bluuebunny/crossref_metadata_2025 huggingface dataset:
Global atlas tree of natural proteins based on sorted composition vectors
Authors: Tian Pu
Published: December 2019

Sequence comparison is the cornerstone of bioinformatics and is traditionally realized by alignment. Unfortunately, exponential computational complexity renders rigorous multiple sequence alignment (MSA) intractable. Approximate algorithms and heuristics provide acceptable performance for relatively small number of sequences but engender prohibitive computational cost and unbounded accumulation of error for massive sequence sets. Alignment free algorithms achieved linear computational cost for sequence pair comparison but the challenge for multiple sequence comparison (MSC) remains. Meanwhile, various number of parameters and procedures need to be empirically adjusted for different MSC tasks with their complex interactions and impact not well understood. Therefore, development of efficient and nonparametric global sequence comparison method is essential for explosive sequencing data. It is shown here that sorted composition vector (SCV), which is based on a physical perspective on sequence composition constraint, is a feasible non-parametric encoding scheme for global protein sequence comparison and classification with linear computational complexity, and provides a global atlas tree for natural protein sequences. This finding renders massive sequence comparison and classification, which is infeasible on supercomputers, routine on a workstation. SCV sets an example of one-way encoding that might revolutionize recognition and classification tasks in general.
Molecular Docking Studies of Phytochemicals of Allophylus serratus Against Cyclooxygenase-2 Enzyme
Authors: Jemal Kero
Published: December 2019

Allophylus serratus is a medicinal plant used traditionally as anti-inflammatory agent. The main objectives of this study are to identify phytochemical compounds that have anti-inflammatory properties from the leaf extracts of Allophylus serratus and to search for cyclooxygenase-2 (COX-2) enzyme inhibitors through molecular docking. From the GC-MS analysis of leaf extracts of this plant, various phytochemicals were identified. About 10of these phytochemical compounds were analyzed for their drug likeliness based on Lipinski’s rule of five and inhibitor property against the cyclooxygenase (COX-2) enzyme, a protein responsible for inflammation The phytochemical compounds which satisfy the Lipinski’s rule such as 1H-Benzocycloheptene, 2,4a,5,6,7,8-hexahydro-3,5,5,9-tetramethyl-,(R) and Sulfurous acid, dipentyl ester were subjected to docking experiments using AutoDock Vina. The results from molecular docking study revealed that 1H-Benzocycloheptene, 2,4a,5,6,7,8-hexahydro-3,5,5,9-tetramethyl-, (R)-, Sulfurous acid, dipentyl ester and 1,2-Benzenedicarboxylic acid, bis(2-methylpropyl) ester bind effectively to the active site region of COX-2 with a binding energy of −8.9, −8.4, and −7.9, respectively. The binding energy of the phyto-compounds were compared with the known antiinflammatory drug Diclofenac that inhibit COX-2 enzyme. It was found that the phytochemical compounds from leaf extracts of Allophylus serratus have strong inhibitory effect on COX-2 enzyme and as a result they have potential anti-inflammatory medicinal values. Thus the study puts forth experimental validation for traditional antidote and these phyto-compounds could be further promoted as potential lead molecule.
A revised mechanism of action of hyperaldosteronism-linked mutations in cytosolic domains of GIRK4 (KCNJ5)
Authors: Shalomov Boris , Handklo-Jamal Reem , Reddy Haritha P. , Theodor Neta , Bera Amal K. , Dascal Nathan
Published: December 2019

G-protein gated, inwardly rectifying potassium channels (GIRK) mediate inhibitory transmission in brain, heart, and adrenal cortex. GIRK4 (KCNJ5) subunits are abundant in the heart and adrenal cortex. Multiple mutations ofKCNJ5cause primary aldosteronism (PA). According to a leading concept, mutations in the pore region of GIRK4 cause loss of K+selectivity; the ensuing Na+influx depolarizes zona glomerulosa cells and activates voltage gated Ca2+channels, inducing hypersecretion of aldosterone. The concept of selectivity loss has been extended to mutations in cytosolic domains of GIRK4 channels, remote from the pore region. We expressed GIRK4R52H, GIRK4E246K, and GIRK4G247Rmutants inXenopusoocytes and human adrenocortical carcinoma cell line (HAC15). Whole-cell currents of heterotetrameric GIRK1/4R52Hand GIRK1/4E246K(but not GIRK1/4G247R) channels were greatly reduced compared to GIRK1/4WT. Nevertheless, all heterotetrameric mutants retained full K+selectivity and inward rectification. When expressed as homotetramers, only GIRK4WT, but none of the mutants, produced whole-cell currents. Confocal imaging, single channel and Förster Resonance Energy Transfer (FRET) analyses showed: 1) reduction of membrane abundance of all mutated channels, especially as homotetramers, 2) impaired interaction with Gβγ subunits, and 3) reduced open probability of GIRK1/4R52H. VU0529331, a GIRK4 opener, activated homotetrameric GIRK4G247Rchannels, but not GIRK4R52Hand GIRK4E246K. Our results suggest impaired gating (GIRK4R52H) and expression in plasma membrane (all mutants). We suggest that, contrary to the previously proposed mechanism, R52H and E246K mutants are loss-of-function rather than gain-of-function/selectivity-loss mutants. Hence, GIRK4 openers may be a potential course of treatment for patients with cytosolic N- and C-terminal mutations.

