Search

[This corrects the article DOI: 10.1371/journal.ppat.1008307.].

Chemical pesticides have an immense role in curbing the infection of plant viruses and soil-borne pathogens of high valued crops. However, the usage of chemical pesticides also contributes to the development of resistance among pathogens. Hence, attempts were made in this study to identify a suitable bacterial antagonist for managing viral and fungal pathogens infecting crop plants. Based on our earlier investigations, we identified Bacillus amyloliquefaciens VB7 as a potential antagonist for managing Sclerotinia sclerotiorum infecting carnation, tobacco streak virus infecting cotton and groundnut bud necrosis infecting tomato. Considering the multifaceted action of B. amyloliquefaciens VB7, attempts were made for whole-genome sequencing to assess the antiviral activity against tomato spotted wilt virus infecting chrysanthemum and antifungal action against Fusarium oxysporum f. sp. cubense (Foc). Genome annotation of the isolate B. amyloliquefaciens VB7 was confirmed as B. velezensis VB7 with accession number CP047587. Genome analysis revealed the presence of 9,231,928 reads with an average read length of 149 bp. Assembled genome had 1 contig, with a total length of 3,021,183 bp and an average G+C content of 46.79%. The protein-coding sequences (CDS) in the genome was 3090, transfer RNA (tRNA) genes were 85 with 29 ribosomal RNA (rRNA) genes and 21 repeat regions. The genome of B. velezensis VB7 had 506 hypothetical proteins and 2584 proteins with functional assignments. VB7 genome had the presence of flagellin protein FlaA with 987 nucleotides and translation elongation factor TU (Ef-Tu) with 1191 nucleotides. The identified ORFs were 3911 with 47.22% GC content. Non ribosomal pepide synthetase cluster (NRPS) gene clusters in the genome of VB7, coded for the anti-microbial peptides surfactin, butirosin A/butirosin B, fengycin, difficidin, bacillibactin, bacilysin, and mersacidin the Ripp lanthipeptide. Antiviral action of VB7 was confirmed by suppression of local lesion formation of TSWV in the local lesion host cowpea (Co-7). Moreover, combined application of B. velezensis VB7 with phyto-antiviral principles M. Jalapa and H. cupanioides increased shoot length, shoot diameter, number of flower buds per plant, flower diameter, and fresh weight of chrysanthemum. Further, screening for antifungal action of VB7 expressed antifungal action against Foc in vitro by producing VOC/NVOC compounds, including hexadecanoic acid, linoelaidic acid, octadecanoic acid, clindamycin, formic acid, succinamide, furanone, 4H-pyran, nonanol and oleic acid, contributing to the total suppression of Foc apart from the presence of NRPS gene clusters. Thus, our study confirmed the scope for exploring B. velezensis VB7 on a commercial scale to manage tomato spotted wilt virus, groundnut bud necrosis virus, tobacco streak virus, S. sclerotiorum, and Foc causing panama wilt of banana.

The ability of HIV-1 to evolve resistance to combined antiretroviral therapies (cARTs) has stimulated research into alternative means of controlling this infection. We assayed >60 modulators of RNA alternative splicing (AS) to identify new inhibitors of HIV-1 RNA processing-a segment of the viral lifecycle not targeted by current drugs-and discovered compound N-[4-chloro-3-(trifluoromethyl)phenyl]-7-nitro-2,1,3-benzoxadiazol-4-amine (5342191) as a potent inhibitor of both wild-type (Ba-L, NL4-3, LAI, IIIB, and N54) and drug-resistant strains of HIV-1 (IC50: ~700 nM) with no significant effect on cell viability at doses tested. 5342191 blocks expression of four essential HIV-1 structural and regulatory proteins (Gag, Env, Tat, and Rev) without affecting total protein synthesis of the cell. This response is associated with altered unspliced (US) and singly-spliced (SS) HIV-1 RNA accumulation (~60% reduction) and transport to the cytoplasm (loss of Rev) whereas parallel analysis of cellular RNAs revealed less than a 0.7% of host alternative splicing (AS) events (0.25-0.67% by ≥ 10-20%), gene expression (0.01-0.46% by ≥ 2-5 fold), and protein abundance (0.02-0.34% by ≥ 1.5-2 fold) being affected. Decreased expression of Tat, but not Gag/Env, upon 5342191 treatment was reversed by a proteasome inhibitor, suggesting that this compound alters the synthesis/degradation of this key viral factor. Consistent with an affect on HIV-1 RNA processing, 5342191 treatment of cells altered the abundance and phosphorylation of serine/arginine-rich splicing factor (SRSF) 1, 3, and 4. Despite the activation of several intracellular signaling pathways by 5342191 (Ras, MEK1/2-ERK1/2, and JNK1/2/3), inhibition of HIV-1 gene expression by this compound could be reversed by pre-treatment with either a G-protein α-subunit inhibitor or two different MEK1/2 inhibitors. These observations demonstrate enhanced sensitivity of HIV-1 gene expression to small changes in host RNA processing and highlights the potential of modulating host intracellular signaling as an alternative approach for controlling HIV-1 infection.

