Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of bacterial cell division: Z ring condensation is essential for cytokinesis

How proteins in the bacterial cell division complex (the divisome) coordinate to divide bacteria remains unknown. To explore how these proteins collectively function, we conducted a complete dynamic characterization of the proteins involved, and then examined the function of FtsZ binding proteins (ZBPs) and their role in cytokinesis. We find that the divisome consists of two dynamically distinct subcomplexes: stationary ZBPs that transiently bind to treadmilling FtsZ filaments, and a directionally-moving complex that includes cell wall synthases. FtsZ filaments treadmill at steady state and the ZBPs have no effect on filament dynamics. Rather, ZBPs bundle FtsZ filaments, condensing them into Z rings. Z ring condensation increases the recruitment of cell wall synthesis enzymes to the division site, and this condensation is necessary for cytokinesis.
A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

Here we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.
Split-wrmScarlet and split-sfGFP: tools for faster, easier fluorescent labeling of endogenous proteins in Caenorhabditis elegans

We create and share a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenous C. elegans proteins with fluorescent tags. CRISPR-mediated fluorescent labeling of C. elegans proteins is an invaluable tool, but it is much more difficult to insert fluorophore-size DNA segments than it is to make small gene edits. In principle, high-affinity asymmetrically split fluorescent proteins solve this problem in C. elegans: the small fragment can quickly and easily be fused to almost any protein of interest and can be detected wherever the large fragment is expressed and complemented. There is currently only one available strain stably expressing the large fragment of a split fluorescent protein, restricting this solution to a single tissue (the germline) in the highly autofluorescent green channel. No available C. elegans lines express unbound large fragments of split red fluorescent proteins, and even state-of-the-art split red fluorescent proteins are dim compared to the canonical split-sfGFP protein. In this study, we engineer a bright, high-affinity new split red fluorophore, split-wrmScarlet, and generate transgenic C. elegans lines to allow easy single-color labeling in muscles and dual-color labeling in somatic cells. We validate these strains by targeting split-wrmScarlet to several genes whose products label distinct organelles, and we provide a protocol for an easy, cloning-free method for CRISPR/Cas9 editing.
A multi-network comparative analysis of transcriptome and translatome in cardiac remodeling

Our understanding of the transition from physiological to pathological cardiac hypertrophy remains elusive and largely based on reductionist hypotheses. Here, we profiled the translatomes of 15 mouse hearts to provide a molecular blueprint of altered gene networks in early cardiac remodeling. Using co-expression analysis, we reveal how sub-networks are orchestrated into functional modules associated with pathological phenotypes. We show how transcriptome networks are only partially reproducible at the translatome level. We find unappreciated hub genes and genes in the transcriptional network that were rewired in the translational network, and associated with semantically different subsets of enriched functional terms, providing novel insights into the complexity of the organization of in vivo cardiac regulatory networks.
Investigating the determinants of mammalian Mastl kinase activation

Mastl (Greatwall) kinase is an essential mitotic protein kinase. Mastl is an atypical member of AGC family with a unique long stretch of non-conserved middle region. The mechanism of its phosphorylation dependent activation has been studied in Xenopus egg extracts, revealing several phosphosites that were suggested to be crucial for kinase activation. These residues correspond to T193 and T206 in the activation loop, and S861 in the C-tail of mouse Mastl. By combining a chemically inducible knockout system to deplete the endogenous Mastl and a viral expression system to ectopically express the mutant variants, we obtained a viable knockout clone that expresses the S861A and S861D mutants. We observed that proliferation rates of the MastlS861A and MastlS861D clones were comparable. Our results have revealed that phosphorylation of the turn motif phosphosite (S861) is auxiliary and it is not indispensable for Mastl function.
Stochastic Analysis Demonstrates the Dual Role of Hfq in Chaperoning E. coli Sugar Shock Response

Small RNAs (sRNAs) play a crucial role in the regulation of bacterial gene expression by silencing the translation of target mRNAs. SgrS is an sRNA that relieves glucose-phosphate stress, or “sugar shock” in E. coli. The power of single cell measurements is their ability to obtain population level statistics that illustrate cell-to-cell variation. Here, we utilize single molecule super-resolution microscopy in single E. coli cells coupled with stochastic modeling to analyze glucose-phosphate stress regulation by SgrS. We present a kinetic model that captures the combined effects of transcriptional regulation, gene replication and chaperone mediated RNA silencing in the SgrS regulatory network. This more complete kinetic description, simulated stochastically, recapitulates experimentally observed cellular heterogeneity and characterizes the binding of SgrS to the chaperone protein Hfq as a slow process that not only stabilizes SgrS but also may be critical in restructuring the sRNA to facilitate association with its target ptsG mRNA.
Transcriptomic and morphological response of SIM-A9 mouse microglia to carbon nanotube neuro-sensors

