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The 3′ end of the 18S ribosomal RNA is formed by the endoribonuclease Nob1. How cells ensure the accuracy of the 3′ end has remained a mystery. A new study in PLOS Biology revealed that there are multiple checkpoints to ensure that only ribosomes containing the correct 3′ end participate in translation. The 3' end of 18S ribosomal RNA is formed by the endoribonuclease Nob1, but how cells ensure the accuracy of the 3' end has been a mystery. A new study in PLOS Biology has revealed multiple checkpoints that ensure only ribosomes containing the correct 3' end participate in translation. [ABSTRACT FROM AUTHOR]

All animals and plants likely require interactions with microbes, often in strong, persistent symbiotic associations. While the recognition of this phenomenon has been slow in coming, it will impact most, if not all, subdisciplines of biology. Research enabled by recent technological advances has revealed that all animals and plants likely require interactions with microbes, often in strong, persistent symbiotic associations. This Perspective article argues that while the recognition of this phenomenon is slow in coming, it will impact most, if not all, subdisciplines of biology. [ABSTRACT FROM AUTHOR]

Many journals in ecology and evolutionary biology encourage or require authors to make their data and code available alongside articles. In this study we investigated how often this data and code could be used together, when both were available, to computationally reproduce results published in articles. We surveyed the data and code sharing practices of 177 meta-analyses published in ecology and evolutionary biology journals published between 2015–17: 60% of articles shared data only, 1% shared code only, and 15% shared both data and code. In each of the articles which had shared both (n = 26), we selected a target result and attempted to reproduce it. Using the shared data and code files, we successfully reproduced the targeted results in 27–73% of the 26 articles, depending on the stringency of the criteria applied for a successful reproduction. The results from this sample of meta-analyses in the 2015–17 literature can provide a benchmark for future meta-research studies gauging the computational reproducibility of published research in ecology and evolutionary biology. [ABSTRACT FROM AUTHOR]

Proteasomes and autophagy constitute the 2 main proteolytic machineries for cytoplasmic content. A new study in PLOS Biology now demonstrates that autophagy stimulation alters proteasome composition, degrading hyperactive immunoproteasomes and thereby limiting inflammation. Proteasomes and autophagy constitute the two main proteolytic machineries for cytoplasmic content. This Primer explores a new study in PLOS Biology which demonstrates that autophagy stimulation alters proteasome composition, degrading hyperactive immunoproteasomes and thereby limiting inflammation. [ABSTRACT FROM AUTHOR]

In mammals, starburst amacrine cells are centrally involved in motion vision and a new study in PLOS Biology, by Yan and colleagues finds that zebrafish have them, too. They coexist with a second pair of starburst-like neurons, but neither appears to be strongly motion selective. In mammals, starburst amacrine cells are centrally involved in motion vision. This primer explores the implications of a PLOS Biology study reporting that zebrafish have amacrine cells, too, and revealing that these cells coexist with a second pair of starburst-like neurons, but neither appears to be strongly motion selective. [ABSTRACT FROM AUTHOR]

Molecular Biology has long tried to discover mechanisms, considering that unless we understand the principles, we cannot develop applications. Now machine learning and artificial intelligence enable direct leaps to application without understanding the principles. Will this herald a decline in mechanistic studies? [ABSTRACT FROM AUTHOR]

Animal and bacterial cells use shared mechanisms to defend against viruses. Analyzing 3 families of immune genes, a new study in PLOS Biology illuminates this evolutionary connection and traces the emergence of antiviral signaling across domains of life. Animal and bacterial cells use shared mechanisms to defend against viruses. This Primer explores a PLOS Biology study which uses analysis of three families of immune genes to illuminate this evolutionary connection and trace the emergence of antiviral signaling across domains of life. [ABSTRACT FROM AUTHOR]

In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (ARG). An ARG extensively encodes the ancestry of the genome(s) and thus is replete with valuable information for addressing diverse questions in evolutionary biology. Despite its potential utility, technological and methodological limitations, along with a lack of approachable literature, have severely restricted awareness and application of ARGs in evolution research. Excitingly, recent progress in ARG reconstruction and simulation have made ARG-based approaches feasible for many questions and systems. In this review, we provide an accessible introduction and exploration of ARGs, survey recent methodological breakthroughs, and describe the potential for ARGs to further existing goals and open avenues of inquiry that were previously inaccessible in evolutionary genomics. Through this discussion, we aim to more widely disseminate the promise of ARGs in evolutionary genomics and encourage the broader development and adoption of ARG-based inference. [ABSTRACT FROM AUTHOR]

