Report on the 11th international workshop on the CCN family of genes,Nice, October 20–24, 2022

In celebration of the twentieth anniversary of the inception of the CCN society, and of the first post-Covid-19 live meeting, the executive board of the ICCNS had chosen Nice as the venue for the 11th International workshop on the CCN family of genes. On this occasion participation in the meeting was extended to colleagues from other cell signaling fields who were invited to present both an overview of their work and the future directions of their laboratory. Also, for the first time, the members of the JCCS Editorial Board were invited to participate in a JCCS special session during which all aspects of the journal « life » were addressed and opened to free critical discussion. The scientific presentations and the discussions that followed showed once more that an expansion of the session topics was beneficial to the quality of the meeting and confirmed that the ARBIOCOM project discussed last April in Nice was now on track to be launched in 2023. The participants unanimously welcomed Professor Attramadal’s proposition to organize the 2024, 12th International CCN workshop in Oslo, Norway.     

2022, a year of the water tiger

According to Chinese astrology, the Tiger is considered as the king of all animals. The Year of the Tiger 2022 was meant to symbolize determinism, vitality, strength, spontaneity and novelty, with the water element making it wiser and thoughtful. Often associated with the defeat of evil, a Water Tiger year occurs only every 60 years. The 2022 version was indeed a year of resilience, even in the time of conflict and the struggles that we have faced both in personal and professional realms. It was a good time to reflect in order to overcome all challenges and difficulties. The revamping of both the International CCN society (ICCNS) and the Journal of Cell Communication and Signaling (JCCS) that I had previously initiated and officially announced in 2019, are on track to becoming a successful reality and will be pursued over the coming years, thanks to the strong support of our colleagues, members of the JCCS Editorial board and representatives of other scientific societies who support our efforts to broaden the scope of the ICCNS and its communication organ. I will schematically draw below the guidelines that we intend to follow in the near future.     

Another Step Forward to the understanding of Biological Signaling Networks

In this editorial I briefly review the new JCCS scientific directions that have emerged from the complicated situations created by the pandemics of COVID- 19, and by the internal audit of both Journal of Cell Communication and Signaling and International CCN Society, that were initiated since my proposal at the 2019 International Workshop on the CCN family of genes.I also welcome the distinguished members of our renewed JCCS Editorial and congratulate all those who have in many different ways participated to the consolidation of the 2021 JCCS Impact Factor attaining 5.908.     

7th international workshop on the CCN family of genes: Nice to be in nice

In this Editorial, I would like to provide our readers with a brief mid-year update about our activities and efforts to bring together researchers working on intercellular signaling proteins at international meetings. The roots emerged about 20 years ago in the discovery of three genes originally designated cyr61, ctgf, and nov. The proteins encoded by these genes were first proposed to constitute a family of proteins (CCN) which now comprises 6 members (CCN1, CCN2, CCN3, CCN4-6) including the wisp proteins. These proteins were recognized to share a striking structural organization and a high degree of identity although they exhibited quite distinct biological properties. After historical considerations regarding the reasons for using the CCN acronym, and how the ICCNS publishing landscape that drove the ICCNS from Cell Communication and Signaling to the Journal of Cell Communication and Signaling, this short update will focus on the 7th edition of the International Workshop on the CCN family of genes to be held in Nice, Oct 16–19, 2013.     

