Abdominal Compartment Syndrome Following Paraesophageal and Diaphragmatic Hernia Repair

Abdominal compartment syndrome (ACS) is defined as a sustained intra-abdominal pressure ≥ 20 mm Hg, associated with new organ dysfunction. Postoperative ACS can occur following repair of hernias with loss-of-domain. Such loss-of-domain hernias are well described involving incisional hernias, less described involving Bochdalek congenital diaphragmatic hernias (CDHs), but not yet described involving paraesophageal hernias (PEHs) or Morgagni CDHs. We describe a case of postoperative ACS following laparoscopic repair of a PEH and Morgagni CDH. This case demonstrates that prophylactic omentectomy should be considered in select patients undergoing repair of large PEHs or CDHs, as ACS is a rare but potential complication.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes a diverse range of genomic sites directly within enhancers and promoters and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites, and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF degradation, reveals that ZNF143 and CTCF collaborate to regulate higher-order topological chromatin organization. Finally, CTCF depletion enlarges direct ZNF143 chromatin looping. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate CTCF/cohesin configuration and TAD (topologically associating domain) formation, whereas directional recognition of genomic DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.

Isolated Extensor Hallucis Longus Compartment Syndrome: A Case Report

We present the case of an isolated extensor hallucis longus compartment syndrome following a diaphyseal fibular fracture. Our subject underwent syndesmotic fixation and experienced ongoing pain post-procedure. This was associated with an isolated loss of power in extension of the hallux. A diagnosis of an isolated extensor hallucis longus compartment syndrome followed. Our case highlights the vulnerability of this muscle belly to ischemia and reiterates the value of complete clinical examination in the postoperative patient.

An Artificial Liposome Compartment with Size Exclusion Molecular Transport

The cellular compartment plays an essential role in organizing the complex and diverse biochemical reactions within the cell. By mimicking the function of such cellular compartments, the challenge of constructing artificial compartments has been taken up to develop new biochemical tools for efficient material production and diagnostics. The important features required for the artificial compartment are that it isolates the interior from the external environment and is further functionalized to control the transport of target chemicals to regulate the interior concentration of both substrate and reaction products. In this study, an artificial compartment with size-selective molecular transport function was constructed by using a DNA origami-guided liposome prepared by modifying the method reported by Perrault et al. This completely isolates the liposome interior, including the DNA origami skeleton, from the external environment and allows the assembly of a defined number of molecules of interest inside and/or outside the compartment. By incorporating a bacterial membrane protein, OmpF, into the liposome, the resulting artificial compartment was shown to transport only the molecule of interest with a molecular weight below 600 Da from the external environment into the interior of the compartment.

Construction of Osmotic Pressure Responsive Vacuole-like Bacterial Organelles with Capsular Polysaccharides as Building Blocks

Many artificial organelles or subcellular compartments have been developed to tune gene expression, regulate metabolic pathways, or endow new cell functions. Most of these organelles or compartments were built using proteins or nucleic acids as building blocks. In this study, we demonstrated that capsular polysaccharide (CPS) retained inside bacteria cytosol assembled into mechanically stable CPS compartments. The CPS compartments were able to accommodate and release protein molecules but not lipids or nucleic acids. Intriguingly, we found that the CPS compartment size responds to osmotic stress and this compartment improves cell survival under high osmotic pressures, which was similar to the vacuole functionalities. By fine-tuning the synthesis and degradation of CPS with osmotic stress-responsive promoters, we achieved dynamic regulation of the size of CPS compartments and the host cells in response to external osmotic stress. Our results shed new light on developing prokaryotic artificial organelles with carbohydrate macromolecules.

Controlled Assembly of Fluorophores inside a Nanoliposome

Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.

Margin Free Resection Achieves Excellent Long Term Outcomes in Parathyroid Cancer

Long-term outcomes of parathyroid cancer remain poorly documented and unsatisfactory. This cohort includes 25 consecutive parathyroid cancer patients with median follow-up of 10.7 years (range 4.1−26.5 years). Pre-operative work-up in the center identified a suspicion of parathyroid cancer in 17 patients. En bloc resection, including the recurrent laryngeal nerve in 4/17 (23.5%), achieved cancer-free resection margins (R0) in 82.4% and lasting loco-regional disease control in 94.1%. Including patients referred after initial surgery elsewhere, R0 resection was achieved in merely 17/25 (68.0%) of patients. Cancer-positive margins (R1) in 8 patients led to local recurrence in 50%. On multivariate analysis, only margin status prevailed as independent predictor of recurrence free survival (χ2 19.5, p < 0.001). Local excision alone carried a 3.5-fold higher risk of positive margins than en bloc resection (CI95: 1.1−11.3; p = 0.03), and a 6.4-fold higher risk of locoregional recurrence (CI95: 0.8−52.1; p = 0.08). R1-status was associated with an 18.0-fold higher risk of recurrence and redo surgery (CI95: 1.1−299.0; p = 0.04), and a 22.0-fold higher probability of radiation (CI95: 1.4−355.5; p = 0.03). In patients at risk, adjuvant radiation reduced the actuarial risk of locoregional recurrence (p = 0.05). When pre-operative scrutiny resulted in upfront oncological surgery achieving cancer free margins, it afforded 100% recurrence free survival at 5- and 10-year follow-up, whilst failure to achieve clear margins caused significant burden by outpatient admissions (176 vs. 4 days; χ2 980, p < 0.001) and exposure to causes for concern (1369 vs. 0 days; χ2 11.3, p = 0.003). Although limited by cohort size, our study emphasizes the paradigm of getting it right the first time as key to improve survivorship in a cancer with excellent long-term prognosis.

A Rare Case of Acute Compartment Syndrome (ACS) Involving the Upper Limb in a Patient on Warfarin

Acute compartment syndrome (ACS) is an acute event characterized by increased pressure in the extremities where fascia encloses muscles, vessels, and nerves, leading to complications in tissue perfusion and, eventually, tissue necrosis and death. This is usually seen after trauma, crush injuries, and fractures. Similar events can also happen in the abdomen and lead to impaired perfusion in the abdominal organs. Hypovolemia, medications, and repeated or suboptimal diagnostic tests tend to worsen a pre-existing ACS, and the mainstay of its management is fasciotomy to prevent ischemic necrosis and rhabdomyolysis. Here we discuss a 64-year-old female with ACS involving the left upper limb, secondary to anticoagulation on warfarin and aspirin for atrial fibrillation. Her history was significant for peripheral vascular disease, above-knee amputation, and congestive heart failure. This article emphasizes the importance of early recognition and management of ACS to salvage limbs.

