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In this study, the nature of the spatial representations of an environment acquired from maps, navigation, and virtual environments (VEs) was assessed. Participants first learned the layout of a simple desktop VE and then were tested in that environment. Then, participants learned two floors of a complex building in one of three learning conditions: from a map, from direct experience, or by traversing through a virtual rendition of the building. VE learners showed the poorest learning of the complex environment overall, and the results suggest that VE learners are particularly susceptible to disorientation after rotation. However, all the conditions showed similar levels of performance in learning the layout of landmarks on a single floor. Consistent with previous research, an alignment effect was present for map learners, suggesting that they had formed an orientation-specific representation of the environment. VE learners also showed a preferred orientation, as defined by their initial orientation when learning the environment. Learning the initial simple VE was highly predictive of learning a real environment, suggesting that similar cognitive mechanisms are involved in the two learning situations. [ABSTRACT FROM AUTHOR]

The first syntheses of the Alpinia officinarum natural products alpinidinoid C and officinine B are reported. These unusual dimeric diarylheptanoids were accessed from a 3-substituted pyridine intermediate via a blue-light-mediated, triple-Minisci-type alkylation. Very few reports utilize N -(acyloxy)phthalimides (NAPs) in the construction of natural products, and the syntheses reported herein highlight the power of this methodology toward the orthogonal construction of highly substituted arenes.

Streptomyces species can form beneficial relationships with hosts as endophytes, including the phytopathogen-inhibiting strain, Streptomyces griseoaurantiacus MH191, isolated from wheat plants. Using genomic characterization and untargeted metabolomics, we explored the capacity of strain MH191 to inhibit a range of fungal phytopathogens through the production of secondary metabolites. Complete genome assembly of strain MH191 predicted 24 biosynthetic gene clusters. Secondary metabolite production was assessed following culture on six different media, with the detection of 205 putative compounds. Members of the manumycin family, undecylprodigiosin, and desferrioxamine were identified as the predominant metabolites. Antifungal activity was validated for undecylprodigiosin and manumycin. These compounds were produced from different BGCs, which showed similarity to asukamycin, undecylprodigiosin, and FW0622 gene clusters, respectively. The growth of strain MH191 on different media illustrated the metabolic regulation of these gene clusters and the strain's extended chemical potential, with the asukamycin gene cluster alone, producing a variety of antifungal metabolites. The study highlights the extended chemical capability of strain MH191, which could be exploited as a biological control agent for designing future crop protection solutions.

The activated B cell (ABC) subset of diffuse large B-cell lymphoma (DLBCL) is characterized by chronic B-cell receptor signaling and associated with poor outcomes when treated with standard therapy. In ABC-DLBCL, MALT1 is a core enzyme that is constitutively activated by stimulation of the B-cell receptor or gain-of-function mutations in upstream components of the signaling pathway, making it an attractive therapeutic target. We discovered a novel small-molecule inhibitor, ABBV-MALT1, that potently shuts down B-cell signaling selectively in ABC-DLBCL preclinical models leading to potent cell growth and xenograft inhibition. We also identified a rational combination partner for ABBV-MALT1 in the BCL2 inhibitor, venetoclax, which when combined significantly synergizes to elicit deep and durable responses in preclinical models. This work highlights the potential of ABBV-MALT1 monotherapy and combination with venetoclax as effective treatment options for patients with ABC-DLBCL., (©2024 The Authors; Published by the American Association for Cancer Research.)