The conduit network is a hallmark of lymph node microanatomy, but lack of suitable imaging technology has prevented comprehensive investigation of its topology. We employed an extended-volume imaging system to capture the conduit network of an entire murine lymph node (comprising over 280,000 segments). The extensive 3D images provide a comprehensive overview of the regions supplied by conduits, including perivascular sleeves and distinctive "follicular reservoirs" within B cell follicles, surrounding follicular dendritic cells. A 3D topology map of conduits within the T-cell zone showed homogeneous branching, but conduit density was significantly higher in the superficial T-cell zone compared with the deep zone, where distances between segments are sufficient for T cells to lose contact with fibroblastic reticular cells. This topological mapping of the conduit anatomy can now aid modeling of its roles in lymph node function, as we demonstrate by simulating T-cell motility in the different T-cell zones.

Dengue virus (DENV) is the most prevalent, medically important mosquito-borne virus. Disease ranges from uncomplicated dengue to life-threatening disease, characterized by endothelial dysfunction and vascular leakage. Previously, we demonstrated that DENV nonstructural protein 1 (NS1) induces endothelial hyperpermeability in a systemic mouse model and human pulmonary endothelial cells, where NS1 disrupts the endothelial glycocalyx-like layer. NS1 also triggers release of inflammatory cytokines from PBMCs via TLR4. Here, we examined the relative contributions of inflammatory mediators and endothelial cell-intrinsic pathways. In vivo, we demonstrated that DENV NS1 but not the closely-related West Nile virus NS1 triggers localized vascular leak in the dorsal dermis of wild-type C57BL/6 mice. In vitro, we showed that human dermal endothelial cells exposed to DENV NS1 do not produce inflammatory cytokines (TNF-α, IL-6, IL-8) and that blocking these cytokines does not affect DENV NS1-induced endothelial hyperpermeability. Further, we demonstrated that DENV NS1 induces vascular leak in TLR4- or TNF-α receptor-deficient mice at similar levels to wild-type animals. Finally, we blocked DENV NS1-induced vascular leak in vivo using inhibitors targeting molecules involved in glycocalyx disruption. Taken together, these data indicate that DENV NS1-induced endothelial cell-intrinsic vascular leak is independent of inflammatory cytokines but dependent on endothelial glycocalyx components.

The present era of nanotechnology has reached to a stage where scientist are able to develop and programme complex machines that are built at molecular level which can work inside the patient body. One such challenge is a nanorobot, which once thought to be a desire as came into reality now. The proposed application of nanorobot can range from common cold to dreadful diseases like cancer, Diabetes, influenza, cerebral aneurysm. This study of nanorobot serves as a lead to the field of nanomedicine. There are many applications for nanorobotic systems and its biggest impact would be in the area of medicine. This article deals with the nanorobotic design and their applications in molecular diagnosis.

n bivalves, many functional parameters show seasonal changes in relation to both abiotic (such as temperature and salinity) and biotic factors (such as gonad maturation, food availability). Available data indicate that also immune parameters can show seasonal fluctuations in the marine mussel Mytilus spp.. In this work we report data on hemocyte lysosomal membrane stability (LMS) and phagocytic activity, as well as on soluble lysozyme activity, in the hemolymph of mussels (Mytilus galloprovincialis) collected over a 24 month period in the Adriatic Sea (2006-2007). The results indicate that all the parameters measured show seasonal fluctuations over the year, with lysozyme activity showing the largest changes. Lowest LMS values were observed in early winter and early autumn, whereas maximal values of phagocytic activity were observed in winter and increasing serum lysozyme activities were recorded in autumn. The observed seasonal fluctuations are discussed in relation to both abiotic (temperature) and biotic (changes in endogenous modulators) factors.

