PLOS Biology (new articles)

Syndicate content PLOS Biology: New Articles
A Peer-Reviewed Open-Access Journal
Updated: 10 hours 39 min ago

Saving the horseshoe crab: A synthetic alternative to horseshoe crab blood for endotoxin detection

Fri, 2018-10-12 23:00

by Tom Maloney, Ryan Phelan, Naira Simmons

Horseshoe crabs have been integral to the safe production of vaccines and injectable medications for the past 40 years. The bleeding of live horseshoe crabs, a process that leaves thousands dead annually, is an ecologically unsustainable practice for all four species of horseshoe crab and the shorebirds that rely on their eggs as a primary food source during spring migration. Populations of both horseshoe crabs and shorebirds are in decline. This study confirms the efficacy of recombinant Factor C (rFC), a synthetic alternative that eliminates the need for animal products in endotoxin detection. Furthermore, our findings confirm that the biomedical industry can achieve a 90% reduction in the use of reagents derived from horseshoe crabs by using the synthetic alternative for the testing of water and other common materials used in the manufacturing process. This represents an extraordinary opportunity for the biomedical and pharmaceutical industries to significantly contribute to the conservation of horseshoe crabs and the birds that depend on them.
Categories: Biology, Journals

Learning what to approach

Thu, 2018-10-11 23:00

by Neir Eshel, Elizabeth E. Steinberg

Most decisions share a common goal: maximize reward and minimize punishment. Achieving this goal requires learning which choices are likely to lead to favorable outcomes. Dopamine is essential for this process, enabling learning by signaling the difference between what we expect to get and what we actually get. Although all animals appear to use this dopamine prediction error circuit, some do so more than others, and this neural heterogeneity correlates with individual variability in behavior. In this issue of PLOS Biology, Lee and colleagues show that manipulating a simple task parameter can bias the animals’ behavioral strategy and modulate dopamine release, implying that how we learn is just as flexible as what we learn.
Categories: Biology, Journals

Partial homologies between sleep states in lizards, mammals, and birds suggest a complex evolution of sleep states in amniotes

Thu, 2018-10-11 23:00

by Paul-Antoine Libourel, Baptiste Barrillot, Sébastien Arthaud, Bertrand Massot, Anne-Laure Morel, Olivier Beuf, Anthony Herrel, Pierre-Hervé Luppi

It is crucial to determine whether rapid eye movement (REM) sleep and slow-wave sleep (SWS) (or non-REM sleep), identified in most mammals and birds, also exist in lizards, as they share a common ancestor with these groups. Recently, a study in the bearded dragon (P. vitticeps) reported states analogous to REM and SWS alternating in a surprisingly regular 80-s period, suggesting a common origin of the two sleep states across amniotes. We first confirmed these results in the bearded dragon with deep brain recordings and electro-oculogram (EOG) recordings. Then, to confirm a common origin and more finely characterize sleep in lizards, we developed a multiparametric approach in the tegu lizard, a species never recorded to date. We recorded EOG, electromyogram (EMG), heart rate, and local field potentials (LFPs) and included data on arousal thresholds, sleep deprivation, and pharmacological treatments with fluoxetine, a serotonin reuptake blocker that suppresses REM sleep in mammals. As in the bearded dragon, we demonstrate the existence of two sleep states in tegu lizards. However, no clear periodicity is apparent. The first sleep state (S1 sleep) showed high-amplitude isolated sharp waves, and the second sleep state (S2 sleep) displayed 15-Hz oscillations, isolated ocular movements, and a decrease in heart rate variability and muscle tone compared to S1. Fluoxetine treatment induced a significant decrease in S2 quantities and in the number of sharp waves in S1. Because S2 sleep is characterized by the presence of ocular movements and is inhibited by a serotonin reuptake inhibitor, as is REM sleep in birds and mammals, it might be analogous to this state. However, S2 displays a type of oscillation never previously reported and does not display a desynchronized electroencephalogram (EEG) as is observed in the bearded dragons, mammals, and birds. This suggests that the phenotype of sleep states and possibly their role can differ even between closely related species. Finally, our results suggest a common origin of two sleep states in amniotes. Yet, they also highlight a diversity of sleep phenotypes across lizards, demonstrating that the evolution of sleep states is more complex than previously thought.
Categories: Biology, Journals

