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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,351 bioRxiv papers from 296,600 authors.

Most tweeted bioRxiv papers, last 7 days

554 results found. For more information, click each entry to expand.

381: Cleavage-furrow formation without F-actin in Chlamydomonas
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Posted to bioRxiv 01 Oct 2019

Cleavage-furrow formation without F-actin in Chlamydomonas
1 tweet cell biology

Masayuki Onishi, James G Umen, Frederick R. Cross, John R. Pringle

It is widely believed that cleavage-furrow formation during cell division is driven by the contraction of a ring containing F-actin and type-II myosin. However, even in cells that have such rings, they are not always essential for furrow formation. Moreover, many taxonomically diverse eukaryotic cells divide by furrowing but have no type-II myosin, making it unlikely that an actomyosin ring drives furrowing. To explore this issue further, we have used one such organism, the green alga Chlamydomonas reinhardtii . We found that although F-actin is concentrated in the furrow region, none of the three myosins (of types VIII and XI) is localized there. Moreover, when F-actin was eliminated through a combination of a mutation and a drug, furrows still formed and the cells divided, although somewhat less efficiently than normal. Unexpectedly, division of the large Chlamydomonas chloroplast was delayed in the cells lacking F-actin; as this organelle lies directly in the path of the cleavage furrow, this delay may explain, at least in part, the delay in cell division itself. Earlier studies had shown an association of microtubules with the cleavage furrow, and we used a fluorescently tagged EB1 protein to show that at least the microtubule plus-ends are still associated with the furrows in the absence of F-actin, consistent with the possibility that the microtubules are important for furrow formation. We suggest that the actomyosin ring evolved as one way to improve the efficiency of a core process for furrow formation that was already present in ancestral eukaryotes.

382: Chemogenetic inhibition in the dorsal striatum reveals regional specificity of direct and indirect pathway control of action sequencing
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Posted to bioRxiv 07 Oct 2019

Chemogenetic inhibition in the dorsal striatum reveals regional specificity of direct and indirect pathway control of action sequencing
1 tweet neuroscience

Eric Garr, Andrew R. Delamater

Animals engage in intricate action sequences that are constructed during instrumental learning. There is broad consensus that the basal ganglia play a crucial role in the formation and fluid performance of action sequences. To investigate the role of the basal ganglia direct and indirect pathways in action sequencing, we virally expressed Cre-dependent Gi-DREADDs in either the dorsomedial (DMS) or dorsolateral (DLS) striatum during and/or after action sequence learning in D1 and D2 Cre rats. Action sequence performance in D1 Cre rats was slowed down early in training when DREADDs were activated in the DMS, but sped up when activated in the DLS. Acquisition of the reinforced sequence was hindered when DREADDs were activated in the DLS of D2 Cre rats. Outcome devaluation tests conducted after training revealed that the goal-directed control of action sequence rates was immune to chemogenetic inhibition—rats suppressed the rate of sequence performance when rewards were devalued. Sequence initiation latencies were generally sensitive to outcome devaluation, except in the case where DREADD activation was removed in D2 Cre rats that previously experienced DREADD activation in the DMS during training. Sequence completion latencies were generally not sensitive to outcome devaluation, except in the case where D1 Cre rats experienced DREADD activation in the DMS during training and test. Collectively, these results suggest that the indirect pathway originating from the DLS is part of a circuit involved in the effective reinforcement of action sequences, while the direct and indirect pathways originating from the DMS contribute to the goal-directed control of sequence completion and initiation, respectively.

383: Genome duplication in Leishmania major relies on DNA replication outside S phase
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Posted to bioRxiv 09 Oct 2019

Genome duplication in Leishmania major relies on DNA replication outside S phase
1 tweet microbiology

Jeziel Damasceno, Catarina Marques, Dario Beraldi, Kathryn Crouch, Craig Lapsley, Ricardo Obonaga, Luiz Tosi, Richard McCulloch