Preventing parasite transmission from humans to mosquitoes is recognised to be critical for achieving elimination and eradication of malaria. Consequently developing new antimalarial drugs with transmission-blocking properties is a priority. Large screening campaigns have identified many new transmission-blocking molecules, however little is known about how they target the mosquito-transmissible Plasmodium falciparum stage V gametocytes, or how they affect their underlying cell biology. To respond to this knowledge gap, we have developed a machine learning image analysis pipeline to characterise and compare the cellular phenotypes generated by transmission-blocking molecules during male gametogenesis. Using this approach, we studied 40 molecules, categorising their activity based upon timing of action and visual effects on the organisation of tubulin and DNA within the cell. Our data both proposes new modes of action and corroborates existing modes of action of identified transmission-blocking molecules. Furthermore, the characterised molecules provide a new armoury of tool compounds to probe gametocyte cell biology and the generated imaging dataset provides a new reference for researchers to correlate molecular target or gene deletion to specific cellular phenotype. Our analysis pipeline is not optimised for a specific organism and could be applied to any fluorescence microscopy dataset containing cells delineated by bounding boxes, and so is potentially extendible to any disease model. Author summary: Interventions that prevent malaria parasite Plasmodium falciparum from transmitting from humans to mosquitoes are highly desirable to prevent both the spread of malaria and crucially the spread of drug resistance. Transmission is caused by the non-pathogenic gametocyte stage of the parasite life cycle which are insensitive to most current antimalarials. Consequently new drugs and new drug targets need to be identified to meet this need. Here we present PhIDDLI–a machine learning image analysis pipeline which we use to characterise the phenotype of male gametocytes treated with 40 novel transmission-blocking molecules. We found that the molecules formed 5 distinct phenotypic clusters according to their putative timing/mode of action within the cell. Molecules with similar chemical structures gave similar phenotypes. Interestingly, by varying the timing of drug exposure, different phenotypes manifest between molecules with seemingly similar initial phenotypes. Our study provides the first insights into the breadth of drug-targetable cell biology in male gametocytes and provides reference images and tool compounds for the identification and validation of new transmission-blocking drug targets. [ABSTRACT FROM AUTHOR]

Why was PLOS Biology launched and how has it changed over the past 20 years? Three editors who have been at the helm of the journal reflect on its beginnings and evolution. In this Editorial, three editors who have previously been at the helm of PLOS Biology reflect on its beginnings and evolution as a journal. [ABSTRACT FROM AUTHOR]

Open science is key to PLOS Biology's mission, both in its daily operations and in the role we aspire to have in the scholarly ecosystem. Here, we reflect on open science at the journal and discuss how and why we shall continue to hold it central to everything we do. Open science is key to PLOS Biology's mission, both in its daily operations and in the role we aspire to have in the scholarly ecosystem. In this Editorial, we reflect on open science at the journal and discuss how and why we shall continue to hold it central to everything we do. [ABSTRACT FROM AUTHOR]

Cellular senescence is a cell fate caused by multiple stresses. A 2008 article in PLOS Biology reported a senescence-associated secretory phenotype that can promote inflammation and cancer, eventually enabling the development of senolytic drugs. In this Perspective, the authors look back at a 2008 PLOS Biology article that reported a senescence-associated secretory phenotype that could promote inflammation and cancer, and discuss how that discovery eventually enabled the development of senolytic drugs. [ABSTRACT FROM AUTHOR]

Hemichordates are close relatives of chordates. Their nervous system patterning is chordate-like, but their neural architecture remains unexplored. A new study in PLOS Biology reveals an unexpected neuroanatomical complexity in these animals, also informing chordate origins. Hemichordates, close relatives of chordates, have a nervous system that is chordate-like in its patterning but their neural architecture remains unexplored. This Primer explores a new study in PLOS Biology that reveals an unexpected neuroanatomical complexity in these animals. [ABSTRACT FROM AUTHOR]

