PNAS Plus Significance Statements

PNAS April 3, 2018 115 (14) 3524-3528; https://doi.org/10.1073/pnas.ss11514

Agricultural origins on the Anatolian plateau

Douglas Baird, Andrew Fairbairn, Emma Jenkins, Louise Martin, Caroline Middleton, Jessica Pearson, Eleni Asouti, Yvonne Edwards, Ceren Kabukcu, Gökhan Mustafaoğlu, Nerissa Russell, Ofer Bar-Yosef, Geraldine Jacobsen, Xiaohong Wu (吴小红), Ambroise Baker, and Sarah Elliott

We demonstrate that the initial spread of farming outside of the area of its first appearance in the Fertile Crescent of Southwest Asia, into Central Anatolia, involved adoption of cultivars by indigenous foragers and contemporary experimentation in animal herding of local species. This represents a rare clear-cut instance of forager adoption and sustained low-level food production. We have also demonstrated that farming uptake was not uniform, with some forager communities rejecting it despite proximity to early farming communities. We also show that adoption of small-scale cultivation could still have significant social consequences for the communities concerned. The evidence suggests forager adoption of cultivation and initiation of herding was not necessarily motivated by simple economic concerns of increasing levels of food production and security. (See pp. E3077–E3086.)

Live births from artificial insemination of microfluidic-sorted bovine spermatozoa characterized by trajectories correlated with fertility

Maria Portia B. Nagata, Kenji Endo, Kazuko Ogata, Kenichi Yamanaka, Junki Egashira, Naoto Katafuchi, Tadayuki Yamanouchi, Hideo Matsuda, Yuki Goto, Miki Sakatani, Takuo Hojo, Hirofumi Nishizono, Kenji Yotsushima, Naoki Takenouchi, Yutaka Hashiyada, and Kenichi Yamashita

Iatrogenic failures of assisted reproduction technology could be associated with routine sperm preparation techniques. Limitations of conventional sperm selection methods include the inability to efficiently sort functional spermatozoa and assess sperm fertilization potential. We developed a robust microfluidic sperm sorting system by using a diffuser-type microfluidic sperm sorter device capable of ultrahigh-throughput selection and separation of motile, DNA-intact, and functionally competent sperm. The strategy inclusively targeted the intrinsic traits related to fertility and successfully produced livebirths from low-dose insemination of microfluidic sorted spermatozoa. The fertile subpopulation was identified based on the kinetic and trajectory patterns as the sinuous, transitional cohort. The clinical significance of microfluidic sperm sorting is reflected by the established pregnancy and live births of calves. (See pp. E3087–E3096.)

Muscle-tendon length and force affect human tibialis anterior central aponeurosis stiffness in vivo

Brent James Raiteri, Andrew Graham Cresswell, and Glen Anthony Lichtwark

Muscle-force production and energy consumption are highly dependent on stiffness of the connecting tendinous tissues (tendon and aponeurosis). Although reduced tendinous tissue stiffness favors greater elastic energy recovery, it permits muscle fiber shortening during fixed-end contractions, which is economically unfavorable for force production. Here, we provide in vivo evidence that the longitudinal central aponeurosis stiffness of human tibialis anterior increases not only with force but also with muscle-tendon unit length. Such a mechanism is likely to be beneficial for different movement scenarios for a range of lower limb muscles. These findings are important for interpreting and modeling muscle-force production and energy consumption during movement and understanding muscle and tendon injury mechanics. (See pp. E3097–E3105.)

Immunization with outer membrane vesicles displaying conserved surface polysaccharide antigen elicits broadly antimicrobial antibodies

Taylor C. Stevenson, Colette Cywes-Bentley, Tyler D. Moeller, Kevin B. Weyant, David Putnam, Yung-Fu Chang, Bradley D. Jones, Gerald B. Pier, and Matthew P. DeLisa

A broad range of bacterial, fungal, and protozoan cells produce the surface polysaccharide poly-N-acetyl-d-glucosamine (PNAG), making this antigen an attractive target for vaccination against multiple human and economically important animal pathogens. While conjugate vaccines involving surface polysaccharides, such as PNAG, are a proven strategy for reducing the incidence of disease caused by bacterial pathogens, their manufacture is technically demanding, inefficient, and expensive, thereby limiting their widespread adoption. Here, we describe an alternative route to producing PNAG-containing glycoconjugates, whereby recombinant PNAG biosynthesis is coordinated with outer membrane vesicle formation in nonpathogenic Escherichia coli strains. The resulting glycosylated outer membrane vesicles effectively deliver PNAG antigens to the immune system while bypassing many of the drawbacks of conventional conjugate vaccines. (See pp. E3106–E3115.)

Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses

Yan-Jiun Lee, Nan Dai, Shannon E. Walsh, Stephanie Müller, Morgan E. Fraser, Kathryn M. Kauffman, Chudi Guan, Ivan R. Corrêa Jr., and Peter R. Weigele

Bacterial viruses (bacteriophages) append a variety of molecules, including sugars, amino acids, and polyamines, to the nucleobases of their genomic DNA to circumvent the endonuclease-based defenses of their hosts. These DNA hypermodifications are formed through bacteriophage-encoded biosynthetic pathways, with steps occurring before and after replication of bacteriophage DNA. We report here the discovery of two thymidine hypermodifications: 5-(2-aminoethoxy)methyluridine replacing 40% of thymidine nucleotides in the Salmonella phage ViI and 5-(2-aminoethyl)uridine replacing 30% of thymidine in the DNA of the Pseudomonas phage M6. Additionally, we show in vitro reconstitution of 5-(2-aminoethyl)uridine biosynthesis from five recombinantly expressed proteins. These findings reveal an expanded diversity in the types of naturally occurring DNA modifications and their biosynthetic pathways. (See pp. E3116–E3125.)

Coordination to lanthanide ions distorts binding site conformation in calmodulin

Sean C. Edington, Andrea Gonzalez, Thomas R. Middendorf, D. Brent Halling, Richard W. Aldrich, and Carlos R. Baiz

Calmodulin is essential to life in all eukaryotic cells and serves as a popular model for ion binding and activation in proteins. Calmodulin transduces complex calcium signals and acts on hundreds of effector proteins, but the sensitivity and complexity of this process make it difficult to characterize. Much work uses lanthanides as luminescent calcium substitutes to study ion binding and activation in calmodulin and other proteins. Using ultrafast 2D IR spectroscopy, we show that lanthanide ions perturb the finely tuned structure and dynamics of calmodulin’s binding sites. The temporal and spatial resolution of our measurements opens a new window into the study of protein−ion binding and demonstrates that seemingly innocuous ligand substitutions can significantly alter protein conformation. (See pp. E3126–E3134.)

Protonation state of inhibitors determines interaction sites within voltage-gated sodium channels

Amanda Buyan, Delin Sun, and Ben Corry

Voltage-gated sodium channels are integral in electrical signaling within the human body and are key targets for anesthetics and antiepileptic compounds used in surgeries and the treatment of neurological disorders. We have used molecular simulations to determine where a number of these compounds bind inside the pore of a voltage-gated sodium channel to aid the design of new compounds for treating chronic pain, heart conditions, and epilepsy. We uncover two distinct binding sites inside the pore harnessed by neutral and charged drugs, respectively. This explains why so many anesthetic compounds have both neutral and charged forms: The neutral form more easily enters the pore, but the charged form binds more tightly to effectively block the pore and prevent electrical signaling. (See pp. E3135–E3144.)

Conformation-dependent partitioning of yeast nutrient transporters into starvation-protective membrane domains

Christos Gournas, Stelios Gkionis, Mélanie Carquin, Laure Twyffels, Donatienne Tyteca, and Bruno André

The plasma membrane of eukaryotic cells is compartmentalized into domains enriched in specific lipids and proteins. However, our understanding of the mechanisms and functions of this lateral segregation remains incomplete. Here, we show that the clustering of the yeast Can1 arginine transporter into domains is dictated by its conformation and requires sustained biogenesis of complex sphingolipids. Furthermore, this clustering confers to Can1 and other transporters protection from ubiquitin-dependent endocytosis. Under nutrient-starvation conditions, this protective role is reinforced, thereby allowing cells to preserve a fraction of their nutrient transporters from bulk endocytosis and to more efficiently resume growth when replenishing compounds are available. Our study reveals nutrient-regulated protection from endocytosis as an important role for protein partitioning into membrane domains. (See pp. E3145–E3154.)

