bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetic feedback on noisy expression boosts evolvability
Authors: Daalman Werner Karl-Gustav , Laan Liedewij
Published: July 2022

Adapting organisms often face fitness valleys, i.e. barriers imposed by ubiquitous genetic interactions, while optimizing functions. Elucidating mechanisms that facilitate fitness valley traversals is integral to understanding evolution. Therefore, we investigated how protein expression noise, mechanistically decomposed into instant variation and epigenetic inheritance of optimal protein dosage (‘transgenerational feedback’), shapes the fitness landscape. For this purpose, we combined a minimal model for expression noise with diverse data of Saccharomyces cerevisiae from literature on e.g. expression and fitness to representatively simulate mutational fitness effects. For our proxy of point mutations, which are very often near-neutral, instant dosage variation by expression noise typically incurs a 8.7% fitness loss (17% in essential genes) for non-neutral point mutations. However, dosage feedback mitigates most of this deleterious effect, and additionally extends the time until extinction when essential gene products are underexpressed. Taken together, we consider dosage feedback as a relevant example of Waddington’s canalization: a mechanism which temporarily drives phenotypes towards the optimum upon a genetic mismatch, thereby promoting fitness valley traversal and evolvability.

Author summary

Gene products frequently interact to generate unexpected phenotypes. This universal phenomenon is known as epistasis, and complicates step-wise evolution to an optimum. Attempts to understand and/or predict how the optimum is found are further compromised by the countless combinations of mutations that are considered by nature, and necessitate the formulation of general rules on how the obstacles that epistasis presents are bridged. To make such a rule as insightful as possible, we reduced cell division to a generation-based model focusing on one protein at a time for reproductive success. Importantly, protein production between divisions is stochastic and we show how the resulting expression noise affects epistasis. After validating the model on experimental fitness landscapes, we combine high-throughput data of budding yeast from multiple sources to make our model predictions on mutational effects on fitness as representative as possible. We find different effects per mutation type: gene duplications have little effect, as genes in our simulated pool are rarely toxic, loss-of-function mutations decrease mutational gains as adaptation progresses, and point mutations permit expression noise to unlock its roles in adaptation. For non-neutral point mutations, noise imposes a sizeable fitness penalty or even induces extinction, which is alleviated by an epigenetic, transgenerational feedback on protein dosage which is never deleterious. Particularly for essential genes, we predict that this effect reduces the obstacles of epistasis and hence significantly increases evolvability, adding to the general rules of evolution.
A scaling law relating the rate of destruction of a solid tumor and the fractal dimension of its boundary
Authors: López Álvaro G. , Sanjuán Lorena R.
Published: July 2022

We investigate the scaling law relating the size of the boundary of a solid tumor and the rate at which it is lysed by a cell population of non-infiltrating cytotoxic lymphocytes. We do it in the context of enzyme kinetics through geometrical, analytical and numerical arguments. Following the Koch island fractal model, a scale-dependent function that describes the constant rate of the decay process and the fractal dimension is obtained in the first place. Then,in silicoexperiments are accomplished by means of a stochastic hybrid cellular automaton model. This model is used to grow several tumors with varying morphology and to test the power decay law when the cell-mediated immune response is effective, confirming its validity.
Impaired bone strength and bone microstructure in a novel early-onset osteoporotic rat model with a clinically relevant PLS3 mutation
Authors: Hu Jing , Zhou Bingna , Lin Xiaoyun , Zhang Qian , Guan Feifei , Sun Lei , Liu Jiayi , Wang Ou , Jiang Yan , Xia Weibo , Xing Xiaoping , Li Mei
Published: July 2022

Osteoporosis is a highly prevalent disorder with a strong genetic component. Recent studies identify PLS3 as a novel bone regulator of bone metabolism and PLS3 mutations lead to a rare monogenic early-onset osteoporosis. However, the mechanism of PLS3 mutation leading to osteoporosis is unknown with no animal models carrying patient-derived PLS3 mutations generated. The effective treatment strategies for PLS3-related have not been established. Here we have constructed a novel rat model with clinically relevant hemizygous E10-16del mutation of PLS3 (PLS3E10-16del/0) that recapitulate the osteoporotic phenotypes with obviously thinner cortical thickness, significant decreases in yield load, maximum load, and breaking load of femora at 3, 6, 9 months compared to WT rats. Histomorphometric analysis indicates a significantly lower mineral apposition rate in PLS3E10-16del/0rats. Treatment with alendronate (ALN, 1.0 ug/kg per day) or teriparatide (TPTD, 40ug/kg five times weekly) for 8 weeks significantly improved bone mass and bone microarchitecture, and bone strength was significantly increased after TPTD treatment (P < 0.05). Thus, our results indicate the roles of PLS3 in the regulation of bone microstructure and bone strength, providing a novel animal model for the study of early-onset osteoporosis. Alendronate and teriparatide treatment could be a potential treatment for early-onset osteoporosis induced by PLS3 mutation.
Dimensionality reduction and statistical modeling of scGET-seq data
Authors: de Pretis Stefano , Cittaro Davide
Published: July 2022