Microglia play a dual role in stroke depending on their pro-inflammatory and anti-inflammatory polarization. A study in PLOS Biology identifies a new mechanism, through which the transcription factor NR4A1 negatively regulates TNF expression in microglia. Microglia play a dual role in stroke depending on their pro-inflammatory and anti-inflammatory polarization. This Primer explores a PLOS Biology study that identifies a new mechanism through which the transcription factor NR4A1 negatively regulates TNF expression in microglia. [ABSTRACT FROM AUTHOR]

2023 saw many important advances in the life sciences. In this editorial, we highlight research from across the breadth of PLOS Biology's scope. [ABSTRACT FROM AUTHOR]

Twenty years ago this month, PLOS Biology was launched, helping to catalyze a movement that has transformed publishing in the life sciences. In this issue, we explore how the community can continue innovating for positive change in the next decades. Twenty years ago this month, PLOS Biology was launched, helping to catalyze a movement that has transformed publishing in the life sciences. This Editorial introduces our October issue, in which we explore how the community can continue innovating for positive change in the next decades. [ABSTRACT FROM AUTHOR]

In the past 2 decades, structural biology has transformed from a single technique used on single proteins to a multimodal integrative approach. Recently, protein structure prediction algorithms have opened new avenues to address challenging biological questions. The past two decades have seen a dramatic transformation take place in the field of structural biology. This Perspective looks back at the changes that have taken place and the promise that protein structure prediction algorithms hold for the future. [ABSTRACT FROM AUTHOR]

Our current understanding of early human development is limited. A study in PLOS Biology found a previously undefined group of cells that diverges from the main lineages and undergo apoptosis through the activity of young transposable elements. [ABSTRACT FROM AUTHOR]

A healing wound is made of cells that paused proliferation and secrete mitogenic factors and cells that proliferate to replace those lost to cell death. A new study in PLOS Biology describes how 2 conserved signaling pathways could repress each other to create these mutually exclusive cell states. [ABSTRACT FROM AUTHOR]

Tumors protect themselves from immune clearance by promoting extramedullary hematopoiesis. A new study in PLOS Biology provides insights into the mechanisms underlying this process, which may hold the key to disrupting generation of the immunosuppressive tumor microenvironment. The mechanisms by which tumors promote hematopoiesis outside the bone marrow have been the subject of intense interest. This Primer explores a new PLOS Biology study that provides new insight into the mechanisms underlying this process, and may hold the key to disrupting generation of the immunosuppressive tumor microenvironment. [ABSTRACT FROM AUTHOR]

To increase the effectiveness of education is appropriate to incorporate varied teaching methods with multisensory stimulation and with an emphasis on personal and emotional experiences. This study aims to compare the knowledge of biology subject matter acquired by second and fourth-grade primary students. The lesson occurred at a farm in the experimental group and at school in the control group. Students' knowledge levels were assessed before the lesson, after the lesson, after 14 days, after a month, and after six months. When the levels of knowledge after the lesson were compared between the groups, significantly better results (p = 0.001) were recorded in students in the control group. Another 14 days after the lesson, there was no significant difference in knowledge between the groups (p = 0.848). The same results were obtained after a month (p = 0.760) and after six months (p = 0.649). In the experimental group, the intra-group analysis did not show any significant difference in the levels of knowledge before and after the lesson; it was recorded only after 14 days. In contrast, the control group showed a significant improvement in knowledge right after the lesson, which was not observed later on. Most often, this phenomenon was observed in second-grade students. The presence of animals in an educational setting can add many benefits, such as mental well-being, an increase in empathy, or support for socio-emotional development. Since the levels of subject matter knowledge acquired at a farm and at school were similar, it seems that farm lessons should not negatively impact education, and it offers many related positive effects. [ABSTRACT FROM AUTHOR]

While heritable symbionts are common in insects, strains that act as male-killers are considered rare. A new study in PLOS Biology identifies a novel male-killer hidden by coinfection and host resistance, highlighting the complexity of host-microbial interactions in natural systems. While heritable symbionts are common in insects, strains that act as male-killers are considered rare. This Primer explores a new study in PLOS Biology which reveals a novel male-killer hidden by co-infection and host resistance, highlighting the complexity of host-microbial interactions in natural systems. [ABSTRACT FROM AUTHOR]

