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Fernandez, D.

Publications and source records attributed to Fernandez, D..

32 records · Page 2Linked to original sources

Lasiodiplodia species associated with mango (Mangifera indica L.) decline in Burkina Faso and influence of climatic factors on the disease distribution

Dieback or decline caused by Lasiodiplodia spp. is a major disease of mango trees (Mangifera indica L.). The main objectives of this study were to identify Lasiodiplodia species associated with mango decline in Burkina Faso, and to asses the climatic and edaphic factors affecting the geographic distribution of the disease in the country. The genetic diversity of 47 Lasiodiplodia isolates was studied based on sequence data of the translation elongation factor 1-alpha gene (tef1-a) and the rDNA internal transcribed spacer region (ITS). Phylogeny analyses grouped the isolates from Burkina Faso with 6 different Lasiodiplodia species, including L. euphorbicola that accounted for 36 of the 47 isolates. Lasiodiplodia isolates tested on mango seedlings induced the typical dieback symptoms. Disease incidence and severity were generally higher in the drier and warmer regions (eastern) of the country. This study provides the required information to establish control strategies against mango decline in Burkina Faso.

microbiology↗

Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies

The hydrophobic pocket found in the N-heptad repeat (NHR) region of HIV-1 gp41 is a highly conserved epitope that is the target of various HIV-1 neutralizing monoclonal antibodies. Although the high conservation of the pocket makes it an attractive vaccine candidate, it has been challenging to elicit potent anti-NHR antibodies via immunization. Here, we solved a high-resolution structure of the NHR mimetic IQN17, and, consistent with previous ligand-bound gp41 pocket structures, we observed remarkable conformational plasticity of the pocket. The high malleability of this pocket led us to test whether we could improve the immunogenicity of the gp41 pocket by stabilizing its conformation. We show that the addition of five amino acids at the C-terminus of IQN17, to generate IQN22, introduces a stabilizing salt bridge at the base of the peptide that rigidifies the pocket. Mice immunized with IQN22 elicited higher avidity antibodies against the gp41 pocket and a more potent, albeit still weak, neutralizing response against HIV-1 compared to IQN17. Stabilized epitope-focused immunogens could serve as the basis for future HIV-1 fusion-inhibiting vaccines.

biochemistry↗

Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2

Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2 site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants. One sentence summaryBroadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.

immunology↗

Modeling the evolutionary history of nonclassical monocytes in mammals

The immune system has experienced major changes in both its organization and function during the evolution of tetrapod animals. Still, the ancestry of specific cell types and the historical relationships between modern immune cells has received little attention. While all tetrapods possess mononuclear blood cells and monocytes, vasculature-patrolling nonclassical monocytes (CD16+CD14- in humans, Ly6C- in mice) have so far only been described in mammals. The question of whether nonclassical monocytes are specific to the mammalian lineage has not been answered. Cell types can be described as traits that persist via the inheritance of core regulatory complexes of transcription factors. We utilized transcriptional network analyses on a human monocyte single-cell RNA-sequencing dataset to highlight the core regulatory complex associated with nonclassical monocyte production (nCoRC). We then applied BLAST-based analyses to quantify the conservation of human nCoRC members amongst mammals and nonmammals. We determined that the average sequence similarity of nCoRC members is highest amongst mammals and that such conservation is not observed in non-mammalian tetrapods. We also discovered that this sequence similarity is specifically driven by boreoeutherian placental mammals. Finally, we found the receptor proteins upstream of nonclassical monocyte assembly are also more homologous in mammals than non-mammals. This work provides an evolutionary model in which the capacity for nonclassical monocyte production is unique to the mammalian lineage.

evolutionary biology↗

Peritubular macrophages phagocyte remains of undifferentiated spermatogonia in mouse testis

The cells involved in spermatogenesis are germ-cells, called spermatogonia, classified as: type A-undifferentiated, type A-intermediate and type B. During the spermatogenesis, more than 75% of the germ-cells undergo apoptosis and most of them are phagocyted by Sertoli cells. Peritubular macrophages in adult mouse testis are macrophages that both stimulate the proliferation and differentiation of undifferentiated spermatogonia in the wall of the seminiferous tubule. They have long processes and ramified appearance that squished between the lateral sides of neighbor myoid cells. We show, that a population of peritubular macrophages, grouped in pairs and activated, phagocyted undifferentiated spermatogonia in apoptosis. In adult mouse testis, 3.3x 105 undifferentiated spermatogonia are in the germinal epithelium and 8,250 of them are in apoptosis. We counted in the testis 2,634.2 {+/-}160 peritubular macrophages with phagocytic activity. If each one phagocyted one undifferentiated spermatogonia in apoptosis, it may indicated that peritubular macrophages phagocyted 31.9 % of the total undifferentiated spermatogonia in apoptosis. According to our knowledges, this is the first time that it is shown that undifferentiated spermatogonia in apoptosis are cleaned by peritubular macrophages. Summary SentenceWe report that peritubular macrophages of adult mouse testis, phagocytic remains of apoptotic undifferentiated spermatogonia. These results show that peritubular macrophages, like Sertoli cells, participate in the remotion of germinal cells in the testis.

