Miracle-dz/UniFAR-FTUs huggingface dataset:
Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources

While many heterologous molecules can be produced via microbial bioconversion processes, maximizing their titers, rates, and yields from lignin-derived carbon streams remains challenging. Growth coupling can not only increase titers and yields but also shift the production period from stationary phase to growth phase. These methods for designing growth-coupling strains however require multi-gene edits for implementation which may be perceived as impractical. Here, we computationally evaluated 4,114 potential solutions for growth coupling para-coumarate to indigoidine production and prototype two cut sets in Pseudomonas putida KT2440. We used adaptive laboratory evolution (ALE) on the initial triple deletion strain to restore growth on p-CA. Using X-ray tomography on this post-ALE strain we revealed increased cell density and decreased cell volume. Proteomics identified upregulated peroxidases that mitigate reactive oxygen species formation. Nine iterative stepwise modifications further informed by model-guided and rational approaches realized a growth coupled strain that produced 7.3 g/L indigoidine at 77% MTY in para-coumarate minimal medium. These ensemble strategies provide a blueprint for producing target molecules at high product titers, rates, and yields. GRAPHICAL ABSTRACT
Effect of cell membrane tension on the lifetime and size of mature clathrin-coated pits and their spatial distribution

Clathrin-mediated endocytosis is the most characterized pathway for cells to internalize diverse receptor-bound cargo such as proteins, nanoparticles, and viruses. However, the effect of membrane tension on clathrin-coated pit (CCP) maturation remains inadequately characterized. This study aimed to figure out the effect of membrane tension on CCP maturation spatially and temporarily, which is still a controversial and elusive issue. We obtained the sizes and spatial distributions of CCPs by the structured illumination microscopy of fixed cells and observed CCP lifetimes in live cells by total internal reflection fluorescence microscopy. The processes of CCP maturation and abortion were reproduced numerically through Monte Carlo simulation. The results showed that the growth time of CCP was more reasonably proportional to its volume rather than its surface area. We further investigated the spatial distribution of the membrane tension and size of CCPs and found a significant positive correlation between the membrane tension and the size of mature CCPs spatially, indicating that the CCPs tended to enrich in the highest-tension region, especially the mature ones. This finding agreed with our numerical prediction that the CCP structure grew larger to overcome a higher energy barrier caused by higher background cell membrane tension. Based on the aforementioned results, we speculated that when the external environment was complex, the cells might choose to reinforce the endocytic vesicles by CCPs in high-tension regions to ensure adequate nutrient uptake.
Seed Longevity is Controlled by Metacaspases

To survive extreme desiccation, seeds enter dormancy that can last millennia. This dormancy involves the accumulation of protective but structurally disordered storage proteins through unknown adjustments of proteolytic surveillance mechanisms. Mutation of all six types II metacaspases (MCAs)-II in the model plant Arabidopsis revealed their essential role in modulating these proteolytic mechanisms. MCA-II mutant seeds fail to properly target at the endoplasmic reticulum (ER) the AAA ATPase Cell Division Cycle 48 (CDC48) to dispose of misfolded proteins. MCA-IIs cleave a CDC48 adaptor, the ubiquitination regulatory X domain-containing (PUX) responsible for localizing CDC48 to the lipid droplets. When cleaved, CDC48-PUX is inactivated and allows a lipid droplet-to-ER shuttling of CDC48, an important step in the regulation of seeds’ lifespan. In sum, we uncover antagonism between proteolytic pathways bestowing longevity. One-Sentence Summary Metacaspase proteases confer seed longevity by antagonizing CDC48 activity.
A Framework for Systematically Evaluating the Representations Learned by A Deep Learning Classifier from Raw Multi-Channel Electroencephalogram Data