Background: Tuberculosis (TB) remains a major public health problem globally, even compared to COVID-19. Genome-wide studies have failed to discover genes that explain a large proportion of genetic risk for adult pulmonary TB, and even fewer have examined genetic factors underlying TB severity, an intermediate trait impacting disease experience, quality of life, and risk of mortality. No prior severity analyses used a genome-wide approach. Methods and findings: As part of our ongoing household contact study in Kampala, Uganda, we conducted a genome-wide association study (GWAS) of TB severity measured by TBScore, in two independent cohorts of culture-confirmed adult TB cases (n = 149 and n = 179). We identified 3 SNPs (P<1.0 x 10–7) including one on chromosome 5, rs1848553, that was GWAS significant (meta-analysis p = 2.97x10-8). All three SNPs are in introns of RGS7BP and have effect sizes corresponding to clinically meaningful reductions in disease severity. RGS7BP is highly expressed in blood vessels and plays a role in infectious disease pathogenesis. Other genes with suggestive associations defined gene sets involved in platelet homeostasis and transport of organic anions. To explore functional implications of the TB severity-associated variants, we conducted eQTL analyses using expression data from Mtb-stimulated monocyte-derived macrophages. A single variant (rs2976562) associated with monocyte SLA expression (p = 0.03) and subsequent analyses indicated that SLA downregulation following MTB stimulation associated with increased TB severity. Src Like Adaptor (SLAP-1), encoded by SLA, is highly expressed in immune cells and negatively regulates T cell receptor signaling, providing a potential mechanistic link to TB severity. Conclusions: These analyses reveal new insights into the genetics of TB severity with regulation of platelet homeostasis and vascular biology being central to consequences for active TB patients. This analysis also reveals genes that regulate inflammation can lead to differences in severity. Our findings provide an important step in improving TB patient outcomes. Author summary: Severity of tuberculosis (TB) is an important determinant of transmission, morbidity, mortality, disease experience and quality of life; it can be affected by human genetic variation. In this study, we performed a genome wide study (GWAS) to examine the role of human genetic variation on TB severity, as measured by the Bandim TBscore, a metric developed for resource-limited environments. Three single nucleotide polymorphisms (SNPs) in one gene, RGS7BP, associated with severity. This gene is expressed in blood vessels and plays a role in infectious disease pathology. In addition, we used the GWAS data to identify pathways linked to TBscore, and found that the platelet homeostasis and transport of organic anion pathways both associated with severity. Functional analyses were also performed, examining the effects of stimulation with Mycobacterium tuberculosis, the causative agent of TB. Down regulation of the gene encoding Src Like Adaptor (SLAP-1) that is highly expressed in immune cells and negatively regulates T cell receptor signaling associated with MTB exposure, providing a potential mechanistic link to TB severity. Together these findings indicate that host factors involved in regulation of platelet homeostasis and vascular biology affect TB severity. These findings may lead to new ways to decrease disease severity. [ABSTRACT FROM AUTHOR]

Viruses arriving late to an individual cell are blocked from replicating, an effect called superinfection exclusion. A study in PLOS Biology indicates that this exclusion at the level of individual cells gives rise to a heterogenous landscape of infection within a host. At the level of individual cells, infection by late-arriving viruses is blocked. At the level of tissues, genetically distinct patches of infection form. Is there a connection? This Primer explores a new PLOS Biology study suggesting that the answer is "yes." [ABSTRACT FROM AUTHOR]

Fibroblasts are known for their ability to make and modify the extracellular matrix. However, there is more to them than meets the eye. It is now clear that they help define tissue microenvironments and support immune responses in organs. As technology advances, we have started to uncover the secrets of fibroblasts. In this Essay, we present fibroblasts as not only the builders and renovators of tissue environments but also the rheostat cells for immune circuits. Although they perform location-specific functions, they do not have badges of fixed identity. Instead, they display a spectrum of functional states and can swing between these states depending on the needs of the organ. As fibroblasts participate in a range of activities both in health and disease, finding the key factors that alter their development and functional states will be an important goal to restore homeostasis in maladapted tissues. Fibroblasts have traditionally been thought of as structural cells, but technological advances have started to uncover important roles for fibroblasts in immune function. This Essay looks at why understanding the biology of fibroblasts really matters for health and disease. [ABSTRACT FROM AUTHOR]