Single cell multiomics approaches are innovative techniques with the ability to profile orthogonal features in the same single cell, giving the opportunity to dig more deeply into the stochastic nature of individual cells. We recently developed scGET-seq, a technique that exploits a Hybrid Transposase (tnH) along with the canonical enzyme (tn5), which is able to profile altogether closed and open chromatin in a single experiment. This technique adds an important feature to the classic scATAC-seq assays. In fact, the lack of a closed chromatin signal in scATAC: (i) restricts sampling of DNA sequence to a very small portion of the chromosomal landscapes, substantially reducing the ability to investigate copy number alteration and sequence variations, and (ii) hampers the opportunity to identify regions of closed chromatin, that cannot be distinguished between non-sampled open regions and truly closed. scGET-seq overcomes these issues in the context of single cells. In this work, we describe the latest advances in the statistical analysis and modeling of scGET-seq data, touching several aspects of the computational framework: from dimensionality reduction, to statistical modeling, and trajectory analysis.
Brain-wide connectivity map of mouse thermosensory cortices
Authors: Bokiniec Phillip , Whitmire Clarissa J. , Leva Tobias M. , Poulet James F.A.
Published: July 2022

In the thermal system, skin cooling is represented in the primary somatosensory cortex (S1) and the posterior insular cortex (pIC). Whether S1 and pIC are nodes in anatomically separated or overlapping thermal sensorimotor pathways is unclear, as the brain-wide connectivity of the thermal system has not been mapped. We address this using functionally targeted, dual injections of anterograde viruses or retrograde tracers into S1 and pIC. Our data show that inputs to S1 and pIC originate from two non-overlapping populations, supporting the existence of parallel input pathways. While outputs from S1 and pIC were more widespread and share a number of cortical and subcortical regions, within target structures axonal projections were often separable. We observed a high degree of reciprocal connectivity with thalamic and cortical regions from both S1 and pIC, but output to the mid- and hind-brain was unidirectional. Notably, pIC showed exclusive connectivity with regions associated with thermal processing. Together, these data indicate that cutaneous thermal information is routed to the cortex via multiple, parallel streams of information which are forwarded to overlapping downstream regions for the binding of complex somatosensory percepts and integration with ongoing behavior.
Gene drive designs for efficient and localisable population suppression using Y-linked editors
Authors: Geci René , Willis Katie , Burt Austin
Published: July 2022

The sterile insect technique (SIT) has been successful in controlling some pest species but is not practicable for many others due to the large numbers of individuals that need to be reared and released. Previous computer modelling has demonstrated that the release of males carrying a Y-linked editor that kills or sterilises female descendants could be orders of magnitude more efficient than SIT while still remaining spatially restricted, particularly if combined with an autosomal sex distorter. In principle, further gains in efficiency could be achieved by using a self-propagating double drive design, in which each of the two components (the Y-linked editor and the sex ratio distorter) boosted the transmission of the other. To better understand the expected dynamics and impact of releasing constructs of this new design, we have analysed a deterministic population genetic and population dynamic model. Our modelling demonstrates that this design can suppress a population from very low release rates, with no invasion threshold. Importantly, the design can work even if homing rates are low and sex chromosomes are silenced at meiosis, potentially expanding the range of species amenable to such control. Moreover, the predicted dynamics and impacts can be exquisitely sensitive to relatively small (e.g., 25%) changes in allele frequencies in the target population, which could be exploited for sequence-based population targeting. Analysis of published Anopheles gambiae genome sequences indicates that even for weakly differentiated populations with an FST of 0.02 there may be thousands of suitably differentiated genomic sites that could be used to restrict the spread and impact of a release. Our proposed design, which extends an already promising development pathway based on Y-linked editors, is therefore a potentially useful addition to the menu of options for genetic biocontrol.
Enabling spectrally resolved single-molecule localization microscopy at high emitter densities
Authors: Martens Koen J.A. , Gobes Martijn , Archontakis Emmanouil , Brillas Roger R. , Zijlstra Niels , Albertazzi Lorenzo , Hohlbein Johannes
Published: July 2022

