WD repeat domain 5 (WDR5) plays an important role in various biological functions through the epigenetic regulation of gene transcription; however, its role in bladder cancer remains largely unknown. Our study investigated the role of WDR5 in bladder cancer and demonstrated that WDR5 was upregulated in bladder cancer tissues, and elevated WDR5 protein levels positively correlated with advanced tumor stage and poor survival. Through gain or loss of function, we demonstrated that WDR5 promoted proliferation, self-renewal and chemoresistance to cisplatin in bladder cancer cells in vitro, and tumor growth in vivo. Mechanistically, WDR5 regulated various functions in bladder cancer by mediating the transcription of cyclin B1, cyclin E1, cyclin E2, UHMK1, MCL1, BIRC3 and Nanog by histone H3 lysine 4 trimethylation. Therefore, we have discovered that WDR5 plays an important role in bladder cancer suggesting that WDR5 is a potential biomarker and a promising target in the treatment of bladder cancer.
Intracellular ISG15 is an interferon (IFN)-α/β-inducible ubiquitin-like modifier which can covalently bind other proteins in a process called ISGylation; it is an effector of IFN-α/β-dependent antiviral immunity in mice1–4. We previously published a study describing humans with inherited ISG15 deficiency but without unusually severe viral diseases5. We showed that these patients were prone to mycobacterial disease and that human ISG15 was non-redundant as an extracellular IFN-γ-inducing molecule. We show here that ISG15-deficient patients also display unanticipated cellular, immunological and clinical signs of enhanced IFN-α/β immunity, reminiscent of the Mendelian autoinflammatory interferonopathies Aicardi–Goutières syndrome and spondyloenchondrodysplasia6–9.We further show that an absence of intracellular ISG15 in the patients’ cells prevents the accumulation of USP1810,11, a potent negative regulator of IFN-α/β signalling, resulting in the enhancement and amplification of IFN-α/β responses. Human ISG15, therefore, is not only redundant for antiviral immunity, but is a key negative regulator of IFN-α/β immunity. In humans, intracellular ISG15 is IFN-α/β-inducible not to serve as a substrate for ISGylation-dependent antiviral immunity, but to ensure USP18-dependent regulation of IFN-α/β and prevention of IFN-α/β-dependent autoinflammation.
This study assessed knowledge of neurotic disorders, and attitudes and preferences toward professional help and treatment for them, among general medical outpatients in general hospitals in Xi’an, China.
General medical outpatients (N=372) from general hospitals in China were recruited by using a stratified cluster sampling method between June and September 2010. In face-to-face interviews, participants age 16 years or older were assessed for their knowledge, attitudes, and help-seeking preferences in regard to neurotic disorders (obsessive-compulsive disorder, social phobia, and panic disorder). Demographic data were also collected.
Lack of insight into neurotic disorders was common among medical outpatients in general hospitals of Xi’an, China. Twenty-four percent to 58% of the outpatients had some knowledge of the symptoms and treatment of neurotic disorders. Only 11% of the outpatients would reveal to others that they or a family member suffered from neurotic disorders. When faced with the problem of neurotic disorders, the preference of the respondents was to visit a psychiatrist in a general hospital (44%), and only 17% would visit a physician in a psychiatric hospital. Major ways for the outpatients to obtain knowledge regarding neurotic disorders were via radio and television (36%), and only 18%223% of outpatients obtained knowledge about neurotic disorders through printed public health materials and by attending lectures.
Study results underscore the need for information campaigns aimed at improving the mental health literacy of general medical outpatients. Such campaigns must consider culturally relevant beliefs to facilitate the development of specific educational programs.
