title: SARS-COV-2 C.1.2 variant is highly mutated but may possess reduced affinity for ACE2 receptor

abstract: SARS-COV-2 evolution generates different variants and drives the pandemic. As the current main driver, delta variant bears little resemblance to the other three variants of concern (alpha, beta and gamma), raising the question what features the future variants of concern may possess. To address this important question, I searched through the GISAID database for potential clues. While investigating how beta variant has been evolving in South Africa, I noticed a small group of genomes mainly classified as C.1.2 variant, with one-year old boy identified in March 2021 being the index case. Over 80% patients are younger than 60. At the average, there are 46-47 mutations per genome, making this variant one of the most mutated lineages identified. A signature substitution is spike Y449H. Like beta and gamma variants, C.1.2 possesses E484K and N501Y. The genomes are heterogenous and encode different subvariants. Like alpha variant, one such subvariant encodes the spike substitution P681H at the furin cleavage site. In a related genome, this substitution is replaced by P681R, which is present in delta variant. In addition, similar to this variant of concern, three C.1.2 subvariants also encode T478K. Mechanistically, spike Y449 recognizes two key residues of the cell-entry receptor ACE2 and Y449H is known to impair the binding to ACE2 receptor, so C.1.2 variant may show reduced affinity for this receptor. If so, this variant needs other mutations to compensate for such deficiency. These results raise the question whether C.1.2 variant is as virulent as suggested by its unexpected high number of mutations.


title: δ1 variant of SARS-COV-2 acquires spike V1176F and yields a highly mutated subvariant in Europe

abstract: Genomic surveillance of SARS-COV-2 has revealed that in addition to many variants of interests, this virus has yielded four variants of concern, , {beta}, {gamma} and {delta}, as designated by the World Health Organization. {delta} variant has recently become the predominant pandemic driver around the world and yielded four different subvariants ({delta}1, {delta}2, {delta}3 and {delta}4). Among them, {delta}1 has emerged as the key subvariant that drives the pandemic in India, Europe and the USA. A relevant question is whether {delta}1 subvariant continues to evolve and acquires additional mutations. Related to this, this subvariant has acquired spike V1176F, a signature substitution of {gamma} variant, and yielded a new sublineage, {delta}1F. The substitution alters heptad repeat 2 of spike protein and is expected to improve interaction with heptad repeat 1 and enhance virus entry. Moreover, there are {delta}1F sublineages encoding spike N501Y, A783S, Q836E and V1264L. While N501Y is a signature substitution shared by , {beta} and {gamma} variants, V1264L is a key substitution in a {delta}1 sublineage that is a major pandemic driver in Southeast Asia. The Q836E-encoding lineage carries an average of 50 mutations per genome, making it the most mutated variant identified so far. Similar to {delta}1 subvariant, {delta}2 subvariant has also acquired spike V1176F and yielded new sublineages. Together, these results suggest that V1176F is a recurrent spike substitution that is frequently acquired by SARS-COV-2 variants to improve viral fitness. It is thus important to track the evolutionary trajectory of related variants for considering and instituting the most effective public health measures.

category: evolutionary biology


title: Negative catalysis by the editing domain of class I aminoacyl-tRNA synthetases

abstract: Aminoacyl-tRNA synthetases (AARS) translate the genetic code by loading tRNAs with the cognate amino acids. The errors in amino acid recognition are cleared at the AARS editing domain through hydrolysis of misaminoacyl-tRNAs. This ensures faithful protein synthesis and cellular fitness. Using Escherichia coli isoleucyl-tRNA synthetase (IleRS) as a model enzyme, we demonstrated that the class I editing domain clears the non-cognate amino acids well-discriminated at the synthetic site with the same rates as the weakly-discriminated fidelity threats. This unveiled low selectivity suggests that evolutionary pressure to optimize the rates against the amino acids that jeopardize translational fidelity did not shape the editing site. Instead, we propose that editing was shaped to safeguard cognate aminoacyl-tRNAs against hydrolysis. Misediting is prevented by the residues that promote negative catalysis through destabilisation of the transition state comprising cognate amino acid. Such powerful design allows broad substrate acceptance of the editing domain along with its exquisite specificity in the cognate aminoacyl-tRNA rejection. Editing proceeds by direct substrate delivery to the editing domain (in cis pathway). However, we found that class I IleRS also releases misaminoacyl-tRNAIle and edits it in trans. This minor editing pathway was up to now recognized only for class II AARSs.

category: biochemistry


title: An improved vector for baculovirus-mediated protein production in mammalian cells

abstract: BacMam system utilizes baculovirus to deliver exogenous genes into mammalian cells and is extensively used for recombinant production of eukaryotic proteins. Here, we described an improved BacMam vector (pBMCL1, Addgene#178203) which allows convenient tracing of virus production, provides higher infection efficiency towards mammalian cells, minimizes unwanted transcription of toxic genes in insect cells, and provides the capability for co-expression of multiple proteins via a single virus. We demonstrate the successful application of the pBMCL1 vector for the expression of not only the human TRPC3 channel but also the heteromeric KATP channel.


title: Rapid and Effective Inactivation of SARS-CoV-2 by a Cationic Conjugated Oligomer with Visible Light: Studies of Antiviral Activity in Solutions and on Supports

abstract: This paper presents results of a study of a new cationic oligomer that contains end groups and a chromophore affording inactivation of SARS-Cov-2 by visible light irradiation in solution or as a solid coating on wipes paper and glass fiber filtration substrates. A key finding of this study is that the cationic oligomer with a central thiophene ring and imidazolium charged groups give outstanding performance in both killing of E. coli bacterial cells and inactivation of the virus at very short times. Our introduction of cationic N-Methyl Imidazolium groups enhances the light-activation process for both E. coli and SARS-Cov-2 but dampens the dark killing of the bacteria and eliminates the dark inactivation of the virus. For the studies with this oligomer in solution at concentration of 1 g/mL and E. coli we obtain 3 log killing of the bacteria with 10 min irradiation with LuzChem cool white lights (mimicking indoor illumination). With the oligomer in solution at a concentration of 10 g/mL, we observe 4 logs inactivation (99.99 %) in 5 minutes of irradiation and total inactivation after 10 min. The oligomer is quite active against E. coli on oligomer-coated wipes papers and glass fiber filter supports. The SARS-Cov-2 is also inactivated by the oligomer coated glass fiber filter papers. This study indicates that these oligomer-coated materials may be very useful as wipes and filtration materials.


title: High Resolution Nanostructure with Two-stages of Exponential Energy Dissipation at the Ultrathin Osteochondral Interface Tissue of Human Knee Joint

abstract: Cartilage adheres to subchondral bone via a specific osteochondral interface tissue where forces are transferred from soft cartilage to hard bone without fatigue damage over a lifetime of load cycles. However, the fine structure and mechanical properties of osteochondral interface tissue remain unclear. Here, we identified an ultrathin [~]20-30 m calcified region with two-layered micro-nano structures of osteochondral interface tissue in human knee joint, which exhibited characteristic biomolecular compositions and complex nanocrystals assembly. Within this region, an exponential increase of modulus (3 orders of magnitude) was conducive to the force transmission which was verified by finite element simulations. The nanoscale heterogeneity of hydroxyapatite, along with enrichment of elastic-responsive protein-titin which is usually present in muscle, endowed the osteochondral tissue with excellent energy dissipation and fatigue resistance properties. Our results provide potential design for high-performance interface materials for osteochondral interface regeneration and functional coatings.

category: bioengineering


title: VSS-Hi-C: Variance-stabilized signals for chromatin 3D contacts

abstract:
Chromatin conformation capture assays output a value for each pair of positions that quantifies their strength of interaction in the nucleus. Hi-C signals lack the property of variance stabilization. That is, a difference between 0 and 200 reads usually has a very different statistical importance from a difference between 2000 and 2200 reads. This deficiency impedes analysis and visualization of Hi-C data.

Here, we propose an approach called VSS-Hi-C that normalizes Hi-C data to produce variance-stabilized signals. It does so by learning the empirical relationship between the mean and variance of Hi-C values and transforming these values such mean and variance of the data are no longer dependent to each other. We show that VSS-Hi-C outperforms the other transformation approaches in stabilizing the variance of the data and using VSS-Hi-C transformed signals improves downstream analysis such as identifying chromosomal subcompartments. Using VSS-Hi-C additionally eliminates the need for complex methods such as negative binomial modeling for downstream analysis and enables expressive visualization of Hi-C data.

category: bioinformatics


title: ADAR2-repressed RNA editing: a novel mechanism contributing to t (8:21) AML leukemogenesis

abstract:
In the past decade, adenosine to inosine (A-to-I) RNA editing, which is catalyzed by adenosine deaminases acting on RNA (ADAR) family of enzymes ADAR1 and ADAR2, has been shown to contribute to the development and progression of multiple cancers; however, very little is known about its role in acute myeloid leukemia (AML) - the second most common type of leukemia making up 31% of all adult leukemia cases. Here, we found that ADAR2, but not ADAR1 and ADAR3, is specifically downregulated in core binding factor (CBF) AML with t(8;21) or inv(16). In t(8;21) AML, RUNX1-driven transcription of ADAR2 transcripts was found to be repressed by the RUNX1-ETO fusion protein. Forced overexpression of two ADAR2-regulated RNA editing targets COPA and COG3 indeed inhibits clonogenic growth of human t(8;21) AML cells. Further in vivo animal studies confirmed that ADAR2 could suppress leukemogenesis of t(8;21) AML through its RNA binding and editing capabilities. Our results suggest a novel RNA editing-mediated mechanism leading to t(8,12) AML.