The application of deep learning methods to raw electroencephalogram (EEG) data is growing increasingly common. While these methods offer the possibility of improved performance relative to other approaches applied to manually engineered features, they also present the problem of reduced explainability. As such, a number of studies have sought to provide explainability methods uniquely adapted to the domain of deep learning-based raw EEG classification. In this study, we present a taxonomy of those methods, identifying existing approaches that provide insight into spatial, spectral, and temporal features. We then present a novel framework consisting of a series of explainability approaches for insight into classifiers trained on raw EEG data. Our framework provides spatial, spectral, and temporal explanations similar to existing approaches. However, it also, to the best of our knowledge, proposes the first explainability approaches for insight into spatial and spatio-spectral interactions in EEG. This is particularly important given the frequent use and well-characterized importance of EEG connectivity measures for neurological and neuropsychiatric disorder analysis. We demonstrate our proposed framework within the context of automated major depressive disorder (MDD) diagnosis, training a high performing one-dimensional convolutional neural network with a robust cross-validation approach on a publicly available dataset. We identify interactions between frontal and central electrodes and other electrodes and identify differences in frontal δ, θ, β, and γlow between healthy controls and individuals with MDD. Our study represents a significant step forward for the field of deep learning-based raw EEG classification, providing new capabilities in interaction explainability and providing direction for future innovations through our proposed taxonomy.
A review and discussion of prospective statistical surveillance in public health

Summary. A review of methods suggested in the literature for sequential detection of changes in public health surveillance data is presented. Many researchers have noted the need for prospective methods. In recent years there has been an increased interest in both the statistical and the epidemiological literature concerning this type of problem. However, most of the vast literature in public health monitoring deals with retrospective methods, especially spatial methods. Evaluations with respect to the statistical properties of interest for prospective surveillance are rare. The special aspects of prospective statistical surveillance and different ways of evaluating such methods are described. Attention is given to methods that include only the time domain as well as methods for detection where observations have a spatial structure. In the case of surveillance of a change in a Poisson process the likelihood ratio method and the Shiryaev–Roberts method are derived.
Bamboozle: A bioinformatic tool for identification and quantification of intraspecific barcodes

Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes amongst strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans a species’ entire genome and identifies allele-rich barcodes that enable direct identification of different strains from a common population, and a single DNA sample, using amplicon sequencing. We demonstrate its usefulness by identifying hypervariable barcoding loci (<500 bp) from genomic data in two microalgal species, the diploid diatom Skeletonema marinoi, and the haploid chlorophyte Chlamydomonas reinhardtii. Across the genomes, only 26 loci capable of resolving all available strains’ genotypes were identified, all of which are within protein-coding genes of variable metabolic function. Single nucleotide polymorphisms (SNPs) provided the most reliable genetic markers, and amongst 55 strains of S. marinoi, three 500 bp loci contained, on average, 46 SNPs, 103 unique alleles, and displayed 100% heterozygosity. The prevalence of heterozygosity was identified as a novel opportunity to improve strain quantification and detect false positive artefacts during denoising of amplicon sequences. Finally, we illustrate how metabarcoding of a single genetic locus can be used to track strain abundances of 58 strains of S. marinoi in an artificial selection experiment. As future genomics datasets become available and DNA sequencing technologies develop, Bamboozle has flexible user settings enabling optimal barcodes to be designed for other species and applications.
Mental simulations and action language are impaired in individuals with aphantasia

Action reading is thought to engage motor simulations, yielding modulations in activity of motor-related cortical regions, and contributing to action language comprehension. To test these ideas, we measured 1) corticospinal excitability during action reading, and 2) reading comprehension ability, in individuals with normal and impaired imagery (i.e., phantasia and aphantasia, respectively). Thirty-four participants (17 phantasic and 17 aphantasic) were asked to read manual action sentences. By means of transcranial magnetic stimulation, we triggered motor-evoked potentials (MEP) in the target right index finger. MEP amplitude, a marker of corticospinal excitability, increased during action reading relative to rest for phantasic individuals, but not for aphantasic individuals. This result provides neurophysiological evidence that individuals living with aphantasia present a real neurophysiological deficit in motor system engagement during action reading. Furthermore, deep-level reading comprehension ability was impaired in individuals with aphantasia, who had difficulty selecting words that best fit the context of sentences. Altogether, these findings support the idea that motor simulations, along with the activation within the motor system, contribute to action language comprehension.
Gain without pain: adaptation and increased virulence of Zika virus in vertebrate host without fitness cost in mosquito vector