The Bahamian Ministry of Education has elected to implement at a national level in all Bahamian government grade six classes an evidence-based HIV prevention intervention [Focus on Youth in the Caribbean (FOYC)]. This study explores fidelity of implementation of the intervention, factors that may influence implementation fidelity, and the impact of variations in implementation fidelity on student outcomes. Data were collected in the first wave of national implementation in 2011, involving 35 government primary schools and 110 teachers and 2811 students. Structural equation modeling was performed to examine the relationships among factors which facilitated or impeded teachers’ implementation of FOYC. Results indicate that teachers taught 16.3 out of 30 core activities, 24.9 out of 46 total activities and 4.4 out of 8 sessions on average. The strongest predictor of implementation fidelity was teacher comfort level with the FOYC curriculum. Teachers who did not perceive the FOYC intervention to be important for their students or who had attended only part of a FOYC training workshop were more likely to change the curriculum. Increased duration of experience as a teacher (>10 years) was negatively associated with fidelity of implementation. Teacher’s perception of the importance of the FOYC intervention and implementation fidelity had direct positive effects on students’ HIV/AIDS knowledge, reproductive health skills, protective intentions and self-efficacy. Youth did not appear to benefit from FOYC if two or fewer sessions were delivered. We concluded that an evidence-based HIV prevention intervention can be implemented at a national level. Prior training of teachers in the intervention curriculum, teacher perception of the importance of the intervention, and fewer years as a teacher are associated with implementation fidelity. Implementation fidelity is associated with improved student outcomes.
Implementation research; HIV prevention; fidelity; adolescents; Bahamas
Parent involvement in prevention efforts targeting adolescents increases the impact of such programs. However, the majority of risk-reduction intervention programs that are implemented through schools do not include parents, in part because most existing parental interventions require significant time commitment by parents. We designed a brief parent-adolescent sexual risk communication intervention to be delivered with an effective HIV prevention intervention as part of a randomized, controlled trial among 2564 grade 10 students and their parents in The Bahamas. Mixed effects modeling analysis was conducted to evaluate the effect of the brief parent-adolescent communication intervention using four waves of longitudinal data. Results indicate that a brief parent-adolescent communication intervention is effective in improving parent-adolescent communication on sex-related issues and perceived parental monitoring as well as the youth's condom use skills and self-efficacy. There is a marginal effect on consistent condom use. In addition, there is an apparent dose effect of the brief parent intervention on perceived parent-adolescent sexual risk communication and adolescent outcomes. These findings suggest that adolescent risk reduction interventions should include a brief parent-adolescent communication intervention which should be reinforced by periodic boosters in order to enhance the impact of adolescent HIV prevention programs.
adolescent; condom use skills; self-efficacy; parent-adolescent communication; brief parental intervention; risk behaviors; The Bahamas
The immune/ inflammation system potentially serves to arrest, eliminate or promote tumor development. Nonetheless, factors that dictate the choice are not comprehensively known yet. Using a B16/F1 syngeneic wild type model, we evaluated the essentiality of initial transformed cells' density for overt tumor development, the molecular trends of inflammatory mediators in the normal tumor-adjacent epithelial tissues (NTAT), and how such local events may reflect systematically in the host. Overt tumors developed, within an observatory period of at least 45 days and 90 days at most, only in mice inoculated with cancer cells above a limiting threshold of 1× 103 cells. Immunoblots showed early, intense and transient presence of IL-1β, IFN-γ, and both the all-thiol and disulfide forms of HMGB1 in the NTAT of non-tumor bearing mice. However, all-thiol form of HMGB1 and delayed but aberrant IL-6 expression characterized chronic inflammation in tumor bearing hosts. These local epithelial tissue events uniquely reflected in host's systemic cytokines dynamics where stable Th1/Th2 signature (IFN-γ/ IL-4) coupled with early Th1 cells polarization (IL-12/ IL-4) evidenced in non-tumor hosts but highly fluctuating Th1/ Th2 profile in tumor hosts, even before tumors became overt. This hypothesizes that the physical quantum of transformed cells that may either spontaneously arise or accrue at a locus may be crucial in orchestrating the mechanism for the type of local epithelial tissue and systemic immune/ inflammatory responses essential for tumor progression or arrest.