Single-walled carbon nanotubes (SWCNT) are used in neuroscience for deep-brain imaging, neuron activity recording, measuring brain morphology, and imaging neuromodulation. However, the extent to which SWCNT-based probes impact brain tissue is not well understood. Here, we study the impact of (GT)6-SWCNT dopamine nanosensors on SIM-A9 mouse microglial cells and show SWCNT-induced morphological and transcriptomic changes in these brain immune cells. Next, we introduce a strategy to passivate (GT)6-SWCNT nanosensors with PEGylated phospholipids to improve both biocompatibility and dopamine imaging quality. We apply these passivated dopamine nanosensors to image electrically stimulated striatal dopamine release in acute mouse brain slices, and show that slices labeled with passivated nanosensor exhibit higher fluorescence response to dopamine and measure more putative dopamine release sites. Hence, this facile modification to SWCNT-based dopamine probes provides immediate improvements to both biocompatibility and dopamine imaging functionality with an approach that is readily translatable to other SWCNT-based neurotechnologies.
A 3-hydroxyacyl-CoA dehydratase (DEH) involved in very long chain fatty acid synthesis is crucial for oocyst mitotic division but not cell size during parasite transmission in Plasmodium

Lipid metabolism is a crucially important area of biochemistry, and cells use fatty acids for membrane biosynthesis, energy storage and the generation of signaling molecules. A 3-hydroxyacyl-CoA dehydratase - DEH - is a key member of this process. Here we further characterized in-depth the location and function of DEH, applying in-silico analysis, live cell imaging, reverse genetics and ultrastructure analysis using the mouse malaria model Plasmodium berghei. We show that DEH is evolutionarily conserved across eukaryotic species, with a single DEH in Plasmodium spp. and up to three orthologs in the other eukaryotes studied. Using DEH-GFP live-cell imaging, we observed strong GFP fluorescence throughout the life-cycle, with areas of localized expression in the cytoplasm and a circular ring pattern around the nucleus that colocalized with ER markers. Functional analysis showed that while {Delta}deh mutants undergo normal oocyst cell growth during early stages of sporogony, endomitotic cell division and sporozoite development are completely ablated, blocking parasite transmission from mosquito to vertebrate host. Ultrastructure analysis confirmed degeneration of {Delta}deh oocysts, and a complete lack of sporozoite budding. Overall, we show that DEH is evolutionarily conserved, localizes to the ER and plays a crucial role in sporogony, potentially through its involvement in fatty acid production.
Arabidopsis Poly(ADP-ribose)-binding protein RCD1 interacts with Photoregulatory Protein Kinases in nuclear bodies

Continuous reprograming of gene expression in response to environmental signals in plants is achieved through signaling hub proteins that integrate external stimuli and transcriptional responses. RADICAL-INDUCED CELL DEATH1 (RCD1) functions as a nuclear hub protein, which interacts with a variety of transcription factors with its C-terminal RST domain and thereby acts as a co-regulator of numerous plant stress reactions. Here a previously function for RCD1 as a novel plant PAR reader protein is shown; RCD1 functions as a scaffold protein, which recruits transcription factors to specific locations inside the nucleus in PAR-dependent manner. The N-terminal WWE- and PARP-like domains of RCD1 bind poly(ADP-ribose) (PAR) and determine its localization to nuclear bodies (NBs), which is prevented by chemical inhibition of PAR synthesis. RCD1 also binds and recruits Photoregulatory Protein Kinases (PPKs) to NBs. The PPKs, which have been associated with circadian clock, abscisic acid, and light signaling pathways, phosphorylate RCD1 at multiple sites in the intrinsically disordered region between the WWE- and PARP-like-domains, which affects the stability and function of RCD1 in the nucleus. Phosphorylation of RCD1 by PPKs provides a mechanism where turnover of a PAR-binding transcriptional co-regulator is controlled by nuclear phosphorylation signaling pathways.
A Bayesian optimization approach for rapidly mapping residual network function in stroke

Post-stroke cognitive and linguistic impairments are debilitating conditions, with current therapies only showing small improvements. Domain-general brain networks seem to play a critical role in stroke recovery and characterising their residual function with functional neuroimaging (fMRI) has the potential to yield biomarkers capable of guiding patient-specific rehabilitation. However, this is currently challenging in patients as such detailed characterisation requires too many different cognitive tasks. Here, we use neuroadaptive Bayesian optimisation to overcome this problem, an approach combining real-time fMRI with machine-learning. By intelligently searching across many tasks, this approach rapidly maps out patient-specific profiles of residual domain-general network function. Whereas controls have highly similar profiles, patients show idiosyncratic profiles of network abnormalities that are associated with behavioural performance. This approach can be extended to diverse brain networks and combined with brain stimulation or other therapeutics, thereby opening new avenues for precision medicine targeting diverse neurological and psychiatric conditions.
Scale-free structure of cancer networks and their vulnerability to hub-directed combination therapy

