Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.     

A Comparison of Bone Mineral Density and Its Predictors in HIV-Infected and HIV-Uninfected Older Men

ObjectiveBone health in older individuals with HIV infection has not been well studied. This study aimed to compare bone mineral density (BMD), trabecular bone score (TBS), and bone markers between HIV-infected men and age- and body mass index (BMI)-matched HIV-uninfected men aged ≥60 years. We investigated the associations of risk factors related to fracture with BMD, TBS, and bone markers in HIV-infected men.MethodsThis cross-sectional study included 45 HIV-infected men receiving antiretroviral therapy and 42 HIV-uninfected men. Medical history, BMD and TBS measurements, and laboratory tests related to bone health were assessed in all the participants. HIV-related factors known to be associated with bone loss were assessed in the HIV-infected men.ResultsThe mean BMD, TBS, and osteopenia or osteoporosis prevalence were similar among the cases and controls. The HIV-infected men had significantly higher mean N-terminal propeptide of type 1 procollagen and C-terminal cross-linking telopeptide of type I collagen levels. Stepwise multiple linear regression analysis demonstrated that low BMI (lumbar spine, P = .015; femoral neck, P = .018; and total hip, P = .005), high C-terminal cross-linking telopeptide of type I collagen concentration (total hip, P = .042; and TBS, P = .010), and low vitamin D supplementation (TBS, P = .035) were independently associated with low BMD and TBS.ConclusionIn older HIV-infected men with a low fracture risk, the mean BMD and TBS were similar to those of the age- and BMI-matched controls. The mean bone marker levels were higher in the HIV group. Traditional risk factors for fracture, including low BMI, high C-terminal cross-linking telopeptide of type I collagen level, and low vitamin D supplementation, were significant predictors of low BMD and TBS.     

An Efficient Regression Type Estimator in Survey Sampling

For the estimation of population mean in simple random sampling, an efficient regression-type estimator is proposed which is more efficient than the conventional regression estimator and hence than mean per unit estimator, ratio and product estimators and many other estimators proposed by various authors. Some numerical examples are included for illustration.     

A novel approach for assessing factors affecting biodiversity based on networks analysis

We propose in this work a novel approach aiming at assessing cause and effect relationships between variables that can affect target biodiversity issues. These cause–effect relations are used to build a network whose nodes represent variables linked by directed arcs. The arcs have associated a value that represents trends of cause–effect relations. An important novelty of this approach is the use of product and addition operations between trends of cause–effect relations for assessing factors that can affect target variables. For the analysis of the network we use the concept of paths. Paths are defined as sequences of cause–effect relations from source variables to target variables. For example, the path from population increment that causes effects on the increment of transport routes, which in turn causes effects on the loss of vegetation cover. This approach was applied to the assessment of vegetation cover in the Morelos State, México during the period 2000–2010. The results show a promising practical alternative to assess the potential effects on biodiversity issues based on the analysis of the paths represented in the network.     

Seasonality of phytoplankton in northern tundra ponds

Thermokarst ponds are the most abundant type of water body in the arctic tundra, with millions occurring in the coastal plains of Alaska, Northwest Territories and Siberia. Because ice covers of at least 2 m in thickness are formed at these latitudes, tundra ponds freeze solid every winter As a result, the growing season is shortened to a range of 60 to 100 days, during which time the photoperiod is altered to a prolonged light phase. Tundra ponds are generally close to neutral in pH and low in ions, contain dissolved gases near saturation and are nutrient poor. In low arctic ponds there are two phytoplankton biomass and primary production peaks, whereas they may be only one in the high arctic. Nanoplanktonic flagellates of the Chrysophyceae and Cryptophyceae dominate the maxima. The mid-summer decline in phytoplankton in the low arctic can be attributed to a combination of phosphorus limitation and heavy grazing pressure. The cryptomonad Rhodomonas minuta Skuja is one of the most widespread phytoplankters in tundra ponds. Because of the altered photoperiods, many species do not form resting spores prior to ice formation but survive freezing in the vegetative state.     

