bluuebunny/crossref_metadata_2025 huggingface dataset:
Elucidating cryptic sympatric speciation in terrestrial orchids
Authors: Pansarin Emerson R. , Ferreira Alessandro W.C.
Published: November 2019

PREMISE

Cryptic sympatric speciation occurs when closely related species arises with no geographic or spatial isolation. Since cryptic species can not usually be detected when investigations are based exclusively on classical plant taxonomy, molecular markers and integrative taxonomy are important tools to elucidate the identity of cryptic taxa.

METHODS

In this paper we aimed to provide a detailed investigation based on molecular data and experimental taxonomy conducted on populations of a plant model occurring inside mesophytic forests and a supposed cryptic sympatric species that is found in marshy areas. Furthermore, a phylogeny was reconstructed by using nrDNA and cpDNA sequences in order to ascertain the position of both sympatric species withinLiparis. The divergence among sequences of the putative cryptic sympatric species and related taxa was also verified based on DNA barcoding.

KEY RESULTS

Our results reveal cryptic sympatric speciation in the orchid genusLiparis. Differences in microhabitat, flowering phenology, morphology of leaves and flowers, and reproductive strategies support the taxon occurring in marshy areas is a cryptic species. The molecular analyses reveal the cryptic species is closely related toL. nervosa.

CONCLUSIONS

PaludalLiparisis a sympatric cryptic species distinguishable fromL. nervosaby differences in habitat, phenology and breeding system. Our conclusions are supported by the molecular investigations. The crypticLiparisemerges as sister toL. nervosa, within a clade with terrestrial habitat and plicate leaves. The discovery of sympatric cryptic speciation in orchids provides increase on the knowledge of diversification and reproductive isolation in flowering plants.
Glutamate and Dysconnection in the Salience Network: Neurochemical, Effective-connectivity, and Computational Evidence in Schizophrenia
Authors: Limongi Roberto , Jeon Peter , Mackinley Michael , Das Tushar , Dempster Kara , Théberge Jean , Bartha Robert , Wong Dickson , Palaniyappan Lena
Published: November 2019

In the dysconnection hypothesis, psychosis is caused by NMDA hypofunction resulting in aberrant network connectivity. Combining a cognitive-control task, functional magnetic resonance spectroscopy, and functional magnetic resonance imaging, we tested this hypothesis in the salience network of 20 first-episode psychosis (FEP) and 20 healthy control (HC) subjects. Across groups, glutamate concentration in the dorsal anterior cingulate cortex (dACC) was associated with higher and lower inhibitory connectivity in the dACC and in the anterior insula (AI) respectively. Crucially, glutamate concentration correlated negatively with the inhibitory influence on the excitatory neuronal population in the dACC of FEP subjects. Furthermore, aberrant computational parameters of the cognitive-control task performance were associated with aberrant inhibitory connections. Finally, the strength of connections from the dACC to the AI correlated negatively with severity of social withdrawal. These findings support a link between glutamate-mediated cortical disinhibition, deficits in effective connectivity, and computational performance in psychosis.
Local Glutamate-Mediated Dendritic Plateau Potentials Change the State of the Cortical Pyramidal Neuron
Authors: Gao Peng P. , Graham Joseph. W. , Zhou Wen-Liang , Jang Jinyoung , Angulo Sergio , Dura-Bernal Salvador , Hines Michael , Lytton William W. , Antic Srdjan D.
Published: November 2019

Dendritic spikes in thin dendritic branches (basal and oblique dendrites) of pyramidal neurons are traditionally inferred from spikelets measured in the cell body. Here, we used laser-spot voltage-sensitive dye imaging in cortical pyramidal neurons (rat brain slices) to investigate the voltage waveforms of dendritic potentials occurring in response to spatially-restricted glutamatergic inputs. Local dendritic potentials lasted 200–500 ms and propagated to the cell body where they caused sustained 10-20 mV depolarizations. Plateau potentials propagating from dendrite to soma, and action potentials propagating from soma to dendrite, created complex voltage waveforms in the middle of the thin basal dendrite, comprised of local sodium spikelets, local plateau potentials, and back-propagating action potentials, superimposed on each other. Our model replicated these experimental observations and made predictions, which were tested in experiments. Dendritic plateau potentials occurring in basal and oblique branches put pyramidal neurons into an activated neuronal state (“prepared state”), characterized by depolarized membrane potential and faster membrane responses. The prepared state provides a time window of 200-500 ms during which cortical neurons are particularly excitable and capable of following afferent inputs. At the network level, this predicts that sets of cells with simultaneous plateaus would provide cellular substrate for the formation of functional neuronal ensembles.

