Quantifying the effects of exceptional fossil preservation on the global availability of phylogenetic data in deep time

Fossil deposits with exceptional preservation ("lagerstätten") provide important details not typically preserved in the fossil record, such that they hold an outsized influence on our understanding of biodiversity and evolution. In particular, the potential bias imparted by this so-called "lagerstätten effect" remains a critical, but underexplored aspect of reconstructing evolutionary relationships. Here, we quantify the amount of phylogenetic information available in the global fossil records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (e.g., lizards, snakes, mosasaurs), and then compare the influence of lagerstätten deposits on phylogenetic information content and taxon selection in phylogenetic analyses to other fossil-bearing deposits. We find that groups that preserve a high amount of phylogenetic information in their global fossil record (e.g., non-avian theropods) are less vulnerable to a "lagerstätten effect" that leads to disproportionate representation of fossil taxa from one geologic unit in an evolutionary tree. Additionally, for each taxonomic group, we find comparable amounts of phylogenetic information in lagerstätten deposits, even though corresponding morphological character datasets vary greatly. Finally, we unexpectedly find that ancient sand dune deposits of the Late Cretaceous Gobi Desert of Mongolia and China exert an anomalously large influence on the phylogenetic information available in the squamate fossil record, suggesting a "lagerstätten effect" can be present in units not traditionally considered lagerstätten. These results offer a phylogenetics-based lens through which to examine the effects of exceptional fossil preservation on biological patterns through time and space, and invites further quantification of evolutionary information in the rock record.

ONC201 in combination with paxalisib for the treatment of H3K27-altered diffuse midline glioma

Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPGs), are the most lethal of childhood cancers. Palliative radiotherapy is the only established treatment, with median patient survival of 9-11 months. ONC201 is a DRD2 antagonist and ClpP agonist that has shown preclinical and emerging clinical efficacy in DMG. However, further work is needed to identify the mechanisms of response of DIPGs to ONC201 treatment and to determine whether recurring genomic features influence response. Using a systems-biological approach, we showed that ONC201 elicits potent agonism of the mitochondrial protease ClpP to drive proteolysis of electron transport chain and tricarboxylic acid cycle proteins. DIPGs harboring PIK3CA-mutations showed increased sensitivity to ONC201, while those harboring TP53-mutations were more resistant. Metabolic adaptation and reduced sensitivity to ONC201 was promoted by redox-activated PI3K/Akt signaling, which could be counteracted using the brain penetrant PI3K/Akt inhibitor, paxalisib. Together, these discoveries coupled with the powerful anti-DIPG/DMG pharmacokinetic and pharmacodynamic properties of ONC201 and paxalisib have provided the rationale for the ongoing DIPG/DMG phase II combination clinical trial NCT05009992.

Synergistic Targeting of DNA-PK and KIT Signaling Pathways in KIT Mutant Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is the most common and aggressive form of acute leukemia, with a 5-year survival rate of just 24%. Over a third of all AML patients harbor activating mutations in kinases, such as the receptor tyrosine kinases FLT3 (receptor-type tyrosine-protein kinase FLT3) and KIT (mast/stem cell growth factor receptor kit). FLT3 and KIT mutations are associated with poor clinical outcomes and lower remission rates in response to standard-of-care chemotherapy. We have recently identified that the core kinase of the non-homologous end joining DNA repair pathway, DNA-PK (DNA-dependent protein kinase), is activated downstream of FLT3; and targeting DNA-PK sensitized FLT3-mutant AML cells to standard-of-care therapies. Herein, we investigated DNA-PK as a possible therapeutic vulnerability in KIT mutant AML, using isogenic FDC-P1 mouse myeloid progenitor cell lines transduced with oncogenic mutant KIT (V560G and D816V) or vector control. Targeted quantitative phosphoproteomic profiling identified phosphorylation of DNA-PK in the T2599/T2605/S2608/S2610 cluster in KIT mutant cells, indicative of DNA-PK activation. Accordingly, proliferation assays revealed that KIT mutant FDC-P1 cells were more sensitive to the DNA-PK inhibitors M3814 or NU7441, compared with empty vector controls. DNA-PK inhibition combined with inhibition of KIT signaling using the kinase inhibitors dasatinib or ibrutinib, or the protein phosphatase 2A activators FTY720 or AAL(S), led to synergistic cell death. Global phosphoproteomic analysis of KIT-D816V cells revealed that dasatinib and M3814 single-agent treatments inhibited extracellular signal-regulated kinase and AKT (RAC-alpha serine/threonine-protein kinase)/MTOR (serine/threonine-protein kinase mTOR) activity, with greater inhibition of both pathways when used in combination. Combined dasatinib and M3814 treatment also synergistically inhibited phosphorylation of the transcriptional regulators MYC and MYB. This study provides insight into the oncogenic pathways regulated by DNA-PK beyond its canonical role in DNA repair and demonstrates that DNA-PK is a promising therapeutic target for KIT mutant cancers.

The femora of Drepanosauromorpha (Reptilia: Diapsida): Implications for the functional evolution of the thigh of Sauropsida

The femora of diapsids have undergone morphological changes related to shifts in postural and locomotor modes, such as the transition from plesiomorphic amniote and diapsid taxa to the apomorphic conditions related to a more erect posture within Archosauriformes. One remarkable clade of Triassic diapsids is the chameleon-like Drepanosauromorpha. This group is known from numerous articulated but heavily compressed skeletons that have the potential to further inform early reptile femoral evolution. For the first time, we describe the three-dimensional osteology of the femora of Drepanosauromorpha, based on undistorted fossils from the Upper Triassic Chinle Formation and Dockum Group of North America. We identify apomorphies and a combination of character states that link these femora to those in crushed specimens of drepanosauromorphs and compare our sample with a range of amniote taxa. Several characteristics of drepanosauromorph femora, including a hemispherical proximal articular surface, prominent asymmetry in the proximodistal length of the tibial condyles, and a deep intercondylar sulcus, are plesiomorphies shared with early diapsids. The femora contrast with those of most diapsids in lacking a crest-like, distally tapering internal trochanter. They bear a ventrolaterally positioned tuberosity on the femoral shaft, resembling the fourth trochanter in Archosauriformes. The reduction of an internal trochanter parallels independent reductions in therapsids and archosauriforms. The presence of a ventrolaterally positioned trochanter is also similar to that of chameleonid squamates. Collectively, these features demonstrate a unique femoral morphology for drepanosauromorphs, and suggest an increased capacity for femoral adduction and protraction relative to most other Permo-Triassic diapsids.