ABSTRACT Zika virus (ZIKV) is now in a post-pandemic period, for which the potential for re-emergence and future spread is unknown. Adding to this uncertainty is the unique capacity of ZIKV to directly transmit between humans via sexual transmission. Recently, we demonstrated that direct transmission of ZIKV between vertebrate hosts leads to rapid adaptation resulting in enhanced virulence in mice and the emergence of three amino acid substitutions (NS2A-A117V, NS2A-A117T, and NS4A-E19G) shared among all vertebrate-passaged lineages. Here, we further characterized these host-adapted viruses and found that vertebrate-passaged viruses do not lose fitness or transmission potential in mosquitoes. To understand the contribution of genetic changes to the enhanced virulence and transmission phenotype, we engineered these amino acid substitutions, singly and in combination, into a ZIKV infectious clone. We found that NS4A-E19G contributed to the enhanced virulence and mortality phenotype in mice. Further analyses revealed that NS4A-E19G results in increased viral loads and distinct transcriptional patterns for innate immune genes in the brain. None of the substitutions contributed to changes in mosquito vector competence. Together, these findings suggest that direct transmission chains could enable the emergence of more virulent ZIKV strains without compromising mosquito transmission capacity, although the underlying genetics of these adaptations are complex. IMPORTANCE Previously, we modeled direct transmission chains of Zika virus (ZIKV) by serially passaging ZIKV in mice and mosquitoes and found that direct mouse transmission chains selected for viruses with increased virulence in mice and the acquisition of non-synonymous amino acid substitutions. Here, we show that these same mouse-passaged viruses also maintain fitness and transmission capacity in mosquitoes. We used infectious clone-derived viruses to demonstrate that the substitution in nonstructural protein 4A contributes to increased virulence in mice. Previously, we modeled direct transmission chains of Zika virus (ZIKV) by serially passaging ZIKV in mice and mosquitoes and found that direct mouse transmission chains selected for viruses with increased virulence in mice and the acquisition of non-synonymous amino acid substitutions. Here, we show that these same mouse-passaged viruses also maintain fitness and transmission capacity in mosquitoes. We used infectious clone-derived viruses to demonstrate that the substitution in nonstructural protein 4A contributes to increased virulence in mice.
Conditionally deleterious mutation load accumulates in genomic islands but can be purged with sufficient genotypic redundancy

Local adaptation frequently evolves in patches or environments that are connected via migration. In these cases, genomic regions that are linked to an adaptive locus experience reduced effective migration rates. Via individual-based simulations of a two-patch system, we show that this reduced effective migration results in the accumulation of conditionally deleterious mutations, but not universally deleterious mutations, adjacent to adaptive loci. When there is redundancy in the genetic basis of local adaptation (i.e. genotypic redundancy), turnover of adaptive loci allows conditionally deleterious mutation load to be purged. The amount of mutational load that accumulates adjacent to adaptive loci is dependent on redundancy, recombination rate, migration rate, population size, strength of selection, and the phenotypic effect size of adaptive alleles. Our results highlight the need to be cautious when interpreting patterns of local adaptation at the level of phenotype or fitness, as the genetic basis of local adaptation can be transient, and evolution may confer a degree of maladaptation to non-local environments.
Forest structural diversity determines tree growth synchrony in response to climate change

After centuries of deforestation, many industrialised countries are experiencing an increase in forest area and biomass due to changes in land- and forest-use since the mid-20th century. At the same time, the impacts of climate change on forests are aggravating, but the interplay between past land- and forest-use (i.e. land- and forest-use legacies) and climate change in forest functioning remains elusive. Here using network theory and linear mixed models, we quantified how land- and forest-use legacies modulate tree growth synchrony in response to climate change. We analysed tree growth data from European beech (Fagus sylvatica L.) stands with different histories of forest management at the species’ rear edge. We found that tree growth synchrony increased following heatwaves, late spring frosts, and reduced precipitation. Interestingly, the greatest tree growth synchrony occurred in recently-established forests, while stands containing large trees and heterogeneous tree sizes showed much lower growth synchrony. Our results highlight the importance of maintaining large trees and structurally heterogeneous forests to mitigate the negative effects of climate change on forest productivity, and thereby, increase forest resilience to future forest climate risks.
TREM2-dependent senescent microglia conserved in aging and Alzheimer’s disease