Spalt and disco define the dorsal-ventral neuroepithelial compartments of the developing Drosophila medulla

Spatial patterning of neural stem cell populations is a powerful mechanism by which to generate neuronal diversity. In the developing Drosophila medulla, the symmetrically dividing neuroepithelial cells of the outer proliferation center crescent are spatially patterned by the nonoverlapping expression of 3 transcription factors: Vsx1 in the center, Optix in the adjacent arms, and Rx in the tips. These spatial genes compartmentalize the outer proliferation center and, together with the temporal patterning of neuroblasts, act to diversify medulla neuronal fates. The observation that the dorsal and ventral halves of the outer proliferation center also grow as distinct compartments, together with the fact that a subset of neuronal types is generated from only one half of the crescent, suggests that additional transcription factors spatially pattern the outer proliferation center along the dorsal-ventral axis. Here, we identify the spalt (salm and salr) and disco (disco and disco-r) genes as the dorsal-ventral patterning transcription factors of the outer proliferation center. Spalt and Disco are differentially expressed in the dorsal and ventral outer proliferation center from the embryo through to the third instar larva, where they cross-repress each other to form a sharp dorsal-ventral boundary. We show that hedgehog is necessary for Disco expression in the embryonic optic placode and that disco is subsequently required for the development of the ventral outer proliferation center and its neuronal progeny. We further demonstrate that this dorsal-ventral patterning axis acts independently of Vsx1-Optix-Rx and thus propose that Spalt and Disco represent a third outer proliferation center patterning axis that may act to further diversify medulla fates.

Compartment-specific Clinical Outcomes in Patients With Soft Tissue Sarcomas of the Thigh

BACKGROUND/AIM

The thigh is divided into the anterior, medial, and posterior compartments, and malignant soft tissue tumours can occur in any compartment of the thigh. This study analysed the relationship between various factors, particularly tumour location and clinical outcome, in patients with primary soft tissue sarcoma of the thigh.

PATIENTS AND METHODS

Seventy-four patients were included in this retrospective study. The relationships between variables and prognosis were statistically analysed.

RESULTS

Multivariate analysis of the patient clinical data demonstrated that seromas developed more often in the medial compartment tumours and postoperative complications excluding seroma occurred more frequently in patients with two or more muscles resected or stage III tumours. A low Musculoskeletal Tumor Society score was associated with a long operative time (more than 120 min), anterior compartment tumours, and more than two muscle resections. In addition, soft tissue sarcomas in the medial compartment and stage III sarcomas were associated with a low 5-year metastasis-free survival.

CONCLUSION

Soft tissue sarcomas in the medial compartment were associated with postoperative seroma and metastasis, whereas sarcomas in the anterior compartment correlated with low postoperative function.

Condensates induced by transcription inhibition localize active chromatin to nucleoli

The proper function of the genome relies on spatial organization of DNA, RNA, and proteins, but how transcription contributes to the organization is unclear. Here, we show that condensates induced by transcription inhibition (CITIs) drastically alter genome spatial organization. CITIs are formed by SFPQ, NONO, FUS, and TAF15 in nucleoli upon inhibition of RNA polymerase II (RNAPII). Mechanistically, RNAPII inhibition perturbs ribosomal RNA (rRNA) processing, releases rRNA-processing factors from nucleoli, and enables SFPQ to bind rRNA. While accumulating in CITIs, SFPQ/TAF15 remain associated with active genes and tether active chromatin to nucleoli. In the presence of DNA double-strand breaks (DSBs), the altered chromatin compartmentalization induced by RNAPII inhibition increases gene fusions in CITIs and stimulates the formation of fusion oncogenes. Thus, proper RNAPII transcription and rRNA processing prevent the altered compartmentalization of active chromatin in CITIs, suppressing the generation of gene fusions from DSBs.

Expression of Maf family proteins in glutamatergic neurons of the mouse olfactory bulb

The fate of neurons in the developing brain is largely determined by the combination of transcription factors they express. In particular, stem cells must follow different transcriptional cascades during differentiation in order to generate neurons with different neurotransmitter properties, such as glutamatergic and GABAergic neurons. In the mouse cerebral cortex, it has been shown that large Maf family proteins, MafA, MafB and c-Maf, regulate the development of specific types of GABAergic interneurons but are not expressed in glutamatergic neurons. In this study, we examined the expression of large Maf family proteins in the developing mouse olfactory bulb (OB) by immunohistochemistry and found that the cell populations expressing MafA and MafB are almost identical, and most of them express Tbr2. As Tbr2 is expressed in glutamatergic neurons in the OB, we further examined the expression of glutamatergic and GABAergic neuronal markers in MafA and MafB positive cells. The results showed that in the OB, MafA and MafB are expressed exclusively in glutamatergic neurons, but not in GABAergic neurons. We also found that few cells express c-Maf in the OB. These results indicate that, unlike the cerebral cortex, MafA and/or MafB may regulate the development of glutamatergic neurons in the developing OB. This study advances our knowledge about the development of glutamatergic neurons in the olfactory bulb, and also might suggest that mechanisms for the generation of projection neurons and interneurons differ between the cortex and the olfactory bulb, even though they both develop from the telencephalon.

SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort

BACKGROUND

Oncological patients have a higher risk of prolonged SARS-CoV-2 shedding, which, in turn, can lead to evolutionary mutations and emergence of novel viral variants. The aim of this study was to analyze biological samples of a cohort of oncological patients by deep sequencing to detect any significant viral mutations.

METHODS

High-throughput sequencing was performed on selected samples from a SARS-CoV-2-positive oncological patient cohort. Analysis of variants and minority variants was performed using a validated bioinformatics pipeline.

RESULTS

Among 54 oncological patients, we analyzed 12 samples of 6 patients, either serial nasopharyngeal swab samples or samples from the upper and lower respiratory tracts, by high-throughput sequencing. We identified amino acid changes D614G and P4715L as well as mutations at nucleotide positions 241 and 3037 in all samples. There were no other significant mutations, but we observed intra-host evolution in some minority variants, mainly in the ORF1ab gene. There was no significant mutation identified in the spike region and no minority variants common to several hosts.