Influence of overwinteringDaphnia on spring zooplankton communities: An experimental study

To evaluate the influence of overwintering individuals of zooplankton on spring zooplankton communities, the dynamics of zooplankton communities with or without overwintering individuals were observed in experimental ponds from fall to spring. An insecticide, carbaryl, was used to regulate the overwintering individuals. In ponds which received insecticide applications in November or January, all cladoceran and rotiferan species were eliminated by the treatments and did not reappear until late March or early April, even when the chemical disappeared rapidly. The low water temperature may delayed the establishment of the populations from resting eggs. In these ponds, populations of various cladoceran and rotiferan species, which seemed to be originated from resting eggs, were built up in the spring. In control ponds,Daphnia ambigua orD. longispina overwintered as juveniles and adults and established a large spring population earlier than other cladocerans and rotifers overwintering as resting eggs. The latter zooplankters did not increase in the spring probably because their growth was suppressed by the precedingDaphnia species through competition. In nature, even if the number of overwintering individuals is small, they may have a potential to build up a large population earlier than the individuals hatching from resting eggs. As a result, the species which have overwintered as individuals seem to predominate in the spring and have a large influence on the spring zooplankton community.     

池鹭繁殖种群数量、活动规律和生物生产量的研究

本文报道池鹭种群数量变动,种群活动,雏鸟生长和生物生产量。种群活动可划分为适到期,运情期,繁殖期,同鸟活动期,集群活动和迁离期。１９９０,１９９１二年繁殖前种群密度分别为１３００只／ｈｍ＾２和１４０１只／ｈｍ＾２,繁殖后增加密度为２０８７只／ｈｍ＾２和２２４８只／ｈｍ＾２。雏鸟体重增长曲线议程为：Ｗ＝２８６／１＋ｅ＾－０．４０９（ｔ－１２．６）１９９０,１９９１年繁殖种群的生物生产量分别为１９７．     

Detection of Nitrosomonas spp. by polymerase chain reaction

Abstract A unique genomic DNA fragment was isolated from Nitrosomonas europaea ATCC 19718. Based on the sequence of this fragment, oligonucleotide primers for polymerase chain reaction amplification were prepared which amplify sequences of 775 and 658 bp. The predicted DNA fragments were both amplified from the genome of N. europaea and a Nitrosomonas spp. isolated from a local oxidation pond. The primers failed to amplify DNA from the genomes of the ammonia oxidiser Nitrosolobous multiformis , the nitrite oxidiser Nitrococcus mobilis as well as from the genomes of other unrelated heterotrophic bacteria. These DNA sequences could be amplified from 0.01 ng of N. europaea genomic DNA or from 100 intact cells, and it was possible to detect Nitrosomonas DNA in a DNA mixture extracted from water samples drawn from a local oxidation pond.     

硫酸盐对淡水养殖池塘表层底泥微生物的影响

硫酸盐引起的生态学效应已得到了越来越多的关注,但目前关于硫酸盐对养殖池塘底泥微生物的影响还知之甚少。【目的】探究不同浓度硫酸盐对养殖池塘底泥微生物的影响规律及可能的机制。【方法】本研究利用采集自养殖池塘的底泥和表层水构建了试验系统,研究了加入约0 mg/L （对照组）、30 mg/L （T1处理组）、150 mg/L （T2处理组）、500 mg/L （T3处理组） Na₂SO₄后表层底泥微生物的丰度、多样性、组成和共生网络的变化规律,并分析了环境影响因素。【结果】孵育第30天前,各实验组底泥微生物变化不大;但到第50天时,T2和T3处理组微生物丰度和多样性相比对照组均明显下降。相比其他实验组,T1处理组酸杆菌门（Acidobacteriota）、拟杆菌门（Bacteroidota）相对丰度出现显著升高（P<0.05）,T3处理组变形菌门（Proteobacteria）和放线菌门（Actinobacteriota）相对丰度出现显著升高（P<0.05）。与对照组相比,T1处理组增加了较多差异类群（62种）,而T3处理组差异类群大量减少（45种）。共生网络图分析显示硫酸盐浓度的增加引起了底泥微生物网络复杂性的增加,说明微生物群落可能通过自身的调节来响应硫酸盐引起的环境改变。冗余分析（redundant analysis,RDA）和相关性分析揭示底泥总有机碳、总氮和氧化还原电位是影响底泥微生物的主要环境因素,提示底泥微生物可能受到硫酸盐和有机质作用的影响。【结论】较长时间的高浓度硫酸盐会对池塘底泥微生物群落造成重要影响,微生物群落自身的转变和硫酸盐引起的有机质分解改变可能是造成微生物群落变化的关键因素。