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Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add ecomorphological characterization of a young cryptic divergence within the carnivorous marsupial genus Antechinus. Specifically, we used 168 museum specimens to characterize the recently proposed clades A. stuartii ‘south’, A. stuartii ‘north’ and A. subtropicus. Beyond slight differences attributable to overall size (and, therefore, not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian diversity.

Background: Genetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the host’s anti-viral immune response, in turn affecting the frequency of variants over time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally. Methods: Deep-sequencing data of SARS-CoV-2 from public databases and from clinical samples were analyzed to identify and map genetic variants and sub-genomic RNA transcripts across the genome. Results: Sequence analysis suggests that the 3 adjacent nucleotide changes that result in the K203/R204 variant have arisen by homologous recombination from the core sequence of the leader transcription-regulating sequence (TRS) rather than by stepwise mutation. The resulting sequence changes generate a novel sub-genomic RNA transcript for the C-terminal dimerization domain of nucleocapsid. Deep-sequencing data from 981 clinical samples confirmed the presence of the novel TRS-CS-dimerization domain RNA in individuals with the K203/R204 variant. Quantification of sub-genomic RNA indicates that viruses with the K203/R204 variant may also have increased expression of sub-genomic RNA from other open reading frames. Conclusions: The finding that homologous recombination from the TRS may have occurred since the introduction of SARS-CoV-2 in humans, resulting in both coding changes and novel sub-genomic RNA transcripts, suggests this as a mechanism for diversification and adaptation within its new host.

Advances in multiplexed imaging technologies have drastically improved our ability to characterize healthy and diseased tissues at the single-cell level. Co-detection by indexing (CODEX) relies on DNA-conjugated antibodies and the cyclic addition and removal of complementary fluorescently labeled DNA probes and has been used so far to simultaneously visualize up to 60 markers in situ. CODEX enables a deep view into the single-cell spatial relationships in tissues and is intended to spur discovery in developmental biology, disease and therapeutic design. Herein, we provide optimized protocols for conjugating purified antibodies to DNA oligonucleotides, validating the conjugation by CODEX staining and executing the CODEX multicycle imaging procedure for both formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues. In addition, we describe basic image processing and data analysis procedures. We apply this approach to an FFPE human tonsil multicycle experiment. The hands-on experimental time for antibody conjugation is ~4.5 h, validation of DNA-conjugated antibodies with CODEX staining takes ~6.5 h and preparation for a CODEX multicycle experiment takes ~8 h. The multicycle imaging and data analysis time depends on the tissue size, number of markers in the panel and computational complexity. This protocol describes co-detection by indexing, a highly multiplexed imaging technology that uses DNA-conjugated antibodies to image up to 60 markers in formalin-fixed, paraffin-embedded and fresh-frozen tissues.

While Canada, like most other nation states, has adopted various aspects of neoliberalism, the recent Cannabis Act presents ideological tensions and practical concerns given its advertising and promotional restrictions. Given the rise of neoliberalism within the dominant social, economic, and cultural system of consumer capitalism, it seems contradictory for the Canadian state to develop legislation that creates (or at least, legalizes) a new market wherein advertising and promotions (i.e., the driving forces of consumer capitalism) are effectively made absent. This article identifies and interrogates the existing tensions and contradictions between the Cannabis Act and the promotional cultures of consumer capitalism, as well as the ways in which the Trailer Park Boys (TPB) “brand” and performers (as promotional intermediaries) have attempted to circumvent the existing promotional restrictions. Beginning with a review of the existing literature regarding relevant theoretical perspectives and key concepts, the article provides a brief overview of the Cannabis Act, its promotional restrictions, and the exemptions and legal loopholes thereof. Finally, in presenting and engaging with a case study, this article concludes that the TPB brand has, effectively, circumvented the Cannabis Act’s existing restrictions and subsequently become a multi-platform promotional intermediary.

A new species of branchiobdellidan, Pterodrilus leiteri n. sp., is described from the anterior cephalothorax of the crayfish Cambarus longulus from north-western North Carolina, USA. Like its 10 co...

Targeted, catalytic degradation of oncoproteins using heterobifunctional small molecules is an attractive modality, particularly for hematologic malignancies, which are often initiated by aberrant transcription factors and are challenging to drug with inhibitors. BRD4, a member of the bromodomain and extraterminal family, is a core transcriptional and epigenetic regulator that recruits the P-TEFb complex, which includes Cdk9 and cyclin T, to RNA polymerase II (pol II). Together, BRD4 and CDK9 phosphorylate serine 2 (pSer2) of heptad repeats in the C-terminal domain of RPB1, the large subunit of pol II, promote transcriptional elongation. Small-molecule degraders of BRD4 have shown encouraging efficacy in preclinical models for several tumor types but less efficacy in other cancers including small-cell lung cancer (SCLC) and pancreatic cancer. Here, we evaluated CFT-2718, a new BRD4-targeting degrader with enhanced catalytic activity and in vivo properties. In vivo, CFT-2718 has significantly greater efficacy than the CDK9 inhibitor dinaciclib in reducing growth of the LX-36 SCLC patient-derived xenograft (PDX) model and performed comparably to dinaciclib in limiting growth of the PNX-001 pancreatic PDX model. In vitro, CFT-2718 reduced cell viability in four SCLC and two pancreatic cancer models. In SCLC models, this activity significantly exceeded that of dinaciclib; furthermore, CFT-2718 selectively increased the expression of cleaved PARP, an indicator of apoptosis. CFT-2718 caused rapid BRD4 degradation and reduced levels of total and pSer2 RPB1 protein. These and other findings suggest that BRD-mediated transcriptional suppression merits further exploration in the setting of SCLC.

Staphylococcus aureus is a common organism in orthopaedic infections, but little is known about the genetic diversity of strains during an infectious process. Using periprosthetic joint infection (PJI) as a model, a prospective study was designed to quantify genetic variation among S. aureus strains both among and within patients. Whole genome sequencing and multilocus sequence typing (MLST) was performed to genotype these two populations at high resolution. In nasal cultures, 78% of strains were of clonal complexes CC5, CC8, and CC30. In PJI cultures, only 63% could be classified in these common clonal complexes. The PJI cultures had a larger proportion of atypical strains, and these atypical strains were associated with poor host status and compromised immune conditions. Mutations in genes involved in fibronectin binding (ebh, fnbA, clfA, clfB) systematically distinguished later PJI isolates from the first PJI isolate from each patient. Repeated mutations in S. aureus genes associated with extracellular matrix binding were identified suggesting an adaptive, parallel evolution in S. aureus during the development of PJI.