Confronting climate change in the age of denial

Tue, 2018-10-09 23:00

by Liza Gross

This Editorial introduces a Collection of articles in which the authors explore the challenges and pitfalls of communicating the science of climate change in an atmosphere where evidence doesn't matter.
Categories: Biology, Journals

The placenta goes viral: Retroviruses control gene expression in pregnancy

Tue, 2018-10-09 23:00

by Edward B. Chuong

The co-option of endogenous retroviruses (ERVs) is increasingly recognized as a recurrent theme in placental biology, which has far-reaching implications for our understanding of mammalian evolution and reproductive health. Most research in this area has focused on ERV-derived proteins, which have been repeatedly co-opted to promote cell–cell fusion and immune modulation in the placenta. ERVs also harbor regulatory sequences that can potentially control placental gene expression, but there has been limited evidence to support this role. In a recent study, Dunn-Fletcher and colleagues discover a striking example of an ERV-derived enhancer element that has been co-opted to regulate a gene important for human pregnancy. Using genomic and experimental approaches, they firmly establish that a primate-specific ERV functions as a placenta-specific enhancer for corticotropin-releasing hormone (CRH), a hormone linked to the control of birth timing in humans. Their findings implicate an extensive yet understudied role for retroviruses in shaping the evolution of placental gene regulatory networks.
Categories: Biology, Journals

(Escaping) the paradox of scientific storytelling

Tue, 2018-10-09 23:00

by Michael F. Dahlstrom, Dietram A. Scheufele

Compelling stories about science can motivate people to engage and respond to relevant problems facing society. While science plays a unique role in society, providing the best available evidence for policy choices, understanding the world, and informing citizens’ daily lives, it does not hold any intrinsic advantage in creating captivating stories for mass audiences. Instead, science must compete with other storytellers, many of whom are not bound to scientific evidence. This presents a paradox—how can science preserve its credibility as curator of knowledge while engaging audiences with a communication format that is agnostic to truth?
Categories: Biology, Journals

Tracking arctic marine mammal resilience in an era of rapid ecosystem alteration

Tue, 2018-10-09 23:00

by Sue E. Moore, Randall R. Reeves

Global warming is significantly altering arctic marine ecosystems. Specifically, the precipitous loss of sea ice is creating a dichotomy between ice-dependent polar bears and pinnipeds that are losing habitat and some cetaceans that are gaining habitat. While final outcomes are hard to predict for the many and varied marine mammal populations that rely on arctic habitats, we suggest a simplified framework to assess status, based upon ranking a population’s size, range, behavior, and health. This basic approach is proposed as a means to prioritize and expedite conservation and management efforts in an era of rapid ecosystem alteration.
Categories: Biology, Journals

Gene expression in response to optical defocus of opposite signs reveals bidirectional mechanism of visually guided eye growth

Tue, 2018-10-09 23:00

by Tatiana V. Tkatchenko, David Troilo, Alexandra Benavente-Perez, Andrei V. Tkatchenko

Myopia (nearsightedness) is the most common eye disorder, which is rapidly becoming one of the leading causes of vision loss in several parts of the world because of a recent sharp increase in prevalence. Nearwork, which produces hyperopic optical defocus on the retina, has been implicated as one of the environmental risk factors causing myopia in humans. Experimental studies have shown that hyperopic defocus imposed by negative power lenses placed in front of the eye accelerates eye growth and causes myopia, whereas myopic defocus imposed by positive lenses slows eye growth and produces a compensatory hyperopic shift in refractive state. The balance between these two optical signals is thought to regulate refractive eye development; however, the ability of the retina to recognize the sign of optical defocus and the composition of molecular signaling pathways guiding emmetropization are the subjects of intense investigation and debate. We found that the retina can readily distinguish between imposed myopic and hyperopic defocus, and identified key signaling pathways underlying retinal response to the defocus of different signs. Comparison of retinal transcriptomes in common marmosets exposed to either myopic or hyperopic defocus for 10 days or 5 weeks revealed that the primate retina responds to defocus of different signs by activation or suppression of largely distinct pathways. We also found that 29 genes differentially expressed in the marmoset retina in response to imposed defocus are localized within human myopia quantitative trait loci (QTLs), suggesting functional overlap between genes differentially expressed in the marmoset retina upon exposure to optical defocus and genes causing myopia in humans. These findings identify retinal pathways involved in the development of myopia, as well as potential new strategies for its treatment.
Categories: Biology, Journals

