Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Putative Promoter Motif Analyses Reinforce the Evolutionary Relationships Among Faustoviruses, Kaumoebavirus, and Asfarvirus

Putative promoter motifs have been described in viruses belonging to the nucleocytoplasmic large DNA viruses (NCLDVs) group; however, few studies have been conducted to search for promoter sequences in newly discovered amoebal giant viruses. Faustovirus and kaumoebavirus are two Asfarviridae-related giant viruses belonging to the NCLDVs group. The phylogenetic relationships among these viruses led us to investigate if the promoter regions previously identified in the asfarvirus genome could be shared by its amoebal virus relatives. Previous studies demonstrated the role of A/T-rich motifs as promoters of asfarvirus. In this study, we reinforce the importance of A/T rich motifs in asfarvirus and show that the TATTT and TATATA motifs are also shared in abundance by faustovirus and kaumoebavirus. Here, we demonstrate that TATTT and TATATA are mostly present in faustovirus and kaumoebavirus genomic intergenic regions (IRs) and that they are widely distributed at 0 to -100 bp upstream to the start codons. We observed that putative promoter motifs are present as one to dozens of repetitions in IRs of faustovirus, kaumoebavirus, and asfarvirus, which is similar to that described previously for marseilleviruses. Furthermore, the motifs were found in most of the upstream regions of the core genes of faustovirus, kaumoebavirus, and asfarvirus, which suggests that the motifs could already be present in the ancestor of these viruses before the irradiation of this group. Our work provides an in-depth analysis of the putative promoter motifs present in asfarvirus, kaumoebavirus, and faustovirus, which reinforces the relationship among these viruses

A long-term prospecting study on giant viruses in terrestrial and marine Brazilian biomes

Abstract The discovery of mimivirus in 2003 prompted the search for novel giant viruses worldwide. Despite increasing interest, the diversity and distribution of giant viruses is barely known. Here, we present data from a 2012–2022 study aimed at prospecting for amoebal viruses in water, soil, mud, and sewage samples across Brazilian biomes, using Acanthamoeba castellanii for isolation. A total of 881 aliquots from 187 samples covering terrestrial and marine Brazilian biomes were processed. Electron microscopy and PCR were used to identify the obtained isolates. Sixty-seven amoebal viruses were isolated, including mimiviruses, marseilleviruses, pandoraviruses, cedratviruses, and yaraviruses. Viruses were isolated from all tested sample types and almost all biomes. In comparison to other similar studies, our work isolated a substantial number of Marseillevirus and cedratvirus representatives. Taken together, our results used a combination of isolation techniques with microscopy, PCR, and sequencing and put highlight on richness of giant virus present in different terrestrial and marine Brazilian biomes

A Brief History of Giant Viruses’ Studies in Brazilian Biomes

Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle sizes, integrating remarkable evolutionary relationships that date as early as the emergence of life on the planet. This year, a decade has passed since the first studies on giant viruses in the Brazilian territory, and since then biomes of rare beauty and biodiversity (Amazon, Atlantic forest, Pantanal wetlands, Cerrado savannas) have been explored in the search for giant viruses. From those unique biomes, novel viral entities were found, revealing never before seen genomes and virion structures. To celebrate this, here we bring together the context, inspirations, and the major contributions of independent Brazilian research groups to summarize the accumulated knowledge about the diversity and the exceptionality of some of the giant viruses found in Brazil

Gene duplication as a major force driving the genome expansion in some giant viruses

International audienceGiant viruses with their gigantic genomes are among the most intriguing components of the virosphere. How these viruses attained such giant genomes remains unclear, despite considerable efforts to understand this phenomenon. Here, we describe the discovery of cedratvirus pambiensis, an amoebal giant virus isolated in Brazil. Although the virion morphology and replication cycle of c. pambiensis are very similar to those described for other cedratviruses, whole genome sequencing revealed the largest cedratvirus genome ever described, with 623,564 base pairs and 842 predicted protein-coding genes (among them, 76 ORFans). Genome analysis has revealed an unprecedented number of paralogous genes, with ~73% of the c. pambiensis genome being composed of genes with two or more copies. Large families of functionally diverse paralogous genes included up to >70 copies and were distributed across the genome. The in-depth investigation of the mechanisms and origins of gene duplications revealed that both tandem-like duplications and distal transfer of syntenic blocks of genes contributed to the c. pambiensis genomic expansion. Finally, a comprehensive genome analysis of viruses from all known giant virus families suggested that gene duplication is one of the key mechanisms underlying genomic gigantism across the phylum Nucleocytoviricota . The expansion of viral genomes through successive duplications followed by subfunctionalization and exaptation of the paralogous gene copies may promote the adaptation of giant viruses to a variety of niches. IMPORTANCE Giant viruses are noteworthy not only due to their enormous particles but also because of their gigantic genomes. In this context, a fundamental question has persisted: how did these genomes evolve? Here we present the discovery of cedratvirus pambiensis, featuring the largest genome ever described for a cedratvirus. Our data suggest that the larger size of the genome can be attributed to an unprecedented number of duplicated genes. Further investigation of this phenomenon in other viruses has illuminated gene duplication as a key evolutionary mechanism driving genome expansion in diverse giant viruses. Although gene duplication has been described as a recurrent event in cellular organisms, our data highlights its potential as a pivotal event in the evolution of gigantic viral genomes

1-Year Outcomes After Transfemoral Transcatheter or Surgical Aortic Valve Replacement: Results From the Italian OBSERVANT Study.

