Learning generative models for protein fold families

We introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN (Generative REgularized ModeLs of proteINs), learns an undirected probabilistic graphical model of the amino acid composition within the MSA. The resulting model encodes both the position-specific conservation statistics and the correlated mutation statistics between sequential and long-range pairs of residues. Existing techniques for learning graphical models from MSA either make strong, and often inappropriate assumptions about the conditional independencies within the MSA (e.g., Hidden Markov Models), or else use suboptimal algorithms to learn the parameters of the model. In contrast, GREMLIN makes no a priori assumptions about the conditional independencies within the MSA. We formulate and solve a convex optimization problem, thus guaranteeing that we find a globally optimal model at convergence. The resulting model is also generative, allowing for the design of new protein sequences that have the same statistical properties as those in the MSA. We perform a detailed analysis of covariation statistics on the extensively studied WW and PDZ domains and show that our method out-performs an existing algorithm for learning undirected probabilistic graphical models from MSA. We then apply our approach to 71 additional families from the PFAM database and demonstrate that the resulting models significantly out-perform Hidden Markov Models in terms of predictive accuracy.     

黄河上游灌区稻田N2O排放特征

黄河上游灌区稻田高产区过量施肥现象十分突出,氮肥过量施用引起土壤氮素盈余,导致N₂O排放量增大,由此引起的温室效应引起广泛关注。采用静态箱-气相色谱法研究黄河上游灌区稻田不同施肥处理下N₂O排放特征。试验设置5个施肥处理,包括常规氮肥300 kg/hm²下单施尿素和有机肥配施2个处理,分别用N300和N300-OM代表;优化氮肥240 kg/hm²下单施尿素和有机肥配施2个处理,分别用N240和N240-OM代表;对照不施氮肥用N0代表。试验结果得出,灌区水稻生长季稻田土壤N₂O排放主要集中在水稻分蘖前及水稻生长的中后期,稻田氮肥施用、灌水及土壤温度的变化对N₂O排放通量影响较大,不同处理水稻各生育阶段N₂O累积排放量与稻田土壤耕层NO^-₃-N含量动态变化显著相关。稻田N₂O排放不是黄河上游灌区稻田氮素损失的主要途径,但灌区稻田N₂O排放的增温潜势较大;稻田氮肥过量施用会显著增加N₂O排放量,在相同氮素水平下,有机肥配施会显著增加稻田土壤N₂O的排放量(P＜0.01)。优化施氮能有效减少灌区稻田水稻生长季N₂O排放量。稻田不同处理的水稻整个生长季土壤N₂O排放总量为2.69-3.87 kg/hm²,肥料氮通过N₂O排放损失的百分率仅为0.43%-0.64%。在灌区习惯灌水和高氮肥300 kg/hm²时,N300-OM处理的稻田N₂O排放量达3.87 kg/hm²,在100 a时间尺度上的全球增温潜势(GWPs)为20.76×10⁷ kg CO₂/hm²;优化施氮240 kg/hm²水平下,N240和N240-OM处理的N₂O累计排放量较N300-OM处理,分别降低了1.18 kg/hm²和0.57 kg/hm²,在100 a尺度上每年由稻田N₂O排放引起的GWPs分别降低了6.33×10⁷ kg CO₂/hm²和3.06×10⁷ kg CO₂/hm²。     

平衡施肥对缺磷红壤性水稻土的生态效应

为了研究平衡施肥对缺磷水稻土的生态效应,对长期缺施磷肥水稻土进行了3.5年平衡施肥试验。试验采取盆栽水稻的方式,在长期缺施磷肥的红壤性水稻土上比较不施磷肥（NK）、平衡施用氮磷钾无机肥（NPK）、无机氮磷钾肥配施硅肥（NPKSi）、无机氮磷钾肥配施有机肥（无机肥占3/5）、NPK基础上增施磷肥（NKhP）、NPKM基础上增施磷肥（NKhPM）处理的土壤肥力、土壤微生物特性、土壤磷的渗漏量以及地上部水稻产量、养分利用率、磷肥利用率的变化。试验表明,平衡施肥处理NPK、NPKSi、NPKM、NKhPM显著提高水稻产量,比不施磷肥（NK）平均增产147%,其中NPKM提高152%;能提高土壤肥力,比不施磷肥土壤有机质含量平均提高18.5%,其中NPKM提高30.1%;显著提高土壤微生物生物量,比不施磷肥土壤微生物生物量碳（MBC）平均提高57.2%,其中NPKM提高87.1%;提高氮素、钾素养分利用率,比不施磷肥平均分别提高120.3%、33.6%,其中NPKM分别提高152%、43%。而长期重施无机磷肥处理（NKhP）虽然水稻产量比不施磷肥处理提高125.1%,但因土壤中磷酸根离子含量过高影响土壤微生物正常生长,土壤微生物活度比不施磷处理降低9.4%,土壤微生物量碳（MBC）降低2.4%,稻田土壤微生物生态系统质量劣化。此外,重施磷肥处理（包括NKhP、NKhPM）易导致稻田水体的磷污染。各处理比较,NPKM综合生态效应最佳,以下依次是NKhPM、NPKSi、NPK,NKhP,NKhP对稻田土壤微生物生态系统产生负效应。根据试验结果,平衡施肥是恢复缺磷水稻土的有效措施,其中在平衡施用氮磷钾化肥的基础上增施有机肥或硅肥效果较好。     