Phospho-heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED) provides real-time phosphoproteomics data to aid in cancer drug selection

Global high-throughput phosphoproteomic profiling is increasingly being applied to cancer specimens to identify the oncogenic signaling cascades responsible for promoting disease initiation and disease progression; pathways that are often invisible to genomics analysis. Hence, phosphoproteomic profiling has enormous potential to inform and improve individualized anti-cancer treatment strategies. However, to achieve the adequate phosphoproteomic depth and coverage necessary to identify the activated, and hence, targetable kinases responsible for driving oncogenic signaling pathways, affinity phosphopeptide enrichment techniques are required and often coupled with offline high-pressure liquid chromatographic (HPLC) separation prior to nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS). These complex and time-consuming procedures, limit the utility of phosphoproteomics for the analysis of individual cancer patient specimens in real-time, and restrict phosphoproteomics to specialized laboratories often outside of the clinical setting. To address these limitations, here we have optimized a new protocol, phospho-heavy-labeled-spiketide FAIMS Stepped-CV DDA (pHASED), that employs online phosphoproteome deconvolution using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and internal phosphopeptide standards to provide accurate label-free quantitation (LFQ) data in real-time. Compared with traditional single-shot LFQ phosphoproteomics workflows, pHASED provided increased phosphoproteomic depth and coverage (phosphopeptides = 4617 pHASED, 2789 LFQ), whilst eliminating the variability associated with offline prefractionation. pHASED was optimized using tyrosine kinase inhibitor (sorafenib) resistant isogenic FLT3-mutant acute myeloid leukemia (AML) cell line models. Bioinformatic analysis identified differential activation of the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) pathway, responsible for sensing and repairing DNA damage in sorafenib-resistant AML cell line models, thereby uncovering a potential therapeutic opportunity. Herein, we have optimized a rapid, reproducible, and flexible protocol for the characterization of complex cancer phosphoproteomes in real-time, a step towards the implementation of phosphoproteomics in the clinic to aid in the selection of anti-cancer therapies for patients.

DIPG-07. Preclinical and case study results underpinning the phase II clinical trial testing the combination of ONC201 and paxalisib for the treatment of patients with diffuse midline glioma (NCT05009992)

Diffuse midline gliomas (DMG), including those of the brainstem (diffuse intrinsic pontine glioma - DIPG), are pediatric CNS tumors recognized as the most lethal of all children’s cancers. Palliative radiotherapy is the only approved treatment, with survival just 9-11–months post-diagnosis. ONC201 shows preclinical and emerging clinical efficacy in early-stage clinical trials, extending survival of DIPG patients by ~9-11–months compared to historic controls. However, patients invariably develop resistance, with some patients completely refractory to treatment. Using a multi-omics approach, including pharmacology, proteomics, genomics, epigenetics, in vitro and in vivo modeling, across ten international laboratories, we have uncovered the inherent mechanisms of resistance to ONC201. We find ONC201 elicits antagonism of the Dopamine receptor D2 (DRD2), whilst also causing mitochondrial degradation through potent agonism of the Mitochondrial protease CLPP, that drives proteolysis of the electron transport chain (ETC) protein Succinate dehydrogenase A (SDHA) and degradation of critical mitochondrial tricarboxylic acid (TCA) cycle regulator Isocitrate dehydrogenase 3B (IDH3B). Loss mitochondrial respiration increased hypoxia and reduced α-ketoglutarate, inhibiting lysine demethylation, increasing methylation of H3K4me3 and H3K27me3, thus altering the epigenome of primary DIPG cells. Loss of SDHA caused oxidation of succinate forming superoxide driving redox regulated PI3K/AKT signaling, counteracted using the PI3K/AKT inhibitor paxalisib. The combination of ONC201 and paxalisib synergically extended survival of two aggressive DIPG PDX models (SU-SIPG-VI vehicle=73 vs. combination=100-days, p=0.0027; SF8626 vehicle=36 vs. combination=43-days, p=0.0002). Compassionate access to this combination (n=2 patients; immediately post-RT and following re-RT) resulted in reductions in tumor volume and complete resolution of disease symptoms, extending overall survival (e.g., diagnosis patient MR axial scan=1554 mm2 , following eight months on the combination, current tumor volume=464 mm2 (<70%), patient remains on treatment). Our findings harness the powerful anti-DMG/DIPG pharmacokinetic/dynamic properties of ONC201 and paxalisib, a combination that is currently in clinical trials (NCT05009992).

Topographic Control of Order in Quasi-2D Granular Phase Transitions

We experimentally investigate the nature of 2D phase transitions in a quasi-2D granular fluid. Using a surface decorated with periodically spaced dimples we observe interfacial tension between coexisting granular liquid and crystal phases. Measurements of the orientational and translational order parameters and associated susceptibilities indicate that the surface topography alters the order of the phase transition from a two-step continuous one to a first-order liquid-solid one. The interplay of boundary inelasticity and geometry, either order promoting or inhibiting, controls whether it is the granular crystal or the granular fluid which makes contact with the edge. This order induced wetting has important consequences, determining how coexisting phases separate spatially.

Exceptionally simple, rapidly replaced teeth in sauropod dinosaurs demonstrate a novel evolutionary strategy for herbivory in Late Jurassic ecosystems

BACKGROUND

Dinosaurs dominated terrestrial environments for over 100 million years due in part to innovative feeding strategies. Although a range of dental adaptations was present in Late Jurassic dinosaurs, it is unclear whether dinosaur ecosystems exhibited patterns of tooth disparity and dietary correlation similar to those of modern amniotes, in which carnivores possess simple teeth and herbivores exhibit complex dentitions. To investigate these patterns, we quantified dental shape in Late Jurassic dinosaurs to test relationships between diet and dental complexity.

RESULTS

Here, we show that Late Jurassic dinosaurs exhibited a disparity of dental complexities on par with those of modern saurians. Theropods possess relatively simple teeth, in spite of the range of morphologies tested, and is consistent with their inferred carnivorous habits. Ornithischians, in contrast, have complex dentitions, corresponding to herbivorous habits. The dentitions of macronarian sauropods are similar to some ornithischians and living herbivorous squamates but slightly more complex than other sauropods. In particular, all diplodocoid sauropods investigated possess remarkably simple teeth. The existence of simple teeth in diplodocoids, however, contrasts with the pattern observed in nearly all known herbivores (living or extinct).

CONCLUSIONS

Sauropod dinosaurs exhibit a novel approach to herbivory not yet observed in other amniotes. We demonstrate that sauropod tooth complexity is related to tooth replacement rate rather than diet, which contrasts with the results from mammals and saurians. This relationship is unique to the sauropod clade, with ornithischians and theropods displaying the patterns observed in other groups. The decoupling of herbivory and tooth complexity paired with a correlation between complexity and replacement rate demonstrates a novel evolutionary strategy for plant consumption in sauropod dinosaurs.

