Miracle-dz/UniFAR-FTUs huggingface dataset:
Variola virus is as old as the earliest historical lines of evidence suggest

Archaeovirology efforts provided a rich portrait of the evolutionary history of variola virus (VARV), the causative agent of smallpox. These studies revealed frequent viral lineage extinction and a relatively recent origin of VARV as a human pathogen (∼ 1,700 years ago, ya). This contrasts with historical records suggesting the presence of smallpox as early as 3,500 ya. By performing an analysis of ancestry components in modern, historic, and ancient VARV genomes, we unveil the progressive drifting of VARV lineages from a common ancestral population and we show that a small proportion of Viking-Age ancestry persisted until the 18th century. After the split of the P-I and P-II lineages, which occurred before the onset of smallpox vaccination, the former (but not the latter) experienced a severe bottleneck. We suggest this was due to the distinct epidemiology of the two lineages, which display remarkably different disease severity. As for the emergence of VARV, we corrected time estimates by accounting for the time-dependent rate phenomenon. Using this approach, we estimate that VARV emerged earlier than 3,800 ya, thus supporting its presence in ancient societies, including Egypt, as pockmarked mummies suggest. Importance Now eradicated, smallpox was one of the most devastating human diseases, causing the death of at least 300 million people in the 20th century. Humans were the only known host of variola virus, but the time-frame of its emergence in our species has been a matter of debate. Specifically, molecular dating suggested a relatively recent origin, whereas historical sources indicated the presence of VARV in ancient societies. By applying population genetic methods, we analyzed the ancestry components in modern and historic VARV genomes, and we found a progressive drifting of VARV lineages from a common ancestral population. By accounting for the common observation that rates of viral evolution scale negatively with the time-frame of measurement, we estimated that VARV emerged earlier than 3800 years ago. Thus, out data settle a controversy and provide novel insight into the origin and evolution of one of the most historically relevant human pathogens.
Unraveling the mystery behind the short-day-specific flowering of tobacco cultivar Maryland Mammoth

Flowering in day-neutral tobacco (Nicotiana tabacum) plants requires the photoperiod-dependent expression of members of the FLOWERING LOCUS T (FT)-like clade of phosphatidylethanolamine-binding proteins. FT-like floral activators and inhibitors compete for interaction with FD proteins to shift from vegetative to reproductive growth. In the short-day (SD) cultivar Maryland Mammoth (MM), vegetative growth persists under long-day (LD) conditions, generating unusually tall plants. We found that the major floral inducer under long-days (NtFT5) was expressed in MM and that NtFT5 overexpression induced flowering in MM plants under LD conditions. However, sequence analysis revealed a 2-bp deletion near the 3′ end of NtFT5 in MM plants resulting in a truncated C-terminus with an altered amino acid sequence. We found that the truncated NtFT5MM protein was still able to interact with tobacco FD proteins. However, constitutive overexpression under LD conditions in SD-specific flowering tobacco plants showed that NtFT5MM is a weaker floral inducer than NtFT5. Our data indicate that the truncation does not impair the stability of the NtFT5MM protein but affects its binding affinity for NtFD1, probably resulting in the weaker expression of target genes. Our results therefore provide a potential explanation for the MM gigantism phenotype first observed more than 100 years ago. Highlight The previously unexplained gigantism of Maryland Mammoth tobacco is caused by a truncated major floral activator protein that results in weaker activation and the inability to flower under long-day conditions.
Molecular mechanism of plasmid-borne resistance to sulfonamides

The sulfonamides (sulfas) are the oldest class of synthetic antibacterial that target the essential, conserved dihydropteroate synthase (DHPS) enzyme, encoded by folP, through chemical mimicry of its substrate p-aminobenzoic acid (pABA). Resistance has complicated their clinical utility and is widespread in pathogenic species. Resistance is mediated by acquisition of sul genes on mobile genetic elements, which code for the so-called Sul enzymes that are divergent DHPS enzymes with intrinsic sulfa-insensitivity. Even decades after the discovery of this resistance mechanism, its molecular details have not been understood. In this study, we elucidate the molecular basis for intrinsic resistance of Sul enzymes using x-ray crystallography, enzymology, mutagenesis, intrinsic tryptophan fluorescence, antibiotic susceptibility of a contemporary ΔfolP strain, and adaptive laboratory evolution of folP. We show that the active sites of Sul enzymes possess a modified pABA-interaction region based on insertion of a Phe-Gly sequence. This insertion is necessary for discrimination between pABA and sulfonamides, more than 1000-fold loss in binding affinity of sulfas to Sul enzymes, and robust pan-sulfonamide resistance. We detect no fitness cost due to this active site modification, as it does not compromise the rate of dihydropteroate biosynthesis and complements the thymidine-auxotrophy of an E. coli folP deletion strain. Lab-evolved sulfa-resistance folP recapitulated this mechanism through the same active site insertion. Finally, we show that this insertion and a nearby loop confer increased active site flexibility of Sul enzymes relative to DHPS. These results provide a molecular foundation for revisiting DHPS-targeted antibacterials to evade resistance.
Presynaptic Rac1 controls synaptic strength through the regulation of synaptic vesicle priming

