CXCR4/CXCL12-mediated entrapment of axons at the injury site compromises optic nerve regeneration

Regenerative failure in the mammalian optic nerve is generally attributed to axotomy-induced retinal ganglion cell (RGC) death, an insufficient intrinsic regenerative capacity, and an extrinsic inhibitory environment. Here, we show that a chemoattractive CXCL12/CXCR4-dependent mechanism prevents the extension of growth-stimulated axons into the distal nerve. The chemokine CXCL12 is chemoattractive toward axonal growth cones in an inhibitory environment, and these effects are entirely abolished by the specific knockout of its receptor, CXCR4 (CXCR4^−/−), in cultured regenerating RGCs. Notably, 8% of naïve RGCs express CXCL12 and transport the chemokine along their axons in the nerve. Thus, axotomy causes its release at the injury site. However, most osteopontin-positive α-RGCs, the main neuronal population that survives optic nerve injury, express CXCR4 instead. Thus, CXCL12-mediated attraction prevents growth-stimulated axons from regenerating distally in the nerve, indicated by axons returning to the lesion site. Accordingly, specific depletion of CXCR4 in RGC reduces aberrant axonal growth and enables long-distance regeneration. Likewise, CXCL12 knockout in RGCs fully mimics these CXCR4^−/− effects. Thus, active CXCL12/CXCR4-mediated entrapment of regenerating axons to the injury site contributes to regenerative failure in the optic nerve.

Retinal ganglion cells (RGCs) convey the visual input from the eye through the optic nerve and optic tract into the brain’s target regions. As typical neurons of the central nervous system (CNS), mammalian RGCs lose most of their capability to regrow injured axons after birth (1, 2), leading to an irreversible functional loss after optic nerve damage. To date, regenerative failure has been mainly attributed to three leading causes: 1) axotomy-induced apoptosis of RGCs, 2) the low intrinsic capacity to regrow axons, and 3) the external inhibitory environment with CNS myelin and glial scar proteins (3, 4).One widely used approach to delay axotomy-induced RGC degeneration and activate the intrinsic regenerative capacity of injured axons is inflammatory stimulation (IS) in the eye induced by a lens injury, intravitreal Pam₃Cys, or zymosan injection (5–7). IS leads to the expression and release of CNTF, LIF, and IL-6 from retinal astrocytes and Müller cells (8–10), which directly interact with RGCs and activate neuroprotective/regenerative signaling such as the JAK/STAT3 pathway (8, 9, 11, 12). IS, therefore, enables moderate axon regeneration beyond the lesion site of the optic nerve. Although combinatorial strategies, together with measures overcoming the inhibitory CNS environment synergistically, further improve IS-mediated optic nerve regeneration (13–17), the overall outcome remains mostly unsatisfactory. Thus, additional unknown mechanisms besides neurodegeneration, low intrinsic capacity, and the inhibitory environment might contribute to optic nerve regeneration failure.The chemokine receptor CXCR4, a seven-transmembrane G protein–coupled receptor, is expressed in embryonic and adult neurons (18–20). We have recently shown that this receptor is also expressed in the somata and axons of adult rat RGCs (18). Next to its role as a coreceptor for HIV entry and cancer-cell migration/proliferation (21, 22), CXCR4 is reportedly involved in neurogenesis and axonal pathfinding during the embryonal development of RGCs (20, 23, 24). CXCR4 regulates different signaling pathways upon binding its ligand CXCL12 (also known as stromal cell–derived factor 1, SDF-1), which is part of the chemokine family of chemotactic cytokines in the immune system involved in the attraction of lymphocytes (25, 26). CXCL12 is also reportedly expressed by some CNS neurons, astrocytes, and microglia (19, 27–30). As the CXCR4/CXCL12 axis is highly conserved between different species (31) and involved in axonal pathfinding during embryonal development of RGCs (20, 32), we speculated that CXCR4 expression in adult RGCs might also play a role in the regenerative processes of mature axons.The current study shows that growth-stimulated axons of RGCs are actively attracted and entrapped at the lesion site of the optic nerve by a CXCL12/CXCR4-dependent mechanism. CXCL12 is expressed in a subpopulation of RGCs and axonally transported, implying its release at the injury site. A different RGC subpopulation expressed CXCR4, causing axons in the distal nerve to return to the injury site. Specific depletion of CXCR4 or CXCL12 in RGCs abolished aberrant growth. It enabled long-distance regeneration in the optic nerve, with some axons reaching the optic chiasm 3 wk after injury. Thus, active CXCL12/CXCR4-mediated entrapment markedly compromises axon extension into the distal optic nerve and contributes to regenerative failure in the optic nerve.     

Scavenging of soluble and immobilized CCL21 by ACKR4 regulates peripheral dendritic cell emigration

Leukocyte homing driven by the chemokine CCL21 is pivotal for adaptive immunity because it controls dendritic cell (DC) and T cell migration through CCR7. ACKR4 scavenges CCL21 and has been shown to play an essential role in DC trafficking at the steady state and during immune responses to tumors and cutaneous inflammation. However, the mechanism by which ACKR4 regulates peripheral DC migration is unknown, and the extent to which it regulates CCL21 in steady-state skin and lymph nodes (LNs) is contested. Specifically, our previous findings that CCL21 levels are increased in LNs of ACKR4-deficient mice [I. Comerford et al., Blood 116, 4130–4140 (2010)] were refuted [M. H. Ulvmar et al., Nat. Immunol. 15, 623–630 (2014)], and no differences in CCL21 levels in steady-state skin of ACKR4-deficient mice were reported despite compromised CCR7-dependent DC egress in these animals [S. A. Bryce et al., J. Immunol. 196, 3341–3353 (2016)]. Here, we resolve these issues and reveal that two forms of CCL21, full-length immobilized and cleaved soluble CCL21, exist in steady-state barrier tissues, and both are regulated by ACKR4. Without ACKR4, extracellular CCL21 gradients in barrier sites are saturated and nonfunctional, DCs cannot home directly to lymphatic vessels, and excess soluble CCL21 from peripheral tissues pollutes downstream LNs. The results identify the mechanism by which ACKR4 controls DC migration in barrier tissues and reveal a complex mode of CCL21 regulation in vivo, which enhances understanding of functional chemokine gradient formation.