Dimeric sorting code for concentrative cargo selection by the COPII coat

Chao Nie (聂超), Huimin Wang (王惠敏), Rui Wang (王锐), David Ginsburg, and Xiao-Wei Chen (陈晓伟)

One-third of the mammalian genome encodes proteins that are transported by the secretory pathway. Coat protein complexes such as COPII generate carrier vesicles and recruit cargos, orchestrated by cognate small GTPases as “molecular switches.” How coat complexes select specific cargos remains incompletely understood. Here we applied proximity-dependent biotinylation, fusing the promiscuous biotin ligase BirA* with the SAR1B GTPase, to track the dynamics of COPII-mediated export from the endoplasmic reticulum. LMAN1, a cargo receptor for COPII, is transiently enriched and released by the coat complex. The enrichment requires a dimeric sorting signal, formed by two copies of LMAN1. Hence, the COPII coat undergoes a dynamic engaging–disengaging cycle to select unique sets of secretory cargos. (See pp. E3155–E3162.)

A pex1 missense mutation improves peroxisome function in a subset of Arabidopsis pex6 mutants without restoring PEX5 recycling

Kim L. Gonzalez, Sarah E. Ratzel, Kendall H. Burks, Charles H. Danan, Jeanne M. Wages, Bethany K. Zolman, and Bonnie Bartel

ATPases have diverse cellular roles, including extracting proteins from membranes to maintain organellar function. The PEX1–PEX6 heterohexameric ATPases are thought to retrotranslocate PEX5 from the peroxisome membrane, and PEX1–PEX6 dysfunction impairs peroxisome biogenesis in humans and plants. We implemented a pex6 suppressor screen in Arabidopsis and recovered a compensatory pex1 allele that rescues several pex6 defects. Preventing autophagy also improved pex6 peroxisome function, and combining the pex1 and autophagy lesions delivered synergistic benefits. Surprisingly, these different alterations ameliorated pex6 symptoms without notably restoring the sole known function of PEX6, suggesting that PEX1–PEX6 has unexplored functions. Because the pex6 mutations ameliorated by pex1 are analogous to those in human pex6 patients, this study informs research on peroxisome dysfunction in other eukaryotes. (See pp. E3163–E3172.)

PDGFRα+ pericryptal stromal cells are the critical source of Wnts and RSPO3 for murine intestinal stem cells in vivo

Gediminas Greicius, Zahra Kabiri, Kristmundur Sigmundsson, Chao Liang, Ralph Bunte, Manvendra K. Singh, and David M. Virshup

Tissue stem cells in vivo reside in highly structured niches that provide signals for proliferation and differentiation. Understanding the role of the niche requires identifying the key cell types that provide these regulators. In the intestine, R-spondins and Wnts are essential regulators of the stem-cell niche. Here we identify subepithelial myofibroblasts of the PDGF receptor α lineage as the specific stromal cell type that secretes these ligands. These data demonstrate the close interaction between epithelial stem cells and the underlying regulatory stroma niche and provide insights into both normal homeostasis and tissue recovery after injury. (See pp. E3173–E3181.)

Division-independent differentiation mandates proliferative competition among stem cells

Amy Reilein, David Melamed, Simon Tavaré, and Daniel Kalderon

Adult stem cells support tissue maintenance throughout life, but they also can be cells of origin for cancer, allowing clonal expansion and long-term maintenance of the first oncogenic mutations. We considered how a mutation that increases the proliferation rate of a stem cell would affect the probability of its competitive survival and amplification for different potential organizations of stem cells. Quantitative modeling showed that the key characteristic predicting the impact of relative proliferation rate on competition is whether differentiation of a stem cell is coupled to its division. We then used Drosophila follicle stem cells to provide definitive experimental evidence for the general prediction that relative proliferation rates dictate stem cell competition specifically for stem cells that exhibit division-independent differentiation. (See pp. E3182–E3191.)