Dementia in general, and Alzheimer’s disease (AD) in particular, are age-related diseases1,2. AD is associated with multiple causative factors3,4, among which local brain inflammation plays a significant role5. Microglia, the brain-resident immune cells6,7, are activated along the disease course7. Yet, their contribution to the disease progression is still controversial. Here, using high-throughput mass cytometry for microglial immuno-phenotyping, we identified accumulation of senescent microglia in several pathologies associated with cognitive decline. These senescent microglia have a unique profile conserved across the multiple conditions investigated, including aging, mouse models of amyloidosis, and tauopathy. Moreover, we found that the expression of markers of senescence correlates with levels of TREM2, whose polymorphism was identified by GWAS as an AD risk factor8,9. A TREM2-null AD mouse model showed lower levels of senescent microglia, relative to TREM2-intact AD mice. Senolysis using the drug ABT-73710,11 in an AD mouse model reduced the abundance of TREM2-senescent microglia without affecting levels of TREM2-dependent activated microglia, ameliorated cognitive deficits, and reduced brain inflammation. These results reveal the unexpected contribution of TREM2 to accumulation of senescent microglia in AD pathology, an effect that must be considered when targeting TREM2 as a therapeutic approach.
RNase R Controls Membrane Fatty Acid Composition in Streptococcus pneumoniae

Previous studies on RNase R have highlighted significant effects of this ribonuclease in several processes of Streptococcus pneumoniae biology. In this work we have studied the global impact of RNase R by comparing the transcriptional landscape of a deleted RNase R mutant to that of the wild-type strain, and this led us investigate specific targets affected by RNase R. RNA-Seq showed that RNase R deletion affects transcripts from several different biological processes. Of particular interest, elimination of RNase R results in overexpression of most of the genes encoding the components of type II fatty acid biosynthesis (FAS-II) cluster. We demonstrate that RNase R governs the turnover of most of genes from this pathway, affecting the outcome of the whole FAS-II cluster, and leading to an unbalanced membrane fatty acid composition. Our results show that the membrane of the deleted strain contains a higher proportion of unsaturated and long-chained fatty acids than the wild type strain. This leads to a higher fluidity of the Δrnr mutant membrane, which is probably related with the increased sensitivity to detergent observed in this strain. We demonstrate that RNase R expression is induced in cells challenged with H2O2, which is suggestive of a role for this ribonuclease on the regulation of membrane homeostasis under oxidative stress. Reprogramming of membrane fluidity is an adaptative cell response crucial for bacterial survival in constantly changing environmental conditions. The fact that RNase R controls the expression of several essential genes to the fatty acid synthesis unveils a new important function of this enzyme.
Lactococcus G423 Ameliorates the Growth Performance of Broilers by Modulation of Gut Microbiota- Metabolites