New & Noteworthy

In cortical pyramidal neurons, we recorded glutamate-mediated dendritic plateau potentials using voltage imaging, and created a computer model that recreated experimental measures from dendrite and cell body. Our model made new predictions, which were then tested in experiments. Plateau potentials profoundly change neuronal state -- a plateau potential triggered in one basal dendrite depolarizes the soma and shortens membrane time constant, making the cell more susceptible to firing triggered by other afferent inputs.
In vivocontrol ofToxoplasma gondiiby zebrafish macrophages
Authors: Yoshida Nagisa , Domart Marie-Charlotte , Yakimovich Artur , Mazon-Moya Maria J. , Collinson Lucy , Mercer Jason , Frickel Eva-Maria , Mostowy Serge
Published: November 2019

Toxoplasma gondiiis an obligate intracellular parasite capable of invading any nucleated cell. Three main clonal lineages (type I, II, III) exist and murine models have driven the understanding of general and strain-specific immune mechanisms underlyingToxoplasmainfection. However, murine models are limited for studying parasite-leukocyte interactionsin vivo, and discrepancies exist between cellular immune responses observed in mouse versus human cells. Here, we develop a zebrafish infection model to study the innate immune response toToxoplasma in vivo. By infecting the zebrafish hindbrain ventricle, and using high-resolution microscopy techniques coupled with computer vision driven automated image analysis, we reveal thatToxoplasmainvades and replicates inside a parasitophorous vacuole to which type I and III parasites recruit host cell mitochondria. We show that type II and III strains maintain a higher infectious burden than type I strains. To understand how parasites are being clearedin vivo, we analyzedToxoplasma-macrophage interactions using time-lapse and correlative light and electron microscopy. Strikingly, macrophages are recruited to the infection site and play a key role inToxoplasmacontrol. These results highlightin vivocontrol ofToxoplasmaby macrophages, and illuminate the possibility to exploit zebrafish for discoveries within the field of parasite immunity.
Concepts for structured illumination microscopy with extended axial resolution through mirrored illumination
Authors: Manton James D. , Ströhl Florian , Fiolka Reto , Kaminski Clemens F. , Rees Eric J.
Published: November 2019

Wide-field fluorescence microscopy, while much faster than confocal microscopy, suffers from a lack of optical sectioning and poor axial resolution. 3D structured illumination microscopy (SIM) has been demonstrated to provide optical sectioning and to double the resolution limit both laterally and axially, but even with this the axial resolution is still worse than the lateral resolution of unmodified wide-field microscopy. Interferometric schemes using two high numerical aperture objectives, such as 4Pi confocal and I5M microscopy, have improved the axial resolution beyond that of the lateral, but at the cost of a significantly more complex optical setup. Here, we investigate a simpler dual-objective scheme which we propose can be easily added to an existing 3D-SIM microscope, providing lateral and axial resolutions in excess of 125 nm with conventional fluorophores and without the need for interferometric detection.
Predicting glaucoma prior to its onset using deep learning
Authors: Thakur Anshul , Goldbaum Michael , Yousefi Siamak
Published: November 2019

Purpose

To assess the accuracy of deep learning models to predict glaucoma development from fundus photographs several years prior to disease onset.

Design

A deep learning model for prediction of glaucomatous optic neuropathy or visual field abnormality from color fundus photographs.

Participants

We retrospectively included 66,721 fundus photographs from 3,272 eyes of 1,636 subjects to develop deep leaning models.

Method

Fundus photographs and visual fields were carefully examined by two independent readers from the optic disc and visual field reading centers of the ocular hypertension treatment study (OHTS). When an abnormality was detected by the readers, subject was recalled for re-testing to confirm the abnormality and further confirmation by an endpoint committee. Using OHTS data, deep learning models were trained and tested using 85% of the fundus photographs and further validated (re-tested) on the remaining (held-out) 15% of the fundus photographs.

Main Outcome Measures

Accuracy and area under the receiver-operating characteristic curve (AUC).

Results

The AUC of the deep learning model in predicting glaucoma development 4-7 years prior to disease onset was 0.77 (95% confidence interval 0.75, 0.79). The accuracy of the model in predicting glaucoma development about 1-3 years prior to disease onset was 0.88 (0.86, 0.91). The accuracy of the model in detecting glaucoma after onset was 0.95 (0.94, 0.96).

Conclusions

Deep learning models can predict glaucoma development prior to disease onset with reasonable accuracy. Eyes with visual field abnormality but not glaucomatous optic neuropathy had a higher tendency to be missed by deep learning algorithms.
Androgen Receptor Signaling Regulates the Transcriptome of Prostate Cancer Cells by Modulating Global Alternative Splicing
Authors: Shah Kalpit , Gagliano Teresa , Garland Lisa , O’Hanlon Timothy , Bortolotti Daria , Gentili Valentina , Rizzo Roberta , Giamas Georgios , Dean Michael
Published: November 2019