Once every cell cycle, DNA replication takes place to allow cells to duplicate their genome and segregate the two resulting copies into offspring cells. In eukaryotes, the number of DNA replication initiation loci, termed origins, is proportional to chromosome size. However, previous studies have suggested that in Leishmania, a group of single-celled eukaryotic parasites, DNA replication starts from just a single origin per chromosome, which is predicted to be insufficient to secure complete genome duplication within S phase. Here, we show that the paucity of origins activated in early S phase is balanced by DNA synthesis activity outside S phase. Simultaneous recruitment of acetylated histone H3 (AcH3), modified base J and the kinetochore factor KKT1 is exclusively found at the origins used in early S phase, while subtelomeric DNA replication can only be linked to AcH3 and displays persistent activity through the cell cycle, including in G2/M and G1 phases. We also show that subtelomeric DNA replication, unlike replication from the previously mapped origins, is sensitive to hydroxyurea and dependent on subunits of the 9-1-1 complex. Our work indicates that Leishmania genome transmission relies on an unconventional DNA replication programme, which may have implications for genome stability in this important parasite.

384: Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform specific start-loss mutations of essential genes can cause genetic diseases
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Posted to bioRxiv 10 Oct 2019

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform specific start-loss mutations of essential genes can cause genetic diseases
1 tweet genetics

Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M Berdowski, Ivan Capo, Herma C van der Linde, Paul van den Berg, Edwin H Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F.J. van IJcken, Walter G de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer F Kohler, Jonathan A. Bernstein, Kristin G Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik-Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcova, Faisal Zafar, Nuzhat Rana, Krishna K Kandaswamy, Jozef Hertecant, Peter Bauer, Stephanie Efthymiou, Henry Houlden, Aida M Bertoli-Avella, Reza Maroofian, Kyle Retterer, Alice S. Brooks, Tjakko J van Ham, Tahsin Stefan Barakat

Developmental and/or epileptic encephalopathies (DEEs) are a group of devastating genetic disorders, resulting in early onset, therapy resistant seizures and developmental delay. Here we report on 12 individuals from 10 families presenting with a severe form of intractable epilepsy, severe developmental delay, progressive microcephaly and visual disturbance. Whole exome sequencing identified a recurrent, homozygous variant (chr2:64083454A>G) in the essential UDP-glucose pyrophosphorylase (UGP2) gene in all probands. This rare variant results in a tolerable Met12Val missense change of the longer UGP2 protein isoform but causes a disruption of the start codon of the shorter isoform. We show that the absence of the shorter isoform leads to a reduction of functional UGP2 enzyme in brain cell types, leading to altered glycogen metabolism, upregulated unfolded protein response and premature neuronal differentiation, as modelled during pluripotent stem cell differentiation in vitro. In contrast, the complete lack of all UGP2 isoforms leads to differentiation defects in multiple lineages in human cells. Reduced expression of Ugp2a/Ugp2b in vivo in zebrafish mimics visual disturbance and mutant animals show a behavioral phenotype. Our study identifies a recurrent start codon mutation in UGP2 as a cause of a novel autosomal recessive DEE. Importantly, it also shows that isoform specific start-loss mutations causing expression loss of a tissue relevant isoform of an essential protein can cause a genetic disease, even when an organism-wide protein absence is incompatible with life. We provide additional examples where a similar disease mechanism applies.

385: Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication
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Posted to bioRxiv 10 Oct 2019

Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication
1 tweet microbiology

Jeziel Dener Damasceno, Joao Reis-Cunha, Kathryn Crouch, Craig Lapsley, Luiz Tosi, Daniella Bartholomeu, Richard McCulloch

Homologous recombination (HR) has an intimate relationship with genome replication, both during repair of DNA lesions that might prevent DNA synthesis and in tackling stalls to the replication fork. Recent studies led us to ask if HR might have a more central role in replicating the genome of Leishmania, a eukaryotic parasite. Conflicting evidence has emerged regarding whether or not HR genes are essential, and genome-wide mapping has provided evidence for an unorthodox organisation of DNA replication initiation sites, termed origins. To answer this question, we have employed a combined CRISPR/Cas9 and DiCre approach to rapidly generate and assess the effect of conditional ablation of RAD51 and three RAD51-related proteins in Leishmania major. Using this approach, we demonstrate that loss of any of these HR factors is not immediately lethal, but in each case growth slows with time and leads to DNA damage, accumulation of cells with aberrant DNA content, and genome-wide mutation. Despite these similarities, we show that only loss of RAD51 and RAD51-3 impairs DNA synthesis, and that the factors act in distinct ways. Finally, we reveal that loss of RAD51 has a profound effect on DNA replication, causing loss of initiation at the major origins and increased DNA synthesis at subtelomeres. Our work clarifies questions regarding the importance of HR to survival of Leishmania and reveals an unanticipated, central role for RAD51 in the programme of genome replication in a microbial eukaryote.