Key pointsO_LIADAR2, but not ADAR1 and ADAR3, was specifically downregulated in CBF-AML
C_LIO_LIRUNX1-ETO suppresses ADAR2 transcription in t(8;21) AML through binding on its promoter
C_LIO_LIRNA editing capability of ADAR2 is essential for its repression of leukemogenesis in an AE9a mouse model
C_LI

category: cancer biology


title: The landscape of extrachromosomal circular DNA in medulloblastoma

abstract: Extrachromosomal circular DNA (ecDNA) is an important driver of aggressive tumor growth, promoting high oncogene copy number, intratumoral heterogeneity, accelerated evolution of drug resistance, enhancer rewiring, and poor outcome. ecDNA has been reported in medulloblastoma (MB), the most common malignant pediatric brain tumor, but the ecDNA landscape and its association with specific MB subgroups, its impact on enhancer rewiring, and its potential clinical implications, are not known. We assembled a retrospective cohort of 468 MB patient samples with available whole genome sequencing (WGS) data covering the four major MB subgroups WNT, SHH, Group 3 and Group 4. Using computational methods for the detection and reconstruction of ecDNA1, we find ecDNA in 82 patients (18%) and observe that ecDNA+ MB patients are more than twice as likely to relapse and three times as likely to die of disease. In addition, we find that individual medulloblastoma tumors often harbor multiple ecDNAs, each containing different amplified oncogenes along with co-amplified non-coding regulatory enhancers. ecDNA was substantially more prevalent among 31 analyzed patient-derived xenograft (PDX) models and cell lines than in our patient cohort. By mapping the accessible chromatin and 3D conformation landscapes of MB tumors that harbor ecDNA, we observe frequent candidate "enhancer rewiring" events that spatially link oncogenes with co-amplified enhancers. Our study reveals the frequency and diversity of ecDNA in a subset of highly aggressive tumors and suggests enhancer rewiring as a frequent oncogenic mechanism of ecDNAs in MB. Further, these results demonstrate that ecDNA is a frequent and potent driver of poor outcome in MB patients.


title: Dynamic Brain Network States during Suspenseful Film Viewing

abstract: Studies of brain activity evoked by naturalistic stimuli have found narrative suspense produces reliable patterns of activation consistent with increased attention to the narrative and decreased processing of non-narrative stimuli (Bezdek et al., 2015). Yet the progression of brain states (i.e. patterns of activity levels across the whole brain) at suspense peaks and how they differ from suspense valleys or resting state scans has not previously been investigated. We used a fast fMRI acquisition sequence to measure sub-second brain states at peaks and valleys of narrative suspense and during rest. We found five brain states that occur during suspenseful film viewing, four of which differ in their frequency near suspense peaks compared to valleys. The pattern of results is consistent with the theoretical view that suspense captures and focuses attentional processing, triggering subsequent cognitive processing of narrative events.

category: neuroscience


title: Sonic Hedgehog Pathway Modulation Normalizes Expression of Olig2 in Rostrally Patterned NPCs with Trisomy 21

abstract: The intellectual disability found in people with Down syndrome (DS) is associated with a decrease in white matter in the central nervous system. To study the mechanism of this myelination deficit, we differentiated two isogenic lines of induced pluripotent stem cells (iPSCs) derived from people with DS into brain-like and spinal cord-like neural progenitor cells (NPCs) and promoted a transition towards oligodendroglial fate by activating the Sonic hedgehog (SHH) pathway. In the spinal cord-like trisomic cells, we found no difference in expression of OLIG2 or NKX2.2, two transcription factors essential for commitment to the oligodendrocyte (OL) lineage. However, in the brain-like trisomic NPCs, OLIG2 is significantly upregulated and is associated with reduced expression of NKX2.2. We found that this gene dysregulation and block in NPC transition can be normalized by increasing the concentration of a SHH pathway agonist (SAG) during differentiation. These results underscore the importance of regional and cell type differences in gene expression in DS and demonstrate that modulation of SHH signaling in trisomic cells can rescue an early perturbed step in neural lineage specification in DS.


title: Survival of hatchery grown native oysters is associated with specific gut-associated bacteria at various locations within the Puget Sound

abstract:
The Olympia oyster (Ostrea lurida) of the Puget Sound suffered a dramatic population crash, but restoration efforts hope to revive this native species. One overlooked variable in the process of assessing ecosystem health is association of bacteria with marine organisms and the environments they occupy. Oyster microbiomes are known to differ significantly between species, tissue type, and the habitat in which they are found. The goals of this study were to determine the impact of field site and habitat on the oyster microbiome and to identify core oyster-associated bacteria in the Puget Sound. Olympia oysters from one parental family were deployed at four sites in the Puget Sound both inside and outside of eelgrass (Zostera marina) beds. Using 16S rRNA gene amplicon sequencing of the oyster gut, shell, surrounding seawater and sediment, we demonstrate that gut-associated bacteria are distinct from the surrounding environment and vary by field site. Furthermore, regional differences in the gut microbiota are associated with the survival rates of oysters at each site after two months of field exposure. However, habitat type had no influence on microbiome diversity. Further work is needed to identify the specific bacterial dynamics that are associated with oyster physiology and survival rates.

ImportanceThe outcomes of this study demonstrate the need to monitor microbial ecology at potential oyster restoration sites, specifically for the native Olympia oyster in the Puget Sound. Some areas of Puget Sound may be less amenable to Olympia oyster restoration than others due to microbiome colonization trends. Furthermore, this study puts the oyster microbiome in the context of its surroundings, providing a holistic perspective on the factors that may influence oyster performance and microbial ecology.

category: microbiology


title: Dynamic proton-dependent motors power Type IX secretion and gliding adhesin movement in Flavobacterium

abstract: Motile bacteria usually rely on external apparatus like flagella for swimming or pili for twitching. By contrast, gliding bacteria do not rely on obvious surface appendages to move on solid surfaces. Flavobacterium johnsoniae and other bacteria in the Bacteroidetes phylum use adhesins whose movement on the cell surface supports motility. In F. johnsoniae, secretion and helicoidal motion of the main adhesin SprB are intimately linked and depend on the type IX secretion system (T9SS). Both processes necessitate the proton motive force (PMF), which is thought to fuel a molecular motor that comprises the GldL and GldM cytoplasmic membrane proteins. Here we show that F. johnsoniae gliding motility is powered by the pH gradient component of the PMF. We further delineate the interaction network between the GldLM transmembrane helices (TMH) and show that conserved glutamate residues in GldL TMH are essential for gliding motility, although having distinct roles in SprB secretion and motion. We then demonstrate that the PMF and GldL trigger conformational changes in the GldM periplasmic domain. We finally show that multiple GldLM complexes are distributed in the membrane suggesting that a network of motors may be present to move SprB along a helical path on the cell surface. Altogether, our results provide evidence that GldL and GldM assemble dynamic membrane channels that use the proton gradient to power both T9SS-dependent secretion of SprB and its motion at the cell surface.


title: Restoration of a pond: monitoring water quality and macroinvertebrate community succession

abstract: To determine the success of restoration programmes, knowledge of the temporal dynamics in community structure and processes is vital. The water quality and macroinvertebrate community structures of a newly created and an established pond within the same ecosystem were sampled bi-monthly over a year to monitor the development of the new pond. The water quality measures of the ponds were significantly different. Conductivity, salinity, and total dissolved solids levels were also different between the ponds. The colonisation of a macroinvertebrate community in the new pond was rapid, resulting in a 75% resemblance to the established pond by the end of the first year. The pond was colonised by non-insect taxa like Crustacea and Gastropod and then by insects. There was a significant difference in the macroinvertebrate communities of the ponds due to temporal taxonomic composition differences. The high abundance of Diplacodes spp. (perchers), Physa spp. (left-handed pond snail), and Ostracod (seed shrimp) in the new pond contributed to the difference in the community between the two ponds. Cladocera (water fleas) dominated the macroinvertebrate community, and the highest abundance was recorded in August for both ponds. Our results suggest that a newly created pond can have a comparable macroinvertebrate community to nearby established ponds within a year.

category: ecology


title: Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks

abstract:
Super-resolution imaging techniques have provided a better understanding of the relationship between the nanoscale organization of function of ryanodine receptors (RyRs) in cardiomy-ocytes. Interestingly recent data have indicated that this relationship is disrupted in heart failure (HF), as RyRs are dispersed into smaller and more numerous clusters. However, RyRs are also hyperphosphorylated in this condition, and this is reported to occur preferentially within the cluster centre. Thus, the combined impact of RyR relocalization and sensitization on Ca2+ spark generation in failing cardiomyocytes is likely complex and these observations suggest that both the nanoscale organization of RyRs and the pattern of phosphorylated RyRs within clusters could be critical determinants of Ca2+ spark dynamics. To test this hypothesis, we used computational modeling to quantify the relationships between RyR cluster geometry, phosphorylation patterns, and sarcoplasmic reticulum (SR) Ca2+ release. We found that RyR cluster disruption results in a decrease in spark fidelity and longer sparks with a lower amplitude. Phosphorylation of some RyRs within the cluster can play a compensatory role, recovering healthy spark dynamics. Interestingly, our model predicts that such compensation is critically dependent on the phosphorylation pattern, as phosphorylation localized within the cluster center resulted in longer Ca2+ sparks and higher spark fidelity compared to a uniformly distributed phosphorylation pattern. Our results strongly suggest that both the phosphorylation pattern and nanoscale RyR reorganization are critical determinants of Ca2+ dynamics in HF.