Androgen receptor (AR), is a transcription factor and a member of a hormone receptor superfamily. AR plays a vital role in the progression of prostate cancer and is a crucial target for therapeutic interventions. While the majority of advanced-stage prostate cancer patients will initially respond to the androgen-deprivation, the disease often progresses to castrate-resistant prostate cancer (CRPC). Interestingly, CRPC tumors continue to depend on hyperactive AR signaling and will respond to potent second-line anti-androgen therapies, including bicalutamide (CASODEX®) and enzalutamide (XTANDI®). However, the progression-free survival rate for the CRPC patients on anti-androgen therapies is only 8 to 19 months. Hence, there is a need to understand the mechanisms underlying CRPC progression and eventual treatment resistance. Here, we have leveraged next-generation sequencing and newly developed analytical methodologies to evaluate the role of AR-signaling in regulating the transcriptome of prostate cancer cells. The genomic and pharmacologic stimulation- and inhibition-of AR activity demonstrates that AR regulates alternative splicing within cancer-relevant genes. Furthermore, by integrating transcriptomic data from in vitro experiments and in prostate cancer patients, we found that a significant number of AR-regulated splicing events are associated with tumor progression. For example, we found evidence for an inadvertent AR-antagonist mediated switch inIDH1andPL2G2Aisoform expression, which is associated with a decrease in overall survival of patients. Mechanistically, we discovered that the epithelial-specific splicing regulators (ESRP1 and ESRP2), flank many AR-regulated alternatively spliced exons. And, using 2D-invasion assays, we show that the inhibition of ESRPs can suppress AR-antagonist driven tumor invasion. In conclusion, until now, AR signaling has been primarily thought to modulate transcriptome of prostate epithelial cells by inducing or suppressing gene expression. Our work provides evidence for a new mechanism by which AR alters the transcriptome of prostate cancer cells by modulating alternative splicing. As such, our work has important implications for CRPC progression and development of resistance to treatment with bicalutamide and enzalutamide.
Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota
Authors: Minich Jeremiah J , Jantawongsri Khattapan , Johnston Colin , Bowie Kate , Bowman John , Knight Rob , Nowak Barbara , Allen Eric
Published: November 2019

Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, and commercial fishing through wild stock enhancements, and aquaculture production. Flow through (FT) hatcheries require more water than Recirculating-Aquaculture-Systems (RAS) which enable up to 99% of water to be recycled thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of the built environment of a hatchery from three Atl salmon hatcheries (RAS n=2, FT n=1). Six juvenile fish were sampled from tanks in each of the hatcheries for a total of 60 fish across 10 tanks. Water and tank side biofilm samples were collected from each of the tanks along with three salmon body sites (gill, skin, and digesta) to assess mucosal microbiota using 16S rRNA sequencing. The water and tank biofilm had more microbial richness than fish mucus while skin and digesta from RAS fish had 2× the richness of FT fish. Body sites each had unique microbial communities (P<0.001) and were influenced by the various hatchery systems (P<0.001) with RAS systems more similar. Water and especially tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin and digesta communities were more similar to the origin tank biofilm vs. all other experimental tanks suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome with the skin microbiome as an important intermediate.

IMPORTANCE

Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide with an annual production of 2,248 million metric tonnes in 2016. Salmon hatcheries are increasingly changing from flow through towards RAS design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies on hatcheries have focused either on the fish mucosal microbiota or the built environment microbiota, but have not combined the two to understand interactions. Our study evaluates how water and tank biofilm microbiota influences fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and furthermore how this can influence the fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for a beneficial phenotype.
The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere
Authors: Karasov Talia L. , Neumann Manuela , Duque-Jaramillo Alejandra , Kersten Sonja , Bezrukov Ilja , Schröppel Birgit , Symeonidi Efthymia , Lundberg Derek S. , Regalado Julian , Shirsekar Gautam , Bergelson Joy , Weigel Detlef
Published: November 2019

A central goal in microbiome research is to learn what distinguishes a healthy from a dysbiotic microbial community. Shifts in diversity and taxonomic composition are important indicators of dysbiosis, but a full understanding also requires knowledge of absolute microbial population sizes. In addition to the number of microbial cells, information on taxonomic composition can provide important insight into microbiome function and disease state. Here we use shotgun metagenomics to simultaneously assess microbiome composition and microbial load in the phyllosphere of wild populations of the plant Arabidopsis thaliana. We find that wild plants vary substantially in the load of colonizing microbes, and that high loads are typically associated with the proliferation of single taxa, with only a few putatively pathogenic taxa achieving high abundances in the field. Our results suggest (i) that the inside of a plant leaf is on average sparsely colonized with an estimated two bacterial genomes per plant genome and an order of magnitude fewer eukaryotic microbial genomes, and (ii) that higher levels of microbial cells often indicate successful colonization by pathogens. Lastly, our results show that load is a significant explanatory variable for loss of estimated Shannon diversity in phyllosphere microbiomes, implying that reduced diversity may be a significant predictor of microbial dysbiosis in a plant leaf.
Batch cultivation of non-transgenic males suitable for SIT programs
Authors: Das Siba , Maselko Maciej , Upadhyay Ambuj , Smanski Michael J.
Published: November 2019