Cinnamomum verum Blume (syn Cinnamomum zeylanicum) commonly known as Ceylon cinnamon, has gained worldwide attention due to its health benefits and its unique quality. Therefore, maintaining the yield quality and quantity is essential, especially for high-end value-added products. Knowledge on floral behaviour and reproductive biology is essential for breeding superior varieties and is critical for commercial cultivation efforts. However, limited literature is available on the floral biology of C. verum. Here in this study, we assessed the seasonal flowering, floral development and pollination of two cultivars of C. verum. Both macroscopic and microscopic data were collected on floral biology, pollination, and male and female floral organs before and after pollination. Cinnamomum verum is morpho-anatomically, structurally, and physiologically adapted for cross-pollination, possible between the two cultivars; type A (Sri Gemunu) and type B (Sri Wijaya) flowers; naturally evolved with Protogynous Dichogamy. However, due to changes in environmental conditions, female and male stages in the same tree overlap for about 45–60 min suggesting possible close-pollination within the same plant. During this event some of the pollens were observed hydrated even during self-pollination. In mean time, 4–8% of the flowers formed fruits after natural close and hand pollination which is between male and female phases of the same tree. Although C. verum is adapted for cross-pollination, natural close-pollination is also possible. The data suggest the complex nature of the sexual reproduction of C. verum. Well-managed breeding attempts with controlled factors like temperature and humidity will help to develop superior C. verum varieties. [ABSTRACT FROM AUTHOR]

Twenty years ago, the first transcriptome of the intraerythrocytic developmental cycle of the malaria parasite Plasmodium falciparum was published in PLOS Biology. Since then, transcriptomics studies have transformed the study of parasite biology. Twenty years ago, the first transcriptome of the intraerythrocytic developmental cycle of the malaria parasite Plasmodium falciparum was published in PLOS Biology. This Perspective looks at how transcriptomics studies have transformed the study of parasite biology in the years following its publication. [ABSTRACT FROM AUTHOR]

The baculum of mammals offers the opportunity to study the reproductive biology of extinct species given that it is a fossilizable part of the male genitalia and that its size and shape correlate with several aspects of the reproductive biology of extant mammals. Fossil bacula, however, are rare. Currently, bacula have been described from only two extinct species of canids, one from the subfamily Caninae and the other from the extinct subfamily Hesperocyoninae. Here, I describe the bacula of five extinct species of Borophaginae, each of which was found with other skeletal elements that have enabled identification to the species level. Two specimens (Aelurodon ferox and Aelurodon stirtoni) are largely complete, while the baculum from Carpocyon compressus is complete but still embedded in matrix that obscures some of its features. The bacula of Paratomarctus euthos and Desmocyon thomsoni are incomplete, but they provide useful information nonetheless. These borophagine bacula are similar to extant canines in being robust, having a urethral groove, and a simple distal end. These features suggest that the Borophaginae had long-lasting copulation and possibly spontaneous ovulation, similar to the extant canines. However, unlike the straight baculum of extant canines, borophagine bacula are ventrally curved (arched), which is also observed in the hesperocyonine baculum. The implication of this curvature for the reproductive biology of these animals remains unknown. [ABSTRACT FROM AUTHOR]

As 2022 draws to a close, we look back at some of the recent changes that have taken place at PLOS Biology, highlight some of our editors' favorite moments from the past year across the life sciences, and thank our editors, authors and peer-reviewers. [ABSTRACT FROM AUTHOR]

Are selection and control of action serial processes of separate neural modules? A new study in PLOS Biology argues against this and in favor of an integrated process distributed across multiple brain regions, each contributing in a distinct way. Are selection and control of action serial processes of separate neural modules? This Primer explores a study in PLOS Biology which argues against this and in favor of an integrated process distributed over multiple brain regions, each contributing in a distinct way. [ABSTRACT FROM AUTHOR]