A novel approach to nonsurgical sterilization; application of menadione-modified gonocyte-targeting M13 bacteriophage for germ cell ablation in utero

There remains a compelling need for the development of nonsurgical sterilizing agents to expand the fertility management options for both domestic and feral animal species. We hypothesize that an efficacious sterilization approach would be to selectively ablate nonrenewable cell types that are essential for reproduction, such as the undifferentiated gonocytes within the embryonic gonad. Here, we report a novel strategy to achieve this goal centered on the use of a chemically modified M13 bacteriophage to effect the targeted delivery of menadione, a redox‐cycling naphthoquinone, to mouse gonocytes. Panning of the M13 random peptide ‘phage display library proved effective in the isolation of gonocyte‐specific targeting clones. One such clone was modified via N‐succinimidyl‐S‐acetylthioacetate (SATA) linkage to the N‐terminus of the major PVIII capsid protein. Subsequent deacetylation of the SATA was undertaken to expose a thiol group capable of reacting with menadione through Michael addition. This chemical modification was confirmed using UV spectrophotometry. In proof‐of‐concept experiments we applied the modified ‘phage to primary cultures of fetal germ cells and induced, an approximately, 60% reduction in the viability of the target cell population. These studies pave the way for in vivo application of chemically modified M13 bacteriophage in order to achieve the selective ablation of nonrenewable cell types in the reproductive system, thereby providing a novel nonsurgical approach the regulation of fertility in target species.

Collision-enhanced friction of a bouncing ball on a rough vibrating surface

We describe experiments and simulations to investigate the dynamics of a ball bouncing on a rough vibrating surface. Directly measuring the impulse due to each bounce we find that the frictional interaction with the surface is strongly enhanced near to the side wall. The enhanced dissipation arises as a consequence of the coupling between the collision, rotation and surface friction. This dissipation, which for our experimental conditions was estimated to be up to three times larger than the more obvious inelastic collision, can result in an enhanced probability density near boundaries and particle–particle spatial correlations. Our findings imply that the effective particle collision properties cannot be considered independently of the surface’s frictional properties.

Preclinical and clinical evaluation of German-sourced ONC201 for the treatment of H3K27M-mutant diffuse intrinsic pontine glioma

Background

Diffuse intrinsic pontine glioma (DIPG) is a fatal childhood brainstem tumor for which radiation is the only treatment. Case studies report a clinical response to ONC201 for patients with H3K27M-mutant gliomas. Oncoceutics (ONC201) is only available in the United States and Japan; however, in Germany, DIPG patients can be prescribed and dispensed a locally produced compound—ONC201 German-sourced ONC201 (GsONC201). Pediatric oncologists face the dilemma of supporting the administration of GsONC201 as conjecture surrounds its authenticity. Therefore, we compared GsONC201 to original ONC201 manufactured by Oncoceutics Inc.

Methods

Authenticity of GsONC201 was determined by high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy. Biological activity was shown via assessment of on-target effects, in vitro growth, proliferation, and apoptosis analysis. Patient-derived xenograft mouse models were used to assess plasma and brain tissue pharmacokinetics, pharmacodynamics, and overall survival (OS). The clinical experience of 28 H3K27M+ mutant DIPG patients who received GsONC201 (2017–2020) was analyzed.

Results

GsONC201 harbored the authentic structure, however, was formulated as a free base rather than the dihydrochloride salt used in clinical trials. GsONC201 in vitro and in vivo efficacy and drug bioavailability studies showed no difference compared to Oncoceutics ONC201. Patients treated with GsONC201 (n = 28) showed a median OS of 18 months (P = .0007). GsONC201 patients who underwent reirradiation showed a median OS of 22 months compared to 12 months for GsONC201 patients who did not (P = .012).

Conclusions

This study confirms the biological activity of GsONC201 and documents the OS of patients who received the drug; however, GsONC201 was never used as a monotherapy.

Osteohistological analyses reveal diverse strategies of theropod dinosaur body-size evolution

The independent evolution of gigantism among dinosaurs has been a topic of long-standing interest, but it remains unclear if gigantic theropods, the largest bipeds in the fossil record, all achieved massive sizes in the same manner, or through different strategies. We perform multi-element histological analyses on a phylogenetically broad dataset sampled from eight theropod families, with a focus on gigantic tyrannosaurids and carcharodontosaurids, to reconstruct the growth strategies of these lineages and test if particular bones consistently preserve the most complete growth record. We find that in skeletally mature gigantic theropods, weight-bearing bones consistently preserve extensive growth records, whereas non-weight-bearing bones are remodelled and less useful for growth reconstruction, contrary to the pattern observed in smaller theropods and some other dinosaur clades. We find a heterochronic pattern of growth fitting an acceleration model in tyrannosaurids, with allosauroid carcharodontosaurids better fitting a model of hypermorphosis. These divergent growth patterns appear phylogenetically constrained, representing extreme versions of the growth patterns present in smaller coelurosaurs and allosauroids, respectively. This provides the first evidence of a lack of strong mechanistic or physiological constraints on size evolution in the largest bipeds in the fossil record and evidence of one of the longest-living individual dinosaurs ever documented.

New fossil lizard specimens from a poorly-known squamate assemblage in the Upper Cretaceous (Campanian) San Juan Basin, New Mexico, USA

Recent collection efforts in the upper Campanian (∼76-73.5 Ma) Fruitland and Kirtland formations of northwestern New Mexico have significantly increased the taxonomic diversity of lizards in this historically poorly understood squamate assemblage. New lizard specimens from the “Hunter Wash Local Fauna” of the upper Fruitland and lower Kirtland formations include: (1) new specimens referable to Chamopsiidae; (2) new material belonging to Scincomorpha, (3) new material belonging to Anguidae; and (4) the first reported predatory lizard (Platynota) material from the Campanian of New Mexico. The increase in lizard diversity in the “Hunter Wash Local Fauna” expands our understanding of Late Cretaceous squamate taxonomy, distribution, and diversity in the Western Interior of North America (Laramidia). Collectively, the described specimens represent family-level diversity similar to that seen in other Campanian foreland basin deposits of the Western Interior, such as the mid-paleolatitude Kaiparowits Formation of southern Utah, the higher paleolatitude Dinosaur Park Formation of southern Alberta, and the lower paleolatitude Aguja Formation of southwestern Texas. The lizards of the “Hunter Wash Local Fauna” represent crucial mid-paleolatitude data from a coastal plain depositional setting in Laramidia—allowing for comparisons to more well-studied assemblages at different latitudes and in different depositional settings.

The Association Between Admiration of Antisocial Peers and Past 30-Day Opioid Misuse Among Justice-Involved children

AIM

Prevention of illicit or nonmedical opioid use, called opioid misuse (OM) is a key public health concern that requires research on the factors that influence OM initiation among high-risk populations. Justice-involved children (JIC) have more risk factors and fewer resources. Antisocial peers have been linked to adolescent substance abuse and delinquency. However, the association between the admiration of antisocial peers and OM among JIC has not yet been studied. This study hypothesizes that admiration of antisocial peers will be associated with a higher likelihood of OM among Florida JIC.