Single-molecule localization microscopy (SMLM) is a powerful technique for elucidating structure and dynamics in the life- and material sciences with sub-50 nm spatial resolution. The simultaneous acquisition of spectral information (spectrally resolved SMLM, sSMLM) enables multiplexing using spectrally distinct fluorophores or enable the probing of local chemical environments by using solvachromatic fluorophores such as Nile Red. Until now, the widespread utilisation of sSMLM was hampered by several challenges: an increased complexity of the optical detection pathway, limited software solutions for data analysis, lower accessible emitter densities or smaller field-of-views, and overall compromised spatio-spectral resolution. Here, we present a low-cost implementation of sSMLM that addresses these challenges. Using a blazed, low-dispersion transmission grating positioned close to the image plane here represented by the camera sensor, the +1st diffraction order is minimally elongated compared to the point spread function of the 0th order and can therefore be analysed using common subpixel single-molecule localization algorithms. The distance between both PSFs provides accurate information on the spectral properties of the emitter. The minimal excess width of 1st order PSFs enables a fivefold higher emitter density compared to other sSMLM approaches whilst achieving a spatio-spectral localization accuracy sufficient to discriminate between fluorophores whose peak emission are less than 15 nm apart as demonstrated using dSTORM, DNA-PAINT and smFRET. We provide an ImageJ/Fiji plugin (sSMLMAnalyzer) and suitable Matlab scripts for data analysis. We envision that our approach will find widespread use in super-resolution applications that rely on distinguishing spectrally different fluorophores under low photon conditions.
A bifunctional CPD/(6-4)- photolyase from the cyanobacteria Synechococcus sp. PCC 7335 constitutes an UV-B inducible operon: new insights into photolyases phylogenetic evolution
Authors: Belén Fernández María , Lucas Latorre , Natalia Correa-Aragunde , Cassia Raúl
Published: July 2022

Photosynthetic organisms are continuously exposed to solar ultraviolet radiation-B (UV-B) because of their autotrophic lifestyle. UV-B provokes DNA damages, as cyclobutane pyrimidine dimers (CPD) or pyrimidine (6-4) pyrimidone photoproducts (6-4 PPs). The cryptochrome/ photolyase family (CPF) comprises flavoproteins that are able to bind damaged or undamaged DNA. Photolyases (PHRs) are enzymes that repair either CPDs or 6-4 PPs. A natural bifunctional CPD/(6-4)- PHR (PhrSph98) was recently isolated from the UV-resistant bacteria Sphingomonas UV9. In this work, phylogenetic studies of bifunctional CPD/(6-4)- photolyases and its evolutionary relationship with other CPF members were performed. Amino acids involved in electron transfer and binding to FAD cofactor and DNA lesions were conserved in proteins from proteobacteria, planctomycete, bacteroidete, acidobacteria and cyanobacteria clades. Genome analysis revealed that the cyanobacteria Synechococcus sp. PCC 7335 encodes a two-gene assembly operon coding for a PHR and a bifunctional CPD/(6-4)- PHR. Operon structure was validated by RT-qPCR analysis and the polycistronic transcript accumulated after 15 minutes of UV-B irradiation. Conservation of structure and evolution is discussed. This is the first report of an UV-B inducible PHRs operon which encodes a CPD/(6-4)- photolyase with putative bifunctional role in the repair of CPDs and 6-4 PPs damages in oxygenic photosynthetic organisms.
Long-range alteration of the physical environment mediates cooperation betweenPseudomonas aeruginosaswarming colonies
Authors: Deforet Maxime
Published: July 2022

Pseudomonas aeruginosamakes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how this rhamnolipids interact with biogels to assist swarming remains unclear. Here I use a combination of optical techniques across scales and genetically-engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances > 10,000x the body size of an individual cell. The swelling front is on the micrometric scale, and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel, but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depends on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically-engineered mutant unable to secrete rhamnolipids (DrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences.

Significance statement

Living organisms have the ability to interact mechanically with their environment.Pseudomonas aeruginosa, a motile bacterium, can spread collectively on biogels, a behavior called swarming. Rhamnolipids, surfactant moleculesP. aeruginosamake and secrete, are required for swarming. Here, I demonstrate rhamnolipids not only physically alter the biogel in the vicinity of the secreting cells, but also over distances much greater than the bacterial cell size, through gel swelling. This long-distance physical alteration can even rescue a remote colony which would not produce rhamnolipids. This work illustrates the remarkable ability of bacteria to change the mechanical property of the world surrounding them.
Gait, physical activity, and tibiofemoral cartilage damage: A longitudinal machine learning analysis in the Multicenter Osteoarthritis Study
Authors: Costello Kerry E. , Felson David T. , Jafarzadeh S. Reza , Guermazi Ali , Roemer Frank W. , Segal Neil A. , Lewis Cora E. , Nevitt Michael C. , Lewis Cara L. , Kolachalama Vijaya B. , Kumar Deepak
Published: July 2022

Objective

To 1) develop and evaluate a machine learning model incorporating gait and physical activity to predict medial tibiofemoral cartilage worsening over two years in individuals without or with early knee osteoarthritis and 2) identify influential predictors in the model and quantify their effect on cartilage worsening.

Design

An ensemble machine learning model was developed to predict worsened cartilage MRI Osteoarthritis Knee Score at follow-up from gait, physical activity, clinical and demographic data from the Multicenter Osteoarthritis Study. Model performance was evaluated in repeated cross-validations. The top 10 predictors of the outcome across 100 held-out test sets were identified by a variable importance measure statistic, and their marginal effect on the outcome was quantified by g-computation.

Results

Of 947 legs in the analysis, 14% experienced medial cartilage worsening at follow-up. The median (2.5th-97.5thpercentile) AUC across the 100 held-out test sets was 0.73 (0.65-0.79). Presence of baseline cartilage damage, higher Kellgren-Lawrence grade, greater pain during walking, higher lateral ground reaction force impulse, greater time spent lying, and lower vertical ground reaction force unloading rate were associated with greater risk of cartilage worsening.

