journal
MENU ▼
Read by QxMD icon Read
search

ELife

journal
https://www.readbyqxmd.com/read/28230529/single-molecule-fret-unveils-induced-fit-mechanism-for-substrate-selectivity-in-flap-endonuclease-1
#1
Fahad Rashid, Paul D Harris, Manal S Zaher, Mohamed A Sobhy, Luay I Joudeh, Chunli Yan, Hubert Piwonski, Susan E Tsutakawa, Ivaylo Ivanov, John A Tainer, Satoshi Habuchi, Samir M Hamdan
Human flap endonuclease 1 (FEN1) and related structure-specific 5'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28230528/biologically-plausible-learning-in-recurrent-neural-networks-reproduces-neural-dynamics-observed-during-cognitive-tasks
#2
Thomas Miconi
Neural activity during cognitive tasks exhibits complex dynamics that flexibly encode task-relevant variables. Chaotic recurrent networks, which spontaneously generate rich dynamics, have been proposed as a model of cortical computation during cognitive tasks. However, existing methods for training these networks are either biologically implausible, and/or require a continuous, real-time error signal to guide learning. Here we show that a biologically plausible learning rule can train such recurrent networks, guided solely by delayed, phasic rewards at the end of each trial...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28230527/phloem-unloading-in-arabidopsis-roots-is-convective-and-regulated-by-the-phloem-pole-pericycle
#3
Timothy J Ross-Elliott, Kaare H Jensen, Katrine S Haaning, Brittney Michaelle Wager, Jan Knoblauch, Alexander H Howell, Daniel L Mullendore, Alexander G Monteith, Danae Paultre, Dawei Yan, Sofia Otero-Perez, Matthieu Bourdon, Ross Sager, Jung-Youn Lee, Ykä Helariutta, Michael Knoblauch, Karl John Oparka
In plants, a complex mixture of solutes and macromolecules is transported by the phloem. Here we examined how solutes and macromolecules are separated when they exit the phloem during the unloading process. We used a combination of approaches (non-invasive imaging, 3D-electron microscopy, and mathematical modelling) to show that phloem unloading of solutes in Arabidopsis roots occurs through plasmodesmata by a combination of mass flow and diffusion (convective phloem unloading). During unloading, solutes and proteins are diverted into the phloem-pole pericycle, a tissue connected to the protophloem by a unique class of 'funnel plasmodesmata'...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28230526/sensitivity-to-image-recurrence-across-eye-movement-like-image-transitions-through-local-serial-inhibition-in-the-retina
#4
Vidhyasankar Krishnamoorthy, Michael Weick, Tim Gollisch
Standard models of stimulus encoding in the retina postulate that image presentations activate neurons according to the increase of preferred contrast inside the receptive field. During natural vision, however, images do not arrive in isolation, but follow each other rapidly, separated by sudden gaze shifts. We here report that, contrary to standard models, specific ganglion cells in mouse retina are suppressed after a rapid image transition by changes in visual patterns across the transition, but respond with a distinct spike burst when the same pattern reappears...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28229860/distinct-contributions-of-the-thin-and-thick-filaments-to-length-dependent-activation-in-heart-muscle
#5
Xuemeng Zhang, Thomas Kampourakis, Ziqian Yan, Ivanka Sevrieva, Malcolm Irving, Yin-Biao Sun
The Frank-Starling relation is a fundamental auto-regulatory property of the heart that ensures the volume of blood ejected in each heartbeat is matched to the extent of venous filling. At the cellular level, heart muscle cells generate higher force when stretched, but despite intense efforts the underlying molecular mechanism remains unknown. We applied a fluorescence-based method, which reports structural changes separately in the thick and thin filaments of rat cardiac muscle, to elucidate that mechanism...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28229859/transient-inflammatory-response-mediated-by-interleukin-1%C3%AE-is-required-for-proper-regeneration-in-zebrafish-fin-fold
#6
Tomoya Hasegawa, Christopher J Hall, Philip S Crosier, Gembu Abe, Koichi Kawakami, Akira Kudo, Atsushi Kawakami