CONCLUSIONS

There was no major and rapid evolution of viral strains in this oncological patient cohort, but there was minority variant evolution, reflecting a dynamic pattern of quasi-species replication.

Did Solid Surfaces Enable the Origin of Life?

In this perspective article, I discuss whether and how solid surfaces could have played a key role in the formation of membranous primitive cells on the early Earth. I argue why surface energy could have been used by prebiotic amphiphile assemblies for unique morphological transformations, and present recent experimental findings showing the surface-dependent formation and behavior of sophisticated lipid membrane structures. Finally, I discuss the possible unique contributions of such surface-adhered architectures to the transition from prebiotic matter to living systems.

Forecasting the Long-Term Trends of Coronavirus Disease 2019 (COVID-19) Epidemic Using the Susceptible-Infectious-Recovered (SIR) Model

A simple model for predicting Coronavirus Disease 2019 (COVID-19) epidemic is presented in this study. The prediction model is presented based on the classic Susceptible-Infectious-Recovered (SIR) model, which has been widely used to describe the epidemic time evolution of infectious diseases. The original version of the Kermack and McKendrick model is used in this study. This included the daily rates of infection spread by infected individuals when these individuals interact with a susceptible population, which is denoted by the parameter β, while the recovery rates to determine the number of recovered individuals is expressed by the parameter γ. The parameters estimation of the three-compartment SIR model is determined through using a mathematical sequential reduction process from the logistic growth model equation. As the parameters are the basic characteristics of epidemic time evolution, the model is always tested and applied to the latest actual data of confirmed COVID-19 cases. It seems that this simple model is still reliable enough to describe the dynamics of the COVID-19 epidemic, not only qualitatively but also quantitatively with a high degree of correlation between actual data and prediction results. Therefore, it is possible to apply this model to predict cases of COVID-19 in several countries. In addition, the parameter characteristics of the classic SIR model can provide information on how these parameters reflect the efforts by each country to prevent the spread of the COVID-19 outbreak. This is clearly seen from the changes of the parameters shown by the classic SIR model.

cAMP at Perinuclear mAKAPα Signalosomes Is Regulated by Local Ca2+ Signaling in Primary Hippocampal Neurons

The second messenger cyclic adenosine monophosphate (cAMP) is important for the regulation of neuronal structure and function, including neurite extension. A perinuclear cAMP compartment organized by the scaffold protein muscle A-kinase anchoring protein α (mAKAPα/AKAP6α) is sufficient and necessary for axon growth by rat hippocampal neurons in vitro. Here, we report that cAMP at mAKAPα signalosomes is regulated by local Ca²⁺ signaling that mediates activity-dependent cAMP elevation within that compartment. Simultaneous Forster resonance energy transfer (FRET) imaging using the protein kinase A (PKA) activity reporter AKAR4 and intensiometric imaging using the RCaMP1h fluorescent Ca²⁺ sensor revealed that membrane depolarization by KCl selectively induced activation of perinuclear PKA activity. Activity-dependent perinuclear PKA activity was dependent on expression of the mAKAPα scaffold, while both perinuclear Ca²⁺ elevation and PKA activation were dependent on voltage-dependent L-type Ca²⁺ channel activity. Importantly, chelation of Ca²⁺ by a nuclear envelope-localized parvalbumin fusion protein inhibited both activity-induced perinuclear PKA activity and axon elongation. Together, this study provides evidence for a model in which a neuronal perinuclear cAMP compartment is locally regulated by activity-dependent Ca²⁺ influx, providing local control for the enhancement of neurite extension.

Chronic exertional compartment syndrome of the forearm: a systematic review

The aim of this systematic review is to understand which surgical procedure provides better results in terms of pain relief and function in the treatment of chronic exertional compartment syndrome (CECS) of the forearm.

We searched Medline (PubMed), Web of Science, Embase and Scopus databases on 8 July 2020. Twelve studies were included in this review.

We assessed the quality of the studies using the Coleman Methodological Score.

Data on demographic features, operative readings, diagnostic methods, follow-up periods, type and rates of complications, survivorship of the procedure, return to sport activity, and outcome measures were recorded.

In conclusion, compared to the other techniques, endoscopic fasciotomy delivers similar success rates and lower incidence of complications.

Cite this article: EFORT Open Rev 2021;6:101-106. DOI: 10.1302/2058-5241.6.200107

Osmosis-Driven Water Transport through a Nanochannel: A Molecular Dynamics Simulation Study

In this work, we study a chemical method to transfer water molecules from a nanoscale compartment to another initially empty compartment through a nanochannel. Without any external force, water molecules do not spontaneously move to the empty compartment because of the energy barrier for breaking water hydrogen bonds in the transport process and the attraction between water molecules and the compartment walls. To overcome the energy barrier, we put osmolytes into the empty compartment, and to remove the attraction, we weaken the compartment-water interaction. This allows water molecules to spontaneously move to the empty compartment. We find that the initiation and time-transient behavior of water transport depend on the properties of the osmolytes specified by their number and the strength of their interaction with water. Interestingly, when osmolytes strongly interact with water molecules, transport immediately starts and continues until all water molecules are transferred to the initially empty compartment. However, when the osmolyte interaction strength is intermediate, transport initiates stochastically, depending on the number of osmolytes. Surprisingly, because of strong water-water interactions, osmosis-driven water transport through a nanochannel is similar to pulling a string at a constant speed. Our study helps us understand what minimal conditions are needed for complete transfer of water molecules to another compartment through a nanochannel, which may be of general concern in many fields involving molecular transfer.

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

Widespread changes to DNA methylation and chromatin are well documented in cancer, but the fate of higher-order chromosomal structure remains obscure. Here we integrated topological maps for colon tumors and normal colons with epigenetic, transcriptional, and imaging data to characterize alterations to chromatin loops, topologically associated domains, and large-scale compartments. We found that spatial partitioning of the open and closed genome compartments is profoundly compromised in tumors. This reorganization is accompanied by compartment-specific hypomethylation and chromatin changes. Additionally, we identify a compartment at the interface between the canonical A and B compartments that is reorganized in tumors. Remarkably, similar shifts were evident in non-malignant cells that have accumulated excess divisions. Our analyses suggest that these topological changes repress stemness and invasion programs while inducing anti-tumor immunity genes and may therefore restrain malignant progression. Our findings call into question the conventional view that tumor-associated epigenomic alterations are primarily oncogenic.