Population trends in Vermivora warblers are linked to strong migratory connectivity

Gunnar R. Kramer, David E. Andersen, David A. Buehler, Petra B. Wood, Sean M. Peterson, Justin A. Lehman, Kyle R. Aldinger, Lesley P. Bulluck, Sergio Harding, John A. Jones, John P. Loegering, Curtis Smalling, Rachel Vallender, and Henry M. Streby

Identifying drivers of population trends in migratory animals is difficult due to their reliance on different geographic regions throughout the annual cycle. Populations of Nearctic–Neotropical migratory birds are often thought to be limited by spatial variation in factors affecting reproduction and survival during the breeding season. We tracked individual songbirds from a two-species complex of New World warblers and discovered unequivocal evidence of a system in which strong associations between breeding areas and nonbreeding areas (i.e., migratory connectivity) is concordant with breeding population trends. The strong migratory connectivity we documented is associated with differential rates of land-use change in population-specific nonbreeding areas. Our results suggest that other migratory species with similar population trends may also exhibit strong migratory connectivity. (See pp. E3192–E3200.)

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity

Arunkumar Krishnan, Lakshminarayan M. Iyer, Stephen J. Holland, Thomas Boehm, and L. Aravind

Mutagenic AID/APOBEC deaminases (AADs) are central to processes such as generation of antibody diversity and antiviral defense in vertebrates. Their presence and role outside vertebrates are poorly characterized. We report the discovery of several AADs, including some that are secreted, across diverse metazoan, dictyosteliid, and algal lineages. They appear to have emerged from an early transfer of an AAD from bacterial toxin systems, followed by extensive diversification into multiple eukaryotic clades, showing dramatic structural innovation, rapid divergence, gene loss, polymorphism, and lineage-specific expansions. We uncover evidence for their divergence in arms-race scenarios with viruses and genomic retroelements and show that AAD-based nucleic acid mutagenesis as a basis of immune defense is widespread across metazoa, slime molds, and algae. (See pp. E3201–E3210.)

Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys

Stephen J. Holland, Lesley M. Berghuis, Justin J. King, Lakshminarayan M. Iyer, Katarzyna Sikora, Heather Fifield, Sarah Peter, Emma M. Quinlan, Fumiaki Sugahara, Prashant Shingate, Inês Trancoso, Norimasa Iwanami, Elena Temereva, Christine Strohmeier, Shigeru Kuratani, Byrappa Venkatesh, Guillaume Evanno, L. Aravind, Michael Schorpp, Mani Larijani, and Thomas Boehm

Cytidine deaminases of the AID/APOBEC family mutate the genetic material of pathogens or contribute to the generation and diversification of antibody repertoires in jawed vertebrates. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the somatic diversification of variable lymphocyte receptor (VLR) repertoires. We discovered an unexpected diversity of cytidine deaminase genes within and among lamprey species. The cytidine deaminases with features comparable to jawed vertebrate AID are always present, suggesting that they are involved in essential processes, such as VLR assembly. In contrast, other genes show a remarkable copy number variation, like the APOBEC3 genes in mammals. This suggests an unexpected similarity in functional deployment of AID/APOBEC cytidine deaminases across all vertebrates. (See pp. E3211–E3220.)

Duplicated TLR5 of zebrafish functions as a heterodimeric receptor

Carlos G. P. Voogdt, Jaap A. Wagenaar, and Jos P. M. van Putten

Toll-like receptors (TLRs) are highly conserved innate receptors that form homo- or heterodimers to detect microbial danger signals and activate the immune system. TLR5 detects flagellin of bacteria and functions as a homodimeric receptor complex. A crystallized fragment of TLR5b of the zebrafish (Danio rerio) serves as a model structure for the homodimeric TLR5–flagellin interaction. Here we report that zebrafish TLR5 unexpectedly functions as a heterodimeric flagellin receptor composed of the duplicated gene products TLR5b and TLR5a. The unique heterodimeric nature of zebrafish TLR5 indicates important receptor differences between species, contributes to a deeper understanding of the activation mechanism of TLRs, and provides an illustrative example of the functional coevolution of duplicated genes. (See pp. E3221–E3229.)