CCL21 is a chemokine that mediates recruitment of multiple leukocyte subsets through CCR7-mediated signaling during the steady state and inflammation. CCL21 plays crucial roles in priming adaptive immunity via governing egress of dendritic cells (DCs) from barrier tissues and T cell entry and positioning in secondary lymphoid organs (1–5). A well-characterized site of CCL21 gradient formation is the skin, where CCL21 is secreted by lymphatic endothelial cells (LECs) and immobilized on extracellular heparan sulfate moieties via interactions with the charged, elongated C-terminal tail of CCL21 (6–8). Here, immobilized CCL21 gradients are essential for interstitial DC trafficking toward lymphatic vessels (LVs) (8), after which CCL21 further contributes to LV attachment (9), infiltration (10), downstream luminal migration (11), and migration from the lymph node (LN) subcapsular sinus (SCS) to the paracortex (12). In-vitro studies have shown that the C-terminal tail of CCL21 can also be proteolytically cleaved by mature DCs to generate solubilized CCL21 (13), with signaling properties distinct from another soluble CCR7 ligand, CCL19 (14, 15). While CCL19 is dispensable for steady-state DC migration (16), important questions regarding the in vivo processing and function of cleaved CCL21 remain.Both forms of CCL21 are also ligands for the atypical chemokine receptor ACKR4 (17), which regulates chemokine bioavailability rather than directly mediating cell migration. ACKR4 expression has been identified in multiple barrier tissues (18–20) and lymphoid tissues (12, 21) where expression is largely restricted to stromal cell populations, with the exception of germinal-center B cells (22). Despite clear evidence of ACKR4 scavenging of CCL21 in vitro, the extent to which it regulates CCL21 in vivo is disputed. We have shown increased CCL21 in the LNs of Ackr4^−/− mice, which was associated with exacerbated Th17 responses in autoimmunity (23) and an ACKR4-dependent increase in CCL21 in tumors that promotes antitumor immunity (24). However, no differences in dermal CCL21 abundance were previously reported in steady-state Ackr4^−/− mice despite steady-state CCR7-dependent DC migratory defects being independent of CCL19 (19), and the contribution of ACKR4 in regulating LN CCL21 abundance has been disputed despite a clear role for ACKR4 in maintaining interfollicular CCL21 gradients in LN (12). These discrepancies have remained unresolved but point to previously unrecognized complexity in ACKR4-dependent regulation of CCL21 in both barrier and lymphoid tissues.     

Cholinergic suppression of hippocampal sharp-wave ripples impairs working memory

Learning and memory are assumed to be supported by mechanisms that involve cholinergic transmission and hippocampal theta. Using G protein–coupled receptor-activation–based acetylcholine sensor (GRAB_ACh3.0) with a fiber-photometric fluorescence readout in mice, we found that cholinergic signaling in the hippocampus increased in parallel with theta/gamma power during walking and REM sleep, while ACh3.0 signal reached a minimum during hippocampal sharp-wave ripples (SPW-R). Unexpectedly, memory performance was impaired in a hippocampus-dependent spontaneous alternation task by selective optogenetic stimulation of medial septal cholinergic neurons when the stimulation was applied in the delay area but not in the central (choice) arm of the maze. Parallel with the decreased performance, optogenetic stimulation decreased the incidence of SPW-Rs. These findings suggest that septo–hippocampal interactions play a task-phase–dependent dual role in the maintenance of memory performance, including not only theta mechanisms but also SPW-Rs.

The neurotransmitter acetylcholine is thought to be critical for hippocampus-dependent declarative memories (1, 2). Reduction in cholinergic neurotransmission, either in Alzheimer’s disease or in experiments with cholinergic antagonists, such as scopolamine, impairs memory function (3–8). Acetylcholine may bring about its beneficial effects on memory encoding by enhancing theta rhythm oscillations, decreasing recurrent excitation, and increasing synaptic plasticity (9–11). Conversely, drugs which activate cholinergic receptors enhance learning and, therefore, are a neuropharmacological target for the treatment of memory deficits in Alzheimer’s disease (5, 12, 13).The contribution of cholinergic mechanisms in the acquisition of long-term memories and the role of the hippocampal–entorhinal–cortical interactions are well supported by experimental data (5, 12, 13). In addition, working memory or “short-term” memory is also supported by the hippocampal–entorhinal–prefrontal cortex (14–16). Working memory in humans is postulated to be a conscious process to “keep things in mind” transiently (16). In rodents, matching to sample task, spontaneous alternation between reward locations, and the radial maze task have been suggested to function as a homolog of working memory [“working memory like” (17)].Cholinergic activity is a critical requirement for working memory (18, 19) and for sustaining theta oscillations (10, 20–22). In support of this contention, theta–gamma coupling and gamma power are significantly higher in the choice arm of the maze, compared with those in the side arms where working memory is no longer needed for correct performance (23–26). It has long been hypothesized that working memory is maintained by persistent firing of neurons, which keep the presented items in a transient store in the prefrontal cortex and hippocampal–entorhinal system (27–31), although the exact mechanisms are debated (32–37). An alternative hypothesis holds that items of working memory are stored in theta-nested gamma cycles (38). Common in these models of working memory is the need for an active, cholinergic system–dependent mechanism (39–41). However, in spontaneous alternation tasks, the animals are not moving continuously during the delay, and theta oscillations are not sustained either. During the immobility epochs, theta is replaced by intermittent sharp-wave ripples (SPW-R), yet memory performance does not deteriorate. On the contrary, artificial blockade of SPW-Rs can impair memory performance (42, 43), and prolongation of SPW-Rs improves performance (44). Under the cholinergic hypothesis of working memory, such a result is unexpected.To address the relationship between cholinergic/theta versus SPW-R mechanism in spontaneous alternation, we used a G protein–coupled receptor-activation–based acetylcholine sensor (GRAB_ACh3.0) (45) to monitor acetylcholine (ACh) activity during memory performance in mice. In addition, we optogenetically enhanced cholinergic tone, which suppresses SPW-Rs by a different mechanism than electrically or optogenetically induced silencing of neurons in the hippocampus (43, 44). We show that cholinergic signaling in the hippocampus increases in parallel with theta power/score during walking and rapid eye movement (REM) sleep and reaches a transient minimum during SPW-Rs. Selective optogenetic stimulation of medial septal cholinergic neurons decreased the incidence of SPW-Rs during non-REM sleep (46–48), as well as during the delay epoch of a working memory task and impaired memory performance. These findings demonstrate that memory performance is supported by complementary theta and SPW-R mechanisms.     