A double-blind study was performed to test the abuse liability of electronic nicotine delivery systems (ENDS) in young adults; in particular, the influence of nicotine on reward sensitivity was assessed. A total of 53 healthy nonusers participated in experimental sessions during which they played a video game made available on a progressive ratio schedule of reinforcement and self-administered nicotine via ENDS. Participants were randomized into one of three groups. Two groups received either a dedicated concentration of nicotine (6 and 12 mg) or a placebo, and whether they received the placebo or their dedicated nicotine dose was randomly determined on a session-by-session basis to mask the sequencing of drug administration. The third group received only a 0 mg (placebo) vaping device during all sessions. In comparison to all placebo conditions, nicotine-induced reward sensitization was evidenced on behavioral measures of video game reinforcement, but not subjective appraisals of the vaping experience. A 1-month follow-up survey provided evidence that reinforcement enhancement by nicotine predicts increased abuse liability of ENDS. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Microbial community structure and function were assessed in the organic and upper mineral soil across a ~4000-year dune-based chronosequence at Big Bay, New Zealand, where total P declined and the proportional contribution of organic soil in the profile increased with time. We hypothesized that the organic and mineral soils would show divergent community evolution over time with a greater dependency on the functionality of phosphatase genes in the organic soil layer as it developed. The structure of bacterial, fungal, and phosphatase-harbouring communities was examined in both horizons across 3 dunes using amplicon sequencing, network analysis, and qPCR. The soils showed a decline in pH and total phosphorus (P) over time with an increase in phosphatase activity. The organic horizon had a wider diversity of Class A (phoN/phoC) and phoD-harbouring communities and a more complex microbiome, with hub taxa that correlated with P. Bacterial diversity declined in both horizons over time, with enrichment of Planctomycetes and Acidobacteria. More complex fungal communities were evident in the youngest dune, transitioning to a dominance of Ascomycota in both soil horizons. Higher phosphatase activity in older dunes was driven by less diverse P-mineralizing communities, especially in the organic horizon., (© 2024 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.)

G-quadruplexes (G4s) are secondary DNA and RNA structures stabilized by positive cations in a central channel formed by stacked tetrads of Hoogsteen base-paired guanines. G4s form from G-rich sequences across the genome, whose biased distribution in regulatory regions points towards a gene-regulatory role. G4s can themselves be regulated by helicases, such as DHX36 (aliases: G4R1 and RHAU), which possess the necessary activity to resolve these stable structures. G4s have been shown to both positively and negatively regulate gene expression when stabilized by ligands, or through the loss of helicase activity. Using DHX36 knockout Jurkat cell lines, we identified widespread, although often subtle, effects on gene expression that are associated with the presence or number of observed G-quadruplexes in promoters or gene regions. Genes that significantly change their expression, particularly those that show a significant increase in RNA abundance under DHX36 knockout, are associated with a range of cellular functions and processes, including numerous transcription factors and oncogenes, and are linked to several cancers. Our work highlights the direct and indirect role of DHX36 in the transcriptome of T-lymphocyte leukemia cells and the potential for DHX36 dysregulation in cancer.

Aim: This study aims to examine opportunities for subsequent injury prevention from the perspectives of people who have recently experienced subsequent injury events., Methods: This qualitative study involved individual semi-structured interviews with people who had >2 injury events in the previous 12 months. Interviews were audio-recorded, transcribed verbatim and thematic analysis undertaken., Results: Sixteen interviews were completed with participants who had experienced a range of index and subsequent injury types. Potential opportunities raised were wide-ranging. Some related to individuals, e.g., motivation to carry out prevention strategies. Other opportunities were related to healthcare providers and the health system. For instance, increasing consultation times to allow a focus on subsequent injury prevention, building rapport and tailoring their approach to the individual, proactively referring people to a range of healthcare providers, and ensuring people are aware of resources and supports available following injury. Broader environmental and societal opportunities were also suggested, such as ensuring adequate social support following injury, ensuring accessibility to rehabilitation and community facilities and the modification of built environments., Conclusion: A broad range of potential opportunities to prevent subsequent injuries were raised. These opportunities are promising and future research to trial interventions raised in this study is warranted to determine their feasibility and effectiveness., Competing Interests: Nil, (© PMA.)