Significance StatementRyRs are ion channels located on the membrane of the sarcoplasmic reticulum that are responsible for an increase in cytosolic Ca2+ during cell excitation. Here, we investigate how the geometry of RyR clusters combined with spatial phosphorylation patterns impacts on Ca2+ spark generation and kinetics. The findings from our study show that both phosphorylation pattern and RyR cluster shape and dispersion have implications on Ca2+ spark activity and provide insights into altered Ca2+ dynamics during HF.

category: biophysics


title: Resolving the 3D rotational and translational dynamics of single molecules using radially and azimuthally polarized fluorescence

abstract: We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5{degrees} orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-{beta}-cyclodextrin (M{beta}CD-chol) causes NRs orientational diffusion to be dramatically reduced, but curiously, NRs median lateral displacements drastically increase from 20.8 nm to 75.5 nm (200 ms time lag). These jump diffusion events overwhelmingly originate from cholesterol-rich nanodomains within the SLB. These detailed measurements of single-molecule rotational and translational dynamics are made possible by raPols high measurement precision and are not detectable in standard SMLM.


title: Antennapedia regulates metallic silver wing scale development and cell shape in Bicyclus anynana butterflies

abstract: Butterfly wing scale cells can develop very intricate cuticular nanostructures that interact with light to produce structural colors including silvery hues, but the genetic basis of such nanostructures is mostly unexplored. Here, we first identified that optix is necessary for metallic scale development in the butterfly Bicyclus anynana. We then characterized different subtypes of wildtype metallic silver scales and addressed the function of five genes - apterous A, Ultrabithorax, doublesex, Antennapedia, and optix - in the differentiation of silver scales, at a single-cell resolution, by leveraging crispants that exhibited either ectopic gains or losses of silver scales. Wildtype silver scales were generally rounded and had low amounts of pigmentation, exhibiting a common ultrastructural modification for metallic broadband reflectance, i.e., an undulatory air layer enclosed by an upper and lower lamina. Our results indicated that the varying air layer thickness was the important parameter of the bilaminate scale for producing a broadband reflectance across visible wavelengths. While a single lamina of the appropriate thickness could also produce broadband colors, the bilaminate structure is advantageous as it increases the overall reflectivity. Crispant brown scales differed from wildtype silver scales via the loss of the continuous upper lamina, increased lower lamina thickness, and increased pigmentation. The reverse was seen when brown scales became silver. We identified Antennapedia and optix as high-level regulators in the network differentiating different silver scale subtypes and determining overall cell shape in both sexes. In addition, Antp exhibits a novel, post-embryonic role in the determination of ridge and crossrib orientation.

category: developmental biology


title: Antennapedia and optix regulate metallic silver wing scale development and cell shape in Bicyclus anynana butterflies


title: A dual involvement of Protocadherin-18a in stromal cell development guides the formation of a functional hematopoietic niche.

abstract: Hematopoietic stem and progenitor cells (HSPCs) emerge from the aorta and migrate to the caudal hematopoietic tissue (CHT) of zebrafish larvae, the hematopoietic equivalent of the mammalian fetal liver, for their proliferation and differentiation. We previously reported that somite-derived stromal cells were a key component of the CHT niche. Here we found that the cell adhesion protein protocadherin-18a (Pcdh18a) is expressed in the stromal cell progenitors (SCPs) emigrating from somites toward the future CHT. Deletion of most of the intracellular domain of Pcdh18a caused a decrease in the number of SCPs, the directionality of their migration, and the cell-contact mediated repulsion that normally occurs between migrating SCPs. These defects were followed by abnormal morphogenesis of the venous plexus that forms the CHT framework, and the inability of the resulting CHT to function as a niche for HSPCs. Finally, we found that the extracellular domain of Pcdh18a mediates trans heterophilic adhesion of stromal cells to endothelial cells in vivo and thereby the reticular vs. perivascular fate of SCPs. Our study demonstrates that Pcdh18a expression in SCPs is essential for the proper development of the hematopoietic niche.


title: Diverse chemical functionalization of nucleobases within long RNAs using sulfinate salts

abstract: We have devised a single pot, low-cost method to modify RNA with sulfinate salts that can directly add almost any desired functional group to nucleobases under mild aqueous conditions. This chemistry modifies the Hoogsteen edge of RNA and DNA nucleobases. It can be applied to RNA or DNA of any size, as well as to individual nucleotides. Existing methods of RNA modification have relatively limited applicability due to constraints on the size of the RNA and the lack of diversity of possible modifications. We have been able to add azide groups for click reactions directly onto the nucleobases of RNA utilizing sulfinate salts. C-H bonds on the nucleobase aromatic rings serve as the sites of attachment, with C-H being replaced with C-R, where R is the azide-containing linker. With the addition of azide functional groups, the modified RNA can easily be reacted with any alkyne-labeled compound of interest, including fluorescent dyes as shown in this work. This methodology enables the exploration of diverse chemical groups on RNA that can potentially confer protection from nucleases, allow for efficient delivery of nucleic acids into cells, or act as new tools for the investigation of nucleic acid structure and function.


title: Observation of reversal in twist-stretch coupling of RNA suggests a unified mechanism for the opposite couplings of DNA and RNA

abstract: The functions of DNA and RNA rely on their deformations. When stretched, both DNA and RNA duplexes change their twist angles through twist-stretch coupling. The coupling is negative for DNA but positive for RNA, which is not yet completely understood. Here, our magnetic tweezers experiments show that the coupling of RNA reverses from positive to negative by multivalent cations. Combining with the previously reported tension-induced negative-to-positive coupling-reversal of DNA, we propose a unified mechanism of the couplings of both RNA and DNA based on molecular dynamics simulations. Two deformation pathways are competing when stretched: shrinking the radius causes positive couplings but widening the major groove causes negative couplings. For RNA whose major groove is clamped by multivalent cations and canonical DNA, their radii shrink when stretched, thus exhibiting positive couplings. For elongated DNA whose radius already shrinks to the minimum and canonical RNA, their major grooves are widened when stretched, thus exhibiting negative coupling.


title: Interleukin-1 is overexpressed in injured muscles following spinal cord injury and promotes neurogenic heterotopic ossification

abstract: Neurogenic heterotopic ossifications (NHOs) form in periarticular muscles following severe spinal cord (SCI) and traumatic brain injuries. The pathogenesis of NHO is poorly understood with no effective preventive treatment. The only curative treatment remains surgical resection of pathological NHOs. In a mouse model of SCI-induced NHO that involves a transection of the spinal cord combined with a muscle injury, a differential gene expression analysis revealed that genes involved in inflammation such as interleukin-1{beta} (IL-1{beta}) were overexpressed in muscles developing NHO. Using mice knocked-out for the gene encoding IL-1 receptor (IL1R1) and neutralizing antibodies for IL-1 and IL-1{beta}, we show that IL-1 signaling contributes to NHO development following SCI in mice. Interestingly, other proteins involved in inflammation that were also overexpressed in muscles developing NHO, such as colony-stimulating factor-1, tumor necrosis factor or C-C chemokine ligand-2 did not promote NHO development. Finally using NHO biopsies from SCI and TBI patients, we show that IL-1{beta} is expressed by CD68+ macrophages. IL-1 and IL-1{beta} produced by activated human monocytes promote calcium mineralization of fibro-adipogenic progenitors isolated from muscles surrounding NHOs. Altogether these data suggest that interleukin-1 promotes NHO development in both humans and mice.

category: physiology


title: HaHB11 transformed maize has improved yield under waterlogging and defoliation in control and field conditions

abstract:
HaHB11 is a sunflower transcription factor previously described as conferring improved yield to maize hybrids and lines. Here we report that transgenic HaHB11 maize lines exhibited a better performance funder waterlogging, both in greenhouse and field trials carried out during three growth cycles. One of these trials was particularly affected by a strong storm during flowering, causing severe defoliation. Controlled defoliation assays indicated that the transgenic genotypes were able to set more grains than controls. Hybrids were generated by crossing B73 HaHB11 lines with the contrasting Mo17 lines and tested in the field. These hybrids exhibited the same beneficial traits as the parental lines when compared with their respective controls. Waterlogging tolerance coursed via the root architecture improvement, including more xylem vessels, reduced tissue damage, less superoxide accumulation, and altered carbohydrate metabolism compared to controls. Multivariate analyses corroborated the robustness of the differential traits observed. Furthermore, canopy spectral reflectance data, computing 29 vegetation indices associated with biomass, chlorophyll, and abiotic stress, helped to identify genotypes as well as their growing conditions. Altogether the results reported here indicate that this sunflower gene constitutes a suitable tool to improve maize plants for environments prone to waterlogging and/or wind defoliation.

One sentence summaryPhenotyping and big data analyses indicate that the transcription factor HaHB11 confers waterlogging and defoliation tolerance, and increased yield to maize lines and hybrids in all tested conditions.

category: plant biology


title: Combinatorial transcriptional codes specify macrophage polarization destinations

abstract: Macrophages are driven to form distinct functional phenotypes in response to different immunological stimuli, in a process widely referred to as macrophage polarization. Transcriptional regulators that guide macrophage polarization in response to a given trigger remain largely unknown. In this study, we interrogate the programmable landscape in macrophages to find regulatory panels that determine the precise polarization state that a macrophage is driven to. Towards this, we configure an integrative network analysis pipeline that utilizes macrophage transcriptomes in response to 28 different stimuli and reconstructs contextualized human gene regulatory networks, and identifies epicentres of perturbations in each case. We find that these contextualized regulatory networks form a spectrum of thirteen distinct clusters with M1 and M2 at the two ends. Using our computational pipeline, we identify combinatorial panels of epicentric transcription factors (TFs) for each polarization state. We demonstrate that a set of three TFs i.e., NFE2L2, BCL3 and CEBPB, is sufficient to change the polarization destination from M1 to M2. siRNA-mediated knockdown of the 3-TF set in THP1 derived M0 cells, despite exposure to an M1 stimulant, significantly attenuated the shift to M1 phenotype, and instead switched to an M2-like phenotype. Further, the siRNA-mediated knockdown of the 3-TF set rendered the macrophages hyper-susceptible to S. aureus infection, clearly showing the effect of the knockdown.