Cancer cell density; minimum tumorigenic threshold; inflammation; overt tumor; Th1/Th2/Th17 cytokines.
Phosphine-catalyzed [3+2] and [4+3]annulation reactions of C,N-cyclic azomethine imines with allenoates have been developed to give a variety of pharmaceutically attractive tetrahydroisoquinoline derivatives in moderate to excellent yields. The two distinct reaction pathways, [3+2] and [4+3]cyclization, depend on the nature of the nucleophilic phosphine and the allenoate. Generally, for α-alkylallenoates, the reactions always proceed with [3 +2]cyclization as the major pathway no matter what phosphine was used; for α-ArCH2-substituted allenoates, the reaction pathway was controlled by the phosphine catalyst used.
allenoates; annulation; azomethine imines; catalysis; phosphines
Inefficient thymic negative selection of self-specific T cells is associated with several autoimmune diseases, including type 1 diabetes (T1D). The factors that influence the efficacy of thymic negative selection, and the kinetics of thymic output of autoreactive T cells remain ill-defined. We investigated thymic production of β cell-specific T cells using a thymus transplantation model. Thymi from different aged NOD mice representing distinct stages of T1D, were implanted into NOD.scid recipients and the diabetogenicity of the resulting T cell pool examined. Strikingly, the development of diabetes-inducing β cell-specific CD4+ and CD8+ T cells was regulated in an age-dependent manner. NOD.scid recipients of newborn NOD thymi developed diabetes. However, recipients of thymi from 7 and 10 d-old NOD donor mice remained diabetes-free, and exhibited a progressive decline in islet infiltration and β cell-specific CD4+ and CD8+ T cells. A similar temporal decrease in autoimmune infiltration was detected in some but not all tissues of recipient mice implanted with thymi from NOD mice lacking expression of the autoimmune regulator transcription factor, which develop multi-organ T cell-mediated autoimmunity. In contrast, recipients of 10 d or older thymi lacked diabetogenic T cells but developed severe colitis marked by increased effector T cells reactive to intestinal microbiota. These results demonstrate that thymic development of autoreactive T cells is limited to a narrow time-window, and occurs in a reciprocal manner compared to colonic microbiota-responsive T cells in NOD mice.
In current clinical practice, the diagnosis of cervical cancer (CC) is mainly through the cervical screening followed by a necessary biopsy, but this method is labor consuming and expensive, and can only detect superficial lesions around the external cervical orifice. In contrast, photoacoustic imaging (PAI) is sensitive to the abnormal angiogenesis deep in the biological tissue, and may be capable for the intact scanning both around the external orifice and in cervical canal. In this paper, we for the first time put forward the photoacoustic diagnosis of CC. A total of 30 in-vitro experiments were carried out in this study, and the obtained depth maximum amplitude projection (DMAP) images were analyzed to evaluate the extent of the angiogenesis for different clinical stages of CC. Stronger absorption from the cervical lesions is observed relative to that of normal tissue. Paired t-test indicates that the difference in mean optical absorption (MOA) between normal tissue and cervical lesion has statistical significance with a confidential coefficient of 0.05. Statistical results also show that the MOAs of the cervical lesions are closely related to the severity of CC. These results imply that PAI may have great utility in the clinical diagnosis of CC.