Significance Statement

Mutations in KCNJ5 gene, which encodes for the GIRK4 subunit of G-protein inwardly rectifying K+ channels, are the main cause of primary aldosteronism, a major contributor to secondary hypertension. We report that three mutations in the cytosolic domain of GIRK4 cause loss-of-function, contrary to the prevailing concept that these mutations cause loss of selectivity and subsequent depolarization, i.e. essentially gain-of-function. Our findings correct the existing misconception regarding the biophysical mechanism that impairs the channel function, and may provide indications for future personalized treatment of the disease.
Phage T5 two-step injection
Authors: Davison John
Published: December 2019

Escherichia colibacteriophage T5 differs from most phages in that it injects its genome in two steps: First Step Transfer, FST, corresponding to leftmost 7.9% of the genome and Second Step Transfer, SST, corresponding to the remainder of the genome. Expression of genesA1andA2is required for SST. DNA injection stops at a site known as the injection stop signal (iss) which is a cis acting site located in the large untranslated region of the Left Terminal Repeat (LTR). Theissregion is extremely complicated with many repeats, inverted repeats and palindromes. This report compares theissregions of 25 T5-like phages and shows that all have a common conserved structure including a series of 8 DnaA boxes arranged in a highly specific manner; reminiscent of the origin of replication(oriC)ofE. coli.DnaA protein, which binds to DnaA boxes, is a mostly membrane bound. A new, radically different, mechanism of T5 2-step injection is proposed whereby injecting T5 DNA stops at the plasma membrane due to the binding of theissDnaA boxes to membrane-bound DnaA protein. Injection of the SST continues later via the combined action of the A1 and A2 proteins which cleave the FST DNA at a site upstream (right) of theissregion, thereby liberating it. They also cleave the incoming SST DNA at the same site on the RTR thus facilitating circularisation of one complete genome via the cohesive ends. Circle formation protects the T5 DNA from the degradative action of the RecBCD nuclease and eventually leads to rolling circle DNA replication.
Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing
Authors: Blattman Sydney B. , Jiang Wenyan , Oikonomou Panos , Tavazoie Saeed
Published: December 2019

Despite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. While single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems, application of scRNA-seq to prokaryotes has been hindered by their extremely low mRNA abundance, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a low-cost, high-throughput, prokaryotic scRNA-seq pipeline that overcomes these technical obstacles. PETRI-seq uses in situ combinatorial indexing to barcode transcripts from tens of thousands of cells in a single experiment. PETRI-seq captures single cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and low bias, with median capture rates >200 mRNAs/cell for exponentially growing E. coli. These characteristics enable robust discrimination of cell-states corresponding to different phases of growth. When applied to wild-type S. aureus, PETRI-seq revealed a rare sub-population of cells undergoing prophage induction. We anticipate broad utility of PETRI-seq in defining single-cell states and their dynamics in complex microbial communities.
GHSR-1a is not Required for Ghrelin’s Anti-inflammatory and Fat-sparing Effects in Cancer Cachexia
Authors: Liu Haiming , Luo Jiaohua , Guillory Bobby , Chen Ji-an , Zang Pu , Yoeli Jordan K. , Hernandez Yamileth , Lee Ian (In-gi) , Anderson Barbara , Storie Mackenzie , Tewnion Alison , Garcia Jose M.
Published: December 2019

Adipose tissue (AT) atrophy is a hallmark of cancer cachexia contributing to increased morbidity/mortality. Ghrelin has been proposed as a treatment for cancer cachexia partly by preventing AT atrophy. However, the mechanisms mediating ghrelin’s effects are incompletely understood, including the extent to which its only known receptor, GHSR-1a, is required for these effects. This study characterizes the pathways involved in AT atrophy in the Lewis Lung Carcinoma (LLC)-induced cachexia model and those mediating the effects of ghrelin in Ghsr+/+ and Ghsr−/− mice. We show that LLC causes AT atrophy by inducing anorexia, and increasing AT inflammation, thermogenesis and energy expenditure. These changes were greater in Ghsr−/−. Ghrelin administration prevented LLC-induced anorexia only in Ghsr+/+, but prevented WAT inflammation and atrophy in both genotypes, although its effects were greater in Ghsr+/+. LLC-induced increases in BAT inflammation, WAT and BAT thermogenesis, and energy expenditure were not affected by ghrelin. In conclusion, ghrelin ameliorates WAT inflammation, fat atrophy and anorexia in LLC-induced cachexia. GHSR-1a is required for ghrelin’s orexigenic effect but not for its anti-inflammatory or fat-sparing effects.
Material aging causes centrosome weakening and disassembly during mitotic exit
Authors: Mittasch Matthäus , Tran Vanna M. , Rios Manolo U. , Fritsch Anatol W. , Enos Stephen J. , Gomes Beatriz Ferreira , Bond Alec , Kreysing Moritz , Woodruff Jeffrey B.
Published: December 2019

