Presence of bark influences the succession of cryptogamic wood-inhabiting communities on conifer fallen logs

Predictors of cryptogamic wood-inhabiting communities need to be examined to understand the drivers of forest biodiversity. We estimated the influence of bark cover on the wood-inhabiting vegetation on conifer logs in early stages of epixylic succession in mature European boreal and hemi-boreal forests. Abundance of substrate groups with respect to log attributes was estimated with generalized linear and generalized linear mixed models. The structure and composition of epixylic communities was analysed using non-metric multidimensional scaling with subsequent environmental fitting. The abundance of true epixylics was inversely related to bark cover. In the first stage, bark cover did not influence the abundance of epiphytes and epigeous species; positively influenced the abundance of facultative epixylics on spruce logs and negatively influenced it on pine logs. In the second stage, the effect of bark cover was positive for epiphytes and epigeous species on spruce logs and for facultative epixylics independent of log species identity and negative for epigeous species on pine logs. Generalist species did not depend on bark cover. Total cover of wood-inhabiting vegetation was marginally influenced by bark cover. The effect of bark cover on epixylic vegetation at community level was negligible. In general, bark cover favours the establishment and growth of species with low substrate specificity. This preference may lead to either burial of logs by epigeous bryophytes, or facilitation of succession towards the dominance of ground vegetation.     

Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart,cerebellum, fin,and retina regeneration

Background

Regeneration is an important biological process for the restoration of organ mass, structure, and function after damage, and involves complex bio-physiological mechanisms including cell differentiation and immune responses. We constructed four regenerative protein-protein interaction (PPI) networks using dynamic models and AIC (Akaike’s Information Criterion), based on time-course microarray data from the regeneration of four zebrafish organs: heart, cerebellum, fin, and retina. We extracted core and organ-specific proteins, and proposed a recalled-blastema-like formation model to uncover regeneration strategies in zebrafish.

Results

It was observed that the core proteins were involved in TGF-β signaling for each step in the recalled-blastema-like formation model and TGF-β signaling may be vital for regeneration. Integrins, FGF, and PDGF accelerate hemostasis during heart injury, while Bdnf shields retinal neurons from secondary damage and augments survival during the injury response. Wnt signaling mediates the growth and differentiation of cerebellum and fin neural stem cells, potentially providing a signal to trigger differentiation.

Conclusion

Through our analysis of all four zebrafish regenerative PPI networks, we provide insights that uncover the underlying strategies of zebrafish organ regeneration.

     

A refined method of quantifying deceleration capacity index for heart rate variability analysis

Background

Phase-rectified signal averaging (PRSA) was often applied to assess the cardiac vagal modulation. Despite its broad use, this method suffers from the confounding effects of anomalous variants of sinus rhythm. This study aimed to improve the original PRSA method in deceleration capacity (DC) quantification.

Methods

The refined deceleration capacity (DC_ref) was calculated by excluding from non-vagally mediated abnormal variants of sinus rhythms. Holter recordings from 202 healthy subjects and 51 patients with end-stage renal disease (ESRD) have been used for validity. The DC_ref was compared to original DC (DC_org) by the area under receiver operating characteristic curve.

Results

Experimental results demonstrate that the original and refined DCs calculated from 24-h, 2-h, and 30-min Holter recordings are significantly lower in patients with ESRD than those in the healthy group. In receiver operating characteristic curve analysis, the DC_ref provides better performance than the DC_org in distinguishing between the patients with ESRD and healthy control subjects. Furthermore, the refined PRSA technique enhances the low frequency and attenuates high frequency components for spectral analysis in ESRD patients.

Conclusions

The DC_ref appears to reduce the influence of non-vagally mediated abnormal variants of sinus rhythm and highlighting the pathological influence. DC_ref, especially assessed from short-term electrocardiography recordings, may be complementary to existing autonomic function assessment, risk stratification, and efficacy prediction strategies.

     

Conformation and activity ofPhaseolus coccineus var. rubronanus lectin

The conformation of native and denaturedPhaseolus coccineus var. rubronanus lectin was studied by circular dichroism (CD) and correlated to the hemagglutinating activity. The far-UV CD spectrum at 25°C showed a broad, negative band around 223 nm and a positive one at 196 nm. CD data analysis of the lectin indicated a -sheet-rich protein. At high temperatures, the spectrum was blue-shifted with increasing magnitude; these changes correlated well with the loss of the activity. The conformation of lectin betweenpH 2 and 10 remained essentially unchanged. AtpH 13 the CD spectrum resembled that of unordered form with a negative band near 200 nm and the activity was completely lost. The denatured lectin in 6 M guanidine hydrochloride would be renatured upon diluting the denaturant to 0.75 M; the changes in CD spectrum again correlated well with the loss of the activity. The effect of sodium dodecyl sulfate on the lectin was drastic; it sharply increased thea-helix at the expense of the -sheet and reduced the activity; the changes reached a plateau above 20 mM surfactant.     