We investigated the antibacterial activity of Anemonia sulcata (Cnidaria, Anthozoa) tentacle and body acidic extracts. Biochemical purification consisted of first step on solid phase Sep-Pak C8 column followed by several HPLC runs on C18 column using different conditions. Anti-Micrococcus lysodeikticus activity has been detected in 40 % acetonitrile fractions. The resulting purified molecule from tentacles had a molecular mass determined by MALDI-TOF mass spectrum of 4946,299 Da and has been completely sequenced. Its aa sequence revealed identity with the Neurotoxin 2 (ATX-II), a Na+ channel blocking toxins. Consequently, ATX-II appeared to display a dual role as toxin and as antibacterial.

Axon pathfinding and synapse formation rely on precise spatiotemporal localization of guidance receptors. However, little is known about the neuron-specific intracellular trafficking mechanisms that underlie the sorting and activity of these receptors. Here we show that loss of the neuron-specific v-ATPase subunit a1 leads to progressive endosomal guidance receptor accumulations after neuronal differentiation. In the embryo and in adult photoreceptors, these accumulations occur after axon pathfinding and synapse formation is complete. In contrast, receptor missorting occurs sufficiently early in neurons of the adult central nervous system to cause connectivity defects. An increase of guidance receptors, but not of membrane proteins without signaling function, causes specific gain-of-function phenotypes. A point mutant that promotes sorting but prevents degradation reveals spatiotemporally specific guidance receptor turnover and accelerates developmental defects in photoreceptors and embryonic motor neurons. Our findings indicate that a neuron-specific endolysosomal degradation mechanism is part of the cell biological machinery that regulates guidance receptor turnover and signaling.

HIV avoids elimination by cytotoxic T-lymphocytes (CTLs) through the evolution of escape mutations. Although there is mounting evidence that these escape pathways are broadly consistent among individuals with similar human leukocyte antigen (HLA) class I alleles, previous population-based studies have been limited by the inability to simultaneously account for HIV codon covariation, linkage disequilibrium among HLA alleles, and the confounding effects of HIV phylogeny when attempting to identify HLA-associated viral evolution. We have developed a statistical model of evolution, called a phylogenetic dependency network, that accounts for these three sources of confounding and identifies the primary sources of selection pressure acting on each HIV codon. Using synthetic data, we demonstrate the utility of this approach for identifying sites of HLA-mediated selection pressure and codon evolution as well as the deleterious effects of failing to account for all three sources of confounding. We then apply our approach to a large, clinically-derived dataset of Gag p17 and p24 sequences from a multicenter cohort of 1144 HIV-infected individuals from British Columbia, Canada (predominantly HIV-1 clade B) and Durban, South Africa (predominantly HIV-1 clade C). The resulting phylogenetic dependency network is dense, containing 149 associations between HLA alleles and HIV codons and 1386 associations among HIV codons. These associations include the complete reconstruction of several recently defined escape and compensatory mutation pathways and agree with emerging data on patterns of epitope targeting. The phylogenetic dependency network adds to the growing body of literature suggesting that sites of escape, order of escape, and compensatory mutations are largely consistent even across different clades, although we also identify several differences between clades. As recent case studies have demonstrated, understanding both the complexity and the consistency of immune escape has important implications for CTL-based vaccine design. Phylogenetic dependency networks represent a major step toward systematically expanding our understanding of CTL escape to diverse populations and whole viral genes.

Wallerian degeneration refers to a loss of the distal part of an axon after nerve injury. Wallerian degeneration slow (Wld(s)) mice overexpress a chimeric protein containing the NAD synthase NMNAT (nicotinamide mononucleotide adenylyltransferase 1) and exhibit a delay in axonal degeneration. Currently, conflicting evidence raises questions as to whether NMNAT is the protecting factor and whether its enzymatic activity is required for such a possible function. Importantly, the link between nmnat and axon degeneration is at present solely based on overexpression studies of enzymatically active protein. Here we use the visual system of Drosophila as a model system to address these issues. We have isolated the first nmnat mutations in a multicellular organism in a forward genetic screen for synapse malfunction in Drosophila. Loss of nmnat causes a rapid and severe neurodegeneration that can be attenuated by blocking neuronal activity. Furthermore, in vivo neuronal expression of mutated nmnat shows that enzymatically inactive NMNAT protein retains strong neuroprotective effects and rescues the degeneration phenotype caused by loss of nmnat. Our data indicate an NAD-independent requirement of NMNAT for maintaining neuronal integrity that can be exploited to protect neurons from neuronal activity-induced degeneration by overexpression of the protein.