category: systems biology


title: Identification of bacterial drug-resistant cells by the convolutional neural network in transmission electron microscope images

abstract: The emergence of bacteria that are resistant to antibiotics is common in areas where antibiotics are used widely. The current standard procedure for detecting bacterial drug resistance is based on bacterial growth under antibiotic treatments. Here we describe the morphological changes in enoxacin-resistant Escherichia coli cells and the computational method used to identify these resistant cells in transmission electron microscopy (TEM) images without using antibiotics. Our approach was to create patches from TEM images of enoxacin-sensitive and enoxacin-resistant E. coli strains, use a convolutional neural network for patch classification, and identify the strains on the basis of the classification results. The proposed method was highly accurate in classifying cells, achieving an accuracy rate of 0.94. Using a gradient-weighted class activation mapping to visualize the region of interest, enoxacin-resistant and enoxacin-sensitive cells were characterized by comparing differences in the envelope. Moreover, Pearsons correlation coefficients suggested that four genes, including lpp, the gene encoding the major outer membrane lipoprotein, were strongly associated with the image features of enoxacin-resistant cells.


title: Fetal neural progenitors process TLR signals from bacterial components to enhance proliferation and rework brain development

abstract: Bacterial cell wall, a universal pathogen-associated molecular pattern (PAMP), crosses the placenta into the fetal brain. We determined that PAMPs interact with TLR2/6 on murine fetal neural progenitor cells (NPCs) to induce overexpansion of all neocortical layers leading to a larger, folded cortex and abnormal postnatal behavior. The NPC overexpansion originated at E10 and targeted ventricular radial glia (vRG), the primary NPC, by shortening cell cycle and increasing self-renewal. The mechanism involved two novel signaling pathways in NPCs mediated by recognition of bacterial PAMPs by TLR2/6 including: a) loss of primary cilia, activation of hedgehog signaling, and increased FOXG1 and b) increased PI3K/AKT activity. These findings reveal PAMP/TLR2/6 acts as a morphogen in fetal neurodevelopment. In addition, the loss of Tlr2 or Tlr6 without pathogenic challenge, increased the number of neurons, establishing the requirement for an endogenous TLR2 signal for normal neurodevelopment in the embryo.


title: Opposing subclasses of Drosophila ellipsoid body neurons promote and suppress sleep

abstract: Recent work in Drosophila has uncovered several neighboring classes of sleep-regulatory neurons within the central complex. However, the logic of connectivity and network motifs remains limited by the incomplete examination of relevant cell types. Using a recent genetic-anatomical classification of ellipsoid body ring neurons, we conducted a thermogenetic screen to assess sleep/wake behavior and discovered two opposing populations: sleep-promoting R3m and wake-promoting R3d neurons. Activation of these neurons influences sleep duration and architecture by prolonging or shortening sleep bouts, suggesting a key role in sleep maintenance. R3m and R3d neurons are GABAergic and require GABA synthesis for their effects on sleep. Finally, we use a fluorescent reporter for putative synaptic partners to embed these neurons within the known sleep-regulatory network; R3m and R3d neurons lay downstream of wake-active Helicon cells, and R3m neurons likely inhibit R3d neurons. Together, the data presented herein suggest a neural mechanism by which previously uncharacterized circuit elements operate within the sleep homeostat to stabilize sleep-wake states.


title: The hallucinogenic serotonin2A receptor agonist, DOI, promotes CREB-dependent gene expression of specific plasticity-associated genes in the rodent neocortex

abstract: Psychedelic compounds that target the 5-HT2A receptor are reported to evoke psychoplastogenic effects, including enhanced dendritic arborization and synaptogenesis. Transcriptional regulation of neuronal plasticity-associated genes is implicated in the cytoarchitectural effects of serotonergic psychedelics, however the transcription factors that drive this regulation are poorly elucidated. Here, we addressed the contribution of the transcription factor cAMP response element binding protein (CREB) in the regulation of neuronal plasticity-associated genes by the hallucinogenic 5-HT2A receptor agonist, DOI. In vitro studies with rat cortical neurons indicated that DOI enhances the phosphorylation of CREB (pCREB) through the MAP kinase and CaMKII pathways, with both cascades contributing to the DOI-evoked upregulation of Arc, Bdnf1, Cebpb and Egr2 expression, whilst the upregulation of Egr1 and cFos mRNA involved the MAP kinase and CaMKII pathway respectively. We observed a robust DOI-evoked increase in the expression of several neuronal plasticity-associated genes in the rat neocortex in vivo. Further, 5-HT2A receptor stimulation enhanced pCREB enrichment at putative cAMP response element (CRE) binding sites in the Arc, Bdnf1, Cebpb, cFos, but not Egr1 and Egr2, promoters in the rodent neocortex. The DOI-mediated transcriptional induction of Arc, cFos and Cebpb was significantly attenuated in the neocortex of CREB deficient (CREB{delta} KO) mice. Collectively, these results indicate that the hallucinogenic 5-HT2A receptor agonist DOI leads to a rapid transcriptional upregulation of several neuronal plasticity-associated genes, with a subset of them exhibiting a CREB-dependent regulation. Our findings raise the intriguing possibility that similar to slow-acting classical antidepressants, rapid-action serotonergic psychedelics that target the 5-HT2A receptor may also recruit the transcription factor CREB to enhance the expression of neuronal plasticity-associated genes in the neocortex, which could in turn contribute to the rapid psychoplastogenic changes evoked by these compounds.


title: Chikungunya virus vaccine candidate incorporating synergistic mutations is attenuated and protects against virulent virus challenge

abstract:
BackgroundChikungunya virus (CHIKV) is an arbovirus that periodically reemerges to cause large epidemics of arthritic disease. While the robust immunity elicited by live-attenuated virus (LAV) vaccine candidates makes them attractive, CHIKV vaccine development has been hampered by a high threshold for acceptable adverse events.

MethodsWe evaluated the vaccine potential of a recently described LAV, SKE, that exhibits diminished replication in skeletal muscle cells due to insertion of target sequences for skeletal muscle-specific miR-206. We also evaluated whether these target sequences could augment safety of a LAV encoding a previously described attenuating mutation, E2 G82R, which on its own was too reactogenic in clinical trials. Attenuation of viruses containing these mutations was compared with a double mutant, SKE G82R.

ResultsSKE was attenuated in both immunodeficient and immunocompetent mice and induced a robust neutralizing antibody response, indicating its vaccine potential. However, only SKE G82R elicited diminished swelling in immunocompetent mice at early time points post-inoculation, indicating that these mutations synergistically enhance safety of the vaccine candidate.

ConclusionsThese data suggest that restriction of LAV replication in skeletal muscle enhances tolerability of reactogenic vaccine candidates and may improve the rational design of CHIKV vaccines.


title: Systematic Discovery of Antimicrobial Polymorphic Toxins

abstract: Microbes employ a large diversity of toxins to kill competing microbes or eukaryotic host cells. Polymorphic toxins are a class of protein toxins abundant in Nature and secreted through various secretion systems. Polymorphic toxins have a modular protein architecture with a toxin domain found at the protein C-terminus. The discovery of microbial toxins is important to improve our understanding of microbial ecology and infectious diseases. Here, we developed a computational approach to discover novel toxin domains of polymorphic toxins and applied it to 105,438 microbial genomes. We validated nine short novel toxins ("PTs") that lead to bacterial cell death; one of them also kills yeast. For four toxins, we also identified a cognate immunity gene ("PIM") that protects the toxin producing cell from toxicity. Additionally, we found that the novel PTs are encoded by ~2.2% of the sequenced bacteria, including numerous Gram-negative and -positive pathogens. We explored two avenues to determine the mechanism of action of these nine PTs. First, we used fluorescence microscopy to observe severe changes in cell size, membrane and chromosome morphology upon expression of the novel toxins. We then identified putative catalytic sites of these toxins, which, upon mutation, abolished their harmful activities. Thus, using this unique hybrid computational-experimental pipeline, we were able to expand the microbial toxins repertoire significantly. These new potent toxins likely play essential roles in inter-microbial competition in Nature and can be utilized in various biotechnological and clinical applications.


title: Overexpression of Zinc finger (GpZF) promotes drought tolerance in grass pea (Lathyrus sativus)

abstract:
The genes encoding Cys2/His2-type zinc finger proteins constitute a large family in higher plants consisting of a family of plant transcription factors. GpZF encodes a Cys2/His2-type zinc finger protein. The purposes of this study are to elucidate further the functions of a novel zinc finger transcription factor in the grass pea (GpZF) gene involved in the drought stress response in the grass pea (Lathyrus sativus) and to investigate its biochemical and physiological parameters under stress conditions. GpZF was expressed in grass pea. Relative gene expression analysis showed the GpZF gene in independent transgenic lines was more under drought mild and severe treatments (50% and 25% field capacity-FC). Furthermore, overexpression of this gene in grass pea results in more relative water content, free proline, and soluble sugars than the wild-type (WT) plants under 50% and 25% FC stresses. Moreover, in 25% FC, the independent transgenic lines revealed an increase in survival rates and dry weight than the WT plants. GpZF thus implies the positive role in drought stress tolerance in Lathyrus sativus. In conclusion, the transgenic grass pea plants generated in this study could be used to farm arid areas.