GPR182 is an endothelium-specific atypical chemokine receptor that maintains hematopoietic stem cell homeostasis

G protein–coupled receptor 182 (GPR182) has been shown to be expressed in endothelial cells; however, its ligand and physiological role has remained elusive. We found GPR182 to be expressed in microvascular and lymphatic endothelial cells of most organs and to bind with nanomolar affinity the chemokines CXCL10, CXCL12, and CXCL13. In contrast to conventional chemokine receptors, binding of chemokines to GPR182 did not induce typical downstream signaling processes, including G_q- and G_i-mediated signaling or β-arrestin recruitment. GPR182 showed relatively high constitutive activity in regard to β-arrestin recruitment and rapidly internalized in a ligand-independent manner. In constitutive GPR182-deficient mice, as well as after induced endothelium-specific loss of GPR182, we found significant increases in the plasma levels of CXCL10, CXCL12, and CXCL13. Global and induced endothelium-specific GPR182-deficient mice showed a significant decrease in hematopoietic stem cells in the bone marrow as well as increased colony-forming units of hematopoietic progenitors in the blood and the spleen. Our data show that GPR182 is a new atypical chemokine receptor for CXCL10, CXCL12, and CXCL13, which is involved in the regulation of hematopoietic stem cell homeostasis.

G protein–coupled receptors (GPCRs) represent the largest group of transmembrane receptors encoded in the genome, and they are the largest group of proteins targeted by approved drugs (1, 2). GPCRs are very versatile and can bind ligands of different physicochemical properties, including ions, lipids, biogenic amines, peptides, or proteins, such as chemokines (3). Primarily by activation of heterotrimeric G proteins, GPCRs regulate multiple functions in basically all cells of mammalian organisms (4). Despite their large physiological and pharmacological relevance, the endogenous ligands, activating mechanisms and physiological functions of more than 100 GPCRs, are still not known and these receptors are therefore referred to as “orphan” receptors (3, 5). G protein–coupled receptor 182 (GPR182) is an orphan receptor, although it has been suggested to bind adrenomedullin (6), but this observation could not be confirmed (7). GPR182 was initially described to be widely expressed in various organs (8). More-detailed analyses in developing zebrafish and in mice revealed that Gpr182 is preferentially expressed in the vascular endothelium (9, 10). Widespread expression in endothelial cells of adult mice was shown using a mouse line expressing β-galactosidase under the control of the Gpr182-promoter (11), and expression of GPR182 in sinusoidal endothelial cells was reported based on immunohistochemical analysis (12). Whereas the role of GPR182 in endothelial cells is unknown, GPR182 expression was also reported in intestinal stem cells, where the receptor was shown to negatively regulate proliferation during regeneration and adenoma formation (11).Chemokine receptors are a family of 22 GPCRs that respond to 52 chemokines (13). Upon activation, they induce G protein–mediated intracellular signaling processes which, in many cases, regulate the migration of leukocytes (14). However, more recent work has shown that the function of chemokines goes beyond the regulation of leukocyte migration and can also affect other cell functions and cell types (13, 15, 16). In addition, and in contrast to other groups of GPCRs, the chemokine receptor family contains several members, which bind chemokines but are unable to signal through G proteins. These so-called “atypical chemokine receptors” (ACKRs) can indirectly regulate the interactions between chemokines and conventional chemokine receptors by controlling chemokine localization, distribution, and abundance (13, 16, 17). As most conventional chemokine receptors, ACKRs typically bind subgroups of chemokines. For instance, ACKR1 binds various chemokines and transports them across endothelial cells or, when expressed on erythrocytes, buffers chemokine levels in the blood (18). ACKR2 functions as a scavenger receptor by binding several C-C motif chemokine ligand (CCL) chemokines and plays various roles in the immune system (19). ACKR3 only binds C-X-C motif chemokine ligand 11 (CXCL11) and CXCL12 and controls the CXCL12–CXCR4 signaling axis by direct interaction with CXCR4 and by scavenging CXCL12 (20, 21). ACKR4 binds the conventional chemokine receptor ligands CCL19, CCL21, CCL25, and CXCL19 (18, 19).Here, we show that GPR182 functions as an atypical chemokine receptor for CXCL10, CXCL12, and CXCL13 and that it is involved in preventing hematopoietic stem cell egress from bone marrow.     

Tropospheric carbonyl sulfide mass balance based on direct measurements of sulfur isotopes

Robust estimates for the rates and trends in terrestrial gross primary production (GPP; plant CO₂ uptake) are needed. Carbonyl sulfide (COS) is the major long-lived sulfur-bearing gas in the atmosphere and a promising proxy for GPP. Large uncertainties in estimating the relative magnitude of the COS sources and sinks limit this approach. Sulfur isotope measurements (³⁴S/³²S; δ³⁴S) have been suggested as a useful tool to constrain COS sources. Yet such measurements are currently scarce for the atmosphere and absent for the marine source and the plant sink, which are two main fluxes. Here we present sulfur isotopes measurements of marine and atmospheric COS, and of plant-uptake fractionation experiments. These measurements resulted in a complete data-based tropospheric COS isotopic mass balance, which allows improved partition of the sources. We found an isotopic (δ³⁴S ± SE) value of 13.9 ± 0.1‰ for the troposphere, with an isotopic seasonal cycle driven by plant uptake. This seasonality agrees with a fractionation of −1.9 ± 0.3‰ which we measured in plant-chamber experiments. Air samples with strong anthropogenic influence indicated an anthropogenic COS isotopic value of 8 ± 1‰. Samples of seawater-equilibrated-air indicate that the marine COS source has an isotopic value of 14.7 ± 1‰. Using our data-based mass balance, we constrained the relative contribution of the two main tropospheric COS sources resulting in 40 ± 17% for the anthropogenic source and 60 ± 20% for the oceanic source. This constraint is important for a better understanding of the global COS budget and its improved use for GPP determination.