Centrosomes must resist microtubule-mediated forces for mitotic chromosome segregation. During mitotic exit, however, centrosomes are deformed and fractured by those same forces, which is a key step in centrosome disassembly. How the functional material properties of centrosomes change throughout the cell cycle, and how they are molecularly tuned remain unknown. Here, we used optically-induced flow perturbations to determine the molecular basis of centrosome strength and ductility in C. elegans embryos. We found that both properties declined sharply at anaphase onset, long before natural disassembly. This mechanical transition required PP2A phosphatase and correlated with inactivation of PLK-1 (Polo Kinase) and SPD-2 (Cep192). In vitro, PLK-1 and SPD-2 directly protected centrosome scaffolds from force-induced disassembly. Our results suggest that, prior to anaphase, PLK-1 and SPD-2 confer strength and ductility to the centrosome scaffold so that it can resist microtubule-pulling forces. In anaphase, centrosomes lose PLK-1 and SPD-2 and transition to a weak, brittle state that enables force-mediated centrosome disassembly.
Exploiting homologous recombination increases SATAY efficiency for loss- and gain-of-function screening
Authors: Michel Agnès H. , van Schie Sabine , Mosbach Andreas , Scalliet Gabriel , Kornmann Benoît
Published: December 2019

The analysis of large-scale transposon mutant libraries is becoming a method of choice for functional genomics in bacteria and fungi. We previously established SAturated Transposon Analysis in Yeast (SATAY) to uncover genes necessary for growth in any condition inS. cerevisiae(Michel et al., 2017). We present an improved version leveraging homologous recombination to increase transposition efficiency by a factor 10, allowing a single experimenter to rapidly perform several parallel screens. We demonstrate its potential by presenting (1) a comparison of the essential gene sets between two yeast laboratory backgrounds, (2) a comprehensive description of essential genes displaying phenotypic delays – we highlight their common features and propose plausible explanations for this phenomenon –, (3) a genome-wide analysis of loss- and gain-of-function mutations conferring sensitivity or resistance to a compendium of 9 anti-fungal compounds. This study highlights the power of this improved SATAY protocol for yeast functional- and pharmaco-genomics.
Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome
Authors: Cho Min-Hyung , Wrabl James O. , Taylor James , Hilser Vincent J.
Published: December 2019

Phosphorylation sites are hyper-abundant in the disordered proteins of eukaryotes, suggesting that conformational dynamics (or heterogeneity) may play a major role in determining to what extent a kinase interacts with a particular substrate. In biophysical terms, substrate selectivity may be determined not just by the structural and chemical complementarity between the kinase and its protein substrates, but also by the free energy difference between the conformational ensembles that are recognized by the kinase and those that are not. To test this hypothesis, we developed an informatics framework based on statistical thermodynamics, which allows us to probe for dynamic contributions to phosphorylation, as evaluated by the ability to predict Ser/Thr/ Tyr phosphorylation sites in the disordered proteome. Essential to this framework is a decomposition of substrate sequence information into two types: vertical information encoding conserved kinase specificity motifs and horizontal (distributed) information encoding substrate conformational dynamics that are embedded, but often not apparent, within position specific conservation patterns. We find not only that conformational dynamics play a major role, but that they are the dominant contribution to substrate selectivity. In fact, the main substrate classifier distinguishing selectivity is the magnitude of change in compaction of the disordered chain upon phosphorylation. Thus, in addition to providing fundamental insights into the underlying mechanistic consequences of phosphorylation across the entire proteome, our approach provides a novel statistical thermodynamic strategy for partitioning any sequence-based search into contributions from direct chemical and structural complementarity and those from changes in conformational dynamics. Using this framework, we developed a high-performance open-source phosphorylation site predictor, PHOSforUS, which is freely available athttps://github.com/bxlab/PHOSforUS.
Reversible Loss of Hippocampal Function in a Mouse Model of Demyelination/Remyelination
Authors: Das Aniruddha , Bastian Chinthasagar , Trestan Lexie , Suh Jason , Dey Tanujit , Trapp Bruce , Baltan Selva , Dana Hod
Published: December 2019

Demyelination of axons in the central nervous system (CNS) is a hallmark of multiple sclerosis (MS) and other demyelinating diseases. Cycles of demyelination, followed by remyelination, appear in the majority of MS patients, and are associated with the onset and quiescence of disease-related symptoms, respectively. Previous studies have shown in human patients and animal models that vast demyelination is accompanied by wide-scale changes to brain activity, but details of this process are poorly understood. We use electrophysiological recordings and nonlinear imaging of fluorescence from genetically-encoded calcium indicators to monitor the activity of hippocampal neurons during demyelination and remyelination processes over a period of 100 days. We find in vitro that synaptic transmission in CA1 neurons is diminished, and in vivo both CA1 and dentate gyrus (DG) neuronal firing rates are substantially reduced during demyelination and partially recover after a short remyelination period. This new approach allows monitoring how synaptic transmission changes, induced by cuprizone diet, are affecting neuronal activity, and can potentially be used to study the effects of therapeutic interventions in protecting the functionality of CNS neurons.
Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms
Authors: Yeh Yi-Chun , McNichol Jesse C. , Needham David M. , Fichot Erin B. , Fuhrman Jed A.
Published: December 2019