Climate communication for biologists: When a picture can tell a thousand words

Tue, 2018-10-09 23:00

by Stephan Lewandowsky, Lorraine Whitmarsh

Pictures often tell a story better than the proverbial 1,000 words. However, in connection with climate change, many pictures can be highly misleading, for example, when a snowball is used to ridicule the notion of global warming or when a picture of a dead crop is supposed to alert people to climate change. We differentiate between such inappropriate pictures and those that can be used legitimately because they capture long-term trends. For example, photos of a glacier’s retreat are legitimate indicators of the long-term mass balance loss that is observed for the vast majority of glaciers around the world.
Categories: Biology, Journals

<i>Candida albicans</i> biofilm–induced vesicles confer drug resistance through matrix biogenesis

Mon, 2018-10-08 23:00

by Robert Zarnowski, Hiram Sanchez, Antonio S. Covelli, Eddie Dominguez, Anna Jaromin, Jörg Berhardt, Christian Heiss, Parastoo Azadi, Aaron Mitchell, David R. Andes

Cells from all kingdoms of life produce extracellular vesicles (EVs). Their cargo is protected from the environment by the surrounding lipid bilayer. EVs from many organisms have been shown to function in cell–cell communication, relaying signals that impact metazoan development, microbial quorum sensing, and pathogenic host–microbe interactions. Here, we have investigated the production and functional activities of EVs in a surface-associated microbial community or biofilm of the fungal pathogen Candida albicans. Crowded communities like biofilms are a context in which EVs are likely to function. Biofilms are noteworthy because they are encased in an extracellular polymeric matrix and because biofilm cells exhibit extreme tolerance to antimicrobial compounds. We found that biofilm EVs are distinct from those produced by free-living planktonic cells and display strong parallels in composition to biofilm matrix material. The functions of biofilm EVs were delineated with a panel of mutants defective in orthologs of endosomal sorting complexes required for transport (ESCRT) subunits, which are required for normal EV production in diverse eukaryotes. Most ESCRT-defective mutations caused reduced biofilm EV production, reduced matrix polysaccharide levels, and greatly increased sensitivity to the antifungal drug fluconazole. Matrix accumulation and drug hypersensitivity of ESCRT mutants were reversed by addition of wild-type (WT) biofilm EVs. Vesicle complementation showed that biofilm EV function derives from specific cargo proteins. Our studies indicate that C. albicans biofilm EVs have a pivotal role in matrix production and biofilm drug resistance. Biofilm matrix synthesis is a community enterprise; prior studies of mixed cell biofilms have demonstrated extracellular complementation. Therefore, EVs function not only in cell–cell communication but also in the sharing of microbial community resources.
Categories: Biology, Journals

Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins

Mon, 2018-10-08 23:00

by Suchismita Panda, Meenakshi Setia, Navjot Kaur, Varsha Shepal, Vivek Arora, Divya Kumari Singh, Abir Mondal, Abhishek Teli, Madhura Tathode, Rajendra Gajula, L. C. Padhy, Anjali Shiras