cell biology↗

Nuanced role for dendritic cell intrinsic IRE1 RNase in the regulation of antitumor adaptive immunity.

The IRE1/XBPls axis of the unfolded protein response (UPR) plays divergent roles in dendritic cell (DC) biology in steady state versus tumor contexts. Whereas tumor associated DCs show dysfunctional IRE1/XBP1s activation that curtails their function, the homeostasis of conventional type 1 DCs (cDC1) in tissues requires intact IRE1 RNase activity. Considering that cDC1s are key orchestrators of antitumor immunity, it is relevant to understand the functional versus dysfunctional roles of IRE1/XBP1s in tumor DC subtypes. Here, we show that cDC1s constitutively activate IRE1 RNase within subcutaneous B16 melanoma and MC38 adenocarcinoma tumor models. Mice lacking XBP1s in DCs display increased melanoma tumor growth, reduced T cell effector responses and accumulation of terminal exhausted CD8+ T cells. Transcriptomic studies revealed that XBP1 deficiency in tumor cDCls decreased expression of mRNAs encoding XBPls and regulated IRE1 dependent decay (RIDD) targets. Finally, we find that the dysregulated melanoma growth and impaired T cell immunity noticed in XBP1 deficient mice are attributed to RIDD induction in DCs. This work indicates that IREl RNase activity in melanoma/MC38-associated DCs fine tunes aspects of antitumor immunity independently of XBP1s, revealing a differential role for the UPR axis that depends on the DC subtype and cancer model.

immunology↗

Planktonic protist diversity across contrasting Subtropical and Subantarctic waters of the southwest Pacific

Planktonic protists are an essential component of marine pelagic ecosystems where they mediate important trophic and biogeochemical functions. Although these functions are largely influenced by their taxonomic affiliation, the composition and spatial variability of planktonic protist communities remain poorly characterized in vast areas of the ocean. Here, we investigated the diversity of these communities in contrasting oceanographic conditions of the southwest Pacific sector (33-58{degrees}S) using DNA metabarcoding of the 18S rRNA gene. Seawater samples collected during twelve cruises (n = 482, 0-2000 m) conducted east of New Zealand were used to characterize protist communities in Subtropical (STW) and Subantarctic (SAW) water masses and the Subtropical Front (STF) that separates them. Diversity decreased with latitude and temperature but tended to be lowest in the STF. Sample ordination resulting from the abundance of amplicon single variants (ASVs) corresponded to the different water masses. Overall, Dinophyceae (34% of standardized total number of reads) and Chlorophyta (27%) co-dominated the euphotic zone, but their relative abundance and composition at class and lower taxonomic levels varied consistently between water masses. Among Chlorophyta, several picoplanktonic algae species of the Mamiellophyceae class including Ostreococcus lucimarinus dominated in STW, while the Chloropicophyceae species Chloroparvula pacifica was most abundant in SAW. Bacillariophyta (7%), Prymnesiophyceae (5%), and Pelagophyceae (3%) classes were less abundant but showed analogous water mass specificity at class and finer taxonomic levels. Protist community composition in the STF had mixed characteristics and showed regional differences with the southern STF (50{degrees}S) having more resemblance with subantarctic communities than the STF over the Chatham Rise region (42-44{degrees}S). Below the euphotic zone, Radiolaria sequences dominated the dataset (52%) followed by Dinophyceae (27%) and other heterotrophic groups like Marine Stramenopiles and ciliates (3%). Among Radiolaria, several unidentified ASVs assigned to Spumellarida were most abundant, but showed significantly different distribution between STW and SAW highlighting the need to further investigate the taxonomy and ecology of this group. This study represents a significant step forward towards characterizing protistan communities composition in relation to major water masses and fronts in the South Pacific providing new insights about the biogeography and ecological preferences of different taxa from class to species and genotypic level. HighlightsO_LIWater-mass preference of different taxa emerged at class, species and genotypic level. C_LIO_LIMamiellophyceae green algae dominated in subtropical waters. C_LIO_LIDinophyceae and Chloropicophyceae green algae dominated in subantarctic waters. C_LIO_LIA diverse assemblage of Radiolaria dominated the mesopelagic zone. C_LIO_LISmall rather than large taxa dominated phytoplankton blooms in subtropical waters. C_LI

ecology↗

Prophylactic and Therapeutic Inhibition of In Vitro SARS-CoV-2 Replication by Oleandrin