This study aimed to explore whether Lactococcus G423 could ameliorate growth performance of broilers by modulation of gut microbiota-metabolites based on the 16S ribosomal RNA (rRNA) and liquid chromatography-mass spectrometry (LC-MS). A total of 640 one-day-old AA broilers were randomly divided into 4 groups (Control (CON), Lac_L, Lac_H, and ABX). Average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) were calculated on the 42nd day. The ileum content was harvested and immediately frozen in liquid nitrogen for 16S rRNA and LC-MS analyses. Then, the results of 16S rRNA analysis were confirmed by quantitative polymerase chain reaction (qPCR). Compared with the CON group, ADG significantly increased in the Lac_H group (P<0.05), and survival rate significantly decreased in the Lac_H, Lac_H, and ABX groups (all P<0.05). A significant difference in microbial diversity was found among the four groups. Compared with the CON group, the abundance rates of Firmicutes and Lactobacillus in the Lac_H group were significantly risen (P<0.05). The global and overview maps and membrane transport in the Lac_L, Lac_H, and ABX groups significantly changed versus those in the CON group (P<0.05). The results of LC-MS demonstrated that Lactococcus could significantly improve the levels of some metabolites (6-hydroxy-5-methoxyindole glucuronide, 9,10-DiHOME, carbamazepine-O-quinone, N-Acetyl-L-phenylalanine, and kynurenine), and these metabolites were involved in 5 metabolic pathways. Among them, the pathways of linoleic acid metabolism, phenylalanine metabolism, and pentose and glucuronate interconversions significantly changed (P<0.05). Lactococcus improved wight and survival rate of broilers through the gut microbiota, regulating the pathways of amino acid metabolism, lipid metabolism, bile acid metabolism, and carbohydrate metabolism. However, antibiotics may negatively influence the gut microbiota. IMPORTANCE Improvements in the growth rate of broiler chickens can be achieved through dietary manipulation of the naturally occurring bacterial populations while mitigating the withdrawal of antibiotic growth promoters. Lactococcus is industrially crucial lactic acid bacteria, can be incorporated into the diets of chickens to improve their growth performance. This study investigated the key mechanisms behind this progression and pinpointed Lactococcus improved wight and survival rate of broilers through the gut microbiota, regulating the pathways of amino acid metabolism, lipid metabolism, bile acid metabolism, and carbohydrate metabolism.
Genetic characterization of extended-β-lactamase (ESBL) plasmids captured from dairy manures

This study was to assess the gene diversity and characterize a large set of plasmids harboring extended β-lactamase (ESBL) genes from raw and digested dairy manure. A total of eighty-four plasmids that were captured in this E. coli recipient were sequenced using Illumina MiSeq sequencing technology. Twenty-four plasmids of interest were subsequently sequenced using MinION technology in order that a hybrid assembly could be performed on short-and long-read sequences to circularize and complete these plasmids. The size of sequenced plasmids ranged between 40 and 260 kb with various incompatibility groups: IncC, IncI1, IncN, IncY, IncB/O/K/Z, IncX1, IncHI2, IncHI2A, IncFIB(K), IncFII. A variety of extended β-lactamase genes were identified: blaCTXM -1, blaCTXM -14, blaCTXM -15, blaCTXM-27, blaCTXM-55, blaCTXM-61, blaPER-1, blaIMP-27. Interestingly, the blaIMP-27 gene, a novel metallo-β-lactamase discovered in the last decade, was found located on an integrated region in the host chromosome. And one plasmid carrying the blaCMY-2 gene, an AmpC gene, also expressed ESBL phenotype. Four virulence factors, including cia, cib, traT and terC, were detected on some of these plasmids. In addition, six type-2 toxin-antitoxin systems were detected: MazF/E, PemK/I, HipA/B, YdcE/D, RelB/E and HigB/A. Twenty-two out of twenty-four complete plasmids carried putative prophage regions; and most of prophage hits were marked as incomplete, except that the largest plasmid pT525A and the IncY plasmid pT415A had prophage hits with higher scores. IMPORTANCE The widespread of antibiotic resistant bacteria is largely due to the exchange of mobile genetic elements such as plasmids. Plasmids harboring extended β-lactamase (ESBL) genes originated from dairy manure potentially become entrained in manured soil, which subsequently enter the human food chain. Currently there is a lack of detailed information on these plasmids in the environment, specifically in dairy manure. This study unveils the abundance and diversity of ESBL-carrying plasmids from both raw and digested manures which were captured in gfp-labelled E. coli CV601. In addition, the study provides insightful information of plasmid characteristics including incompatibility groups, ESBL genes combined with other resistance genes, mobile genetic elements (transposons, insertion sequence), toxin-antitoxin systems, virulence factors and prophage sequences.