(170.5120) Photoacoustic imaging; (170.3880) Medical and biological imaging; (170.2150) Endoscopic imaging
Various cochlear pathologies, such as acoustic trauma, ototoxicity and age-related degeneration, cause hearing loss. These pre-existing hearing losses can alter cochlear responses to subsequent acoustic overstimulation. So far, the knowledge on the impacts of pre-existing hearing loss caused by genetic alteration of cochlear genes is limited. Prestin is the motor protein expressed exclusively in outer hair cells in the mammalian cochlea. This motor protein contributes to outer hair cell motility. At present, it is not clear how the interference of prestin function affects cochlear responses to acoustic overstimulation. To address this question, a genetic model of prestin dysfunction in mice was created by inserting an internal ribosome entry site (IRES)-CreERT2-FRT-Neo-FRT cassette into the prestin locus after the stop codon. Homozygous mice exhibit a threshold elevation of auditory brainstem responses with large individual variation. These mice also display a threshold elevation and a shift of the input/output function of the distortion product otoacoustic emission, suggesting a reduction in outer hair cell function. The disruption of prestin function reduces the threshold shifts caused by exposure to a loud noise at 120 dB (sound pressure level) for 1 h. This reduction is positively correlated with the level of pre-noise cochlear dysfunction and is accompanied by a reduced change in Cdh1 expression, suggesting a reduction in molecular responses to the acoustic overstimulation. Together, these results suggest that prestin interference reduces cochlear stress responses to acoustic overstimulation.
Asymptomatic infection is an important obstacle for controlling disease in countries where malaria is endemic. Because asymptomatic carriers do not seek treatment for their infections, they can have high levels of gametocytes and constitute a reservoir available for new infection. We employed a sample pooling/PCR-based molecular detection strategy for screening malaria infection in residents from areas of Myanmar where malaria is endemic. Blood samples (n = 1,552) were collected from residents in three areas of malaria endemicity (Kayin State, Bago, and Tanintharyi regions) of Myanmar. Two nested PCR and real-time PCR assays showed that asymptomatic infection was detected in about 1.0% to 9.4% of residents from the surveyed areas. The sensitivities of the two nested PCR and real-time PCR techniques were higher than that of microscopy examination (sensitivity, 100% versus 26.4%; kappa values, 0.2 to 0.5). Among the three regions, parasite-positive samples were highly detected in subjects from the Bago and Tanintharyi regions. Active surveillance of residents from regions of intense malaria transmission would reduce the risk of morbidity and mitigate transmission to the population in these areas of endemicity. Our data demonstrate that PCR-based molecular techniques are more efficient than microscopy for nationwide surveillance of malaria in countries where malaria is endemic.
Community-based participatory research principles have been successfully applied to public health research in U.S. settings. While there is a long history of collaboration between government and communities in China, to date, community-based participatory research has not been used in children’s environmental health studies.
This article describes how community-based participatory research principles were applied by an international research group to the China Jintan Child Cohort Study, a longitudinal study of malnutrition and lead exposure on cognitive and neurobehavioral development. Challenges emerged and lessons learned from implementing the study were discussed and recommendations were presented.
We conclude that the community-based participatory research model can be applied in conducting and promoting environmental health research in China and researchers should be prepared for special challenges and cultural constraints in the implementation of the research in regards to human subject regulations, information dissemination, and culture.
Community-based participatory research; CBPR; Lead; Children; China; Environmental health
In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.
While the majority of cancer patients are exposed to ionizing radiation during diagnostic and therapeutic procedures, age-dependent differences in radiation sensitivity are not yet well understood. Radiation sensitivity is characterized by the appearance of side effects to radiation therapy, such as secondary malignancies, developmental deficits, and compromised immune function. However, the knowledge of the molecular mechanisms that trigger these side effects is incomplete. Here we used an in vitro system and showed that low-senescent normal human diploid fibroblasts (WI-38) senesce in response to 5 Gy IR, while highly senescent cultures do not show changes in cell cycle regulation and only a slight increase in the percentage of senescent cells. Our study shows that this is associated with changes in the expression of genes responsible for cell cycle progression, apoptosis, DNA repair, and aging, as well as transcriptional and epigenetic regulators. Furthermore, we propose a role of the downregulation of SUV39H1 expression, a histone methyltransferase that specifically trimethylates H3K9, and the corresponding reduction in H3K9me3 levels in the establishment of IR-induced senescence.
senescence; aging; ionizing radiation; epigenetics; SUV39H1; DNA methylation
Recent studies observed that altered energy metabolism has become widespread in cancer cells along with other cancer-associated traits that have been accepted as hallmarks of cancer. Akt signaling pathway is involved in the aerobic glycolysis program. However, mechanisms underlying the regulation of aerobic glycolysis and Akt activity in gliomas remain unclear. MicroRNAs are a group of small non-coding RNAs that can function as endogenous RNA interference to regulate expression of targeted genes. This study was conducted to detect the function of miR-7 targeting insulin-like growth factor 1 receptor (IGF-1R), which is an upstream regulator of Akt.