Since Mendel, maize has been a powerhouse of fundamental genetics research. From testing the Mendelian laws of inheritance, to the first genetic and cytogenetic maps, to the use of whole-genome sequencing data for crop improvement, maize is at the forefront of genetics advances. Underpinning much of this revolutionary work are the classic morphological mutants; the "freaks" that stood out in the field to even the untrained eye. Here we review some of these classic developmental mutants and their importance in the history of genetics, as well as their key role in our fundamental understanding of plant development., (� American Society of Plant Biologists 2022. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: Previous research has shown that spatial performance (e.g. navigation, visuospatial memory, attention) can be influenced by acute stress; however, studies have produced mixed findings sometimes showing an improvement after stress, other times showing impairment or no overall effect. Some of these discrepancies may be related to: the type of stress system activated by the stressor (sympathetic adrenal medulla [SAM] or hypothalamic-pituitary-adrenocortical [HPA]); whether cortisol responders vs. nonresponders are analyzed subsequent to main effects; and sex differences in stress responses. In the present study, we examine the influence of HPA activation from an acute laboratory stressor (Socially Evaluated Cold Pressor test [SECPT]) on performance during two spatial tasks: Useful Field of View (UFOV; a measure of spatial attention) and virtual reality (VR) navigation. We assigned 31 males and 30 females to either the SECPT or a Non-Stress condition prior to the two spatial tasks. Cardiovascular measures including heart rate and blood pressure, and salivary cortisol biosamples were obtained at specific time points., Results: Participants in the Stress condition showed increases in heart rate, systolic and diastolic blood pressure indicating sympathetic adrenal medulla (SAM) axis activation. Stress also led to increases in salivary cortisol, suggesting hypothalamic-pituitary-adrenocortical (HPA) activation. Stress did not influence overall performance in the spatial attention UFOV or the VR navigation task. However, a sex difference in spatial attention was detected when participants were divided into Stress-cortisol responders and non-responders in the UFOV task. Male Stress-cortisol responders (n = 9) showed better UFOV accuracy than female Stress-cortisol responders (n = 6); no sex differences were found among the Non-Stress control group. Furthermore, for females in the stress condition (n = 14), higher cortisol responses were associated with lower spatial attention performance., Conclusions: Socially Evaluated Cold Pressor stress resulted in no change in speed or accuracy in a VR navigation task. For the spatial attention task, the SECPT led to a sex difference among Stress-cortisol responders with males showing improved accuracy over females. The relationship between HPA activation and prefrontal cortex activity may be necessary to understand sex differences in spatial attention performance., (© 2022. The Author(s).)

Phosphorus (P) is an essential element to all living beings but also a finite resource. P-related problems center around broken P cycles from local to global scales. This paper presents outcomes from the 9th International Phosphorus Workshop (IPW9) held 2019 on how to move towards a sustainable P management. It is based on two sequential discussion rounds with all participants. Important progress was reported regarding the awareness of P as finite mineable resource, technologies to recycle P, and legislation towards a circular P economy. Yet, critical deficits were identified such as how to handle legacy P, how climate change may affect ecosystem P cycling, or working business models to up-scale existing recycling models. Workshop participants argued for more transdisciplinary networks to narrow a perceived science-practice/policy gap. While this gap may be smaller in reality as illustrated with a Swiss example, we formulate recommendations how to bridge this gap more effectively., (© 2021. The Author(s).)

Introduction: Many individuals who experience an injury go on to have subsequent injuries. This study examined the views of health professionals about potential opportunities to prevent subsequent injuries., Methods: Semi-structured individual interviews were held with a range of health professionals involved in treating injuries. Interviews examined opportunities for the prevention of subsequent injuries, particularly opportunities that may be implemented by health professionals. A thematic analysis of the data was undertaken., Results: Thirteen health professionals were interviewed, including physiotherapists, occupational therapists, and emergency department staff. Opportunities to prevent subsequent injuries aligned with the Dahlgren-Whitehead model of health determinants, representing opportunities to focus on demographic factors (e.g. older adults), individual lifestyle factors (e.g. alcohol consumption), social and community networks (e.g. social isolation), living and working conditions (e.g. access to preventive healthcare), and general socioeconomic, cultural, and environmental conditions (e.g. changes in legislation)., Conclusions: Health professionals identified a number of opportunities for subsequent injury prevention, ranging from individually oriented interventions to broader societal interventions. Within their roles, health professionals highlighted potential opportunities to provide education, modify attitudes, engage in multi-disciplinary teamwork, and serve as advocates. Use of these strategies could help to reduce the disability burden presented by subsequent injuries., Competing Interests: Declaration of Competing Interest The authors declare that there is no conflict of interest., (Copyright © 2021. Published by Elsevier Ltd.)