386: Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals
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Posted to bioRxiv 19 Oct 2019

Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals
1 tweet molecular biology

Jae-Hyun Yang, Patrick T. Griffin, Daniel L. Vera, John K. Apostolides, Motoshi Hayano, Margarita V. Meer, Elias L. Salfati, Qiao Su, Elizabeth M Munding, Marco Blanchette, Mital Bhakta, Zhixun Dou, Caiyue Xu, Jeffrey W. Pippin, Michael L. Creswell, Brendan L. O'Connell, Richard E. Green, Benjamin A Garcia, Shelley L Berger, Philipp Oberdoerffer, Stuart J. Shankland, Vadim N Gladyshev, Luis A. Rajman, Andreas R Pfenning, David A. Sinclair

All living things experience entropy, manifested as a loss of inherited genetic and epigenetic information over time. As budding yeast cells age, epigenetic changes result in a loss of cell identity and sterility, both hallmarks of yeast aging. In mammals, epigenetic information is also lost over time, but what causes it to be lost and whether it is a cause or a consequence of aging is not known. Here we show that the transient induction of genomic instability, in the form of a low number of non-mutagenic DNA breaks, accelerates many of the chromatin and tissue changes seen during aging, including the erosion of the epigenetic landscape, a loss of cellular identity, advancement of the DNA methylation clock and cellular senescence. These data support a model in which a loss of epigenetic information is a cause of aging in mammals.

387: Respiratory supercomplexes provide metabolic efficiency in zebrafish
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Posted to bioRxiv 25 Oct 2019

Respiratory supercomplexes provide metabolic efficiency in zebrafish
1 tweet physiology

Carolina Garcia-Poyatos, Sara Cogliati, Enrique Calvo, Pablo Hernansanz-Agustin, Sylviane Lagarrigue, Ricardo Magini, Marius Botos, Xavier Langa, Francesca Amati, Jesus Vazquez, Nadia Mercader, Jose Antonio Enriquez

The oxidative phosphorylation (OXPHOS) system is a dynamic system in which the respiratory complexes coexist with super-assembled quaternary structures called supercomplexes (SCs). The physiological role of SCs is still disputed. Here we used zebrafish to study the relevance of respiratory SCs. We combined immunodetection analysis and deep data-independent proteomics to characterize these structures and found similar SCs to those described in mice, as well as novel SCs including III2+IV2, I+IV and I+III2+IV2. To study the physiological role of SCs, we generated two null allele zebrafish lines for supercomplex assembly factor 1 (SCAF1). SCAF1-/- fish displayed altered OXPHOS activity due to the disrupted interaction of complex III and IV. SCAF1-/- fish were smaller in size, and showed abnormal fat deposition and decreased female fertility. These physiological phenotypes were rescued by doubling the food supply, which correlated with improved bioenergetics and alterations in the metabolic gene expression program. These results reveal that SC assembly by SCAF1 modulates OXPHOS efficiency and allows for the optimization of metabolic resources.

388: Multi-region exome sequencing of ovarian teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components
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Posted to bioRxiv 28 Oct 2019

Multi-region exome sequencing of ovarian teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components
1 tweet cancer biology

Michael B. Heskett, John Z. Sanborn, Christopher Boniface, Benjamin Goode, Jocelyn Chapman, Karuna Garg, Joseph T. Rabban, Charles Zaloudek, Stephen C. Benz, Paul T. Spellman, David A. Solomon, Raymond J. Cho

