Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions.

In 2020, the world faced the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic that drastically altered people's lives. Since then, many countries have been forced to suspend public gatherings, leading to many conference cancellations, postponements, or reorganizations. Switching from a face-to-face to a remote conference became inevitable and the ultimate solution to sustain scientific exchanges at the national and the international levels. The same year, as a committee, we were in charge of organizing the major French annual conference that covers all computational biology areas: The "Journées Ouvertes en Biologie, Informatique et Mathématiques" (JOBIM). Despite the health crisis, we succeeded in changing the conference format from face to face to remote in a very short amount of time. Here, we propose 10 simple rules based on this experience to modify a conference format in an optimized and cost-effective way. In addition to the suggested rules, we decided to emphasize an unexpected benefit of this situation: a significant reduction in greenhouse gas (GHG) emissions related to travel for scientific conference attendance. We believe that even once the SARS-CoV-2 crisis is over, we collectively will have an opportunity to think about the way we approach such scientific events over the longer term.

Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas.

BACKGROUND AND AIMS: Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. METHODS: Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. KEY RESULTS: Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. CONCLUSIONS: The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.

High-Resolution Photonic Force Microscopy Based on Sharp Nanofabricated Tips.

Although near-field imaging techniques reach sub-nanometer resolution on rigid samples, it remains extremely challenging to image soft interfaces, such as biological membranes, due to the deformations induced by the probe. In photonic force microscopy, optical tweezers are used to manipulate and measure the scanning probe, allowing imaging of soft materials without force-induced artifacts. However, the size of the optically trapped probe still limits the maximum resolution. Here, we show a novel and simple nanofabrication protocol to massively produce optically trappable quartz particles which mimic the sharp tips of atomic force microscopy. Imaging rigid nanostructures with our tips, we resolve features smaller than 80 nm. Scanning the membrane of living malaria-infected red blood cells reveals, with no visible artifacts, submicron features termed knobs, related to the parasite activity. The use of nanoengineered particles in photonic force microscopy opens the way to imaging soft samples at high resolution.

New Export Pathway in Plasmodium falciparum-Infected Erythrocytes: Role of the Parasite Group II Chaperonin, PfTRiC.

The export of numerous proteins to the plasma membrane of its host erythrocyte is essential for the virulence and survival of the malaria parasite Plasmodium falciparum. The Maurer's clefts, membrane structures transposed by the parasite in the cytoplasm of its host erythrocyte, play the role of a marshal platform for such exported parasite proteins. We identify here the export pathway of three resident proteins of the Maurer's clefts membrane: the proteins are exported as soluble forms in the red cell cytoplasm to the Maurer's clefts membrane in association with the parasite group II chaperonin (PfTRIC), a chaperone complex known to bind and address a large spectrum of unfolded proteins to their final location. We have also located the domain of interaction with PfTRiC within the amino-terminal domain of one of these Maurer's cleft proteins, PfSBP1. Because several Maurer's cleft membrane proteins with different export motifs seem to follow the same route, we propose a general role for PfTRiC in the trafficking of malarial parasite proteins to the host erythrocyte.

Proteomic analysis of detergent-resistant membrane microdomains in trophozoite blood stage of the human malaria parasite Plasmodium falciparum.

Intracellular pathogens contribute to a significant proportion of infectious diseases worldwide. The successful strategy of evading the immune system by hiding inside host cells is common to all the microorganism classes, which exploit membrane microdomains, enriched in cholesterol and sphingolipids, to invade and colonize the host cell. These assemblies, with distinct biochemical properties, can be isolated by means of flotation in sucrose density gradient centrifugation because they are insoluble in nonionic detergents at low temperature. We analyzed the protein and lipid contents of detergent-resistant membranes from erythrocytes infected by Plasmodium falciparum, the most deadly human malaria parasite. Proteins associated with membrane microdomains of trophic parasite blood stages (trophozoites) include an abundance of chaperones, molecules involved in vesicular trafficking, and enzymes implicated in host hemoglobin degradation. About 60% of the identified proteins contain a predicted localization signal suggesting a role of membrane microdomains in protein sorting/trafficking. To validate our proteomic data, we raised antibodies against six Plasmodium proteins not characterized previously. All the selected candidates were recovered in floating low-density fractions after density gradient centrifugation. The analyzed proteins localized either to internal organelles, such as the mitochondrion and the endoplasmic reticulum, or to exported membrane structures, the parasitophorous vacuole membrane and Maurer's clefts, implicated in targeting parasite proteins to the host erythrocyte cytosol or surface. The relative abundance of cholesterol and phospholipid species varies in gradient fractions containing detergent-resistant membranes, suggesting heterogeneity in the lipid composition of the isolated microdomain population. This study is the first report showing the presence of cholesterol-rich microdomains with distinct properties and subcellular localization in trophic stages of Plasmodium falciparum.