The sheathing leaf found in grasses and other monocots is an evolutionary innovation, yet its origin has been a subject of long-standing debate. Here, we revisit the problem in the light of developmental genetics and computational modeling. We show that the sheathing leaf likely arose through WOX- gene-dependent extension of a primordial zone straddling concentric domains around the shoot apex. Patterned growth within this zone, oriented by two polarity fields, accounts for wild-type, mutant and mosaic grass leaf development, whereas zone contraction and growth remodeling accounts for eudicot leaf development. In contrast to the prevailing view, our results suggest that the sheath derives from petiole, whereas the blade derives from the lamina of the eudicot leaf, consistent with homologies proposed in the 19th century.

Certain soil microorganisms can improve plant growth, and practices that encourage their proliferation around the roots can boost production and reduce reliance on agrochemicals. The beneficial effects of the microbial inoculants currently used in agriculture are inconsistent or short-lived because their persistence in soil and on roots is often poor. A complementary approach could use root exudates to recruit beneficial microbes directly from the soil and encourage inoculant proliferation. However, it is unclear whether the release of common organic metabolites can alter the root microbiome in a consistent manner and if so, how those changes vary throughout the whole root system. In this study, we altered the expression of transporters from the ALUMINUM-ACTIVATED MALATE TRANSPORTER and the MULTIDRUG AND TOXIC COMPOUND EXTRUSION families in rice (Oryza sativa L.) and wheat (Triticum aestivum L.) and tested how the subsequent release of their substrates (simple organic anions, including malate, citrate, and γ-amino butyric acid) from root apices affected the root microbiomes. We demonstrate that these exudate compounds, separately and in combination, significantly altered microbiome composition throughout the root system. However, the root type (seminal or nodal), position along the roots (apex or base), and soil type had a greater influence on microbiome structure than the exudates. These results reveal that the root microbiomes of important cereal species can be manipulated by altering the composition of root exudates, and support ongoing attempts to improve plant production by manipulating the root microbiome., (© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Differences in root morphology and acclimation to low-phosphorus (P) soil were examined among eight legume species from the Trifolium Section Tricocephalum to understand how these root attributes determine P acquisition. Ornithopus sativus was included as a highly P-efficient benchmark species. Plants were grown as microswards in pots with five rates of P supplied in a topsoil layer to mimic uneven P distribution within a field soil profile. Topsoil and subsoil roots were harvested separately to enable measurement of the nutrient-foraging responses. Critical P requirement (lowest P supply for maximum yield) varied over a threefold range, reflecting differences in root morphology and acclimation of nutrient-foraging roots to P stress. Among the species, there was a 3.2-fold range in root length density, a 1.7-fold range in specific root length, and a 2.1-fold range in root hair length. O. sativus had the lowest critical P requirement, displayed a high root length density, the highest specific root length, and the longest root hairs. Acquisition of P from P-deficient soil was facilitated by development of a large root hair cylinder (i.e. a large root-soil interface). This, in turn, was determined by the intrinsic root morphology attributes of each genotype, and the plasticity of its root morphology response to internal P stress. Root acclimation in low-P soil by all species was mostly associated with preferential allocation of mass to nutrient-foraging roots. Only O. sativus and four of the Trifolium species adjusted specific root length beneficially, and only O. sativus increased its root hair length in low-P soil., (© 2021 Scandinavian Plant Physiology Society.)

There is increasing interest in understanding how the microbial communities on roots can be manipulated to improve plant productivity. Root systems are not homogeneous organs but are comprised of different root types of various ages and anatomies that perform different functions. Relatively little is known about how this variation influences the distribution and abundance of microorganisms on roots and in the rhizosphere. Such information is important for understanding how root-microbe interactions might affect root function and prevent diseases. This study tested specific hypotheses related to the spatial variation of bacterial and fungal communities on wheat (Triticum aestivum L.) and rice (Oryza sativa L.) roots grown in contrasting soils. We demonstrate that microbial communities differed significantly between soil type, between host species, between root types, and with position along the root axes. The magnitude of variation between different root types and along individual roots was comparable with the variation detected between different plant species. We discuss the general patterns that emerged in this variation and identify bacterial and fungal taxa that were consistently more abundant on specific regions of the root system. We argue that these patterns should be measured more routinely so that localised root-microbe interactions can be better linked with root system design, plant health and performance.