Signaling from multiple receptor tyrosine kinases (RTK) contributes to therapeutic resistance in glioblastoma (GBM). Heparan sulfate (HS), present on cell surfaces and in the extracellular matrix, regulates cell signaling via several mechanisms. To investigate the role for HS in promoting RTK signaling in GBM, we generated neural progenitor cells deficient for HS by knockout of the essential HS-biosynthetic enzyme Ext1, and studied tumor initiation and progression. HS-null cells had decreased proliferation, invasion, and reduced activation of multiple RTKs compared with control. In vivo tumor establishment was significantly decreased, and rate of tumor growth reduced with HS-deficient cells implanted in an HS-poor microenvironment. To investigate if HS regulates RTK activation through platelet-derived growth factor receptor α (PDGFRα) signaling, we removed cell surface HS in patient-derived GBM lines and identified reduced cell surface PDGF-BB ligand. Reduced ligand levels were associated with decreased phosphorylation of PDGFRα, suggesting HS promotes ligand–receptor interaction. Using human GBM tumorspheres and a murine GBM model, we show that ligand-mediated signaling can partially rescue cells from targeted RTK inhibition and that this effect is regulated by HS. Indeed, tumor cells deficient for HS had increased sensitivity to EGFR inhibition in vitro and in vivo. Implications: Our study shows that HS expressed on tumor cells and in the tumor microenvironment regulates ligand-mediated signaling, promoting tumor cell proliferation and invasion, and these factors contribute to decreased tumor cell response to targeted RTK inhibition.

Synthesis of septal peptidoglycan (sPG) is crucial for bacterial cell division. FtsW, an indispensable component of the cell division machinery in all walled bacterial species, was recently identified in vitro as a peptidoglycan glycosyltransferase (PGTase). Despite its importance, the septal PGTase activity of FtsW has not been demonstrated in vivo. How its activity is spatiotemporally regulated in vivo has also remained elusive. Here, we confirmed FtsW as an essential septum-specific PGTase in vivo using an N-acetylmuramic acid analogue incorporation assay. Next, using single-molecule tracking coupled with genetic manipulations, we identified two populations of processively moving FtsW molecules: a fast-moving population correlated with the treadmilling dynamics of the essential cytoskeletal FtsZ protein and a slow-moving population dependent on active sPG synthesis. We further identified that FtsN, a potential sPG synthesis activator, plays an important role in promoting the slow-moving population. Our results suggest a two-track model, in which inactive sPG synthases follow the ‘Z-track’ to be distributed along the septum and FtsN promotes their release from the Z-track to become active in sPG synthesis on the slow ‘sPG-track’. This model provides a mechanistic framework for the spatiotemporal coordination of sPG synthesis in bacterial cell division. Single-molecule tracking of the septal peptidoglycan glycosyltransferase FtsW reveals two populations: a fast-moving one that follows treadmilling FtsZ and a slow-moving one that is involved in peptidoglycan synthesis.

New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening platform for bacterial cultures by combining droplet microfluidics, search algorithms, and imaging with a wide field of view. We remotely alter the chemical microenvironment around cells and test 12 combinations of resistant cell types and chemicals. Fluorescence intensity readouts allow us to infer bacterial resistance to specific antibiotics within 8 hours. The platform has potential to detect and identify parameters of bacterial resilience in cell cultures, biofilms, and microbial aggregates., 2 pages

Among the virulence factors in Neisseria infections, a major inducer of inflammatory cytokines is the lipooligosaccharide (LOS). The activation of NF-κB via extracellular binding of LOS or lipopolysaccharide (LPS) to the toll-like receptor 4 and its coreceptor, MD-2, results in production of pro-inflammatory cytokines that initiate adaptive immune responses. LOS can also be absorbed by cells and activate intracellular inflammasomes, causing the release of inflammatory cytokines and pyroptosis. Studies of LOS and LPS have shown that their inflammatory potential is highly dependent on lipid A phosphorylation and acylation, but little is known on the location and pattern of these posttranslational modifications. Herein, we report on the localization of phosphoryl groups on phosphorylated meningococcal lipid A, which has two to three phosphate and zero to two phosphoethanolamine substituents. Intact LOS with symmetrical hexa-acylated and asymmetrical penta-acylated lipid A moieties was subjected to high-resolution ion mobility spectrometry MALDI-TOF MS. LOS molecular ions readily underwent in-source decay to give fragments of the oligosaccharide and lipid A formed by cleavage of the ketosidic linkage, which enabled performing MS/MS (pseudo-MS3). The resulting spectra revealed several patterns of phosphoryl substitution on lipid A, with certain species predominating. The extent of phosphoryl substitution, particularly phosphoethanolaminylation, on the 4′-hydroxyl was greater than that on the 1-hydroxyl. The heretofore unrecognized phosphorylation patterns of lipid A of meningococcal LOS that we detected are likely determinants of both pathogenicity and the ability of the bacteria to evade the innate immune system.

SummaryIn this manuscript, we describe the second of two field demonstrations of microbially induced calcium carbonate precipitation (MICP) performed in a failed waterflood injection well in Indiana. In 2012, fracture-related flow pathways developed in the wellbore cement, causing injection water to bypass the oil-bearing formation and enter a high-permeability sandstone thief zone, thereby substantially decreasing injection pressure. In the first field demonstration, our study team characterized the well's mode of failure and successfully applied MICP to decrease flow through the defective cement. However, because the MICP treatment was conducted using a bailer delivery system, the degree of permeability reduction achievable was not adequate to fully restore the historic injection pressure of 1,400 psi at 1 gal/min. For the second field demonstration (reported herein), a direct injection system was developed that substantially increased the injection volume of MICP-promoting fluids. Two strategies were implemented to produce more ureolytic microbes: resuspending concentrated frozen cells immediately before injection and scaling up the bioreactor growth capacity. Multiple pulses of microbes and urea-calcium media were pumped into a string of 1-in.-diameter tubing separated by brine spacers and injected continuously at a flow rate of 3.4 to 1.4 gal/min. During the third day of injection, an injection pressure of 1,384 psi at a flow rate of 1.4 gal/min was achieved, and the experiment was terminated. This study demonstrates that MICP can be successfully used in large-volume applications where the time frame for the delivery of reactants is limited. This finding has significant relevance for commercialization of the MICP biotechnology in the oil and gas industry.