Innate responses to gene knockouts impact overlapping gene networks and vary with respect to resistance to viral infection

Yonghong Liu, Yuanyuan Liu, Jiaming Wu, Bernard Roizman, and Grace Guoying Zhou

Analyses of 10 cell lines from which individual genes associated with innate immunity had been knocked out revealed the following: knockout of some genes is associated with increases in the expression of overlapping networks of genes and significant loss of ability to support the replication of HSV-1; knockout of other genes is associated with decreases in the expression of overlapping networks of genes and, overall, no effect on viral replication; the phenotype of cells from which a gene was deleted reflects the sum total of the effects of genes up- or down-regulated as a consequence of the deletion; and key functions associated with innate immunity are normally repressed and must be activated in response to infection. (See pp. E3230–E3237.)

Data-driven model for the assessment of Mycobacterium tuberculosis transmission in evolving demographic structures

Sergio Arregui, María José Iglesias, Sofía Samper, Dessislava Marinova, Carlos Martin, Joaquín Sanz and Yamir Moreno

Even though tuberculosis (TB) is acknowledged as a strongly age-dependent disease, it remains unclear how TB epidemics would react, in the following decades, to the generalized aging that human populations are experiencing worldwide. This situation is partly caused by the limitations of current transmission models at describing the relationship between demography and TB transmission. Here, we present a data-driven epidemiological model that, unlike previous approaches, explicitly contemplates relevant aspects of the coupling between age structure and TB dynamics, such as demographic evolution and contact heterogeneities. Using our model, we identify substantial biases in epidemiological forecasts rooted in an inadequate description of these aspects, at the level of both aggregated incidence and mortality rates and their distribution across age strata. (See pp. E3238–E3245.)

Ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryotomography

Poorna Subramanian, Sahand Pirbadian, Mohamed Y. El-Naggar, and Grant J. Jensen

Recent findings from in vivo fluorescence and immunolabeling measurements hinted at the possible role of outer membrane (OM) extensions as Shewanella oneidensis MR-1 nanowires. However, a detailed understanding of the architecture and electron transport mechanism along OM extensions was lacking. In this work, we report a unique setup for correlative light and electron microscopy of Shewanella OM extensions and demonstrate that they are chains of interconnected outer membrane vesicles with densities, consistent with periplasmic and OM cytochromes, distributed along their length. We propose, based on the packing density of cytochromes measured from electron cryotomograms, that the electron transport mechanism involves a combination of direct electron hopping and diffusion of electron carriers. (See pp. E3246–E3255.)

Haemophilus influenzae genome evolution during persistence in the human airways in chronic obstructive pulmonary disease

Melinda M. Pettigrew, Christian P. Ahearn, Janneane F. Gent, Yong Kong, Mary C. Gallo, James B. Munro, Adonis D’Mello, Sanjay Sethi, Hervé Tettelin, and Timothy F. Murphy

Nontypeable Haemophilus influenzae (NTHi) exclusively colonize and infect humans and play an important role in the course and pathogenesis of chronic obstructive pulmonary disease (COPD). We conducted whole-genome sequencing of 269 NTHi isolates from a 15-y prospective study of COPD to assess in vivo adaption of NTHi. NTHi uses slipped-strand mispairing in simple sequence repeats to regulate critical virulence functions as the primary mechanism to adapt to survival in the human airways. Analyses of changes in 12 candidate vaccine antigens during persistence provided data with important implications for guiding vaccine development. These results advance understanding of how an exclusively human pathogen alters its genome to adapt to survival in the hostile environment of the human respiratory tract. (See pp. E3256–E3265.)

Endogenous superoxide is a key effector of the oxygen sensitivity of a model obligate anaerobe

Zheng Lu, Ramakrishnan Sethu, and James A. Imlay

Microbes display profound differences in their tolerance for oxygen, and this trait organizes the structure of many microbial communities. However, the molecular basis of oxygen sensitivity is not well understood. In this study we determined that Bacteroides thetaiotaomicron, an abundant member of the human intestinal flora, is incapacitated by superoxide stress when it enters a fully oxic environment. The key difference from oxygen-tolerant bacteria lies not in its defensive systems, nor in the nature of the affected enzymes, but in the rate of endogenous oxidant formation. Anaerobes thrive in oxygen-poor environments because they deploy low-potential electron-transfer pathways; these results suggest that an ancillary effect is the reactivity of these pathways with oxygen, thereby generating enough reactive oxygen species to preclude oxic growth. (See pp. E3266–E3275.)

