustrate that reliable evidence for survival senescence can be obtained using highly heterogeneous data from non site‐faithful individuals. We then design a tailored application for a dataset from a colony of black‐headed gull Chroicocephalus ridibundus. Survival probabilities do not appear individually variable, but evidence for survival senescence becomes significant only when accounting for other sources of heterogeneity. This result suggests that not accounting for heterogeneity leads to flawed inference and/or that emigration heterogeneity mimics survival heterogeneity and biases senescence estimates.     

Systematic discovery of drug interaction mechanisms

Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome‐wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions.     

History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement

We propose an evolutionary scenario that could have shaped the modern Arabidopsis thaliana genome, which began with the reduction in chromosome number from n=8 to n=5 in the past 4 million to 5 million years as a result of chromosome fusion. The scenario also includes three ancient polyploidizations: the most recent occurred in an early Brassicaceae with n=4 chromosomes 24 million to 40 million years ago. The two other polyploidizations occurred after the emergence of the Eudicots and the Angiosperms, respectively. Angiosperm evolution includes recurrent cycles of genome duplication and gene and chromosome reorganizations.