During evolution, animals have returned from land to water, adapting with morphological modifications to life in an aquatic environment. We compared the osteochondral units of the humeral head of marine and terrestrial mammals across species spanning a wide range of body weights, focusing on microstructural organization and biomechanical performance. Aquatic mammals feature cartilage with essentially random collagen fiber configuration, lacking the depth-dependent, arcade-like organization characteristic of terrestrial mammalian species. They have a less stiff articular cartilage at equilibrium with a significantly lower peak modulus, and at the osteochondral interface do not have a calcified cartilage layer, displaying only a thin, highly porous subchondral bone plate. This totally different constitution of the osteochondral unit in aquatic mammals reflects that accommodation of loading is the primordial function of the osteochondral unit. Recognizing the crucial importance of the microarchitecture-function relationship is pivotal for understanding articular biology and, hence, for the development of durable functional regenerative approaches for treatment of joint damage, which are thus far lacking.

Rab GTPases are molecular switches that regulate membrane trafficking in all cells. Neurons have particular demands on membrane trafficking and express numerous Rab GTPases of unknown function. Here, we report the generation and characterization of molecularly defined null mutants for all 26 rab genes in Drosophila. In flies, all rab genes are expressed in the nervous system where at least half exhibit particularly high levels compared to other tissues. Surprisingly, loss of any of these 13 nervous system-enriched Rabs yielded viable and fertile flies without obvious morphological defects. However, all 13 mutants differentially affected development when challenged with different temperatures, or neuronal function when challenged with continuous stimulation. We identified a synaptic maintenance defect following continuous stimulation for six mutants, including an autophagy-independent role of rab26. The complete mutant collection generated in this study provides a basis for further comprehensive studies of Rab GTPases during development and function in vivo.

Invasive insects threaten ecosystem stability, public health, and food security. Documenting newly invasive species and understanding how they reach into new territories, establish populations, and interact with other species remain vitally important. Here, we report on the invasion of the South American leafhopper, Curtara insularis into Africa, where it has established populations in Ghana, encroaching inland at least 350 km off the coast. Importantly, 80% of the specimens collected were intercepted between 160 and 190 m above ground. Further, the fraction of this species among all insects collected was also higher at altitude, demonstrating its propensity to engage in high-altitude windborne dispersal. Its aerial densities at altitude translate into millions of migrants/km over a year, representing massive propagule pressure. Given the predominant south-westerly winds, these sightings suggest an introduction of C. insularis into at least one of the Gulf of Guinea ports. To assess the contribution of windborne dispersal to its spread in a new territory, we examine records of C. insularis range-expansion in the USA. Reported first in 2004 from central Florida, it reached north Florida (Panhandle) by 2008–2011 and subsequently spread across the southeastern and south-central US. Its expansion fits a “diffusion-like” process with 200—300 km long “annual displacement steps”—a pattern consistent with autonomous dispersal rather than vehicular transport. Most “steps” are consistent with common wind trajectories from the nearest documented population, assuming 2—8 hours of wind-assisted flight at altitude. Curtara insularis has been intercepted at US ports and on trucks. Thus, it uses multiple dispersal modalities, yet its rapid overland spread is better explained by its massive propagule pressure linked with its high-altitude windborne dispersal. We propose that high-altitude windborne dispersal is common yet under-appreciated in invasive insect species.

Abstract Building models that allow phenotypic evaluation of complex agronomic traits in crops of global economic interest, such as grain yield (GY) in soybean and maize, is essential for improving the efficiency of breeding programs. In this sense, understanding the relationships between agronomic variables and those obtained by high-throughput phenotyping (HTP) is crucial to this goal. Our hypothesis is that vegetation indices (VIs) obtained from HTP can be used to indirectly measure agronomic variables in annual crops. The objectives were to study the association between agronomic variables in maize and soybean genotypes with VIs obtained from remote sensing and to identify computational intelligence for predicting GY of these crops from VIs as input in the models. Comparative trials were carried out with 30 maize genotypes in the 2020/2021, 2021/2022 and 2022/2023 crop seasons, and with 32 soybean genotypes in the 2021/2022 and 2022/2023 seasons. In all trials, an overflight was performed at R1 stage using the UAV Sensefly eBee equipped with a multispectral sensor for acquiring canopy reflectance in the green (550 nm), red (660 nm), near-infrared (735 nm) and infrared (790 nm) wavelengths, which were used to calculate the VIs assessed. Agronomic traits evaluated in maize crop were: leaf nitrogen content, plant height, first ear insertion height, and GY, while agronomic traits evaluated in soybean were: days to maturity, plant height, first pod insertion height, and GY. The association between the variables were expressed by a correlation network, and to identify which indices are best associated with each of the traits evaluated, a path analysis was performed. Lastly, VIs with a cause-and-effect association on each variable in maize and soybean trials were adopted as independent explanatory variables in multiple regression model (MLR) and artificial neural network (ANN), in which the 10 best topologies able to simultaneously predict all the agronomic variables evaluated in each crop were selected. Our findings reveal that VIs can be used to predict agronomic variables in maize and soybean. Soil-adjusted Vegetation Index (SAVI) and Green Normalized Dif-ference Vegetation Index (GNDVI) have a positive and high direct effect on all agronomic variables evaluated in maize, while Normalized Difference Vegetation Index (NDVI) and Normalized Difference Red Edge Index (NDRE) have a positive cause-and-effect association with all soybean variables. ANN outperformed MLR, providing higher accuracy when predicting agronomic variables using the VIs select by path analysis as input. Future studies should evaluate other plant traits, such as physiological or nutritional ones, as well as different spectral variables from those evaluated here, with a view to contributing to an in-depth understanding about cause-and-effect relationships between plant traits and spectral variables. Such studies could contribute to more specific HTP at the level of traits of interest in each crop, helping to develop genetic materials that meet the future demands of population growth and climate change.

