Viruses often coinfect single host organisms in nature. Depending on the combination of viruses in such coinfections, the interplay between them may be synergistic, apparently neutral with no effect on each other, or antagonistic. RNA silencing is responsible for many cases of interference or cross-protection between viruses, but such antagonistic...

The first stages of productive bacteriophage infections of bacterial host cells require efficient adsorption to the cell surface followed by ejection of phage DNA into the host cytoplasm. To achieve this goal, a phage virion must undergo significant structural remodeling. For phage T4, the most obvious change is the contraction...

Midbrain dopaminergic (mDA) neurons are implicated in cognitive functions, neuropsychiatric disorders, and pathological conditions; hence understanding genes regulating their homeostasis has medical relevance. Transcription factors FOXA1 and FOXA2 (FOXA1/2) are key determinants of mDA neuronal identity during development, but their roles in adult mDA neurons are unknown. We used a...

Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young...

Increasingly, evidence argues that many neurodegenerative diseases, including progressive supranuclear palsy (PSP), are caused by prions, which are alternatively folded proteins undergoing self-propagation. In earlier studies, PSP prions were detected by infecting human embryonic kidney (HEK) cells expressing a tau fragment [TauRD(LM)] fused to yellow fluorescent protein (YFP). Here, we...

F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have...

IMMUNOLOGY AND INFLAMMATION Correction for “Inducible RNAi in vivo reveals that the transcription factor BATF is required to initiate but not maintain CD8+ T-cell effector differentiation,” by Jernej Godec, Glenn S. Cowley, R. Anthony Barnitz, David E. Root, Arlene H. Sharpe, and W. Nicholas Haining, which appeared in issue 2,...

NEUROSCIENCE Correction for “Fluid intelligence loss linked to restricted regions of damage within frontal and parietal cortex,” by Alexandra Woolgar, Alice Parr, Rhodri Cusack, Russell Thompson, Ian Nimmo-Smith, Teresa Torralva, Maria Roca, Nagui Antoun, Facundo Manes, and John Duncan, which appeared in issue 33, August 17, 2010, of Proc Natl...

NEUROSCIENCE Correction for “Selectivity for the configural cues that identify the gender, ethnicity, and identity of faces in human cortex,” by Minna Ng, Vivian M. Ciaramitaro, Stuart Anstis, Geoffrey M. Boynton, and Ione Fine, which appeared in issue 51, December 19, 2006, of Proc Natl Acad Sci USA (103:19552–19557; first...

BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction to Supporting Information for “Homologous ligands accommodated by discrete conformations of a buried cavity,” by Matthew Merski, Marcus Fischer, Trent E. Balius, Oliv Eidam, and Brian K. Shoichet, which appeared in issue 16, April 21, 2015, of Proc Natl Acad Sci USA (112:5039–5044; first published...

Microbiomes and risk of preterm birth Microbiomes might indicate risk of preterm birth. Image courtesy of iStockphoto/Eraxion. Preterm birth, which occurs before 37 weeks of gestation, afflicts 11% of pregnant women worldwide and has been inconclusively tied to the relative abundances of microbes in and on the human body. In...

The paper by Ozawa et al. (1) presents numerical results for the configurational entropy density, sc, of a model glass-forming liquid in the presence of random pinning. The location of a “phase boundary” in the pin density (c) − temperature (T) plane, which separates an “ideal glass” phase from the...

In their letter, Chakrabarty et al. (1) point out that their data on the relaxation dynamics are inconsistent with the thermodynamic data presented in our paper (2). They argue that from their results and the predictions of the random first-order transition theory (3) one must conclude that our configurational entropy...

Booth and Doolittle (1) criticize three supposed flaws in our argument (2) that the energetic advantage of mitochondria enabled the prokaryote to eukaryote transition. Their critique, not our paper, is flawed. A reply is in order. First, Booth and Doolittle (1) claim that our paper (2) argued that the energetic...

In their letter, Lane and Martin (1) take us to task for our treatment (2) of their earlier paper (3). In that paper (3), there is much about genes, albeit mostly about the cost of their expression, not their replication. The focus is on how many additional genes mitochondria allow...

Proteins catalyze crucial reactions via unstable, high-energy chemical intermediates. In the absence of physiological substrates, activated redox cofactors become ticking time bombs, capable of producing oxidative damage to the protein. In PNAS, Gray and Winkler (1) propose that chains of tryptophan (Trp) and tyrosine (Tyr) residues may serve as escape...

Although Pacific salmon never swim within 2,000 km of the equatorial Pacific Ocean, this does not mean they are beyond the reach of El Niño and the Southern Oscillation (ENSO). Pacific salmon habitats are subject to robust long-distance climate linkages; tropical ENSO indicators are well correlated with the dominant pattern...

The world of 120 million years ago was one of dynamic biological processes. During that time the flowering plants emerged as the dominant global floristic element, a transformative event that ultimately altered the character of the entire planet. Understandably, the rapid rise of angiosperms has intrigued paleoecologists and evolutionary biologists,...

“He will win who knows when to fight and when not to fight.” ― Sun Tzu, The Art of War, circa 500 BC (1) Microbes are remarkably social. They live in complex, interdependent communities where they share and exchange a variety of beneficial compounds ranging from cell−cell signals to iron-scavenging...

The trillions of bacteria that make up the human microbiome are believed to encode functions that are important to human health; however, little is known about the specific effectors that commensal bacteria use to interact with the human host. Functional metagenomics provides a systematic means of surveying commensal DNA for...