MicroRNA expression data for gliomas and normal controls were downloaded from The Cancer Genome Atlas (TCGA) database. Quantitative real-time PCR was used to measure the microRNA-7 (miR-7) expression level, and Western blot was performed to detect protein expression in U87 and U251 cells. Colony formation assay and glycolysis stress test were also conducted. Luciferase reporter assay was used to identify the mechanism of IGF-1R and miR-7 regulation.
miR-7 was downregulated in human glioma tissues based on TCGA database. Forced expression of miR-7 or IGF-1R knockdown inhibited colony formation and glucose metabolic capabilities of glioma cells in vitro and decreased the p-Akt expression level. Bioinformatics analysis results indicated that IGF-1R could be a target of miR-7. Western blot and luciferase reporter assays showed that miR-7 modulated IGF-1R expression by directly targeting the binding site within the 3′-untranslated region.
This study provides the first evidence that miR-7 inhibits cellular growth and glucose metabolism in gliomas, at least partially, by regulating the IGF-1R/Akt signaling pathway. Therefore, miR-7 is a promising molecular drug for glioma treatment.
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_211
Glioblastoma multiforme; miR-7; IGF-1R; AKT
Interleukin-34 (IL-34) is a novel cytokine, which is composed of 222 amino acids and forms homodimers. It binds to the macrophage colony-stimulating factor (M-CSF) receptor and plays an important role in innate immunity and inflammatory processes. In the present study, we identified the completed IL-34 gene in 25 various mammalian genomes and found that IL-34 existed in all types of vertebrates, including fish, amphibians, birds and mammals. These species have a similar 7 exon/6 intron gene organization. The phylogenetic tree indicated that the IL-34 gene from the primate lineage, rodent lineage and teleost lineage form a species-specific cluster. It was found mammalian that IL-34 was under positive selection pressure with the identified positively selected site, 196Val. Fifty-five functionally relevant single nucleotide polymorphisms (SNPs), including 32 SNPs causing missense mutations, 3 exonic splicing enhancer SNPs and 20 SNPs causing nonsense mutations were identified from 2,141 available SNPs in the human IL-34 gene. IL-34 was expressed in various types of cancer, including blood, brain, breast, colorectal, eye, head and neck, lung, ovarian and skin cancer. A total of 5 out of 40 tests (1 blood cancer, 1 brain cancer, 1 colorectal cancer and 2 lung cancer) revealed an association between IL-34 gene expression and cancer prognosis. It was found that the association between the expression of IL-34 and cancer prognosis varied in different types of cancer, even in the same types of cancer from different databases. This suggests that the function of IL-34 in these tumors may be multidimensional. The upstream transcription factor 1 (USF1), regulatory factor X-1 (RFX1), the Sp1 transcription factor 1, POU class 3 homeobox 2 (POU3F2) and forkhead box L1 (FOXL1) regulatory transcription factor binding sites were identified in the IL-34 gene upstream (promoter) region, which may be involved in the effects of IL-34 in tumors.
interleukin-34; comparative genomics; cancer; prognosis; meta-analysis
KDP single crystals were grown in aqueous solution by using “point seeds” with a defined crystallographic direction of 59° to the Z axis. When hillock slopes on the (100) face of KDP crystals were measured within the supersaturation (σ) range of 0 < σ ≤ 0.06, the slope of hillocks with hollow cores depended nonlinearly on supersaturation. Below σ = 0.02, the hillock slope depended on supersaturation, but when σ was ≥ 0.02, the hillock slope increased more gradually and was less dependent on supersaturation. Hollow funnel-shaped growth dislocation on the (100) face of KDP crystals was observed at σ = 0.04, characterized by large holes with micro-steps and step bunching inside, the formation of which were analyzed. The result verified that the reversed growth appears to occur within hollow channels found on growth hillocks.