Plant and animal chromatin three-dimensional organization: similar structures but different functions

Chromatin is the main carrier of genetic information and is non-randomly distributed within the nucleus. Next-generation sequence-based chromatin conformation capture technologies have enabled us to directly examine its three-dimensional organization at an unprecedented scale and resolution. In the best-studied mammalian models, chromatin folding can be broken down into three hierarchical levels, compartment, domains, and loops, which play important roles in transcriptional regulation. Although similar structures have now been identified in plants, they might not possess exactly the same functions as the mammalian ones. Here, we review recent Hi-C studies in plants, compare plant chromatin structures with their mammalian counterparts, and discuss the differences between plants with different genome sizes.

Thigh Compartment Syndrome After Thrombolytic Therapy of an Occluded Lower Extremity Bypass Graft

Compartment syndrome is caused by increased pressure within fascial compartment. We present a unique case of a thigh compartment syndrome that occurred after overnight catheter delivered Tissue plasminogen activator (tPA) thrombolysis of an acutely thrombosis femoral-to above knee popliteal artery Propaten^® PTFE (WL Gore & Associates, Flagstaff, AZ) bypass graft. The condition was treated by emergency fasciotomy and the patient recovered uneventfully.

Mechanisms and Functions of Chromosome Compartmentalization

Active and inactive chromatin are spatially separated in the nucleus. In Hi-C data, this is reflected by the formation of compartments, whose interactions form a characteristic checkerboard pattern in chromatin interaction maps. Only recently have the mechanisms that drive this separation come into view. Here, we discuss new insights into these mechanisms and possible functions in genome regulation. Compartmentalization can be understood as a microphase-segregated block co-polymer. Microphase separation can be facilitated by chromatin factors that associate with compartment domains, and that can engage in liquid-liquid phase separation to form subnuclear bodies, as well as by acting as bridging factors between polymer sections. We then discuss how a spatially segregated state of the genome can contribute to gene regulation, and highlight experimental challenges for testing these structure-function relationships.

Stereotyped Combination of Hearing and Wind/Gravity-Sensing Neurons in the Johnston's Organ of Drosophila

The antennal ear of the fruit fly, called the Johnston's organ (JO), detects a wide variety of mechanosensory stimuli, including sound, wind, and gravity. Like many sensory cells in insect, JO neurons are compartmentalized in a sensory unit (i.e., scolopidium). To understand how different subgroups of JO neurons are organized in each scolopidial compartment, we visualized individual JO neurons by labeling various subgroups of JO neurons in different combinations. We found that vibration-sensitive (or deflection-sensitive) neurons rarely grouped together in a single scolopidial compartment. This finding suggests that JO neurons are grouped in stereotypical combinations each with a distinct response property in a scolopidium.

Orbital Compartment Syndrome: An Update With Review Of The Literature

Orbital compartment syndrome (OCS) is a potentially blinding condition characterized by a rapid increase in intra-orbital pressure. OCS is most commonly seen in the context of intra-orbital hemorrhage secondary to either trauma or surgery. A review of the literature indicates that better visual outcomes are achieved when interventions occur within the first 2 hrs. There are reports of visual recovery after a delay in management and consideration should be given to intervention even when presentation is delayed. Reported interventions include: lateral canthotomy with cantholysis, bony orbital decompression and treatment of the underlying cause.

Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells

Cohesin exists in two variants carrying either STAG/SA1 or SA2. Here we have addressed their specific contributions to the unique spatial organization of the mouse embryonic stem cell genome, which ensures super-enhancer-dependent transcription of pluripotency factors and repression of lineage-specification genes within Polycomb domains. We find that cohesin-SA2 facilitates Polycomb domain compaction through Polycomb repressing complex 1 (PRC1) recruitment and promotes the establishment of long-range interaction networks between distant Polycomb-bound promoters that are important for gene repression. Cohesin-SA1, in contrast, disrupts these networks, while preserving topologically associating domain (TAD) borders. The diverse effects of both complexes on genome topology may reflect two modes of action of cohesin. One, likely involving loop extrusion, establishes overall genome arrangement in TADs together with CTCF and prevents excessive segregation of same-class compartment regions. The other is required for organization of local transcriptional hubs such as Polycomb domains and super-enhancers, which define cell identity.

Investigating Prebiotic Protocells for A Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective

Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.

What can we learn from the construction of in vitro replication systems?

Replication is a central function of living organisms. Several types of replication systems have been constructed in vitro from various molecules, including peptides, DNA, RNA, and proteins. In this review, I summarize the progress in the construction of replication systems over the past few decades and discuss what we can learn from their construction. I introduce various types of replication systems, supporting the feasibility of the spontaneous appearance of replication early in Earth's history. In the latter part of the review, I focus on parasitic replicators, one of the largest obstacles for sustainable replication. Compartmentalization is discussed as a possible solution.

Regional differences in mitral cell development in mouse olfactory bulb

Olfactory sensory neurons (OSNs) located in the dorsomedial and ventromedial regions of the olfactory epithelium (OE) are distinguished from one another based on their molecular expression patterns. This difference is reflected in the separation of the glomerular layer of the olfactory bulb (OB) into dorsomedial and ventrolateral regions. However, it is unclear whether a complementary separation is also evident in the projection neurons that innervate the OB glomeruli. In this study, we compared the development of the OB between different regions by focusing on the transcription factor, Tbx21, which is expressed by mitral and tufted cells in the mature OB. Examining the OB at different developmental ages, we found that Tbx21 expression commenced in the anteromedial region called the tongue-shaped area, followed by the dorsomedial and then ventrolateral areas. We also showed that the tongue-shaped area was innervated by the OSNs located in the most dorsomedial part of the ventrolateral OE, the V-zone:DM. Interestingly, the generation of OSNs occurred first in the dorsomedial zone including the V-zone:DM, suggesting a correlation between the time course of OSN generation in the OE and Tbx21 expression in their target region of the OB. In contrast, expression of vGluT1, which is also found in all mitral cells in the mature OB, was first detected in the ventrolateral region during development. Our findings demonstrate that the development of projection neurons occurs in a compartmentalized manner in the OB; tongue-shaped, dorsomedial, and ventrolateral areas, and that not all projection neurons follow the same developmental pathway.