Preexisting immune response to SARS-CoV-2 Robust T cell responses to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus occur in most individuals with coronavirus disease 2019 (COVID-19). Several studies have reported that some people who have not been exposed to SARS-CoV-2 have preexisting reactivity to SARS-CoV-2 sequences. The immunological mechanisms underlying this preexisting reactivity are not clear, but previous exposure to widely circulating common cold coronaviruses might be involved. Mateus et al. found that the preexisting reactivity against SARS-CoV-2 comes from memory T cells and that cross-reactive T cells can specifically recognize a SARS-CoV-2 epitope as well as the homologous epitope from a common cold coronavirus. These findings underline the importance of determining the impacts of preexisting immune memory in COVID-19 disease severity. Science , this issue p. 89

Newcomers often have trouble being taken seriously, or even noticed in the first place. This challenge, often referred to as the “liability of newness” (Freeman et al. 1983, Stinchcombe 1965), underscores the idea that to survive and thrive, new entrants must be recognized as legitimate by their audiences — employees, investors, customers, analysts, or simply followers. One way for new entrants to gain legitimacy is by leveraging affiliations. Such connections can increase the likelihood that the new entrant will be recognized as legitimate because they can affect whether audiences notice the new entrant, thereby allowing for its evaluation, such that affiliations act as market signals (Kim and Jensen 2013, Spence 1974). In this regard, a sizeable literature has looked at whether and how affiliations can enhance a new entrant’s visibility, with a particular focus on prominent affiliates (Chen et al. 2008, Jensen 2003, Pollock et al. 2010). A recurring line of argument in this area draws from the literature on social capital (Adler and Kwon 2002, Coleman 1988) to suggest how affiliations are assumed to provide distinct advantages to new entrants by acting as attention filters (Benjamin and Podolny 1999), providing them with access to information or resources (Ingram and Baum 1997, Podolny 2001), and shielding them from failure (Fischer and Pollock 2004, Miner et al. 1990). Furthermore, prominent affiliates often have signaling value, functioning as endorsements to actors who need legitimacy such as newlyestablished organizations like startups (e.g. Stuart et al. 1999). In other words, an affiliation “between two market actors is an informational cue on which others rely to make inferences about the underlying quality of one or both of the market actors” (Podolny 2001: 34).

BACKGROUND Patients with antiphospholipid antibodies (aPL) and thromboembolism (TE) are at risk for recurrent TE. Few studies, however, distinguish patients based on the initial event. OBJECTIVES We performed a systematic review and meta-analysis to investigate patients with aPL and venous TE (VTE), provoked or unprovoked, and patients with arterial TE (ATE). PATIENTS/METHODS We conducted searches in PubMed, CINAHL, Cochrane, and EMBASE. Inclusion criteria were prospective trials or cohort studies investigating patients with aPL and ATE or VTE. Excluded studies did not provide estimated recurrence rates, did not specify whether the incident event was ATE or VTE, included patients with multiple events, or included

With more than 700 described species, leeches include morphological, physiological, and behavioral diversity and occur in terrestrial and aquatic habitats, including freshwater, estuarine, and marine ecosystems. Leeches inhabit a number of extreme environments, including extremes in temperature, moisture, salinity, pressure, light, and pollution. In some cases, leeches in extreme environments have specialized morphological, physiological, or behavioral adaptations to survive these conditions, yet unique adaptations are not apparent in some species. Leeches that inhabit inhospitable habitats occur in more than one branch or family of leech phylogeny suggesting that there have been independent invasions of environments with extreme conditions. Herein, we review examples of leeches that live in extreme conditions and the exceptional biology that has contributed to leeches being the most extreme annelids., Graphical abstract Image 1, Highlights • Leeches occur in terrestrial, freshwater, estuarine, and marine ecosystems. • Leeches inhabit extremes in temperature, moisture, salinity, pressure, light, and pollution. • Not all leech species living in inhospitable conditions have unique adaptations. • There were multiple independent invasions of leeches into extreme environments.

The biogeographic distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy‐focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences—geometric morphometrics—to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behavior, and phenotypic differentiation, allowing us to ask whether populations can be distinguished and whether patterns of variation indicate adaptability to changing environmental conditions. We analyzed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using principal component analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbor similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size‐adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation—76%—remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross‐breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g., specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetic‐based conservation studies., The diversity among populations of threatened mammalian species is generally investigated through population genetics. Here, we characterize shape intraspecific diversity with geometric morphometrics in the skull of an endangered marsupial. Our results suggest a uniform within‐species scope for shape variation, possibly due to phenotypic plasticity or allometric constraints. Thus, the potential for heritable morphological variation, such as specialization to local diets, seems exceedingly limited.

Abacavir hypersensitivity syndrome (ABC HSS) is strongly associated with carriage of human leukocyte antigen (HLA)-B*57:01, which has a 100% negative predictive value for the development of ABC HSS. However, 45% of individuals who carry HLA-B*57:01 can tolerate ABC. We investigated immune and non-immune related genes in ABC HSS (n = 95) and ABC tolerant (n = 43) HLA-B*57:01 + patients to determine other factors required for the development of ABC HSS. Assignment of phenotype showed that ABC HSS subjects were significantly less likely than tolerants to carry only ERAP1 hypoactive trimming allotypes (p = 0.02). An altered self-peptide repertoire model by which abacavir activates T cells is in keeping with observation that endoplasmic reticulum aminopeptidase 1 (ERAP1) allotypes that favour efficient peptide trimming are more common in ABC HSS patients compared to patients who tolerate ABC. Independently, non-specific immune activation via soluble cluster of differentiation antigen 14 (sCD14) may also influence susceptibility to ABC HSS.

Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the

Antibody-drug conjugates have become one of the most actively developed classes of drugs in recent years. Their great potential comes from combining the strengths of large and small molecule therapeutics: the exquisite specificity of antibodies and the highly potent nature of cytotoxic compounds. More recently, the approach of engineering antibody-drug conjugate scaffolds to achieve highly controlled drug to antibody ratios has focused on substituting or inserting cysteines to facilitate site-specific conjugation. Herein, we characterize an antibody scaffold engineered with an inserted cysteine that formed an unexpected disulfide bridge during manufacture. A combination of mass spectrometry and biophysical techniques have been used to understand how the additional disulfide bridge forms, interconverts, and changes the stability and structural dynamics of the antibody intermediate. This quantitative and structurally resolved model of the local and global changes in structure and dynamics associated with the engineering and subsequent disulfide-bonded variant can assist future engineering strategies.

Cutaneous T cell lymphomas (CTCL) are rare but aggressive cancers without effective treatments. While a subset of patients derive benefit from PD-1 blockade, there is a critically unmet need for predictive biomarkers of response. Herein, we perform CODEX multiplexed tissue imaging and RNA sequencing on 70 tumor regions from 14 advanced CTCL patients enrolled in a pembrolizumab clinical trial (NCT02243579). We find no differences in the frequencies of immune or tumor cells between responders and non-responders. Instead, we identify topographical differences between effector PD-1+ CD4+ T cells, tumor cells, and immunosuppressive Tregs, from which we derive a spatial biomarker, termed the SpatialScore, that correlates strongly with pembrolizumab response in CTCL. The SpatialScore coincides with differences in the functional immune state of the tumor microenvironment, T cell function, and tumor cell-specific chemokine recruitment and is validated using a simplified, clinically accessible tissue imaging platform. Collectively, these results provide a paradigm for investigating the spatial balance of effector and suppressive T cell activity and broadly leveraging this biomarker approach to inform the clinical use of immunotherapies., PD-1 blockade is effective for only a subset of patients with cutaneous T cell lymphomas. Here, the authors report a spatial biomarker that uses immune and cancer cell topography to predict response to PD-1 blockade in this disease.