Abstract Spatially resolved molecular assays provide high dimensional genetic, transcriptomic, proteomic, and epigenetic information in situ and at various resolutions. Pairing these data across modalities with histological features enables powerful studies of tissue pathology in the context of an intact microenvironment and tissue structure. Increasing dimensions across molecular analytes and samples require new data science approaches to functionally annotate spatially resolved molecular data. A specific challenge is data-driven cross-sample domain detection that allows for analysis within and between consensus tissue compartments across high volumes of multiplex datasets stemming from tissue atlasing efforts. Here, we present MILWRM (multiplex image labeling with regional morphology)—a Python package for rapid, multi-scale tissue domain detection and annotation at the image- or spot-level. We demonstrate MILWRM’s utility in identifying histologically distinct compartments in human colonic polyps, lymph nodes, mouse kidney, and mouse brain slices through spatially-informed clustering in two different spatial data modalities from different platforms. We used tissue domains detected in human colonic polyps to elucidate the molecular distinction between polyp subtypes, and explored the ability of MILWRM to identify anatomical regions of the brain tissue and their respective distinct molecular profiles.

Abstract Objective To obtain physicians’ “real-world” perspectives on early experiences with triamcinolone acetonide suprachoroidal injection (SCS-TA) for treatment of patients with uveitic macular edema (UME). Results Twelve retina/uveitis specialists in the United States were surveyed about SCS-TA injection procedure and patient outcomes. Survey participants administered ≥ 291 SCS-TA injections to 243 patients with UME with various disease characteristics (etiologies, chronicity, and anatomical subtypes). Commonly reported reasons for SCS-TA adoption included potential for lowering the risk of steroid-associated intraocular pressure elevations versus intravitreal injections or implants (100%), potential for longer duration of action versus intravitreal steroid injections or implants (92%), and desire to use a new delivery modality (83%). Nearly all participants (92%) found injection procedure relatively easy post-training, with most (75%) procedurally comfortable after completing 2–5 injections. 58% of participants indicated that their patients gained 2–3 lines of vision by first follow-up visit, and 92% reported having patients who experienced 100–150 μm or greater reduction in central subfield thickness. Overall, 92% of participants were satisfied with SCS-TA treatment outcomes. Findings from this survey of early adopters of SCS-TA indicate that the suprachoroidal injection technique was easy to learn and resulted in favorable patient outcomes consistent with clinical trial data.

Abstract Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on α-mannooligosaccharides (MOS) and β-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their impact on its gut microbiome composition and functionalities. Our multi-omic analysis revealed that the investigated MDFs (two α-mannans and an acetylated β-galactoglucomannan), at a dose of 0.2% in the diet, had negligible effects on both host gene expression, and gut microbiome structure and function under the studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of β-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of β-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline previously unreported and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon.

Abstract The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short-read, de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target capture short-read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short-read data. MHConstructor facilitates wide-spread access to high-quality, alignment-free MHC sequence analysis.