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization

Interaction domains in Drosophila chromosomes form by segregation of active and inactive chromatin in the absence of CTCF loops, but the role of transcription versus other architectural proteins in chromatin organization is unclear. Here, we find that positioning of RNAPII via transcription elongation is essential in the formation of gene loops, which in turn interact to form compartmental domains. Inhibition of transcription elongation or depletion of cohesin decreases gene looping and formation of active compartmental domains. In contrast, depletion of condensin II, which also localizes to active chromatin, causes increased gene looping, formation of compartmental domains, and stronger intra-chromosomal compartmental interactions. Condensin II has a similar role in maintaining inter-chromosomal interactions responsible for pairing between homologous chromosomes, whereas inhibition of transcription elongation or cohesin depletion has little effect on homolog pairing. The results suggest distinct roles for cohesin and condensin II in the establishment of 3D nuclear organization in Drosophila.

Release of fascial compartment boundaries reduces muscle force output

Most limb muscles operate within a compartment defined by fascial layers that enclose a muscle or groups of muscles within a defined space. These compartments are important clinically, because fluid accumulation can cause ischemia and tissue necrosis if untreated. Little is known, however, about how fascial enclosures influence healthy muscle function. One previous study showed that removing a fascial covering reduced the force output of a muscle under maximal stimulation. We hypothesized that such reduction in force output was due to a change in the muscle length following fasciotomy and that a reduced force output could be explained by the length-tension relationship of muscle. Thus we predicted that the maximum force across a range of lengths would be unchanged following fasciotomy. We measured maximal tetanic force output in a wing muscle in wild turkeys both before and after removal of fascia that enclosed the muscle in a compartment. Our hypothesis was not supported. The length-tension curve of this muscle showed that removal of fascia reduced maximum force output to 72 ± 10% of the prefascial release condition. Thus a reduction in muscle force following fasciotomy was not explained by a change in muscle length. The mechanism underlying reduction in force is unclear, but it suggests that the assumption underlying most isolated muscle experiments, i.e., removal of a muscle from its situation in vivo does not influence its maximal mechanical output, may need reexamining. NEW & NOTEWORTHY Most limb muscles are enclosed within compartments bound by robust fascial sheets. The mechanical significance of the close packing of muscle and fascia is largely unexplored. We used an animal model to show that removal of a fascial covering reduces the maximal force developed during contraction. These results raise questions about the use of isolated muscles to estimate muscle performance and suggest that a muscle's mechanical surrounding influences performance by mechanisms that are not understood.

Bilateral Compartment Syndrome in Intravenous Drug Abuse

Compartment syndrome is an orthopedic emergency in which the neurovasculature of the extremity is compromised. Typically, it presents unilaterally and is the consequence of major trauma to the extremity in the form of fracture. However, more uncommon etiologies of compartment syndrome have been reported, which includes reperfusion injury, burns, and congenital or acquired bleeding disorders.

We present an extremely rare case of bilateral posterior thigh compartment syndrome thought to be due to intravenous drug abuse (IVDA) causing prolonged ischemia with subsequent reperfusion. This case is particularly relevant in today’s clinical setting given the current opioid epidemic and subsequent rise in intravenous drug use.

Pathways of host cell exit by intracellular pathogens

Host cell exit is a critical step in the life-cycle of intracellular pathogens, intimately linked to barrier penetration, tissue dissemination, inflammation, and pathogen transmission. Like cell invasion and intracellular survival, host cell exit represents a well-regulated program that has evolved during host-pathogen co-evolution and that relies on the dynamic and intricate interplay between multiple host and microbial factors. Three distinct pathways of host cell exit have been identified that are employed by three different taxa of intracellular pathogens, bacteria, fungi and protozoa, namely (i) the initiation of programmed cell death, (ii) the active breaching of host cellderived membranes, and (iii) the induced membrane-dependent exit without host cell lysis. Strikingly, an increasing number of studies show that the majority of intracellular pathogens utilize more than one of these strategies, dependent on life-cycle stage, environmental factors and/or host cell type. This review summarizes the diverse exit strategies of intracellular-living bacterial, fungal and protozoan pathogens and discusses the convergently evolved commonalities as well as system-specific variations thereof. Key microbial molecules involved in host cell exit are highlighted and discussed as potential targets for future interventional approaches.

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types

Processes like cellular senescence are characterized by complex events giving rise to heterogeneous cell populations. However, the early molecular events driving this cascade remain elusive. We hypothesized that senescence entry is triggered by an early disruption of the cells' three-dimensional (3D) genome organization. To test this, we combined Hi-C, single-cell and population transcriptomics, imaging, and in silico modeling of three distinct cells types entering senescence. Genes involved in DNA conformation maintenance are suppressed upon senescence entry across all cell types. We show that nuclear depletion of the abundant HMGB2 protein occurs early on the path to senescence and coincides with the dramatic spatial clustering of CTCF. Knocking down HMGB2 suffices for senescence-induced CTCF clustering and for loop reshuffling, while ectopically expressing HMGB2 rescues these effects. Our data suggest that HMGB2-mediated genomic reorganization constitutes a primer for the ensuing senescent program.

Mastering Complexity: Towards Bottom-up Construction of Multifunctional Eukaryotic Synthetic Cells

With the ultimate aim to construct a living cell, bottom-up synthetic biology strives to reconstitute cellular phenomena in vitro - disentangled from the complex environment of a cell. Recent work towards this ambitious goal has provided new insights into the mechanisms governing life. With the fast-growing library of functional modules for synthetic cells, their classification and integration become increasingly important. We discuss strategies to reverse-engineer and recombine functional parts for synthetic eukaryotes, mimicking the characteristics of nature's own prototype. Particularly, we focus on large outer compartments, complex endomembrane systems with organelles, and versatile cytoskeletons as hallmarks of eukaryotic life. Moreover, we identify microfluidics and DNA nanotechnology as two technologies that can integrate these functional modules into sophisticated multifunctional synthetic cells.