Synapses contain a limited number of synaptic vesicles (SVs) that can be released in response to action potentials (APs). Therefore, sustaining synaptic transmission over a wide range of AP firing rates and timescales depends on both SV release and replenishment. Although actin dynamics impact synaptic transmission, how regulators of actin dynamics control SV release and replenishment remain unresolved. Rac1 is a regulator of actin signaling cascades that control synaptogenesis, neuronal development, and postsynaptic function, however, its presynaptic role in regulating synaptic transmission is unclear. To unravel the regulatory roles of presynaptic Rac1 in synaptic transmission, we ablated presynaptic Rac1 at the mature mouse calyx of Held. Presynaptic Rac1 deletion leads to increased synaptic strength due to increased SV release probability which results in faster SV replenishment and increased spontaneous SV release rates. Based on our data, we conclude that presynaptic Rac1 controls synaptic strength by regulating the intrinsic SV release probability through SV priming. Therefore, we propose that presynaptic Rac1 controls actin dynamics and acts as a key regulator of synaptic transmission and plasticity.
Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations

Understanding the benefits and costs of recombination under different scenarios of evolutionary adaptation remains an open problem for theoretical and experimental research. In this study, we focus on finite populations evolving on neutral networks comprising viable and unfit genotypes. We provide a comprehensive overview of the effects of recombination by jointly considering different measures of evolvability and mutational robustness over a broad parameter range, such that many evolutionary regimes are covered. We find that several of these measures vary non-monotonically with the rates of mutation and recombination. Moreover, the presence of unfit genotypes that introduce inhomogeneities in the network of viable states qualitatively alters the effects of recombination. We conclude that conflicting trends induced by recombination can be explained by an emerging trade-off between evolvability on the one hand, and mutational robustness on the other. Finally, we discuss how different implementations of the recombination scheme in theoretical models can affect the observed dependence on recombination rate through a coupling between recombination and genetic drift. Author summary Many genetic mechanisms have been invoked to explain the advantage of sex, but a coherent picture is still to emerge. Here we present a systematic theoretical and computational investigation of the effects of recombination in populations evolving on neutral fitness landscapes with unfit genotypes. We focus on populations that are large enough to be polymorphic, but nevertheless strongly affected by drift, which causes them to diffuse across the neutral network of viable genotypes. We identify a novel trade-off between evolvability, robustness and fitness that can lead to a dramatic reduction of the genetic diversity at large recombination rates. This disproves the common notion (often referred to as Weismann’s hypothesis) that recombination generally increases diversity and evolvability, and instead highlights the interplay of recombination and mutational robustness.
Modelling the contributions to hyperexcitability in a mouse model of Alzheimer’s disease