The Earth system is going through rapid changes as the climate warms and CO₂ level rises. This rise in CO₂ is mitigated by plant uptake; hence, it is important to estimate global and regional photosynthesis rates and trends (1). Yet, robust tools for investigating these processes at a large scale are scarce (2). Recent studies suggest that carbonyl sulfide (COS) could provide an improved constraint on terrestrial photosynthesis (gross primary production, GPP) (2–12). COS is the major long-lived sulfur-bearing gas in the atmosphere and the main supplier of sulfur to the stratospheric sulfate aerosol layer (13), which exerts a cooling effect on the Earth’s surface and regulates stratospheric ozone chemistry (14).During terrestrial photosynthesis, COS diffuses into leaf stomata and is consumed by photosynthetic enzymes in a similar manner to CO₂ (3–5). Contrary to CO₂, COS undergoes rapid and irreversible hydrolysis mainly by the enzyme carbonic-anhydrase (6, 7). Thus, COS can be used as a proxy for the one-way flux of CO₂ removal from the atmosphere by terrestrial photosynthesis (2, 8–11). However, the large uncertainties in estimating the COS sources weaken this approach (10–12, 15). Tropospheric COS has two main sources: the oceans and anthropogenic emissions, and one main sink–terrestrial plant uptake (8, 10–13). Smaller sources include biomass burning, soil emissions, wetlands, volcanoes, and smaller sinks include OH destruction, stratospheric destruction, and soil uptake (12). The largest source of COS to the atmosphere is the ocean, both as direct COS emission, and as indirect carbon disulfide (CS₂) and dimethylsulfide (DMS) emissions that are rapidly oxidized to COS (10, 16–20). Recent studies suggest oceanic COS emissions are in the range of 200–4,000 GgS/y (19–22). The second major COS source is the anthropogenic source, which is dominated by indirect emissions derived from CS₂ oxidation, mainly from the use of CS₂ as an industrial solvent. Direct emissions of COS are mainly derived from coal and fuel combustion (17, 23, 24). Recent studies suggest that anthropogenic emissions are in the range of 150–585 GgS/y (23, 24). The terrestrial plant uptake is estimated to be in the range of 400–1,360 GgS/y (11). Measurements of sulfur isotope ratios (δ³⁴S) in COS may be used to track COS sources and thus reduce the uncertainties in their flux estimations (15, 25–27). However, the isotopic mass balance approach works best if the COS end members are directly measured and have a significantly different isotopic signature. Previous δ³⁴S measurements of atmospheric COS are scarce and there have been no direct measurements of two important components: the δ³⁴S of oceanic COS emissions, and the isotopic fractionation of COS during plant uptake (15, 25–27). In contrast to previous studies that used assessments for these isotopic values, our aim was to directly measure the isotopic values of these missing components, and to determine the tropospheric COS δ³⁴S variability over space and time.     

Replisome bypass of a protein-based R-loop block by Pif1

Efficient and faithful replication of the genome is essential to maintain genome stability. Replication is carried out by a multiprotein complex called the replisome, which encounters numerous obstacles to its progression. Failure to bypass these obstacles results in genome instability and may facilitate errors leading to disease. Cells use accessory helicases that help the replisome bypass difficult barriers. All eukaryotes contain the accessory helicase Pif1, which tracks in a 5′–3′ direction on single-stranded DNA and plays a role in genome maintenance processes. Here, we reveal a previously unknown role for Pif1 in replication barrier bypass. We use an in vitro reconstituted Saccharomyces cerevisiae replisome to demonstrate that Pif1 enables the replisome to bypass an inactive (i.e., dead) Cas9 (dCas9) R-loop barrier. Interestingly, dCas9 R-loops targeted to either strand are bypassed with similar efficiency. Furthermore, we employed a single-molecule fluorescence visualization technique to show that Pif1 facilitates this bypass by enabling the simultaneous removal of the dCas9 protein and the R-loop. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.

Efficient and faithful replication of the genome is essential to maintain genome stability and is carried out by a multiprotein complex called the replisome (1–4). There are numerous obstacles to progression of the replisome during the process of chromosome duplication. These obstacles include RNA-DNA hybrids (R-loops), DNA secondary structures, transcribing RNA polymerases, and other tightly bound proteins (5–9). Failure to bypass these barriers may result in genome instability, which can lead to cellular abnormalities and genetic disease. Cells contain various accessory helicases that help the replisome bypass these difficult barriers (10–20). A subset of these helicases act on the opposite strand of the replicative helicase (1, 2, 14, 19).All eukaryotes contain an accessory helicase, Pif1, which tracks in a 5′–3′ direction on single-stranded DNA (ssDNA) (11–16). Pif1 is important in pathways such as Okazaki-fragment processing and break-induced repair that require the removal of DNA-binding proteins as well as potential displacement of R-loops (11–13, 21, 15–18, 22–25). Genetic studies and immunoprecipitation pull-down assays indicate that Pif1 interacts with PCNA (the DNA sliding clamp), Pol ε (the leading-strand polymerase), the MCMs (the motor subunits of the replicative helicase CMG), and RPA (the single-stranded DNA-binding protein) (15, 26, 27). Pif1 activity in break-induced repair strongly depends on its interaction with PCNA (26). These interactions with replisomal components suggest that Pif1 could interact with the replisome during replication. In Escherichia coli, the replicative helicase is the DnaB homohexamer that encircles the lagging strand and moves in a 5′–3′ direction (20). E. coli accessory helicases include the monomeric UvrD (helicase II) and Rep, which move in the 3′–5′ direction and operate on the opposite strand from the DnaB hexamer. It is known that these monomeric helicases promote the bypass of barriers during replication such as stalled RNA polymerases (5). The eukaryotic replicative helicase is the 11-subunit CMG (Cdc45, Mcm2–7, GINS) and tracks in the 3′–5′ direction, opposite to the direction of Pif1 (25, 28). Once activated by Mcm10, the MCM motor domains of CMG encircle the leading strand (29–32). We hypothesized that, similar to UvrD and Rep in E. coli, Pif1 interacts with the replisome tracking in the opposite direction to enable bypass of replication obstacles.In this report, we use an in vitro reconstituted Saccharomyces cerevisiae replisome to study the role of Pif1 in bypass of a “dead” Cas9 (dCas9), which is a Cas9 protein that is deactivated in DNA cleavage but otherwise fully functional in DNA binding. As with Cas9, dCas9 is a single-turnover enzyme that can be programmed with a guide RNA (gRNA) to target either strand. The dCas9–gRNA complex forms a roadblock consisting of an R-loop and a tightly bound protein (dCas9), a construct that is similar to a stalled RNA polymerase. This roadblock (hereafter dCas9 R-loop) arrests replisomes independent of whether the dCas9 R-loop is targeted to the leading or lagging strand (30). Besides its utility due to its programmable nature (33), the use of the dCas9 R-loop allows us to answer several mechanistic questions. For example, the ability to program the dCas9 R-loop block to any specific sequence enables us to observe whether block removal is different depending on whether the block is on the leading or lagging strand. Furthermore, the inner diameter of CMG can accommodate double-stranded DNA (dsDNA) and possibly an R-loop, but not a dCas9 protein. Using the dCas9 R-loop block allows us to determine the fate of each of its components.Here, we report that Pif1 enables the bypass of the dCas9 R-loop by the replisome. Interestingly, dCas9 R-loops targeted to either the leading or lagging strand are bypassed with similar efficiency. In addition, the PCNA clamp is not required for bypass of the block, indicating that Pif1 does not need to interact with PCNA during bypass of the block. We used a single-molecule fluorescence imaging to show that both the dCas9 and the R-loop are displaced as an intact nucleoprotein complex. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.     

ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating

Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14–ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA–VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid–RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.

Human rhinoviruses are the cause of more than half of common colds (1). Medical visits and missed days of school and work cost tens of billions of US dollars annually (2, 3). There is currently no cure for rhinovirus infections, and the available treatments are only symptomatic. Rhinoviruses belong to the family Picornaviridae, genus Enterovirus, and are classified into species A, B, and C (4). Rhinoviruses A and B can belong to either “major” or “minor” groups, based on their utilization of intercellular adhesion molecule-1 (ICAM-1) or low-density lipoprotein receptor for cell entry (5–7). Type C rhinoviruses use CDHR3 as a receptor (8). Rhinovirus 14 belongs to the species rhinovirus B and uses ICAM-1 as a receptor. Receptors recognized by rhinoviruses and other enteroviruses can be divided into two groups based on their function in the infection process (9). Attachment receptors such as DAF, PSGL1, KREMEN1, CDHR3, and sialic acid enable the binding and endocytosis of virus particles into cells (10–13). In contrast, uncoating receptors including ICAM-1, CD155, CAR, and SCARB2 enable virus cell entry but also promote genome release from virus particles (5, 14–16).Virions of rhinoviruses are nonenveloped and have icosahedral capsids (17). Genomes of rhinoviruses are 7,000 to 9,000 nucleotide-long single-stranded positive-sense RNA molecules (1, 17). The rhinovirus genome encodes a single polyprotein that is co- and posttranslationally cleaved into functional protein subunits. Capsid proteins VP1, VP3, and VP0, originating from one polyprotein, form a protomer, 60 of which assemble into a pseudo-T = 3 icosahedral capsid. To render the virions mature and infectious, VP0 subunits are cleaved into VP2 and VP4 (18, 19). VP1 subunits form pentamers around fivefold symmetry axes, whereas subunits VP2 and VP3 form heterohexamers centered on threefold symmetry axes. The major capsid proteins VP1 through 3 have a jelly roll β-sandwich fold formed by two β-sheets, each containing four antiparallel β-strands, which are conventionally named B to I (20–22). The two β-sheets contain the strands BIDG and CHEF, respectively. The C termini of the capsid proteins are located at the virion surface, whereas the N termini mediate interactions between the capsid proteins and the RNA genome on the inner surface of the capsid. VP4 subunits are attached to the inner face of the capsid formed by the major capsid proteins. The surfaces of rhinovirus virions are characterized by circular depressions called canyons, which are centered around fivefold symmetry axes of the capsids (21).The VP1 subunits of most rhinoviruses, but not those of rhinovirus 14, contain hydrophobic pockets, which are filled by molecules called pocket factors (17, 21, 23, 24). It has been speculated that pocket factors are fatty acids or lipids (25). The pockets are positioned immediately below the canyons. The exposure of rhinoviruses to acidic pH induces expulsion of the pocket factors, which leads to the formation of activated particles and genome release (17, 26–32). The activated particles are characterized by capsid expansion, a reduction in interpentamer contacts, the release of VP4 subunits, externalization of N termini of VP1 subunits, and changes in the distribution of RNA genomes (17, 26–29, 33, 34). Artificial hydrophobic compounds that bind to VP1 pockets with high affinity inhibit infection by rhinoviruses (35, 36).ICAM-1 is an endothelial- and leukocyte-associated protein that stabilizes cell–cell interactions and facilitates the movement of leukocytes through endothelia (37). ICAM-1 can be divided into an extracellular amino-terminal part composed of five immunoglobulin domains, a single transmembrane helix, and a 29-residue–long carboxyl-terminal cytoplasmic domain. The immunoglobulin domains are characterized by a specific fold that consists of seven to eight β-strands, which form two antiparallel β-sheets in a sandwich arrangement (38–40). The immunoglobulin domains of ICAM-1 are stabilized by disulfide bonds and glycosylation (38–41). The connections between the immunoglobulin domains are formed by flexible linkers that enable bending of the extracellular part of ICAM-1. For example, the angle between domains 1 and 2 differs by 8° between molecules in distinct crystal forms (38, 42). As a virus receptor, ICAM-1 enables the virus particles to sequester at the cell surface and mediates their endocytosis (5). The structures of complexes of rhinoviruses 3, 14, and 16, and CVA21 with ICAM-1 have been determined to resolutions of 9 to 28 Å (42–46). It was shown that ICAM-1 molecules bind into the canyons at the rhinovirus surface, approximately between fivefold and twofold symmetry axes (42–46). ICAM-1 interacts with residues from all three major capsid proteins. It has been speculated that the binding of ICAM-1 triggers the transition of virions of rhinovirus 14 to activated particles and initiates genome release (45, 47). However, the limited resolution of the previous studies prevented characterization of the corresponding molecular mechanism.Here, we present the cryo-electron microscopy (cryo-EM) reconstruction of the rhinovirus 14 virion, which contains resolved density of octanucleotide segments of the RNA genome that interact with VP2 subunits. Furthermore, we show that the binding of ICAM-1 to rhinovirus 14 induces changes in its capsid and genome, which are required for subsequent virus activation and genome release at acidic pH.     