Immature teratoma is a subtype of malignant germ cell tumor of the ovary that occurs most commonly in the first three decades of life, frequently with bilateral ovarian disease. Despite being the second most common malignant germ cell tumor of the ovary, little is known about its genetic underpinnings. Here we performed multi-region whole exome sequencing to interrogate the genetic zygosity, clonal relationship, DNA copy number, and mutational status of 52 pathologically distinct tumor components from 10 females with ovarian immature teratomas, with bilateral tumors present in 5 cases and peritoneal dissemination in 7 cases. We found that ovarian immature teratomas are genetically characterized by 2N near-diploid genomes with extensive loss of heterozygosity and an absence of genes harboring recurrent somatic mutations or known oncogenic variants. All components within a single ovarian tumor (immature teratoma, mature teratoma with different histologic patterns of differentiation, and yolk sac tumor) were found to harbor an identical pattern of loss of heterozygosity across the genome, indicating a shared clonal origin. In contrast, the 4 analyzed bilateral teratomas showed distinct patterns of zygosity changes in the right versus left sided tumors, indicating independent clonal origins. All disseminated teratoma components within the peritoneum (including gliomatosis peritonei) shared a clonal pattern of loss of heterozygosity with either the right or left primary ovarian tumor. The observed genomic loss of heterozygosity patterns indicate that diverse meiotic errors contribute to the formation of ovarian immature teratomas, with 11 out of the 15 genetically distinct clones determined to result from the failure of meiosis I or II. Overall, these findings suggest that copy-neutral loss of heterozygosity resulting from meiotic abnormalities may be sufficient to generate ovarian immature teratomas from germ cells.

389: Land productivity dynamics in and around protected areas globally from 1999 to 2013
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Posted to bioRxiv 28 Oct 2019

Land productivity dynamics in and around protected areas globally from 1999 to 2013
1 tweet ecology

Begoña de la Fuente, Mélanie Weynants, Bastian Bertzky, Giacomo Delli, Andrea Mandrici, Eduardo Garcia Bendito, Gregoire Dubois

Tracking changes in total biomass production or land productivity is an essential part of monitoring land transformations and long-term alterations of the health and productive capacity of land that are typically associated with land degradation. Persistent declines in land productivity impact many terrestrial ecosystem services that form the basis for sustainable livelihoods of human communities. Protected areas (PAs) are a key strategy in global efforts to conserve biodiversity and ecosystem services that are critical for human well-being, and cover about 15% of the land worldwide. Here we globally assess the trends in land productivity in PAs of at least 10 km2 and in their unprotected surroundings (10 km buffers) from 1999 to 2013. We quantify the percentage of the protected and unprotected land that shows stable, increasing or decreasing trends in land productivity, quantified as long-term (15 year) changes in above-ground biomass derived from satellite-based observations with a spatial resolution of 1 km. We find that 44% of the land in PAs globally has retained the productivity at stable levels from 1999 to 2013, compared to 42% of stable productivity in the unprotected land around PAs. Persistent increases in productivity are more common in the unprotected lands around PAs (32%) than within PAs (18%) globally, which may be related to more active management and vegetation cover changes in some of these unprotected lands. About 14% of the protected land and 12% of the unprotected land around PAs has experienced declines in land productivity from 1999 to 2013 globally. Oceania has the highest percentage of land with stable productivity in PAs (57%) followed by Asia (52%). Europe is the continent with the lowest percentage of land with stable productivity levels in PAs (38%) and with the largest share of protected land with increasing land productivity (32%), which may be related to the high population density and share of agricultural land within PAs as well as to rural land abandonment processes in many regions of Europe. In conclusion, we provide a relevant indicator and assessment of land productivity dynamics that contributes to characterise the state, pressures and changes in and around protected areas globally. Further research may focus on more detailed analyses to disentangle the relative contribution of specific drivers (from climate change to land use change) and their interaction with land productivity dynamics and potential land degradation in different regions of the world.