Neuronal hyperexcitability is a feature of Alzheimer’s disease (AD). Three main mechanisms have been proposed to explain it: i), dendritic degeneration leading to increased input resistance, ii), ion channel changes leading to enhanced intrinsic excitability, and iii), synaptic changes leading to excitation-inhibition (E/I) imbalance. However, the relative contribution of these mechanisms is not fully understood. Therefore, we performed biophysically realistic multi-compartmental modelling of excitability in reconstructed CA1 pyramidal neurons of wild-type and APP/PS1 mice, a well-established animal model of AD. We show that, for synaptic activation, the excitability promoting effects of dendritic degeneration are cancelled out by excitability decreasing effects of synaptic loss. We find an interesting balance of excitability regulation with enhanced degeneration in the basal dendrites of APP/PS1 cells potentially leading to increased excitation by the apical but decreased excitation by the basal Schaffer collateral pathway. Furthermore, our simulations reveal that three additional pathomechanistic scenarios can account for the experimentally observed increase in firing and bursting of CA1 pyramidal neurons in APP/PS1 mice. Scenario 1: increased excitatory burst input; scenario 2: enhanced E/I ratio and scenario 3: alteration of intrinsic ion channels (IAHP down-regulated; INap, INa and ICaT up-regulated) in addition to enhanced E/I ratio. Our work supports the hypothesis that pathological network and ion channel changes are major contributors to neuronal hyperexcitability in AD. Overall, our results are in line with the concept of multi-causality and degeneracy according to which multiple different disruptions are separately sufficient but no single disruption is necessary for neuronal hyperexcitability. In brief Using a computational model, we find that changes in the extrinsic network and intrinsic biophysical neuronal properties rather than dendritic degeneration alone explain the altered firing behaviour observed in Alzheimer’s disease (AD). Highlights Simulations of synaptically driven responses in PCs with AD-related dendritic degeneration. Dendritic degeneration alone alters PC responses to layer-specific input but additional pathomechanistic scenarios are required to explain neuronal hyperexcitability in AD. Possible scenario 1: Burst hyperactivity of the surrounding network can explain hyper-excitability of PCs during AD. Possible scenario 2: AD-related increased excitatory input together with decreased inhibitory input (E/I imbalance) can lead to hyperexcitability in PCs. Possible scenario 3: Changes in E/I balance combined with altered ion channel properties can account for hyperexcitability in AD.
Thalamocortical contributions to cognitive task activity

Thalamocortical interaction is a ubiquitous functional motif in the mammalian brain. Previously (Hwang et al., 2021), we reported that lesions to network hubs in the human thalamus are associated with multi-domain behavioral impairments in language, memory, and executive functions. Here we show how task-evoked thalamic activity and thalamocortical interactions are organized to support these broad cognitive abilities. To address this question, we analyzed functional MRI data from human subjects that performed 127 tasks encompassing a broad range of cognitive representations. We first investigated the spatial organization of task-evoked activity and found that multi-task thalamic activity converged onto a low-dimensional structure, through which a basis set of activity patterns are evoked to support processing needs of each task. Specifically, the anterior, medial, and posterior-medial thalamus exhibit hub-like activity profiles that are suggestive of broad functional participation. These thalamic task hubs overlapped with network hubs interlinking cortical systems. To further determine the cognitive relevance of thalamocortical interactions, we built a data-driven thalamocortical interaction model to test whether thalamocortical functional connectivity transformed thalamic activity to cortical task activity. The thalamocortical model predicted task-specific cortical activity patterns, and outperformed comparison models built on cortical, hippocampal, and striatal regions. Simulated lesions to low-dimensional, multi-task thalamic hub regions impaired task activity prediction. This simulation result was further supported by profiles of neuropsychological impairments in human patients with focal thalamic lesions. In summary, our results suggest a general organizational principle of how thalamocortical interactions support cognitive task activity. Impact Statement Human thalamic activity transformed via thalamocortical functional connectivity to support task representations across functional domains.
Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common

Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host’s reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
High-throughput platform for depolarization-induced Ca2+ release for skeletal muscle disease mutation validation and drug discovery

In skeletal muscle excitation-contraction (E-C) coupling, depolarization of the plasma membrane triggers Ca2+ release from the sarcoplasmic reticulum (SR), referred to as depolarization-induced Ca2+ release (DICR). DICR occurs via the type 1 ryanodine receptor (RyR1), which physically interacts with the dihydropyridine receptor Cav1.1 subunit in specific machinery formed with additional components. Exome sequencing has accelerated the discovery of many novel mutations in DICR machinery genes in various skeletal muscle diseases. However, functional validation is time-consuming because it must be performed in a skeletal muscle environment. Here, we describe a high-throughput platform for DICR that is reconstituted in non-muscle HEK293 cells. We demonstrate that Cav1.1 mutations implicated in malignant hyperthermia and myopathy exhibit divergent effects on DICR. We also tested several RyR1 inhibitors and DICR modulators. This high-throughput DICR platform will accelerate validation of mutations and drug discovery for skeletal muscle diseases.
Formate-induced CO tolerance and innovative methanogenesis inhibition in co-fermentation of syngas and plant biomass for carboxylate production