PURPOSE OF REVIEW: The goal of this article is to provide an updated understanding and evidence-based approach where possible for antifungal hypersensitivity. This includes recognition of clinical phenotype, implications for cross-reactivity and diagnostic, and management strategy for immediate and delayed hypersensitivity reactions. RECENT FINDINGS: Antifungal hypersensitivity reactions can be classified according to their latency (immediate or delayed) and clinical phenotype. The majority of the cases described in the literature are delayed T-cell mediated reactions of various severities but immediate reactions consistent with non-Immunoglobulin E (IgE)-mediated mast cell activation and IgE-mediated reactions have also been described. Ancillary information such as skin testing, drug challenge and ex vivo experimental approaches can aid causality assessments and inform antifungal class cross-reactivity, which help optimize antifungal prescribing and stewardship. SUMMARY: This review will update the clinician on mechanisms of drug hypersensitivity as well as providing a structured approach to the recognition, diagnosis and management of antifungal hypersensitivity reaction.

Extracellular sulfatases (SULF1 and SULF2) selectively remove 6-O-sulfate groups (6OS) from heparan sulfate proteoglycans (HSPGs) and by this process control important interactions of HSPGs with extracellular factors including morphogens, growth factors, and extracellular matrix (ECM) components. The expression of SULF1 and SULF2 is dynamically regulated during development and is altered in pathological states such as glioblastoma (GBM), a highly malignant and highly invasive brain cancer. SULF2 protein is increased in an important subset of human GBM and it helps regulate receptor tyrosine kinase (RTK) signaling and tumor growth in a murine model of the disease. By altering ligand binding to HSPGs SULF2 has the potential to modify the extracellular availability of factors important in a number of cell processes including proliferation, chemotaxis, and migration. Diffuse invasion of malignant tumor cells into surrounding healthy brain is a characteristic feature of GBM that makes therapy challenging. Here, we describe methods to assess SULF2 expression in human tumor tissue and cell lines and how to relate this to tumor cell invasion.

We and many others have noted the advantages of using heterogeneous (HS) animals to map genes and gene networks associated with both behavioral and non-behavioral phenotypes. Importantly, genetically complex Mus musculus crosses provide substantially increased resolution to examine old and new relationships between gene expression and behavior. Here we report on data obtained from two HS populations: the HS/NPT derived from eight inbred laboratory mouse strains and the HS-CC derived from the eight collaborative cross inbred mouse strains that includes three wild-derived strains. Our work has focused on the genes and gene networks associated with risk for excessive ethanol consumption, individual variation in ethanol consumption and the consequences, including escalation, of long-term ethanol consumption. Background data on the development of HS mice is provided, including advantages for the detection of expression quantitative trait loci. Examples are also provided of using HS animals to probe the genes associated with ethanol preference and binge ethanol consumption.

The century-oldMycobacterium bovisBacillus Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Despite this, there is still a lot to learn about the immune response induced by BCG, both in terms of phenotype and specificity. Here, we investigated immune responses in adult individuals pre and 8 months post BCG vaccination. We specifically determined changes in gene expression, cell subset composition, DNA methylome, and the TCR repertoire induced in PBMCs and CD4 memory T cells associated with antigen stimulation by either BCG or aMycobacterium tuberculosis(Mtb)-derived peptide pool. Following BCG vaccination, we observed increased frequencies of CCR6+ CD4 T cells, which includes both Th1* and Th17 subsets, and mucosal associated invariant T cells (MAITs). A large number of immune response genes and pathways were upregulated post BCG vaccination with similar patterns observed in both PBMCs and memory CD4 T cells, thus suggesting a substantial role for CD4 T cells in the cellular response to BCG. These upregulated genes and associated pathways were also reflected in the DNA methylome. We described both qualitative and quantitative changes in the BCG-specific TCR repertoire post vaccination, and importantly found evidence for similar TCR repertoires across different subjects. The immune signatures defined herein can be used to track and further characterize immune responses induced by BCG, and can serve as reference for benchmarking novel vaccination strategies.

Sensitivity to rewarding and reinforcing drug effects has a critical role in initial use, but the role of initial aversive drug effects has received less attention. Methamphetamine effects on dopamine re-uptake and efflux are associated with its addiction potential. However, methamphetamine also serves as a substrate for the trace amine-associated receptor 1 (TAAR1). Growing evidence in animal models indicates that increasing TAAR1 function reduces drug self-administration and intake. We previously determined that a non-synonymous single nucleotide polymorphism (SNP) in Taar1 predicts a conformational change in the receptor that has functional consequences. A Taar1m1J mutant allele existing in DBA/2J mice expresses a non-functional receptor. In comparison to mice that possess one or more copies of the reference Taar1 allele (Taar1+/+ or Taar1+/m1J), mice with the Taar1m1J/m1J genotype readily consume methamphetamine, express low sensitivity to aversive effects of methamphetamine, and lack sensitivity to acute methamphetamine-induced hypothermia. We used three sets of knock-in and control mice in which one Taar1 allele was exchanged with the alternative allele to determine if other methamphetamine-related traits and an opioid trait are impacted by the same Taar1 SNP proven to affect MA consumption and hypothermia. First, we measured sensitivity to conditioned rewarding and aversive effects of methamphetamine to determine if an impact of the Taar1 SNP on these traits could be proven. Next, we used multiple genetic backgrounds to study the consistency of Taar1 allelic effects on methamphetamine intake and hypothermia. Finally, we studied morphine-induced hypothermia to confirm prior data suggesting that a gene in linkage disequilibrium with Taar1, rather than Taar1, accounts for prior observed differences in sensitivity. We found that a single SNP exchange reduced sensitivity to methamphetamine conditioned reward and increased sensitivity to conditioned aversion. Profound differences in methamphetamine intake and hypothermia consistently corresponded with genotype at the SNP location, with only slight variation in magnitude across genetic backgrounds. Morphine-induced hypothermia was not dependent on Taar1 genotype. Thus, Taar1 genotype and TAAR1 function impact multiple methamphetamine-related effects that likely predict the potential for methamphetamine use. These data support further investigation of their potential roles in risk for methamphetamine addiction and therapeutic development.