METHODS

Cross-sectional data on 79,960 JIC from the Florida Department of Juvenile Justice (FLDJJ) were examined. To test the hypothesis, bivariate and multivariate logistic regression analyses were employed. The multivariate models controlled for gender, race, age in 2007, family income, history of mental health, history of depression, and optimism.

RESULTS

Nearly 2.7% of the sample met the criteria for past 30-day OM, and over 75% of those current users admired or somewhat admired their antisocial peers. Compare to JIC who did not admire their antisocial peers, those who had some admiration of antisocial peers were 2.39 times more likely to misuse opioids in the past 30-days and those who admired their antisocial peers were 4.40 times more likely to meet the criteria for past 30-day OM.

CONCLUSIONS

Cultivating positive peer interactions and providing positive peer role models may help to reduce illicit opioid use among JIC.

Integrating gross morphology and bone histology to assess skeletal maturity in early dinosauromorphs: new insights from Dromomeron (Archosauria: Dinosauromorpha)

Understanding growth patterns is central to properly interpreting paleobiological signals in tetrapods, but assessing skeletal maturity in some extinct clades may be difficult when growth patterns are poorly constrained by a lack of ontogenetic series. To overcome this difficulty in assessing the maturity of extinct archosaurian reptiles—crocodylians, birds and their extinct relatives—many studies employ bone histology to observe indicators of the developmental stage reached by a given individual. However, the relationship between gross morphological and histological indicators of maturity has not been examined in most archosaurian groups. In this study, we examined the gross morphology of a hypothesized growth series of Dromomeron romeri femora (96.6–144.4 mm long), the first series of a non-dinosauriform dinosauromorph available for such a study. We also histologically sampled several individuals in this growth series. Previous studies reported that D. romeri lacks well-developed rugose muscle scars that appear during ontogeny in closely related dinosauromorph taxa, so integrating gross morphology and histological signal is needed to determine reliable maturity indicators for early bird-line archosaurs. We found that, although there are small, linear scars indicating muscle attachment sites across the femur, the only rugose muscle scar that appears during ontogeny is the attachment of the M. caudofemoralis longus, and only in the largest-sampled individual. This individual is also the only femur with histological indicators that asymptotic size had been reached, although smaller individuals possess some signal of decreasing growth rates (e.g., decreasing vascular density). The overall femoral bone histology of D. romeri is similar to that of other early bird-line archosaurs (e.g., woven-bone tissue, moderately to well-vascularized, longitudinal vascular canals). All these data indicate that the lack of well-developed femoral scars is autapomorphic for this species, not simply an indication of skeletal immaturity. We found no evidence of the high intraspecific variation present in early dinosaurs and other dinosauriforms, but a limited sample size of other early bird-line archosaur growth series make this tentative. The evolutionary history and phylogenetic signal of gross morphological features must be considered when assessing maturity in extinct archosaurs and their close relatives, and in some groups corroboration with bone histology or with better-known morphological characters is necessary.

Amino acids and proteomic acclimation of Staphylococcus aureus when incubated in a defined minimal medium supplemented with 5% sodium chloride

Staphylococcus aureus is a versatile bacterium that can adapt to survive and grow in a wide range of salt concentrations. This study investigated whether the cells could mount a response to survive a challenge of 5% NaCl in a minimal incubation medium that would not support cell replication. Cells were grown in liquid culture, washed and then incubated for 90 min at 37°C in a medium that contained only glycine and glucose as substrates in PBS plus trace elements. The control cells were compared with a treatment group which was incubated with an additional 5% NaCl. Significantly more glycine was taken up by the cells exposed to 5% NaCl compared with control cells, and both groups consumed 99% of the glucose supplied. The NaCl treated cells had significantly higher cytoplasmic levels of proline and glutamic acid as well as lower levels of alanine and methionine compared with the controls (p < 0.05). The levels of the two major cytoplasmic amino acids, aspartic acid and glycine, remained constant in control and treated cells. Proteomic analyses revealed that 10 proteins showed differential responses between the control and treatment groups. The reductions in proteins were primarily associated with processes of protein biosynthesis, pathogenicity, and cell adhesion. Since cell numbers remained constant during the incubation period in minimal medium, it was concluded that there was no cell division to support population growth. The results provided evidence that the cells in the minimal medium exposed to the NaCl treatment underwent in situ homeostatic changes to adjust to the new environmental conditions. It was proposed that this represented a phenotypic shift to form cells akin to small colony variants, with lower metabolic rates and lower levels of key proteins associated with pathogenicity.

The serine protease testisin is present on the surface of capacitated stallion spermatozoa and interacts with key zona pellucida binding proteins

BACKGROUND AND OBJECTIVES

Serine proteases are emerging as important players in the spermatozoon's acquisition of functional competence. This study aimed to characterize the serine protease testisin (PRSS21) in stallion spermatozoa, examining its surface expression, possible origins in the testis and epididymis, and changes in response to capacitation and acrosome reaction, as well as its capacity to form high molecular weight complexes and interact with other proteins.

MATERIALS AND METHODS

The role of serine proteases in spontaneous capacitation and acrosome reaction of stallion spermatozoa was established using the serine protease inhibitor, AEBSF. Testisin localization, before and after exposure of stallion spermatozoa to capacitating conditions and calcium ionophore, was examined using live cell immunofluorescence and flow cytometry. Immunohistochemistry of testicular and epididymal tissues was used to further dissect the origins of sperm testisin. Testisin's participation in high molecular weight protein complexes and identification of its interacting partner proteins were investigated using Blue Native PAGE, co-immunoprecipitation, and mass spectrometry, with interrogation of protein-protein interaction databases and gene ontology analysis of partner proteins used to further explore the potential roles of the testisin-containing complex in sperm function.

RESULTS

Testisin surface expression increased significantly in capacitated spermatozoa (p < 0.001), increased further following acrosome reaction (p < 0.01), and was localized to the equatorial region of the sperm head. Testisin was also detected in luminal fluid within the caput and corpus regions of the epididymis, epididymal spermatozoa, and epididymal epithelial cells. Testisin formed several multiprotein complexes; co-immunoprecipitation revealed interactions of testisin with a multitude of zona pellucida-binding proteins, including ZPBP, ZAN, acrosin, several heat-shock proteins, and components of the TCP1 complex.

CONCLUSION

Testisin appears to form part of the zona pellucida-binding complex in stallion spermatozoa and may be involved in the proteolytic cascade that prepares the sperm surface for interaction with the oocyte.