Dan Salah Tawfik (1955‐2021)—A giant of protein evolution

It was with great sorrow that we have learned of the untimely death of our friend, mentor, collaborator, and hero, Dan Tawfik. Danny was a true legend in the field of protein function and evolution. He had an incredibly creative mind and a breadth of knowledge—his interests spanned chemistry and engineering to genetics and evolution—that allowed him to see connections that the rest of us could not. More importantly, he made solving biochemical mysteries fun: He was passionate about his work, and his face lit up with joy whenever he talked about scientific topics that excited him (of which there were a lot). Conversations with Danny made us all smarter by osmosis.Danny’s own evolution in science began with physical organic chemistry and biochemistry. His PhD at the Weizmann Institute of Science, awarded in 1995, was on catalytic antibodies under the supervision of Zelig Eshhar and Michael Sela. It was followed by a highly productive period at the University of Cambridge’s Centre for Protein Engineering, first as a postdoctoral fellow with Alan Fersht and Tony Kirby, and then as a senior researcher. Among his many achievements during his time in Cambridge was the demonstration that off‐the‐shelf proteins—the serum albumins—could rival the best catalytic antibodies in accelerating the Kemp elimination reaction due to non‐specific medium effects. This work was an early example of unexpected catalytic promiscuity, and it sowed the seed for Danny’s later fascination with “esoteric, niche enzymology” that went far beyond convenient model systems.It was also in Cambridge where Danny first realized the power of the then new field of directed evolution, both for biotechnology and for elucidating evolutionary processes. He and Andrew Griffiths pioneered emulsion‐based in vitro compartmentalization. The idea of controlling biochemical reactions in separate aqueous droplets inspired emulsion PCR and next‐generation sequencing technologies, whereas Danny used it to solve a long‐standing problem in directed evolution; in vitro selection techniques had always been good at identifying ligand‐binding proteins, but compartmentalization finally enabled the directed evolution of ultra‐fast catalysts.Danny returned to Israel in 2001 to join the faculty of the Weizmann Institute of Science where his scientific trajectory further evolved, diverged, and even “drifted”. He developed new methods for enzyme engineering and applied his evolutionary insights into de novo protein design efforts. In this context, Danny’s interest was always focused on how proteins evolve, particularly the connection between promiscuity, conformational diversity, and evolvability. His depth of understanding underpinned both applied research, such as engineering enzymes to detoxify nerve agents, and fundamental research, such as the evolution of enzymes from non‐catalytic scaffolds.Through it all, Danny retained his sense of joy and wonder at the “beautiful aspects of Nature’s chemistry”. This includes his discovery of an exquisite molecular specificity mechanism mediated by a single, short H‐bond that enables microbes to scavenge phosphate in arsenate‐rich environments. In recent years, he deciphered the biosynthetic mechanism of dimethyl sulfide, “the smell of the sea”, and homed in on the interplay between the evolution of an enzyme, its host organism, and environmental complexity. His insights into how the first proteins emerged caused tremendous excitement in the field. He established the roots of two common enzyme lineages, the Rossmann and P‐loop NTPases, as simple polypeptides, and suggested ornithine as the first cationic amino acid. Prior to his death, he published the results of another tour de force: evidence that the first organisms to utilize oxygen may have appeared much earlier than thought.His work impacted many research fields, and he won many significant awards. Most recently, Danny was awarded the EMET Prize for Art, Science and Culture (2020), informally dubbed “Israel’s Nobel Prize”. He was an active and valued member of the EMBO community, having been elected in 2009, and, until his passing, served on the Editorial Advisory Board of EMBO Reports.Danny was also a superb science communicator. Both his research articles and reviews are a joy to read. What stood out just as much as his brilliance was his personality, as he embodied the Yiddish concept of being a true “mensch”. Danny was humble, was down‐to‐earth, and treated all his colleagues—including the most junior members of our research teams—as equals. He championed the careers of others, both those who worked directly for him and those who were lucky enough to be “just” his friends and collaborators. He believed in us even when we did not believe in ourselves, and he was always there to answer questions both scientific and professional. While he loved to share his own ideas, he would be just as excited about ours. Despite his own busy schedule, he always found the time to help others. He was also excellent company, with a great, very dry, sense of humor, and endless interesting stories, including from his own colorful life. In the days after his untimely death, an often‐repeated phrase was “he was my best friend”. Danny’s former group members have gone on to be highly successful in both industry and academia, including more than 15 former doctoral and postdoctoral researchers who are now faculty. The network of researchers Danny has trained, mentored, or influenced is broad, and this legacy is testament to his qualities as both a scientist and a person.Danny was born in Jerusalem to an Iraqi Jewish family, and his Arabic Jewish identity was important to him. He believed strongly in coexistence and peace, and very much valued the Arabic part of his heritage. In his own words: “I am an Israeli, a Jew, an Arab, but first and foremost a human being”. He would often speak of the achievements of his children with immense pride. Danny also had a passion for being outdoors, especially climbing and hiking—when the best discussions were often to be had (Fig ​(Fig1).1). One of the easiest ways to persuade him to come for a seminar, a collaborative visit, or a conference was to have access to high‐quality climbing in the area. He passed away in a tragic rock‐climbing accident, doing what he loved most outside of science. Our thoughts are with his partner Ita and his children, and we join the much broader community of friends, collaborators, and colleagues whose hearts are broken by his sudden loss.Open in a separate windowFigure 1Dan Salah Tawfik (1955–2021)Photo courtesy of Prof. Joel Mackay, The University of Sydney.     

