An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis

Multiplexed quantitative proteomics using tandem mass tag (TMT) is increasingly used in –omic study of complex samples. While TMT-based proteomics has the advantages of the higher quantitative accuracy, fewer missing values, and reduced instrument analysis time, it is limited by the additional reagent cost. In addition, current TMT labeling workflows involve repeated small volume pipetting of reagents in volatile solvents, which may increase the sample-to-sample variations and is not readily suitable for high throughput applications. In this study, we demonstrated that the TMT labeling procedures could be streamlined by using pre-aliquoted dry TMT reagents in a 96 well plate or 12-tube strip. As little as 50 μg dry TMT per channel was used to label 6–12 μg peptides, yielding high TMT labeling efficiency (∼99%) in both microbiome and mammalian cell line samples. We applied this workflow to analyze 97 samples in a study to evaluate whether ice recrystallization inhibitors improve the cultivability and activity of frozen microbiota. The results demonstrated tight sample clustering corresponding to groups and consistent microbiome responses to prebiotic treatments. This study supports the use of TMT reagents that are pre-aliquoted, dried, and stored for robust quantitative proteomics and metaproteomics in high throughput applications.     

Isoform switching of the sarco(endo)plasmic reticulum Ca2+ pump during differentiation of BC3H1 myoblasts

We have studied the expression of the gene 2 for the sarco(endo)plasmic reticulum Ca2+ pump (SERCA2) in BC3H1 cells. Myogenic differentiation not only activated the SERCA2 expression but it also induced an isoform switch. Undifferentiated myoblasts only expressed the SERCA2b isoform (non-muscle) whereas differentiated myocytes predominantly contained the SERCA2a isoform (cardiac/slow skeletal muscle). The isoform switch was documented by immunoblot analysis with isoform-specific antibodies. This observation was confirmed at the mRNA level by using antisense RNA probes specific for class 1 (SERCA2a) or class 2 (SERCA2b) messengers. The expression of the SERCA2a isoform after differentiation was accompanied by a decreased sensitivity of the Ca2+ uptake in permeabilized cells to the Ca2+ pump inhibitor thapsigargin.     

Who's Watching Me: Female Siamese Fighting Fish Alter Their Interactions in Response to an Audience

It is well established that interactions between conspecifics are often influenced by the presence of passive bystanders. Individuals have been found to alter their behavior in a variety of contexts, from foraging to aggression, based on the presence, sex, or identity of an audience. This audience effect may influence not only the nature of a signaling event but also the evolution of signal structure as signals may have to convey information across a distance. Additionally, audience individuals may use information obtained by watching in later encounters with these individuals, which may act as a selection pressure on communication. Communication networks in Siamese fighting fish, Betta splendens, are particularly well studied, with audience effects influencing both male–male interactions and male–female interactions. However, the effects of an audience on female–female interactions have not been examined in this species or any other. This study examined the interactions of pairs of females in three different audience conditions (male, female, and no audience). The results suggest that female–female interactions are affected by the presence of an audience as interactant‐directed gill flaring, the most commonly performed behavior, was performed more with an audience present. Additionally, the sex of the audience seemed to be influential, reflected by a difference in the frequency of interactant‐directed behaviors when a female vs. a male audience was present. This study is one of the first to demonstrate that females modify their behavior as a result of being watched and stresses the importance of examining audience effects in a variety of social contexts.