The field performance of Sterile Insect Technique (SIT) is improved by sex-sorting and releasing only the sterile males. This can be accomplished by resource-intensive separation of males from females by morphology. Alternatively, sex-ratio biasing genetic constructs can be used to selectively kill one sex without the need for manual or automated sorting, but the resulting genetically engineered (GE) control agents would be subject to additional governmental regulation. Here we describe and demonstrate a method for the batch production of non-GE males that is applicable for sex-selective production of males suitable for genetic biocontrol programs. This method could be applied to generate the heterogametic sex (XY, or WZ) in any organism with chromosomal sex determination. We observed up to 100% sex-selection with batch cultures of more than 103individuals. Using a stringent transgene detection assay, we demonstrate the potential of mass rearing of transgene free males.
Detection of a novel African-lineage-like Zika virus naturally infecting free-living neotropical primates in Southern Brazil
Authors: de Almeida Paula Rodrigues , Ehlers Luiza Presser , Demoliner Meriane , Eisen Ana Karolina Antunes , Girardi Viviane , De Lorenzo Cíntia , Bianchi Matheus Viezzer , Mello Lauren , Pavarini Saulo Pettinati , Driemeier David , Sonne Luciana , Spilki Fernando Rosado
Published: November 2019

Mosquito borne flaviviruses cause a series of important diseases in humans and animals. These viruses are maintained in cycles involving replication in mosquito and in vertebrate hosts. Most natural hosts are vertebrate animals living in sylvatic or peridomestic environments. Human contact with these environments may result in host shifts that lead to the establishment of urban transmission cycles. Zika virus is aFlavivirusthat persists in nature in a transmission cycle involving non-human primates (NHP). Its recent emergence in Brazil has shed light upon the importance of surveying this agent in Brazilian sylvatic environments. Here we present histopathological and molecular evidence that free ranging howler monkeys (Alouatta guariba) in Southern Brazil are infected by ZIKV closely related to African lineage MR766. Nine NHP were nested RT-PCR positive for ZIKV RNA. Sequence analysis revealed 96 to 98% identity to ZIKV MR766 and 85% identity to ZIKV P6-740, the current epidemic strain. The affected howler monkeys presented discrete inflammatory infiltrates in several tissues and immunohistochemichal (IHC) labeling of viral antigen was observed in placenta. These findings point to the circulation of African lineage Zika virus in the Americas in non-human primates. And raises the possibility that ZIKV was introduced into the Americas on more than one occasion.
Dynamic macromolecular composition and high exudation rates inProchlorococcus
Authors: Roth-Rosenberg Dalit , Aharonovich Dikla , Omta Anne-Willem , Follows Michael J. , Sher Daniel
Published: November 2019

Every living cell is composed of macromolecules such as proteins, DNA, RNA and pigments. The ratio between these macromolecular pools depends on the allocation of resources within the organism to different physiological requirements, and in turn affects biogeochemical cycles of elements such as carbon, nitrogen and phosphorus. Here, we present detailed measurements of the macromolecular composition ofProchlorococcusMIT9312, a representative strain of a globally abundant marine primary producer, as it grows and declines due to nitrogen starvation in laboratory batch cultures. As cells reached stationary stage and declined, protein per cell decreased by ∼30% whereas RNA per cell and pigments per cell decreased by ∼75%. The decline stage was associated with the appearance of chlorotic cells which had higher forward scatter (a proxy for cell size) but lower chlorophyll autofluorescence, as well as with changes in photosynthetic pigment composition. Specifically, during culture decline divinyl-chlorophyll-like pigments emerged, which were not observed during exponential growth. These divinyl-chlorophyll-like pigments were also observed in natural samples from the Eastern Mediterranean. Around >80% of the carbon fixed byProchlorococcusMIT9312 (but not of a different strain, NATL2A) was released into the growth media as dissolved organic carbon under these laboratory conditions. Variations in RNA/protein indicate that, broadly defined, the macromolecular composition ofProchlorococcusMIT9312 is more similar to eukaryotic phytoplankton than to marine heterotrophic bacteria, possibly due to the significant investment in photosynthetic machinery of phototrophs.
Lymphatic metastases have more diverse roots than distant metastases
Authors: Reiter Johannes G. , Nagpal Shriya , Naxerova Kamila
Published: November 2019

Both lymphatic and distant metastases arise through cancer cell migration and colonization of ectopic sites. Nonetheless, the two metastasis types are associated with significantly different clinical outcomes, suggesting that distinct biological mechanisms may drive their formation. Here we show fundamental differences in the seeding patterns of lymphatic and distant metastases. Analyzing the reconstructed phylogenies of human colorectal cancers, we find that distant metastases typically are monophyletic, originating from one common ancestor. Lymphatic metastases, in contrast, are almost exclusively polyphyletic and can be seeded from many primary tumor regions. We develop a rigorous mathematical framework for quantifying the phylogenetic diversity of metastases while accounting for differential lesion sampling among patients. Our results indicate that a smaller fraction of primary tumor cells gives rise to distant metastases than lymphatic metastases. Thus, the two metastasis types exhibit profoundly distinct phylogenetic traits, indicating that different evolutionary mechanisms may drive their formation and influence their clinical behavior.
Selective protein O-GlcNAcylation in cells by a proximity-directed O-GlcNAc transferase
Authors: Ramirez Daniel H. , Aonbangkhen Chanat , Wu Hung-Yi , Naftaly Jeffrey A. , Tang Stephanie , O’Meara Timothy R. , Woo Christina M.
Published: November 2019