Universal SSU rRNA primers allow comprehensive quantitative profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show all rRNA gene relative gene abundances, they are rarely used due to concerns about length bias against 18S amplicons and bioinformatic challenges converting mixed 16S/18S sequences into amplicon sequence variants. We thus developed 16S and 18S rRNA mock communities and a bioinformatic pipeline to validate this three-domain approach. To test for length biases, we mixed eukaryotic and prokaryotic mocks before PCR, and found consistent two-fold underestimation of longer 18S sequences due to sequencing but not PCR bias. Using these mocks, we show universal V4-V5 primers (515Y/926R) outperformed eukaryote-specific V4 primers in observed vs. expected abundance correlations and sequences with single mismatches to the primer were strongly underestimated (3-8 fold). A year of monthly time-series data from a protist-enriched 1.2-80 μm size fraction yielded an average of 9% 18S, 17% chloroplast 16S, and 74% prokaryote 16S rRNA gene amplicons. These data demonstrate the potential for universal primers to generate quantitative and comprehensive microbiome profiles, although gene copy and genome size variability should be considered - as for any quantitative genetic analysis.
Neural speech restoration at the cocktail party: Auditory cortex recovers masked speech of both attended and ignored speakers
Authors: Brodbeck Christian , Jiao Alex , Hong L. Elliot , Simon Jonathan Z.
Published: December 2019

Humans are remarkably skilled at listening to one speaker out of an acoustic mixture of several speech sources. Two speakers are easily segregated, even without binaural cues, but the neural mechanisms underlying this ability are not well understood. One possibility is that early cortical processing performs a spectro-temporal decomposition of the acoustic mixture, allowing the attended speech to be reconstructed via optimally weighted recombinations that discount spectro-temporal regions where sources heavily overlap. Using human magnetoencephalography (MEG) responses to a two-talker mixture, we show evidence for an alternative possibility, in which early, active segregation occurs even for strongly spectro-temporally overlapping regions. Early (∼70 ms) responses to non-overlapping spectro-temporal features are seen for both talkers. When competing talkers’ spectro-temporal features mask each other, the individual representations persist, but they occur with a ∼20 ms delay. This suggests that the auditory cortex recovers acoustic features that are masked in the mixture, even if they occurred in the ignored speech. The existence of such noise-robust cortical representations, of features present in attended as well as ignored speech, suggests an active cortical stream segregation process, which could explain a range of behavioral effects of ignored background speech.
Environment affects specialisation of plants and pollinators
Authors: Cagua E. Fernando , Lustig Audrey , Tylianakis Jason M. , Stouffer Daniel B.
Published: December 2019

What determines whether or not a species is a generalist or a specialist? Evidence that the environment can influence species interactions is rapidly accumulating. However, a systematic link between environment and the number of partners a species interacts with has been elusive so far. Presumably, because environmental gradients appear to have contrasting effects on species depending on the environmental variable. Here, we test for a relationship between the stresses imposed by the environment, instead of environmental gradients directly, and species specialisation using a global dataset of plant-pollinator interactions. We found that the environment can play a significant effect on specialisation, even when accounting for community composition, likely by interacting with species’ traits and evolutionary history. Species that have a large number of interactions are more likely to focus on a smaller number of, presumably higher-quality, interactions under stressful environmental conditions. Contrastingly, the specialists present in multiple locations are more likely to broaden their niche, presumably engaging in opportunistic interactions to cope with increased environmental stress. Indeed, many apparent specialists effectively behave as facultative generalists. Overall, many of the species we analysed are not inherently generalist or specialist. Instead, species’ level of specialisation should be considered on a relative scale depending on where they are found and the environmental conditions at that location.
d-Lysergic acid diethylamide has major potential as a cognitive enhancer
Authors: Cini Felipe Augusto , Ornelas Isis , Marcos Encarni , Goto-Silva Livia , Nascimento Juliana , Ruschi Sergio , Salerno José , Karmirian Karina , Costa Marcelo , Sequerra Eduardo , de Araújo Dráulio , Tófoli Luis Fernando , Rennó-Costa César , Martins-de-Souza Daniel , Feilding Amanda , Rehen Stevens , Ribeiro Sidarta
Published: December 2019