Interleukin-2 (IL-2) is a critical cytokine for the homeostasis and function of forkhead box p3–expressing regulatory T cells (Foxp3+Tregs). Dysregulation of the IL-2–IL-2 receptor axis is associated with aberrant Foxp3+Tregs and T cell–mediated autoimmune diseases such as type 1 diabetes. Treatment with recombinant IL-2 has been reported to enhance Foxp3+Tregs and suppress different models of autoimmunity. However, efficacy of IL-2 therapy is dependent on achieving sufficient levels of IL-2 to boost tissue-resident Foxp3+Tregs while avoiding the potential toxic effects of systemic IL-2. With this in mind, adeno-associated virus (AAV) vector gene delivery was used to localize IL-2 expression to the islets of NOD mice. Injection of a double-stranded AAV vector encoding IL-2 driven by a mouse insulin promoter (dsAAVmIP-IL2) increased Foxp3+Tregs in the islets but not the draining pancreatic lymph nodes. Islet Foxp3+Tregs in dsAAVmIP-IL2–treated NOD mice exhibited enhanced fitness marked by increased expression of Bcl-2, proliferation, and suppressor function. In contrast, ectopic IL-2 had no significant effect on conventional islet-infiltrating effector T cells. Notably, β-cell–specific IL-2 expression suppressed late preclinical type 1 diabetes in NOD mice. Collectively, these findings demonstrate that β-cell–specific IL-2 expands an islet-resident Foxp3+Tregs pool that effectively suppresses ongoing type 1 diabetes long term.
The literature suggests that parental monitoring can best be conceptualized and measured through the domains of parental knowledge, youth disclosure, parental solicitation, and parental control. Using longitudinal data on 913 grade-six Bahamian students followed over a period of three years, we examined the unique and independent roles of these domains of parental monitoring and parent–adolescent communication in relation to adolescent involvement in delinquency, substance use, and sexual risk behaviors. The results obtained with mixed-effects models indicate that parental knowledge, youth disclosure, and parental control are negatively associated with both delinquency and substance use. Open parent—adolescent communication was associated with decreased sexual risk behavior, whereas problematic parent–adolescent communication was associated with increased sexual risk behavior. The results obtained with path models indicate that youth disclosure is a significant longitudinal predictor of reduced adolescent delinquency and that parental control during early adolescence predicted reduced substance use in middle adolescence. The findings suggest that parental knowledge, youth disclosure and parental control differ in their impacts on substance use, delinquency and sexual risk behaviors. Problematic parent–adolescent communication is consistently associated with increases in all three types of adolescent risk behaviors. Future parental monitoring interventions should focus on enhancing parents’ interpersonal communication skills and emphasize the differences in and importance of the unique components of parental monitoring.
adolescent; parental knowledge; youth disclosure; parental solicitation; parental control; parent–adolescent communication; risk behaviors; Bahamas
Age of the target audience at time of intervention is thought to be a critical variable influencing the effectiveness of adolescent sexual risk reduction interventions. Despite this postulated importance, to date studies have not been designed to enable a direct comparison of outcomes according to age at time of intervention delivery.
We examined outcomes of 598 youth who were sequentially involved in two randomized controlled trials of sexual risk prevention interventions, the first one delivered in grade 6 [Focus on Youth in the Caribbean (FOYC)] and the second one in grade ten [Bahamian Focus on Older Youth (BFOOY)]. Four groups were examined, including those who received: 1) both treatment conditions, FOYC and BFOOY; 2) FOYC in grade 6 and the control condition in grade 10; 3) the control condition in grade 6 and BFOOY in grade 10; and 4) both control conditions. Intentions, perceptions, condom-use skills as well as HIV-related knowledge were assessed over 60 months.