Extracellular vesicles with altered tetraspanin CD9 and CD151 levels confer increased prostate cell motility and invasion

To facilitate intercellular communication, cells release nano-sized, extracellular vesicles (EVs) to transfer biological cargo to both local and distant sites. EVs are enriched in tetraspanins, two of which (CD9 and CD151) have altered expression patterns in many solid tumours, including prostate cancer, as they advance toward metastasis. We aimed to determine whether EVs from prostate cells with altered CD9 and CD151 expression could influence cellular behaviour and increase the metastatic capabilities of non-tumourigenic prostate cells. EVs were isolated by ultrafiltration and characterised for their tetraspanin expression and size distribution. iTRAQ was used to identify differences between RWPE1 and tetraspanin-modified RWPE1 EV proteomes, showing an enrichment in protein degradation pathways. Addition of EVs from RWPE1 cells with reduced CD9 or increased CD151 abundance resulted in increased invasion of RWPE1 cells, and increased migration in the case of high CD151 abundance. We have been able to show that alteration of CD9 and CD151 on prostate cells alters the proteome of their resultant EVs, and that these EVs can enhance the migratory and invasive capabilities of a non-tumourigenic prostate cellular population. This work suggests that cellular tetraspanin levels can alter EVs, potentially acting as a driver of metastasis in prostate cancer.

Cell-Free DNA Blood Collection Tubes Are Appropriate for Clinical Proteomics: A Demonstration in Colorectal Cancer

BACKGROUND

Optimized blood collection tubes (BCT) have been developed to expand the utility of plasma cell-free DNA (cfDNA) and are in clinical use. The appropriateness of plasma collected and stored in these tubes for proteomic analysis is unknown.

METHODS

Paired blood samples were collected in BCT and traditional K3EDTA (EDTA) tubes from healthy controls and from colorectal cancer (CRC) patients before and after surgery, and stored for between 45 min and 48 h at room temperature. Plasma proteins were analyzed following high-abundant plasma protein depletion in quantitative discovery and targeted proteomics by liquid chromatography tandem-mass spectrometry (LC-MS/MS).

RESULTS

BCT reduced cellular protein contamination in healthy controls over time, and increased the number of high confident low-abundant protein identifications in CRC blood samples compared to matched samples collected in EDTA tubes. The known CRC plasma protein biomarker, carcinoembryonic antigen (CEA), showed elevated levels across patients pre-operatively when collected and stored in BCT compared to EDTA tubes. Emerging CRC biomarkers, Dickkopf-3 (DKK3) and Gelsolin (GSN), showed elevated levels pre-operatively when collected in BCT.

CONCLUSIONS

Optimized BCT are appropriate for low-abundant plasma protein analysis and can be used with confidence for clinical proteomics.

Boundary effects in a quasi-two-dimensional driven granular fluid

The effect of a confining boundary on the spatial variations in granular temperature of a driven quasi-two-dimensional layer of particles is investigated experimentally. The radial drop in the relative granular temperature ΔT/T exhibits a maximum at intermediate particle numbers which coincides with a crossover from kinetic to collisional transport of energy. It is also found that at low particle numbers, the distributions of radial velocities are increasingly asymmetric as one approaches the boundary. The radial and tangential granular temperatures split, and in the tails of the radial velocity distribution there is a higher population of fast moving particles traveling away rather than towards the boundary.

Electrophilic aldehyde products of lipid peroxidation selectively adduct to heat shock protein 90 and arylsulfatase A in stallion spermatozoa

Oxidative stress is a major determinant of mammalian sperm function stimulating lipid peroxidation cascades that culminate in the generation of potentially cytotoxic aldehydes. The aim of this study was to assess the impact of such aldehydes on the functionality of stallion spermatozoa. The impact of exposure to exogenous acrolein (ACR) and 4-hydroxynonenal (4HNE) was manifested in a highly significant dose- and time-dependent increase in mitochondrial reactive oxygen species (ROS), total cellular ROS, a decrease in sperm motility, and a time-dependent increase in lipid peroxidation. Notably, low doses of ACR and 4HNE also caused a significant decrease in zona binding. In contrast, exogenous malondialdehyde, a commonly used marker of oxidative stress, had little impact on the various sperm parameters assessed. In accounting for the negative physiological impact of ACR and 4HNE, it was noted that both aldehydes readily adducted to sperm proteins located predominantly within the head, proximal centriole, and tail. The detoxifying activity of mitochondrial aldehyde dehydrogenase 2 appeared responsible for a lack of adduction in the midpiece; however, this activity was overwhelmed by 24 h of electrophilic aldehyde exposure. Sequencing of the dominant proteins targeted for ACR and 4HNE covalent modification identified heat shock protein 90 alpha (cytosolic) class A member 1 and arylsulfatase A, respectively. These collective findings may prove useful in the identification of diagnostic biomarkers of stallion fertility and resolving the mechanistic basis of sperm dysfunction in this species.

Determination of Thermodynamic Properties of Alkaline Earth-liquid Metal Alloys Using the Electromotive Force Technique

A novel electrochemical cell based on a CaF₂ solid-state electrolyte has been developed to measure the electromotive force (emf) of binary alkaline earth-liquid metal alloys as functions of both composition and temperature in order to acquire thermodynamic data. The cell consists of a chemically stable solid-state CaF₂-AF₂ electrolyte (where A is the alkaline-earth element such as Ca, Sr, or Ba), with binary A-B alloy (where B is the liquid metal such as Bi or Sb) working electrodes, and a pure A metal reference electrode. Emf data are collected over a temperature range of 723 K to 1,123 K in 25 K increments for multiple alloy compositions per experiment and the results are analyzed to yield activity values, phase transition temperatures, and partial molar entropies/enthalpies for each composition.

The Australian saltwater crocodile (Crocodylus porosus) provides evidence that the capacitation of spermatozoa may extend beyond the mammalian lineage

Although mammalian spermatozoa only acquire functional maturity as they are conveyed through the male (epididymal maturation) and female (capacitation) reproductive tracts, the degree of post-testicular development necessary to achieve fertilization in other vertebrate species remains far less clear. Indeed, despite reports that the epididymis of birds and reptiles is capable of secreting proteins that bind and modify the sperm surface characteristics, it remains unclear whether capacitation is a pre-requisite for fertilization in these species. Using the ancient reptilian Australian saltwater crocodile as a model, this study was undertaken to explore whether reptile sperm do undergo capacitation-like changes following ejaculation. Our studies revealed that crocodile spermatozoa experienced a rapid and sustained, cyclic-AMP mediated increase in progressive motility following incubation under conditions optimized for the induction of capacitation in mammalian species such as the mouse and human. This response was coupled with elevated levels of phosphorylation associated with both protein kinase A and tyrosine kinase substrates, the latter of which were predominantly localized within the sperm flagellum. In findings that also accord with mammalian spermatozoa, we confirmed a homologue of outer dense fibre 2 as one of the principal substrates for tyrosine phosphorylation. Overall, our findings support the concept that crocodile spermatozoa do undergo a process that is homologous to capacitation in preparation for fertilization of an ovum.