Psychedelic agonists of serotonin receptors induce neural plasticity and synaptogenesis, but their potential to enhance learning remains uncharted. Here we show that a single dose of d-LSD, a potent serotonergic agonist, increased novel object preference in young and adult rats several days after treatment. d-LSD alone did not increase preference in old animals, but could rescue it to young levels when followed by a 6-day exposure to enriched environment (EE). Mass spectrometry-based proteomics in human brain organoids treated with d-LSD showed upregulation of proteins from the presynaptic active zone. A computational model of synaptic connectivity in the hippocampus and prefrontal cortex suggests that d-LSD enhances novelty preference by combining local synaptic changes in mnemonic and executive regions, with alterations of long-range synapses. Better pattern separation within EE explained its synergy with d-LSD in rescuing novelty preference in old animals. These results advance the use of d-LSD in cognitive enhancement.
Deep learning enables structured illumination microscopy with low light levels and enhanced speed
Authors: Jin Luhong , Liu Bei , Zhao Fenqiang , Hahn Stephen , Dong Bowei , Song Ruiyan , Elston Tim , Xu Yingke , Hahn Klaus M.
Published: December 2019

Using deep learning to augment structured illumination microscopy (SIM), we obtained a fivefold reduction in the number of raw images required for super-resolution SIM, and generated images under extreme low light conditions (100X fewer photons). We validated the performance of deep neural networks on different cellular structures and achieved multi-color, live-cell super-resolution imaging with greatly reduced photobleaching.
Gut-associated bacteria invade the midgut epithelium of Aedes aegypti and stimulate innate immunity and suppress Zika virus infection in cells
Authors: Hegde Shivanand , Voronin Denis , Casas-Sanchez Aitor , Saldaña Miguel A. , Heinz Eva , Acosta-Serrano Alvaro , Popov Vsevolod L. , Chopra Ashok K. , Hughes Grant L.
Published: December 2019

Microbiota within mosquitoes influence nutrition, immunity, fecundity, and the capacity to transmit pathogens. Despite their importance, we have a limited understanding of host-microbiota interactions, especially at the cellular level. It is evident bacterial symbionts that are localized within the midgut also infect other organs within the mosquito; however, the route these symbionts take to colonize other tissues is unknown. Here, utilizing the gentamicin protection assay, we showed that the bacterial symbionts Cedecea and Serratia have the capacity to invade and reside intracellularly within mosquito cells. Symbiotic bacteria were found within a vacuole and bacterial replication was observed in mosquito cell by transmission electron microscopy, indicating bacteria were adapted to the intracellular milieu. Using gene silencing, we determined that bacteria exploited host factors, including actin and integrin receptors, to actively invade mosquito cells. As microbiota can affect pathogens within mosquitoes, we examined the influence of intracellular symbionts on Zika virus (ZIKV) infection. Mosquito cells harbouring intracellular bacteria had significantly less ZIKV compared to uninfected cells or cells exposed to non-invasive bacteria. Intracellular bacteria were observed to substantially upregulate the Toll and IMD innate immune pathways, providing a possible mechanism mediating these anti-viral effects. Examining mono-axenically infected mosquitoes using transmission electron and fluorescent microscopy revealed that bacteria occupied an intracellular niche in vivo. Our results provided evidence that bacteria that associate with the midgut of mosquitoes have intracellular lifestyles which likely have implications for mosquito biology and pathogen infection. This study expands our understanding of host-microbiota interactions in mosquitoes, which is important as symbiont microbes are being exploited for vector control strategies.
Forecasting the potential distribution of the invasive vegetable leafminer using ‘top-down’ and ‘bottom-up’ models
Authors: Maino James L. , Pirtle Elia I. , Ridland Peter M. , Umina Paul A.
Published: December 2019

The vegetable leafminer, Liriomyza sativae, is an internationally significant pest of vegetable and flower crops, that was detected for the first time on the Australian mainland in 2015. Due to the early stage of its invasion in Australia, it is unclear how climatic conditions are likely to support and potentially restrict the distribution of L. sativae as it expands into a novel range and threatens agricultural production regions. Here we predicted the future establishment potential of L. sativae in Australia, using both a novel ‘bottom-up’ process-based model and a popular ‘top-down’ correlative species distribution model (SDM), leveraging the unique strengths of each approach. Newly compiled global distribution data spanning 42 countries was used to validate the process-based model of establishment potential based on intrinsic population growth rates, as well as parameterise the correlative SDM. Both modelling approaches successfully captured the international distribution of L. sativae based on environmental variables and predicted the high suitability of non-occupied ranges, including northern regions of Australia. The largely unfilled climatic niche available to L. sativae in Australia demonstrates the early stage of its Australian invasion, and highlights locations where important vegetable and nursery production regions in Australia are highly vulnerable to L. sativae establishment.
Changing the Waddington landscape to control mesendoderm competence
Authors: Valcourt James R. , Huang Roya , Kundu Sharmistha , Venkatasubramanian Divya , Kingston Robert E. , Ramanathan Sharad
Published: December 2019