Cellular responses to injury are recognized to be crucial for complete tissue regeneration, but their underlying processes remain incompletely elucidated. We have previously reported that myeloid-defective zebrafish mutants display apoptosis of regenerative cells during fin fold regeneration. Here, we found that the apoptosis phenotype is induced by the prolonged expression of interleukin 1 beta (il1b). Myeloid cells have been considered to be the principal source of Il1b, but we show that epithelial cells express il1b in response to tissue injury and initiate the inflammatory response, and that its resolution by macrophages is necessary for the survival of regenerative cells...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28226243/bottom-up-and-top-down-computations-in-word-and-face-selective-cortex
#7
Kendrick N Kay, Jason D Yeatman
The ability to read a page of text or recognize a person's face depends on category-selective visual regions in ventral temporal cortex (VTC). To understand how these regions mediate word and face recognition, it is necessary to characterize how stimuli are represented and how this representation is used in the execution of a cognitive task. Here, we show that the response of a category-selective region in VTC can be computed as the degree to which the low-level properties of the stimulus match a category template...
February 22, 2017: ELife
https://www.readbyqxmd.com/read/28226242/p-falciparum-ligand-binding-to-erythrocytes-induce-alterations-in-deformability-essential-for-invasion
#8
Xavier Sisquella, Thomas Nebl, Jennifer K Thompson, Lachlan Whitehead, Brian M Malpede, Nichole D Salinas, Kelly Rogers, Niraj H Tolia, Andrea Fleig, Joseph O'Neill, Wai-Hong Tham, F David Horgen, Alan F Cowman
The most lethal form of malaria in humans is caused by Plasmodium falciparum. These parasites invade erythrocytes, a complex process involving multiple ligand-receptor interactions. The parasite makes initial contact with the erythrocyte followed by dramatic deformations linked to the function of the Erythrocyte binding antigen family and P. falciparum reticulocyte binding-like families. We show EBA-175 mediates substantial changes in deformability of erythrocytes by binding to glycophorin A and activating a phosphorylation cascade that includes erythrocyte cytoskeletal proteins resulting in changes in the viscoelastic properties of the host cell...
February 22, 2017: ELife
https://www.readbyqxmd.com/read/28226241/catsper%C3%AE-regulates-the-structural-continuity-of-sperm-ca-2-signaling-domains-and-is-required-for-normal-fertility
#9
Jean-Ju Chung, Kiyoshi Miki, Doory Kim, Sang-Hee Shim, Huanan F Shi, Jae Yeon Hwang, Xinjiang Cai, Yusuf Iseri, Xiaowei Zhuang, David E Clapham
We report that the Gm7068 (CatSperε) and Tex40 (CatSperζ) genes encode novel subunits of a 9-subunit CatSper ion channel complex. Targeted disruption of CatSperζ reduces CatSper current and sperm rheotactic efficiency in mice, resulting in severe male subfertility. Normally distributed in linear quadrilateral nanodomains along the flagellum, the complex lacking CatSperζ is disrupted at ~0.8 μm intervals along the flagellum. This disruption renders the proximal flagellum inflexible and alters the 3D flagellar envelope, thus preventing sperm from reorienting against fluid flow in vitro and efficiently migrating in vivo...
February 22, 2017: ELife
https://www.readbyqxmd.com/read/28226240/position-and-hippo-signaling-dependent-plasticityduring-lineage-segregation-in-the-early-mouse-embryo
#10
Eszter Posfai, Sophie Petropoulos, Flavia Ro de Barros, John Paul Schell, Igor Jurisica, Rickard Sandberg, Fredrik Lanner, Janet Rossant
The segregation of the trophectoderm (TE) from the inner cell mass (ICM) in the mouse blastocyst is determined by position-dependent Hippo signaling. However, the window of responsiveness to Hippo signaling, the exact timing of lineage commitment and the overall relationship between cell commitment and global gene expression changes are still unclear. Single-cell RNA sequencing during lineage segregation revealed that the TE transcriptional profile stabilizes earlier than the ICM and prior to blastocyst formation...