Abstract Background Ecological barriers can shape the movement strategies of migratory animals that navigate around or across them, creating migratory divides. Wind plays a large role in facilitating aerial migrations and can temporally or spatially change the challenge posed by an ecological barrier, with beneficial winds potentially converting a barrier into a corridor. Here, we explore the role wind plays in shaping initial southbound migration strategy among individuals breeding at two sites along an ecological barrier. Methods Using GPS satellite transmitters, we tracked the southbound migrations of Short-billed Dowitchers (Limnodromus griseus caurinus) from two breeding sites in Alaska to nonbreeding sites in coastal Mexico. The breeding sites were positioned in distinct regions along an ecological barrier – the Gulf of Alaska. We investigated potential differences in migratory timing, wind availability, and tailwind support en route across the Gulf of Alaska between individuals breeding at the two sites. Results Route choice and arrival timing to wintering sites differed markedly between the two breeding sites: individuals departing from the more westerly site left at the same time as those from further east but crossed the Gulf of Alaska farther west and arrived along the Pacific coast of Mexico an average of 19 days earlier than their counterparts. Dowitchers from both sites departed with slight tailwinds, but once aloft over the Gulf of Alaska, birds from the more westerly site had up to twelve times more tailwind assistance than birds from the more easterly one. Conclusions The distinct migration strategies and degree of wind assistance experienced by birds at these two breeding sites demonstrates how differences in wind availability along migratory routes can form the basis for intraspecific variation in migration strategies with potential carryover effects. Future changes in wind regimes may therefore interact with changes in habitat availability to influence migration patterns and migratory bird conservation.

Water is an essential nutrient for living beings and is fundamental to metabolic processes. Under free-living conditions, primate individuals can use different strategies, skills, and resources to access water. Here, we report on observations of water consumption in Ateles chamek and Sapajus apella; describe the environmental conditions in which such events were observed, as well as the behavior of the individuals; and compare these observations with similar records in neotropical primates. Water consumption was observed during primate surveys in a forest fragment of approximately 52 ha bordered by the Jaru River, located southwest of the Brazilian Amazon, Vale do Paraíso municipality, state of Rondônia, Brazil. To access water, individuals of A. chamek used their tails, whereas S. apella used a leaf as a tool. Our observations suggest that tree holes may be important water sources for primates in forest fragments and that individuals of different species use different strategies to collect water from tree holes. Access and consumption strategies are directly associated with different cognitive skills and behaviors, which may include using tools, as in the case of capuchins. As water consumption records are limited, these findings highlight the need for continuous reporting to better understand water acquisition. Such reports are especially needed in the context of fragmented and degraded habitats, where water availability is affected by edge effects and the reduction in both fleshy fruits and moisture, which are important for primate species.

Abstract We describe the geographical variation in tree species composition across Amazonian forests and show how environmental conditions are associated with species turnover. Our analyses are based on 2023 forest inventory plots (1 ha) that provide abundance data for a total of 5188 tree species. Within-plot species composition reflected both local environmental conditions (especially soil nutrients and hydrology) and geographical regions. A broader-scale view of species turnover was obtained by interpolating the relative tree species abundances over Amazonia into 47,441 0.1-degree grid cells. Two main dimensions of spatial change in tree species composition were identified. The first was a gradient between western Amazonia at the Andean forelands (with young geology and relatively nutrient-rich soils) and central–eastern Amazonia associated with the Guiana and Brazilian Shields (with more ancient geology and poor soils). The second gradient was between the wet forests of the northwest and the drier forests in southern Amazonia. Isolines linking cells of similar composition crossed major Amazonian rivers, suggesting that tree species distributions are not limited by rivers. Even though some areas of relatively sharp species turnover were identified, mostly the tree species composition changed gradually over large extents, which does not support delimiting clear discrete biogeographic regions within Amazonia.

Abstract The neurexin superfamily, consisting of neurexins and Casprs, play important roles in the development, maintenance, function, and plasticity of neuronal circuits. Caspr/CNTNAP genes are linked to alterations in neuronal circuits and associated with neurodevelopmental and neurodegenerative conditions. Casprs are implicated in multiple neuronal signaling pathways, including dopamine; however, the molecular mechanisms by which Casprs differentially alter specific signaling pathways and downstream behaviors are unclear. We find that the C. elegans Caspr nlr-1 functions in neurons to control foraging behaviors, acting in distinct monoamine neurons to modulate locomotor activity in the presence or absence of food. nlr-1 functions in dopamine neurons to reduce activity in the absence of food, similar to the role of dopamine, and regulates dopamine signaling through D2-like receptors. Furthermore, nlr-1 contributes to proper morphology and presynaptic structure of dopamine neurons, dopamine receptor expression and localization, and the behavioral response to dopamine. We find that nlr-1 similarly regulates another dopamine-dependent behavior, the basal slowing response. Therefore, spatial manipulation of a broadly expressed neuronal gene is sufficient to alter neural circuits and behavior and uncovers important functions masked by global manipulation, highlighting the importance of genetic variation and mechanisms that impact spatial expression of genes to behavior.