Basic versus applied research: Julius Sachs (1832–1897) and the experimental physiology of plants

The German biologist Julius Sachs was the first to introduce controlled, accurate, quantitative experimentation into the botanical sciences, and is regarded as the founder of modern plant physiology. His seminal monograph Experimental-Physiologie der Pflanzen (Experimental Physiology of Plants) was published 150 y ago (1865), when Sachs was employed as a lecturer at the Agricultural Academy in Poppelsdorf/Bonn (now part of the University). This book marks the beginning of a new era of basic and applied plant science. In this contribution, I summarize the achievements of Sachs and outline his lasting legacy. In addition, I show that Sachs was one of the first biologists who integrated bacteria, which he considered to be descendants of fungi, into the botanical sciences and discussed their interaction with land plants (degradation of wood etc.). This “plant-microbe-view” of green organisms was extended and elaborated by the laboratory botanist Wilhelm Pfeffer (1845–1920), so that the term “Sachs-Pfeffer-Principle of Experimental Plant Research” appears to be appropriate to characterize this novel way of performing scientific studies on green, photoautotrophic organisms (embryophytes, algae, cyanobacteria).     

A special issue of the Australian society for Biophysics

On behalf of the Australian Society for Biophysics (ASB) and the Editors of this Special Issue, I would like to express our appreciation to Editor-in-Chief, Damien Hall, for arranging the publication of this Special Issue. The ASB is about five times smaller than our sister the Biophysical Society for Japan (BSJ) and tenfold smaller than the US Biophysical Society (USBS), but our meetings are notable because of the encouragement the Society gives to emerging biophysicists. It can be a terrifying experience for a PhD student to have to face a roomful of professors and senior academics, but invariably they appreciate the experience. Another feature of the ASB meetings is the inclusion of contributions from the Asian Pacific region. We now have formal ties with our New Zealand colleagues and our meetings with the BSJ contain joint sessions (see below). In 2020, despite the impact of COVID-19 (see Adam Hill’s Commentary), there is a joint session with the University of California Davis. This Special Issue comprises 2 Editorials, 3 Commentaries, and 25 reviews.