The field of optimal experimental design uses mathematical techniques to determine experiments that are maximally informative from a given experimental setup. Here we apply a technique from artificial intelligence—reinforcement learning—to the optimal experimental design task of maximizing confidence in estimates of model parameter values. We show that a reinforcement learning approach performs favourably in comparison with a one-step ahead optimisation algorithm and a model predictive controller for the inference of bacterial growth parameters in a simulated chemostat. Further, we demonstrate the ability of reinforcement learning to train over a distribution of parameters, indicating that this approach is robust to parametric uncertainty. Author summary: Biological systems are often complex and typically exhibit non-linear behaviour, making accurate model parametrisation difficult. Optimal experimental design tools help address this problem by identifying experiments that are predicted to provide maximally informative data for parameter inference. In this work we use reinforcement learning, an artificial intelligence method, to determine such experiments. Our simulation studies show that this approach allows uncertainty in model parameterisation to be directly incorporated into the search for optimal experiments, opening a practical avenue for training an experimental controller. We present this method as complementary to existing optimisation approaches and we anticipate that artificial intelligence has a valuable role to play in the future of optimal experimental design. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) pandemic has led to a reimagining of many aspects of higher education, including how instructors interact with their students and how they encourage student participation. Text-based chatting during synchronous remote instruction is a simple form of student-student and student-instructor interaction. The importance of student participation has been documented, as have clear disparities in participation between those well-represented and those under-represented in science disciplines. Thus, we conducted an investigation into who is texting, what students are texting, and how these texts align with course content. We focused on two sections of a large-enrollment, introductory biology class offered remotely during Fall 2020. Using an analysis of in-class chatting, in combination with student survey responses, we find that text-based chatting suggests not only a high level of student engagement, but a type of participation that is disproportionately favored by women. Given the multiple lines of evidence indicating that women typically under-participate in their science courses, any vehicle that counters this trend merits further exploration. We conclude with suggestions for further research, and ideas for carrying forward text-based chatting in the post-COVID-19, in-person classroom. [ABSTRACT FROM AUTHOR]

Genome integrity in animals depends on silencing of mobile elements by Piwi-interacting RNAs (piRNAs). A new study in this issue of PLOS Biology reveals recent evolutionary losses of key piRNA biogenesis factors in flies, highlighting adaptability by rapid shift to alternative piRNA biogenesis strategies. Genome integrity in animals depends on silencing of mobile elements by piRNAs. This Primer explores a new study in PLOS Biology that reveals recent evolutionary losses of key piRNA biogenesis factors in flies, highlighting adaptability by rapid shifts to alternative piRNA biogenesis strategies. [ABSTRACT FROM AUTHOR]

The transition from dormant spore to germling has been topic of study and debate. A recent discovery in PLOS Biology shows that chaperone Hsp42 plays a crucial role in resolubilizing the proteome during dormancy breaking, although a role of trehalose cannot be excluded. The transition from dormant fungal spore to germling has been topic of study and debate. This Primer explores a recent discovery in PLOS Biology showing that chaperone Hsp42 plays a crucial role in re-solubilizing the proteome during dormancy breaking, although a role of trehalose cannot be excluded. [ABSTRACT FROM AUTHOR]

Neurons lack the ability to regenerate after injury. A new Preregistered Article in PLOS Biology finds that pharmacologically boosting regenerative capacity long after injury in mice, together with an enriched animal environment, promotes axonal and synaptic plasticity. Neurons lack the ability to regenerate after injury. This Primer explores a new Preregistered Article in PLOS Biology that found that pharmacologically boosting regenerative capacity long after injury in mice, together with an enriched animal environment, promotes axonal and synaptic plasticity. [ABSTRACT FROM AUTHOR]

Leaf veins provide a vital transport route in plants. The formation of leaf vein patterns has fascinated many scientists. In PLOS Biology, Linh and Scarpella reveal that transport through plasmodesmata plays a key role in vein patterning. Leaf veins provide a vital transport route in plants, and the formation of vein patterns has fascinated many scientists over the years. This Primer explores a new PLOS Biology study which reveals how transport through plasmodesmata plays a key role in vein patterning. [ABSTRACT FROM AUTHOR]

The roles for glycolytic and respiratory metabolism in supporting in vivo tumor growth in different contexts are not well understood. In this issue of PLOS Biology, a new study reveals that primary and metastatic tumors demonstrate divergent metabolic requirements. [ABSTRACT FROM AUTHOR]

Identifying the neural correlates of visual serial dependence has lagged behind the behavioral understanding. A new study in PLOS Biology provides a model of interpreting the complex relationship between physiology and behavior in studies of serial dependence. Our senses are barraged with discontinuous and uncertain visual input, but the brain smooths experience by making perception serially dependent. Neural correlates of this have been elusive but this Primer explores a new PLOS Biology study that provides a model for interpreting the complex relationship between physiology and behavior in studies of serial dependence. [ABSTRACT FROM AUTHOR]