HighlightGpZF is a positive regulator in drought stress tolerance in grass pea.

category: molecular biology


title: In an arms race between host and parasite, a lungworm's ability to infect a toad is determined by host susceptibility, not parasite preference

abstract: Evolutionary arms races can alter both parasite infectivity and host resistance, and it is difficult to separate the effects of these twin determinants of infection outcomes. Using a co-introduced, invasive host-parasite system (the lungworm Rhabdias pseudosphaerocephala and the cane toad Rhinella marina), we quantified behavioural responses of parasite larvae to skin-chemical cues of toads from different invasive populations, and rates at which hosts became infected following standardised exposure to lungworms. Chemical cues from toad skin altered host-seeking behaviour by parasites, similarly among populations. The number of infection attempts (parasite larvae entering the hosts body) also did not differ between populations, but rates of successful infection (establishment of adult worm in host lungs) was higher for range-edge toads than for range-core conspecifics. Thus, lower resistance to parasite infection in range-edge toads appears to be due to less effective immune defences of the host rather than differential behavioural responses of the parasite. In this ongoing host-parasite arms-race, changing outcomes appear to be driven by shifts in host immunocompetence.


title: Design, 3D-printing, and characterisation of a low-cost, open-source centrifuge adaptor for separating large volume clinical blood samples

abstract: Blood plasma separation is a prerequisite in numerous biomedical assays involving low abundance plasma-borne biomarkers and thus is the fundamental step before many bioanalytical steps. Conventionally, plasma separation is performed using high-capacity refrigerated centrifuges which have the advantage of handling large volume blood samples. These centrifuges are bulky, and prohibitively expensive for low-resource settings, with prices starting from $1,500. Although commercial and existing open-source micro-centrifuges are relatively low-cost, they cannot handle large volume blood samples. Microfluidic blood plasma separation also has been adopted by many researchers to enable low-cost plasma separation, however, these systems still present yield and purity issues for extremely low abundance biomarker detection such as the detection of various fractions of circulating cell-free DNA. To overcome this, we customised the rotor of a commercially available micro-centrifuge [~]$125) using fused filament fabrication to enable centrifugation of large clinical blood samples in resource poor-settings. Our designed adaptor ($15) can hold two 9 mL S-Monovette tubes and maintain the same separation performance (yield, cell count, hemolysis, albumin levels) as the control benchtop refrigerated centrifuge. This low-cost open-source centrifugation system capable of processing clinical blood tubes could be valuable to low-funded laboratories or low-resource settings where centrifugation is required immediately after blood withdrawal for further testing.


title: Controlling Selectivity of Modular Microbial Biosynthesis of Butyryl-CoA-Derived Designer Esters

abstract: Short-chain esters have broad utility as flavors, fragrances, solvents, and biofuels. Controlling selectivity of ester microbial biosynthesis has been an outstanding metabolic engineering problem. Here, we present a generalizable framework to enable the de novo fermentative microbial biosynthesis of butyryl-CoA-derived designer esters (e.g., butyl acetate, ethyl butyrate, butyl butyrate) with controllable selectivity. Using the modular design principles, we generated the butyryl-CoA-derived ester pathways as exchangeable production modules compatible with an engineered chassis cell for anaerobic production of designer esters. We designed these modules derived from an acyl-CoA submodule (e.g., acetyl-CoA, butyryl-CoA), an alcohol submodule (e.g., ethanol, butanol), a cofactor regeneration submodule (e.g., NADH), and an alcohol acetyltransferase (AAT) submodule (e.g., ATF1, SAAT) for rapid module construction and optimization by manipulating replication (e.g., plasmid copy number), transcription (e.g., promoters), translation (e.g., codon optimization), pathway enzymes, and pathway induction conditions. To further enhance production of designer esters with high selectivity, we systematically screened various strategies of protein solubilization using protein fusion tags and chaperones to improve the soluble expression of multiple pathway enzymes. Finally, our engineered ester-producing strains could achieve 19-fold increase in butyl acetate production (0.64 g/L, 96% selectivity), 6-fold increase in ethyl butyrate production (0.41 g/L, 86% selectivity), and 13-fold increase in butyl butyrate production (0.45 g/L, 54% selectivity) as compared to the initial strains. Overall, this study presented a generalizable framework to engineer modular microbial platforms for anaerobic production of butyryl-CoA-derived designer esters from renewable feedstocks.

category: synthetic biology


title: Genetic Mouse Models of Autism Spectrum Disorder Present Subtle Heterogenous Cardiac Abnormalities.

abstract:
BackgroundAutism Spectrum Disorder (ASD) and Congenital Heart Disease (CHD) are strongly linked on a functional and genetic level. Most work has been focused on neurodevelopmental abnormalities in CHD. Conversely, cardiac abnormalities in ASD have been less studied. In this work we investigate the prevalence of cardiac comorbidities relative to genetic contributors of ASD.

MethodsUsing high frequency ultrasound imaging, we screened 9 mouse models with ASD-related genetic alterations (Arid1b(+/-), Chd8(+/-), 16p11.2 (deletion), Sgsh(+/-), Sgsh(-/-), Shank3 {Delta}exon 4-9(+/-), Shank3 {Delta}exon 4-9(-/-), Fmr1(-/-), Vps13b(+/-)), and pooled wild-type littermates (WT). Using a standardised imaging protocol, we measured heart rate (HR), aorta diameter (AoD), thickness and thickening of the left-ventricular (LV) anterior and posterior walls, LV chamber diameter, fractional shortening, stroke volume and cardiac output, Peak E and A velocity ratio of mitral inflow, Velocity Time Integral (VTI) through the ascending aorta.

ResultsMutant groups presented small-scale alterations in cardiac structure and function compared to WTs. A greater number of significant differences was observed among mutant groups than between mutant groups and WTs. Mutant groups differed primarily in measures of structure (LV chamber diameter and anterior wall thickness, HR, AoD). When compared to WTs, they differed in both structure and function (LV anterior wall thickness and thickening, chamber diameter and fractional shortening, HR). The mutant groups with most differences to WTs were 16p11.2 (deletion), Fmrl(-/-), Arid1b(+/-). Among mutant groups, the groups differing most from others were 16p11.2 (deletion), Sgsh(+/-), Fmrl(-/-). Our results broadly recapitulate the associated clinical findings.

LimitationsVarious genetically driven cardiac abnormalities occur early in life, so repeating this work in non-adult mice may be valuable. To identify possible sex differences, we must extend this work to female mice. The downsampling procedure used (total correlation calculation) must be verified. Only indirect comparison between our results and clinical literature is possible due to differing study designs.

ConclusionsThe characteristic heterogeneity of ASD was recapitulated in the observed cardiac phenotype. The type of measures (morphological, functional) mutant groups differ in can highlight common underlying mechanisms. Clinically, knowledge of cardiac abnormalities in ASD can be essential as even non-lethal cardiac abnormalities can impact normal development.


title: Single cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney

abstract: Cutaneous lupus is commonly present in patients with systemic lupus erythematosus (SLE) but can also exist as an isolated manifestation without further systemic involvement. T cells have been strongly suspected to contribute to the pathology of cutaneous lupus, yet our understanding of the T cell phenotypes and functions in the skin in lupus remains incomplete, and the extent to which lupus T cell infiltrates in skin resemble those in other tissue beds is unknown. Here, we present a detailed single-cell RNA sequencing profile of T and NK cell populations present within lesional and non-lesional skin biopsies of patients with cutaneous lupus. We identified multiple lymphocyte clusters, including both CD4 and CD8 T cells, NK cells, regulatory T cells, and a population of strongly interferon-responding cells that was present in patients with cutaneous lupus but absent in healthy donors. T cells across clusters from both lesional and non-lesional skin biopsies expressed elevated levels of interferon simulated genes (ISGs); however, compared to T cells from control skin, T cells from cutaneous lupus lesions did not show elevated expression profiles of activation, cytotoxicity, or exhaustion. Integrated analyses comparing skin T/NK cells to lupus nephritis kidney T/NK cells indicated that skin lymphocytes appeared less activated and lacked the expanded cytotoxic populations prominent in lupus nephritis. An integrated comparison of skin T cells from lupus and systemic sclerosis revealed similar activation profiles but an elevated ISG signature specific to cells from lupus skin biopsies. Overall, these data represent the first detailed transcriptomic analysis of the of T and NK cells in cutaneous lupus at the single cell level and have enabled a cross-tissue comparison that highlighted the stark differences in composition and activation of T/NK cells in distinct tissues in lupus.

category: immunology


title: Cyclooxygenase production of PGE2 promotes phagocyte control of A. fumigatus hyphal growth in larval zebrafish

abstract:
Invasive aspergillosis is a common opportunistic infection, causing >50% mortality in infected immunocompromised patients. The specific molecular mechanisms of the innate immune system that prevent pathogenesis of invasive aspergillosis in immunocompetent individuals are not fully understood. Here, we used a zebrafish larva-Aspergillus infection model to identify cyclooxygenase (COX) enzyme signaling as one mechanism that promotes host survival. Larvae exposed to the pan-COX inhibitor indomethacin succumb to infection at a significantly higher rate than control larvae. COX signaling is both macrophage- and neutrophil-mediated. However, indomethacin treatment has no effect on phagocyte recruitment. Instead, COX signaling promotes phagocyte-mediated inhibition of germination and invasive hyphal growth. Protective COX-mediated signaling requires the receptor EP2 and exogenous prostaglandin E2 (PGE2) rescues indomethacin-induced decreased immune control of fungal growth. Collectively, we find that COX signaling activates the PGE2-EP2 pathway to increase control A. fumigatus hyphal growth by phagocytes in zebrafish larvae.

Author SummaryInvasive aspergillosis causes mortality in >50% of infected patients. It is caused by a free-living fungus Aspergillus fumigatus which releases thousands of airborne spores. While healthy individuals clear inhaled spores efficiently, in immunocompromised individuals these spores grow into filamentous hyphae and destroy lungs and other tissues causing invasive aspergillosis. The immune mechanisms that control this fungal growth in healthy people are still largely unknown. Here, we used a larval zebrafish model of A. fumigatus infection to determine that cyclooxygenase enzymes, which are the target of non-steroidal anti-inflammatory drugs such as aspirin and ibuprofen, are important to control the fungus. Innate immune cells use cyclooxygenase signaling to prevent hyphal growth and tissue destruction. Our study provides new insights into the mechanisms that immune cells deploy to stop invasive growth of A. fumigatus and inform development of future strategies to combat invasive aspergillosis.


title: Expert annotation and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) highlight the role of cold shock proteins in dormancy exit

abstract: Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster - two of the most represented TF families in fungi-indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The cold shock protein (CSP) family showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, strengthening their implication in dormancy exit. This study addresses for the first time TF involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.


title: Specificities and commonalities of carbapenemase producing Escherichia coli isolated in France from 2012 to 2015.

abstract:
Carbapenemase-producing Escherichia coli (CP-Ec) represent a major public health threat with a risk of dissemination in the community as it has occurred for lineages producing extended spectrum {beta}-lactamases. To characterize the extend of CP-Ec spread in France, isolates from screening and infection samples received at the French National Reference Centre laboratory (F-NRC) for carbapenemase-producing Enterobacterales were investigated. Six hundred and ninety one CP-Ec isolates collected between 2012 and 2015 and 22 before were fully sequenced. Analysis of their genome sequences revealed some disseminating multidrug resistant (MDR) lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex (CC) 23 (ST 410) and CC10 (ST10, ST167) and sporadic isolates including rare ST131 isolates (n=17). However, the most represented ST was ST38 (n=92) with four disseminated lineages carrying blaOXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n=457) was blaOXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid pOXA-48 in France and its high frequency of conjugation. In contrast blaOXA-181 or blaNDM genes were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC.

