Insight into the recognition mechanism of DNA cytosine-5 methyltransferases (DNMTs) by incorporation of acyclic 5-fluorocytosine (FC) nucleosides into DNA

DNA cytosine-5 methyltransferase (DNMT) catalyzes methylation at the C5 position of cytosine in the CpG sequence in double stranded DNA to give 5-methylCpG (mCpG) in the epigenetic regulation step in human cells. The entire reaction mechanism of DNMT is divided into six steps, which are scanning, recognition, flipping, loop locking, methylation, and releasing. The methylation and releasing mechanism are well-investigated; however, few reports are known about other reaction steps. To obtain insight into the reaction mechanism, we planned the incorporation of acyclic nucleosides, which make it easy to flip out the target nucleobase, into oligodeoxynucleotides (ODNs) and investigated the interaction between the ODN and DNMT. Here, we describe the design and synthesis of ODNs containing new acyclic 5-fluorocytosine nucleosides and their physiological and biological properties, including their interactions with DNMT. We found that the ODNs containing the acyclic 5-fluorocytosine nucleoside showed higher flexibility than those that contain 5-fluoro-2′-deoxycytidine. The observed flexibility of ODNs is expected to influence the scanning and recognition steps due to the decrease in helicity of the B-form.     

Development of the first small molecule histone deacetylase 6 (HDAC6) degraders

Histone deacetylases (HDACs) decrease the acetylation level of histones and other non-histone proteins. Over expression of HDACs have been observed in cancers and other diseases. Targeted protein degradation by “hijacking” the natural ubiquitin-proteasome-system (UPS) recently emerged as a novel technology to “knock-out” endogenous disease-causing proteins. We applied this strategy to the development of the first small molecule degraders for zinc-dependent HDACs by conjugating non-selective HDAC inhibitors with E3 ubiquitin ligase ligands. Through cell-based assays, we discovered novel bifunctional molecules (dHDAC6) that could selectively degrade HDAC6. Further mechanistic studies indicated that HDAC6 was selectively removed by the UPS.     

Simulation of a fluid phase lipid bilayer membrane: Incorporation of the surface tension into system boundary conditions

Modeling membranes is not just modeling another kind of macromolecule, but modeling an entire environment for a large class of biomolecular processes. Membrane modeling poses quite a different set of technical problems and scientific isues from modeling proteins. This paper reviews some of these issues and suggests approaches that seem promising for resolving them based on work in our laboratories and that of others.     

Time series analysis supporting the hypothesis that enhanced cosmic radiation during germ cell formation can increase breast cancer mortality in germ cell cohorts

 Techniques from cancer epidemiology and time series analysis were used to explore the hypothesis that cosmic radiation can induce germ cell changes leading to increases in future breast cancer mortality. A birth cohort time series for female breast cancer mortality was obtained using a model-independent, age-period-cohort analysis on age-specific mortality data for 1940–1990. The birth cohort series contained several oscillatory components, which were isolated and compared to the corresponding frequency components of a cosmic ray surrogate time series – Greenland ice-core ¹⁰Be concentrations. A technique, referred to as component wave-train alignment, was used to show that the breast cancer and cosmic ray oscillations were phase-locked approx. 25 years before the time of birth. This is consistent with the time of germ cell formation, which occurs during the fetal development stage of the preceding generation. Evidence is presented that the observable oscillations in the birth cohort series were residues of oscillations of much larger amplitude in the germ cell cohort, which were attenuated by the effect of the broad maternal age distribution. It is predicted that a minimum of 50% of breast cancer risk is associated with germ cell damage by cosmic radiation (priming event), which leads to the development of individuals with a higher risk of breast cancer. It is proposed that the priming event, by preceding other steps of carcinogenesis, works in concert with risk factor exposure during life. The priming event is consistent with epigenetic changes such as imprinting. Received: 10 June 1996 / Revised: 4 December 1996 / Accepted: 19 December 1996     

A size dependent predator-prey interaction: who pursues whom?

We investigate the properties of an (age, size) -structured model for a population of Daphnia that feeds on a dynamical algal food source. The stability of the internal equilibrium is studied in detail and combined with numerical studies on the dynamics of the model to obtain insight in the relation between individual behaviour and population dynamical phenomena. Particularly the change in the (age, size)-relation with a change in the food availability seems to be an important behavioural mechanism that strongly influences the dynamics. This influence is partly stabilizing and partly destabilizing and leads to the coexistence of a stable equilibrium and a stable limit cycle or even coexistence of two stable limit cycles for the same parameter values. The oscillations in this case are characterized by drastic changes in the size-structure of the population during a cycle. In addition the model exhibits the usual predator-prey oscillations that characterize Lotka-Volterra models.     