Erroneous taxonomic attributions in GenBank accessions can mislead phylogenetic inference and appear to be widespread within genera. We investigate the influence of taxonomic misattributions for reconstructing the phylogeny of three-striped dasyures, which include four recognized Myoictis species (Marsupialia: Dasyuridae) that are distributed across New Guinea and nearby islands. Molecular phylogenetic studies that have focused on dasyurids consistently resolve the interrelationships of these small carnivores, grouping M. leucura with M. wavicus, and placing M. wallacei and M. melas as successively deeper divergences from these. Two recent marsupial and mammalian supermatrix phylogenies instead favour an alternative Myoictis topology that is discordant with each of these relationships. We add new nuclear and mitochondrial sequences and employ randomized accession resampling that shows the supermatrix topologies are an artefact of several outdated taxonomic attributions in GenBank. Updating these accessions brings agreement across Myoictis phylogenies with randomly resampled accessions. We encourage authors to update GenBank taxonomic attributions and we argue that an option is needed for flagging accessions that are not demonstrably incorrect, but that provide anomalous results. This would serve both as a caution for future supermatrix construction and to highlight accessions of potentially significant biological interest for further study.

Methamphetamine (MA) impairs vesicular monoamine transporter 2 (VMAT2) and dopamine transporter (DAT) function and expression, increasing intracellular DA levels that lead to neurotoxicity. The trace amine–associated receptor 1 (TAAR1) is activated by MA, but when the receptor is not activated, MA-induced neurotoxicity is increased. To investigate interactions among TAAR1, VMAT2, and DAT, transporter function and expression were measured in transgenic Taar1 knockout (KO) and wild-type (WT) mice 24 hours following a binge-like regimen (four intraperitoneal injections, 2 hours apart) of MA (5 mg/kg) or the same schedule of saline treatment. Striatal synaptosomes were separated by fractionation to examine the function and expression of VMAT2 localized to cytosolic and membrane-associated vesicles. DAT was measured in whole synaptosomes. VMAT2-mediated [(3)H]DA uptake inhibition was increased in Taar1 KO mice in synaptosomal and vesicular fractions, but not the membrane-associated fraction, compared with Taar1 WT mice. There was no difference in [(3)H]dihydrotetrabenazine binding to the VMAT2 or [(125)I]RTI-55 binding to the DAT between genotypes, indicating activation of TAAR1 does not affect VMAT2 or DAT expression. There was also no difference between Taar1 WT and KO mice in DAT-mediated [(3)H]DA uptake inhibition following in vitro treatment with MA. These findings provide the first evidence of a TAAR1-VMAT2 interaction, as activation of TAAR1 mitigated MA-induced impairment of VMAT2 function, independently of change in VMAT2 expression. Additionally, the interaction is localized to intracellular VMAT2 on cytosolic vesicles and did not affect expression or function of DAT in synaptosomes or VMAT2 at the plasmalemmal surface, i.e., on membrane-associated vesicles. SIGNIFICANCE STATEMENT: Methamphetamine stimulates the G protein-coupled receptor TAAR1 to affect dopaminergic function and neurotoxicity. Here we demonstrate that a functional TAAR1 protects a specific subcellular fraction of VMAT2, but not the dopamine transporter, from methamphetamine-induced effects, suggesting new directions in pharmacotherapeutic development for neurodegenerative disorders.

Tau protein is found to be aggregated and hyperphosphorylated (p-tau) in many neurologic disorders, including Parkinson disease (PD) and related parkinsonisms, Alzheimer disease, traumatic brain injury, and even in normal aging. Although not known to produce autoimmune responses, we hypothesized that the appearance of aggregated tau and p-tau with disease could activate the immune system. We thus compared T cell responses to tau and p-tau–derived peptides between PD patients, age-matched healthy controls, and young healthy controls (

Leeches (Hirudinida) comprise a charismatic, yet often maligned group of organisms. Despite their ecological, economic, and medical importance, a general consensus on the phylogenetic relationships of major hirudinidan lineages is lacking. This absence of a consistent, robust phylogeny of early-diverging lineages has hindered our understanding of the underlying processes that enabled evolutionary diversification of this clade. Here, we used an anchored hybrid enrichment-based phylogenomic approach, capturing hundreds of loci to investigate phylogenetic relationships among major hirudinidan lineages and their closest living relatives. Our results suggest that a dramatic reinterpretation of early leech evolution is warranted. We recovered Branchiobdellida as sister to a clade that includes all major lineages of hirudinidans, but found Acanthobdella to be nested within Oceanobdelliformes. These results cast doubt on the utility of Acanthobdella as a “missing link” used to explain the origin of blood-feeding in hirudineans. Further, our results support a deep divergence between predominantly marine and freshwater lineages, while not supporting the reciprocal monophyly of jawed and proboscis-bearing leeches. To sum up, our phylogenomic resolution of early-diverging leeches provides a necessary foundation for illuminating the evolution of host–symbiont associations and key adaptations that have allowed leeches to colonize a wide diversity of habitats worldwide.

The kinetics of urea hydrolysis (ureolysis) and induced calcium carbonate (CaCO3) precipitation for engineering use in the subsurface was investigated under aerobic conditions using Sporosarcina pasteurii (ATCC strain 11859) as well as Bacillus sphaericus strains 21776 and 21787. All bacterial strains showed ureolytic activity inducing CaCO3 precipitation aerobically. Rate constants not normalized to biomass demonstrated slightly higher-rate coefficients for both ureolysis (kurea) and CaCO3 precipitation (kprecip) for B. sphaericus 21776 (kurea=0.10±0.03 h−1, kprecip=0.60±0.34 h−1) compared to S. pasteurii (kurea=0.07±0.02 h−1, kprecip=0.25±0.02 h−1), though these differences were not statistically significantly different. B. sphaericus 21787 showed little ureolytic activity but was still capable of inducing some CaCO3 precipitation. Cell growth appeared to be inhibited during the period of CaCO3 precipitation. Transmission electron microscopy (TEM) images suggest this is due to the encasement of cells and was reflected in lower kurea values observed in the presence of dissolved Ca. However, biomass regrowth could be observed after CaCO3 precipitation ceased, which suggests that ureolysis-induced CaCO3 precipitation is not necessarily lethal for the entire population. The kinetics of ureolysis and CaCO3 precipitation with S. pasteurii was further analyzed under anaerobic conditions. Rate coefficients obtained in anaerobic environments were comparable to those under aerobic conditions; however, no cell growth was observed under anaerobic conditions with NO3-, SO42- or Fe3+ as potential terminal electron acceptors. These data suggest that the initial rates of ureolysis and ureolysis-induced CaCO3 precipitation are not significantly affected by the absence of oxygen but that long-term ureolytic activity might require the addition of suitable electron acceptors. Variations in the ureolytic capabilities and associated rates of CaCO3 precipitation between strains must be fully considered in subsurface engineering strategies that utilize microbial amendments.