O-LinkedN-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Yet, the study of post-translational modifications like O-GlcNAc has been limited by the lack of strategies to induce O-GlcNAcylation on a target protein in cells. Here, we report a generalizable genetic strategy to induce O-GlcNAc to specific target proteins in cells using a nanobody as a proximity-directing agent fused to O-GlcNAc transferase (OGT). Fusion of a nanobody that recognizes GFP (nGFP) or a nanobody that recognizes the four-amino acid sequence EPEA (nEPEA) to OGT(4), a truncated form of OGT, yielded a nanobody-OGT(4) construct that selectively delivered O-GlcNAc to the target protein (e.g., JunB, cJun, Nup62) and reduced alteration of global O-GlcNAc levels in the cell. Quantitative chemical proteomics confirmed the selective increase in O-GlcNAc to the target protein by nanobody-OGT(4). Glycoproteomics revealed that nanobody-OGT(4) or full-length OGT produced a similar glycosite profile on the target protein. Finally, we demonstrate the ability to selectively target endogenous α-synuclein for glycosylation in HEK293T cells. Thus, the use of nanobodies to redirect OGT substrate selection is a versatile strategy to induce glycosylation of desired target proteins in cells that will facilitate discovery of O-GlcNAc functions and provide a mechanism to engineer O-GlcNAc signaling. The proximity-directed OGT approach for protein-selective O-GlcNAcylation is readily translated to additional protein targets and nanobodies that may constitute a generalizable strategy to control post-translational modifications in cells.

Significance Statement

Nature uses post-translational modifications (PTMs) like glycosylation as a mechanism to alter protein signaling and function. However, the study of these modified proteins in cells is confined to loss-of-function strategies, such as mutagenic elimination of the modification site. Here, we report a generalizable strategy for induction of O-GlcNAc to a protein target in cells. The O-GlcNAc modification is installed by O-GlcNAc transferase (OGT) to thousands of nucleocytoplasmic proteins. Fusion of a nanobody to OGT enables the selective increase of O-GlcNAc levels on a series of target proteins. The described approach will facilitate direct studies of O-GlcNAc and its regulatory enzymes and drive new approaches to engineer protein signaling via a strategy that may be conceptually translatable to additional PTMs.
The dynamic equilibrium of nascent and parental MCMs safeguards replicating genomes
Authors: Sedlackova Hana , Rask Maj-Britt , Gupta Rajat , Choudhary Chunaram , Somyajit Kumar , Lukas Jiri
Published: November 2019

The MCM2-7 (minichromosome maintenance) protein complex is a DNA unwinding motor required for the eukaryotic genome duplication1. Although a huge excess of MCM2-7 is loaded onto chromatin in G1 phase to form pre-replication complexes (pre-RCs), only 5-10 percent are converted into a productive CDC45-MCM-GINS (CMG) helicase in S phase – a perplexing phenomenon often referred to as the ‘MCM paradox’2. Remaining pre-RCs stay dormant but can be activated under replication stress (RS)3. Remarkably, even a mild reduction in MCM pool results in genome instability4, 5, underscoring the critical requirement for high-level MCM maintenance to safeguard genome integrity across generations of dividing cells. How this is achieved remains unknown. Here, we show that for daughter cells to sustain error-free DNA replication, their mothers build up a stable nuclear pool of MCMs both by recycling of chromatin-bound MCMs (referred to as parental pool) and synthesizing new MCMs (referred to as nascent pool). We find that MCMBP, a distant MCM paralog6, ensures the influx of nascent MCMs to the declining recycled pool, and thereby sustains critical levels of MCMs. MCMBP promotes nuclear translocation of nascent MCM3-7 (but not MCM2), which averts accelerated MCM proteolysis in the cytoplasm, and thereby fosters assembly of licensing-competent nascent MCM2-7 units. Consequently, lack of MCMBP leads to reduction of nascent MCM3-7 subunits in mother cells, which translates to poor MCM inheritance and grossly reduced pre-RCs formation in daughter cells. Unexpectedly, whereas the pre-RC paucity caused by MCMBP deficiency does not alter the overall bulk DNA synthesis, it escalates the speed and asymmetry of individual replisomes. This in turn increases endogenous replication stress and renders cells hypersensitive to replication perturbations. Thus, we propose that surplus of MCMs is required to safeguard replicating genomes by modulating physiological dynamics of fork progression through chromatin marked by licensed but inactive MCM2-7 complexes.
A genomic dating tool resolves the origins of ancient Eurasian genomes
Authors: Esposito U. , Holland G. , Alshehab G. , Dobre A. M. , Pirooznia M. , Brimacombe C. S. , Elhaik E.
Published: November 2019

Radiocarbon dating is the gold-standard in archaeology to estimate the age of skeletons, a key to studying their origins. Nearly half of all published ancient human genomes lack reliable and direct dates, which results in obscure and contradictory reports. Here, we developed the Temporal Population Structure (TPS), the first DNA-based dating method for ancient genomes ranging from the Upper Palaeolithic to modern-day samples and applied it to 1559 ancient Europeans, Asians, and Caucasus individuals and to 2117 modern worldwide individuals. We show that TPS predictions for dated skeletons align with their known dates and correctly account for kin relationships. The TPS-dating of poorly dated Eurasian samples resolves conflicts and sheds new light on disputed findings, as illustrated by four test cases. We discuss the phenotypic traits of the Time Informative Markers (TIMs) that underlie TPS.

