The Interplay between Scientific Overlap and Cooperation and the Resulting Gain in Co-Authorship Interactions

Considering the importance of scientific interactions, understanding the principles that govern fruitful scientific research is crucial to policy makers and scientists alike. The outcome of an interaction is to a large extent dependent on the balancing of contradicting motivations accompanying the establishment of collaborations. Here, we assembled a dataset of nearly 20,000 publications authored by researchers affiliated with ten top universities. Based on this data collection, we estimated the extent of different interaction types between pairwise combinations of researchers. We explored the interplay between the overlap in scientific interests and the tendency to collaborate, and associated these estimates with measures of scientific quality and social accessibility aiming at studying the typical resulting gain of different interaction patterns. Our results show that scientists tend to collaborate more often with colleagues with whom they share moderate to high levels of mutual interests and knowledge while cooperative tendency declines at higher levels of research-interest overlap, suggesting fierce competition, and at the lower levels, suggesting communication gaps. Whereas the relative number of alliances dramatically differs across a gradient of research overlap, the scientific impact of the resulting articles remains similar. When considering social accessibility, we find that though collaborations between remote researchers are relatively rare, their quality is significantly higher than studies produced by close-circle scientists. Since current collaboration patterns do not necessarily overlap with gaining optimal scientific quality, these findings should encourage scientists to reconsider current collaboration strategies.     

PfSR1 controls alternative splicing and steady‐state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs

Plasmodium species have evolved complex biology to adapt to different hosts and changing environments throughout their life cycle. Remarkably, these adaptations are achieved by a relatively small genome. One way by which the parasite expands its proteome is through alternative splicing (AS). We recently identified PfSR1 as a bona fide Ser/Arg‐rich (SR) protein that shuttles between the nucleus and cytoplasm and regulates AS in Plasmodium falciparum. Here we show that PfSR1 is localized adjacent to the Nuclear Pore Complex (NPC) clusters in the nucleus of early stage parasites. To identify the endogenous RNA targets of PfSR1, we adapted an inducible overexpression system for tagged PfSR1 and performed RNA immunoprecipitation followed by microarray analysis (RIP‐chip) to recover and identify the endogenous RNA targets that bind PfSR1. Bioinformatic analysis of these RNAs revealed common sequence motifs potentially recognized by PfSR1. RNA‐EMSAs show that PfSR1 preferentially binds RNA molecules containing these motifs. Interestingly, we find that PfSR1 not only regulates AS but also the steady‐state levels of mRNAs containing these motifs in vivo.     

Increasing global agricultural production by reducing ozone damages via methane emission controls and ozone‐resistant cultivar selection

Meeting the projected 50% increase in global grain demand by 2030 without further environmental degradation poses a major challenge for agricultural production. Because surface ozone (O₃) has a significant negative impact on crop yields, one way to increase future production is to reduce O₃‐induced agricultural losses. We present two strategies whereby O₃ damage to crops may be reduced. We first examine the potential benefits of an O₃ mitigation strategy motivated by climate change goals: gradual emission reductions of methane (CH₄), an important greenhouse gas and tropospheric O₃ precursor that has not yet been targeted for O₃ pollution abatement. Our second strategy focuses on adapting crops to O₃ exposure by selecting cultivars with demonstrated O₃ resistance. We find that the CH₄ reductions considered would increase global production of soybean, maize, and wheat by 23–102 Mt in 2030 – the equivalent of a ~2–8% increase in year 2000 production worth $3.5–15 billion worldwide (USD₂₀₀₀), increasing the cost effectiveness of this CH₄ mitigation policy. Choosing crop varieties with O₃ resistance (relative to median‐sensitivity cultivars) could improve global agricultural production in 2030 by over 140 Mt, the equivalent of a 12% increase in 2000 production worth ~$22 billion. Benefits are dominated by improvements for wheat in South Asia, where O₃‐induced crop losses would otherwise be severe. Combining the two strategies generates benefits that are less than fully additive, given the nature of O₃ effects on crops. Our results demonstrate the significant potential to sustainably improve global agricultural production by decreasing O₃‐induced reductions in crop yields.     

Association between translation efficiency and horizontal gene transfer within microbial communities

Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an additional central barrier to HGT-the lack of co-adaptation between the codon usage of the transferred gene and the tRNA pool of the recipient organism. Analyzing the genomic sequences of more than 190 microorganisms and the HGT events that have occurred between them, we show that the number of genes that were horizontally transferred between organisms is positively correlated with the similarity between their tRNA pools. Those genes that are better adapted to the tRNA pools of the target genomes tend to undergo more frequent HGT. At the community (or environment) level, organisms that share a common ecological niche tend to have similar tRNA pools. These results remain significant after controlling for diverse ecological and evolutionary parameters. Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them. Similar tRNA pools between a donor and a host tend to increase the probability that a horizontally acquired gene will become fixed in its new genome. Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.     