Data showed that those who received both interventions had the greatest increase in condom-use skills. Youth who received FOYC in grade 6 had greater scores in knowledge and intention.
These results suggest that youth receive the most protection with early and repeated exposure to interventions. These findings suggest that educators should consider implementing HIV prevention and risk reduction programs as a fixed component of education curriculum beginning in the pre-adolescent years and if possible also during the adolescent years.
HIV Prevention Intervention; Adolescence; Condom-use skills; Randomized Controlled Trials; Risk Reduction Behavior
The terpenoid compositions of the Late Cretaceous Xixia amber from Central China and the middle Miocene Zhangpu amber from Southeast China were analyzed by gas chromatography-mass spectrometry (GC-MS) to elucidate their botanical origins. The Xixia amber is characterized by sesquiterpenoids, abietane and phyllocladane type diterpenoids, but lacks phenolic abietanes and labdane derivatives. The molecular compositions indicate that the Xixia amber is most likely contributed by the conifer family Araucariaceae, which is today distributed primarily in the Southern Hemisphere, but widely occurred in the Northern Hemisphere during the Mesozoic according to paleobotanical evidence. The middle Miocene Zhangpu amber is characterized by amyrin and amyrone-based triterpenoids and cadalene-based sesquiterpenoids. It is considered derived from the tropical angiosperm family Dipterocarpaceae based on these compounds and the co-occurring fossil winged fruits of the family in Zhangpu. This provides new evidence for the occurrence of a dipterocarp forest in the middle Miocene of Southeast China. It is the first detailed biomarker study for amber from East Asia.
End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal•mol−1 highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10). But larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the non-polar and entropy components, rather than a better representation of the electrostatics. SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by pre-scoring protein-ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the non-polar components of MM-GBSA and MM-PBSA, but not the electrostatic components, showed strong correlation to the ITC free energy; the computed entropies did not correlate with the ITC entropy.
Scatter-hoarding rodents are known to play a crucial role in the seed dispersal of many plant species. Numerous studies have indicated that both seed size and the energy content of seeds can affect rodent foraging behavior. However, seed size is usually associated with energy content per seed, making it difficult to isolate how seed size and energy affect rodent foraging preferences. This study used 99 treatments of artificial seeds (11 seed sizes×9 levels of energy content) to tease apart the effect of seed size and energy content on rodent seed-caching behavior. Both seed traits showed significant effects, but their details depended on the stage of the rodent foraging process. Seeds with higher energy content were harvested more rapidly while seed size only had a modest effect on harvest rate. However, after harvesting, seed size showed a much stronger effect on rodent foraging behavior. Rodents’ choice of which seeds to remove and cache, as well as seed dispersal distance, seemed to reflect an optimal seed size. Our findings could be adapted in future studies to gain a better understanding of scatter-hoarding rodent foraging behavior, and the co-evolutionary dynamics between plant seed production and seed dispersers.
4D pathological anatomy modeling is key to understanding complex pathological brain images. It is a challenging problem due to the difficulties in detecting multiple appearing and disappearing lesions across time points and estimating dynamic changes and deformations between them. We propose a novel semi-supervised method, called 4D active cut, for lesion recognition and deformation estimation. Existing interactive segmentation methods passively wait for user to refine the segmentations which is a difficult task in 3D images that change over time. 4D active cut instead actively selects candidate regions for querying the user, and obtains the most informative user feedback. A user simply answers ‘yes’ or ‘no’ to a candidate object without having to refine the segmentation slice by slice. Compared to single-object detection of the existing methods, our method also detects multiple lesions with spatial coherence using Markov random fields constraints. Results show improvement on the lesion detection, which subsequently improves deformation estimation.
Active learning; graph cuts; longitudinal MRI; Markov Random Fields; semi-supervised learning