February 22, 2017: ELife
https://www.readbyqxmd.com/read/28226239/structural-basis-for-the-hijacking-of-endosomal-sorting-nexin-proteins-by-chlamydia-trachomatis
#11
Blessy Paul, Hyun Sung Kim, Markus C Kerr, Wilhelmina M Huston, Rohan D Teasdale, Brett M Collins
During infection chlamydial pathogens form an intracellular membrane-bound replicative niche termed the inclusion, which is enriched with bacterial transmembrane proteins called Incs. Incs bind and manipulate host cell proteins to promote inclusion expansion and provide camouflage against innate immune responses. Sorting nexin (SNX) proteins that normally function in endosomal membrane trafficking are a major class of inclusion-associated host proteins, and are recruited by IncE/CT116. Crystal structures of the SNX5 phox-homology (PX) domain in complex with IncE define the precise molecular basis for these interactions...
February 22, 2017: ELife
https://www.readbyqxmd.com/read/28221136/an-essential-dual-function-complex-mediates-erythrocyte-invasion-and-channel-mediated-nutrient-uptake-in-malaria-parasites
#12
Daisuke Ito, Marc A Schureck, Sanjay A Desai
Malaria parasites evade immune detection by growth and replication within erythrocytes. After erythrocyte invasion, the intracellular pathogen must increase host cell uptake of nutrients from plasma. Here, we report that the parasite-encoded RhopH complex contributes to both invasion and channel-mediated nutrient uptake. As rhoph2 and rhoph3 gene knockouts were not viable in the human P. falciparum pathogen, we used conditional knockdowns to determine that the encoded proteins are essential and to identify their stage-specific functions...
February 21, 2017: ELife
https://www.readbyqxmd.com/read/28221135/impaired-respiration-elicits-srrab-dependent-programmed-cell-lysis-and-biofilm-formation-in-staphylococcus-aureus
#13
Ameya A Mashruwala, Adriana Van De Guchte, Jeffrey M Boyd
Biofilms are communities of microorganisms attached to a surface or each other. Biofilm associated cells are the etiologic agents of recurrent Staphylococcus aureus infections. Infected human tissues are hypoxic or anoxic. S. aureus increases biofilm formation in response to hypoxia, but how this occurs is unknown. In the current study we report that oxygen influences biofilm formation in its capacity as a terminal electron acceptor for cellular respiration. Genetic, physiological, or chemical inhibition of respiratory processes elicited increased biofilm formation...
February 21, 2017: ELife
https://www.readbyqxmd.com/read/28221134/human-nup98-regulates-the-localization-and-activity-of-dexh-d-box-helicase-dhx9
#14
Juliana S Capitanio, Ben Montpetit, Richard W Wozniak
Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98, binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, we focused on identifying novel binding partners and understanding the significance of these interactions. Here we report on the identification of the DExH/D-box helicase DHX9 as an intranuclear Nup98 binding partner. Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner...
February 21, 2017: ELife
https://www.readbyqxmd.com/read/28220754/the-ap-2-complex-has-a-specialized-clathrin-independent-role-in-apical-endocytosis-and-polar-growth-in-fungi
#15
Olga Martzoukou, Sotiris Amillis, Amalia Zervakou, Savvas Christoforidis, George Diallinas
Filamentous fungi provide excellent systems for investigating the role of the AP-2 complex in polar growth. Using Aspergillus nidulans, we show that AP-2 has a clathrin-independent essential role in polarity maintenance and growth. This is in line with a sequence analysis showing that the AP-2 β subunit (β2) of higher fungi lacks a clathrin-binding domain, and experiments showing that AP-2 does not co-localize with clathrin. We provide genetic and cellular evidence that AP-2 interacts with endocytic markers SlaB(End4) and SagA(End3) and the lipid flippases DnfA and DnfB in the sub-apical collar region of hyphae...