TPS is a novel method to date humans from the Upper Palaeolithic to modern time from their DNA sequences.

Accurate dating is essential to the interepretation of paleogemonic data.. The gold-standard method in archaeology is radiocarbon dating1. However, a major limitation of radiocarbon dating is the high amount of collagen extraction (500 mg) involved in the process2. Consequently, half of all published ancient human genomes lack reliable and direct dates, which results in obscure and contradictory reports. Here, we present the Temporal Population Structure (TPS), the first genomic dating method for ancient genomes ranging from the Upper Palaeolithic to modern-day samples. We show that TPS predictions for 961 radiocarbon-dated Eurasian skeletons align with their known dates. We replicate these findings on 598 other Europeans, Asians and Caucasus individuals. Using kin-pairs, we demonstrate that TPS has produced more accurate results than radiocarbon and other dating. We show how our findings resolve conflicts and sheds new light on disputed findings as illustrated by four test cases. Finally, we discuss the phenotypic traits of the Time Informative Markers (TIMs) that underlie TPS. TPS is a novel dating technique, which can be used when radiocarbon dating is unfeasible or uncertain or to develop alternative hypotheses. TPS cannot be used for older (<14,000 years ago) samples, and its accuracy depends on the temporal and geographical breadth of radiocarbon-dated samples in the training dataset, though this limitation can be improved over time. Overall, TPS can improve the accuracy of archeological and paleogenomic studies.
Disinfection exhibits systematic impacts on the drinking water microbiome
Authors: Dai Zihan , Sevillano-Rivera Maria C. , Calus Szymon T. , Bautista-de los Santos Q. Melina , Eren A. Murat , van der Wielen Paul W.J.J. , Ijaz Umer Z. , Pinto Ameet J.
Published: November 2019

Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without the use of a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We utilized genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiomes across multiple full-scale drinking water systems utilizing these two-distinct microbial growth control strategies. Microbial communities cluster together at the structural- and functional potential-level based on the presence or absence of a disinfectant residual. Disinfectant residual concentrations alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including samples from multiple drinking water systems with variable source waters and source water communities, treatment strategies, and chemical compositions. The drinking water microbiome is structurally and functionally less diverse and less variable across disinfected systems as compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and γ-aminobutyrate metabolism in disinfected systems which may be associated with the recycling of amino acids. Metagenome-assembled genome-level analyses for a subset of phylogenetically related microorganisms suggests that disinfection may select for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic and consistent selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection inactivated microorganisms.
Single-molecule nanopore sensing of actin dynamics and drug binding
Authors: Wang Xiaoyi , Wilkinson Mark D. , Lin Xiaoyan , Ren Ren , Willison Keith , Ivanov Aleksandar P. , Baum Jake , Edel Joshua B.
Published: November 2019

Actin is a key protein in the dynamic processes within the eukaryotic cell. To date, methods exploring the molecular state of actin are limited to insights gained from structural approaches, providing a snapshot of protein folding, or methods that require chemical modifications compromising actin monomer thermostability. Nanopore sensing permits label-free investigation of native proteins and is ideally suited to study proteins such as actin that require specialised buffers and cofactors. Using nanopores we determined the state of actin at the macromolecular level (filamentous or globular) and in its monomeric form bound to inhibitors. We revealed urea-dependent and voltage-dependent transitional states and observed unfolding process within which sub-populations of transient actin oligomers are visible. We detected, in real-time, drug-binding and filament-growth events at the single-molecule level. This enabled us to calculate binding stoichiometries and to propose a model for protein dynamics using unmodified, native actin molecules, demostrating the promise of nanopores sensing for in-depth understanding of protein folding landscapes and for drug discovery.
High-resolution Introgressive Region Map Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication
Authors: Ohyanagi Hajime , Goto Kosuke , Negrão Sónia , Wing Rod A. , Tester Mark A. , McNally Kenneth L. , Bajic Vladimir B. , Mineta Katsuhiko , Gojobori Takashi
Published: November 2019

Domestication is anthropogenic evolution that fulfills mankind’s critical food demand. As such, elucidating the molecular mechanisms behind this process promotes the development of future new food resources including crops. With the aim of understanding the long-term domestication process of Asian rice and by employing the Oryza sativa subspecies (indica and japonica) as an Asian rice domestication model, we scrutinized past genomic introgressions between them as traces of domestication. Here we show the genome-wide introgressive region (IR) map of Asian rice, by utilizing 4,587 accession genotypes with a stable outgroup species, particularly at the finest resolution through a machine learning-aided method. The IR map revealed that 14.2% of the rice genome consists of IRs, including both wide IRs (recent) and narrow IRs (ancient). This introgressive landscape with their time calibration indicates that introgression events happened in multiple genomic regions over multiple periods. From the correspondence between our wide IRs and the so-called selective sweep regions, we provide a definitive answer to a long-standing controversy over the evolutionary origin of Asian rice domestication, single or multiple origins: It heavily depends upon which regions you pay attention to, implying that wider genomic regions represent immediate short history of Asian rice domestication as a likely support to the single origin, while its ancient history is interspersed in narrower traces throughout the genome as a possible support to the multiple origin.
Magnetic resonance image‐guided focal laser ablation in clinically localized prostate cancer: safety and efficacy
Authors: Al‐Hakeem Yasser , Raz Orit , Gacs Zita , Maclean Fiona , Varol Celi
Published: November 2019

Background

To evaluate the safety and efficacy of focal laser ablation (FLA) in low‐intermediate risk prostate cancer.