Long noncoding RNAs constitute a major fraction of the eukaryotic transcriptome, and together with proteins, they intricately fine-tune various growth regulatory signals to control cellular homeostasis. Here, we describe the functional characterisation of a novel pair of long intergenic noncoding RNAs (lincRNAs) comprised of complementary, fully overlapping sense and antisense transcripts Genomic Instability Inducing RNA (Ginir) and antisense RNA of Ginir (Giniras), respectively, from mouse cells. This transcript pair is expressed in a spatiotemporal manner during embryonic development. The individual levels of the sense and antisense transcripts are finely balanced during embryonic growth and in adult tissues. Functional studies of the individual transcripts performed using overexpression and knock-down strategies in mouse cells has led to the discovery that Ginir RNA is a regulator of cellular proliferation and can act as an oncogene having a preeminent role in malignant transformation. Mechanistically, we demonstrate that the oncogenic function of Ginir is mediated by its interaction with centrosomal protein 112 (Cep112). Additionally, we establish here a specific interaction between Cep112 with breast cancer type 1 susceptibility protein (Brca1), another centrosome-associated protein. Next, we prove that the mutual interaction between Cep112 with Brca1 is significant for mitotic regulation and maintenance of genomic stability. Furthermore, we demonstrate that the Cep112 protein interaction with Brca1 protein is impaired when an elevated level of Ginir RNA is present in the cells, resulting in severe deregulation and abnormality in mitosis, leading to malignant transformation. Inhibiting the Ginir RNA function in transformed cells attenuates transformation and restores genomic stability. Together, these findings unravel, to our knowledge, a hitherto-unknown mechanism of oncogenesis mediated by a long noncoding RNA and establishes a unique role of Cep112–Brca1 interaction being modulated by Ginir RNA in maintaining mitotic fidelity.
Categories: Biology, Journals

Crafting your scientist brand

Fri, 2018-10-05 23:00

by Peter J. Hotez

That a scientist might shape and cultivate a personal brand is a relatively new concept but one that is finding increasing acceptance in this new age of rapid communications and social media. A key driver is the abrupt rise in well-funded and organized antiscience movements, especially in North America and Europe, such that society now benefits from scientists with strong personal brands and public personas who are willing to engage general audiences. In this sense, branding itself can advance science, the sharing of information, and the promotion of science as a public good. Still another dimension to branding is that it affords an opportunity to mentor younger scientists and helps you to become an important role model for the next generation. There is also a practical side, as today, fewer scientists spend their entire career at a single institution, so owning a strong brand can sometimes create easier paths for transitions and mobility. However, brand cultivation ideally begins in collaboration with your institutional office of communications and is done in a way that is seen as a win for both you and your university or research institution. Described here are some steps to consider when embarking on brand cultivation and how to avoid some of the potential pitfalls.
Categories: Biology, Journals

Birds, blooms, and evolving diversity

Thu, 2018-10-04 23:00

by Lauren A. Richardson

In this Open Highlight, Senior Editor Lauren Richardson features exciting new Open Access research into how species evolve their characteristic traits.
Categories: Biology, Journals

The fault in his seeds: Lost notes to the case of bias in Samuel George Morton’s cranial race science

Thu, 2018-10-04 23:00

by Paul Wolff Mitchell

The discovery of nearly 180-year-old cranial measurements in the archives of 19th century American physician and naturalist Samuel George Morton can address a lingering debate, begun in the late 20th century by paleontologist and historian of science Stephen Jay Gould, about the unconscious bias alleged in Morton’s comparative data of brain size in human racial groups. Analysis of Morton’s lost data and the records of his studies does not support Gould’s arguments about Morton’s biased data collection. However, historical contextualization of Morton with his scientific peers, especially German anatomist Friedrich Tiedemann, suggests that, while Morton’s data may have been unbiased, his cranial race science was not. Tiedemann and Morton independently produced similar data about human brain size in different racial groups but analyzed and interpreted their nearly equivalent results in dramatically different ways: Tiedemann using them to argue for equality and the abolition of slavery, and Morton using them to entrench racial divisions and hierarchy. These differences draw attention to the epistemic limitations of data and the pervasive role of bias within the broader historical, social, and cultural context of science.
Categories: Biology, Journals

GABAergic modulation of olfactomotor transmission in lampreys

Thu, 2018-10-04 23:00

by Gheylen Daghfous, François Auclair, Felix Clotten, Jean-Luc Létourneau, Elias Atallah, Jean-Patrick Millette, Dominique Derjean, Richard Robitaille, Barbara S. Zielinski, Réjean Dubuc