February 21, 2017: ELife
https://www.readbyqxmd.com/read/28211790/flpstop-a-tool-for-conditional-gene-control-in-drosophila
#16
Yvette Erica Fisher, Helen H Yang, Jesse Isaacman-Beck, Marjorie Xie, Daryl M Gohl, Thomas R Clandinin
Manipulating gene function cell type-specifically is a common experimental goal in Drosophila research and has been central to studies of neural development, circuit computation, and behavior. However, current cell type-specific gene disruption techniques in flies often reduce gene activity incompletely or rely on cell division. Here we describe FlpStop, a generalizable tool for conditional gene disruption and rescue in post-mitotic cells. In proof-of-principle experiments, we manipulated apterous, a regulator of wing development...
February 17, 2017: ELife
https://www.readbyqxmd.com/read/28211789/the-cortical-connectivity-of-the-periaqueductal-gray-and-the-conditioned-response-to-the-threat-of-breathlessness
#17
Olivia K Faull, Kyle Ts Pattinson
Previously we observed differential activation in individual columns of the periaqueductal grey (PAG) during breathlessness and its conditioned anticipation (Faull et al., 2016). Here, we have extended this work by determining how the individual columns of the PAG interact with higher cortical centres, both at rest and in the context of breathlessness threat. Activation was observed in ventrolateral PAG (vlPAG) and lateral PAG (lPAG), where activity scaled with breathlessness intensity ratings, revealing a potential interface between sensation and cognition during breathlessness...
February 17, 2017: ELife
https://www.readbyqxmd.com/read/28198700/towards-a-mechanistic-foundation-of-evolutionary-theory
#18
Michael Doebeli, Yaroslav Ispolatov, Burt Simon
Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics...
February 15, 2017: ELife
https://www.readbyqxmd.com/read/28198699/longitudinal-imaging-of-hiv-1-spread-in-humanized-mice-with-parallel-3d-immunofluorescence-and-electron-tomography
#19
Collin Kieffer, Mark S Ladinsky, Allen Ninh, Rachel P Galimidi, Pamela J Bjorkman
Dissemination of HIV-1 throughout lymphoid tissues leads to systemic virus spread following infection. We combined tissue clearing, 3D-immunofluorescence, and electron tomography (ET) to longitudinally assess early HIV-1 spread in lymphoid tissues in humanized mice. Immunofluorescence revealed peak infection density in gut at 10-12 days post-infection when blood viral loads were low. Human CD4+ T-cells and HIV-1-infected cells localized predominantly to crypts and the lower third of intestinal villi. Free virions and infected cells were not readily detectable by ET at 5-days post-infection, whereas HIV-1-infected cells surrounded by pools of free virions were present in ~10% of intestinal crypts by 10-12 days...
February 15, 2017: ELife
https://www.readbyqxmd.com/read/28198698/a-role-for-cerebellum-in-the-hereditary-dystonia-dyt1
#20
Rachel Fremont, Ambika Tewari, Chantal Angueyra, Kamran Khodakhah
DYT1 is a debilitating movement disorder caused by loss-of-function mutations in torsinA. How these mutations cause dystonia remains unknown. Mouse models which have embryonically targeted torsinA have failed to recapitulate the dystonia seen in patients, possibly due to differential development compensation between rodents and humans. To address this issue, torsinA was acutely knocked down in select brain regions of adult mice using shRNAs. TorsinA knockdown in the cerebellum, but not in the basal ganglia, was sufficient to induce dystonia...
February 15, 2017: ELife
journal
journal
43971
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"