As pluripotent human embryonic stem cells progress towards one germ layer fate, they lose the ability to adopt alternative fates. It is unknown how the cells’ competence for these alternative fates changes along their developmental trajectory or if this competence can be modulated. Here, we show that a differentiating stem cell’s probability of adopting a mesendodermal fate when given the appropriate signal falls sharply at a specific point along the ectodermal trajectory, and we further demonstrate that this point can be moved using genetic perturbations. Using a low-dimensional reaction coordinate to monitor progression towards ectoderm, we can determine the probability that individual cells at different points along this path can transition to the mesendodermal fate upon BMP4 and Activin A signal exposure. Knowing this probability allows us to prospectively isolate and profile differentiating cells based on their mesendoderm competence. Analysis and validation of these RNA-seq and ATAC-seq profiles identified transcription factors that can independently control the cell’s mesendoderm competence and its progression along the ectodermal developmental trajectory. In the classical picture of a Waddington landscape, these effects correspond to altering the barrier between fates and changing the cell’s location on the landscape, respectively. The ability of the underlying gene regulatory network to modulate these two aspects of the developmental landscape could allow separate control of the dynamics of differentiation and tissue size proportions.
Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic
Authors: Vihani Aashutosh , Hu Xiaoyang Serene , Gundala Sivaji , Koyama Sachiko , Block Eric , Matsunami Hiroaki
Published: December 2019

Abstract

Understanding how genes and experiences work in concert to generate phenotypic variability will provide a better understanding of individuality. Here, we considered this in the context of the main olfactory epithelium, a chemosensory structure with over a thousand distinct cell-types, in mice. We identified a subpopulation of at least three types of olfactory sensory neurons, defined by receptor expression, whose abundances were sexually dimorphic. This subpopulation of olfactory sensory neurons was over-represented in sex-separated female mice and responded robustly to the male-specific semiochemicals 2-sec-butyl-4,5-dihydrothaizole and (methylthio)methanethiol. Sex-combined housing led to a robust attenuation of the female over-representation. Testing of Bax null mice revealed a Bax-dependence in generating the sexual dimorphism in sex-separated mice. Altogether, our results suggest a profound role of experience in influencing homeostatic neural lifespan mechanisms to generate a robust sexually dimorphic phenotype in the main olfactory epithelium.
Juvenile hormone regulation on the flight capability of Bactrocera dorsalis (Diptera: Tephritidae)
Authors: Chen Peng , Chen Min , Ye Hui , Yuan Ruiling , Du Chunhua , Ong Su Ping
Published: December 2019

The oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), is considered a major economic threat in many regions worldwide. In order to better understand the flight capacity of B. dorsalis and its physiological basis, the functions and regulatory roles of juvenile hormone (JH) in the flight muscle of B. dorsalis were studied under a controlled environment. JH titer of B. dorsalis varied with age and sex. Females, irrespective of age, have higher JH than males for ovarian development and maturation in addition to better flight capabilities. The flight duration and distance of both males and females increased with the gradual increase of JH titer after adult emergences. JH titer peaked in 15-d-old adult and declined subsequently with age. Flight activity stimulated the production of JH as adults flown for 24 hours on the flight mills have the highest JH titers compare to adults tethered on shorter flight durations. Furthermore, JH III-treated adults were able to perform long-duration and long-distance flights. The mutual reinforcement of JH and flight activity provides fundamental understanding on the physiological aspects of the flight capability and dispersal, which facilitates strategies for the long-term control of this destructive pest.
Effect of Assembly Method on Nanoparticle Attachment Density, Growth Rate, and Motility of Nanoscale Bacteria Enabled Autonomous Drug Delivery System (NanoBEADS)
Authors: Zhan Ying , Fergusson Austin , McNally Lacey R. , Davis Richey M. , Behkam Bahareh
Published: December 2019

Microbial-mediated drug delivery systems have the potential to significantly enhance the efficacy of nanomedicine for cancer therapy through improved specificity and interstitial transport. The Nanoscale Bacteria-Enabled Autonomous Drug Delivery System (NanoBEADS) is a bacteria-based bio-hybrid drug delivery system designed to carry nanotherapeutics cargo deep into poorly vascularized cancerous tissue. The effect of bacteria-nanoparticle conjugation method and NanoBEADS assembly parameters (i.e., mixing method, volume, and duration) was investigated to maximize particle attachment density. The nanoparticle attachment capacity, viability, growth rate and motility of the original NanoBEADS and an antibody-free variant NanoBEADS were characterized and compared. It is found that the assembly parameters affect the attachment outcome and the binding mechanism impacts the attachment number, the growth rate and motility of NanoBEADS. The NanoBEADS platform provides an opportunity to load nanoparticles with different materials and sizes for applications beyond cancer therapy, such as imaging agents for high-resolution medical imaging.
Controlling the speed and trajectory of evolution with counterdiabatic driving
Authors: Iram Shamreen , Dolson Emily , Chiel Joshua , Pelesko Julia , Krishnan Nikhil , Güngör Özenç , Kuznets-Speck Benjamin , Deffner Sebastian , Ilker Efe , Scott Jacob G. , Hinczewski Michael
Published: December 2019