Accessible biometrics: A frustrated total internal reflection approach to imaging fingerprints

Fingerprints are widely used as a means of identifying persons of interest because of the highly individual nature of the spatial distribution and types of features (or minuta) found on the surface of a finger. This individuality has led to their wide application in the comparison of fingerprints found at crime scenes with those taken from known offenders and suspects in custody. However, despite recent advances in machine vision technology and image processing techniques, fingerprint evidence is still widely being collected using outdated practices involving ink and paper - a process that can be both time consuming and expensive. Reduction of forensic service budgets increasingly requires that evidence be gathered and processed more rapidly and efficiently. However, many of the existing digital fingerprint acquisition devices have proven too expensive to roll out on a large scale. As a result new, low-cost imaging technologies are required to increase the quality and throughput of the processing of fingerprint evidence. Here we describe an inexpensive approach to digital fingerprint acquisition that is based upon frustrated total internal reflection imaging. The quality and resolution of the images produced are shown to be as good as those currently acquired using ink and paper based methods. The same imaging technique is also shown to be capable of imaging powdered fingerprints that have been lifted from a crime scene using adhesive tape or gel lifters.

A new rauisuchid (Archosauria, Pseudosuchia) from the Upper Triassic (Norian) of New Mexico increases the diversity and temporal range of the clade

Rauisuchids are large (2–6 m in length), carnivorous, and quadrupedal pseudosuchian archosaurs closely related to crocodylomorphs. Though geographically widespread, fossils of this clade are relatively rare in Late Triassic assemblages. The middle Norian (∼212 Ma) Hayden Quarry of northern New Mexico, USA, in the Petrified Forest Member of the Chinle Formation, has yielded isolated postcranial elements and associated skull elements of a new species of rauisuchid. Vivaron haydeni gen. et. sp. nov. is diagnosed by the presence of two posteriorly directed prongs at the posterior end of the maxilla for articulation with the jugal. The holotype maxilla and referred elements are similar to those of the rauisuchid Postosuchus kirkpatricki from the southwestern United States, but V. haydeni shares several maxillary apomorphies (e.g., a distinct dropoff to the antorbital fossa that is not a ridge, a straight ventral margin, and a well defined dental groove) with the rauisuchid Teratosaurus suevicus from the Norian of Germany. Despite their geographic separation, this morphological evidence implies a close phylogenetic relationship between V. haydeni and T. suevicus. The morphology preserved in the new Hayden Quarry rauisuchid V. haydeni supports previously proposed and new synapomorphies for nodes within Rauisuchidae. The discovery of Vivaron haydeni reveals an increased range of morphological disparity for rauisuchids from the low-paleolatitude Chinle Formation and a clear biogeographic connection with high paleolatitude Pangea.

An Unusual New Theropod with a Didactyl Manus from the Upper Cretaceous of Patagonia, Argentina

BACKGROUND

Late Cretaceous terrestrial strata of the Neuquén Basin, northern Patagonia, Argentina have yielded a rich fauna of dinosaurs and other vertebrates. The diversity of saurischian dinosaurs is particularly high, especially in the late Cenomanian-early Turonian Huincul Formation, which has yielded specimens of rebacchisaurid and titanosaurian sauropods, and abelisaurid and carcharodontosaurid theropods. Continued sampling is adding to the known vertebrate diversity of this unit.

METHODOLOGY/ PRINCIPAL FINDINGS

A new, partially articulated mid-sized theropod was found in rocks from the Huincul Formation. It exhibits a unique combination of traits that distinguish it from other known theropods justifying erection of a new taxon, Gualicho shinyae gen. et sp. nov. Gualicho possesses a didactyl manus with the third digit reduced to a metacarpal splint reminiscent of tyrannosaurids, but both phylogenetic and multivariate analyses indicate that didactyly is convergent in these groups. Derived characters of the scapula, femur, and fibula supports the new theropod as the sister taxon of the nearly coeval African theropod Deltadromeus and as a neovenatorid carcharodontosaurian. A number of these features are independently present in ceratosaurs, and Gualicho exhibits an unusual mosaic of ceratosaurian and tetanuran synapomorphies distributed throughout the skeleton.

CONCLUSIONS/ SIGNIFICANCE

Gualicho shinyae gen. et sp. nov. increases the known theropod diversity of the Huincul Formation and also represents the first likely neovenatorid from this unit. It is the most basal tetatanuran to exhibit common patterns of digit III reduction that evolved independently in a number of other tetanuran lineages. A close relationship with Deltadromaeus from the Kem Kem beds of Niger adds to the already considerable biogeographic similarity between the Huincul Formation and coeval rock units in North Africa.

Characterization of transient noise in Advanced LIGO relevant to gravitational wave signal GW150914

On September 14, 2015, a gravitational wave signal from a coalescing black hole binary system was observed by the Advanced LIGO detectors. This paper describes the transient noise backgrounds used to determine the significance of the event (designated GW150914) and presents the results of investigations into potential correlated or uncorrelated sources of transient noise in the detectors around the time of the event. The detectors were operating nominally at the time of GW150914. We have ruled out environmental influences and non-Gaussian instrument noise at either LIGO detector as the cause of the observed gravitational wave signal.

GW151226: Observation of Gravitational Waves from a 22-Solar-Mass Binary Black Hole Coalescence

We report the observation of a gravitational-wave signal produced by the coalescence of two stellar-mass black holes. The signal, GW151226, was observed by the twin detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO) on December 26, 2015 at 03:38:53 UTC. The signal was initially identified within 70 s by an online matched-filter search targeting binary coalescences. Subsequent off-line analyses recovered GW151226 with a network signal-to-noise ratio of 13 and a significance greater than 5σ. The signal persisted in the LIGO frequency band for approximately 1 s, increasing in frequency and amplitude over about 55 cycles from 35 to 450 Hz, and reached a peak gravitational strain of 3.4_{-0.9}^{+0.7}×10^{-22}. The inferred source-frame initial black hole masses are 14.2_{-3.7}^{+8.3}M_{⊙} and 7.5_{-2.3}^{+2.3}M_{⊙}, and the final black hole mass is 20.8_{-1.7}^{+6.1}M_{⊙}. We find that at least one of the component black holes has spin greater than 0.2. This source is located at a luminosity distance of 440_{-190}^{+180}  Mpc corresponding to a redshift of 0.09_{-0.04}^{+0.03}. All uncertainties define a 90% credible interval. This second gravitational-wave observation provides improved constraints on stellar populations and on deviations from general relativity.