Production of monocarboxylates using microbial communities is highly dependent on local and degradable biomass feedstocks. Syngas or different mixtures of H2, CO, and CO2 can be co-fed to a fermenter to alleviate this dependence. To understand the effects of adding these gases during anaerobic fermentation of plant biomass, a series of batch experiments was carried out with different syngas compositions and corn silage (pH 6.0, 32°C). Co-fermentation of syngas with corn silage increased the overall carboxylate yield per gram of volatile solids (VS) by up to 44% (0.36 ± 0.07 g gVS-1; in comparison to 0.23 ± 0.04 g gVS-1 with a N2/CO2 headspace), despite slowing down biomass degradation. Ethylene and CO exerted a synergistic effect in preventing methanogenesis, leading to net carbon fixation. Less than 12% of the electrons were misrouted to CH4 when either 15 kPa CO or 5 kPa CO + 1.5 kPa ethylene was used. CO increased the selectivity to acetate and propionate, which accounted for 86% (electron equivalents) of all products at 49 kPa CO, by favoring lactic acid bacteria and actinobacteria over n-butyrate and n-caproate producers. This happened even when an inoculum pre-acclimatized to syngas and lactate was used. Intriguingly, the effect of CO on n-butyrate and n-caproate production was reversed when formate was present in the broth. The concept of co-fermenting syngas and plant biomass shows promise in two aspects: by making anaerobic fermentation a carbon-fixing process and by increasing the production of propionate and acetate. Testing the concept in a continuous process could improve selectivity to n-butyrate and n-caproate by enriching chain-elongating bacteria adapted to CO and complex biomass.
Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes

Maize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The northwestern region of Argentina (NWA) constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the “Banco Activo de Germoplasma INTA Pergamino, Argentina” (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers. In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.
Students co-creating curriculum: navigating complexity and uncertainty

Engaging students in curriculum has the potential to enhance student agency, authentic learning and hence effective preparation for work in an ever-changing world. However, curriculum design is often bounded by the complexities of professional requirements and academic priorities and expectations, without consideration to what students might contribute to the process. Processes which bridge these boundaries and encourage student engagement are needed to facilitate graduate capabilities. This project investigated ways to interrogate student involvement in the curriculum and enhance their agency as learners. In the context of a Bachelor of Nursing (BN) program, the aim was to develop a practice model for engaging students as co-creators of curriculum. Action research was utilised to engage students in exploring their curriculum and their location as learners and partners. Students reflected on their recent work integrated learning (WIL) experience and identified sentinel learning experiences and practice development needs. Students then worked with the project team to discuss ways to enhance WIL preparation in the undergraduate BN curriculum. In phase one, students reported being well prepared for basic care skills and communication in the workplace environment. Students reported feeling underprepared for challenging professional behaviours and for confronting clinical situations such as death. In phase two, students’ workshopped solutions in the form of student narratives or real life stories that they could produce and embed in curriculum and opportunities to harness real time support via mobile communication tools. The activities and results inform a guided process to involve students in creating and interacting with their curriculum. ; NURTURE Publication awards 2015: Best collaborative interdisciplinary paper; ;
Drugs and Alcohol Today

Purpose – The purpose of this paper is to map the presence of the Cannabis Social Club (CSC) model in Belgium since its emergence in the country and to analyze the inter-organizational relations among CSCs and between the CSCs and other supportive actors engaged in the wider cannabis movement. Design/methodology/approach – This analysis draws on qualitative interviews (n ¼ 42) with directors of seven currently active and one former Belgian CSC(s), as well as with organizations or individuals reportedly collaborating with the Belgian CSCs. That data are complemented by fieldwork observations and a review of CSC internal documents. Findings – Despite an uninterrupted presence in the country over the last decade, CSC presence in Belgium remains rather volatile and vulnerable to external control pressure. The CSC landscape is a somewhat segmented field as cooperation among CSCs remains limited. At the same time, the support base for the movement is diverse, encompassing different types of secondary organizations ranging from national and international advocacy groups, to cannabis industry entrepreneurs and other consultants. Originality/value – This paper contributes to the yet limited body of knowledge on CSCs, by providing a first comprehensive overview of the presence of CSCs in one of the key settings associated with the model, by shedding light into the interplay between CSCs, and between other organizations supportive of the cannabis movement.