Background The effectiveness of many targeted therapies is limited by toxicity and the rise of drug resistance. A growing appreciation of the inherent redundancies of cancer signaling has led to a rise in the number of combination therapies under development, but a better understanding of the overall cancer network topology would provide a conceptual framework for choosing effective combination partners. In this work, we explore the scale-free nature of cancer protein-protein interaction networks in 14 indications. Scale-free networks, characterized by a power-law degree distribution, are known to be resilient to random attack on their nodes, yet vulnerable to directed attacks on their hubs (their most highly connected nodes). Results Consistent with the properties of scale-free networks, we find that lethal genes are associated with ∼5-fold higher protein connectivity partners than non-lethal genes. This provides a biological rationale for a hub-centered combination attack. Our simulations show that combinations targeting hubs can efficiently disrupt 50% of network integrity by inhibiting less than 1% of the connected proteins, whereas a random attack can require inhibition of more than 30% of the connected proteins. Conclusions We find that the scale-free nature of cancer networks makes them vulnerable to focused attack on their highly connected protein hubs. Thus, we propose a new strategy for designing combination therapies by targeting hubs in cancer networks that are not associated with relevant toxicity networks.
The impact of allometry on vomer shape and its implications for the taxonomy and cranial kinesis of crown-group birds

Crown birds are subdivided into two main groups, Palaeognathae and Neognathae, that can be distinguished, among others, by the organization of the bones in their pterygoid-palatine complex (PPC). Shape variation to the vomer, which is the most anterior part of the PPC, was recently analysed by Hu et al. (2019) with help of geometric morphometrics to discover morphological differences between palaeognath and neognath birds. Based on this study, the vomer was identified as sufficient to distinguish the two main groups (and even more inclusive neognath groups) and their cranial kinetic system. As there are notable size differences between the skulls of palaeognaths and neognaths, we here investigate the impact of allometry on vomeral shape and its implication for taxonomic classification by re-analysing the data of the previous study. Different types of multivariate statistical analyses reveal that taxonomic identification based on vomeral shape is strongly impaired by allometry, as the error of correct identification is high when shape data is corrected for size. This finding is evident by a great overlap between palaeognath and neognath subclades in morphospace. The correct identification is further influenced by the convergent presence of a flattened vomeral morphotype in multiple neognath subclades. As the evolution of cranial kinesis has been linked to vomeral shape in the original study, the existing correlation between shape and size of the vomer across different bird groups found in the present study questions this conclusion. In fact, cranial kinesis in crown birds results from the loss of the jugal-postorbital bar in the temporal region and ectopterygoid in the PPC and the combination of a mobilized quadrate-zygomatic arch complex and a flexible PPC. Therefore, we can conclude that the vomer itself is not a suitable proxy for exploring the evolution of cranial kinesis in crown birds and their ancestors.
Biochemical Analysis of Lannea coromandelica L leaf Galls Induced by Odeniadiplosis odinae

Lannea coromandelica L. commonly known as Indian Ash tree, moya, wodeer, mohin, gudau belongs to Anacardiaceae family. This plant is of great economic value for wound healing, bone strengthening and stomach related diseases. In the present investigation the biochemical analysis of Lannea coromandelica L leaf galls induced by Odeniadiplosis odinae. Total soluble sugar, starch, total protein contents, amino acid contents, total phenolic contents, invertase activity, alpha amylase activity, auxin contents, IAA oxidase activity, peroxidase activity and polyphenol oxidase have been carried out in normal and induced leaf galls of Lannea coromandelica L. The results showed the changes in the metabolic activities of the plant.
Nitrogen metabolism in the ovine stomach: 4. Nitrogenous components of the abomasal secretions

SUMMARY The major nitrogenous components of gastric juice were determined in sheep with innervated pouches in the fundic and pyloric regions of the abomasum. Fundic secretions contained mean levels of 36–55 mg total-N/100 ml in the fluid fraction, and pyloric secretions contained 38–70 mg/100 ml. Of this, 65–76% and 75–91% could be attributed to protein, in the fundic and pyloric secretions respectively. Tungstic acid was found to be the most suitable precipitant of proteins in the gastric juice. Dissolved mucin accounted for 2–16% of the total-N in the fluid fraction of the fundic secretions, and for 6–14% in the pyloric secretions. Urea + ammonia contributed 2·8–13·4% of the total-N. The daily output of nitrogen by the fundic region of the abomasum, including that contributed by the cellular debris and visible mucus, was calculated at 0·46–2·4 g. The comparable values for the pyloric region varied between 0·05 and 0·37 g N/day. The electrophoretic patterns of the abomasal secretions were similar to those reported for human gastric juice.
Three times NO: no relationship between frontal alpha asymmetry and depressive disorders in a multiverse analysis of three studies