Slow-cycling and treatment-resistant cancer cells escape therapy, providing a rationale for regrowth and recurrence in patients. Much interest has focused on identifying the properties of slow-cycling tumor cells in glioblastoma (GBM), the most common and lethal primary brain tumor. Despite aggressive ionizing radiation (IR) and treatment with the alkylating agent temozolomide (TMZ), GBM patients invariably relapse and ultimately succumb to the disease. In patient biopsies, we demonstrated that GBM cells expressing the proliferation markers Ki67 and MCM2 displayed a larger cell volume compared to rare slow-cycling tumor cells. In optimized density gradients, we isolated a minor fraction of slow-cycling GBM cells in patient biopsies and tumorsphere cultures. Transcriptional profiling, self-renewal, and tumorigenicity assays reflected the slow-cycling state of high-density GBM cells (HDGCs) compared to the tumor bulk of low-density GBM cells (LDGCs). Slow-cycling HDGCs enriched for stem cell antigens proliferated a few days after isolation to generate LDGCs. Both in vitro and in vivo, we demonstrated that HDGCs show increased treatment-resistance to IR and TMZ treatment compared to LDGCs. In conclusion, density gradients represent a non-marker based approach to isolate slow-cycling and treatment-resistant GBM cells across GBM subgroups.

Since 2012 the number of recognized taxa in the Australian carnivorous marsupial genus Antechinus has increased from 10 to 15 species. The systematic relationships among these species and others in the genus are not well resolved. We undertook the first comprehensive, molecular systematic analysis of the genus, incorporating all known species and subspecies of Antechinus. Two mitochondrial (mtDNA) and four autosomal nuclear genes were sequenced. Four clades of Antechinus were consistently reconstructed in the concatenated and mtDNA analyses: (1) dusky antechinuses (A. arktos, A. swainsonii, A. vandycki and A. mimetes) and A. minimus; (2) A. godmani; (3) A. agilis, A. stuartii and A. subtropicus; (4) A. argentus, A. mysticus, A. adustus, A. flavipes, A. leo and A. bellus. The inclusion of A. adustus in clade 4 is surprising, because previous morphology-based studies suggested it was a member of clade 3. However, analysis of the nuclear dataset and multi-species coalescence analysis did not separate clades 3 and 4. Within clade 3, A. stuartii is not monophyletic and may be more appropriately classified as two species. Timing of cladogenesis is estimated for all 15 species of Antechinus, permitting us to posit an evolutionary scenario for the group. BEAST analysis dated the divergence of Antechinus from extant congeners to the Late Miocene and cladogenesis among all extant Antechinus to the Plio-Pleistocene. Wet, closed habitat was reconstructed as the most probable ancestral state for the genus Antechinus and the four main Antechinus clades. Overall, increasing aridity from the Miocene to the Pleistocene and a number of well-known biogeographic barriers to mesic species, appear to have driven speciation in Antechinus.

Mammalian hairs are internally patterned from both a morphological and proteomic perspective to exhibit specific functional traits, including curvature, which is important for coat structure affecting thermo-insulation. Most functional traits in mammalian coats are complex emergent phenomena associated with single-fibre properties that are themselves multi-variate and poorly understood. Here we compare hair curvature, ultrastructure, microstructure, protein composition and felting (a functional attribute) between fibres from natural straight-wool mutants of domestic sheep (felting lustre-mutant sheep), their wild-type relatives and also with a straight-haired semi-lustrous breed, English Leicester. Proteomic and structural results confirmed that the straight lustre mutant fibres had a normal cuticle and the same cortical protein and ultrastructural building blocks as wild-type fibres, but differed from equivalent fibres from wild-type relatives and English Leicester in layout and relative proportions. While curved wild-type fibres had bilaterally arranged orthocortex and paracortex, and English Leicester fibres had a scatter of paracortex on a background of orthocortex, lustre mutant fibres typically had a complete or partial ring of orthocortex surrounding a paracortex core, and sometimes a central orthocortex (similar to straight human and goat hairs). Lustre mutant fibres also had a reduced abundance of some high glycine-tyrosine proteins, normally associated with the orthocortex, with a possible relationship between the protein expression of the KAP8 and KAP16 protein families and fibre felting properties. We conclude that through control of the internal fibre patterning, multiple-solutions to hair curvature are possible, and variation may affect mechanical phenotype differently. Felting lustre mutant sheep will be a useful tool for discriminating cause and effect from non-causative correlation in mammalian fibre development.

Kangaroos and wallabies of the Macropus complex include the largest extant marsupials and hopping mammals. They have traditionally been divided among the genus Macropus (with three subgenera: Macropus, Osphranter and Notamacropus) and the monotypic swamp wallaby, Wallabia bicolor. Recent retrotransposon and genome-scale phylogenetic analyses clarify the placement of Wallabia as sister to Notamacropus, with Osphranter and Macropus branching successively deeper. In view of the traditional Macropus concept being paraphyletic, we undertake to resolve the species-level phylogeny and genus-level taxonomy of the Macropus complex. For the first time, we include nuclear and mitochondrial DNA covering all extant species, and the first DNA sequences from the extinct Toolache wallaby (Notamacropus greyi), which we find groups with the black-gloved wallaby (Notamacropus irma). Morphological variation was examined using geometric morphometric methods on three-dimensional surface-scanned skulls. Wallabia skull shape fell close to Notamacropus (or Thylogale when controlling for allometry). We recommend the subgenera Macropus, Osphranter and Notamacropus be elevated to genera, alongside Wallabia, based on comparisons with other established macropodine genera for cranial disparity, ecology and molecular divergence. Our time tree estimates that all four ‘Macropus’ genera diverged close to the Miocene–Pliocene boundary (~6–5 Mya), then diversified coincident with Pliocene expansion of grasslands in Australia.

Accumulating evidence demonstrates that CD8(+) T cells contribute to protection from severe dengue virus (DENV) disease and vaccine efficacy. Nevertheless, molecular programs associated with DENV-specific CD8(+) T cell subsets have not been defined. Here, we studied the transcriptomic profiles of human DENV-specific CD8(+) T cells isolated after stimulation with DENV epitopes from donors who had been infected with DENV multiple times and would therefore be expected to have significant levels of adaptive immunity. We found that DENV-specific CD8(+) T cells mainly consisted of effector memory subsets, namely CD45RA(−)CCR7(−) effector memory (Tem) and CD45RA(+)CCR7(−) effector memory re-expressing CD45RA (Temra) cells, which enacted specific gene expression profiles upon stimulation with cognate antigens. DENV-specific CD8(+) T cell subsets in general, and Temra cells in particular, were fully activated and polyfunctional, yet associated with relatively narrow transcriptional responses. Furthermore, we found that DENV-specific CD8(+) Tem and Temra cells showed some unique T cell receptor features in terms of overlap and variable (V) gene usage. This study provides a transcriptomic definition of DENV-specific activated human CD8(+) T cell subsets and defines a benchmark profile that vaccine-specific responses could aim to reproduce.