Characterization of a serine hydrolase targeted by acyl-protein thioesterase inhibitors in Toxoplasma gondii.

In eukaryotic organisms, cysteine palmitoylation is an important reversible modification that impacts protein targeting, folding, stability, and interactions with partners. Evidence suggests that protein palmitoylation contributes to key biological processes in Apicomplexa with the recent palmitome of the malaria parasite Plasmodium falciparum reporting over 400 substrates that are modified with palmitate by a broad range of protein S-acyl transferases. Dynamic palmitoylation cycles require the action of an acyl-protein thioesterase (APT) that cleaves palmitate from substrates and conveys reversibility to this posttranslational modification. In this work, we identified candidates for APT activity in Toxoplasma gondii. Treatment of parasites with low micromolar concentrations of ß-lactone- or triazole urea-based inhibitors that target human APT1 showed varied detrimental effects at multiple steps of the parasite lytic cycle. The use of an activity-based probe in combination with these inhibitors revealed the existence of several serine hydrolases that are targeted by APT1 inhibitors. The active serine hydrolase, TgASH1, identified as the homologue closest to human APT1 and APT2, was characterized further. Biochemical analysis of TgASH1 indicated that this enzyme cleaves substrates with a specificity similar to APTs, and homology modeling points toward an APT-like enzyme. TgASH1 is dispensable for parasite survival, which indicates that the severe effects observed with the ß-lactone inhibitors are caused by the inhibition of non-TgASH1 targets. Other ASH candidates for APT activity were functionally characterized, and one of them was found to be resistant to gene disruption due to the potential essential nature of the protein.

Novel Plasmodium falciparum Maurer's clefts protein families implicated in the release of infectious merozoites.

The pathogenicity of the most deadly human malaria parasite, Plasmodium falciparum, relies on the export of virulence factors to the surface of infected erythrocytes. A novel membrane compartment, referred to as Maurer's clefts, is transposed to the host erythrocyte, acting as a marshal platform in the red blood cell cytoplasm, for exported parasite proteins addressed to the host cell plasma membrane. We report here the characterization of three new P. falciparum multigene families organized in 9 highly conserved clusters with the Pfmc-2tm genes in the subtelomeric regions of parasite's chromosomes and expressed at early trophozoite stages. Like the PfMC-2TM proteins, the PfEPF1, 3 and 4 proteins encoded by these families are exported to the Maurer's clefts, as peripheral or integral proteins of the Maurer's cleft membrane and largely exposed to the red cell cytosolic face of this membrane. A promoter titration approach was used to question the biological roles of these P. falciparum-specific exported proteins. Using the Pfepf1 family promoter, we observed the specific downregulation of all four families, correlating with the inefficient release of merozoites while the parasite intra-erythrocytic maturation and Maurer's clefts morphology were not impacted.

A novel mechanism for egress of malarial parasites from red blood cells.

The culminating step of the intraerythrocytic development of Plasmodium falciparum, the causative agent of malaria, is the spectacular release of multiple invasive merozoites on rupture of the infected erythrocyte membrane. This work reports for the first time that the whole process, taking place in time scales as short as 400 milliseconds, is the result of an elastic instability of the infected erythrocyte membrane. Using high-speed differential interference contrast (DIC) video microscopy and epifluorescence, we demonstrate that the release occurs in 3 main steps after osmotic swelling of the infected erythrocyte: a pore opens in ~ 100 milliseconds, ejecting 1-2 merozoites, an outward curling of the erythrocyte membrane is then observed, ending with a fast eversion of the infected erythrocyte membrane, pushing the parasites forward. It is noteworthy that this last step shows slight differences when infected erythrocytes are adhering. We rationalize our observations by considering that during the parasite development, the infected erythrocyte membrane acquires a spontaneous curvature and we present a subsequent model describing the dynamics of the curling rim. Our results show that sequential erythrocyte membrane curling and eversion is necessary for the parasite efficient angular dispersion and might be biologically essential for fast and numerous invasions of new erythrocytes.

Dematin, a component of the erythrocyte membrane skeleton, is internalized by the malaria parasite and associates with Plasmodium 14-3-3.