390: Neuronal transcriptome analyses reveal novel neuropeptide modulators of excitation and inhibition imbalance in C. elegans
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Posted to bioRxiv 28 Oct 2019

Neuronal transcriptome analyses reveal novel neuropeptide modulators of excitation and inhibition imbalance in C. elegans
1 tweet genetics

Katherine A. McCulloch, Kingston Zhou, Yishi Jin

Neuropeptides are secreted molecules that have conserved roles modulating many processes, including mood, reproduction, and feeding.  Dysregulation of neuropeptide signaling is also implicated in neurological disorders such as epilepsy. However, much is unknown about the mechanisms regulating specific neuropeptides to mediate behavior. Here, we report that the expression levels of dozens of neuropeptides are up-regulated in response to circuit activity imbalance in C. elegans . acr-2 encodes a homolog of human nicotinic receptors, and functions in the cholinergic motoneurons. A hyperactive mutation, acr-2(gf), causes an activity imbalance in the motor circuit. We performed cell-type specific transcriptomic analysis and identified genes differentially expressed in acr-2(gf) , compared to wild type. The most over-represented class of genes are neuropeptides, with insulin-like-peptides (ILPs) the most affected. Moreover, up-regulation of neuropeptides occurs in motoneurons, as well as sensory neurons.  In particular, the induced expression of the ILP ins-29 occurs in the BAG neurons, which are previously shown to function in gas-sensing. We also show that this up-regulation of ins-29 in acr-2(gf) animals is activity-dependent.  Our genetic and molecular analyses support cooperative effects for ILPs and other neuropeptides in promoting motor circuit activity in the acr-2(gf) background. Together, this data reveals that a major transcriptional response to motor circuit dysregulation is in up-regulation of multiple neuropeptides, and suggests that BAG sensory neurons can respond to intrinsic activity states to feedback on the motor circuit.

391: Host-microbiome protein-protein interactions capture mechanisms in human disease
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Posted to bioRxiv 29 Oct 2019

Host-microbiome protein-protein interactions capture mechanisms in human disease
1 tweet microbiology

Juan Felipe Beltran, Ilana Brito

Host-microbe interactions are crucial for normal physiological and immune system development and are implicated in a wide variety of diseases, including inflammatory bowel disease (IBD), obesity, colorectal cancer (CRC), and type 2 diabetes (T2D). Despite large-scale case-control studies aimed at identifying microbial taxa or specific genes involved in pathogeneses, the mechanisms linking them to disease have thus far remained elusive. To better identify potential mechanisms linking human-associated bacteria with host health, we leveraged publicly-available interspecies protein-protein interaction (PPI) data to identify clusters of homologous microbiome-derived proteins that bind human proteins. By detecting human-interacting bacterial genes in metagenomic case-control microbiome studies and applying a tailored machine learning algorithm, we are able to identify bacterial-human PPIs strongly linked with disease. In 9 independent case studies, we discover the microbiome broadly targets human immune, oncogenic, apoptotic, and endocrine signaling pathways, among others. This host-centric analysis strategy illuminates human pathways targeted by the commensal microbiota, provides a mechanistic hypothesis-generating platform for any metagenomics cohort study, and extensively annotates bacterial proteins with novel host-relevant functions.

392: Reanalysis and Integration of Public Microarray Datasets Reveals Novel Host Genes Modulated in Leprosy
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Posted to bioRxiv 30 Oct 2019

Reanalysis and Integration of Public Microarray Datasets Reveals Novel Host Genes Modulated in Leprosy
1 tweet genomics