Circular swimming motility and disordered hyperuniform state in an algae system

Active matter comprises individually driven units that convert locally stored energy into mechanical motion. Interactions between driven units lead to a variety of nonequilibrium collective phenomena in active matter. One of such phenomena is anomalously large density fluctuations, which have been observed in both experiments and theories. Here we show that, on the contrary, density fluctuations in active matter can also be greatly suppressed. Our experiments are carried out with marine algae (Effrenium voratum), which swim in circles at the air–liquid interfaces with two different eukaryotic flagella. Cell swimming generates fluid flow that leads to effective repulsions between cells in the far field. The long-range nature of such repulsive interactions suppresses density fluctuations and generates disordered hyperuniform states under a wide range of density conditions. Emergence of hyperuniformity and associated scaling exponent are quantitatively reproduced in a numerical model whose main ingredients are effective hydrodynamic interactions and uncorrelated random cell motion. Our results demonstrate the existence of disordered hyperuniform states in active matter and suggest the possibility of using hydrodynamic flow for self-assembly in active matter.

Active matter exists over a wide range of spatial and temporal scales (1–6) from animal groups (7, 8) to robot swarms (9–11), to cell colonies and tissues (12–16), to cytoskeletal extracts (17–20), to man-made microswimmers (21–25). Constituent particles in active matter systems are driven out of thermal equilibrium at the individual level; they interact to develop a wealth of intriguing collective phenomena, including clustering (13, 22, 24), flocking (11, 26), swarming (12, 13), spontaneous flow (14, 20), and giant density fluctuations (10, 11). Many of these observed phenomena have been successfully described by particle-based or continuum models (1–6), which highlight the important roles of both individual motility and interparticle interactions in determining system dynamics.Current active matter research focuses primarily on linearly swimming particles which have a symmetric body and self-propel along one of the symmetry axes. However, a perfect alignment between the propulsion direction and body axis is rarely found in reality. Deviation from such a perfect alignment leads to a persistent curvature in the microswimmer trajectories; examples of such circle microswimmers include anisotropic artificial micromotors (27, 28), self-propelled nematic droplets (29, 30), magnetotactic bacteria and Janus particles in rotating external fields (31, 32), Janus particle in viscoelastic medium (33), and sperm and bacteria near interfaces (34, 35). Chiral motility of circle microswimmers, as predicted by theoretical and numerical investigations, can lead to a range of interesting collective phenomena in circular microswimmers, including vortex structures (36, 37), localization in traps (38), enhanced flocking (39), and hyperuniform states (40). However, experimental verifications of these predictions are limited (32, 35), a situation mainly due to the scarcity of suitable experimental systems.Here we address this challenge by investigating marine algae Effrenium voratum (41, 42). At air–liquid interfaces, E. voratum cells swim in circles via two eukaryotic flagella: a transverse flagellum encircling the cellular anteroposterior axis and a longitudinal one running posteriorly. Over a wide range of densities, circling E. voratum cells self-organize into disordered hyperuniform states with suppressed density fluctuations at large length scales. Hyperuniformity (43, 44) has been considered as a new form of material order which leads to novel functionalities (45–49); it has been observed in many systems, including avian photoreceptor patterns (50), amorphous ices (51), amorphous silica (52), ultracold atoms (53), soft matter systems (54–61), and stochastic models (62–64). Our work demonstrates the existence of hyperuniformity in active matter and shows that hydrodynamic interactions can be used to construct hyperuniform states.     

Collagen IV differentially regulates planarian stem cell potency and lineage progression

The extracellular matrix (ECM) provides a precise physical and molecular environment for cell maintenance, self-renewal, and differentiation in the stem cell niche. However, the nature and organization of the ECM niche is not well understood. The adult freshwater planarian Schmidtea mediterranea maintains a large population of multipotent stem cells (neoblasts), presenting an ideal model to study the role of the ECM niche in stem cell regulation. Here we tested the function of 165 planarian homologs of ECM and ECM-related genes in neoblast regulation. We identified the collagen gene family as one with differential effects in promoting or suppressing proliferation of neoblasts. col4-1, encoding a type IV collagen α-chain, had the strongest effect. RNA interference (RNAi) of col4-1 impaired tissue maintenance and regeneration, causing tissue regression. Finally, we provide evidence for an interaction between type IV collagen, the discoidin domain receptor, and neuregulin-7 (NRG-7), which constitutes a mechanism to regulate the balance of symmetric and asymmetric division of neoblasts via the NRG-7/EGFR pathway.