Properties of the Binary Black Hole Merger GW150914

On September 14, 2015, the Laser Interferometer Gravitational-Wave Observatory (LIGO) detected a gravitational-wave transient (GW150914); we characterize the properties of the source and its parameters. The data around the time of the event were analyzed coherently across the LIGO network using a suite of accurate waveform models that describe gravitational waves from a compact binary system in general relativity. GW150914 was produced by a nearly equal mass binary black hole of masses 36_{-4}^{+5}M_{⊙} and 29_{-4}^{+4}M_{⊙}; for each parameter we report the median value and the range of the 90% credible interval. The dimensionless spin magnitude of the more massive black hole is bound to be <0.7 (at 90% probability). The luminosity distance to the source is 410_{-180}^{+160}  Mpc, corresponding to a redshift 0.09_{-0.04}^{+0.03} assuming standard cosmology. The source location is constrained to an annulus section of 610  deg^{2}, primarily in the southern hemisphere. The binary merges into a black hole of mass 62_{-4}^{+4}M_{⊙} and spin 0.67_{-0.07}^{+0.05}. This black hole is significantly more massive than any other inferred from electromagnetic observations in the stellar-mass regime.

GW150914: First results from the search for binary black hole coalescence with Advanced LIGO

On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-wave Observatory (LIGO) simultaneously observed the binary black hole merger GW150914. We report the results of a matched-filter search using relativistic models of compact-object binaries that recovered GW150914 as the most significant event during the coincident observations between the two LIGO detectors from September 12 to October 20, 2015. GW150914 was observed with a matched filter signal-to-noise ratio of 24 and a false alarm rate estimated to be less than 1 event per 203000 years, equivalent to a significance greater than 5.1 σ.

GW150914: First results from the search for binary black hole coalescence with Advanced LIGO

On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-wave Observatory (LIGO) simultaneously observed the binary black hole merger GW150914. We report the results of a matched-filter search using relativistic models of compact-object binaries that recovered GW150914 as the most significant event during the coincident observations between the two LIGO detectors from September 12 to October 20, 2015. GW150914 was observed with a matched filter signal-to-noise ratio of 24 and a false alarm rate estimated to be less than 1 event per 203000 years, equivalent to a significance greater than 5.1 σ.

Tests of General Relativity with GW150914

The LIGO detection of GW150914 provides an unprecedented opportunity to study the two-body motion of a compact-object binary in the large-velocity, highly nonlinear regime, and to witness the final merger of the binary and the excitation of uniquely relativistic modes of the gravitational field. We carry out several investigations to determine whether GW150914 is consistent with a binary black-hole merger in general relativity. We find that the final remnant's mass and spin, as determined from the low-frequency (inspiral) and high-frequency (postinspiral) phases of the signal, are mutually consistent with the binary black-hole solution in general relativity. Furthermore, the data following the peak of GW150914 are consistent with the least-damped quasinormal mode inferred from the mass and spin of the remnant black hole. By using waveform models that allow for parametrized general-relativity violations during the inspiral and merger phases, we perform quantitative tests on the gravitational-wave phase in the dynamical regime and we determine the first empirical bounds on several high-order post-Newtonian coefficients. We constrain the graviton Compton wavelength, assuming that gravitons are dispersed in vacuum in the same way as particles with mass, obtaining a 90%-confidence lower bound of 10^{13}  km. In conclusion, within our statistical uncertainties, we find no evidence for violations of general relativity in the genuinely strong-field regime of gravity.

GW150914: Implications for the Stochastic Gravitational-Wave Background from Binary Black Holes

The LIGO detection of the gravitational wave transient GW150914, from the inspiral and merger of two black holes with masses ≳30M_{⊙}, suggests a population of binary black holes with relatively high mass. This observation implies that the stochastic gravitational-wave background from binary black holes, created from the incoherent superposition of all the merging binaries in the Universe, could be higher than previously expected. Using the properties of GW150914, we estimate the energy density of such a background from binary black holes. In the most sensitive part of the Advanced LIGO and Advanced Virgo band for stochastic backgrounds (near 25 Hz), we predict Ω_{GW}(f=25  Hz)=1.1_{-0.9}^{+2.7}×10^{-9} with 90% confidence. This prediction is robustly demonstrated for a variety of formation scenarios with different parameters. The differences between models are small compared to the statistical uncertainty arising from the currently poorly constrained local coalescence rate. We conclude that this background is potentially measurable by the Advanced LIGO and Advanced Virgo detectors operating at their projected final sensitivity.

GW150914: The Advanced LIGO Detectors in the Era of First Discoveries

Following a major upgrade, the two advanced detectors of the Laser Interferometer Gravitational-wave Observatory (LIGO) held their first observation run between September 2015 and January 2016. With a strain sensitivity of 10^{-23}/sqrt[Hz] at 100 Hz, the product of observable volume and measurement time exceeded that of all previous runs within the first 16 days of coincident observation. On September 14, 2015, the Advanced LIGO detectors observed a transient gravitational-wave signal determined to be the coalescence of two black holes [B. P. Abbott et al., Phys. Rev. Lett. 116, 061102 (2016)], launching the era of gravitational-wave astronomy. The event, GW150914, was observed with a combined signal-to-noise ratio of 24 in coincidence by the two detectors. Here, we present the main features of the detectors that enabled this observation. At full sensitivity, the Advanced LIGO detectors are designed to deliver another factor of 3 improvement in the signal-to-noise ratio for binary black hole systems similar in mass to GW150914.

Observation of Gravitational Waves from a Binary Black Hole Merger

On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-Wave Observatory simultaneously observed a transient gravitational-wave signal. The signal sweeps upwards in frequency from 35 to 250 Hz with a peak gravitational-wave strain of 1.0×10(-21). It matches the waveform predicted by general relativity for the inspiral and merger of a pair of black holes and the ringdown of the resulting single black hole. The signal was observed with a matched-filter signal-to-noise ratio of 24 and a false alarm rate estimated to be less than 1 event per 203,000 years, equivalent to a significance greater than 5.1σ. The source lies at a luminosity distance of 410(-180)(+160)  Mpc corresponding to a redshift z=0.09(-0.04)(+0.03). In the source frame, the initial black hole masses are 36(-4)(+5)M⊙ and 29(-4)(+4)M⊙, and the final black hole mass is 62(-4)(+4)M⊙, with 3.0(-0.5)(+0.5)M⊙c(2) radiated in gravitational waves. All uncertainties define 90% credible intervals. These observations demonstrate the existence of binary stellar-mass black hole systems. This is the first direct detection of gravitational waves and the first observation of a binary black hole merger.