水稻土中铁还原菌多样性

微生物介导的异化Fe(III) 还原是非硫厌氧环境中Fe(III) 还原生成Fe(II) 的主要途径,然而相关的铁还原菌还不是很清楚,特别是在水稻土中.本文采用富集培养的方法,以乙酸和氢气作为电子供体,水铁矿和针铁矿作为电子受体,通过末端限制性片段长度多态性（T-RFLP）技术和16S rRNA基因克隆测序相结合的分子生物学方法研究了水稻土中铁还原菌的多样性.结果表明：无论是以乙酸或氢气为电子供体,水铁矿或针铁矿为电子受体,地杆菌（Geobacter）和梭菌（Clostridiales）是富集到的主要微生物群落;乙酸为电子供体时,富集到的主要微生物群落还包括红环菌（Rhodocyclaceae）;因此,除地杆菌外,梭菌和红环菌很可能也是水稻土中重要的铁还原菌.     

Environmental factors associated with the distribution of floodwater mosquito eggs in irrigated fields in Wrocław,Poland

A survey of distribution patterns of floodwater mosquito eggs related to environmental conditions such as moisture and plant associations was conducted by using soil samples from irrigated fields in Wroc?aw, Poland. Mosquito egg distribution was determined by repeatedly flooding the soil samples with aerated water at a temperature of 25° C. Under laboratory conditions, hatching in installments of Aedes caspius (Pallas) and Aedes vexans (Meigen) were commonly observed. The results show that ～75% of the larvae of Ae. caspius and Ae. vexans hatched after the first flooding under summer‐like conditions, whereas, following the second and third flooding, the numbers of hatched larvae were significantly lower. In our study, within one intermediate flooded field, a total of 66 plant species was identified and classified into six communities. All vegetation types were associated by varied egg densities and showed differences both in richness and Shannon‐Wiener diversity index as well as in ecological indices for moisture, soil reaction, and nutrient level. Small changes in elevation along the slope within the study area showed a large difference in the distribution of mosquito eggs. The highest average egg density was observed in zones with high occurrence of Phalaris arundinacea, usually prevalent in intermediate flooded and fertile areas. Knowledge of the indicators for the distribution of floodwater mosquito eggs in temporary breeding sites may be essential for organizing a successful, integrated mosquito control program with special regard to microbial control agents.     

Net annual global warming potential and greenhouse gas intensity in Chinese double rice‐cropping systems: a 3‐year field measurement in long‐term fertilizer experiments

The impact of agricultural management on global warming potential (GWP) and greenhouse gas intensity (GHGI) is not well documented. A long‐term fertilizer experiment in Chinese double rice‐cropping systems initiated in 1990 was used in this study to gain an insight into a complete greenhouse gas accounting of GWP and GHGI. The six fertilizer treatments included inorganic fertilizer [nitrogen and phosphorus fertilizer (NP), nitrogen and potassium fertilizer (NK), and balanced inorganic fertilizer (NPK)], combined inorganic/organic fertilizers at full and reduced rate (FOM and ROM), and no fertilizer application as a control. Methane (CH₄) and nitrous oxide (N₂O) fluxes were measured using static chamber method from November 2006 through October 2009, and the net ecosystem carbon balance was estimated by the changes in topsoil (0–20 cm) organic carbon (SOC) density over the 10‐year period 1999–2009. Long‐term fertilizer application significantly increased grain yields, except for no difference between the NK and control plots. Annual topsoil SOC sequestration rate was estimated to be 0.96 t C ha^?1 yr^?1 for the control and 1.01–1.43 t C ha^?1 yr^?1 for the fertilizer plots. Long‐term inorganic fertilizer application tended to increase CH₄ emissions during the flooded rice season and significantly increased N₂O emissions from drained soils during the nonrice season. Annual mean CH₄ emissions ranged from 621 kg CH₄ ha^?1 for the control to 1175 kg CH₄ ha^?1 for the FOM plots, 63–83% of which derived from the late‐rice season. Annual N₂O emission averaged 1.15–4.11 kg N₂O–N ha^?1 in the double rice‐cropping systems. Compared with the control, inorganic fertilizer application slightly increased the net annual GWPs, while they were remarkably increased by combined inorganic/organic fertilizer application. The GHGI was lowest for the NP and NPK plots and highest for the FOM and ROM plots. The results of this study suggest that agricultural economic viability and GHGs mitigation can be simultaneously achieved by balanced fertilizer application.     