Thyago Leal-Calvo, Milton Ozório Moraes

Background Leprosy is an insidious disease caused primarily by mycobacteria. The difficulties in culturing this slow-growing bacteria together with the chronic progression of the disease have hampered the development of accurate methods for diagnosis. Host gene expression profiling is an important tool to assess overall tissue activity, whether in health or disease conditions. High-throughput gene expression experiments have become popular over the last decade or so, and public databases have been created to easily store and retrieve these data. This has enabled researchers to reuse and reanalyze existing datasets with the aim of generating novel and or more robust information. In this work, after a systematic search, nine microarray datasets evaluating host gene expression in leprosy were reanalyzed and the information was integrated to strengthen evidence of differential expression for several genes. Results Reanalysis of individual datasets revealed several differentially expressed genes (DEGs). Then, five integration methods were tested, both at the P-value and effect size level. In the end, random effects model ( REM ) and ratio association ( sdef ) were selected as the main methods to pinpoint DEGs. Overall, some classic gene/pathways were found corroborating previous findings and validating this approach for analysis. Also, various original DEGs related to poorly understood processes in leprosy were described. Nevertheless, some of the novel genes have already been associated with leprosy pathogenesis by genetic or functional studies, whilst others are, as yet, unrelated or poorly studied in these contexts. Conclusions This study reinforces evidences of differential expression of several genes and presents novel genes and pathways associated with leprosy pathogenesis. Altogether, these data are useful in better understanding host responses to the disease and, at the same time, provide a list of potential host biomarkers that could be useful in complementing leprosy diagnosis based on transcriptional levels. * sdef : ratio association method REM : random effects model rOP : r-th ordered p-value maxP : maximum P-value SR : sum of ranks MB : multibacillary leprosy PB : paucibacillary leprosy DEG : differentially expressed gene FDR : false discovery rate BH : Benjamini-Hochberg LL : lepromatous lepromatous leprosy ENL : erythema nodosum leprosum BT : borderline-tuberculoid FC : fold change GEO : Gene Expression Omnibus NCBI : National Center for Biotechnology Information

393: A geostatistical approach to modelling human Holocene migrations in Europe using ancient DNA
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Posted to bioRxiv 31 Oct 2019

A geostatistical approach to modelling human Holocene migrations in Europe using ancient DNA
1 tweet evolutionary biology

Fernando Racimo, Jessie Woodbridge, Ralph Fyfe, Martin Sikora, Karl-Goran Sjogren, Kristian Kristiansen, Marc Vander Linden

The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants, via admixture and population replacement processes. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. Here, we use a combination of paleogenomics and geostatistical modelling to produce detailed maps of the movement of these populations over time and space, and to understand how these movements impacted the European vegetation landscape. We find that the dilution of hunter-gatherer ancestries and the Yamnaya steppe migration coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture lands in the continent. We also show that climate played a role in these vegetational changes. Additionally, we find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings based on patterns of the cultural spread of farming from radiocarbon-dated archaeological sites. With thousands of ancient genomes publicly available and in production, we foresee that the integration of ancient DNA with geostatistical techniques and large-scale archaeological datasets will revolutionize the study of ancient populations movements, and their effects on local fauna and flora.

394: Evaluation of haplotype callers for next-generation sequencing of viruses
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Posted to bioRxiv 01 Nov 2019

Evaluation of haplotype callers for next-generation sequencing of viruses
1 tweet bioinformatics

Anton Eliseev, Keylie M Gibson, Pavel M Avdeyev, Dmitry Novik, Matthew L. Bendall, Marcos Pérez-Losada, Nikita Alexeev, Keith A Crandall

Currently, the standard practice for assembling next-generation sequencing (NGS) reads of viral genomes is to summarize thousands of individual short reads into a single consensus sequence, thus confounding useful intra-host diversity information for molecular phylodynamic inference. It is hypothesized that a few viral strains may dominate the intra-host genetic diversity with a variety of lower frequency strains comprising the rest of the population. Several software tools currently exist to convert NGS sequence variants into haplotypes. However, previous studies suggest that current approaches of haplotype reconstruction greatly underestimate intra-host diversity. Here, we tested twelve NGS haplotype reconstruction methods using viral populations simulated under realistic evolutionary dynamics. Parameters for the simulated data spanned known fast evolving viruses (e.g., HIV-1) diversity estimates to test the limits of the haplotype reconstruction methods and ensured coverage of predicted intra-host viral diversity levels. Using those parameters, we simulated HIV-1 viral populations of 216-1,185 haplotypes per host at a frequency <7%. All twelve investigated haplotype callers showed variable performance and produced drastically different results that were mainly driven by differences in mutation rate and, to a lesser extent, in effective population size. Most methods were able to accurately reconstruct haplotypes when genetic diversity was low. However, under higher levels of diversity (e.g., those seen intra-host HIV-1 infections), haplotype reconstruction accuracy was highly variable and, on average, poor. High diversity levels led to severe underestimation of, with a few tools greatly overestimating, the true number of haplotypes. PredictHaplo and PEHaplo produced estimates close to the true number of haplotypes, although their haplotype reconstruction accuracy was worse than that of the other ten tools. We conclude that haplotype reconstruction from NGS short reads is unreliable due to high genetic diversity of fast-evolving viruses. Local haplotype reconstruction of longer reads to phase variants may provide a more reliable estimation of viral variants within a population.