The malaria parasite invades the terminally differentiated erythrocytes, where it grows and multiplies surrounded by a parasitophorous vacuole. Plasmodium blood stages translocate newly synthesized proteins outside the parasitophorous vacuole and direct them to various erythrocyte compartments, including the cytoskeleton and the plasma membrane. Here, we show that the remodeling of the host cell directed by the parasite also includes the recruitment of dematin, an actin-binding protein of the erythrocyte membrane skeleton and its repositioning to the parasite. Internalized dematin was found associated with Plasmodium 14-3-3, which belongs to a family of conserved multitask molecules. We also show that, in vitro, the dematin-14-3-3 interaction is strictly dependent on phosphorylation of dematin at Ser(124) and Ser(333), belonging to two 14-3-3 putative binding motifs. This study is the first report showing that a component of the erythrocyte spectrin-based membrane skeleton is recruited by the malaria parasite following erythrocyte infection.

Human erythrocyte remodelling during Plasmodium falciparum malaria parasite growth and egress.

The intra-erythrocyte growth and survival of the malarial parasite Plasmodium falciparum is responsible for both uncomplicated and severe malaria cases and depends on the parasite's ability to remodel its host cell. Host cell remodelling has several functions for the parasite, such as acquiring nutrients from the extracellular milieu because of the loss of membrane transporters upon erythrocyte differentiation, avoiding splenic clearance by conferring cytoadhesive properties to the infected erythrocyte, escaping the host immune response by exporting antigenically variant proteins at the red blood cell surface. In addition, parasite-induced changes at the red blood cell membrane and sub-membrane skeleton are also necessary for the efficient release of the parasite progeny from the host cell. Here we review these cellular and molecular changes, which might not only sustain parasite growth but also prepare, at a very early stage, the last step of egress from the host cell.

Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas.

Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.

Draft Genome Sequence of Fusarium oxysporum f. sp. cubense Tropical Race 4 from Peru, Obtained by Nanopore and Illumina Hybrid Assembly.

Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is the causal agent of Fusarium wilt, a major threat to the banana industry worldwide. Here, we report the genome of a Foc TR4 strain from Peru, sequenced using a combination of Illumina and Oxford Nanopore Technologies.

The banana genome hub: a community database for genomics in the Musaceae.

The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.

Export of PfSBP1 to the Plasmodium falciparum Maurer's clefts.

The human malaria parasite Plasmodium falciparum exports determinants of virulence and pathology to destinations within the host erythrocyte, including the erythrocyte cytoplasm, plasma membrane and membrane profiles of parasite origin termed Maurer's clefts. Most of the exported proteins contain a conserved pentameric motif termed plasmodial export element (PEXEL)/vacuolar transfer signal (VTS) that functions as a cleavable sorting signal permitting export to the host erythrocyte. However, there are some exported proteins, such as the skeleton-binding protein 1 (PfSBP1) that lack the PEXEL/VTS motif and that are not N-terminally processed, suggesting the presence of alternative sorting signals and/or mechanisms. In this study, we have investigated trafficking of PfSBP1 to the Maurer's clefts. Our data show that the transmembrane domain of PfSBP1 functions as an internal signal sequence for entry into the parasite's secretory pathway and for transport to the parasite plasma membrane. Trafficking beyond the parasite's plasma membrane required additional N-terminal domains, which are characterized by a high negative net charge. Biochemical data indicate that these domains affect the solubility and extraction profile, the orientation of the protein within the membrane and the subcellular localization. Our findings suggest new principles of protein export in P. falciparum-infected erythrocytes.

A Dual-Successive-Screen Model at Pollen/Stigma and Pollen Tube/Ovary Explaining Paradoxical Self-Incompatibility Diagnosis in the Olive Tree-An Interpretative Update of the Literature.

The 'pollen test' and 'fruit set test' following controlled crossing combinations of parents are the most commonly used methods for pollination incompatibility studies in Olea europaea L. Self-incompatibility (SI), with diagnoses based on the pollen test and pollen germination, indicating self-compatibility, is not always followed by fruit set in this species. To solve this dispute, we have reconciled all observations into a new model. Mismatches between field and laboratory data and between methods are resolved by the dual-successive-screen model (DSSM) supposing two different loci for the expression of the two SI mechanisms. Pollen/stigma is controlled by diallelic SI, or DSI, inferring two G1 and G2 compatibility/incompatibility (C/I) groups for varieties, whereas pollen tubes in ovaries are controlled by poly-allelic SI or PASI with twenty C/I groups. To explain the selfing of varieties, we have suggested that some determinants in the pollen tube and stigma are unstable and degrade (DS-D for degradation of S-determinant) after three to five days, enabling some pollen tubes to avoid being rejected, hence reaching ovules. DSI and PASI in the DSSM and DS-D mechanisms, plus the andromonoecy of the olive tree, complexify SI studies. Inferences from DSSM and DS-D mechanisms in olive orchard practice are detailed.

Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes.