Abstract The continuous emergence of SARS-CoV-2 variants of concern has rendered many therapeutic monoclonal antibodies (mAbs) ineffective. To date, there are no clinically authorized therapeutic antibodies effective against the recently circulating Omicron sub-lineages BA.2.86 and JN.1. Here, we report the isolation of broad and potent neutralizing human mAbs (HuMabs) from a healthcare worker infected with SARS-CoV-2 early in the pandemic. These include a genetically unique HuMab, named K501SP6, which can neutralize different Omicron sub-lineages, including BQ.1, XBB.1, BA.2.86 and JN.1, by targeting a highly conserved epitope on the N terminal domain, as well as an RBD-specific HuMab (K501SP3) with high potency towards earlier circulating variants that was escaped by the more recent Omicron sub-lineages through spike F486 and E484 substitutions. Characterizing SARS-CoV-2 spike-specific HuMabs, including broadly reactive non-RBD-specific HuMabs, can give insight into the immune mechanisms involved in neutralization and immune evasion, which can be a valuable addition to already existing SARS-CoV-2 therapies.

Understanding the dynamics of physiological changes involved in the acclimation responses of plants after their exposure to repeated cycles of water stress is crucial to selecting resilient genotypes for regions with recurrent drought episodes. Under such background, we tried to respond to questions as: (1) Are there differences in the stomatal-related and non-stomatal responses during water stress cycles in different clones of Coffea canephora Pierre ex A. Froehner? (2) Do these C. canephora clones show a different response in each of the two sequential water stress events? (3) Is one previous drought stress event sufficient to induce a kind of “memory” in C. canephora? Seven-month-old plants of two clones (’3V’ and ‘A1’, previously characterized as deeper and lesser deep root growth, respectively) were maintained well-watered (WW) or fully withholding the irrigation, inducing soil water stress (WS) until the soil matric water potential (Ψmsoil) reached ≅ −0.5 MPa (−500 kPa) at a soil depth of 500 mm. Two sequential drought events (drought-1 and drought-2) attained this Ψmsoil after 19 days and were followed by soil rewatering until a complete recovery of leaf net CO2 assimilation rate (Anet) during the recovery-1 and recovery-2 events. The leaf gas exchange, chlorophyll a fluorescence, and leaf reflectance parameters were measured in six-day frequency, while the leaf anatomy was examined only at the end of the second drought cycle. In both drought events, the WS plants showed reduction in stomatal conductance and leaf transpiration. The reduction in internal CO2 diffusion was observed in the second drought cycle, expressed by increased thickness of spongy parenchyma in both clones. Those stomatal and anatomical traits impacted decreasing the Anet in both drought events. The ‘3V’ was less influenced by water stress than the ‘A1’ genotype in Anet, effective quantum yield in PSII photochemistry, photochemical quenching, linear electron transport rate, and photochemical reflectance index during the drought-1, but during the drought-2 event such an advantage disappeared. Such physiological genotype differences were supported by the medium xylem vessel area diminished only in ‘3V’ under WS. In both drought cycles, the recovery of all observed stomatal and non-stomatal responses was usually complete after 12 days of rewatering. The absence of photochemical impacts, namely in the maximum quantum yield of primary photochemical reactions, photosynthetic performance index, and density of reaction centers capable of QA reduction during the drought-2 event, might result from an acclimation response of the clones to WS. In the second drought cycle, the plants showed some improved responses to stress, suggesting “memory” effects as drought acclimation at a recurrent drought.

Abstract Disease recurrence following chemotherapy is a major clinical challenge in ovarian cancer (OC), but little is known regarding how the tumour epigenome regulates transcriptional programs underpinning chemoresistance. We determine the single cell chromatin accessibility landscape of omental OC metastasis from treatment-naïve and neoadjuvant chemotherapy-treated patients and define the chromatin accessibility profiles of epithelial, fibroblast, myeloid and lymphoid cells. Epithelial tumour cells display open chromatin regions enriched with motifs for the oncogenic transcription factors MEIS and PBX. Post chemotherapy microenvironments show profound tumour heterogeneity and selection for cells with accessible chromatin enriched for TP53, TP63, TWIST1 and resistance-pathway-activating transcription factor binding motifs. An OC chemoresistant tumour subpopulation known to be present prior to treatment, and characterised by stress-associated gene expression, is enriched post chemotherapy. Nuclear receptors RORa, NR2F6 and HNF4G are uncovered as candidate transcriptional drivers of these cells whilst closure of binding sites for E2F2 and E2F4 indicate post-treated tumour having low proliferative capacity. Delineation of the gene regulatory landscape of ovarian cancer cells surviving chemotherapy treatment therefore reveals potential core transcriptional regulators of chemoresistance, suggesting novel therapeutic targets for improving clinical outcome.