A novel postpriming regulatory check point of effector/memory T cells dictated through antigen density threshold-dependent anergy

CTLs act as the effector arm of the cell-mediated immune system to kill undesirable cells. Two processes regulate these effector cells to prevent self reactivity: a thymic selection process that eliminates autoreactive clones and a multistage activation or priming process that endows them with a license to kill cognate target cells. Hitherto no subsequent regulatory restrictions have been ascribed for properly primed and activated CTLs that are licensed to kill. In this study we show that CTLs possess a novel postpriming regulatory mechanism(s) that influences the outcome of their encounter with cognate target cells. This mechanism gauges the degree of Ag density, whereupon reaching a certain threshold significant changes occur that induce anergy in the effector T cells. The biological consequences of this Ag-induced postpriming control includes alterations in the expression of cell surface molecules that control immunological synapse activity and cytokine profiles and induce retarded cell proliferation. Most profound is genome-wide microarray analysis that demonstrates changes in the expression of genes related to membrane potential, TCR signal transduction, energy metabolism, and cell cycle control. Thus, a discernible and unique gene expression signature for anergy as a response to high Ag density has been observed. Consequently, activated T cells possess properties of a self-referential sensory organ. These studies identify a new postpriming control mechanism of CTL with anergenic-like properties. This mechanism extends our understanding of the control of immune function and regulation such as peripheral tolerance, viral infections, antitumor immune responses, hypersensitivity, and autoimmunity.     

A Tradeoff in the Neural Code across Regions and Species

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Amberlite IR-120 Modified with 8-Hydroxyquinoline as Efficient Adsorbent for Solid-Phase Extraction and Flame Atomic Absorption Determination of Trace Amounts of Some Metal Ions

In this study, a solid-phase extraction method combined with atomic absorption spectrometry for extraction, preconcentration, and determination of iron (Fe³⁺), copper (Cu²⁺), and lead (Pb²⁺) ions at trace levels in water samples has been reported. The influences of effective parameters such as flow rate, pH, eluent conditions (type, volume, and concentration), sample volumes, and interference of matrix ions on metal ions recoveries were studied. Under optimized conditions, the limits of detection were found in the range of 0.7–2.2 μg L⁻¹, while preconcentration factors for Fe³⁺, Cu²⁺, and Pb²⁺ ions were found to be 166, 200, and 250, respectively, and loading half time (t _1/2) values were less than 2 min for all analyte ions. The proposed procedure was applied for the determination of metal ions in different water samples with recovery of >94.4% and relative standard deviation less than 4.4% for N = 5.     

Ce-emerin and LEM-2: essential roles in Caenorhabditis elegans development, muscle function, and mitosis

Emerin and LEM2 are ubiquitous inner nuclear membrane proteins conserved from humans to Caenorhabditis elegans. Loss of human emerin causes Emery-Dreifuss muscular dystrophy (EDMD). To test the roles of emerin and LEM2 in somatic cells, we used null alleles of both genes to generate C. elegans animals that were either hypomorphic (LEM-2-null and heterozygous for Ce-emerin) or null for both proteins. Single-null and hypomorphic animals were viable and fertile. Double-null animals used the maternal pool of Ce-emerin to develop to the larval L2 stage, then arrested. Nondividing somatic cell nuclei appeared normal, whereas dividing cells had abnormal nuclear envelope and chromatin organization and severe defects in postembryonic cell divisions, including the mesodermal lineage. Life span was unaffected by loss of Ce-emerin alone but was significantly reduced in LEM-2-null animals, and double-null animals had an even shorter life span. In addition to striated muscle defects, double-null animals and LEM-2-null animals showed unexpected defects in smooth muscle activity. These findings implicate human LEM2 mutations as a potential cause of EDMD and further suggest human LEM2 mutations might cause distinct disorders of greater severity, since C. elegans lacking only LEM-2 had significantly reduced life span and smooth muscle activity.     

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

The evolutionary origins of genetic robustness are still under debate: it may arise as a consequence of requirements imposed by varying environmental conditions, due to intrinsic factors such as metabolic requirements, or directly due to an adaptive selection in favor of genes that allow a species to endure genetic perturbations. Stratifying the individual effects of each origin requires one to study the pertaining evolutionary forces across many species under diverse conditions. Here we conduct the first large-scale computational study charting the level of robustness of metabolic networks of hundreds of bacterial species across many simulated growth environments. We provide evidence that variations among species in their level of robustness reflect ecological adaptations. We decouple metabolic robustness into two components and quantify the extents of each: the first, environmental-dependent, is responsible for at least 20% of the non-essential reactions and its extent is associated with the species'' lifestyle (specialized/generalist); the second, environmental-independent, is associated (correlation = ∼0.6) with the intrinsic metabolic capacities of a species—higher robustness is observed in fast growers or in organisms with an extensive production of secondary metabolites. Finally, we identify reactions that are uniquely susceptible to perturbations in human pathogens, potentially serving as novel drug-targets.