When we began to put together an editorial on the contributions to this Special Issue of the 44th meeting of the Australian Society for Biophysics (ASB), we were struck by the sheer diversity of what we call “Biophysics”. Biophysics is actually not easy to define. The glib answer is “Biophysics is what biophysicists do”, but what do they do? If we asked an Australian Minister for Science to tell us what biophysicists do, he or she could tell us what immunologists and virologists do, but would probably have no idea what a biophysicist does. So how should we explain biophysics to the Minister? The US Biophysical Society defines “biophysics” as the field that applies the theories and methods of physics to understand how biological systems work. Operationally, biophysicists analyse the structure of biological molecules like DNA and proteins, they develop computer models to understand how drugs bind to the receptors in the body, and they investigate how gene mutations change the function of proteins.We thought a good example of biophysics research is the article by Boris Martinac at the beginning of this Special Issue. Boris has worked for much of his research life on trying to figure out how a mechanosensitive ion channel works. His “babies” are molecules encoded by the MscL and MscS genes and more recently also by the Piezo1 gene. He realised that bacteria needed to have sensors embedded in their surface membrane so they can quickly produce electrical or chemical signals in response to a mechanical force which occurs in the form of osmotic pressure. This of course is what enables the bacterium to survive when exposed to a hypoosmotic shock. More recently he and his colleagues turned their attention to investigating whether Piezo1 channels are the inherently mechanosensitive channels in vertebrates (Syeda et al. 2016) like MscL and MscS channels are in bacteria. They explained how Piezo receptors respond to changes in mechanical curvature of the cell membranes that open non-specific cation channels, thereby generating an electrical signal. In 2013 Boris was elected to the Australian Academy of Science in recognition of his discovery of bacterial mechanosensitive channels and the physical principles of mechanosensitive channel gating. More recently his work has expanded into the roles of mechanosensitive channels in nerves and heart disease. While we all hope he would get the “big” prize in science, it was his colleague, Ardem Patapoutian, who was awarded a share for the 2021 Nobel Prize in Physiology or Medicine for his research on Piezo1 and Piezo2.The 44th meeting of the Australian Society for Biophysics (ASB) was notable for two other reasons. It was either despite the fact or because it was a virtual meeting that the Society concurrently ran an international symposium with our sister society in Japan the Japanese Society for Biophysics. There is a close connection between the ABS and JSB. For years they have encouraged Australian biophysicists to travel to the large JSB meetings in Japan and they regularly send a strong contingent to Australia. A lot of hard work was put in by Kumiko Hayashi and her colleagues Risa Shibuya and Emi Hibino and the meeting attracted Japanese biophysicists from Tsukuba, Osaka, Kyoto, Shinjuku, Okayama, Kawasaki and Nagoya.The Society also hosted a virtual Early Career Researcher symposium which involved ASB and the University of California Davis. This was chaired by Dr Adam Hill and we refer you to his Commentary where he writes about the challenges and successes of running a virtual meeting “Biophysics in the time of COVID”.The ASB has had a long-standing policy to encourage presentations from early career biophysicists, even as early as PhD students. These young biophysicists prepare carefully and seem to enjoy what can be a terrifying experience. Professor Jamie Vandenberg moderated a session on careers in biophysics where participants discussed the latest technology in ultrasound, the Victor Chang Innovation Centre, strategies for careers outside of traditional biophysics, the importance of scientific communication and advocacy, and the importance intellectual property law, and finally, there were some encouraging words on a career in biophysics from Boris Martinac.Our friends across the “ditch” in New Zealand had a session that discussed calcium imaging in mouse models of disease, the impact fibrosis on Ca signalling, high-content super-resolution microscopy, effects of ryanodine receptor clustering on arrhythmia, the impact of fibrosis on cardiac Ca signalling, how N-glycans affect shear force activation of Na channels, and a fascinating analysis of how insects have managed to adapt their flight muscles to achieve high-frequency flapping flight.The meeting finished with a presentation of the McAuley-Hope prize for a biophysicist who crosses boundaries in biophysics and develops new techniques and methods. It is not always presented but Dr Till Boecking at the University of New South Wales was the well-deserved winner of this much sought-after Prize.     

The 11th international workshop on the CCN family of genes in pictures

The 11th International Workshop on the CCN Family of Genes organized in Nice from October 20th to October 24th, 2022, was the occasion to celebrate the 20th anniversary of the ICCNS meetings.

In order to mark this special event, and as a co-organizer of the workshop, I shot pictures to illustrate the nice days that we spent with all the scientists who accepted to participate in this new episode of the ICCNS workshop series.     

A quantitative analysis of the voltage-current relationships of fixed charge membranes and the associated property of "punch-through"

A theoretical analysis of the voltage-current relationship is carried out in a membrane consisting of two fixed charge regions, of opposite sign, in contact. This is achieved by applying the diffusion equations to this system in conjunction with the Poisson-Boltzmann equation. The latter has been successfully applied by Mauro to determine the profiles of the electrostatic potential in his treatment of the capacitative property of such a system. It is shown that the system displays the property of rectification and is very similar in many respects to a solid state P-N junction diode. It is also shown that for the case of reverse bias, an electrical breakdown phenomena can occur. This is referred to as the “punch-through” effect. “Punch-through” was observed in experiments on the electrical characteristics of the membranes of Chara australis and Nitella sp. The experimental results are discussed in relation to the theoretical analysis.     

A Novel Rickettsia Species Detected in Vole Ticks (Ixodes angustus) from Western Canada

The genomic DNA of ixodid ticks from western Canada was tested by PCR for the presence of Rickettsia. No rickettsiae were detected in Ixodes sculptus, whereas 18% of the I. angustus and 42% of the Dermacentor andersoni organisms examined were PCR positive for Rickettsia. The rickettsiae from each tick species were characterized genetically using multiple genes. Rickettsiae within the D. andersoni organisms had sequences at four genes that matched those of R. peacockii. In contrast, the Rickettsia present within the larvae, nymphs, and adults of I. angustus had novel DNA sequences at four of the genes characterized compared to the sequences available from GenBank for all recognized species of Rickettsia and all other putative species within the genus. Phylogenetic analyses of the sequence data revealed that the rickettsiae in I. angustus do not belong to the spotted fever, transitional, or typhus groups of rickettsiae but are most closely related to “Candidatus Rickettsia kingi” and belong to a clade that also includes R. canadensis, “Candidatus Rickettsia tarasevichiae,” and “Candidatus Rickettsia monteiroi.”     