Conclusions

An ensemble machine learning approach incorporating gait, physical activity, and clinical/demographic features showed good performance for predicting cartilage worsening over two years. While identifying potential intervention targets from the model is challenging, these results suggest that lateral ground reaction force impulse, time spent lying, and vertical ground reaction force unloading rate should be investigated further as potential early intervention targets to reduce medial tibiofemoral cartilage worsening.

Summary box

What are the findings?

Machine learning models predicted cartilage worsening in persons without or with early knee osteoarthritis from gait, physical activity, and clinical and demographic characteristics with a median AUC of 0.73 across 100 held-out test sets.

High lateral ground reaction force impulse, more time spent lying, and low vertical ground reaction force unloading rate were associated with increased risk of cartilage worsening over two years.

How might it impact on clinical practice in the future?

Gait and physical activity are some of the only modifiable risk factors for knee osteoarthritis; this study identified three potential intervention targets to slow early knee osteoarthritis progression.
Development of allosteric, selective cyclin-dependent kinase 2 (CDK2) inhibitors that are negatively cooperative with cyclin binding and show potential as contraceptive agents
Authors: Faber Erik B. , Tang Jian , Roberts Emily , Ganeshkumar Sornakala , Sun Luxin , Wang Nan , Rasmussen Damien , Majumdar Abir , John Kristen , Yang An , Khalid Hira , Hawkinson Jon E. , Levinson Nicholas M. , Schönbrunn Ernst , Chennathukuzhi Vargheese , Harki Daniel A. , Georg Gunda I.
Published: July 2022

Compared to most ATP-site kinase inhibitors, small molecules that target an allosteric pocket have the potential for improved selectivity due to the often observed lower structural similarity at these distal sites. Despite their promise, relatively few examples of structurally confirmed, high-affinity allosteric kinase inhibitors exist. Cyclin-dependent kinase 2 (CDK2) is a target for many therapeutic indications, including non-hormonal contraception.1 However, an inhibitor against this kinase with exquisite selectivity has not reached the market because of the structural similarity between CDKs.1-2 In this paper, we describe the development and mechanism of action of new type III inhibitors that bind CDK2 with nanomolar affinity, making them the highest affinity, structurally confirmed allosteric CDK inhibitors reported. Notably, these anthranilic acid inhibitors exhibit a strong negative cooperative relationship with cyclin binding, which remains an underexplored mechanism for CDK2 inhibition. Furthermore, the binding profile of these compounds in both biophysical and cellular assays demonstrate the promise of this series for further development into a therapeutic selective for CDK2 over highly similar kinases like CDK1. The potential of these inhibitors as efficacious contraceptive agents is seen by incubation with mouse testicular explants, where they recapitulate Cdk2-/- and Spdya-/- phenotypes.
Sediment substrate size influences fish diversity in tributary mouth areas in impounded boreal rivers in Sweden
Authors: Näslund J. , Bowes R. , Sandin L. , Bergman E. , Greenberg L.
Published: July 2022

Large boreal rivers in Sweden are generally impounded by hydropower dams and a large proportion of their main stem shallow flowing habitats have been lost. Tributaries often contain relatively undisturbed habitats and could be important for the conservation of species diversity. Tributary mouth areas could be biodiversity hot-spots, due to the vicinity to the main stem and favorable environmental conditions. In this study, we investigate whether tributary mouth areas in two impounded boreal rivers (Ume- and Lule River) could be regarded as biodiversity hot spots for fish. Based on electrofishing in 20 tributary mouths, we found that overall fish diversity is generally low. The highest species richness and diversity was found in mouth areas dominated by intermediate substrate sizes (gravel – cobble). Few, if any, species were found in association with fine sediment substrates (smaller than sand). The tributary mouth areas had similar species richness and diversity as areas in the tributaries located 1-km upstream of the mouth, but the fish community composition often differed between these sites. Management action favoring fish diversity in the tributary mouth areas could include protection or rehabilitation of areas dominated by medium sized substrate and reduction of erosion and transport of fine sediments in the tributaries. Overall, we find no support for tributary mouths being hot-spots for fish biodiversity and while some patterns in diversity gives hints on suitable management action, it is important to further understand impacts in tributaries and their mouths especially in relation to temporal dynamics of the fish community.
Stromal transdifferentiation drives lymph node lipomatosis and induces extensive vascular remodeling
Authors: Bekkhus Tove , Olofsson Anna , Sun Ying , Magnusson Peetra , Ulvmar Maria H.
Published: July 2022