Multiplicative mixing of object identity and image attributes in single inferior temporal neurons

N. Apurva Ratan Murty and S. P. Arun

Vision is a challenging problem because the same object can produce a variety of images on the retina, mixing signals related to its identity with signals related to its viewing attributes, such as size, position, rotation, etc. Precisely how the brain separates these signals to form an efficient representation is unknown. Here, we show that single neurons in high-level visual cortex encode object identity and attribute multiplicatively and that doing so allows for better decoding of each signal. (See pp. E3276–E3285.)

Sensorineural hearing loss degrades behavioral and physiological measures of human spatial selective auditory attention

Lengshi Dai, Virginia Best, and Barbara G. Shinn-Cunningham

Listeners with hearing loss have trouble communicating in many social settings. In such situations, listeners with normal hearing suppress the neural representation of competing sounds, a process known as auditory selective attention. We compared hearing-impaired (HI) and normal-hearing (NH) listeners on a spatial selective attention task while measuring neural responses using electroencephalography. Compared with NH listeners, HI listeners have poorer sensitivity to spatial cues, perform more poorly on the selective attention task, and show weaker neural suppression of competing sounds. Moreover, these different measures are correlated both for HI and for NH listeners. These results suggest that poor spatial acuity produces problems with selective attention. These findings have implications both for basic science and for development of next-generation hearing aids. (See pp. E3286–E3295.)

mTOR signaling in VIP neurons regulates circadian clock synchrony and olfaction

Dong Liu, Adam Stowie, Nuria de Zavalia, Tanya Leise, Salil Saurav Pathak, Lester R. Drewes, Alec J. Davidson, Shimon Amir, Nahum Sonenberg, and Ruifeng Cao

The mammalian/mechanistic target of rapamycin (mTOR) kinase resides at the crux of an intracellular signaling network that controls fundamental biological processes. Dysregulation of mTOR signaling is linked to neurological and psychiatric diseases. However, the physiological functions of mTOR signaling in the adult brain are not fully understood. In the current study, we discovered that mTOR in vasoactive intestinal peptide (VIP) neurons plays a key role in regulating neurophysiology in the brain circadian clock and the olfactory system. The conditional mTOR knockout mouse will be a useful model for future investigations of mTOR and/or VIP. (See pp. E3296–E3304.)

Flexible egocentric and allocentric representations of heading signals in parietal cortex

Xiaodong Chen (陈晓冬), Gregory C. DeAngelis, and Dora E. Angelaki

Body-centered (egocentric) and world-centered (allocentric) spatial reference frames are both important for spatial navigation. We have previously shown that vestibular heading signals, which are initially coded in a head-centered reference frame, are no longer head-centered in the ventral intraparietal (VIP) area, but instead are represented in either a body- or world-centered frame, as the two frames were not dissociated. Here, we report a flexible switching between egocentric and allocentric reference frames in a subpopulation of VIP neurons, depending on gaze strategy. Other VIP neurons continue to represent heading in a body-centered reference frame despite changes in gaze strategy. These findings suggest that the vestibular representation of heading in VIP is dynamic and may be modulated by task demands. (See pp. E3305–E3312.)

Schema learning for the cocktail party problem

Kevin J. P. Woods and Josh H. McDermott

The “cocktail party problem” is encountered when sounds from different sources in the world mix in the air before arriving at the ear, requiring the brain to estimate individual sources from the received mixture. Sounds produced by a given source often exhibit consistencies in structure that might be useful for separating sources if they could be learned. Here we show that listeners rapidly learn the abstract structure shared by sounds from novel sources and use the learned structure to extract these sounds when they appear in mixtures. The involvement of learning and memory in our ability to hear one sound among many opens an avenue to understanding the role of statistical regularities in auditory scene analysis. (See pp. E3313–E3322.)

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PNAS Plus Significance Statements
Proceedings of the National Academy of Sciences Apr 2018, 115 (14) 3524-3528; DOI: 10.1073/pnas.ss11514
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