IMPORTANCECarbapenemase-producing Escherichia coli (CP-Ec) might be difficult to detect, as minimal inhibitory concentrations can be very low. However, their absolute number and their proportion among carbapenem-resistant Enterobacterales have been increasing, as reported by WHO and national surveillance programs. This suggests a still largely uncharacterized community spread of these isolates. Here we have characterized the diversity and evolution of CP-Ec isolated in France before 2016. We show that carbapenemase genes are associated with a wide variety of E. coli genomic backgrounds and a small number of dominant phylogenetic lineages. In a significant proportion of CP-Ec, the most frequent carbapenemase gene blaOXA-48, was detected in isolates lacking any other resistance gene, reflecting the dissemination of pOXA-48 plasmids, likely in the absence of any antibiotic pressure. In contrast carbapenemase gene transfer may also occur in multi-drug resistant E. coli, ultimately giving rise to at-risk lineages encoding carbapenemases with a high potential of dissemination.


title: Interaction of human Crx and Nrl in live cells measured using fluorescence resonance energy transfer (FRET)

abstract: CRX and NRL are retina-specific transcription factors that control rod photoreceptor differentiation and synergistically activate rod phototransduction gene expression. Previous experiments showed they interact in vitro and in yeast two-hybrid assays. Here, we examined CRX-NRL interaction in live HEK293T cells using two fluorescence resonance energy transfer (FRET) approaches: confocal microscopy and flow cytometry (FC-FRET). FC-FRET can provide measurements from many cells having wide donor-acceptor expression ranges. FRET efficiencies were calibrated with a series of donor (EGFP)-acceptor (mCherry) fusion proteins separated with linkers between 6-45 amino acids. CRX and NRL were fused at either terminus with EGFP or mCherry to create fluorescent proteins, and all combinations were tested in transiently transfected cells. FRET signals between CRX or NRL homo-pairs were highest with both fluorophores fused to the DNA binding domains (DBD), lower with both fused to the activation domains (AD), and not significant when fused on opposite termini. NRL had stronger FRET signals than CRX. A significant FRET signal between CRX and NRL hetero-pairs was detected when donor was fused to the CRX DNA binding domain and the acceptor fused to the NRL activation domain. FRET signals increased with CRX or NRL expression levels at a rate much higher than expected for collisional FRET alone. Together, our results show the formation of CRX-NRL complexes in live HEK293T cells that are close enough for FRET.


title: In vitro experiments and kinetic models of pollen hydration show that MSL8 is not a simple tension-gated osmoregulator

abstract: Pollen, a neighbor-less cell that contains the male gametes, undergoes multiple mechanical challenges during plant sexual reproduction, including desiccation and rehydration. It was previously showed that the pollen-specific mechanosensitive ion channel MscS-Like (MSL)8 is essential for pollen survival during hydration and proposed that it functions as a tension-gated osmoregulator. Here we test this hypothesis with a combination of mathematical modeling and laboratory experiments. Time-lapse imaging revealed that wild-type pollen grains swell and then stabilize in volume rapidly during hydration. msl8 mutant pollen grains, however, continue to expand and eventually burst. We found that a mathematical model wherein MSL8 acts as a simple tension-gated osmoregulator does not replicate this behavior. A better fit was obtained from variations of the model wherein MSL8 inactivation is independent of its membrane tension gating threshold or MSL8 strengthens the cell wall without osmotic regulation. Experimental and computational testing of several perturbations, including hydration in an osmolyte-rich solution, hyper-desiccation of the grains, and MSL8-YFP overexpression, indicated that the Cell Wall Strengthening Model best simulated experimental responses. Finally, expression of a non-conducting MSL8 variant did not complement the msl8 overexpansion phenotype. These data indicate that, contrary to our hypothesis and to known MS ion channel function in single-cell systems, MSL8 does not act as a simple membrane tension-gated osmoregulator. Instead, they support a model wherein ion flux through MSL8 is required to alter pollen cell wall properties. These results demonstrate the utility of pollen as a cellular-scale model system and illustrate how mathematical models can correct intuitive hypotheses.


title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human pathogenic Escherichia

abstract:
Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans.

We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two different types of the NEL C-terminal domain. Only the ipaH9.8 gene was found in Escherichia derived from both human and non-human hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.


title: Analysing and identifying miRNAs from RNA-seq data using miRDeep2 tool in Galaxy, a practical guide.

abstract: Micro-RNAs (miRNAs) analysis from RNA-seq experiment data provides additional depth into the cellular gene regulation. Such analysis has been simplified using miRDeep2 tool available in freely accessible Galaxy Europe server and miRBase database that compiled the miRNAs in many organisms. Here, we are describing a step by step protocol on how to ultilised the tool and most importantly on how to prepared and compiled miRDeep2 results to be used for downstream analysis such as investigating the differential expression of the detected miRNAs. Currently miRDeep2 miRNAs count result output in the Galaxy are in the broken HTML page and processing such data are troublesome for further analysis unless the user setting up their software dependencies for the tool to run. Hence, we proposed a method to process this output so that it is usable for downstream processing without a single coding required.


title: Tuning the Pennes Perfusion Rate to Model Large Vessel Cooling Effects in Hepatic Radiofrequency Ablation

abstract: Radio-frequency ablation (RFA) has become a popular method for the minimally invasive treatment of liver cancer. However, the success rate of these treatments depends heavily on the amount of experience the clinician possesses. Mathematical modelling can help mitigate this problem by providing an indication of the treatment outcome. Thermal lesions in RFA are affected by the cooling effect of both fine-scale and large-scale blood vessels. The exact model for large-scale blood vessels is advection-diffusion, i.e. a model capable of producing directional effects, which are known to occur in certain cases. In previous research, in situations where directional effects do not occur, the advection term in the blood vessel model has been typically replaced with the Pennes perfusion term, albeit with a higher-than usual perfusion rate. Whether these values of the perfusion rate appearing in literature are optimal for the particular vessel radii in question, has not been investigated so far. The present work aims to address this issue. An attempt has been made to determine, for values of vessel radius between 0.55 mm and 5 mm, best estimates for the perfusion rate which minimize the error in thermal lesion volumes between the perfusion-based model and the advection-based model. The results for the best estimate of the perfusion rate presented may be used in existing methods for fast estimation of RFA outcomes. Furthermore, the possible improvements to the presented methodology have been highlighted.


title: Base editors for citrus gene editing

abstract: Base editors, such as adenine base editors (ABE) and cytosine base editors (CBE), provide alternatives for precise genome editing without generating double-strand breaks (DSBs), thus avoiding the risk of genome instability and unpredictable outcomes caused by DNA repair. Precise gene editing mediated by base editors in citrus has not been reported. Here, we have successfully adapted the ABE to edit the TATA box in the promoter region of the canker susceptibility gene LOB1 from TATA to CACA in grapefruit (Citrus paradise) and sweet orange (Citrus sinensis). TATA-edited plants are resistant to the canker pathogen Xanthomonas citri subsp. citri (Xcc). In addition, CBE was successfully used to edit the acetolactate synthase (ALS) gene in citrus. ALS-edited plants were resistant to the herbicide chlorsulfuron. Two ALS-edited plants did not show green fluorescence although the starting construct for transformation contains a GFP expression cassette. The Cas9 gene was undetectable in the herbicide-resistant citrus plants. This indicates that the ALS edited plants are transgene-free, representing the first transgene-free gene-edited citrus using the CRISPR technology. In summary, we have successfully adapted the base editors for precise citrus gene editing. The CBE base editor has been used to generate transgene-free citrus via transient expression.


title: CombPDX: a unified statistical framework for evaluating drug synergism in patient-derived xenografts

abstract:
MotivationAnticancer combination therapy has been developed to increase efficacy by enhancing synergy. Patient-derived xenografts (PDXs) have emerged as reliable preclinical models to develop effective treatments in translational cancer research. However, in most PDX combination experiments, PDXs are tested on single dose levels and dose-response surface methods are not applicable for testing synergism.

ResultsWe propose a comprehensive statistical framework to assess joint action of drug combinations from PDX tumor growth curve data. We provide various metrics and robust statistical inference procedures that locally (at a fixed time) and globally (across time) access combination effects under classical drug interaction models. Integrating genomic and pharmacological profiles in non-small-cell lung cancer (NSCLC), we have shown the utilities of combPDX in discovering effective therapeutic combinations and relevant biological mechanisms.

AvailabilityWe provide an interactive web server, combPDX (https://licaih.shinyapps.io/CombPDX/), to analyze PDX tumor growth curve data and perform power analyses.