With continued expansion of the COVID-19 pandemic, antiviral drugs are desperately needed to treat patients at high risk of life-threatening disease and even to limit spread if administered early during infection. Typically, the fastest route to identifying and licensing a safe and effective antiviral drug is to test those already shown safe in early clinical trials for other infections or diseases. Here, we tested in vitro oleandrin, derived from the Nerium oleander plant and shown previously to have inhibitory activity against several viruses. Using Vero cells, we found that prophylactic oleandrin administration at concentrations down to 0.05 g/ml exhibited potent antiviral activity against SARS-CoV-2, with an 800-fold reduction in virus production, and a 0.1 g/ml dose resulted in a greater than 3,000-fold reduction in infectious virus production. The EC50 values were 11.98ng/ml when virus output was measured at 24 hours post-infection, and 7.07ng/ml measured at 48 hours post-infection. Therapeutic (post-infection) treatment up to 24 hours after infection of Vero cells also reduced viral titers, with the 0.1 g/ml dose causing greater than 100-fold reductions as measured at 48 hours, and the 0.05 g/ml dose resulting in a 78-fold reduction. The potent prophylactic and therapeutic antiviral activities demonstrated here strongly support the further development of oleandrin to reduce the severity of COVID-19 and potentially also to reduce spread by persons diagnosed early after infection. IMPORTANCECOVID-19, a pandemic disease caused by infection with SARS-CoV-2, has swept around the world to cause millions of infections and hundreds-of-thousands of deaths due to the lack of vaccines and effective therapeutics. We tested oleandrin, derived from the Nerium oleander plant and shown previously to reduce the replication of several viruses, against SARS-CoV-2 infection of Vero cells. When administered both before and after virus infection, nanogram doses of oleandrin significantly inhibited replication by up to 3,000-fold, indicating the potential to prevent disease and virus spread in persons recently exposed to SARS-CoV-2, as well as to prevent severe disease in persons at high risk. These results indicate that oleandrin should be tested in animal models and in humans exposed to infection to determine its medical usefulness in controlling the pandemic.

microbiology↗

Structure-aided development of small molecule inhibitors of ENPP1, the extracellular phosphodiesterase of the immunotransmitter cGAMP

Cancer cells initiate an innate immune response by synthesizing and exporting the small molecule immunotransmitter cGAMP, which activates the anti-cancer Stimulator of Interferon Genes (STING) pathway in the host. An extracellular enzyme, ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1), hydrolyzes cGAMP and negatively regulates this anti-cancer immune response. Small molecule ENPP1 inhibitors are much needed as tools to study basic biology of extracellular cGAMP and as investigational cancer immunotherapy drugs. Here, we surveyed structure-activity relationships around a series of cell-impermeable and thus extracellular-targeting phosphonate inhibitors of ENPP1. Additionally, we solved the crystal structure of an exemplary phosphonate inhibitor to elucidate the interactions that drive potency. This study yielded several best-in-class compounds with Ki < 2 nM and excellent physicochemical and pharmacokinetic properties. Finally, we demonstrate that an ENPP1 inhibitor delays tumor growth in a breast cancer mouse model. Together, we have developed ENPP1 inhibitors that are excellent tool compounds and potential therapeutics.

biochemistry↗

Early-Career Coordinated Distributed Experiments: Empowerment Through Collaboration

Coordinated distributed experiments (CDEs) enable the study of large-scale ecological patterns in geographically dispersed areas, while simultaneously providing broad academic and personal benefits for the participants. However, the effective involvement of early-career researchers (ECRs) presents major challenges. Here, we analyze the benefits and challenges of the first CDE exclusively led and conducted by ECRs (i.e. ECR-CDE), which sets a baseline for similar CDEs, and we provide recommendations for successful CDE execution. ECR-CDEs achieve most of the outcomes identified in conventional CDEs as well as extensive benefits for the young cohort of researchers, including: (i) receiving scientific credit, (ii) peer-training in new concepts and methods, (iii) developing leadership and communication skills, (iv) promoting a peer network among ECRs, and (v) building on individual engagement and independence. We also discuss the challenges of ECR-CDEs, which are mainly derived from the lack of independence and instability of the participants, and we suggest mechanisms to address them, such as resource re-allocation and communication strategies.