For decades, the frontal alpha asymmetry (FAA) - a disproportion in EEG alpha oscillations power between right and left frontal channels - has been one of the most popular measures of depressive disorders (DD) in electrophysiology studies. Patients with DD often manifest a left-sided FAA: relatively higher alpha power in the left versus right frontal lobe. Recently, however, multiple studies failed to confirm this effect, questioning its reproducibility. Our purpose is to thoroughly test the validity of FAA in depression by conducting a multiverse analysis - running many related analyses and testing the sensitivity of the effect to changes in the analytical approach - on data from three independent studies. Only two of the 81 analyses revealed significant results. We conclude the paper by discussing theoretical assumptions underlying the FAA and suggest a list of guidelines for improving and expanding the EEG data analysis in future FAA studies.
Photosynthetic features and primary productivity of phytoplankton in the Oyashio and Kuroshio–Oyashio transition regions of the northwest Pacific

Diel and seasonal changes in the photosynthetic physiology of phytoplankton and primary productivity were investigated during 2005, together with community composition in the Oyashio (OY) and Kuroshio – Oyashio transition (TR) regions of the northwest Pacific. In both regions, diel changes in the maximum photosynthetic rate (P* max) and the light saturation index (Ek) in the photosynthesis – irradiance (P –E) curve were observed, due to diel differences in photo-physiology. In the OY region, the highest values of chlorophyll a concentration, depth-integrated primary production and the maximum quantum yield of carbon fixation in photosynthesis (Fc max) were observed in May when diatom blooms occurred. Furthermore, a higher water-column light utilization efficiency (C) of photosynthesis for phytoplankton was found in the OY region in both May and September. In contrast, in the TR and warm-core ring regions, Fc max was nearly constant, while depth-integrated primary production in May was significantly lower than in the OY region. These results show that the spring phytoplankton assemblages in OY waters had a higher light utilization ability during photosynthesis. Such a high photosynthetic property would contribute to the highest seasonal biological drawdown of surface pCO2 among the world’s oceans (Takahashi, T., Sutherland, S. C., Sweeney, C. et al. (2002) Global sea – air CO2 flux based on climatological surface ocean pCO2, and seasonal biological and temperature effects. Deep-Sea Res. II, 49, 1601– 1622).
Effects of clam rake harvesting on the intertidal Ruditapes habitat of the English Channel

Recreational and professional clam fishing was an important activity on the extensive intertidal zone of the western Cotentin coast (western English Channel). A variety of fishing gear was used to harvest the target species: the European clam Ruditapes decussatus (Linnaeus, 1758) and the introduced Manila clam R. philippinarum (Adams and Reeve, 1850). In this study, we studied the effect of rake harvesting during the spring tides of February–March 2014, following an experimental design with a control station and three stations impacted by rake harvesting in three sediment types: sandy, gravelly, and mixed gravelly rocky habitats. No significant sediment and macrofauna changes occurred at the three sites after rake harvesting. Nevertheless, the number of clams decreased significantly after raking on the gravelly habitat, whereas in the other two habitats, sediment transport in this high-energy hydrodynamic environment was able to transfer clams and other macrofauna species across the fishing sites, thus minimizing the effects of rake harvesting. Therefore, although the effect of rake harvesting appeared limited during winter, the regional impact (high fishing pressure along 60 km of coast) and increase of recreational fishers during summer needed to be studied in the future.
Carbon and nitrogen release from cover crop residues and implications for cropping systems management

Cover cropping is an effective management practice for reducing nitrogen (N) losses to the environment from agriculture fields in the Upper Mississippi River Basin (UMRB). Cereal rye (CR; Secale cereale L.) and hairy vetch (HV; Vicia villosa Roth) are two of the most common cover crop species grown in the UMRB. Few studies have examined the effect of corn (Zea mays L.) or soybean (Glycine max L.) management on the rate and timing of N and carbon (C) release from CR and HV residue. The objective of this study was to measure the effect of cash crop rotation (continuous corn, corn–soybean, and soybean–corn), cover crop selection (CR, HV, and a CR/HV mixture), and tillage (spring disk or transitional no-till) on the rate and timing of N and C loss from litterbags as an estimate of N and C release from cover crop residue. Our results demonstrated that rotation did not impact cover crop N and C release. However, HV released both N and C at rates 2.1 and 1.6 times faster, respectively, than treatments that included CR. Furthermore, where residue was incorporated, rates of N and C release were 2.7 and 3.0 times faster, respectively, than where residue was not incorporated. When averaged across cover crop species and tillage, 17% to 56% of nutrient release occurred, after planting, during vegetative cash crop growth stages. Results from this study advanced the understanding of how cropping systems management can influence release of N and C from cover crop residue.