Methods

Inclusion criteria were men aged 50–75 years, prostate‐specific antigen (PSA) ≤15 ng/mL, clinical stage T1c–T2a, one or two lesions (PI‐RADS ≥3) on magnetic resonance imaging (MRI), and Gleason score 6 (>3 mm) or Gleason 7 on targeted biopsy. Treatment success was defined as no clinically significant cancer in ablated areas. The study is prospective. Under MRI guidance, laser ablation was applied to the visible lesion(s). International Prostate Symptoms Score, Sexual Health Inventory in Men score and PSA levels were assessed at baseline and repeated at 1, 3, 6, 12 and 18 months. MRI was repeated at 3 and 12 months. Cancer control was assessed at 6 months using targeted and systematic biopsies.

Results

FLA was performed in 49 patients. Gleason scores were 3 + 3 in 13 patients (26.5%), 3 + 4 in 29 (59.2%) and 4 + 3 in 7 (14.3%). No significant complications were noticed. International Prostate Symptoms Score measurements up to 18 months were not different from baseline (all P > 0.05). Sexual Health Inventory in Men scores dropped in the first year (all P < 0.05), but were not different from baseline levels at 18 months (P = 0.097). PSA levels dropped significantly at 3–18 months (all P < 0.05). Treatment was successful in 39 patients (79.6%). Persistent cancer in treated areas was found in 10 patients (20.4%).

Conclusions

FLA is safe with no impact on urinary and sexual functions at 18 months follow‐up. Oncologic control is encouraging. Larger scale studies and longer follow‐up are required.
The grade index model as a rationale for autogenic nonequilibrium responses of deltaic clinoform to relative sea‐level rise
Authors: Wang Junhui , Naruse Hajime , Muto Tetsuji
Published: November 2019

Grade index (Gindex) is a dimensionless number given as the volume‐in‐unit‐time ratio of subaerial allocation to both subaerial and subaqueous allocations of sediment supplied to a delta from upstream. It was originally proposed for understanding the effect of basin water depth on the morphodynamics of delta distributary channels under stationary relative sea level. We here examine how rising relative sea level modulates the Gindex, using geometrical reasoning and numerical simulations. We find that the grade index model can account for autoretreat of the deltaic shoreline, autodrowning of the whole system, and autobreak of the deltaic sedimentation, all of which are the consequences of autogenic nonequilibrium responses to steadily rising relative sea level. The regressive‐to‐transgressive threshold (i.e. the onset of autoretreat) is crossed when the delta plain's dimensionless basal area (At*) encounters a critical value that is expressed in terms of Gindex: regression and transgression are sustained when At* is below and above the threshold, respectively. The mode of transgression depends on the slope conditions. If the hinterland slope (γ) is steeper than the foreset slope (β), both At* and Gindex decrease as the relative sea‐level rises. Eventually, the depositional system experiences autodrowning when At* = Gindex = 0. If γ < β; on the other hand, both At* and Gindex increase. This latter slope condition eventually causes autobreak of the deltaic sedimentation, afterward of which At* = Gindex = 1. The grade index model is useful for interpreting and predicting the stratigraphic responses of natural deltaic clinoforms in conditions of rising relative sea level.
Cortical responses to tactile stimuli in preterm infants
Authors: Leikos Susanna , Tokariev Anton , Koolen Ninah , Nevalainen Päivi , Vanhatalo Sampsa
Published: November 2019

The conventional assessment of preterm somatosensory functions using averaged cortical responses to electrical stimulation ignores the characteristic components of preterm somatosensory evoked responses (SERs). Our study aimed to systematically evaluate the occurrence and development of SERs after tactile stimulus in preterm infants. We analysed SERs performed during 45 electroencephalograms (EEGs) from 29 infants at the mean post‐menstrual age of 30.7 weeks. Altogether 2,087 SERs were identified visually at single‐trial level from unfiltered signals capturing also their slowest components. We observed salient SERs with a high‐amplitude slow component at a high success rate after hand (95%) and foot (83%) stimuli. There was a clear developmental change in both the slow wave and the higher‐frequency components of the SERs. Infants with intraventricular haemorrhage (IVH; eleven infants) had initially normal SERs, but those with bilateral IVH later showed a developmental decrease in the ipsilateral SER occurrence after 30 weeks of post‐menstrual age. Our study shows that tactile stimulus applied at bedside elicits salient SERs with a large slow component and an overriding fast oscillation, which are specific to the preterm period. Prior experimental research indicates that such SERs allow studying both subplate and cortical functions. Our present findings further suggest that they might offer a window to the emergence of neurodevelopmental sequelae after major structural brain lesions and, hence, an additional tool for both research and clinical neurophysiological evaluation of infants before term age.
Survey on Bactrocera spp. (Tephritidae, Diptera) in Austria
Authors: Egartner A. , Lethmayer C. , Gottsberger R. A. , Blümel S.
Published: November 2019