GGGGCC (G 4 C 2 ) hexanucleotide repeat expansions in the endosomal trafficking gene C9orf72 are the most common genetic cause of ALS and frontotemporal dementia. Repeat-associated non-AUG (RAN) translation of this expansion through near-cognate initiation codon usage and internal ribosomal entry generates toxic proteins that accumulate in patients' brains and contribute to disease pathogenesis. The helicase protein DEAH-box helicase 36 (DHX36-G4R1) plays active roles in RNA and DNA G-quadruplex (G4) resolution in cells. As G 4 C 2 repeats are known to form G4 structures in vitro, we sought to determine the impact of manipulating DHX36 expression on repeat transcription and RAN translation. Using a series of luciferase reporter assays both in cells and in vitro, we found that DHX36 depletion suppresses RAN translation in a repeat length-dependent manner, whereas overexpression of DHX36 enhances RAN translation from G 4 C 2 reporter RNAs. Moreover, upregulation of RAN translation that is typically triggered by integrated stress response activation is prevented by loss of DHX36. These results suggest that DHX36 is active in regulating G 4 C 2 repeat translation, providing potential implications for therapeutic development in nucleotide repeat expansion disorders., Competing Interests: Conflict of interest P. K. T. served as a paid consultant for Denali Therapeutics, holds a joint patent with Ionis Therapeutics, and receives publishing royalties from UpToDate. None of these are directly relevant to his role on this article, and none of these organizations have any role in the conception, preparation, or editing of this article. All other authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Research examining psychological distress in people who have experienced an injury has focused on those with serious injuries or specific injury types, and has not involved long-term follow up. The aims of this investigation were to describe the prevalence of, and factors contributing to, psychological distress in a cohort of people with a broad range of injuries., Methods: The Prospective Outcomes of Injury Study (POIS) is a longitudinal cohort study of 2856 injured New Zealanders recruited from a national insurance entitlement claims register between 2007 and 2009. Participants were interviewed approximately 3, 12, and 24 months after their injury. The Kessler Psychological Distress Scale (K6) was used to measure psychological distress at each interview., Results: 25% of participants reported clinically relevant distress (K6 ≥ 8) 3 months post-injury, 15% reported distress at 12 months, and 16% reported distress at 24 months. Being 45 years or older, Māori or Pacific ethnicity, experiencing pre-injury mental health conditions, having inadequate pre-injury income, reporting poor pre-injury health or trouble accessing healthcare, having a severe injury or an injury resulting from assault, and reporting clinically relevant distress 3 months post-injury were independently associated with an increased risk of distress 12 months post-injury. The majority of these associations were also evident with respect to distress 24 months post-injury., Conclusions: Distress is common after injury among people with a broad range of injury types and severities. Screening for distress early after injury is important to identify individuals in need of targeted support.

The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2)., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)

Phosphate-solubilising microorganisms (PSM) are often reported to have positive effects on crop productivity through enhanced phosphorus (P) nutrition. Our aim was to evaluate the validity of this concept. Most studies that report 'positive effects' of PSM on plant growth have been conducted under controlled conditions, whereas field experiments more frequently fail to demonstrate a positive response. Many studies have indicated that the mechanisms seen in vitro do not translate into improved crop P nutrition in complex soil-plant systems. Furthermore, associated mechanisms are often not rigorously assessed. We suggest that PSM do not mobilise sufficient P to change the crops' nutritional environment under field conditions. The current concept, in which PSM solubilise P 'for the plant' should thus be revised. Although PSM have the capacity to solubilise P to meet their own needs, it is the turnover of the microbial biomass that subsequently provides P to plants over a longer time. Therefore, the existing concept of PSM function is unlikely to deliver a reliable strategy for increasing crop P nutrition. A further mechanistic understanding is needed to determine how P mobilisation by PSM as a component of the whole soil community can be manipulated to become more effective for plant P nutrition., (© 2020 The Authors New Phytologist © 2020 New Phytologist Trust.)