The pace and unpredictability of evolution are critically relevant in a variety of modern challenges: combating drug resistance in pathogens and cancer, understanding how species respond to environmental perturbations like climate change, and developing artificial selection approaches for agriculture. Great progress has been made in quantitative modeling of evolution using fitness landscapes, allowing a degree of prediction for future evolutionary histories. Yet fine-grained control of the speed and the distributions of these trajectories remains elusive. We propose an approach to achieve this using ideas originally developed in a completely different context – counterdiabatic driving to control the behavior of quantum states for applications like quantum computing and manipulating ultra-cold atoms. Implementing these ideas for the first time in a biological context, we show how a set of external control parameters (i.e. varying drug concentrations / types, temperature, nutrients) can guide the probability distribution of genotypes in a population along a specified path and time interval. This level of control, allowing empirical optimization of evolutionary speed and trajectories, has myriad potential applications, from enhancing adaptive therapies for diseases, to the development of thermotolerant crops in preparation for climate change, to accelerating bioengineering methods built on evolutionary models, like directed evolution of biomolecules.
A longitudinal study of perceived stress and cortisol responses in an undergraduate student population from India
Authors: Batabyal Anuradha , Bhattacharya Anindita , Thaker Maria , Mukherjee Shomen
Published: December 2019

Young adults entering into college experience immense shifts in both personal and professional environments and this may result in some of them experiencing a lot of stress and difficulty in coping with their new surroundings. Such potentially stressful events may trigger multiple psychological as well as physiological effects. The current study investigated multiple psychological parameters such as PSS14 (Perceived Stress Scale), K10 (distress scale) and positive mood measures, along with salivary cortisol levels, in a repeated measures longitudinal study of first year students (~ 19 years of age) enrolled at a residential college in India. Six salivary cortisol samples were collected over a one-year period from 20 students. On each sampling day, a questionnaire designed to evaluate (K10, PSS14 and Mood) psychological parameters was also administered.

Overall, men showed a significantly lower level of salivary cortisol compared to women. Men also showed a decrease in perceived stress (PSS14) and distress (K10) with time. However, women reported similar perceived stress and distress levels all year round. Academic stress was reported by the students to be the most important stressor, whereas financial stress was reported the least number of times by all participants. Our results suggest that men seem to have a better capability to adjust to the new environment of a residential program with time. In contrast, women show an elevation in salivary cortisol at the end of the semester (the final assessment stage) in spite of a continuous assessment curricular design. This study not only provides an important glimpse into the sex differences in stress response in the first one year of joining an undergraduate program, but it also provides a valuable longitudinal dataset from the Indian undergraduate student cohort which is lacking in literature.
Polymorphisms in Human Cytomegalovirus gO Exert Epistatic Influences on Cell-Free and Cell-To-Cell Spread, and Antibody Neutralization on gH Epitopes
Authors: Day Le Zhang , Stegmann Cora , Schultz Eric P. , Lanchy Jean-Marc , Yu Qin , Ryckman Brent J.
Published: December 2019

The human cytomegalovirus (HCMV) glycoproteins H and L (gH/gL) can be bound by either gO, or the UL128-131 proteins to form complexes that facilitate entry and spread and the complexes formed are important targets of neutralizing antibodies. Strains of HCMV vary considerably in the levels of gH/gL/gO and gH/gL/UL128-131 and this can impact infectivity and cell tropism. In this report, we investigated how natural interstrain variation in the amino acid sequence of gO influences the biology of HCMV. Heterologous gO recombinants were constructed in which 6 of the 8 alleles or genotypes (GT) of gO were analyzed in the backgrounds of strain TR and Merlin (ME). The levels of gH/gL complexes were not affected, but there were impacts on entry, spread and neutralization by anti-gH antibodies. AD169 (AD) gO (GT1a) drastically reduced cell-free infectivity of both strains on fibroblasts and epithelial cells. PHgO(GT2a) increased cell-free infectivity of TR in both cell types, but spread in fibroblasts was impaired. In contrast, spread of ME in both cell types was enhanced by Towne (TN) gO (GT4), despite similar cell-free infectivity. TR expressing TNgO(GT4) was resistant to neutralization by anti-gH antibodies AP86 and 14-4b, whereas ADgO(GT1a) conferred resistance to 14-4b, but enhanced neutralization by AP86. Conversely, ME expressing ADgO(GT1a) was more resistant to 14-4b. These results suggest; 1) mechanistically distinct roles for gH/gL/gO in cell-free and cell-to-cell spread, 2) gO isoforms can differentially shield the virus from neutralizing antibodies, and 3) effects of gO polymorphisms are epistatically dependent on other variable loci.

IMPORTANCE

Advances in HCMV population genetics have greatly outpaced understanding of the links between genetic diversity and phenotypic variation. Moreover, recombination between genotypes may shuffle variable loci into various combinations with unknown outcomes. UL74(gO) is an important determinant of HCMV infectivity, and one of the most diverse loci in the viral genome. By analyzing interstrain heterologous UL74(gO) recombinants, we show that gO diversity can have dramatic impacts on cell-free and cell-to-cell spread as well as on antibody neutralization and that the manifestation of these impacts can be subject to epistatic influences of the global genetic background. These results highlight the potential limitations of laboratory studies of HCMV biology that use single, isolated genotypes or strains.
Antagonistic plants preferentially target arbuscular mycorrhizal fungi that are highly connected to mutualistic plants
Authors: Gomes Sofia IF , Fortuna Miguel A , Bascompte Jordi , Merckx Vincent SFT
Published: December 2019

How antagonists – mycoheterotrophic plants that obtain carbon and soil nutrients from fungi – are integrated in the usually mutualistic arbuscular mycorrhizal networks is unknown. Here, we compare mutualistic and antagonistic plant associations with arbuscular mycorrhizal fungi and use network analysis to investigate fungal association preferences in the tripartite network.