Resonance phenomena in the cochlea of the mustache bat and their contribution to neuronal response characteristics in the cochlear nucleus

Summary The cochlea of the mustache bat, Pteronotus parnellii, is very sensitive and sharply tuned to the frequency range of the dominant second harmonic of the echolocation call around 61 kHz. About 900 Hz above this frequency the cochlear microphonic potential (CM) reaches its maximum amplitude and lowest threshold. At exactly the same frequency, pronounced evoked otoacoustic emissions (OAE) can be measured in the outer ear canal, indicating mechanical resonance. The CM amplitude maximum and the OAE are most severely masked by simultaneous exposure to tones within the range from about 61–62 kHz up to about 70 kHz. The data suggest that the mechanism of mechanical resonance involves cochlear loci basal to the 61 kHz position.The resonance contributes to auditory sensitivity and sharp tuning: At the frequency of the OAE, single unit responses in the cochlear nucleus have the lowest thresholds. Maximum tuning sharpness occurs at frequencies about 300 Hz below the OAE-frequency, where the threshold is about 10 dB less sensitive than at the OAE-frequency. In addition, in the frequency range around the OAE-frequency several specialized neuronal response features can be related to mechanical resonance: Long lasting excitation after the end of the stimulus, asymmetrical tuning curves with a shallow high frequency slope and phasic on-off neuronal response patterns. In particular the latter phenomenon indicates the occurrence of local mechanical cancellations in the cochlea.Abbreviations CF constant frequency component of echolocation calls - CM cochlear microphonic potential - FM frequency modulated component of echolocation calls - N1 compound action potential of the auditory nerve - OAE octoacoustic emission - SEOAE synchronous evoked OAE     

A pilot study on clinicopathological features and intestinal microflora changes in colorectal cancer patients born over a nine-year period encompassing three years before and after the Great Chinese famine

BackgroundExposure to energy restriction during childhood is associated with a lower risk of developing colorectal cancer (CRC). To date, the association between this critical period of growth and prognosis of CRC has rarely been investigated. Changes in microbiota and epigenetic dysregulation may be key underlying mechanisms.MethodologyTissues collected from patients born between 1956 and 1964 were grouped based on time-period. The differences in overall survival among patients from the three time-periods were examined via univariate analysis. The 16S rRNA gene sequencing approach was to determine differences in microbiota among the groups. Samples were randomly selected to detect BRAF mutations, microsatellite instability (MSI) and promoter CpG island methylator phenotype (CIMP) status. The chi-square test was to assess the relationship between alterations in these molecules and microbiota differences.ResultsPatients from the three groups differed in terms of location of CRC (P = 0.034) and carcinoembryonic antigen (CEA) level (P = 0.036). A survival advantage was observed in the famine group compared with the other two groups. Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were more abundant in the two comparing groups. Abundance of B. fragilis was associated with BRAF mutations, microsatellite instability (MSI) and abundance of E. coli. Moreover, the incidence of CIMP and MSI was higher in patients with greater abundance of F. nucleatum.ConclusionsLimitation of energy intake during childhood may affect the composition of gut microbiota, resulting in persistent epigenetic changes that subsequently influence the prognosis of patients with CRC.     

Spectral call features provide information about the aggression level of greater mouse-eared bats (Myotis myotis) during agonistic interactions

Bats rely heavily on acoustic signals in order to communicate with each other in a variety of social contexts. Among those, agonistic interactions and accompanying vocalizations have received comparatively little study. Here, we studied the communicational behaviour between male greater mouse-eared bats (Myotis myotis) during agonistic encounters. Two randomly paired adult males were placed in a box that allowed us to record video and sound synchronously. We describe their vocal repertoire and compare the acoustic structure of vocalizations between two aggression levels, which we quantified via the bats’ behaviour. By inspecting thirty, one-minute long encounters, we identified a rich variety of social calls that can be described as two basic call types: echolocation-like, low-frequency sweeps and long, broadband squawks. Squawks, the most common vocalization, were often noisy, i.e. exhibited a chaotic spectral structure. We further provide evidence for individual signatures and the presence of nonlinear phenomena in this species’ vocal repertoire. As the usage and acoustic structure of vocalizations is known to encode the internal state of the caller, we had predicted that the spectral structure of squawks would be affected by the caller’s aggression level. Confirming our hypothesis, we found that increased aggression positively correlated with an increase in call frequency and tonality. We hypothesize that the extreme spectral variability between and within squawks can be explained by small fluctuations in vocal control parameters (e.g. subglottal pressure) that are caused by the elevated arousal, which is in turn influenced by the aggression level.