Butterfly diversity at the ecotone between agricultural and semi‐natural habitats across a climatic gradient

Aim Understanding the response of species to ecotones and habitat edges is essential to designing conservation management, especially in mosaic agricultural landscapes. This study examines how species diversity and composition change with distance from semi‐natural habitats, over ecotones into agricultural fields, and how within‐site patterns of community transition change across a climatic gradient and differ between crop types. Location A total of 19 sites in Israel where semi‐natural habitats border agricultural fields (wheat fields or olive groves) distributed along a sharp climatic gradient ranging between 100 and 800 mm mean annual rainfall. Methods  We performed butterfly surveys in 2006. We analysed species richness (α‐diversity), diversity, community nestedness and species turnover (β‐diversity) within sites and between sites (γ‐diversity). We also assessed where species of conservation concern occurred. Results In wheat sites, richness and diversity declined abruptly from ecotones to fields and remained homogenously poor throughout the fields, regardless of climate. In olive sites, despite the sharp structural boundary, richness and diversity remained high from the semi‐natural habitat to the grove margins and then declined gradually into groves. Species of conservation concern occurred across all habitats at olive sites, but none were found inside wheat fields or at their ecotones. The contrast in community structure between semi‐natural habitats and fields was affected by both climate and field type. Irrigation in arid regions did not augment species diversity. Main conclusions Our results indicate that consideration of crop type, within a climatic context, should receive high priority in biodiversity conservation in agricultural areas. In ‘hostile’ crops, such as wheat, we suggest favouring a combination of high‐intensity management and wide margins over less intensive management without margins, which may merely aid generalist butterfly species. The scarcity of butterflies in arid irrigated fields suggests a need to carefully assess the effects of irrigation and agrochemicals on species’ communities.     

Mechanism of interaction between electromagnetic fields and living organisms

Based on nonlinear phenomena of biophoton emission observed in the past, an interference model concerning with the mechanism of interaction between living organisms and electromagnetic fields was raised. Caused by biological nonlinearly polarizable double layer, destructive interference of incoming and reflected waves establishes in the outside. As a consequence, in the inside constructive interference takes place at the same time. The interference patterns may play an important role in biological self organization and in biological functions. We investigate the boundary conditions necessary for explaining these non-linear optical effects in terms of the phase conjugation. It turns out that there are solutions of the Maxwell equations which satisfy destructive interference of biophotons in agreement with the experimental results. Necessary provisions are nonlinearly polarizable optically active double layers of distances which are small compared to the wavelength of light. In addition, they have to be able to move into the nodal planes of the impinging waves within a small time interval compared to the coherence time. These conditions are likely fulfilled in the optically dense, but ordered and optically excited, highly polarizable living matter.     

Skin temperature increase caused by a mobile phone: a methodological infrared camera study

Mobile phone users often complain about burning sensations or a heating of the ear region. The increase in temperature may be due to thermal insulation by the phone, heating of the mobile phone resulting from its electrical power dissipation, and radio frequency (RF) exposure. The main objective of this study was to use infrared (IR) camera techniques to find how much each of these factors contributes to the increase in skin temperature resulting from the use of one GSM 900 phone. One subject, a healthy male, took part in the study. He was holding the phone in a normal position when the phone was switched off, when it was switched on but with the antenna replaced by a 50 Omega load to eliminate the RF exposure, and when it was transmitting RF fields. The output power could be fixed, and the minimal and the maximal power levels of the phone were used. The study was designed as a double blind experiment. The changes in temperature after 15 and 30 min of mobile phone use were calculated on the exposed side of the head relative to the unexposed side. The insulation and the electrical power dissipation led to statistically significant rises in the skin temperature, while the RF exposure did not.     

Effect of weak, interrupted sinusoidal low frequency magnetic field on neural regeneration in rats: functional evaluation

A study of the effect of weak, interrupted sinusoidal low frequency magnetic field (ISMF) stimulation on regeneration of the rat sciatic nerve was carried out. In the experiment, 60 Wistar rats were used: 24 rats underwent unilateral sciatic nerve transection injury and immediate surgical nerve repair, 24 rats underwent unilateral sciatic nerve crush injury, and the remaining 12 rats underwent a sham surgery. Half of the animals (n = 12) with either sciatic nerve lesion were randomly chosen and exposed between a pair of Helmholtz coils for 3 weeks post-injury, 4 h/day, to an interrupted (active period to pause ratio = 1.4 s/0.8 s) sinusoidal 50 Hz magnetic field of 0.5 mT. The other half of the animals (n = 12) and six rats with sham surgery were used for two separate controls. Functional recovery was followed for 6 weeks for the crush injuries and 7(1/2) months for the transection injuries by video assisted footprint analysis in static conditions and quantified using a recently revised static sciatic index (SSI) formula. We ascertained that the magnetic field influence was weak, but certainly detectable in both injury models. The accuracy of ISMF influence detection, determined by the one-way repeated measures ANOVA test, was better for the crush injury model: F(1, 198) = 9.0144, P = .003, than for the transection injury model: F(1, 198) = 6.4826, P = .012. The Student-Newman-Keuls range test for each response day yielded significant differences (P < .05) between the exposed and control groups early in the beginning of functional recovery and later on from the points adjacent to the beginning of the plateau, or 95% of functional recovery, and the end of observation. These differences probably reflect the ISMF systemic effect on the neuron cell bodies and increased and more efficient reinnervation of the periphery.