CCN proteins in the musculoskeletal system: current understanding and challenges in physiology and pathology

The acronym for the CCN family was recently revised to represent “cellular communication network”. These six, small, cysteine-enriched and evolutionarily conserved proteins are secreted matricellular proteins, that convey and modulate intercellular communication by interacting with structural proteins, signalling factors and cell surface receptors. Their role in the development and physiology of musculoskeletal system, constituted by connective tissues where cells are interspersed in the cellular matrix, has been broadly studied. Previous research has highlighted a crucial balance of CCN proteins in mesenchymal stem cell commitment and a pivotal role for CCN1, CCN2 and their alter ego CCN3 in chondrogenesis and osteogenesis; CCN4 plays a minor role and the role of CCN5 and CCN6 is still unclear. CCN proteins also participate in osteoclastogenesis and myogenesis. In adult life, CCN proteins serve as mechanosensory proteins in the musculoskeletal system providing a steady response to environmental stimuli and participating in fracture healing. Substantial evidence also supports the involvement of CCN proteins in inflammatory pathologies, such as osteoarthritis and rheumatoid arthritis, as well as in cancers affecting the musculoskeletal system and bone metastasis. These matricellular proteins indeed show involvement in inflammation and cancer, thus representing intriguing therapeutic targets. This review discusses the current understanding of CCN proteins in the musculoskeletal system as well as the controversies and challenges associated with their multiple and complex roles, and it aims to link the dispersed knowledge in an effort to stimulate and guide readers to an area that the writers consider to have significant impact and relevant potentialities.     

Socio-Demographic Predictors and Distribution of Pulmonary Tuberculosis (TB) in Xinjiang,China: A Spatial Analysis

Objectives

Xinjiang is one of the high TB burden provinces of China. A spatial analysis was conducted using geographical information system (GIS) technology to improve the understanding of geographic variation of the pulmonary TB occurrence in Xinjiang, its predictors, and to search for targeted interventions.

Methods

Numbers of reported pulmonary TB cases were collected at county/district level from TB surveillance system database. Population data were extracted from Xinjiang Statistical Yearbook (2006~2014). Spatial autocorrelation (or dependency) was assessed using global Moran’s I statistic. Anselin’s local Moran’s I and local Getis-Ord statistics were used to detect local spatial clusters. Ordinary least squares (OLS) regression, spatial lag model (SLM) and geographically-weighted regression (GWR) models were used to explore the socio-demographic predictors of pulmonary TB incidence from global and local perspectives. SPSS17.0, ArcGIS10.2.2, and GeoDA software were used for data analysis.

Results

Incidence of sputum smear positive (SS+) TB and new SS+TB showed a declining trend from 2005 to 2013. Pulmonary TB incidence showed a declining trend from 2005 to 2010 and a rising trend since 2011 mainly caused by the rising trend of sputum smear negative (SS-) TB incidence (p<0.0001). Spatial autocorrelation analysis showed the presence of positive spatial autocorrelation for pulmonary TB incidence, SS+TB incidence and SS-TB incidence from 2005 to 2013 (P <0.0001). The Anselin’s Local Moran’s I identified the “hotspots” which were consistently located in the southwest regions composed of 20 to 28 districts, and the “coldspots” which were consistently located in the north central regions consisting of 21 to 27 districts. Analysis with the Getis-Ord Gi* statistic expanded the scope of “hotspots” and “coldspots” with different intensity; 30 county/districts clustered as “hotspots”, while 47 county/districts clustered as “coldspots”. OLS regression model included the “proportion of minorities” and the “per capita GDP” as explanatory variables that explained 64% the variation in pulmonary TB incidence (adjR² = 0.64). The SLM model improved the fit of the OLS model with a decrease in AIC value from 883 to 864, suggesting “proportion of minorities” to be the only statistically significant predictor. GWR model also improved the fitness of regression (adj R² = 0.68, AIC = 871), which revealed that “proportion of minorities” was a strong predictor in the south central regions while “per capita GDP” was a strong predictor for the southwest regions.