Ubr1 is a conserved ubiquitin ligase involved in the degradation of aberrant proteins in eukaryotic cells. The human enzyme is found mutated in patients with Johanson-Blizzard syndrome. We hypothesized that Ubr1 is necessary for optimal cellular fitness in conditions associated with elevated abundance of aberrant and misfolded proteins. Indeed, we found that loss of Ubr1 in the model eukaryotic microorganism Saccharomyces cerevisiae strongly sensitizes cells to hygromycin B, which reduces translational fidelity by causing ribosome A site distortion. Our results are consistent with a prominent role for Ubr1 in protein quality control. We speculate that disease manifestations in patients with Johanson-Blizzard syndrome are linked, at least in part, to defects in protein quality control caused by loss of Ubr1 function.

G-quadruplexes (G4s) are nucleic acid structures found enriched within gene regulatory sequences. G4s control fundamental cellular processes, including replication, transcription, and translation. Proto-oncogenes are enriched with G4 sequences, while tumor-suppressor genes are depleted, suggesting roles for G4s in cell survival and proliferation. Specialized helicases participate in G4-mediated gene regulation via enzymatic unwinding activity. One such enzyme, DHX36/G4R1, is the major G4-helicase and is a master regulator of G4-DNAs and mRNAs. G4-resolution promotes the expression of proproliferative genes; as such, DHX36/G4R1 promotes cell proliferation. Little is known about how DHX36/G4R1 itself is regulated in nondividing cells. We hypothesized that DHX36/G4R1 protein binding partners are altered when a cell transitions from a dividing to a quiescent state. We found that DHX36/G4R1 co-purifies with a distinct set of proteins under quiescent conditions, which may represent a novel complex that regulates DHX36/G4R1 during cell cycle transitions and have implications for development and cancer., Competing Interests: The authors declare no competing financial interest.

Aim: The purpose of this systematic review is to identify psychological interventions that have been effective at improving quality of life and reducing psychological distress (depression and anxiety) in patients with head and neck cancer., Methods: All relevant peer-reviewed articles published between March 1980 and March 2017 were identified through an electronic search of five databases: Medline, Embase, PsycINFO, Scopus, and Academic Search Complete. Risk of bias was independently assessed by two reviewers using the Crowe Critical Appraisal Tool (CCAT). Following this, a narrative synthesis of the findings was completed., Results: Twenty-one unique intervention studies were identified. Interventions tested included cognitive behavioural therapy (CBT), psychoeducation, meditation/mindfulness, group therapy, and telehealth initiatives. Ten studies utilised a randomised controlled design. Five of these investigated CBT and three examined psychoeducation, with the greatest empirical support found for these intervention types. However, the majority of studies were underpowered to detect significant effects and did not examine whether improvements in quality of life and psychological well-being were sustained over time., Conclusions: Further research is needed to investigate the effects of psychological interventions among patients with head and neck cancer, using randomised controlled designs, adequately powered samples, and long-term follow-up. This would allow evidence-based recommendations to be made regarding the most appropriate interventions to implement in clinical practice., Trial Registration: CRD42017069851.

Delineation between distinct populations of cells is essential for organ development. Boundary formation is necessary for the maintenance of pluripotent meristematic cells in the shoot apical meristem (SAM) and differentiation of developing organs. Boundaries form between the meristem and organs, as well as between organs and within organs. Much of the research into the boundary gene regulatory network (GRN) has been carried out in the eudicot model Arabidopsis thaliana . This work has identified a dynamic network of hormone and gene interactions. Comparisons with other eudicot models, like tomato and pea, have shown key conserved nodes in the GRN and species-specific alterations, including the recruitment of the boundary GRN in leaf margin development. How boundaries are defined in monocots, and in particular the grass family which contains many of the world's staple food crops, is not clear. In this study, we review knowledge of the grass boundary GRN during vegetative development. We particularly focus on the development of a grass-specific within-organ boundary, the ligule, which directly impacts leaf architecture. We also consider how genome engineering and the use of natural diversity could be leveraged to influence key agronomic traits relative to leaf and plant architecture in the future, which is guided by knowledge of boundary GRNs.