Although closed-note exams have traditionally been used to evaluate students in undergraduate biology classes, open-note exams are becoming increasingly common, though little is known about how students prepare for these types of exams. We investigated student perceptions of and their preparation habits for online open-note exams in an undergraduate biology class, as compared to their previous experiences with closed-note exams in other classes. Specifically, we explored the following research questions: (1a) How do students perceive open-note exams impact their exam scores, their anxiety, the amount they studied, and the amount their peers studied? (1b) How do these perceptions impact performance outcomes? (2a) How do students prepare for open-note exams? (2b) How do these preparation methods impact performance outcomes? Results demonstrate students perceived increased exam scores, decreased exam-anxiety, decreased study time spent personally, and decreased study time spent by their peers for open-note exams, as compared to past experiences with closed-note exams. Open-ended survey responses analyzed through first- and second-cycle analyses showed students adapted their study habits by focusing on note preparation and broad conceptual understanding rather than rote memorization. Using linear mixed effects models to assess student performance, we found students who focused on understanding, note preparation and using external resources outperformed students who did not report those study habits. As institutions shift towards flexible and scalable assessments that can be used in face-to-face or online environments, the use of open-note exams can promote effective study habits and reward higher-order thinking with intentional guidance from the instructor. [ABSTRACT FROM AUTHOR]

Genotyping Plasmodium vivax relapses can provide insights into hypnozoite biology. We performed targeted amplicon sequencing of 127 relapses occurring in Indonesian soldiers returning to malaria-free Java after yearlong deployment in malarious Eastern Indonesia. Hepatic carriage of multiple hypnozoite clones was evident in three-quarters of soldiers with two successive relapses, yet the majority of relapse episodes only displayed one clonal population. The number of clones detected in relapse episodes decreased over time and through successive relapses, especially in individuals who received hypnozoiticidal therapy. Interrogating the multiplicity of infection in this P. vivax relapse cohort reveals evidence of independent activation and slow depletion of hypnozoites over many months by multiple possible mechanisms, including parasite senescence and host immunity. Author summary: Investigating relapse patterns in infections of Plasmodium vivax, a parasite that causes malaria, is challenging due to concurrent reinfection events alongside true relapses in most clinical cohorts. We performed sequencing on P. vivax samples from a cohort of Indonesian soldiers who were exposed to the parasite while deployed in a malaria-endemic region and then experienced relapses after their return to a region with no current malaria transmission. From these true relapses, we show that most infected individuals harbor multiple lineages of hypnozoites (latent liver stage parasites that reactivate to cause relapse) but individual relapses are largely driven by a single hypnozoite lineage or clone. Additionally, the average number of parasite clones detected in each relapse decreases over time. These findings suggest that P. vivax hypnozoites activate independently from each other and that their population in the liver decreases over time after the initial infection, possibly due to immune clearance or loss of parasite viability. [ABSTRACT FROM AUTHOR]

Suppression of recombination along the Y chromosome leads to its degeneration, so why does a process with such potentially deleterious consequences arise? In this issue of PLOS Biology, a new model reveals how and why this might be. We know that suppression of recombination leads to degeneration of Y chromosomes, but it has remained difficult to understand how features with such strong negative effects actually arise. This Primer explores a new model published in PLOS Biology that reveals how this could happen. [ABSTRACT FROM AUTHOR]

Nucleotide modifications can markedly influence mRNA processing and metabolism. New studies, one in PLOS Biology, show that approximately 130 yeast mRNAs contain dihydrouridine, a derivative of uridine. Functional studies show that dihydrouridine, in some cases, can affect mRNA splicing. Nucleotide modifications can markedly influence mRNA processing and metabolism. This Primer explores two new studies, one in PLOS Biology, showing that ~130 yeast mRNAs contain dihydrouridine, a derivative of uridine. Functional studies show that dihydrouridine, in some cases, can affect mRNA splicing. [ABSTRACT FROM AUTHOR]

In a new PLOS Biology paper, de Oliveira Caetano and colleagues presented an innovative method to estimate extinction risk in reptile species worldwide. The method shows a promising avenue to support Red List assessment, alongside some well-known challenges. This Primer explores the implications of a new PLOS Biology study that presents an innovative method for estimating extinction risk in reptile species worldwide; this method represents a promising avenue to support Red List assessment, alongside some well-known challenges. [ABSTRACT FROM AUTHOR]