In Situ Caging of Biomolecules in Graphene Hybrids for Light Modulated Bioactivity

Remote and noninvasive modulation of protein activity is essential for applications in biotechnology and medicine. Optical control has emerged as the most attractive approach owing to its high spatial and temporal resolutions; however, it is challenging to engineer light responsive proteins. In this work, a near-infrared (NIR) light-responsive graphene-silica-trypsin (GST) nanoreactor is developed for modulating the bioactivity of trypsin molecules. Biomolecules are spatially confined and protected in the rationally designed compartment architecture, which not only reduces the possible interference but also boosts the bioreaction efficiency. Upon NIR irradiation, the photothermal effect of the GST nanoreactor enables the ultrafast in situ heating for remote activation and tuning of the bioactivity. We apply the GST nanoreactor for remote and ultrafast proteolysis of proteins, which remarkably enhances the proteolysis efficiency and reduces the bioreaction time from the overnight of using free trypsin to seconds. We envision that this work not only provides a promising tool of ultrafast and remotely controllable proteolysis for in vivo proteomics in study of tissue microenvironment and other biomedical applications but also paves the way for exploring smart artificial nanoreactors in biomolecular modulation to gain insight in dynamic biological transformation.

Segmental architecture, compartmentalization, and lineage anatomy

The subesophageal zone (SEZ) of the Drosophila brain houses the circuitry underlying feeding behavior and is involved in many other aspects of sensory processing and locomotor control. Formed by the merging of four neuromeres, the internal architecture of the SEZ can be best understood by identifying segmentally reiterated landmarks emerging in the embryo and larva, and following the gradual changes by which these landmarks become integrated into the mature SEZ during metamorphosis. In previous works, the system of longitudinal fibers (connectives) and transverse axons (commissures) has been used as a scaffold that provides internal landmarks for the neuromeres of the larval ventral nerve cord. We have extended the analysis of this scaffold to the SEZ and, in addition, reconstructed the tracts formed by lineages and nerves in relationship to the connectives and commissures. As a result, we establish reliable criteria that define boundaries between the four neuromeres (tritocerebrum, mandibular neuromere, maxillary neuromere, labial neuromere) of the SEZ at all stages of development. Fascicles and lineage tracts also demarcate seven columnar neuropil domains (ventromedial, ventro-lateral, centromedial, central, centrolateral, dorsomedial, dorsolateral) identifiable throughout development. These anatomical subdivisions, presented in the form of an atlas including confocal sections and 3D digital models for the larval, pupal and adult stage, allowed us to describe the morphogenetic changes shaping the adult SEZ. Finally, we mapped MARCM-labeled clones of all secondary lineages of the SEZ to the newly established neuropil subdivisions. Our work will facilitate future studies of function and comparative anatomy of the SEZ.

Eradication of HIV from Tissue Reservoirs: Challenges for the Cure

The persistence of HIV infection, even after lengthy and successful combined antiretroviral therapy (cART), has precluded an effective cure. The anatomical locations and biological mechanisms through which the viral population is maintained remain unknown. Much research has focused nearly exclusively on circulating resting T cells as the predominant source of persistent HIV, a strategy with limited success in developing an effective cure strategy. In this study, we review research supporting the importance of anatomical tissues and other immune cells for HIV maintenance and expansion, including the central nervous system, lymph nodes, and macrophages. We present accumulated research that clearly demonstrates the limitations of using blood-derived cells as a proxy for tissue reservoirs and sanctuaries throughout the body. We cite recent studies that have successfully used deep-sequencing strategies to uncover the complexity of HIV infection and the ability of the virus to evolve despite undetectable plasma viral loads. Finally, we suggest new strategies and highlight the importance of tissue banks for future research.

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.

3D Chromatin Structures of Mature Gametes and Structural Reprogramming during Mammalian Embryogenesis

High-order chromatin structure plays important roles in gene expression regulation. Knowledge of the dynamics of 3D chromatin structures during mammalian embryo development remains limited. We report the 3D chromatin architecture of mouse gametes and early embryos using an optimized Hi-C method with low-cell samples. We find that mature oocytes at the metaphase II stage do not have topologically associated domains (TADs). In sperm, extra-long-range interactions (>4 Mb) and interchromosomal interactions occur frequently. The high-order structures of both the paternal and maternal genomes in zygotes and two-cell embryos are obscure but are gradually re-established through development. The establishment of the TAD structure requires DNA replication but not zygotic genome activation. Furthermore, unmethylated CpGs are enriched in A compartment, and methylation levels are decreased to a greater extent in A compartment than in B compartment in embryos. In summary, the global reprogramming of chromatin architecture occurs during early mammalian development.

Compartmentalized cGMP Responses of Olfactory Sensory Neurons in Caenorhabditis elegans

Cyclic guanosine monophosphate (cGMP) plays a crucial role as a second messenger in the regulation of sensory signal transduction in many organisms. In AWC olfactory sensory neurons of Caenorhabditis elegans, cGMP also has essential and distinctive functions in olfactory sensation and adaptation. According to molecular genetic studies, when nematodes are exposed to odorants, a decrease in cGMP regulates cGMP-gated channels for olfactory sensation. Conversely, for olfactory adaptation, an increase in cGMP activates protein kinase G to modulate cellular physiological functions. Although these opposing cGMP responses in single neurons may occur at the same time, it is unclear how cGMP actually behaves in AWC sensory neurons. A hypothetical explanation for opposing cGMP responses is region-specific behaviors in AWC: for odor sensation, cGMP levels in cilia could decrease, whereas odor adaptation is mediated by increased cGMP levels in soma. Therefore, we visualized intracellular cGMP in AWC with a genetically encoded cGMP indicator, cGi500, and examined spatiotemporal cGMP responses in AWC neurons. The cGMP imaging showed that, after odor exposure, cGMP levels in AWC cilia decreased transiently, whereas levels in dendrites and soma gradually increased. These region-specific responses indicated that the cGMP responses in AWC neurons are explicitly compartmentalized. In addition, we performed Ca²⁺ imaging to examine the relationship between cGMP and Ca²⁺ These results suggested that AWC sensory neurons are in fact analogous to vertebrate photoreceptor neurons.SIGNIFICANCE STATEMENT Cyclic guanosine monophosphate (cGMP) plays crucial roles in the regulation of sensory signal transduction in many animals. In AWC olfactory sensory neurons of Caenorhabditis elegans, cGMP also has essential and distinctive functions involving olfactory sensation and adaptation. Here, we visualized intracellular cGMP in AWC neurons with a genetically encoded cGMP indicator and examined how these different functions could be regulated by the same second messenger in single neurons. cGMP imaging showed that, after odor application, cGMP levels in cilia decreased transiently, whereas levels in dendrites and soma gradually increased. These region-specific responses indicated that the responses in AWC neurons are explicitly compartmentalized. In addition, by combining cGMP and Ca²⁺ imaging, we observed that AWC neurons are analogous to vertebrate photoreceptor neurons.