Different attributes of membrane protein substrates have been proposed and characterized as translocation-pathway determinants. However, several gaps in our understanding of the mechanism of targeting, insertion, and assembly of inner-membrane proteins exist. Specifically, the role played by hydrophilic N-terminal tails in pathway selection is unclear. In this study, we have evaluated length and charge density as translocase determinants using model proteins. Strikingly, the 36-residue N-tail of 2Pf3-Lep translocates independent of YidC-Sec. This is the longest known substrate of this pathway. We confirmed this using a newly constructed YidC-Sec double-depletion strain. Increasing its N-tail length with uncharged spacer peptides led to YidC dependence and eventually YidC-Sec dependence, hence establishing that length has a linear effect on translocase dependence. Tails longer than 60 residues were not inserted; however, an MBP-2Pf3-Lep fusion protein could be ranslocated. This suggests that longer N-tails can be translocated if it can engage SecA. In addition, we have examined how the positioning of charges within the translocated N-tail affects the insertion pathway. Additional charges can be translocated by the Lep TM when the charges are distributed across a longer N-tail. We tested charge density as a translocase determinant and confirmed that the addition of positive or negatives charges led to a greater dependence on YidC-Sec when they were placed close to each other than away. Findings from this work make an important advance in our existing knowledge about the different insertion mechanisms of membrane proteins in Escherichia coli.

Trichloromethane (TCM) is a frequently detected and persistent groundwater contaminant. Recent studies have reported that two closely related Dehalobacter strains (UNSWDHB and CF) transform TCM to dichloromethane, with inconsistent carbon isotope effects (e(13)C(UNSWDHB) = -4.3 +/- 0.45 parts per thousand; e13C(CF) = -27.5 +/- 0.9 parts per thousand). This study uses dual element compound specific isotope analysis (C; Cl) to explore the underlying differences. TCM transformation experiments using strain CF revealed pronounced normal carbon and chlorine isotope effects (e13C(CF) = -27.9 +/- 1.7 parts per thousand; e37Cl(CF) = -4.2 +/- 0.2 parts per thousand). In contrast, small carbon and unprecedented inverse chlorine isotope effects were observed for strain UNSWDHB (e13C(UNSWDHB) = -3.1 +/- 0.5 parts per thousand; e37Cl(UNSWDHB) = 2.5 +/- 0.3 parts per thousand) leading to opposing dual element isotope slopes (?CF = 6.64 +/- 0.14 vs lambda(UNSWDHB) = -1.20 +/- 0.18). Isotope effects of strain CF were identical to experiments with TCM and Vitamin B12 (e13C(Vitamin B12) = -26.0 +/- 0.9 parts per thousand, e37Cl(Vitamin B12) = -4.0 +/- 0.2 parts per thousand, lambda(Vitamin) (B12) = 6.46 +/- 0.20). Comparison to previously reported isotope effects suggests outer-sphere-single-electron transfer or S(N)2 as possible underlying mechanisms. Cell suspension and cell free extract experiments with strain UNSWDHB were both unable to unmask the intrinsic KIE of the reductive dehalogenase (TmrA) suggesting that enzyme binding and/or mass-transfer into the periplasm were rate-limiting. Nondirected intermolecular interactions of TCM with cellular material were ruled out as reason for the inverse isotope effect by gas/water and gas/hexadecane partitioning experiments indicating specific, yet uncharacterized interactions must be operating prior to catalysis.

Background The proliferative phase of infantile hemangiomas (IHs) is usually complete by 9 months of life. Late growth beyond age 3 years is rarely reported. Objective To describe the demographic and clinic characteristics of a cohort of patients with late growth of IH, defined as growth in a patient >3 years of age. Methods A multicenter, retrospective cohort study. Results In total, 59 patients, 85% of which were female, met the inclusion criteria. The mean first episode of late growth was 4.3 (range 3-8.5) years. Head and neck location (55/59; 93%) and presence of deep hemangioma (52/59; 88%) were common characteristics. P osterior fossa malformations, h emangiomas, a rterial anomalies, c ardiac defects, e ye abnormalities (PHACE) syndrome was noted in 20 of 38 (53%) children with segmental facial IH. Systemic therapy (corticosteroid or β-blocker) was given during infancy in 58 of 59 (98%) and 24 of 59 (41%) received systemic therapy (β-blockers) for late IH growth. Limitations The retrospective nature and ascertainment by investigator recall are limitations of the study. Conclusion Late IH growth can occur in children after 3 years of age. Risk factors include head and neck location, segmental morphology, and involvement of deep dermal/subcutaneous tissues.

Despite considerable attention, the mechanisms by which the microbiota affect brain function and host behaviour via the gut-brain axis remain undefined. Identifying microbe-specific pathways that influence neuronal function and bi-directional communication between the gut microbiota and the host central nervous system is challenging due to the extreme microbial diversity in the gut of conventionally-reared mice. Herein, we describe the use of the altered Schaedler flora (ASF) mouse model as an alternative to conventionally-reared and germ-free animals. Colonized with only 8 bacterial species, use of ASF mice greatly simplifies the examination of microbiota-host interactions. We assessed the extent to which behaviour differed between mice with a limited consortium of bacteria compared with a complex, conventional microbiota. The elevated plus maze and open-field assays were utilized to assess murine behaviour. Histological analysis of ileum and colon was performed to evaluate intestinal morphology, and 16 s rRNA gene taxonomic profiling was performed to determine host-stress induced changes in fecal microbial communities. Behavioural and serum corticosterone differences were observed between ASF and conventionally-reared mice, while no differences were found between the intestinal morphology of these two groups. The stress of the behavioural tests induced significant changes in the ASF fecal microbial community but not in that of the conventionally-reared mice. In contrast to the conventionally-reared mice, the results indicated that the ASF mice displayed a marked anxiogenic-like behaviour. These data indicate that ASF mice represent a unique model to elucidate mechanisms governing microbiota-gut-brain communication affecting behaviour.