Asexual proliferation of the Plasmodium parasites that cause malaria follows a developmental program that alternates non-canonical intraerythrocytic replication with dissemination to new host cells. We carried out a functional analysis of the Plasmodium falciparum homolog of Protein Phosphatase 1 (PfPP1), a universally conserved cell cycle factor in eukaryotes, to investigate regulation of parasite proliferation. PfPP1 is indeed required for efficient replication, but is absolutely essential for egress of parasites from host red blood cells. By phosphoproteomic and chemical-genetic analysis, we isolate two functional targets of PfPP1 for egress: a HECT E3 protein-ubiquitin ligase; and GCα, a fusion protein composed of a guanylyl cyclase and a phospholipid transporter domain. We hypothesize that PfPP1 regulates lipid sensing by GCα and find that phosphatidylcholine stimulates PfPP1-dependent egress. PfPP1 acts as a key regulator that integrates multiple cell-intrinsic pathways with external signals to direct parasite egress from host cells.

The RhopH complex is transferred to the host cell cytoplasm following red blood cell invasion by Plasmodium falciparum.

The high-molecular mass rhoptry protein complex (PfRhopH), which comprises three distinct gene products, RhopH1, RhopH2, and RhopH3, is known to be secreted and transferred to the parasitophorous vacuole membrane upon invasion of a red blood cell by the malaria parasite Plasmodium falciparum. Here we show that the merozoite-acquired RhopH complex is also transferred to defined domains of the red blood cell cytoplasm, and possibly transiently associated with Maurer's clefts. This is the first report of trafficking in the host cell cytoplasm for P. falciparum rhoptry proteins secreted upon red blood cell invasion. Based on its newly identified sub-cellular location and the phenotype of RhopH1 mutants, we propose that the RhopH complex participate in the assembly of the cytoadherence complex.

Reply to Saumitou-Laprade et al. (2017) "Controlling for genetic identity of varieties, pollen contamination and stigma receptivity is essential to characterize the self-incompatibility system of Olea europaea L.". Eva:https://doi.org/10.1111/eva.12498.

This study was carried out to examine the validity of previous studies on the intercompatibility of olive and to compare the approach and techniques used for proposing the diallelic self-incompatibility system and the sporophytic self-incompatibility system. Analysis of the literature indicates that the mating system of the olive tree is a controversial issue and requires further studies to clearly and fully comprehend it. All possible approaches should be used to maximize reliability of the final conclusions on the olive mating system.

Sequential Membrane Rupture and Vesiculation during Plasmodium berghei Gametocyte Egress from the Red Blood Cell.

Malaria parasites alternate between intracellular and extracellular stages and successful egress from the host cell is crucial for continuation of the life cycle. We investigated egress of Plasmodium berghei gametocytes, an essential process taking place within a few minutes after uptake of a blood meal by the mosquito. Egress entails the rupture of two membranes surrounding the parasite: the parasitophorous vacuole membrane (PVM), and the red blood cell membrane (RBCM). High-speed video microscopy of 56 events revealed that egress in both genders comprises four well-defined phases, although each event is slightly different. The first phase is swelling of the host cell, followed by rupture and immediate vesiculation of the PVM. These vesicles are extruded through a single stabilized pore of the RBCM, and the latter is subsequently vesiculated releasing the free gametes. The time from PVM vesiculation to completion of egress varies between events. These observations were supported by immunofluorescence microscopy using antibodies against proteins of the RBCM and PVM. The combined results reveal dynamic re-organization of the membranes and the cortical cytoskeleton of the erythrocyte during egress.

'Comment on Saumitou et al. (2017): Elucidation of the genetic architecture of self-incompatibility in olive: evolutionary consequences and perspectives for orchard management'.

The new self-incompatibility system (SI) was presented by Saumitou-Laprade, Vernet, Vekemans et al. (2017). Evolutionary Applications based on 89 crosses between varieties in the olive tree. Four main points are not clear. We are examining here as follows: (i) the assertion that the self-incompatibility system is sporophytic was not sustained by pollen germination data; (ii) surprisingly, the new model does not explain that about one-third of pairwise combinations of olive varieties leads to asymmetric fruit setting; (iii) DNA preparation from one seed may contain two embryos, and thus, embryos should be separated before seed extraction; (iv) although effective self-fertility in olive varieties was reported by many studies, the DSI model fails to explain self-fertility in some olive varieties. Moreover, we cannot discuss result data, as science cannot be verified because variety names were encoded, this does not allow comparison of data with previous works. The DSI model on olive self-incompatibility should explain more features than the model based on four dominance levels shared by six S-alleles. Perspectives for orchard management based on this model may face serious limitations. An olive variety does not have a fifty percent chance of cross-incompatibility, but surely fewer, and thus, the sporophytic system limits fruit production. Evolutionary perspectives of self-incompatibility in Oleaceae should include data from the Jasmineae tribe that displays heterostyly SI.