Across the animal kingdom, stem cell function is regulated by the microenvironment in the surrounding niche (1), where the concentration of molecular signals for self-renewal and differentiation can be precisely regulated (2). The niche affects stem cell biology in many processes, such as aging and tissue regeneration, as well as pathological conditions such as cancer (3). Most studies have been done in tissues with large stem cell populations, such as the intestinal crypt (4) and the hair follicle (5) in mice. Elucidation of the role of the stem cell niche in tissue regeneration requires the study of animals with high regenerative potential, such as freshwater planarians (flatworms) (6). Dugesia japonica and Schmidtea mediterranea are two well-studied species that possess the ability to regenerate any missing body part (6, 7).Adult S. mediterranea maintain a high number of stem cells (neoblasts)—∼10 to 30% of all somatic cells in the adult worm—with varying potency, including pluripotent cells (8–14). Neoblasts are the only proliferating somatic cells: they are molecularly heterogeneous, but all express piwi-1 (15–18). Lineage-committed neoblasts are “progenitors” that transiently express both piwi-1 and tissue-specific genes (15, 19). Examples include early intestinal progenitors (γ neoblast, piwi-1⁺/hnf4⁺) (8, 10, 15, 19–21) and early epidermal progenitors (ζ neoblast, piwi-1⁺/zfp-1⁺) (8, 15). Other progenitor markers include collagen for muscles (22), ChAT for neurons (23), and cavII for protonephridia (24, 25). During tissue regeneration, neoblasts are recruited to the wound site, where they proliferate then differentiate to replace the missing cell types (16, 26). Some neoblasts express the pluripotency marker tgs-1, and are designated as clonogenic neoblasts (cNeoblasts) (10, 11). cNeoblasts are located in the parenchymal space adjacent to the gut (11).Neoblasts are sensitive to γ-irradiation and can be preferentially depleted in the adult planarian (27). After sublethal γ-irradiation, remaining cNeoblasts can repopulate the stem cell pool within their niche (10, 11). The close proximity of neoblasts to the gut suggests gut may be a part of neoblast niche (28, 29). When gut integrity was impaired by silencing gata4/5/6, the egfr-1/nrg-1 ligand-receptor pair, or wwp1, maintenance of non–γ-neoblasts were also disrupted (20, 30, 31), but whether that indicates the gut directly regulates neoblast remains unclear. There is evidence indicating the dorsal-ventral (D/V) transverse muscles surrounding the gut may promote neoblast proliferation and migration, with the involvement of matrix metalloproteinase mt-mmpB (32, 33). The central nervous system has also been implicated in influencing neoblast maintenance through the expression of EGF homolog neuregulin-7 (nrg-7), a ligand for EGFR-3, affecting the balance of neoblast self-renewal (symmetric or asymmetric division) (34).In other model systems, an important component of the stem-cell niche is the extracellular matrix (ECM) (35). Germline stem cells in Drosophila are anchored to niche supporting cells with ECM on one side, while the opposite side is exposed to differentiation signals, allowing asymmetric cell fate outcomes for self-renewal or differentiation following division (36–38). Few studies have addressed the ECM in planarians, largely due to the lack of genetic tools to manipulate the genome, the absence of antibodies to specific planarian ECM homologs, or the tools required to study cell fate changes. However, the genomes of D. japonica (39–41) and S. mediterranea (41–45), and single-cell RNA-sequencing (scRNA-seq) datasets for S. mediterranea are now available (11, 46–50). A recent study of the planarian matrisome demonstrated that muscle cells are the primary source of many ECM proteins (51), which, together with those produced by neoblasts and supporting parenchymal cells, may constitute components of the neoblast niche. For example, megf6 and hemicentin restrict neoblast’s localization within the parenchyma (51, 52). Functional studies also implicate ECM-modifiers, such as matrix metalloproteases (MMPs) in neoblast migration and regeneration. For example, reducing the activity of the ECM-degrading enzymes mt-mmpA (26, 33), mt-mmpB (53), or mmp-1 (33) impaired neoblast migration, proliferation, or overall tissue growth, respectively. Neoblasts are also likely to interact with ECM components of the niche via cell surface receptors, such as β1 integrin, inactivation of which impairs brain regeneration (54, 55).Here, we identified planarian ECM homologs in silico, followed by systematic functional assessment of 165 ECM and ECM-related genes by RNA interference (RNAi), to determine the effect on neoblast repopulation in planarians challenged by a sublethal dose of γ-irradiation (10). Surprisingly, multiple classes of collagens were shown to have the strongest effects. In particular, we show that the type IV collagens (COLIV) of basement membranes (BMs), were required to regulate the repopulation of neoblasts as well as lineage progression to progenitor cells. Furthermore, our data support an interaction between COLIV and the discoidin domain receptor (DDR) in neurons that activates signaling of NRG-7 in the neoblasts to regulate neoblast self-renewal versus differentiation. Together, these data demonstrate multifaceted regulation of planarian stem cells by ECM components.     

ATM controls the extent of DNA end resection by eliciting sequential posttranslational modifications of CtIP

DNA end resection is a critical step in the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR). However, the mechanisms governing the extent of resection at DSB sites undergoing homology-directed repair remain unclear. Here, we show that, upon DSB induction, the key resection factor CtIP is modified by the ubiquitin-like protein SUMO at lysine 578 in a PIAS4-dependent manner. CtIP SUMOylation occurs on damaged chromatin and requires prior hyperphosphorylation by the ATM protein kinase. SUMO-modified hyperphosphorylated CtIP is targeted by the SUMO-dependent E3 ubiquitin ligase RNF4 for polyubiquitination and subsequent degradation. Consequently, disruption of CtIP SUMOylation results in aberrant accumulation of CtIP at DSBs, which, in turn, causes uncontrolled excessive resection, defective HR, and increased cellular sensitivity to DSB-inducing agents. These findings reveal a previously unidentified regulatory mechanism that regulates CtIP activity at DSBs and thus the extent of end resection via ATM-dependent sequential posttranslational modification of CtIP.