395: FtsK in motion reveals its mechanism for double-stranded DNA translocation
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Posted to bioRxiv 01 Nov 2019

FtsK in motion reveals its mechanism for double-stranded DNA translocation
1 tweet molecular biology

Nicolas L. Jean, Trevor J. Rutherford, Jan Löwe

FtsK protein contains a fast DNA motor involved in bacterial chromosome dimer resolution. To understand how FtsK moves DNA, we solved the 3.6 Å resolution cryo-EM structure of the motor domain of FtsK while translocating double-stranded DNA. Each subunit of the hexameric ring adopts a unique conformation and one of three nucleotide states. Two DNA-binding loops within four subunits form a pair of spiral staircases within the ring, interacting with the two DNA strands. This suggests that simultaneous conformational changes in all ATPase domains at each catalytic step generate movement through a mechanism related to filament treadmilling. While the ring is only rotating around the DNA slowly, it is instead the conformational states that rotate around the ring as the DNA substrate is pushed through.

396: Maternal Odor Reduces the Neural Threat Response in Human Infants
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Posted to bioRxiv 01 Nov 2019

Maternal Odor Reduces the Neural Threat Response in Human Infants
1 tweet neuroscience

Sarah Jessen

Maternal odor is known to play an important role in mother-infant-interaction in many altricial species such as rodents. However, we only know very little about its role in early human development. The present study therefore investigated the impact of maternal odor on infant brain responses to threat signals. We recorded the electroencephalographic (EEG) signal of seven-month-old infants watching happy and fearful facial expressions. While infants in two control groups showed the expected EEG fear response, this response was markedly absent in the group exposed to their mother's odor. Thus, infants respond differently to fear signals in the presence of their mother and the mother's odor is a sufficiently strong signal to elicit this effect. Our data suggest that olfaction, a sensory modality that has been largely neglected as a social signal in our own species, might function as a crucial modulator in early social learning.

397: Functional role of respiratory supercomplexes in mice: segmentation of the Qpool and SCAF1
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Posted to bioRxiv 02 Nov 2019

Functional role of respiratory supercomplexes in mice: segmentation of the Qpool and SCAF1
1 tweet molecular biology

Enrique Calvo, Sara Cogliati, Pablo Hernansanz-Agustin, Marta Loureiro-Lopez, Adela Guaras, Rafael A Casuso, Fernando Garcia-Marques, Rebeca Acin-Perez, Yolanda Marti-Mateos, Juan Carlos Silla-Castro, Marta Carro-Alvarellos, Jesus R Huertas, Jesus Vazquez, Jose Antonio Enriquez

Mitochondrial respiratory complexes assemble into different forms of supercomplexes (SC). In particular, SC III2+IV require the SCAF1 protein. However, the structural role of this factor in the formation of the respirasome (I+III2+IV) and the physiological role of SCs are controversial. Here, we study C57BL/6J mice harbouring either non-functional SCAF1, the full knock-out for SCAF1 or the wild-type version of the protein, and found a growth and exercise phenotype due to the lack of functional SCAF1. By combining quantitative data-independent proteomics, high resolution 2D Blue Native Gel Electrophoresis and functional analysis of enriched respirasome fractions, we show that SCAF1 confers structural attachment between III2 and IV within the respirasome, increases NADH-dependent respiration and reduces ROS production. Furthermore, through the expression of AOX in cells and mice we confirm that CI-CIII superassembly segments the CoQ in two pools and modulates CI-NADH oxidative capacity. These data demonstrate that SC assembly, regulated by SCAF1, modulates the functionality of the electron transport chain.