Lymph node (LN) lipomatosis is a common, but rarely discussed phenomenon, associated with aging, involving a gradual exchange of the LN parenchyma into adipose tissue. The mechanisms behind these changes and the effects on the LN have been unknown. We show that LN lipomatosis starts in the medullary regions of the human LN and link the initiation of lipomatosis to transdifferentiation of LN medullary fibroblasts into adipocytes. The latter is associated with a downregulation of lymphotoxin beta expression. We also show that, medullary fibroblasts, in contrast to the reticular cells in the T-cell zone, display an inherent higher sensitivity for adipogenesis. Progression of lipomatosis leads to a gradual loss of the medullary lymphatic network, but at later stages, collecting-like lymphatic vessels, are found inside the adipose tissue. The stromal dysregulation includes a dramatic remodeling and dilation of the high endothelial venules associated with reduced density of naïve T-cells. Abnormal clustering of plasma cells is also observed. Thus, LN lipomatosis causes widespread stromal dysfunction with consequences for the immune contexture of the human LN. Our data warrant an increased awareness of LN lipomatosis as a factor contributing to decreased immune functions in the elderly and in disease.

Graphical abstract

In lymph nodes (LNs) of young patients there is a normal lymph flow, normal and functioning high endothelial venules (HEVs) with a high density of surrounding naïve T-cells. With aging lymphotoxin beta (LTB) is downregulated in the medulla of the LN and the fibroblasts of the medulla, namely the medullary reticular cells (MedRCs), transdifferentiate into adipocytes inducing LN lipomatosis. LN lipomatosis leads to loss of lymphoid tissue, medullary sinuses and can be predicted to result in a shortcut of the lymph flow based on the presence of collecting-like vessels in the adipose tissue in late stage lipomatosis. Lipomatosis also induce extensive vascular remodeling with loss of medullary lymphatic vessels and dysfunctional, highly dilated HEVs with lower density of naïve T-cells and trapped plasma cells.
A Versatile Agrobacterium-Based Transformation System for Genetic Engineering of Diverse Citrus Cultivars
Authors: Dominguez Michelle M. , Padilla Carmen S. , Mandadi Kranthi K.
Published: July 2022

Developing an efficient transformation system is vital in genetically engineering recalcitrant crops, particularly trees. Here, we outline an Agrobacterium tumefaciens-based transformation methodology for citrus genetic engineering. The process was optimized to suit the requirements of fourteen citrus varieties by establishing appropriate infection, co-cultivation, selection, and culture media conditions. The procedure includes transforming seedling-derived epicotyl segments with an A. tumefaciens strain, then selecting and regenerating transformed tissues. Transgenic shoots were further identified by a visual reporter (e.g., β-glucuronidase) and confirmed by Northern and Southern blot analysis. Transgene integrations among the transgenic lines ranged between one to four. The methodology can yield transformation efficiencies of up to 11%, and transgenic plants can be recovered as early as six months, depending on the variety. In addition, we show that incorporating A. tumefaciens helper virulence genes (virG and virE), spermidine, and lipoic acid in the resuspension buffer before transformation improved the transformation efficiency of specific recalcitrant cultivars, presumably by enhancing T-DNA integration and alleviating oxidative stress on the explant tissues. In conclusion, the optimized methodology can be utilized to engineer diverse recalcitrant citrus varieties towards trait improvement or functional genetics applications.
The genetic architecture of local adaptation in a cline
Authors: Laroche Fabien , Lenormand Thomas
Published: July 2022

Local adaptation is pervasive. It occurs whenever selection favors different phenotypes in different environments, provided that there is genetic variation for the corresponding traits and that the effect of selection is greater than the effect of drift and migration. In many cases, ecologically relevant traits are quantitative and controlled by many genes. It has been repeatedly proposed that the localization of these genes in the genome may not be random, but could be an evolved feature. In particular, the clustering of local adaptation genes may be theoretically expected and has been observed in several situations. Previous theory has focused on two-patch or continent-island models to investigate this phenomenon, reaching the conclusion that such clustering could evolve, but in relatively limited conditions. In particular, it required that migration rate was neither too low nor too large and that the full optimization of trait values could not be eventually achieved by a mutation at a single locus. Here, we investigate this question in a spatially-explicit model, considering two contiguous habitats with distinct trait optima on a circular stepping-stone. We find that clustering of local-adaptation genes is pervasive within clines during both the establishment phase of local adaptation and the subsequent “reconfiguration” phase where different genetic architectures compete with each other. We also show that changing the fitness function relating trait to fitness has a strong impact on the overall evolutionary dynamics and resulting architecture.
H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements
Authors: Tafessu Amanuel , O’Hara Ryan , Martire Sara , Dube Altair L. , Saha Purbita , Banaszynski Laura A.
Published: July 2022

Background

The histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are highly accessible, creating an environment that is permissive to transcription factor binding and the recruitment of transcriptional coactivators that establish a unique chromatin post-translational landscape. How H3.3 contributes to the establishment and function of chromatin states at these regions is poorly understood.