DNA double-strand breaks (DSBs) constitute one of the most severe forms of DNA damage and can result in a wide variety of genetic alterations including mutations, deletions, translocations, and chromosome loss (1, 2). Extensive studies have shown that DSBs can be repaired primarily via two pathways, classical nonhomologous end joining and homologous recombination (HR), both of which are highly conserved among all eukaryotes (3–5). Classical nonhomologous end joining, which directly rejoins the two broken ends of a DSB, occurs throughout interphase (3–5). In contrast, DSB repair by HR requires the presence of a sister chromatid and is therefore restricted to the late S and G2 phases of the cell cycle (3–5). HR is initiated by resection of the 5′ strand of the DSB ends, yielding 3′ single-stranded DNA (ssDNA) tails that are initially coated with the replication protein A (RPA) complex (3–5). The resulting RPA-coated ssDNA is an essential intermediate not only in HR repair but also in ATR-CHK1 pathway activation (3–5). Studies conducted in yeast and mammalian cells have established that resection of DSB ends is a two-step process (3–5). First, the conserved MRE11/RAD50/NBS1 complex (MRE11/RAD50/XRS2 in Saccharomyces cerevisiae) cooperates with the key resection factor CtIP (Sae2 in S. cerevisiae, Ctp1 in Schizosaccharomyces pombe) to catalyze limited resection of broken DNA ends (3–6). Second, the resulting short 3′ overhangs are further processed through the action of either the 5′–3′ exonuclease EXO1 or the nuclease–helicase protein complex DNA2–BLM (DNA2–Sgs1 in S. cerevisiae) (3–5). Whereas extensive end resection is required for HR initiation and full checkpoint activation, uncontrolled and excessive processing of DSB ends can have deleterious consequences such as large deletions at DSB sites, persistent checkpoint signaling, and cell death (7–11). However, the mechanisms by which cells precisely control the extent of end resection at DSB sites undergoing homology-directed repair remain obscure.It has been well established that posttranslational modifications of DNA repair proteins play crucial roles in the cellular response to genotoxic stress (12, 13). For example, phosphorylation of CtIP at threonine 847 (serine 267 in Sae2) by CDK1/2 restricts its activity to the S and G2 phases of the cell cycle (14–17), and promotes its capacity to stimulate the MRE11 endonuclease activity (18) as well as the annealing of broken DNA ends (19). In addition, phosphorylation of CtIP at serine 327 by CDK2 and/or Aurora A is a prerequisite for its interactions with BRCA1 and PLK1 (20–23). Furthermore, CtIP undergoes phosphorylation at threonine 315 by CDK2, and this phosphorylation event regulates CtIP protein stability by facilitating its interaction with the phosphorylation-specific prolyl isomerase PIN1 (24). In addition to acting as a CDK substrate, CtIP can also be hyperphosphorylated by ATM (or ATR in Xenopus) at multiple serine/threonine–glutamine sites in response to DSBs, which is manifested by the appearance of a slow-migrating form of CtIP (25, 26). ATM-dependent hyperphosphorylation of CtIP not only facilitates its association with damaged DNA (27) but also promotes the recruitment of BLM and EXO1 to DSB sites (25). Moreover, a previous study showed that the putative ATM-targeted residues serine 231, serine 664, and serine 745 as well as the CDK-targeted residues serine 276, threonine 315, and serine 347 within CtIP are critical for its endonuclease activity, although the relative contributions of the individual modifications have not been fully characterized (28). In addition to phosphorylation, CtIP is also subject to other posttranslational modifications, such as ubiquitination and acetylation (21, 29–36). Strict regulation of CtIP activity via various posttranslational modifications is crucial for accurate processing and repair of DSBs; however, precisely how these modifications are regulated in a coordinated manner remains unclear.In this study, we provide evidence that CtIP becomes SUMOylated primarily at lysine 578 upon exposure to DSB-inducing agents, and that this modification controls the activated CtIP level at DSBs and thereby the extent of DSB end resection. CtIP SUMOylation at lysine 578 is dependent on its prior hyperphosphorylation by the protein kinase ATM. SUMO-modified hyperphosphorylated CtIP can be targeted by the SUMO-dependent E3 ubiquitin ligase RNF4 for polyubiquitination and subsequent degradation. As a consequence, cells expressing non-SUMOylatable CtIP mutants exhibit aberrant accumulation of CtIP at DSB sites, uncontrolled excessive end resection, and defective HR. Our results suggest that active CtIP triggers its own SUMOylation and degradation, establishing a negative feedback loop that restricts CtIP activity at DSBs and thereby prevents excessive end resection and genome instability.     

Multiscale photonic imaging of the native and implanted cochlea

The cochlea of our auditory system is an intricate structure deeply embedded in the temporal bone. Compared with other sensory organs such as the eye, the cochlea has remained poorly accessible for investigation, for example, by imaging. This limitation also concerns the further development of technology for restoring hearing in the case of cochlear dysfunction, which requires quantitative information on spatial dimensions and the sensorineural status of the cochlea. Here, we employed X-ray phase-contrast tomography and light-sheet fluorescence microscopy and their combination for multiscale and multimodal imaging of cochlear morphology in species that serve as established animal models for auditory research. We provide a systematic reference for morphological parameters relevant for cochlear implant development for rodent and nonhuman primate models. We simulate the spread of light from the emitters of the optical implants within the reconstructed nonhuman primate cochlea, which indicates a spatially narrow optogenetic excitation of spiral ganglion neurons.

In the case of profound sensorineural hearing impairment, cochlear implants (CIs) partially restore hearing by providing auditory information to the brain via electrical stimulation of the spiral ganglion neurons (SGNs). CIs enable speech understanding in the majority of the ∼700,000 users worldwide. However, current clinical CIs are limited by their wide current spread (1) resulting in poor coding of spectral information (2). Recently, cochlear optogenetics was proposed for stimulating the auditory nerve by light (3–10). As light can be better confined in space, the spread of excitation in the cochlea is lower (3, 9–11) and, hence, future optical CIs (oCIs) promise improved speech comprehension—especially in noisy background—as well as greater music appreciation.For the technical development of oCIs toward a future medical device, major efforts are currently being undertaken to devise multichannel optical stimulators for the cochlea (10, 12–17). As is the case for the electrodes of current CIs, future oCIs will place multiple stimulation channels, here microscale emitters, along the tonotopic axis of the cochlea. Further development of the oCIs requires precise estimates of parameters such as scala tympani size, optimal probe stiffness, and bending radius. Moreover, cochlear optogenetics employs gene transfer to the SGNs for which adeno-associated viruses (AAVs) seem promising candidate vectors (3–5, 8). AAV delivery has used injection of virus suspension via the round window (4, 8) or directly into Rosenthal’s canal (5, 9, 10). Therefore, the volumes of Rosenthal’s canal and the scalae tympani, vestibuli and media needed to be evaluated in order to estimate the required virus load for injection. Finally, the sensorineural status of the cochlea is highly relevant for future gene therapy and CI stimulation, and hence, quantitative imaging of sensory cells and neurons is an important objective.Here, we employed multiscale X-ray phase-contrast tomography (XPCT) and light-sheet fluorescence microscopy (LSFM) and provide an analysis of cochlear morphology for mice, rats, gerbils, guinea pigs, and marmosets. Each of these animal models offers unique advantages for auditory research. The mouse is readily available for genetic manipulation (e.g., ref. 18). Channelrhodopsin-expressing transgenic lines are available also for rats (19, 20) that offer a larger cochlea and can carry heavier implants than mice (21–24). Similarly, gerbils and guinea pigs are established rodent models for auditory research with larger-sized cochleae. Moreover, gerbils, which have low-frequency hearing more similar to humans, have already been employed for cochlear optogenetics (5, 9, 10, 24). Finally, we analyzed the cochlea of the common marmoset, as an established nonhuman primate model for auditory research (e.g., refs. 25, 26). Marmosets possess a rich vocalization repertoire and share a pitch perception mechanism with humans (27). Therefore, we compared cochlear insertion of newly designed oCIs with electrical cochlear implants (eCI) and modeled the optical spread of excitation in the marmoset cochlea.