The presence of delaminations, apertures, fractures, voids and other unrestricted flow channels in the wellbore environment substantially reduces wellbore integrity. Compromised cement may cause a loss of zonal isolation leading to deleterious flow of fluids between zones or to the surface with multiple potential negative impacts including: loss of resource production, reduction of sweep efficiency in EOR operations, and regulatory non-compliance. One potential solution to enhance wellbore integrity is microbially induced calcite precipitation (MICP) to plug preferential flow pathways. MICP is promoted with micrometer-sized organisms and low viscosity (aqueous) solutions thereby facilitating fluid transport into small aperture, potentially tortuous leakage flow paths within the cement column. In this study, MICP treatment of compromised wellbore cement was demonstrated at a depth interval of 310.0–310.57 m (1017–1019 feet) below ground surface (bgs) using conventional oil field subsurface fluid delivery technologies (packer, tubing string, and a slickline deployed bailer). After 25 urea/calcium solution and 10 microbial (Sporosarcina pasteurii) suspension injections, injectivity was reduced from the initial 0.29 cubic meters per hour (m3/h) (1.28 gallons per minute (gpm)) to less than 0.011 m3/h (0.05 gpm). The flow rate was decreased while maintaining surface pumping pressure below a maximum pressure of 81.6 bar (1200 psi) to minimize the potential for fracturing a shale formation dominant in this interval. The pressure decay immediately after each injection ceased decreased after MICP treatment. Comparison of pre- and post-test cement evaluation logs revealed substantial deposition of precipitated solids along the original flow channel. This study suggests MICP is a promising tool for enhancing wellbore cement integrity.

Over the last decade, multiple studies have highlighted the essential role of gut microbiota in normal infant development. However, the sensitive periods during which gut bacteria are established and become associated with physical growth and maturation of the brain are still poorly defined. This study tracked the assembly of the intestinal microbiota during the initial nursing period, and changes in community structure after transitioning to solid food in infant rhesus monkeys (Macaca mulatta). Anthropometric measures and rectal swabs were obtained at 2-month intervals across the first year of life and bacterial taxa identified by 16S rRNA gene sequencing. At 12 months of age, total brain and cortical regions volumes were quantified through structural magnetic resonance imaging. The bacterial community structure was dynamic and characterized by discrete maturational phases, reflecting an early influence of breast milk and the later transition to solid foods. Commensal microbial taxa varied with diet similar to findings in other animals and human infants; however, monkeys differ in the relative abundances of Lactobacilli and Bifidobacteria, two taxa predominant in breastfed human infants. Higher abundances of taxa in the phylum Proteobacteria during nursing were predictive of slower growth trajectories and smaller brain volumes at one year of age. Our findings define discrete phases of microbial succession in infant monkeys and suggest there may be a critical period during nursing when endogenous differences in certain taxa can shift the community structure and influence the pace of physical growth and the maturational trajectory of the brain.

Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add eco-morphological characterisation of a young cryptic divergence within the marsupial carnivorous genusAntechinus. Specifically, we used 168 museum specimens to characterise the recently proposed cladesA. stuartii“south”,A. stuartii“north” andA. subtropicus. Beyond slight differences attributable to overall size (and therefore not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian diversity.

Atopic dermatitis (AD) is a chronic illness that is associated with immune dysregulation. NK cell function has previously been associated with AD. NK cells directly interact with polymorphic HLA class I ligand variants using killer cell Ig-like receptors (KIRs). The purpose of this study was to identify potential associations between NK cell function and AD by evaluating variation in the presence of KIR genes as well as KIR gene interactions with the appropriate HLA class I KIR–specific ligands. Human DNA from the genetics of AD case–control study was used to genotype HLA class I KIR–specific ligands and the presence of KIR genes. In the full cohort, an increased risk of AD was noted for KIR2DL5 (1.51 [1.13, 2.01]), KIR2DS5 (1.72 [1.26, 2.34]), and KIR2DS1 (1.41 [1.04, 1.91]). Individuals with KIR2DS5 or KIR2DS1 and the HLA-C*C2 epitope were at an increased risk of AD (1.74 [1.21, 2.51] and 1.48 [1.04, 2.12], respectively). The HLA-B*-21T (TT) leader sequence increased the risk of AD across ethnicity. African Americans with KIR2DL2, KIR2DS1, KIR2DL5, and KIR2DS5 are more likely to have AD, and the risk increased for KIR2DS1 and KIR2DS5 in the presence of appropriate HLA-C C2 epitope. The risk of AD also increased for individuals with the HLA-B*-21T leader sequence. Future studies should focus on KIR gene allelic variation as well as consider cell-based measurements of KIR and the associated HLA class I epitopes.

The gut microbiota is critical to immune homeostasis, but our understanding of the underlying molecular mechanisms is very limited. Here, we demonstrate a division of labor among members of the eight-membered “model microbiome” altered Schaedler flora in promoting distinct immunophenotypes. We report that Parabacteroides goldsteinii ASF519 induces immune tolerance by promoting interleukin (IL)-10 production in a variety of myeloid-derived immune cells. The IL-10 induction is dependent on the activation of adenosine receptor A2a by microbial enzymes of the methionine cycle. ASF519 colonization in mice increased the level of adenosine in ceca and induced IL-10 secreting dendritic cells in colonic lamina propria. These immunophenotypes were pharmacologically reversed by A2a blockage. In mouse models of human autoimmune diseases, ASF519 supplementation significantly ameliorated insulitis in type 1 diabetes and collagen-induced arthritis. This study unveils a novel paradigm of gut microbiota-adenosine receptor interactions in immune tolerance and potentially provides a new therapeutic strategy for immune disorders.

Chronic demyelination in the human CNS is characterized by an inhibitory microenvironment that impairs recruitment and differentiation of oligodendrocyte progenitor cells (OPCs) leading to failed remyelination and axonal atrophy. By network-based transcriptomics, we identified sulfatase 2 (Sulf2) mRNA in activated human primary OPCs. Sulf2, an extracellular endosulfatase, modulates the signaling microenvironment by editing the pattern of sulfation on heparan sulfate proteoglycans. We found that Sulf2 was increased in demyelinating lesions in multiple sclerosis and was actively secreted by human OPCs. In experimental demyelination, elevated OPC Sulf1/2 expression directly impaired progenitor recruitment and subsequent generation of oligodendrocytes thereby limiting remyelination. Sulf1/2 potentiates the inhibitory microenvironment by promoting BMP and WNT signaling in OPCs. Importantly, pharmacological sulfatase inhibition using PI-88 accelerated oligodendrocyte recruitment and remyelination by blocking OPC-expressed sulfatases. Our findings define an important inhibitory role of Sulf1/2 and highlight the potential for modulation of the heparanome in the treatment of chronic demyelinating disease., Demyelination results in impairments in oligodendrocyte progenitor cell recruitment. Here the authors identify sulfatase 1/2 as a potential modulator of myelination by modulating the microenvironment around oligodendrocyte progenitor cells.