In eukaryotic organisms, noncoding RNAs (ncRNAs) have been implicated as important regulators of multifaceted biological processes, including transcriptional, posttranscriptional, and epigenetic regulation of gene expression. In recent years, it is becoming clear that protozoan parasites encode diverse ncRNA transcripts; however, little is known about their cellular functions. Recent advances in high-throughput "omic" studies identified many novel long ncRNAs (lncRNAs) in apicomplexan parasites, some of which undergo splicing, polyadenylation, and encode small proteins. To date, only a few of them are characterized, leaving a big gap in our understanding regarding their origin, mode of action, and functions in parasite biology. In this review, we focus on lncRNAs of the human malaria parasite Plasmodium falciparum and highlight their cellular functions and possible mechanisms of action. [ABSTRACT FROM AUTHOR]

PLOS began publishing influential open access science in 2003. As PLOS Biology enters its third decade, we reflect on our mission, what has changed, what remains to be done and our wishes for the future. As PLOS Biology enters its third decade, we reflect on our mission, what has changed, what remains to be done and our wishes for the future. [ABSTRACT FROM AUTHOR]

Fitness usually increases when a male mates with more females, but is the same true for females? A new meta-analysis in PLOS Biology shows that females, like males, tend to have a positive relationship between the number of mates and their reproductive output. But why? Fitness usually increases when a male mates with more females, but is the same true for females? A new meta-analysis in PLOS Biology shows that females, like males, tend to have a positive relationship between the number of mates and their reproductive output. This Primer asks why. [ABSTRACT FROM AUTHOR]

New findings in PLOS Biology show that visual gamma oscillations are greatly attenuated by small spatial discontinuities in visual stimuli, suggesting that their genesis occurs in response to predictable regularities in the visual world. This Primer explores the implications of a recent PLOS Biology study showing that gamma synchrony in visual cortex is disrupted when small discontinuities are added to visual stimuli. This suggests that gamma synchrony is highly sensitive to regularities in the visual world and potentially play a role in predictive processing. [ABSTRACT FROM AUTHOR]

Recently reported specimens of the enigmatic Ediacaran fossil Dickinsonia from Russia show damage and repair that provides evidence of how they grew, and of their biological affinities. Marginal and terminal areas of wilting deformation are necrotic zones separating regenerated growth, sometimes on two divergent axes, rather than a single axis. Necrotic zones of damage to Dickinsonia are not a thick scar or callus, like a wound or amputation. Nor are they smooth transitions to a regenerated tail or arm. The wilted necrotic zone is most like damage by freezing, salt, or sunburn of leaves and lichens, compatible with evidence of terrestrial habitat from associated frigid and gypsic paleosols. Dickinsonia did not regrow by postembryonic addition of modules from a subterminal or patterned growth zone as in earthworms, myriapods, trilobites, crustaceans, and lizards. Rather Dickinsonia postembryonic regrowth from sublethal damage was from microscopic apical and lateral meristems, as in plants and lichens. Considered as fungal, Dickinsonia, and perhaps others of Class Vendobionta, were more likely Glomeromycota or Mucoromycotina, rather than Ascomycota or Basidiomycota. [ABSTRACT FROM AUTHOR]

The mechanism of symbiont-induced cytoplasmic incompatibility (CI) has been a long-standing mystery. A new study on Wolbachia's Cif proteins in PLOS Biology provides supportive evidence for the "Host modification model," although the alternative "Toxin–antidote model" is still in the running. The mechanism of symbiont-induced cytoplasmic incompatibility has been a long-lasting mystery. This Primer explores a new study on Wolbachia's Cif proteins in PLOS Biology that provides supportive evidence for the "Host-Modification Model," although the alternative "Toxin-Antidote Model" is still in the running. [ABSTRACT FROM AUTHOR]

In this issue of PLOS Biology, van Rijnberk and colleagues show how polyploidy, via binucleation, enables Caenorhabditis elegans intestinal cells to ramp up gene expression supplying the oocytes with the necessary lipids for optimal organismal growth and reproductive fitness. This Primer explores the implications of a new PLOS Biology study that shows how polyploidy, via binucleation, enables Caenorhabditis elegans intestinal cells to ramp up gene expression, supplying oocytes with the necessary lipids for optimal organismal growth and reproductive fitness. [ABSTRACT FROM AUTHOR]