Comparison of the Proteomes of Three Yeast Wild Type Strains: CEN.PK2, FY1679 and W303

Yeast deletion strains created during gene function analysis projects very often show drastic phenotypic differences depending on the genetic background used. These results indicate the existence of important molecular differences between the CEN.PK2, FY1679 and W303 wild type strains. To characterise these differences we have compared the protein expression levels between CEN.PK2, FY1679 and W303 strains using twodimensional gel electrophoresis and identified selected proteins by mass spectrometric analysis. We have found that FY1679 and W303 strains are more similar to each other than to the CEN.PK2 strain. This study identifies 62 proteins that are differentially expressed between the strains and provides a valuable source of data for the interpretation of yeast mutant phenotypes observed in CEN.PK2, FY1679 and W303 strains

Retrospective Loss: Looking Back to Improve Training of Deep Neural Networks

Deep neural networks (DNNs) are powerful learning machines that have enabled breakthroughs in several domains. In this work, we introduce a new retrospective loss to improve the training of deep neural network models by utilizing the prior experience available in past model states during training. Minimizing the retrospective loss, along with the task-specific loss, pushes the parameter state at the current training step towards the optimal parameter state while pulling it away from the parameter state at a previous training step. Although a simple idea, we analyze the method as well as to conduct comprehensive sets of experiments across domains - images, speech, text, and graphs - to show that the proposed loss results in improved performance across input domains, tasks, and architectures.Comment: Accepted at KDD 2020; The first two authors contributed equall

Biomechanics of ramp descent in unilateral trans-tibial amputees: Comparison of a microprocessor controlled foot with conventional ankle–foot mechanisms

yesBackground Walking down slopes and/or over uneven terrain is problematic for unilateral trans-tibial amputees. Accordingly, ‘ankle’ devices have been added to some dynamic-response feet. This study determined whether use of a microprocessor controlled passive-articulating hydraulic ankle–foot device improved the gait biomechanics of ramp descent in comparison to conventional ankle–foot mechanisms. Methods Nine active unilateral trans-tibial amputees repeatedly walked down a 5° ramp, using a hydraulic ankle–foot with microprocessor active or inactive or using a comparable foot with rubber ball-joint (elastic) ‘ankle’ device. When inactive the hydraulic unit's resistances were those deemed to be optimum for level-ground walking, and when active, the plantar- and dorsi-flexion resistances switched to a ramp-descent mode. Residual limb kinematics, joints moments/powers and prosthetic foot power absorption/return were compared across ankle types using ANOVA. Findings Foot-flat was attained fastest with the elastic foot and second fastest with the active hydraulic foot (P < 0.001). Prosthetic shank single-support mean rotation velocity (p = 0.006), and the flexion (P < 0.001) and negative work done at the residual knee (P = 0.08) were reduced, and negative work done by the ankle–foot increased (P < 0.001) when using the active hydraulic compared to the other two ankle types. Interpretation The greater negative ‘ankle’ work done when using the active hydraulic compared to other two ankle types, explains why there was a corresponding reduction in flexion and negative work at the residual knee. These findings suggest that use of a microprocessor controlled hydraulic foot will reduce the biomechanical compensations used to walk down slopes

Opportunities for behavioral rescue under rapid environmental change

Laboratory measurements of physiological and demographic tolerances are important in understanding the impact of climate change on species diversity; however, it has been recognized that forecasts based solely on these laboratory estimates overestimate risk by omitting the capacity for species to utilize microclimatic variation via behavioral adjustments in activity patterns or habitat choice. The complex, and often context‐dependent nature, of microclimate utilization has been an impediment to the advancement of general predictive models. Here, we overcome this impediment and estimate the potential impact of warming on the fitness of ectotherms using a benefit/cost trade‐off derived from the simple and broadly documented thermal performance curve and a generalized cost function. Our framework reveals that, for certain environments, the cost of behavioral thermoregulation can be reduced as warming occurs, enabling behavioral buffering (e.g., the capacity for behavior to ameliorate detrimental impacts) and “behavioral rescue” from extinction in extreme cases. By applying our framework to operative temperature and physiological data collected at an extremely fine spatial scale in an African lizard, we show that new behavioral opportunities may emerge. Finally, we explore large‐scale geographic differences in the impact of behavior on climate‐impact projections using a global dataset of 38 insect species. These multiple lines of inference indicate that understanding the existing relationship between thermal characteristics (e.g., spatial configuration, spatial heterogeneity, and modal temperature) is essential for improving estimates of extinction risk

Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.

A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible for MRSA infections worldwide, and those of different lineages carry unique Type I restriction-modification (RM) variants. We have identified the specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and ST239. We experimentally demonstrate that this RM system is sufficient to block horizontal gene transfer between clinically important MRSA, confirming the bioinformatic evidence that each lineage is evolving independently. Target sites are distributed randomly in S. aureus genomes, except in a set of large conjugative plasmids encoding resistance genes that show evidence of spreading between two successful MRSA lineages. This analysis of the identification and distribution of target sites explains evolutionary patterns in a pathogenic bacterium. We show that a lack of specific target sites enables plasmids to evade the Type I RM system thereby contributing to the evolution of increasingly resistant community and hospital MRSA