Odor-guided behaviors, including homing, predator avoidance, or food and mate searching, are ubiquitous in animals. It is only recently that the neural substrate underlying olfactomotor behaviors in vertebrates was uncovered in lampreys. It consists of a neural pathway extending from the medial part of the olfactory bulb (medOB) to locomotor control centers in the brainstem via a single relay in the caudal diencephalon. This hardwired olfactomotor pathway is present throughout life and may be responsible for the olfactory-induced motor behaviors seen at all life stages. We investigated modulatory mechanisms acting on this pathway by conducting anatomical (tract tracing and immunohistochemistry) and physiological (intracellular recordings and calcium imaging) experiments on lamprey brain preparations. We show that the GABAergic circuitry of the olfactory bulb (OB) acts as a gatekeeper of this hardwired sensorimotor pathway. We also demonstrate the presence of a novel olfactomotor pathway that originates in the non-medOB and consists of a projection to the lateral pallium (LPal) that, in turn, projects to the caudal diencephalon and to the mesencephalic locomotor region (MLR). Our results indicate that olfactory inputs can induce behavioral responses by activating brain locomotor centers via two distinct pathways that are strongly modulated by GABA in the OB. The existence of segregated olfactory subsystems in lampreys suggests that the organization of the olfactory system in functional clusters may be a common ancestral trait of vertebrates.
Categories: Biology, Journals

Cross-resistance is modular in bacteria–phage interactions

Wed, 2018-10-03 23:00

by Rosanna C. T. Wright, Ville-Petri Friman, Margaret C. M. Smith, Michael A. Brockhurst

Phages shape the structure of natural bacterial communities and can be effective therapeutic agents. Bacterial resistance to phage infection, however, limits the usefulness of phage therapies and could destabilise community structures, especially if individual resistance mutations provide cross-resistance against multiple phages. We currently understand very little about the evolution of cross-resistance in bacteria–phage interactions. Here we show that the network structure of cross-resistance among spontaneous resistance mutants of Pseudomonas aeruginosa evolved against each of 27 phages is highly modular. The cross-resistance network contained both symmetric (reciprocal) and asymmetric (nonreciprocal) cross-resistance, forming two cross-resistance modules defined by high within- but low between-module cross-resistance. Mutations conferring cross-resistance within modules targeted either lipopolysaccharide or type IV pilus biosynthesis, suggesting that the modularity of cross-resistance was structured by distinct phage receptors. In contrast, between-module cross-resistance was provided by mutations affecting the alternative sigma factor, RpoN, which controls many lifestyle-associated functions, including motility, biofilm formation, and quorum sensing. Broader cross-resistance range was not associated with higher fitness costs or weaker resistance against the focal phage used to select resistance. However, mutations in rpoN, providing between-module cross-resistance, were associated with higher fitness costs than mutations associated with within-module cross-resistance, i.e., in genes encoding either lipopolysaccharide or type IV pilus biosynthesis. The observed structure of cross-resistance predicted both the frequency of resistance mutations and the ability of phage combinations to suppress bacterial growth. These findings suggest that the evolution of cross-resistance is common, is likely to play an important role in the dynamic structure of bacteria–phage communities, and could inform the design principles for phage therapy treatments.
Categories: Biology, Journals

Cryptochrome: The magnetosensor with a sinister side?

Tue, 2018-10-02 23:00

by Lukas Landler, David A. Keays

Over the last three decades, evidence has emerged that low-intensity magnetic fields can influence biological systems. It is now well established that migratory birds have the capacity to detect the Earth's magnetic field; it has been reported that power lines are associated with childhood leukemia and that pulsed magnetic fields increase the production of reactive oxidative species (ROS) in cellular systems. Justifiably, studies in this field have been viewed with skepticism, as the underlying molecular mechanisms are unknown. In the accompanying paper, Sherrard and colleagues report that low-flux pulsed electromagnetic fields (PEMFs) result in aversive behavior in Drosophila larvae and ROS production in cell culture. They further report that these responses require the presence of cryptochrome, a putative magnetoreceptor. If correct, it is conceivable that carcinogenesis associated with power lines, PEMF-induced ROS generation, and animal magnetoreception share a common mechanistic basis.
Categories: Biology, Journals

Is adaptive therapy natural?