Background: Plant roots release a variety of organic compounds into the soil which alter the physical, chemical and biological properties of the rhizosphere. Root exudates are technically challenging to measure in soil because roots are difficult to access and exudates can be bound by minerals or consumed by microorganisms. Exudates are easier to measure with hydroponically-grown plants but, even here, simple compounds such as sugars and organic acids can be rapidly assimilated by microorganisms. Sterile hydroponic systems avoid this shortcoming but it is very difficult to maintain sterility for long periods especially for larger crop species. As a consequence, studies often use small model species such as Arabidopsis to measure exudates or use seedlings of crop plants which only have immature roots systems., Results: We developed a simple hydroponic system for cultivating large crop plants in sterile conditions for more than 30 days. Using this system wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.) plants were grown in sterile conditions for 30 days by which time they had reached the six-leaf stage and developed mature root systems with seminal, nodal and lateral roots. To demonstrate the utility of this system we characterized the aluminium-activated exudation of malate from the major types of wheat roots for the first time. We found that all root types measured released malate but the amounts were two-fold greater from the seminal and nodal axile roots compared with the lateral roots. Additionally, we showed that this sterile growth system could be used to collect exudates from intact whole root systems of barley., Conclusions: We developed a simple hydroponic system that enables cereal plants to be grown in sterile conditions for longer periods than previously recorded. Using this system we measured, for the first time, the aluminium-activated efflux of malate from the major types of wheat roots. We showed the system can also be used for collecting exudates from intact root systems of 30-day-old barley plants. This hydroponic system can be modified for various purposes. Importantly it enables the study of exudates from crop species with mature root systems.

Increased extracellular matrix (ECM) formation and matrix metalloprotease (MMP)-mediated ECM degradation are parts of tumorgenesis and generates collagen fragments that are released into circulation. We evaluated the association of specific collagen fragments measured in serum with outcomes in two independent metastatic breast cancer (MBC) cohorts. ELISAs were used to measure C1M (MMP-generated type I collagen fragment), C3M (MMP-generated type III collagen fragment), C4M (MMP-generated type IV collagen fragment), and PRO-C3 (pro-peptide of type III collagen) in pretreatment serum from a phase 3 randomized clinical trial of second-line hormone therapy (HR+, n = 148), and a first-line trastuzumab-treated cohort (HER2+, n = 55). All sites of metastases were included. The collagen fragments were evaluated by Cox-regression analysis for their association with time-to-progression (TTP) and overall survival (OS). In the HR+ cohort, higher C1M and C3M levels (75th percentile cut-off) were associated with shorter TTP; all fragments were associated with shorter OS. In the HER2+ cohort, higher levels of all fragments were associated with shorter TTP; higher PRO-C3 was associated with shorter OS. In multivariate analysis of the HR+ trial for OS, higher levels of all fragments were significant for reduced OS when added separately (C1M HR = 2.1, p < 0.001; C3M HR = 1.8, p = 0.028; C4M HR = 1.8, p = 0.018; PRO-C3 HR = 1.8, p = 0.017); none other clinical covariates were significant. In conclusion, collagen fragments quantified in pretreatment serum was associated with shorter TTP and OS in two independent MBC cohorts receiving systemic therapy. If validated, quantification of ECM remodeling in serum has potential as prognostic and/or predictive biomarkers in MBC., (© 2018 UICC.)

N 6 -isopentenyladenosine RNA modifications are functionally diverse and highly conserved among prokaryotes and eukaryotes. One of the most highly conserved N 6 -isopentenyladenosine modifications occurs at the A37 position in a subset of tRNAs. This modification improves translation efficiency and fidelity by increasing the affinity of the tRNA for the ribosome. Mutation of enzymes responsible for this modification in eukaryotes are associated with several disease states, including mitochondrial dysfunction and cancer. Therefore, understanding the substrate specificity and biochemical activities of these enzymes is important for understanding of normal and pathologic eukaryotic biology. A diverse array of methods has been employed to characterize i 6 A modifications. Herein is described a direct approach for the detection of isopentenylation by Mod5. This method utilizes incubation of RNAs with a recombinant isopentenyl transferase, followed by RNase T1 digestion, and 1-dimensional gel electrophoresis analysis to detect i 6 A modifications. In addition, the potential adaptability of this protocol to characterize other RNA-modifying enzymes is discussed.