ContactMJHa@mdanderson.org

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Overground Gait Kinematics and Muscle Activation Patterns in the Yucatan Mini Pig

abstract: A growing number of spinal cord injury, neuromodulation, and cell therapy studies on porcine models, especially the Yucatan minipigs (YMPs), have been recently reported. This is due to the large similarities between human and porcine neuroanatomy and biomechanics. To assess treatment modalities and locomotor recovery in this model, there is an obvious need for detailed characterization of normative overground gait in neurologically intact YMPs. The objective of this study was to assess gait biomechanics and the effect of overground walking speed on gait parameters, kinematics, and electromyographic (EMG) activity in the hindlimb muscles of YMPs. Nine neurologically-intact adult YMPs were trained to walk overground in a straight line. Whole-body kinematics and EMG activity of hindlimb muscles were recorded and analyzed at 6 different speed ranges (0.4-0.59, 0.6-0.79, 0.8-0.99, 1.0-1.19, 1.2-1.39, and 1.4-1.6 m/s). A MATLAB program was developed to detect strides and gait events automatically from motion-captured data. Significant decreases in stride duration, stance and swing times and an increase in stride length were observed with increasing speed. A transition in gait pattern occurred at the 1.0m/s walking speed. Significant increases in the range of motion of the knee and ankle joints were observed at higher speeds. Also, the points of minimum and maximum knee and ankle joint angles occurred earlier in the gait cycle at higher speeds. The onset of EMG activity in the biceps femoris muscle occurred significantly earlier in the gait cycle with increasing speed. A comprehensive characterization of overground walking in neurologically-intact YMPs is provided. These normative measures set the basis against which the effects of future interventions on locomotor capacity in YMPs can be compared.


title: Neural network embedding of functional microconnectome.

abstract:
Our brain works as a complex network system. Experiential knowledge seems to be coded into the organisms network architecture rather than retaining only properties of individual neurons.

In order to be better able to consider the high complexity of this network architecture, extracting simple rules through both automated as well as interpretable analysis of topological patterns will be necessary in order to allow more useful observations of interrelationships within the complex neural architecture.

By combining these two types of analysis methods, we could automatically compress and naturally interpret topological patterns of functional connectivities, which produced electrical activities from many neurons simultaneously from acute slices of mice brain for 2.5 hours [Kajiwara et al. 2021].

As the first type of analysis, this study trained an artificial neural network system called Neural Network Embedding (NNE), and automatically compressed the functional connectivities into only small (25%) dimensions.

As the second type of analysis, we widely compared the compressed features with ~15 representative network metrics, having clear interpretations, including > 5 centrality-type metrics and newly developed network metrics, that quantify degrees or ratio of hubs distanced by several-nodes from initially focused hubs.

As the result, although we could give interpretations for only 55-60% of the extracted features, these new metrics, together with the commonly utilized network metrics, enabled interpretations for 80-100% features, using automated analysis.

The result demonstrates not only the fact that the NNE method surpasses limitations of commonly used human-made variables, but also the possibility that acknowledgement of our own limitations drives us to extend interpretable possibilities by developing new analytic methodologies.


title: Visual Motion Coherence Responses in Human Visual Cortex

abstract: 1Random dot kinematograms (RDKs) have recently been used to train subjects with cortical scotomas to perform direction of motion discrimination, partially restoring visual motion perception. To study recovery of visual perception, it is important to understand how visual areas in normal subjects and subjects with cortical scotomas respond to RDK stimuli. Studies in normal subjects have shown that Blood Oxygen Level Dependent (BOLD) responses in human area hV5/MT+ increase monotonically with coherence, in general agreement with electrophysiology studies in primates. However, RDK responses in prior studies were obtained while the subject was performing fixation, not a motion discrimination condition. Furthermore, BOLD responses were gauged against a baseline condition of uniform illumination or static dots, potentially decreasing the specificity of responses for the spatial integration of local motion signals (motion coherence). Here we revisit this question starting from a baseline RDK condition of no coherence, thereby isolating the component of BOLD response due specifically to the spatial integration of local motion signals. In agreement with prior studies, we found that responses in area hV5/MT+ of healthy subjects were monotonically increasing when subjects fixated without performing a motion discrimination task. In contrast, when subjects were performing an RDK direction of motion discrimination task, responses in area hV5/MT+ remained flat, changing minimally, if at all, as a function of motion coherence. A similar pattern of responses was seen in area hV5/MT+ of subjects with dense cortical scotomas performing direction of motion discrimination for RDKs presented inside the scotoma. Passive RDK presentation within the scotoma elicited no significant hV5/MT+ responses. These observations shed further light on how visual cortex responses behave as a function of motion coherence, helping to prepare the ground for future studies using these methods to study visual system recovery after injury.


title: Quantitative MRI reveals differences in striatal myelin in children with DLD

abstract: Developmental Language Disorder (DLD) is a common neurodevelopmental disorder characterised by receptive or expressive language difficulties or both. While theoretical frameworks and empirical studies support the idea that there may be neural correlates of DLD in frontostriatal loops, findings are inconsistent across studies. Here, we use a novel semiquantitative imaging protocol - multiparameter mapping (MPM) - to investigate microstructural neural differences in children with DLD. The MPM protocol allows us to reproducibly map specific indices of tissue microstructure. In 56 typically developing children and 34 children with DLD, we derived maps of: 1) longitudinal relaxation rate R1 (1/T1); 2) the transverse relaxation rate R2* (1/T2*); and 3) Magnetization Transfer Saturation (MTsat). R1 and MTsat predominantly index myelin, while R2* is sensitive to iron content. Children with DLD showed reductions in MTsat values in the caudate nucleus bilaterally, as well as in the left ventral sensorimotor cortex and Heschls gyrus. They also had globally lower R1 values. No group differences were noted in R2* maps. Differences in MTsat and R1 were coincident in the caudate nucleus bilaterally. These findings support our hypothesis of corticostriatal abnormalities in DLD and indicate abnormal levels of myelin in the dorsal striatum in children with DLD.


title: Expression level of the reprogramming factor NeuroD1 is critical for neuronal conversion efficiency from different cell types

abstract:
Several transcription factors, including NeuroD1, have been shown to act as neuronal reprogramming factors (RFs) that induce neuronal conversion from somatic cells. However, it remains unexplored whether expression levels of RFs in the original cells affect reprogramming efficiency. Here, we show that the neuronal reprogramming efficiency from two distinct glial cell types, microglia and astrocytes, is substantially dependent on the expression level of NeuroD1: low expression failed to induce neuronal reprogramming, whereas elevated NeuroD1 expression dramatically improved reprogramming efficiency in both cell types. Moreover, even under conditions where NeuroD1 expression was too low to induce effective conversion by itself, combined expression of three RFs (Ascl1, Brn2, and NeuroD1) facilitated the breaking down of cellular barriers, inducing neuronal reprogramming. Thus, our results suggest that a sufficiently high expression level of RFs or alternatively their combinatorial expression, is the key to achieving efficient neuronal reprogramming from different cells.

Highlights{blacksquare} High expression of NeuroD1 is required for neuronal conversion.
{blacksquare}Multiple infections with NeuroD1-expressing virus enhance neuronal reprogramming
{blacksquare}Combinatorial expression of NeuroD1 with other RFs facilitates neuronal conversion

eTOC blurbIn this article, Matsuda-Ito et al. demonstrate that the efficacy of conversion into neurons from two distinct glial cells, microglia and astrocytes, depends on the NeuroD1 expression level. They also show that increased NeuroD1 expression alone enables efficient neuronal reprogramming in non-reactive astrocytes that were previously shown to be difficult to convert into neurons.


title: Clonally expanded CD38hi cytotoxic CD8 T cells define the T cell infiltrate in checkpoint inhibitor-associated arthritis

abstract: Immune checkpoint inhibitor (ICI) therapies that promote T cell activation have improved outcomes for advanced malignancies yet also elicit harmful autoimmune reactions. The T cell mechanisms mediating these iatrogenic autoimmune events remain unclear. Here we assayed T cells from joints of patients affected by ICI-induced inflammatory arthritis (ICI-arthritis), which can present clinically indistinguishable from rheumatoid arthritis (RA). Compared to the autoimmune arthritides RA and psoriatic arthritis (PsA), ICI-arthritis joints contained an expanded CD38hi CD127- CD8+ T cell subset that displays cytotoxic, effector, and interferon (IFN) response signatures. The abundance of CD38hi CD8 T cells in ICI-arthritis resulted from a limited number of clones that could be found proliferating in the joint. Exposure of synovial T cells to Type I IFN, more so than IFN-{gamma}, induces the CD38hi cytotoxic phenotype. Relative to other CD8+ T cell subsets in the joints, the CD38hi population is distinct from a dysfunctional population and clonally most related to TCF7+ memory populations. Examination of synovial tissue from bilateral knee arthroplasty demonstrated considerable sharing of TCR clonotypes in the CD38hi CD8 T cell fraction from both knees. These results define a distinct CD8 T cell subset that may be directly activated by ICI therapy and mediate a tissue-specific autoimmune cellular reaction in patient joints.


title: Contribution of rsaC, a small non-coding RNA, towards the pathogenicity of Staphylococcus aureus in a mouse systemic infection model

abstract:
Understanding how a pathogen responds to the host stimuli and succeeds in causing disease is crucial for developing a novel treatment approach against the pathogen. Transcriptomic analysis facilitated by RNA-Seq technologies is used to examine bacterial responses at the global level. However, the ability to understand pathogen behavior inside the host tissues is hindered by much lower pathogen biomass than host tissue. Recently, we succeeded in establishing a method to enrich Staphylococcus aureus cells from infected organs. In this research, we analyzed the small non-coding RNA (sRNA) transcriptome of S. aureus inside the host and found that rsaC was among the highly expressed sRNAs. Furthermore, by gene disruption and complementation, we demonstrated that rsaC was required for full pathogenicity of S. aureus in a murine model. Besides, we found that {Delta}rsaC showed a difference in gene expression depending on the oxygen and host stress. The findings of this study suggest rsaC acts as a novel virulence factor in S. aureus and might facilitate the adaptation of staphylococci within the host.