Conclusion

The SS+TB incidence of Xinjiang had a decreasing trend during 2005–2013, but it still remained higher than the national average in China. Spatial analysis showed significant spatial autocorrelation in pulmonary TB incidence. Cluster analysis detected two clusters—the “hotspots”, which were consistently located in the southwest regions, and the “coldspots”, which were consistently located in the north central regions. The exploration of socio-demographic predictors identified the “proportion of minorities” and the “per capita GDP” as predictors and may help to guide TB control programs and targeting intervention.     

Distributional records of Ross Sea (Antarctica) Tanaidacea from museum samples stored in the collections of the Italian National Antarctic Museum (MNA) and the New Zealand National Institute of Water and Atmospheric Research (NIWA)

Here we present distributional records for Tanaidacea specimens collected during several Antarctic expeditions to the Ross Sea: the Italian PNRA expeditions (“V”, 1989/1990; “XI”, 1995/1996; “XIV”, 1998/1999; “XIX”, 2003/2004; “XXV”, 2009/2010) and the New Zealand historical (New Zealand Oceanographic Institute, NZOI, 1958-1961) and recent (“TAN0402 BIOROSS” voyage, 2004 and “TAN0802 IPY-CAML Oceans Survey 20/20” voyage, 2008) expeditions. Tanaidaceans were obtained from bottom samples collected at depths ranging from 16 to 3543 m by using a variety of sampling gears. On the whole, this contribution reports distributional data for a total of 2953 individuals belonging to 33 genera and 50 species. All vouchers are permanently stored in the Italian National Antarctic Museum collection (MNA), Section of Genoa (Italy) and at the National Institute of Water and Atmospheric Research (NIWA Invertebrate Collection), Wellington (New Zealand).     

Editorial for Issue 1, Jan 2016 title of the editorial 2016 : A year for JCCS Editorial changes and CCN3 KO mice at ICCNS

The year 2016 will see significant improvements for the Journal of Cell Communication and Signaling with the earning of an official Impact Factor and the merger of Springer Science + Business Media and part of Macmillan Sciences and Education. It will also be an important year for the International CCN Society (ICCNS) with the nomination of a new Scientific Board and reinforcement of interactions with other major scientific societies interested in various aspects of Cell Signaling. Starting this year the ICCNS will become an official provider of CCN3 knock out mice to ICCNS members. This first step in opening up access to certified reagents as a service for our CCN scientific community is part of our intention and efforts to attain the highest degree of assistance and enabler of scientific cooperation and communication in Science Communication.     

It's a Wonderful Life: A Career as an Academic Scientist

Many years of training are required to obtain a job as an academic scientist. Is this investment of time and effort worthwhile? My answer is a resounding “yes.” Academic scientists enjoy tremendous freedom in choosing their research and career path, experience unusual camaraderie in their lab, school, and international community, and can contribute to and enjoy being part of this historical era of biological discovery. In this essay, I further elaborate by listing my top ten reasons why an academic job is a desirable career for young people who are interested in the life sciences.Students are attracted to careers in academic science because of their interest in the subject rather than for financial reward. But then they hear messages that make them think twice about this career choice. It is difficult to find a job: “Hear about Joe? Three publications as a postdoc and still no job offers.” The NIH pay line is low: “Poor Patricia, she is now on her third submission of her first NIH grant.” Publishing is painful: “Felix''s grad school thesis work has been rejected by three journals!” Academic jobs are demanding: “Cathy has spent her last three weekends writing grants rather than being with her family.”Such scenarios do take place, but if you think that this is what a career in academic science is about, then you need to hear the other side of the story. And this is the purpose of this article—a chance to reflect on the many good things about the academic profession. In the classic movie It''s a Wonderful Life, George Bailey is at the point of despair but regains his confidence through the wisdom and perspective of a guardian angel, Clarence. Doubt and setbacks also are bound to happen in science (as is true of other careers), but pessimism should not rule the day. It is a great profession and there are many happy endings. I would like to share my top ten reasons of why being an academic professor is a “wonderful life,” one that bright and motivated young people should continue to aspire to pursue.     