398: CTP synthase forms cytoophidia in archaea
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Posted to bioRxiv 04 Nov 2019

CTP synthase forms cytoophidia in archaea
1 tweet cell biology

Shuang Zhou, Hua Xiang, Ji-Long Liu

CTP synthase (CTPS) is an important metabolic enzyme that catalyzes the rate-limiting reaction of de novo synthesis of the nucleotide CTP. Since 2010, a series studies have demonstrated that CTPS can form filamentous structures termed cytoophidia in bacteria and eukaryotes. However, it remains unknown whether cytoophidia exist in archaea, the third domain of life. Using Haloarcula hispanica as a model system, here we demonstrate that CTPS forms distinct intracellular compartments in archaeal cells. Under stimulated emission depletion (STED) microscopy, we find that those HhCTPS compartments are elongated filamentous structure, resembling cytoophidia in bacteria and eukaryotes. When Haloarcula cells cultured in low-salt medium, the occurrence of cytoophidia increases dramatically. Moreover, overexpression CTPS or glutamine analog treatment promote cytoophidium assembly in H. hispanica. Our study reveals that CTPS forms cytoophidia in all three domains of life, suggesting that forming cytoophidia is an ancient property of CTPS.

399: The impact of reporter kinetics on the interpretation of data gathered with fluorescent reporters
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Posted to bioRxiv 07 Nov 2019

The impact of reporter kinetics on the interpretation of data gathered with fluorescent reporters
1 tweet neuroscience

Bernardo Sabatini

Fluorescent reporters of biological functions are used to monitor biochemical events and signals in cells and tissue. For neurobiology, these have been particularly useful for monitoring signals in the brains of behaving animals. In order to enhance signal-to-noise, fluorescent reporters typically have kinetics that are slower than that of the underlying biological process. This low-pass filtering by the reporter renders the fluorescence transient a leaking integrated version of the biological signal. Here I discuss the effects that low-pass filtering, or more precisely of integrating by convolving with an exponentially decaying kernel, has on the interpretation of the relationship between the reporter fluorescence transient and the events that underlie it. Unfortunately, when the biological events being monitored are impulse-like, such as the firing of an action potential or the release of neurotransmitter, filtering greatly reduces the maximum correlation coefficient that can be found between the events and the fluorescence signal. This can erroneously support the conclusion that the fluorescence transient and the biological signal that it reports are only weakly related. Furthermore, when examining the encoding of behavioral state variables by nervous system, filtering by the reporter kinetics will favor the interpretation that fluorescence transients encode integrals of measured variables as opposed to the variables themselves. For these reasons, it is necessary to take into account the filtering effects of the indicator by deconvolving with the convolution kernel and recovering the underlying biological events before making conclusions about what is encoded in the signals emitted by fluorescent reporters.

400: Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure
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Posted to bioRxiv 07 Nov 2019

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure
1 tweet genomics

Netha Ulahannan, Matthew Pendleton, Aditya S Deshpande, Stefan Schwenk, Julie M. Behr, Xiaoguang Dai, Carly Tyer, Priyesh Rughani, Sarah Kudman, Emily Adney, Huasong Tian, David Wilkes, Juan Miguel Mosquera, David Stoddart, Daniel J Turner, Sissel Juul, Eoghan Harrington, Marcin Imielinski

Higher-order chromatin structure arises from the combinatorial physical interactions of many genomic loci. To investigate this aspect of genome architecture we developed Pore-C, which couples chromatin conformation capture with Oxford Nanopore Technologies (ONT) long reads to directly sequence multi-way chromatin contacts without amplification. In GM12878, we demonstrate that the pairwise interaction patterns implicit in Pore-C multi-way contacts are consistent with gold standard Hi-C pairwise contact maps at the compartment, TAD, and loop scales. In addition, Pore-C also detects higher-order chromatin structure at 18.5-fold higher efficiency and greater fidelity than SPRITE, a previously published higher-order chromatin profiling technology. We demonstrate Pore-C's ability to detect and visualize multi-locus hubs associated with histone locus bodies and active / inactive nuclear compartments in GM12878. In the breast cancer cell line HCC1954, Pore-C contacts enable the reconstruction of complex and aneuploid rearranged alleles spanning multiple megabases and chromosomes. Finally, we apply Pore-C to generate a chromosome scale de novo assembly of the HG002 genome. Our results establish Pore-C as the most simple and scalable assay for the genome-wide assessment of combinatorial chromatin interactions, with additional applications for cancer rearrangement reconstruction and de novo genome assembly.

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