We sequenced root tips from mutualistic and antagonistic plants in a tropical forest to assemble the combined tripartite network between mutualistic plants, mycorrhizal fungi, and antagonistic plants. We compared the fungal ecological similarity between mutualistic and antagonist networks, and searched for modules (an antagonistic and a mutualistic plant interacting with the same pair of fungi) to investigate whether pairs of fungi simultaneously linked to plant species from each interaction type were overrepresented throughout the network.

Antagonistic plants interacted with approximately half the fungi detected in mutualistic plants. Antagonists were indirectly linked to any of the detected mutualistic plants, and fungal pairwise ecological distances were correlated in both network types. Moreover, pairs of fungi sharing the same antagonistic and mutualistic plant species occurred more often than expected by chance.

We hypothesize that the maintenance of antagonistic interactions is maximized by targeting well-linked mutualistic fungi, thereby minimizing the risk of carbon supply shortages.
A new symbiotic lineage related toNeisseriaandSnodgrassellaarises from the dynamic and diverse microbiomes in sucking lice
Authors: Říhová Jana , Batani Giampiero , Rodríguez-Ruano Sonia M. , Martinů Jana , Nováková Eva , Hypša Václav
Published: December 2019

Phylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have experienced a complex history of symbiont acquisition, loss, and replacement during their evolution. By combining metagenomics and amplicon screening across several populations of two louse genera (PolyplaxandHoplopleura) we describe a novel louse symbiont lineage related toNeisseriaandSnodgrassella, and show its’ independent origin within dynamic lice microbiomes. While the genomes of these symbionts are highly similar in both lice genera, their respective distributions and status within lice microbiomes indicate that they have different functions and history. InHoplopleura acanthopus, theNeisseria-related bacterium is a dominant obligate symbiont universally present across several host’s populations, and seems to be replacing a presumably older and more degenerated obligate symbiont. In contrast, thePolyplaxmicrobiomes are dominated by the obligate symbiontLegionella polyplacis, with theNeisseria-related bacterium co-occurring only in some samples and with much lower abundance.
The virus integrations in gut microbes associated with dysbiosis of microbial community in tumorigenesis of colorectal carcinoma
Authors: Cui Boyu , Wang Xiaodan , Xu Wenqiu , Zheng Caihong , Cai Jun
Published: December 2019

Patients with colorectal cancer (CRC) have a different gut microbial and viral communities from healthy individuals. But little is known about the ways and functions of interaction of virus-bacteria, let alone its correlation with the aetiology of CRC. In this study we aimed to identify the association between the genetic integration of virusbacteria and the expansion of some microbial population during tumorigenesis of human colorectum. Using a gut metagenomics sequencing data of healthy controls, advanced adenoma and carcinoma patients, to our knowledge, we demonstrate for the first time that the viral genetic integrations in gut microbes tend to occur in CRC patients and are potentially associated with the carcinogenesis. We found that almost all of the genetic integrations were happened between bacteriophages and bacteria, which could be influenced by the abundance of the phage communities. Importantly, the integrations of phage-carried positive effective genes offered selective advantages to the commensal and potential pathogenic bacteria, as a result, potentially led to a microbial dysbiosis along with the increasing bacterial diversity in carcinoma patients. Consequently, our work opens a new way to understand the carcinogenicity in complex intestinal ecosystems.
Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Authors: Patrick Ralph , Humphreys David T. , Janbandhu Vaibhao , Oshlack Alicia , Ho Joshua W.K. , Harvey Richard P. , Lo Kitty K.
Published: December 2019

High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology. We validate Sierra by comparing cardiac scRNA-seq cell-types to bulk RNA-seq of matched populations, finding significant overlap in differential transcripts. Sierra detects differential transcript usage across human peripheral blood mononuclear cells and the Tabula Muris, and 3’UTR shortening in cardiac fibroblasts. Sierra is available at https://github.com/VCCRI/Sierra.
Early replacement of West Eurasian male Y chromosomes from the east
Authors: Hallast Pille , Agdzhoyan Anastasia , Balanovsky Oleg , Xue Yali , Tyler-Smith Chris
Published: December 2019

The genomes of humans outside Africa originated almost entirely from a single migration out ∼50,000-60,000 years ago1,2, followed closely by mixture with Neanderthals contributing ∼2% to all non-Africans3,4. However, the details of this initial migration remain poorly-understood because no ancient DNA analyses are available from this key time period, and present-day autosomal data are uninformative due to subsequent population movements/reshaping5. One locus, however, does retain extensive information from this early period: the Y-chromosome, where a detailed calibrated phylogeny has been constructed6. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations6,7. We show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to East/South-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model8,9, and thus informing and constraining models of the initial expansion.