An Evolutionarily Conserved Network Mediates Development of the zona limitans intrathalamica, a Sonic Hedgehog-Secreting Caudal Forebrain Signaling Center

Recent studies revealed new insights into the development of a unique caudal forebrain-signaling center: the zona limitans intrathalamica (zli). The zli is the last brain signaling center to form and the first forebrain compartment to be established. It is the only part of the dorsal neural tube expressing the morphogen Sonic Hedgehog (Shh) whose activity participates in the survival, growth and patterning of neuronal progenitor subpopulations within the thalamic complex. Here, we review the gene regulatory network of transcription factors and cis-regulatory elements that underlies formation of a shh-expressing delimitated domain in the anterior brain. We discuss evidence that this network predates the origin of chordates. We highlight the contribution of Shh, Wnt and Notch signaling to zli development and discuss implications for the fact that the morphogen Shh relies on primary cilia for signal transduction. The network that underlies zli development also contributes to thalamus induction, and to its patterning once the zli has been set up. We present an overview of the brain malformations possibly associated with developmental defects in this gene regulatory network (GRN).

Diagnostic accuracy of intracellular uptake rates calculated using dynamic Gd-EOB-DTPA-enhanced MRI for hepatic fibrosis stage

PURPOSE

To assess the diagnostic accuracy of intracellular uptake rates (K_i ), and other quantitative pharmacokinetic (PK) parameters, for hepatic fibrosis stage; to compare this accuracy with a previously published semiquantitative metric, contrast enhancement index (CEI); and to assess variability of these parameters between liver regions.

MATERIALS AND METHODS

This was a case-control study design. Dynamic Gd-EOB-DTPA-enhanced 1.5T magnetic resonance imaging (MRI) was performed prospectively in 22 subjects with varying known stages of hepatic fibrosis. PK parameters and CEI were derived from the whole livers and from three fixed regions of interest (ROIs) in all subjects. Spearman rank correlation coefficients were computed to assess the relationship between fibrosis stages and each parameter. Receiver operating characteristic (ROC) curves were constructed to discriminate severe fibrosis (stages 3-4) from nonsevere fibrosis (stages 0-2). The coefficient of variation (CV) was calculated to assess variability in parameters between ROIs.

RESULTS

K_i and fibrosis stage were significantly correlated (R = -0.55, 95% confidence interval [CI] [-0.79, -0.14], P = 0.01). Area under ROC curve (AUC) in distinguishing severe from nonsevere fibrosis for K_i was 0.84 (95% CI [0.65,1.00]), and for CEI was 0.64 (95% CI [0.39, 0.89]) (P = 0.0248). CV for K_i and CEI were 33.4 and 5.8, respectively. The only other parameter in the PK model having significant correlation with fibrosis stage was absolute arterial blood flow (F_a ) (R = -0.48, 95% CI [-0.75,-0.05], P = 0.03).

CONCLUSION

Hepatocyte intracellular uptake rate, K_i , derived from dynamic contrast-enhanced MRI, correlates with fibrosis stage and may contribute to a noninvasive biomarker of hepatic fibrosis.

LEVEL OF EVIDENCE

2 J. Magn. Reson. Imaging 2017;45:1177-1185.

[Characteristics of Microbial Community in Each Compartment of ABR ANAMMOX Reactor Based on High-throughput Sequencing]

In order to investigate the characteristics of microbial community in each compartment of ABR anammox reactor, a five-compartment ABR reactor was used to analyze the microbial community by Miseq High-throughput Sequencing during the steady operational process. The results indicated that the denitrifying bacteria coexisted in the reactor, such as Proteobacteria, Planctomycete, and Nitrospirae bacteria, and the percentages of these three microbial populations in the sludge were 11.66%-20.28%, 2.18%-7.94% and 0.19%-6.30%, respectively. In addition, there were four dominant genera in the phylum Proteobacteria:Rhodoplanes, Dok59, Rubrivivax and Bdellovibrio. Furthermore, Candidatus brocadia and Candidatus kuenenia were the main genera in the phylum Planctomycete. The color of sludge in the five compartments, in turn, varied from red to black. In addition, the biodiversity index of Chao, ACE, Shannon and Simpson indicated that the richness and diversity of microbial community increased gradually, and at the same time, the relative abundance of Proteobacteria increased while that of Planctomycetes gradually decreased. The above conclusion was consistent with the laws of substrate degradation and enrichment of functional microorganisms.

Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system

To date, various cellular functions have been reconstituted in vitro such as self-replication systems using DNA, RNA, and proteins. The next important challenges include the reconstitution of the interactive networks of self-replicating species and investigating how such interactions generate complex ecological behaviors observed in nature. Here, we synthesized a simple replication system composed of two self-replicating host and parasitic RNA species. We found that the parasitic RNA eradicates the host RNA under bulk conditions; however, when the system is compartmentalized, a continuous oscillation pattern in the population dynamics of the two RNAs emerges. The oscillation pattern changed as replication proceeded mainly owing to the evolution of the host RNA. These results demonstrate that a cell-like compartment plays an important role in host-parasite ecological dynamics and suggest that the origin of the host-parasite coevolution might date back to the very early stages of the evolution of life.

Estimation of the Number of Compartments Associated With the Apparent Diffusion Coefficient in MRI: The Theoretical and Experimental Investigations

OBJECTIVE

The goal of the present study was to estimate the number of compartments and the mean apparent diffusion coefficient (ADC) value with the use of the DWI signal curve.

MATERIALS AND METHODS

A useful new mathematic model that includes internal correlation among subcompartments with a distinct number of compartments was proposed. The DWI signal was simulated to estimate the approximate association between the number of subcompartments and the molecular density, with density corresponding to the ratio of the ADC values of the compartments, as determined using the Monte Carlo method.