Tamburino C, Barbanti M, D'Errigo P, Ranucci M, Onorati F, Covello RD, Santini F, Rosato S, Santoro G, Fusco D, Grossi C, Seccareccia F; OBSERVANT Research Group. Collaborators (209) Marra S, Marra S, D'Amico M, Gaita F, Moretti C, De Benedictis M, Aranzulla T, Pistis G, Reale M, Bedogni F, Brambilla N, Ferrario M, Ferrero L, Vicinelli P, Colombo A, Chieffo A, Ferrari A, Inglese L, Casilli F, Ettori F, Frontini M, Antona C, Piccaluga E, Klugmann S, De Marco F, Tespili M, Saino A, Leonzi O, Rizzi A, Grisolia E, Franceschini Grisolia E, Isabella G, Fraccaro C, Bernardi G, Bisceglia T, Armellini I, Vischi M, Parodi E, Vignali L, Ardissimo D, Marzocchi A, Marrozzini C, Cremonesi A, Colombo F, Giannini C, Pierli C, Iadanza A, Santoro G, Meucci F, Berti S, Mariani M, Tomai F, Ghini A, Violini R, Confessore P, Crea F, Giubilato S, Sardella G, Mancone M, Ribichini F, Vassanelli C, Dandale R, Giudice P, Vigorito F, Liso A, Specchia L, Indolfi C, Spaccarotella C, Stabile A, Gandolfo C, Tamburino C, Ussia G, Comoglio C, Dyrda O, Rinaldi M, Salizzoni S, Micalizzi E, Grossi C, Di Gregorio O, Scoti P, Costa R, Casabona R, Del Ponte S, Panisi P, Spira G, Troise G, Messina A, Viganò M, Aiello M, Alfieri O, Denti P, Menicanti L, Agnelli B, Donatelli F, Muneretto C, Frontini M, Rambaldini M, Frontini M, Gamba A, Tasca G, Ferrazzi P, Terzi A, Antona C, Gelpi G, Martinelli L, Bruschi G, Graffigna AC, Mazzucco A, Pappalardo A, Gatti G, Livi U, Pompei E, Coppola R, Gucciardo M, Parodi E, Albertini A, Caprili L, Ghidoni I, Gabbieri D, La Marra M, Aquino T, Gherli T, Policlinico S, Di Bartolomeo R, Savini C, Popoff G, Innocenti D, Bortolotti U, Pratali S, Stefano P, Blanzola C, Glauber M, Cerillo A, Chiaramonti F, Pardini A, Fioriello F, Torracca L, Rescigno G, De Paulis R, Nardella S, Musumeci F, Luzi G, Possati G, Bonalumi G, Covino E, Pollari F, Sinatra R, Roscitano A, Chiariello L, Nardi P, Lonobile T, Baldascino F, Di Benedetto G, Mastrogiovanni G, Piazza L, Marmo J, Vosa C, De Amicis V, Speziale G, Visicchio G, Spirito R, Gregorini R, Specchia L, Villani M, Pano MA, Bortone A, De Luca Tupputi Schinosa L, De Cillis E, Gaeta R, Di Natale M, Cassese M, Antonazzo A, Argano V, Santaniello E, Patanè L, Gentile M, Tribastone S, Follis F, Montalbano G, Pilato M, Stringi V, Patanè F, Salamone G, Ruvolo G, Pisano C, Mignosa C, Bivona A, Cirio EM, Lixi G, Seccareccia F, D'Errigo P, Rosato S, Maraschini A, Badoni G, Tamburino C, Santoro G, Santini F, Grossi C, Ranucci M, Covello RD, Fusco D, Onorato F, De Palma R, Scandotto S, Orlando A, Copello F, Borgia P, Marchetta F, Porcu R. BACKGROUND: There is a paucity of prospective and controlled data on the comparative effectiveness of transcatheter aortic valve replacement (TAVR) versus surgical aortic valve replacement (SAVR) in a real-world setting. OBJECTIVES: This analysis aims to describe 1-year clinical outcomes of a large series of propensity-matched patients who underwent SAVR and transfemoral TAVR. METHODS: The OBSERVANT (Observational Study of Effectiveness of SAVR-TAVI Procedures for Severe Aortic Stenosis Treatment) trial is an observational prospective multicenter cohort study that enrolled patients with aortic stenosis (AS) who underwent SAVR or TAVR. The propensity score method was applied to select 2 groups with similar baseline characteristics. All outcomes were adjudicated through a linkage with administrative databases. The primary endpoints of this analysis were death from any cause and major adverse cardiac and cerebrovascular events (MACCE) at 1 year. RESULTS: The unadjusted enrolled population (N = 7,618) included 5,707 SAVR patients and 1,911 TAVR patients. The matched population had a total of 1,300 patients (650 per group). The propensity score method generated a low-intermediate risk population (mean logistic EuroSCORE 1: 10.2 ± 9.2% vs. 9.5 ± 7.1%, SAVR vs. transfemoral TAVR; p = 0.104). At 1 year, the rate of death from any cause was 13.6% in the surgical group and 13.8% in the transcatheter group (hazard ratio [HR]: 0.99; 95% confidence interval [CI]: 0.72 to 1.35; p = 0.936). Similarly, there were no significant differences in the rates of MACCE, which were 17.6% in the surgical group and 18.2% in the transcatheter group (HR: 1.03; 95% CI: 0.78 to 1.36; p = 0.831). The cumulative incidence of cerebrovascular events, and rehospitalization due to cardiac reasons and acute heart failure was similar in both groups at 1 year. CONCLUSIONS: The results suggest that SAVR and transfemoral TAVR have comparable mortality, MACCE, and rates of rehospitalization due to cardiac reasons at 1 year. These data need to be confirmed in longer term and dedicated ongoing randomized trial