Tue, 2018-10-02 23:00

by Frédéric Thomas, Emmanuel Donnadieu, Guillaume M. Charriere, Camille Jacqueline, Aurélie Tasiemski, Pascal Pujol, François Renaud, Benjamin Roche, Rodrigo Hamede, Joel Brown, Robert Gatenby, Beata Ujvari

Research suggests that progression-free survival can be prolonged by integrating evolutionary principles into clinical cancer treatment protocols. The goal is to prevent or slow the proliferation of resistant malignant cell populations. The logic behind this therapy relies on ecological and evolutionary processes. These same processes would be available to natural selection in decreasing the probability of an organism’s death due to cancer. We propose that organisms’ anticancer adaptions include not only ones for preventing cancer but also ones for directing and retarding the evolution of life-threatening cancer cells. We term this last strategy natural adaptive therapy (NAT). The body’s NAT might include a lower than otherwise possible immune response. A restrained immune response might forego maximum short-term kill rates. Restraint would forestall immune-resistant cancer cells and produce long-term durable control of the cancer population. Here, we define, develop, and explore the possibility of NAT. The discovery of NAT mechanisms could identify new strategies in tumor prevention and treatments. Furthermore, we discuss the potential risks of immunotherapies that force the immune system to ramp up the short-term kill rates of malignant cancer cells in a manner that undermines the body’s NAT and accelerates the evolution of immune resistance.
Categories: Biology, Journals

Should police have access to genetic genealogy databases? Capturing the Golden State Killer and other criminals using a controversial new forensic technique

Tue, 2018-10-02 23:00

by Christi J. Guerrini, Jill O. Robinson, Devan Petersen, Amy L. McGuire

On April 24, 2018, a suspect in California’s notorious Golden State Killer cases was arrested after decades of eluding the police. Using a novel forensic approach, investigators identified the suspect by first identifying his relatives using a free, online genetic database populated by individuals researching their family trees. In the wake of the case, media outlets reported privacy concerns with police access to personal genetic data generated by or shared with genealogy services. Recent data from 1,587 survey respondents, however, provide preliminary reason to question whether such concerns have been overstated. Still, limitations on police access to genetic genealogy databases in particular may be desirable for reasons other than current public demand for them.
Categories: Biology, Journals

Low-intensity electromagnetic fields induce human cryptochrome to modulate intracellular reactive oxygen species

Tue, 2018-10-02 23:00

by Rachel M. Sherrard, Natalie Morellini, Nathalie Jourdan, Mohamed El-Esawi, Louis-David Arthaut, Christine Niessner, Francois Rouyer, Andre Klarsfeld, Mohamed Doulazmi, Jacques Witczak, Alain d’Harlingue, Jean Mariani, Ian Mclure, Carlos F. Martino, Margaret Ahmad

Exposure to man-made electromagnetic fields (EMFs), which increasingly pollute our environment, have consequences for human health about which there is continuing ignorance and debate. Whereas there is considerable ongoing concern about their harmful effects, magnetic fields are at the same time being applied as therapeutic tools in regenerative medicine, oncology, orthopedics, and neurology. This paradox cannot be resolved until the cellular mechanisms underlying such effects are identified. Here, we show by biochemical and imaging experiments that exposure of mammalian cells to weak pulsed electromagnetic fields (PEMFs) stimulates rapid accumulation of reactive oxygen species (ROS), a potentially toxic metabolite with multiple roles in stress response and cellular ageing. Following exposure to PEMF, cell growth is slowed, and ROS-responsive genes are induced. These effects require the presence of cryptochrome, a putative magnetosensor that synthesizes ROS. We conclude that modulation of intracellular ROS via cryptochromes represents a general response to weak EMFs, which can account for either therapeutic or pathological effects depending on exposure. Clinically, our findings provide a rationale to optimize low field magnetic stimulation for novel therapeutic applications while warning against the possibility of harmful synergistic effects with environmental agents that further increase intracellular ROS.
Categories: Biology, Journals