Ecotones between distinct ecosystems have been the focus of many studies as they offer valuable insights into key drivers of community structure and ecological processes that underpin function. While previous studies have examined a wide range of above-ground parameters in ecotones, soil microbial communities have received little attention. Here we investigated spatial patterns, composition, and co-occurrences of archaea, bacteria, and fungi, and their relationships with soil ecological processes across a woodland-grassland ecotone. Geostatistical kriging and network analysis revealed that the community structure and spatial patterns of soil microbiota varied considerably between three habitat components across the ecotone. Woodland samples had significantly higher diversity of archaea while the grassland samples had significantly higher diversity of bacteria. Microbial co-occurrences reflected differences in soil properties and ecological processes. While microbial networks were dominated by bacterial nodes, different ecological processes were linked to specific microbial guilds. For example, soil phosphorus and phosphatase activity formed the largest clusters in their respective networks, and two lignolytic enzymes formed joined clusters. Bacterial ammonia oxidizers were dominant over archaeal oxidizers and showed a significant association ( p  < 0.001) with potential nitrification (PNR), with the PNR subnetwork being dominated by Betaproteobacteria . The top ten keystone taxa comprised six bacterial and four fungal OTUs, with Random Forest Analysis revealing soil carbon and nitrogen as the determinants of the abundance of keystone taxa. Our results highlight the importance of assessing interkingdom associations in soil microbial networks. Overall, this study shows how ecotones can be used as a model to delineate microbial structural patterns and ecological processes across adjoining land-uses within a landscape.

European earthworms have colonised many parts of Australia, although their impact on soil microbial communities remains largely uncharacterised. An experiment was conducted to contrast the responses to Aporrectodea trapezoides introduction between soils from sites with established (Talmo, 64 A. trapezoides m-2) and rare (Glenrock, 0.6 A. trapezoides m-2) A. trapezoides populations. Our hypothesis was that earthworm introduction would lead to similar changes in bacterial communities in both soils. The effects of earthworm introduction (earthworm activity and cadaver decomposition) did not lead to a convergence of bacterial community composition between the two soils. However, in both soils, the Firmicutes decreased in abundance and a common set of bacteria responded positively to earthworms. The increase in the abundance of Flavobacterium, Chitinophagaceae, Rhodocyclaceae and Sphingobacteriales were consistent with previous studies. Evidence for possible soil resistance to earthworms was observed, with lower earthworm survival in Glenrock microcosms coinciding with A. trapezoides rarity in this site, lower soil organic matter and clay content and differences in the diversity and abundance of potential earthworm mutualist bacteria. These results suggest that while the impacts of earthworms vary between different soils, the consistent response of some bacteria may aid in predicting the impacts of earthworms on soil ecosystems.

Citrate and phytase root exudates contribute to improved phosphorus (P) acquisition efficiency in Nicotiana tabacum (tobacco) when both exudates are produced in a P deficient soil. To test the importance of root intermingling in the interaction of citrate and phytase exudates, Nicotiana tabacum plant-lines with constitutive expression of heterologous citrate (Cit) or fungal phytase (Phy) exudation traits were grown under two root treatments (roots separated or intermingled) and in two soils with contrasting soil P availability. Complementarity of plant mixtures varying in citrate efflux rate and mobility of the expressed phytase in soil was determined based on plant biomass and P accumulation. Soil P composition was evaluated using solution 31 P NMR spectroscopy. In the soil with limited available P, positive complementarity occurred in Cit+Phy mixtures with roots intermingled. Root separation eliminated positive interactions in mixtures expressing the less mobile phytase (Aspergillus niger PhyA) whereas positive complementarity persisted in mixtures that expressed the more mobile phytase (Peniophora lycii PhyA). Soils from Cit+Phy mixtures contained less inorganic P and more organic P compared to monocultures. Exudate-specific strategies for the acquisition of soil P were most effective in P-limited soil and depended on citrate efflux rate and the relative mobility of the expressed phytase in soil. Plant growth and soil P utilization in plant systems with complementary exudation strategies are expected to be greatest where exudates persist in soil and are expressed synchronously in space and time., (This article is protected by copyright. All rights reserved.)