Ethical Considerations and Change Recipients’ Reactions: ‘It’s Not All About Me’

An implicit assumption in most works on change recipient reactions is that employees are self-centred and driven by a utilitarian perspective. According to large parts of the organizational change literature, employees’ reactions to organizational change are mainly driven by observations around the question ‘what will happen to me?’ We analysed change recipients’ reactions to 26 large-scale planned change projects in a policing context on the basis of 23 in-depth interviews. Our data show that change recipients drew on observations with three foci (me, colleagues and organization) to assess change, making sense of change as multidimensional and mostly ambivalent in nature. In their assessment of organizational change, recipients care not only about their own personal outcomes, but go beyond self-interested concerns to show a genuine interest in the impact of change on their colleagues and organization. Meaningful engagement of employees in organizational change processes requires recognizing that reactions are not simply ‘all about me’. We add to the organizational change literature by introducing a behavioural ethics perspective on change recipients’ reactions highlighting an ethical orientation where moral motives that trigger change reactions get more attention than is common in the change management literature. Beyond the specifics of our study, we argue that the genuine concern of change recipients for the wellbeing of others, and the impact of the organizations’ activities on internal and external stakeholders, needs to be considered more systematically in research on organizational change

1-Year Outcomes After Transfemoral Transcatheter or Surgical Aortic Valve Replacement: Results From the Italian OBSERVANT Study.

BACKGROUND: There is a paucity of prospective and controlled data on the comparative effectiveness of transcatheter aortic valve replacement (TAVR) versus surgical aortic valve replacement (SAVR) in a real-world setting. OBJECTIVES: This analysis aims to describe 1-year clinical outcomes of a large series of propensity-matched patients who underwent SAVR and transfemoral TAVR. METHODS: The OBSERVANT (Observational Study of Effectiveness of SAVR-TAVI Procedures for Severe Aortic Stenosis Treatment) trial is an observational prospective multicenter cohort study that enrolled patients with aortic stenosis (AS) who underwent SAVR or TAVR. The propensity score method was applied to select 2 groups with similar baseline characteristics. All outcomes were adjudicated through a linkage with administrative databases. The primary endpoints of this analysis were death from any cause and major adverse cardiac and cerebrovascular events (MACCE) at 1 year. RESULTS: The unadjusted enrolled population (N = 7,618) included 5,707 SAVR patients and 1,911 TAVR patients. The matched population had a total of 1,300 patients (650 per group). The propensity score method generated a low-intermediate risk population (mean logistic EuroSCORE 1: 10.2 ± 9.2% vs. 9.5 ± 7.1%, SAVR vs. transfemoral TAVR; p = 0.104). At 1 year, the rate of death from any cause was 13.6% in the surgical group and 13.8% in the transcatheter group (hazard ratio [HR]: 0.99; 95% confidence interval [CI]: 0.72 to 1.35; p = 0.936). Similarly, there were no significant differences in the rates of MACCE, which were 17.6% in the surgical group and 18.2% in the transcatheter group (HR: 1.03; 95% CI: 0.78 to 1.36; p = 0.831). The cumulative incidence of cerebrovascular events, and rehospitalization due to cardiac reasons and acute heart failure was similar in both groups at 1 year. CONCLUSIONS: The results suggest that SAVR and transfemoral TAVR have comparable mortality, MACCE, and rates of rehospitalization due to cardiac reasons at 1 year. These data need to be confirmed in longer term and dedicated ongoing randomized trials