Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists

Comparative genomics has proven a fruitful approach to acquire many functional and evolutionary insights into core cellular processes. Here it is argued that in order to perform accurate and interesting comparative genomics, one first and foremost has to be able to recognize, postulate, and revise different evolutionary scenarios. After all, these studies lack a simple protocol, due to different proteins having different evolutionary dynamics and demanding different approaches. The authors here discuss this challenge from a practical (what are the observations?) and conceptual (how do these indicate a specific evolutionary scenario?) viewpoint, with the aim to guide investigators who want to analyze the evolution of their protein(s) of interest. By sharing how the authors draft, test, and update such a scenario and how it directs their investigations, the authors hope to illuminate how to execute molecular evolution studies and how to interpret them. Also see the video abstract here https://youtu.be/VCt3l2pbdbQ .     

Asymptomatic Middle East Respiratory Syndrome Coronavirus Infection in Rabbits

The ability of Middle East respiratory syndrome coronavirus (MERS-CoV) to infect small animal species may be restricted given the fact that mice, ferrets, and hamsters were shown to resist MERS-CoV infection. We inoculated rabbits with MERS-CoV. Although virus was detected in the lungs, neither significant histopathological changes nor clinical symptoms were observed. Infectious virus, however, was excreted from the upper respiratory tract, indicating a potential route of MERS-CoV transmission in some animal species.     

Connexins: substrates and regulators of autophagy

Connexins mediate intercellular communication by assembling into hexameric channel complexes that act as hemichannels and gap junction channels. Most connexins are characterized by a very rapid turn-over in a variety of cell systems. The regulation of connexin turn-over by phosphorylation and ubiquitination events has been well documented. Moreover, different pathways have been implicated in connexin degradation, including proteasomal and lysosomal-based pathways. Only recently, autophagy emerged as an important connexin-degradation pathway for different connexin isoforms. As such, conditions well known to induce autophagy have an immediate impact on the connexin-expression levels. This is not only limited to experimental conditions but also several pathophysiological conditions associated with autophagy (dys)function affect connexin levels and their presence at the cell surface as gap junctions. Finally, connexins are not only substrates of autophagy but also emerge as regulators of the autophagy process. In particular, several connexin isoforms appear to recruit pre-autophagosomal autophagy-related proteins, including Atg16 and PI3K-complex components, to the plasma membrane, thereby limiting their availability and capacity for regulating autophagy.

     

Identification of CANT1 Mutations in Desbuquois Dysplasia

Desbuquois dysplasia is a severe condition characterized by short stature, joint laxity, scoliosis, and advanced carpal ossification with a delta phalanx. Studying nine Desbuquois families, we identified seven distinct mutations in the Calcium-Activated Nucleotidase 1 gene (CANT1), which encodes a soluble UDP-preferring nucleotidase belonging to the apyrase family. Among the seven mutations, four were nonsense mutations (Del 5′ UTR and exon 1, p.P245RfsX3, p.S303AfsX20, and p.W125X), and three were missense mutations (p.R300C, p.R300H, and p.P299L) responsible for the change of conserved amino acids located in the seventh nucleotidase conserved region (NRC). The arginine substitution at position 300 was identified in five out of nine families. The specific function of CANT1 is as yet unknown, but its substrates are involved in several major signaling functions, including Ca²⁺ release, through activation of pyrimidinergic signaling. Importantly, using RT-PCR analysis, we observed a specific expression in chondrocytes. We also found electron-dense material within distended rough endoplasmic reticulum in the fibroblasts of Desbuquois patients. Our findings demonstrate the specific involvement of a nucleotidase in the endochondral ossification process.     

Predicted insect diversity declines under climate change in an already impoverished region

Being ectotherms, insects are predicted to suffer more severely from climate change than warm-blooded animals. We forecast possible changes in diversity and composition of butterflies, grasshoppers and dragonflies in Belgium under increasingly severe climate change scenarios for the year 2100. Two species distribution modelling techniques (Generalised Linear Models and Generalised Additive Models), were combined via a conservative version of the ensemble forecasting strategy to predict present-day and future species distributions, considering the species as potentially present only if both modelling techniques made such a prediction. All models applied were fair to good, according to the AUC (area under the curve of the receiver operating characteristic plot), sensitivity and specificity model performance measures based on model evaluation data. Butterfly and grasshopper diversity were predicted to decrease significantly in all scenarios and species-rich locations were predicted to move towards higher altitudes. Dragonfly diversity was predicted to decrease significantly in all scenarios, but dragonfly-rich locations were predicted to move upwards only in the less severe scenarios. The largest turnover rates were predicted to occur at higher altitudes for butterflies and grasshoppers, but at intermediate altitudes for dragonflies. Our results highlight the challenge of building conservation strategies under climate change, because the changes in the sites important for different groups will not overlap, increasing the area needed for protection. We advocate that possible conservation and policy measures to mitigate the potentially strong impacts of climate change on insect diversity in Belgium should be much more pro-active and flexible than is the case presently.     

Adenosine Deaminase Acts as a Natural Antagonist for Dipeptidyl Peptidase 4-Mediated Entry of the Middle East Respiratory Syndrome Coronavirus

Middle East respiratory syndrome coronavirus (MERS-CoV) replicates in cells of different species using dipeptidyl peptidase 4 (DPP4) as a functional receptor. Here we show the resistance of ferrets to MERS-CoV infection and inability of ferret DDP4 to bind MERS-CoV. Site-directed mutagenesis of amino acids variable in ferret DPP4 thus revealed the functional human DPP4 virus binding site. Adenosine deaminase (ADA), a DPP4 binding protein, competed for virus binding, acting as a natural antagonist for MERS-CoV infection.     

How to Use Secondary Data on Seafood Contamination for Probabilistic Exposure Assessment Purposes? Main Problems and Potential Solutions

Seafood consumption is related to both favorable health benefits of nutrients and to potential adverse health impacts of chemical contamination. To quantify the magnitude of this dilemma, probabilistic intake assessments can be performed. One step in such a procedure involves the determination of nutrient and contaminant concentrations in seafood for which data need to be collected. This article describes the process of building up a database containing previously published contaminant concentrations in seafood, and defining input distributions characterizing the variability. During the constitution of the database, several problems influencing the comparability of the data were encountered related to (1) sampling plans of the published data; (2) sample handling prior to analysis; (3) analytical methodologies; (4) the format of reporting results; and (5) missing data. Different solutions for these methodological problems have been developed. Contaminant concentrations ranges per gram fresh weight of 2.4–4390.0 ng for mercury, 0.1–5736.6 ng for the sum of indicator PCB, 0.002–115.000 pg TEQ for the sum of all PCBs, 0.002–34.400 pg TEQ for dioxins, and 0.006–126.000 pg TEQ for total of dioxin-like compounds were found. This work confirms that more guidelines are needed to standardize the analytical methodologies to be used and the format for result reporting in order to improve the comparability of data critical to conduct a human intake and risk-benefit assessment.