During early development of biopharmaceuticals, suboptimal producing clones and production conditions can result in limited quantities of high-purity products. Here we describe a systematic approach, which requires minimal amounts of protein (~10 mg) to assess critical quality attributes of a monoclonal antibody (mAb). A commercial anti-PCSK9 IgG2 (evolocumab, Repatha®) and an early-stage biosimilar candidate were compared head-to-head using a range of high-throughput physicochemical and in-vitro binding analytical methods. Overall, both mAbs were shown to be highly pure and primarily monomeric, to share an identical primary structure, and to have similar higher-order structural integrity, apparent solubility, aggregation propensity, and physical stability profiles under temperature and pH stress conditions. Low levels of dimers were detected for the innovator (1.2%) and the biosimilar candidate mAb (0.3%), which also presented fragments (1.2%). Regarding charge heterogeneity, the amount of the main charge isoform was 53.6% for the innovator and 61.6% for the biosimilar candidate mAb. Acidic species were 38% for the innovator and 30% for the biosimilar candidate. Variations in the relative content of a few N-glycan species were found. The in-vitro binding affinity to PCSK9 was monitored, and no differences were detected. The mathematical approach called “error spectral difference” (ESD), proposed herein, enabled a quantitative comparison of the biophysical datasets. The workflow used in the present work to characterize CQAs at early stages is helpful in supporting the development of biosimilar mAb candidates.

Abstract A seed recovered during archaeological excavations of a cave in the Judean desert was germinated, with radiocarbon analysis indicating an age of 993 CE– 1202 calCE. DNA sequencing and phylogenetic analysis identified the seedling as belonging to the angiosperm genus Commiphora Jacq., sister to three Southern African Commiphora species, but unique from all other species sampled to date. The germinated seedling was not closely related to Commiphora species commonly harvested for their fragrant oleoresins including Commiphora gileadensis (L.) C.Chr., candidate for the locally extinct “Judean Balsam” or “Balm of Gilead” of antiquity. GC-MS analysis revealed minimal fragrant compounds but abundance of those associated with multi-target bioactivity and a previously undescribed glycolipid compound series. Several hypotheses are offered to explain the origins, implications and ethnobotanical significance of this unknown Commiphora sp., to the best of our knowledge the first identified from an archaeological site in this region, including identification with a resin producing tree mentioned in Biblical sources and possible agricultural relationship with the historic Judean Balsam.

In this paper, we describe modifications to a sampling technique for surface, stream-dwelling salamanders for use in subterranean settings. Leaf litter bags are an effective and commonly used trap for salamanders, and their construction purposefully allows animals to move freely in and out of the trap. However, this presents a problem in subterranean deployment because retrieving the trap over long vertical distances, such as well sampling, allows time and space for the animals to escape. To overcome this challenge, we enclosed a leaf litter bag in a suspended net system contained by a lanyard to sample a 3-meter deep well. Our trap modifications resulted in the live capture of adult and immature federally threatened Salado Salamanders (Eurycea chisholmensis) from the well in addition to aquatic invertebrates. This represents a novel trapping technique within a habitat system for which stygofauna sampling options are limited.

Abstract SARS-CoV-2 continues to be a public health burden, driven in-part by its continued antigenic diversification and resulting emergence of new variants. By increasing herd immunity, current vaccines have improved infection outcomes for many. However, prophylactic and treatment interventions that are not compromised by viral evolution of the Spike protein are still needed. Using a differential staining strategy with a rationally designed SARS-CoV-2 Receptor Binding Domain (RBD) – ACE2 fusion protein and a native Omicron RBD protein, we developed a recombinant human monoclonal antibody (hmAb) from a convalescent individual following SARS-CoV-2 Omicron infection. The resulting hmAb, 1301B7 potently neutralized a wide range of SARS-CoV-2 variants including the original Wuhan-1, the more recent Omicron JN.1 strain, and SARS-CoV. 1301B7 contacts the ACE2 binding site of RBD exclusively through its VH1-69 heavy chain. Broad specificity is achieved through 1301B7 binding to many conserved residues of Omicron variants including Y501 and H505. Consistent with its extensive binding epitope, 1301B7 is able to potently diminish viral burden in the upper and lower respiratory tract and protect mice from challenge with Omicron XBB1.5 and Omicron JN.1 viruses. These results suggest 1301B7 has broad potential to prevent or treat clinical SARS-CoV-2 infections and to guide development of RBD-based universal SARS-CoV-2 prophylactic vaccines and therapeutic approaches.