The Search for Significance: A Few Peculiarities in the Distribution of P Values in Experimental Psychology Literature

In this project I investigate the use and possible misuse of p values in papers published in five (high-ranked) journals in experimental psychology. I use a data set of over 135’000 p values from more than five thousand papers. I inspect (1) the way in which the p values are reported and (2) their distribution. The main findings are following: first, it appears that some authors choose the mode of reporting their results in an arbitrary way. Moreover, they often end up doing it in such a way that makes their findings seem more statistically significant than they really are (which is well known to improve the chances for publication). Specifically, they frequently report p values “just above” significance thresholds directly, whereas other values are reported by means of inequalities (e.g. “p<.1”), they round the p values down more eagerly than up and appear to choose between the significance thresholds and between one- and two-sided tests only after seeing the data. Further, about 9.2% of reported p values are inconsistent with their underlying statistics (e.g. F or t) and it appears that there are “too many” “just significant” values. One interpretation of this is that researchers tend to choose the model or include/discard observations to bring the p value to the right side of the threshold.     

Fossil and Genetic Evidence for the Polyphyletic Nature of the Planktonic Foraminifera "Globigerinoides", and Description of the New Genus Trilobatus

Planktonic foraminifera are one of the most abundant and diverse protists in the oceans. Their utility as paleo proxies requires rigorous taxonomy and comparison with living and genetically related counterparts. We merge genetic and fossil evidence of “Globigerinoides”, characterized by supplementary apertures on spiral side, in a new approach to trace their “total evidence phylogeny” since their first appearance in the latest Paleogene. Combined fossil and molecular genetic data indicate that this genus, as traditionally understood, is polyphyletic. Both datasets indicate the existence of two distinct lineages that evolved independently. One group includes “Globigerinoides” trilobus and its descendants, the extant “Globigerinoides” sacculifer, Orbulina universa and Sphaeroidinella dehiscens. The second group includes the Globigerinoides ruber clade with the extant G. conglobatus and G. elongatus and ancestors. In molecular phylogenies, the trilobus group is not the sister taxon of the ruber group. The ruber group clusters consistently together with the modern Globoturborotalita rubescens as a sister taxon. The re-analysis of the fossil record indicates that the first “Globigerinoides” in the late Oligocene are ancestral to the trilobus group, whereas the ruber group first appeared at the base of the Miocene with representatives distinct from the trilobus group. Therefore, polyphyly of the genus "Globigerinoides" as currently defined can only be avoided either by broadening the genus concept to include G. rubescens and a large number of fossil species without supplementary apertures, or if the trilobus group is assigned to a separate genus. Since the former is not feasible due to the lack of a clear diagnosis for such a broad genus, we erect a new genus Trilobatus for the trilobus group (type species Globigerina triloba Reuss) and amend Globoturborotalita and Globigerinoides to clarify morphology and wall textures of these genera. In the new concept, Trilobatus n. gen. is paraphyletic and gave rise to the Praeorbulina / Orbulina and Sphaeroidinellopsis / Sphaeroidinella lineages.     

Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae)

Species of Osmanthus are economically important ornamental trees, yet information regarding their plastid genomes (plastomes) have rarely been reported, thus hindering taxonomic and evolutionary studies of this small but enigmatic genus. Here, we performed comparative genomics and evolutionary analyses on plastomes of 16 of the 28 currently accepted species, with 11 plastomes newly sequenced. Phylogenetic studies identified four main lineages within the genus that are here designated the: “Caucasian Osmanthus” (corresponding to O. decorus), “Siphosmanthus” (corresponding to O. sect. Siphosmanthus), “O. serrulatus + O. yunnanensis,” and “Core Osmanthus: (corresponding to O. sect. Osmanthus + O. sect. Linocieroides). Molecular clock analysis suggested that Osmanthus split from its sister clade c. 15.83 Ma. The estimated crown ages of the lineages were the following: genus Osmanthus at 12.66 Ma; “Siphosmanthus” clade at 5.85 Ma; “O. serrulatus + O. yunnanensis” at 4.89 Ma; and “Core Osmanthus: clade at 6.2 Ma. Ancestral state reconstructions and trait mapping showed that ancestors of Osmanthus were spring flowering and originated at lower elevations. Phylogenetic principal component analysis clearly distinguished spring‐flowering species from autumn‐flowering species, suggesting that flowering time differentiation is related to the difference in ecological niches. Nucleotide substitution rates of 80 common genes showed slow evolutionary pace and low nucleotide variations, all genes being subjected to purifying selection.