scientific communication and education↗

Chemical precision glyco-mutagenesis by glycosyltransferase engineering in living cells

Studying posttranslational modifications classically relies on experimental strategies that oversimplify the complex biosynthetic machineries of living cells. Protein glycosylation contributes to essential biological processes, but correlating glycan structure, underlying protein and disease-relevant biosynthetic regulation is currently elusive. Here, we engineer living cells to tag glycans with editable chemical functionalities while providing information on biosynthesis, physiological context and glycan fine structure. We introduce a non-natural substrate biosynthetic pathway and use engineered glycosyltransferases to incorporate chemically tagged sugars into the cell surface glycome of the living cell. We apply the strategy to a particularly redundant yet disease-relevant human glycosyltransferase family, the polypeptide N-acetylgalactosaminyl transferases. This approach bestows a gain-of-function modification on cells where the products of individual glycosyltransferases can be selectively characterized or manipulated at will.

synthetic biology↗

HAVE IT, KNOW IT, BUT DO NOT SHOW IT: EXAMINING PHYSIOLOGICAL AROUSAL, ANXIETY, AND FACIAL EXPRESSIONS OVER THE COURSE OF A SOCIAL SKILLS INTERVENTION FOR AUTISTIC ADOLESCENTS

Facial expressions provide a nonverbal mechanism for social communication, a core challenge for autistic people. Little is known regarding the association between arousal, self-report of anxiety, and facial expressions among autistic adolescents. Therefore, this study investigated session-by-session facial expressions, self-report of anxiety, and physiological arousal via Electrodermal Activity (EDA), of 12 autistic male adolescents in a didactic social skills intervention setting. The goals of this study were threefold: 1) identify physiological arousal levels (\"have-it\"), 2) examine if autistic adolescents facial expressions indicated arousal (\"show-it\"), and 3) determine whether autistic adolescents were self-aware of their anxiety (\"know-it\"). Our results showed that autistic adolescents self-rated anxiety was significantly associated with peaks in EDA. Both machine learning algorithms and human participant-based methods, however, had low accuracy in predicting autistic adolescents arousal state from facial expressions, suggesting that autistic adolescents facial expressions did not coincide with their arousal. Implications for understanding social communication difficulties among autistic adolescents, as well as future targets for intervention, are discussed. This project is registered with ClinicalTrials.gov, Identifier: NCT02680015.

bioinformatics↗

STING polymer structure reveals mechanisms for activation, hyperactivation, and inhibition

How the central innate immune protein, STING, is activated by its ligands remains unknown. Here, using structural biology and biochemistry, we report that the metazoan second messenger 23-cGAMP induces closing of the human STING homodimer and release of the STING C-terminal tail, which exposes a polymerization interface on the STING dimer and leads to the formation of disulfide-linked polymers via cysteine residue 148. Disease-causing hyperactive STING mutations either flank C148 and depend on disulfide formation or reside in the C-terminal tail binding site and cause constitutive C-terminal tail release and polymerization. Finally, bacterial cyclic-di-GMP induces an alternative active STING conformation, activates STING in a cooperative manner, and acts as a partial antagonist of 23-cGAMP signaling. Our insights explain the tight control of STING signaling given varying background activation signals and provide a novel therapeutic hypothesis for autoimmune syndrome treatment.

biochemistry↗

Distinct ipRGC subpopulations mediate light’s acute and circadian effects on body temperature and sleep

The light environment greatly impacts human alertness, mood, and cognition by acute regulation of physiology and indirect alignment of circadian rhythms. Both processes require the melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs), but the relevant downstream brain areas remain elusive. ipRGCs project widely in the brain, including to the central circadian pacemaker, the suprachiasmatic nucleus (SCN). Here we show that body temperature and sleep responses to light are absent after genetic ablation of all ipRGCs except a subpopulation that projects to the SCN. Furthermore, by chemogenetic activation of the ipRGCs that avoid the SCN, we show that these cells are sufficient for acute changes in body temperature. Our results challenge the idea that the SCN is a major relay for the acute effects of light on non-image forming behaviors and identify the sensory cells that initiate lights profound effects on body temperature and sleep.

neuroscience↗