Results

We performed genomic analyses of features associated with active promoter chromatin in mouse embryonic stem cells (ESCs) and found evidence of subtle yet widespread promoter dysregulation in the absence of H3.3. Loss of H3.3 deposition at promoters reduces chromatin accessibility and transcription factor (TF) footprinting for nearly all TFs expressed in ESCs. H3.3 deletion leads to reduced promoter enrichment of the transcriptional coactivator and histone acetyltransferase, p300. Subsequently, histone H3 acetylation at lysine 27 (H3K27ac) is reduced at promoters in the absence of H3.3, along with reduced enrichment of the bromodomain-containing protein BRD4, an acetyl lysine reader. Despite the observed chromatin dysregulation, H3.3 KO ESCs maintain transcription from ESC-specific genes. However, upon undirected differentiation, H3.3 KO cells retain footprinting of ESC-specific TFs motifs and fail to generate footprints of lineage-specific TF motifs, in line with their diminished capacity to differentiate.

Conclusions

H3.3 facilitates DNA accessibility, TF binding, and histone post-translational modification at active promoters. While H3.3 is not required for maintaining transcription in ESCs, it is required for TF binding at new promoters during differentiation.
Cavity geometry shapes overall ant colony organization through spatial limits but workers maintain fidelity zones
Authors: Chism Greg T. , Nichols William , Dornhaus Anna
Published: July 2022

Many animals inhabit nests that protect them from adverse environments. However, the effects of living in a built or found structure are not limited to protection: the physical space can shape and organize behavior, particularly in self-organized collective systems. In addition, the geometry of nest space may not be under the animal’s control, raising the question whether animals can compensate for the effects that unexpected or suboptimal geometries may have. Here we examine how the shape of a nest cavity affects spatial organization of colonies in the antTemnothorax rugatulus, a species that adapted to nest cavities of unmodifiable internal dimensions, since they inhabit rock crevices with rigid walls. We show that the emerging spatial relationships of workers, brood, queens, and young alates, as well as their relationships and distances to significant points in the nest, are all significantly influenced by nest shape, with the brood distributions most affected. However, we also found that the size of worker spatial fidelity zones, i.e. the areas in the nest that individual workers occupy and that may be key regulators of division of labor, are overall not affected by nest shape. These findings indicate that ants may actively regulate which areas of a nest they occupy, and that they may compensate for effects of nest architecture constraints. Physical properties of nests can thus influence the organization of ant colonies, highlighting the need to explore spatial constraints as a direct influence on the organization, movement, and communication of evolved or engineered self-organized systems.
Functional analysis of recurrent non-coding variants in human melanoma
Authors: Godoy Paula M. , Zarov Anna P. , Kaufman Charles K.
Published: July 2022

Small nucleotide variants in non-coding regions of the genome can alter transcriptional regulation, leading to changes in gene expression which can activate oncogenic gene regulatory networks. Melanoma is heavily burdened by non-coding variants, representing over 99% of total genetic variation, including the well-characterized TERT promoter mutation. However, the compendium of regulatory non-coding variants is likely still functionally under-characterized. We developed a pipeline to identify hotspots, i.e. recurrently mutated regions, in melanoma containing putatively functional non-coding somatic variants that are located within predicted melanoma-specific regulatory regions. We identified hundreds of statistically significant hotspots, including the hotspot containing the TERT promoter variants, and focused in on a hotspot in the promoter of CDC20. We found that variants in the promoter of CDC20, which putatively disrupt an ETS motif, lead to lower transcriptional activity in reporter assays. Using CRISPR/Cas9, we generated an indel in the CDC20 promoter in a human A375 melanoma cell line and observed decreased expression of CDC20, changes in migration capabilities, and an altered transcriptional state previously associated with neural crest transcriptional programs and melanoma initiation. Overall, our analysis prioritized several recurrent functional non-coding variants that, through downregulation of CDC20, led to perturbation of key melanoma phenotypes.
Pitfalls of genotyping microbial communities with rapidly growing genome collections
Authors: Zhao Chunyu , Shi Zhou Jason , Pollard Katherine S.
Published: July 2022

Detecting genetic variants in metagenomic data is a priority for understanding the evolution, ecology, and functional characteristics of microbial communities. Many recent tools that perform this metagenotyping rely on aligning reads of unknown origin to a reference database of sequences from many species before calling variants. Using simulations designed to represent a wide range of scenarios, we demonstrate that diverse and closely related species both reduce the power and accuracy of reference-based metagenotyping. We identify multi-mapping reads as a prevalent source of errors and illustrate a tradeoff between retaining correct alignments versus limiting incorrect alignments, many of which map reads to the wrong species. Then we quantitatively evaluate several actionable mitigation strategies and review emerging methods with promise to further improve metagenotyping. These findings document a critical challenge that has come to light through the rapid growth of genome collections that push the limits of current alignment algorithms. Our results have implications beyond metagenotyping to the many tools in microbial genomics that depend upon accurate read mapping.

HIGHLIGHTS

Most microbial species are genetically diverse. Their single nucleotide variants can be genotyped using metagenomic data aligned to databases constructed from genome collections (“metagenotyping”).

Microbial genome collections have grown and now contain many pairs of closely related species.

Closely related species produce high-scoring but incorrect alignments while also reducing the uniqueness of correct alignments. Both cause metagenotype errors.