RESULTS

Various factors, such as energy depletion, temperature, intracellular water accumulation, changes in the tortuosity of the extracellular diffusion paths, and changes in cell membrane permeability, have all been implicated as factors contributing to changes in the ADC of water (ADCw); therefore, one may consider them as pseudocompartments in the new model proposed in this study. The lower the coefficient is, the lower the contribution of the compartment to the net signal will be. The results of the simulation indicate that when the number of compartments increases, the signal will become significantly lower, because the gradient factor (i.e., the b value) will increase. In other words, the signal curve is approximately linear at all b values when the number of compartments in which the tissues have been severely damaged is low; however, when the number of compartments is high, the curve will become constant at high b values, and the perfusion parameters will prevail on the diffusion parameters at low b values. Therefore, normal tissues will be investigated when the number of compartments and the ADC values are high and the b values are low, whereas damaged tissues will be evaluated when the number of compartments and the ADC values are low and the b values are high.

CONCLUSION

The present study investigates damaged tissues at high b values for which the effect of eddy currents will also be compensated. These b values will probably be used in functional MRI.

The Drosophila melanogaster Mutants apblot and apXasta Affect an Essential apterous Wing Enhancer

The selector gene apterous (ap) plays a key role during the development of the Drosophila melanogaster wing because it governs the establishment of the dorsal-ventral (D-V) compartment boundary. The D-V compartment boundary is known to serve as an important signaling center that is essential for the growth of the wing. The role of Ap and its downstream effectors have been studied extensively. However, very little is known about the transcriptional regulation of ap during wing disc development. In this study, we present a first characterization of an essential wing-specific ap enhancer. First, we defined an 874-bp fragment about 10 kb upstream of the ap transcription start that faithfully recapitulates the expression pattern of ap in the wing imaginal disc. Analysis of deletions in the ap locus covering this element demonstrated that it is essential for proper regulation of ap and formation of the wing. Moreover, we showed that the mutations ap^blot and ap^Xasta directly affect the integrity of this enhancer, leading to characteristic wing phenotypes. Furthermore, we engineered an in situ rescue system at the endogenous ap gene locus, allowing us to investigate the role of enhancer fragments in their native environment. Using this system, we were able to demonstrate that the essential wing enhancer alone is not sufficient for normal wing development. The in situ rescue system will allow us to characterize the ap regulatory sequences in great detail at the endogenous locus.

Barriers in the brain: resolving dendritic spine morphology and compartmentalization

Dendritic spines are micron-sized protrusions that harbor the majority of excitatory synapses in the central nervous system. The head of the spine is connected to the dendritic shaft by a 50-400 nm thin membrane tube, called the spine neck, which has been hypothesized to confine biochemical and electric signals within the spine compartment. Such compartmentalization could minimize interspinal crosstalk and thereby support spine-specific synapse plasticity. However, to what extent compartmentalization is governed by spine morphology, and in particular the diameter of the spine neck, has remained unresolved. Here, we review recent advances in tool development - both experimental and theoretical - that facilitate studying the role of the spine neck in compartmentalization. Special emphasis is given to recent advances in microscopy methods and quantitative modeling applications as we discuss compartmentalization of biochemical signals, membrane receptors and electrical signals in spines. Multidisciplinary approaches should help to answer how dendritic spine architecture affects the cellular and molecular processes required for synapse maintenance and modulation.

Bicompartmental phase transfer vehicles based on colloidal dimers

Colloidal particles have been used extensively for stabilizing oil-water interfaces in petroleum, food, and cosmetics industries. They have also demonstrated promising potential in the encapsulation and delivery of drugs. Our work is motivated by challenging applications that require protecting and transporting active agents across the water-oil interfaces, such as delivering catalysts to underground oil phase through water flooding for in situ cracking of crude oil. In this Research Article, we successfully design, synthesize, and test a unique type of bicompartmental targeting vehicle that encapsulates catalytic molecules, finds and accumulates at oil-water interface, releases the catalysts toward the oil phase, and performs hydrogenation reaction of unsaturated oil. This vehicle is based on colloidal dimers that possess structural anisotropy between two compartments. We encapsulate active species, such as fluorescent dye and catalytic molecules in one lobe which consists of un-cross-linked polymers, while the other polymeric lobe is highly cross-linked. Although dimers are dispersible in water initially, the un-cross-linked lobe swells significantly upon contact with a trace amount of oil in aqueous phase. The dimers then become amphiphilic, migrate toward, and accumulate at the oil-water interface. As the un-cross-linked lobe swells and eventually dissolves in oil, the encapsulated catalysts are fully released. We also show that hydrogenation of unsaturated oil can be performed subsequently with high conversion efficiency. By further creating the interfacial anisotropy on the dimers, we can reduce the catalyst release time from hundred hours to 30 min. Our work demonstrates a new concept in making colloidal emulsifiers and phase-transfer vehicles that are important for encapsulation and sequential release of small molecules across two different phases.

Subcellular transcriptome alterations in a cell culture model of spinal muscular atrophy point to widespread defects in axonal growth and presynaptic differentiation

Neuronal function critically depends on coordinated subcellular distribution of mRNAs. Disturbed mRNA processing and axonal transport has been found in spinal muscular atrophy and could be causative for dysfunction and degeneration of motoneurons. Despite the advances made in characterizing the transport mechanisms of several axonal mRNAs, an unbiased approach to identify the axonal repertoire of mRNAs in healthy and degenerating motoneurons has been lacking. Here we used compartmentalized microfluidic chambers to investigate the somatodendritic and axonal mRNA content of cultured motoneurons by microarray analysis. In axons, transcripts related to protein synthesis and energy production were enriched relative to the somatodendritic compartment. Knockdown of Smn, the protein deficient in spinal muscular atrophy, produced a large number of transcript alterations in both compartments. Transcripts related to immune functions, including MHC class I genes, and with roles in RNA splicing were up-regulated in the somatodendritic compartment. On the axonal side, transcripts associated with axon growth and synaptic activity were down-regulated. These alterations provide evidence that subcellular localization of transcripts with axonal functions as well as regulation of specific transcripts with nonautonomous functions is disturbed in Smn-deficient motoneurons, most likely contributing to the pathophysiology of spinal muscular atrophy.