Diversity among bacteria isolated from the deep subsurface

Culturable bacteria from the deep subsurface (179 m) at Cerro Negro, New Mexico were isolated and characterized. The average number of viable aerobic bacteria was estimated to be 5×10⁵g^–1 of sediment, but only about 0.1% of these could be recovered on agar medium when incubated under aerobic conditions. Of 158 strains isolated from this depth, 92 were characterized by cellular fatty acid profiles (FAME), 36 by analysis of partial 16S rDNA sequences, and 44 by rep-PCR genome fingerprint analysis using three different sets of oligonucleotide primers (REP, BOX, or ERIC). These analyses showed the majority of isolates (67%) were Gram-positive bacteria and primarily members of genera with a high %G+C DNA. The remaining isolates were -subdivisionProteobacteria (19%) and members of the flavobacteria group (14%). The diversity indices based on these different methods of characterization were very high suggesting this subsurface habitat harbors a highly diverse microbial community.     

钙离子对PSII颗粒放氧活性的影响

外加5 mmol/L Ca~(2 )可以使菠菜PSⅡ颗粒的放氧活性增高。PSⅡ颗粒经EGTA透析、低pH值、光照、2 mol/L NaCl等处理后,放氧活性下降,同时,这些颗粒的钙含量也相应降低。但当外加 5 mmol/L Ca~(2 )时,可使这些颗粒全部或部分地恢复放氧活性。PSⅡ颗粒中存在的钙对放氧起着重要作用;钙在PSⅡ颗粒中的结合位点不止一个,其结合状态有紧密和松散之别。     

Spring bloom dynamics in Kongsfjorden,Svalbard: nutrients,phytoplankton, protozoans and primary production

The marine ecosystem in Kongsfjorden (79°N), a glacial fjord in Svalbard, is to a large extent well known with regard to hydrography, mesozooplankton and higher trophic levels. Research on primary production and lower trophic levels is still scare and especially investigations from winter and spring periods. The spring bloom dynamics in Kongsfjorden were investigated in 2002. The development in nutrient conditions, phytoplankton, protozoans and primary production were followed from 15 April until 22 May. The winter/spring in 2002 was categorized as a cold year with sea ice cover and water masses dominated by local winter-cooled water. The spring bloom started around 18 April and lasted until the middle of May. The bloom probably peaked in late April, but break-up of sea ice made it impossible to sample frequently in this period. Diatoms dominated the phytoplankton assemblage. We estimated the total primary production during the spring bloom in 2002 to range 27–35 g C m⁻². There was a mismatch situation between the mesozooplankton and the phytoplankton spring bloom in 2002.     

The evolution of antennal courtship in diplazontine parasitoid wasps (Hymenoptera,Ichneumonidae, Diplazontinae)

Background

As predicted by theory, traits associated with reproduction often evolve at a comparatively high speed. This is especially the case for courtship behaviour which plays a central role in reproductive isolation. On the other hand, courtship behavioural traits often involve morphological and behavioural adaptations in both sexes; this suggests that their evolution might be under severe constraints, for instance irreversibility of character loss. Here, we use a recently proposed method to retrieve data on a peculiar courtship behavioural trait, i.e. antennal coiling, for 56 species of diplazontine parasitoid wasps. On the basis of a well-resolved phylogeny, we reconstruct the evolutionary history of antennal coiling and associated morphological modifications to study the mode of evolution of this complex character system.

Results

Our study reveals a large variation in shape, location and ultra-structure of male-specific modifications on the antennae. As for antennal coiling, we find either single-coiling, double-coiling or the absence of coiling; each state is present in multiple genera. Using a model comparison approach, we show that the possession of antennal modifications is highly correlated with antennal coiling behaviour. Ancestral state reconstruction shows that both antennal modifications and antennal coiling are highly congruent with the molecular phylogeny, implying low levels of homoplasy and a comparatively low speed of evolution. Antennal coiling is lost on two independent occasions, and never reacquired. A zero rate of regaining antennal coiling is supported by maximum parsimony, maximum likelihood and Bayesian approaches.