ImportanceDrug-resistant Staphylococcus aureus is among the pathogen for which new treatment options are urgently needed. However, limited understanding of S. aureus pathogenesis in the host has hindered unearthing potential strategies to treat the infections. Here, based on the in vivo transcriptomic analysis, we present the identification of a small non-coding RNA (sRNA) rsaC as a novel virulence factor of S. aureus. Furthermore, we performed transcriptomic analysis of the rsaC disrupted mutant and identified different pathways, possibly controlled by rsaC, during aerobic, anaerobic, and in vivo conditions. These findings contribute to reveal the role of sRNA rsaC and broadens our understanding of the adaptation of S. aureus to host environments.


title: A single-cell approach reveals variation in cellular phage-producing capacities

abstract:
Virus burst size, a component of viral fitness, is the average number of viral particles released from a single infected cell. In this study, we estimated bacteriophage lambda ({lambda}) burst size mean and distribution at different lysis times. To estimate phage {lambda} burst sizes at single-cell level, we employed a lysis-deficient E. coli lysogen, which allowed chemical lysis at desired times after the induction of lytic cycle. Induced cultures of E. coli lysogen were diluted and aliquoted into the wells of 96-well plates. A high dilution rate results in mostly empty wells and minimizes the probability of having multiple cells in wells that do receive cells. Burst size was estimated by titering single-cell lysates obtained after chemical lysis at desired times. Our data shows that the viral burst size initially increases exponentially with the lysis time, and then saturates at longer lysis times. We also demonstrate that cell-to-cell variation or "noise" in lysis timing does not significantly contribute to the burst size noise. The burst size noise remains constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise is that cell-to-cell differences in burst size originate from differences in cellular capacity to produce phages. The mean burst size measured at different lysis times is positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicates that there are other factors in addition to cell size that determine this cellular capacity.

ARTICLE IMPORTANCEPhages produce offspring by hijacking a cells replicative machinery. Previously, it was noted that the variation in the number of phages produced by single infected cells far exceeded cell size variation. It has been hypothesized that this variation is a consequence of variation in the timing of host cell lysis. Here we show that cell-to-cell variation in lysis timing does not significantly contribute to the burst size variation. We suggest that the constant burst size variation across different host lysis times results from cell-to-cell differences in capacity to produce phages. We find that the mean burst size measured at different lysis times is positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicates that there are other factors in addition to cell size that determine this cellular capacity.


title: Two type II phosphatidylinositol 4-kinases function sequentially in tubule-mediated cargo delivery from early endosomes to melanosomes

abstract:
Melanosomes are pigment cell-specific lysosome-related organelles in which melanin pigments are synthesized and stored. Melanosome maturation requires delivery of melanogenic cargoes via tubular transport carriers that emanate from early endosomes and that require BLOC-1 for their formation. Here we show that phosphatidylinositol-4-phosphate (PtdIns4P) and the type II PtdIns-4-kinases (PI4KII and PI4KII{beta}) support BLOC-1-dependent tubule formation to regulate melanosome biogenesis. Depletion of either PI4KII or PI4KII{beta} with shRNAs in melanocytes reduced melanin content and misrouted BLOC-1-dependent cargoes to late endosomes/lysosomes. Genetic epistasis, cell fractionation, and quantitative live-cell imaging analyses show that PI4KII and PI4KII{beta} function sequentially and non-redundantly downstream of BLOC-1 during tubule elongation towards melanosomes by generating local pools of PtdIns4P. The data show that both type II PtdIns-4-kinases are necessary for efficient BLOC-1-dependent tubule elongation and subsequent melanosome contact and content delivery during melanosome biogenesis. The independent functions of PtdIns-4-kinases in tubule extension are downstream of likely redundant functions in BLOC-1-dependent tubule initiation.

SUMMARYContents are delivered to maturing melanosomes from early endosomal intermediates through tubular transport carriers. Zhu et al show that two type II phosphatidylinositol kinases, PI4KII and PI4KII{beta}, sequentially generate phosphatidylinositol-4-phosphate during tubule initiation and elongation for ultimate melanosome content delivery.

category: cell biology


title: Sculpting rupture-free nuclear shapes in fibrous environments

abstract: Cytoskeleton-mediated force transmission regulates nucleus morphology. How nuclei shaping occurs in fibrous in vivo environments remains poorly understood. Here a suspended nanofiber assay of precisely-tunable (nm-m) diameters is used to quantify nucleus plasticity in fibrous environments mimicking the natural extracellular matrix. In contrast to the apical cap over the nucleus in cells on 2-dimensional surfaces, the cellular cytoskeleton of cells on fibers displays a uniform actin network caging the nucleus. The role of contractility-driven caging in sculpting nuclear shapes is investigated as cells spread on aligned single fibers, doublets, and multiple fibers of varying diameters. Cell contractility increases with fiber diameter due to increased focal adhesion clustering and density of actin stress fibers, which correlates with increased mechanosensitive transcription factor YAP translocation to the nucleus. Unexpectedly, large- and small-diameter fiber combinations lead to teardrop-shaped nuclei due to stress-fiber anisotropy across the cell. As cells spread on fibers, diameter-dependent invaginations that run the nucleuss length are formed at contact sites. The deepest and sharpest invaginations are insufficient to trigger nucleus rupture, often observed in 2D or confined systems. Overall, we describe the unknown adaptability of nuclei to fibrous environments and resultant sculpting of the nucleus shapes, with pathophysiological implications.


title: Single-Cell Analysis of Human Testis Aging, and Impact of Elevated Body Mass Index

abstract: Aging human males display reduced reproductive health, however testis aging is poorly understood at the molecular and genomic level. Here, we utilized single-cell RNA-seq to profile over 44,000 cells from both young and older men (>60 years old) - and examined age-related changes in germline development and in the somatic niche. Interestingly, age-related changes in spermatogonial stem cells appeared modest, whereas age-related dysregulation of spermatogenesis and the somatic niche ranged from moderate to severe. Altered pathways included signaling and inflammation in multiple cell types, metabolic signaling in Sertoli cells, hedgehog signaling and testosterone production in Leydig cells, cell death and growth in testicular peritubular cells, and possible developmental regression in both Leydig and peritubular cells. Remarkably, the extent of dysregulation correlated with body mass index in older, but not younger men. Taken together, we reveal candidate molecular mechanisms underlying the complex testicular changes conferred by aging, and their exacerbation by concurrent chronic conditions such as obesity.


title: Similar geographic patterns but distinct assembly processes of abundant and rare bacterioplankton communities in river networks of the Taihu Basin

abstract: Bacterioplankton play an important role in the biochemical cycling in rivers. The dynamics of hydrologic conditions in rivers were believed to affect geographic pattern and assembly process of these microorganisms, which have not been widely investigated. In this study, the geographic pattern and community assembly process of bacterioplankton in river networks of the Taihu Basin were systematically explored using amplicon sequencing of the 16S rRNA gene. The results showed that community structure, diversity, and taxonomic composition of bacterioplankton all exhibited significant temporal variation during wet, normal, and dry seasons (p<0.01). The neutral community model and null model were applied to reveal the assembly process of bacterioplankton community. The stochastic process and deterministic process both shaped the bacterioplankton community with greater influence of deterministic process. In addition, the abundant and rare bacterioplankton communities were comparatively analyzed. The abundant and rare bacterioplankton communities exhibited similar temporal dynamics (principal coordinates analysis) and spatial variations (distance-decay relationship), indicating similar geographic patterns. Meanwhile, distinct assembly processes were observed for the abundant and rare bacterioplankton communities. Stochastic process (dispersal limitation) shaped the abundant bacterioplankton community while deterministic process (heterogeneous selection) dominated the assembly process of rare bacterioplankton community. Mantel test, redundancy analysis, and correlation analysis together indicated that pH and dissolved oxygen were the major environmental attributes that affected the bacterioplankton community structure and assembly process. These results expanded our understanding of the geographic patterns, assembly processes, and driving factors of the bacterioplankton community in river networks and provided clues provided clues for the underlying mechanisms.


title: Facing the green threat: A waterflea's defenses against a carnivorous plant

abstract:
Water fleas of the family Daphniidae are keystone species in many lentic ecosystems and, as most abundant filter feeders, link the primary production to higher trophic levels. As a response to the high predatory pressures, water fleas have evolved a range of defenses, including inducible defenses against animal predators. Here we show in Ceriodaphnia dubia a first example of such defenses induced by the presence of a coexisting plant predator, i.e. the carnivorous southern bladderwort (Utricularia australis, Lentibulariaceae), which possesses ultrafast underwater suction traps. When the bladderwort is present, C. dubia shows changes in morphology, life-history and behavior. While the morphological and behavioral adaptations improve C. dubias survival rate in the presence of this predator, the life-history parameters likely reflect trade-offs for the defense. Our study demonstrates plant-induced animal defenses, implying their potential relevance in freshwater ecosystems and contributing to an overall yet underestimated biodiversity of inducible defenses.

Open Research StatementData is not finally prepared for upload yet. Once most fitting file types are determined and metadata is created we aim to upload all raw data as supporting information.


title: Multiple Sex Chromosome Drivers in a Mammal with Three Sex Chromosomes

abstract: A few mammals have unusual sex determining systems whereby fertile XY females live alongside XX females and XY males. These systems are regarded as evolutionary paradoxes because of the production of sex-reversed individuals and non-viable embryos, but they nevertheless seem stable over evolutionary time. Several hypotheses have been proposed to account for their stability, including models involving sex chromosome drive (i.e., biased transmission of sex chromosomes to the next generation). Here we corroborate this hypothesis in Mus minutoides, a close relative of the house mouse in which the presence of XY females is due to the evolution of a third sex chromosome: a feminizing X. Through extensive molecular sexing of pups at weaning, we reveal the existence of a remarkable male sex chromosome drive system in this species, whereby direction and strength of drive is conditional upon the genotype of males partners: males transmit their Y to almost 80% of their offspring when mating with XX females, and only 36% when mating with XY females. Using mathematical modelling, we explore the joint evolution of these unusual sex-determining and drive systems, revealing that different sequences of events could have led to the evolution of this bizarre system, and that the "conditional" nature of sex chromosome drive stabilizes the feminizing X, and even precludes a return to a standard XX/XY system.

category: evolutionary biology