This dilemma can be mitigated by leveraging paired-end reads, customizing databases to species detected in the sample, and adjusting post-alignment filters.
Interactive analysis of functional residues in protein families
Authors: Price Morgan N. , Arkin Adam P.
Published: July 2022

A protein’s function depends on functional residues that determine its binding specificity or its catalytic activity, but these residues are typically not considered when annotating a protein’s function. To help biologists investigate the functional residues of proteins, we developed two interactive web-based tools, SitesBLAST and Sites on a Tree. Given a protein sequence, SitesBLAST finds homologs that have known functional residues and shows whether the functional residues are conserved. Sites on a Tree shows how functional residues vary across a protein family by showing them on a phylogenetic tree. These tools are available at http://papers.genomics.lbl.gov/sites.
Transcriptional Profiles Analysis of COVID-19 and Malaria Patients Reveals Potential Biomarkers in Children
Authors: Lambert Nzungize , Kengne-Ouafo Jonas A. , Rissy Wesonga Makokha , Diane Umuhoza , Murithi Ken , Kimani Peter , Awe Olaitan I. , Dillman Allissa
Published: July 2022

The clinical presentation overlap between malaria and COVID-19 poses special challenges for rapid diagnosis in febrile children. In this study, we collected RNA-seq data of children with malaria and COVID-19 infection from the public databases as raw data in fastq format paired end files. A group of six, five and two biological replicates of malaria, COVID-19 and healthy donors respectively were used for the study. We conducted differential gene expression analysis to visualize differences in the expression profiles. Using edgeR, we explored particularly gene expression levels in different phenotype groups and found that 1084 genes and 2495 genes were differentially expressed in the malaria samples and COVID-19 samples respectively when compared to healthy controls. The highly expressed gene in the COVID-19 group we found CD151 gene which is facilitates in T cell proliferation, while in the malaria group, among the highly expressed gene we identified GBP5 gene which involved in inflammatory response and response to bacterium. By comparing both malaria and COVID-19 infections, the overlap of 62 differentially expressed genes patterns were identified. Among them, three genes (ENSG00000234998, H2AC19 and TXNDC5) were highly upregulated in both infections. Strikingly, we observed 13 genes such as HBQ1, HBM, SLC7A5, SERINC2, ATP6V0C, ST6GALNAC4, RAD23A, PNPLA2, GAS2L1, TMEM86B, SLC6A8, UBALD1, RNF187 were downregulated in children with malaria and uniquely upregulated in children with COVID-19, thus may be further validated as potential biomarkers to delineate COVID-19 from malaria-related febrile infection. The hemoglobin complexes and lipid metabolism biological pathways are highly expressed in both infections. Our study provided new insights for further investigation of the biological pattern in hosts with malaria and COVID-19 coinfection.
D/E-rich peptides are less suitable than D/E-deficient peptides for identification by negative-ion HCD due to scarce production of sequencing ions from multiply charged precursors
Authors: Zuo Mei-Qing , Sun Rui-Xiang , Dong Meng-Qiu
Published: July 2022

Highly acidic, D/E-rich peptides or proteins are difficult to identify by positive-ion-mode mass spectrometry (MS), and negative-ion-mode MS is an attractive but insufficiently explored alternative. Based on high-resolution and accurate-mass MS analysis of 115 synthetic peptides of 5-28 amino acids, we confirmed that higher-energy collisional dissociation (HCD) of deprotonated peptides induced abundant backbone or side-chain neutral losses (NL), and updated the ranking list of NLs by abundance. The most abundant fragment ion types arey->x-, z->c-if the NL ions are included, orc->y->z->b-if not. The most frequent side-chain NLs involve amino acids C, S, T, D, E, N, Q, and R. Although NL of CO2is common for all peptides, it is markedly enhanced in D/E-containing peptides. Long peptides and D/E-rich peptides are prone to carrying multiple negative charges. HCD spectra produced from multiply deprotonated peptides have a lower fraction of sequencing ions (i.e.,a-, b-, c-, x-, y-, z-ions) than those produced from 1-([M-H]-) and 2-([M-2H]2-) precursors. Based on the above findings, we predict that under negative-ion HCD, D/E-rich peptides should be difficult to identify and that choosing a protease to generate peptides containing fewer D/E residues will improve identification of highly acidic proteins.
BmHen1 plays an essential role in the regulation of eupyrene sperm development in Bombyx mori
Authors: Yang Xu , Chen Dongbin , Zheng Shirui , Yi Meiyan , Liu Zulian , Liu Yongjian , Yang Dehong , Liu Yujia , Tang Linmeng , Zhu Chenxu , Huang Yongping
Published: July 2022