L-carnitine and pyruvate are prosurvival factors during the storage of stallion spermatozoa at room temperature

The spermatozoa of many stallions do not tolerate being cooled, restricting the commercial viability of these animals and necessitating the development of a chemically defined room temperature (RT) storage medium. This study examined the impact of two major modulators of oxidative phosphorylation, pyruvate (Pyr) and L-carnitine (L-C), on the storage of stallion spermatozoa at RT. Optimal concentrations of Pyr (10 mM) and L-C (50 mM) were first identified and these concentrations were then used to investigate the effects of these compounds on sperm functionality and oxidative stress at RT. Mitochondrial and cytosolic reactive oxygen species, along with lipid peroxidation, were all significantly suppressed by the addition of L-C (48 h MitoSOX Red negative: 46.2% vs. 26.1%; 48 and 72 h dihydroethidium negative: 61.6% vs. 43.1% and 64.4% vs. 46.9%, respectively; 48 and 72 h 4-hydroxynonenal negative: 37.1% vs. 23.8% and 41.6% vs. 25.7%, respectively), while the Pyr + L-C combination resulted in significantly higher motility compared to the control at 72 h (total motility: 64.2% vs. 39.4%; progressive motility: 34.2% vs. 15.2%). In addition, supplementation with L-C significantly reduced oxidative DNA damage at 72 h (9.0% vs. 15.6%). To investigate the effects of L-C as an osmolyte, comparisons were made between media that were osmotically balanced with NaCl, choline chloride, or L-C. This analysis demonstrated that spermatozoa stored in the L-C balanced medium had significantly higher total motility (55.0% vs. 39.0%), rapid motility (44.0% vs. 25.7%), and ATP levels (70.9 vs. 12.8 ng/ml) following storage compared with the NaCl treatment, while choline chloride did not significantly improve these parameters compared to the control. Finally, mass spectrometry was used to demonstrate that a combination of Pyr and L-C produced significantly higher acetyl-L-carnitine production than any other treatment (6.7 pg/10(6) spermatozoa vs. control at 4.0 pg/10(6) spermatozoa). These findings suggest that Pyr and L-C could form the basis of a novel, effective RT storage medium for equine spermatozoa.

Metabolomic and proteomic responses of Staphylococcus aureus to prolonged cold stress

The high pathogenicity of Staphylococcus aureus is thought to be due to its extraordinary capacity to rapidly adapt to changes in environmental conditions. This study was carried out to investigate whether the cytoplasmic profiles of metabolites and proteins of S. aureus were altered in response to prolonged exposure to cold stress. Metabolic profiling and proteomics were used to characterise alterations in cytoplasmic proteins and metabolites in cells from the mid-exponential phase of growth under ideal conditions at 37°C and compared with equivalent cells exposed to prolonged cold stress for 2 weeks at 4°C. Principle component analysis (PCA) of the metabolomic and proteomic data indicated that, at the mid-exponential phase of growth, prolonged cold stress conditions generated cells with different metabolite and protein profiles compared with those grown at 37°C. Nine ribosomal proteins and citric acid were substantially elevated in the cytoplasmic fractions from the cells adapted to cold-stress but most amino acids showed a reduction in their concentration in cold-stressed samples. The data provided strong evidence supporting the hypothesis that specific changes in metabolic homeostasis and protein composition were critical to the adaptive processes required for survival under cold stress.

BIOLOGICAL SIGNIFICANCE

Work in our laboratory has shown that prolonged exposure of S. aureus to cold stress can result in the formation of small colony variants (SCVs) associated with significant alterations in the cell wall composition. Further studies revealed that S. aureus altered cell size and cell wall thickness in response to exposure to cold temperatures, alterations in pH and exposure to antibiotics. The current study has utilised the prolonged exposure to cold stress as a model system to explore changes in the proteome and associated metabolic homeostasis following environmental challenges. The study provides an improved understanding of how S. aureus adapts to the changing environment whilst in transition between human hosts. The results indicated an unexpected production of 9 ribosomal proteins and citric acid in response to cold stress suggesting specific survival roles for these proteins and citric acid as an adaptation mechanism for empowering survival under these conditions.

Investigation of the stallion sperm proteome by mass spectrometry

Stallion spermatozoa continue to present scientific and clinical challenges with regard to the biological mechanisms responsible for their survival and function. In particular, deeper understanding of sperm energy metabolism, defence against oxidative damage and cell–cell interactions should improve fertility assessment and the application of advanced reproductive technologies in the equine species. In this study, we used highly sensitive LC–MS/MS technology and sequence database analysis to identify and characterise the proteome of Percoll-isolated ejaculated equine spermatozoa, with the aim of furthering our understanding of this cell's complex biological machinery. We were able to identify 9883 peptides comprising 1030 proteins, which were subsequently attributed to 975 gene products. Gene ontology analysis for molecular and cellular processes revealed new information about the metabolism, antioxidant defences and receptors of stallion spermatozoa. Mitochondrial proteins and those involved in catabolic processes constituted dominant categories. Several enzymes specific to β-oxidation of fatty acids were identified, and further experiments were carried out to ascertain their functional significance. Inhibition of carnitine palmitoyl transferase 1, a rate-limiting enzyme of β-oxidation, reduced motility parameters, indicating that β-oxidation contributes to maintenance of motility in stallion spermatozoa.

Activity-associated miRNA are packaged in Map1b-enriched exosomes released from depolarized neurons

Rapid input-restricted change in gene expression is an important aspect of synaptic plasticity requiring complex mechanisms of post-transcriptional mRNA trafficking and regulation. Small non-coding miRNA are uniquely poised to support these functions by providing a nucleic-acid-based specificity component for universal-sequence-dependent RNA binding complexes. We investigated the subcellular distribution of these molecules in resting and potassium chloride depolarized human neuroblasts, and found both selective enrichment and depletion in neurites. Depolarization was associated with a neurite-restricted decrease in miRNA expression; a subset of these molecules was recovered from the depolarization medium in nuclease resistant extracellular exosomes. These vesicles were enriched with primate specific miRNA and the synaptic-plasticity-associated protein MAP1b. These findings further support a role for miRNA as neural plasticity regulators, as they are compartmentalized in neurons and undergo activity-associated redistribution or release into the extracellular matrix.

Furin processing dictates ectodomain shedding of human FAT1 cadherin

Fat1 is a single pass transmembrane protein and the largest member of the cadherin superfamily. Mouse knockout models and in vitro studies have suggested that Fat1 influences cell polarity and motility. Fat1 is also an upstream regulator of the Hippo pathway, at least in lower vertebrates, and hence may play a role in growth control. In previous work we have established that FAT1 cadherin is initially cleaved by proprotein convertases to form a noncovalently linked heterodimer prior to expression on the cell surface. Such processing was not a requirement for cell surface expression, since melanoma cells expressed both unprocessed FAT1 and the heterodimer on the cell surface. Here we further establish that the site 1 (S1) cleavage step to promote FAT1 heterodimerisation is catalysed by furin and we identify the cleavage site utilised. For a number of other transmembrane receptors that undergo heterodimerisation the S1 processing step is thought to occur constitutively but the functional significance of heterodimerisation has been controversial. It has also been generally unclear as to the significance of receptor heterodimerisation with respect to subsequent post-translational proteolysis that often occurs in transmembrane proteins. Exploiting the partial deficiency of FAT1 processing in melanoma cells together with furin-deficient LoVo cells, we manipulated furin expression to demonstrate that only the heterodimer form of FAT1 is subject to cleavage and subsequent release of the extracellular domain. This work establishes S1-processing as a clear functional prerequisite for ectodomain shedding of FAT1 with general implications for the shedding of other transmembrane receptors.