Fruit fly species (Diptera: Tephritidae) of the genus Bactrocera are among the most serious orchard pests worldwide but are not native to Austria. The unexpected finding of one Bactrocera zonata adult in Vienna in 2011 initiated increasing survey efforts in Austria since 2012. Traps with male attracting lures were employed at several sites during the fruiting periods and catches were analysed. At sites in Vienna (urban area) Bactrocera specimens were trapped between 2012 and 2018, whereas no Bactrocera specimens were caught in agricultural areas or commercial orchards outside the city. Twelve specimens were identified as B. zonata and nine specimens as B. dorsalis sensu lato, though for the latter it was not possible to distinguish between B. dorsalis s.l. and B. carambolae using molecular analysis (ITS1). Molecular sequencing showed that the specimens caught were genetically different (with only a few exceptions), indicating genetically different origins. It is evident that the repeated findings of Bactrocera specimens in Vienna, where winter temperatures do not allow the establishment of tropical fruit flies, are linked to repeated entries of juveniles with infested fruits (in luggage or consignments). The results of our study reveal the need to strengthen phytosanitary import requirements for fruit commodities and travellers’ luggage in order to protect fruit production in Austria and probably in other countries.
Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori
Authors: Song He , Dharmasena Madushini N. , Wang Chao , Shaw Gary X. , Cherry Scott , Tropea Joseph E. , Jin Ding J. , Ji Xinhua
Published: November 2019

Rapid adaptation to environmental changes is crucial for bacterial survival. Almost all bacteria possess a conserved stringent response system to prompt transcriptional and metabolic responses toward stress. The adaptive process relies on alarmones, guanosine pentaphosphate (pppGpp), and tetraphosphate (ppGpp), to regulate global gene expression. The ppGpp is more potent than pppGpp in the regulatory activity, and pppGpp phosphohydrolase (GppA) plays a key role in (p)ppGpp homeostasis. Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX), which mediates the metabolism of cellular inorganic polyphosphate. Here, our phylogenetic analysis of PPX/GppA homologs in bacteria shows a wide distribution with several distinct subfamilies, and our structural and functional analysis of Escherichia coli GppA and Helicobacter pylori PPX/GppA reveals unique properties of each homolog. These results explain how each homolog possesses its distinct functionality.
Sequencing two Tyr::CreERT2 transgenic mouse lines
Authors: Aktary Zackie , Corvelo Andre , Estrin Camille , Larue Lionel
Published: November 2019

The Cre/loxP system is a powerful tool that has allowed the study of the effects of specific genes of interest in various biological settings. The Tyr::CreERT2 system allows for the targeted expression and activity of the Cre enzyme in the melanocyte lineage following treatment with tamoxifen, thus providing spatial and temporal control of the expression of specific target genes. Two independent transgenic mouse models, each containing a Tyr::CreERT2 transgene, have been generated and are widely used to study melanocyte transformation. In this study, we performed whole genome sequencing (WGS) on genomic DNA from the two Tyr::CreERT2 mouse models and identified their sites of integration in the C57BL/6 genome. Based on these results, we designed PCR primers to accurately, and efficiently, genotype transgenic mice. Finally, we discussed some of the advantages of each transgenic mouse model.
Zero Hunger and Sustainable Development Goals: Model of Food Bank Centre By Lembaga Zakat Negeri Kedah
Authors: Zainal Hafizah , Mustaffa Mohd Faisal , Othman Zakaria
Published: November 2019

Food banks are normally owned by non-profit organizations which responsible for distributes food items to a person or charitable organizations in need. The implementation of Food Bank Centre is very suitable as the Malaysia government’s focus to ease burden among the B40 group in 11th Malaysia Plan. In addition, Malaysia also focuses on Sustainable Development Goals (SDGs) whereby to ensure everyone can access food and end hunger by 2030. However, poverty rates are higher in rural area especially in Kedah, Malaysia. This article explores Model of Food Bank Centre offer to the needy and poor by Lembaga Zakat Negeri Kedah (LZNK). In 2019, The Food Bank covering 574 mosques in Kedah, to cover 17,220 families of the needy and poor in need to access food every month.  Maqasid shariah theory is used as a guideline and conjunction to implement the SDGs 2030 as maqasid syariah itself already highlight on the elements of SDGs. The result of this program created aid to the needy and the poor in term of virtuous and moral matters. Furthermore, it also gives a positive impact to stakeholder towards LZNK. Therefore, it is suggested stakeholders should engage and do a collaboration with LZNK in order to sustain supplying food for Food Bank Centre.