In lepidopteran insects, sperm polymorphism is a remarkable feature, in which males exhibit two different types of sperms. Both sperm morphs are essential for fertilization as eupyrene (nucleate) sperm carries DNA and fertilizes the egg, while apyrene (anucleate) sperm is necessary for transporting eupyrene sperm into females. To date, the functional genetic study on dichotomous spermatogenesis has been limited. It is known that, in the model species including mice, worms, and flies, the components in piRNA biogenesis pathway play an important role in gonad development. In this study, we characterize BmHen1 as a new critical component involved in the regulation of eupyrene sperm development in B. mori. We generated the loss-of-function mutant of BmHen1 (ΔBmHen1) through CRISPR/Cas9-based gene editing, and found that it is both female- and male-sterile. ΔBmHen1 females lay significantly fewer eggs than wild-type, which display morphological defects. Fluorescence staining assays show that the ΔBmHen1 eupyrene sperms exhibit severe defects in nuclei formation, while its apyrene sperms are normal. We then constructed the loss-of-function mutants of Siwi and BmAgo3 (ΔSiwi and ΔBmAgo3) through CRISPR/Cas9-based gene editing, which encode PIWI proteins acting as the core elements in piRNA biogenesis, and explored whether they might be involved in spermatogenesis. To our surprise, ΔSiwi and ΔBmAgo3 mutants develop normal male reproduction system, indicating that they don’t participate in sperm development. As the activity of BmHen1 depends on BmPnldc1 during piRNA biogenesis, and ΔBmHen1 and ΔBmPnldc1 mutants display similar defects in sperm development, we performed RNA sequencing analysis to look for the genes that might be co-regulated by BmHen1 and BmPnldc1. Our results indicate that the defects in ΔBmHen1 and ΔBmPnldc1 eupyrene sperms could be attributed to dysregulated genes involved in energy metabolism and cell differentiation. Furthermore, we found that the piRNA biogenesis is inhibited in ΔBmHen1 and ΔBmPnldc1 sperm bundles, whereas the transposon activity was induced. Taken together, our findings suggest that BmHen1 is a new crucial component regulating eupyrene sperm development in B. mori, whereas the PIWI proteins Siwi and BmAgo3 are not involved in this process. Our results may provide a potential gene target for genetic modification of sterility in B. mori.
Lepidopteran prolegs are novel traits, not leg homologs
Authors: Matsuoka Yuji , Murugesan Suriya Narayanan , Prakash Anupama , Monteiro Antónia
Published: July 2022

Lepidopteran larvae have both thoracic legs and abdominal prolegs, yet it is unclear whether these are serial homologs. We examined the role of three Hox genes in proleg development in Bicyclus anynana butterflies using CRISPR-Cas9 and discovered that under a partial segment abdominal-A (abd-A) knockout, both types of appendages can develop in the same segment, arguing for prolegs being a novel trait, not a leg serial homolog. We also discover that specificity protein (sp) genes do not co-localize with Distal-less (Dll) in prolegs, as they do in legs, and that the proleg gene-regulatory network (GRN) mostly resembles the head-horn GRN, another novel trait in the lepidoptera. We propose that larval prolegs evolved from the co-option of a partial limb GRN into novel embryonic coordinates in the abdomen.

One-Sentence Summary

The chubby legs of caterpillars are evolutionary innovations
Hydroxychloroquine pre-exposure prophylaxis to prevent SARS-CoV-2 among health care workers at risk for SARS-CoV-2 exposure: A nonrandomized controlled trial
Authors: Raabe Vanessa N. , Fleming Andrew , Samanovic Marie I. , Lai Lilin , Belli Hayley M. , Mulligan Mark J. , Belmont H. Michael
Published: July 2022

Background

Aerosol-generating procedures increase the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among health care workers (HCWs). An effective pre-exposure prophylaxis would mitigate this risk.

Objective

To determine the efficacy of pre-exposure prophylactic hydroxychloroquine for the prevention of SARS-CoV-2 infection and symptomatic coronavirus 19 disease (COVID-19) among HCWs at high occupational risk of SARS-CoV-2 exposure.

Methods

130 HCWs in the New York University Langone Health System (NYULHS) who performed aerosol-generating procedures on patients with COVID-19 or provided bedside care for inpatients with COVID-19 or persons with suspected COVID-19 in an emergency department, for at least three shifts in a 7-day period, during the first 2020 COVID-19 wave in New York City were enrolled. Participants elected to take oral hydroxychloroquine, 600 mg on day 1 followed by 200 mg daily, or not take hydroxychloroquine for up to 90 days. Participants self-collected dried blood spots and completed digital questionnaires regarding COVID-19 symptoms, adverse events, and other COVID-19 medication use.

Results

Six participants (7.5%) seroconverted during the trial: four who took hydroxychloroquine (6.8%) and two who declined hydroxychloroquine (9.5%). All participants not taking hydroxychloroquine reported COVID-19 symptoms at seroconversion compared to one of four participants (25%) who took hydroxychloroquine. Adverse events occurred in eight participants (9.6%) on hydroxychloroquine and were mostly mild.

Conclusions

This study (ClinicalTrials.govNCT04354870) did not demonstrate a statistically significant difference in SARS-CoV-2 seroconversion associated with hydroxychloroquine pre-exposure prophylaxis among HCWs at high risk of occupational SARS-CoV-2 exposure, although was underpowered and a high rate of hydroxychloroquine discontinuation was observed.