Glutathione S-transferase M1 and T1 gene polymorphism and COPD risk in smokers: an updated analysis

We evaluated the association between GSTM1 and GSTT1 gene polymorphisms and susceptibility to chronic obstructive pulmonary disease (COPD) in smokers. A meta-analysis of the published case–control studies was performed. Published literature was retrieved from PubMed, EMBASE, and China National Knowledge Infrastructure (CNKI), with last update in February, 2011. Data were extracted and a fixed- or random-effects model was used to calculate pooled odds ratios with 95% confidence intervals depending on statistical heterogeneity. Fourteen eligible studies, comprising 1,665 COPD cases and 1,614 controls, were included in the meta-analysis. The combined analyses showed that there was a significant difference in GSTM1 genotype distribution between COPD cases and controls among Caucasians, but not among Asians. The combined GSTM1/GSTT1 null genotype conferred a 1.36-fold greater risk for COPD in Asian smokers. The GSTT1 null genotype alone was not associated with enhanced risk for COPD. The GSTM1 null genotype is significantly associated with an increasing susceptibility to COPD in Caucasian smokers, but not in Asian smokers. The GSTM1/GSTT1 null genotype is a significant risk factor for developing COPD in Asian smokers. The GSTT1 null genotype, however, was not associated with COPD.     

High-level production of 1,3-propanediol from crude glycerol by <Emphasis Type="Italic">Clostridium butyricum</Emphasis> AKR102a

The aim of this study was to optimize a biotechnological process for the production of 1,3-propanediol (1,3-PD) based on low-quality crude glycerol derived from biodiesel production. Clostridium butyricum AKR102a was used in fed-batch fermentations in 1-L and 200-L scale. The newly discovered strain is characterized by rapid growth, high product tolerance, and the ability to use crude glycerol at the lowest purity directly gained from a biodiesel plant side stream. Using pure glycerol, the strain AKR102 reached 93.7 g/L 1,3-PD with an overall productivity of 3.3 g/(L*h). With crude glycerol under the same conditions, 76.2 g/L 1,3-PD was produced with a productivity of 2.3 g/(L*h). These are among the best results published so far for natural producers. The scale up to 200 L was possible. Due to the simpler process design, only 61.5 g/L 1,3-PD could be reached with a productivity of 2.1 g/(L*h).     

Traveling EEG slow oscillation along the dorsal attention network initiates spontaneous perceptual switching

An ambiguous figure such as the Necker cube causes spontaneous perceptual switching (SPS). The mechanism of SPS in multistable perception has not yet been determined. Although early psychological studies suggested that SPS may be caused by fatigue or satiation of orientation, the neural mechanism of SPS is still unknown. Functional magnetic resonance imaging (fMRI) has shown that the dorsal attention network (DAN), which mainly controls voluntary attention, is involved in bistable perception of the Necker cube. To determine whether neural dynamics along the DAN cause SPS, we performed simultaneous electroencephalography (EEG) and fMRI during an SPS task with the Necker cube, with every SPS reported by pressing a button. This EEG–fMRI integrated analysis showed that (a) 3–4 Hz spectral EEG power modulation at fronto-central, parietal, and centro-parietal electrode sites sequentially appeared from 750 to 350 ms prior to the button press; and (b) activations correlating with the EEG modulation traveled along the DAN from the frontal to the parietal regions. These findings suggest that slow oscillation initiates SPS through global dynamics along the attentional system such as the DAN.     

The effects of riparian forest disturbance on stream temperature,sedimentation, and morphology

Forested headwater streams rely on their riparian areas for temperature regulation, woody debris inputs, and sediment retention. These products and services may be altered by disturbances such as timber harvest, windthrow, or development. This study investigated the effects of riparian forest disturbance by removing trees using 50 and 90% basal area harvests and by directly felling some trees into eight streams in eastern West Virginia. On summer afternoons, water temperature increased in the 50 and 90% BAH treatments at average rates of 0.18 and 0.79°C/100 m, respectively. The 90% BAH treatments had the potential to disrupt fish and invertebrate communities via increased water temperature. New roads and log landings associated with the riparian logging had no detectable effect on sedimentation or turbidity. Large woody debris (LWD) additions increased habitat complexity but no net increase in pool area was observed. Greater morphological instability was observed within the LWD addition sections as pools were both created and destroyed at significantly higher rates. Experimentally manipulating small riparian patches may be an analog for small-scale natural and anthropogenic disturbances. These common events are assumed to alter streams, but there are few experimental studies quantifying their effects.     

Detecting nonculturable bacteria in the active mycorrhizal zone of the pine mushroom <Emphasis Type="Italic">Tricholoma matsutake</Emphasis>

The fungus Tricholoma matsutake forms an ectomycorrhizal relationship with pine trees. Its sporocarps often develop in a circle, which is commonly known as a fairy ring. The fungus produces a solid, compact, white aggregate of mycelia and mycorrhizae beneath the fairy ring, which in Japanese is called a ’shiro’. In the present study, we used soil dilution plating and molecular techniques to analyze the bacterial communities within, beneath, and outside the T. matsutake fairy ring. Soil dilution plating confirmed previous reports that bacteria and actinomycetes are seldom present in the soil of the active mycorrhizal zone of the T. matsutake shiro. In addition, the results showed that the absence of bacteria was strongly correlated with the presence of T. matsutake mycorrhizae. The results demonstrate that bacteria, especially aerobic and heterotrophic forms, and actinomycetes, are strongly inhibited by T. matsutake. Indeed, neither bacteria nor actinomycetes were detected in 11.3% of 213 soil samples from the entire shiro area by culture-dependent methods. However, molecular techniques demonstrated that some bacteria, such as individual genera of Sphingomonas and Acidobacterium, were present in the active mycorrhizal zone, even though they were not detected in soil assays using the dilution plating technique.