Conclusions

Our study provides the first comparative evidence for a tight correlation between male-specific antennal modifications and the use of the antennae during courtship. Antennal coiling in Diplazontinae evolved at a comparatively low rate, and was never reacquired in any of the studied taxa. This suggests that the loss of antennal coiling is irreversible on the timescale examined here, and therefore that evolutionary constraints have greatly influenced the evolution of antennal courtship in this group of parasitoid wasps. Further studies are needed to ascertain whether the loss of antennal coiling is irreversible on larger timescales, and whether evolutionary constraints have influenced courtship behavioural traits in a similar way in other groups.

     

Identification of methylation markers for the prediction of nodal metastasis in oral and oropharyngeal squamous cell carcinoma

Hypermethylation is an important mechanism for the dynamic regulation of gene expression, necessary for metastasizing tumour cells. Our aim is to identify methylation tumour markers that have a predictive value for the presence of regional lymph node metastases in patients with oral and oropharyngeal squamous cell carcinoma (OOSCC). Significantly differentially expressed genes were retrieved from four reported microarray expression profiles comparing pN0 and pN+ head-neck tumours, and one expression array identifying functionally hypermethylated genes. Additional metastasis-associated genes were included from the literature. Thus genes were selected that influence the development of nodal metastases and might be regulated by methylation. Methylation-specific PCR (MSP) primers were designed and tested on 8 head-neck squamous cell carcinoma cell lines and technically validated on 10 formalin-fixed paraffin-embedded (FFPE) OOSCC cases. Predictive value was assessed in a clinical series of 70 FFPE OOSCC with pathologically determined nodal status. Five out of 28 methylation markers (OCLN, CDKN2A, MGMT, MLH1 and DAPK1) were frequently differentially methylated in OOSCC. Of these, MGMT methylation was associated with pN0 status (P = 0.02) and with lower immunoexpression (P = 0.02). DAPK1 methylation was associated with pN+ status (P = 0.008) but did not associate with protein expression. In conclusion, out of 28 candidate genes, two (7%) showed a predictive value for the pN status. Both genes, DAPK1 and MGMT, have predictive value for nodal metastasis in a clinical group of OOSCC. Therefore DNA methylation markers are capable of contributing to diagnosis and treatment selection in OOSCC. To efficiently identify additional new methylation markers, genome-wide methods are needed.     

Export or retention? Copepod abundance,faecal pellet production and vertical flux in the marginal ice zone through snap shots from the northern Barents Sea

The balance between faecal pellet (FP) production and destruction that accelerates or diminishes vertical export has an effect on pelagic-benthic coupling, but is inadequately known. Production, export and retention of copepod FP were investigated in the marginal ice zone (MIZ) of the northern Barents Sea in July 2003. Older stages of Calanus finmarchicus and C. glacialis dominated the copepod biomass and FP production experiments revealed that more than 90% of the FP were produced in the upper 50 m where most of the copepods were located both day and night. Copepod pellets typically made up ∼10% of the vertical particulate organic carbon flux, and significantly less than what was produced by the copepod community. This implies a variable but significant retention of pellets. We suggest that retention of FP is caused partly by the zooplankton themselves and that retention of FP is the rule rather than the exception in the Barents Sea, particularly during non-bloom scenarios.     

广义隐Markov模型在基因识别中的应用

广义隐Markov模型(GHMM)是基因识别的一种重要模型,但是其计算量比传统的隐Markov模型大得多,以至于不能直 接在基因识别中使用。根据原核生物基因的结构特点,提出了一种高效的简化算法,其计算量是序列长度的线性函数。在此 基础上,构建了针对原核生物基因的识别程序GeneMiner,对实际数据的测试表明,此算法是有效的。