Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared with outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep sea. Various other microbial functional genes that are relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments.     

Microbes inside—from diversity to function: the case of Akkermansia

The human intestinal tract is colonized by a myriad of microbes that have developed intimate interactions with the host. In healthy individuals, this complex ecosystem remains stable and resilient to stressors. There is significant attention on the understanding of the composition and function of this intestinal microbiota in health and disease. Current developments in metaomics and systems biology approaches allow to probe the functional potential and activity of the intestinal microbiota. However, all these approaches inherently suffer from the fact that the information on macromolecules (DNA, RNA and protein) is collected at the ecosystem level. Similarly, all physiological and other information collected from isolated strains relates to pure cultures grown in vitro or in gnotobiotic systems. It is essential to integrate these two worlds of predominantly chemistry and biology by linking the molecules to the cells. Here, we will address the integration of omics- and culture-based approaches with the complexity of the human intestinal microbiota in mind and the mucus-degrading bacteria Akkermansia spp. as a paradigm.     

Screening for antibacterial and antifungal activities in marine benthic invertebrates from northern Norway

Benthic marine invertebrates collected from sub-Arctic regions of northern Norway, were found to be a promising source of novel bioactive compounds against human and fish pathogenic bacteria and fungi. Lyophilized material from seven species of ascidians, six sponges and one soft alcyonid coral were extracted with 60% acidified acetonitrile (ACN). After separation into an ACN-rich phase (ACN-extract) and an aqueous phase, and subsequent solid-phase extraction of the aqueous phase, fractions differing in polarity were obtained and screened for antibacterial and antifungal activities, along with the more lipophilic ACN-extracts. Antimicrobial activity was determined against two Gram-negative, two Gram-positive bacteria, and two strains of fungi. Notably, all the invertebrate species in the study showed activity against all four strains of bacteria and the two strains of fungi. In general, the aqueous fractions displayed highest antimicrobial activity, and the most potent extracts were obtained from the colonial ascidian Synoicum pulmonaria which displayed activity against bacteria and fungi at a concentration of 0.02 mg/ml; the lowest concentration tested.     

Importance for absorption of Na+ from freshwater of lysine, valine and serine substitutions in the alpha1a-isoform of Na,K-ATPase in the gills of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar)

In the gills of rainbow trout and Atlantic salmon, the alpha1a- and alpha1b-isoforms of Na,K-ATPase are expressed reciprocally during salt acclimation. The alpha1a-isoform is important for Na(+) uptake in freshwater, but the molecular basis for the functional differences between the two isoforms is not known. Here, three amino acid substitutions are identified in transmembrane segment 5 (TM5), TM8 and TM9 of the alpha1a-isoform compared to the alpha1b-isoform, and the functional consequences are examined by mutagenesis and molecular modeling on the crystal structures of Ca-ATPase or porcine kidney Na,K-ATPase. In TM5 of the alpha1a-isoform, a lysine substitution, Asn783 --> Lys, inserts the epsilon-amino group in cation site 1 in the E(1) form to reduce the Na(+)/ATP ratio. In the E(2) form the epsilon-amino group approaches cation site 2 to force ejection of Na(+) to the blood phase and to interfere with binding of K(+). In TM8, a Asp933 --> Val substitution further reduces K(+) binding, while a Glu961 --> Ser substitution in TM9 can prevent interaction of FXYD peptides with TM9 and alter Na(+) or K(+) affinities. Together, the three substitutions in the alpha1a-isoform of Na,K-ATPase act to promote binding of Na(+) over K(+) from the cytoplasm, to reduce the Na(+)/ATP ratio and the work done in one Na,K pump cycle of active Na(+) transport against the steep gradient from freshwater (10-100 microM: Na(+)) to blood (160 mM: Na(+)) and to inhibit binding of K(+) to allow Na(+)/H(+) rather than Na(+)/K(+) exchange.     

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin

Conventional myosin is representative of biomolecular motors in which the hydrolysis of adenosine triphosphate (ATP) is coupled to large-scale structural transitions both in and remote from the active site. The mechanism that underlies such “mechanochemical coupling,” especially the causal relationship between hydrolysis and allosteric structural changes, has remained elusive despite extensive experimental and computational analyses. In this study, using combined quantum mechanical and molecular mechanical simulations and different conformations of the myosin motor domain, we provide evidence to support that regulation of ATP hydrolysis activity is not limited to residues in the immediate environment of the phosphate. Specifically, we illustrate that efficient hydrolysis of ATP depends not only on the proper orientation of the lytic water but also on the structural stability of several nearby residues, especially the Arg238-Glu459 salt bridge (the numbering of residues follows myosin II in Dictyostelium discoideum) and the water molecule that spans this salt bridge and the lytic water. More importantly, by comparing the hydrolysis activities in two motor conformations with very similar active-site (i.e., Switches I and II) configurations, which distinguished this work from our previous study, the results clearly indicate that the ability of these residues to perform crucial electrostatic stabilization relies on the configuration of residues in the nearby N-terminus of the relay helix and the “wedge loop.” Without the structural support from those motifs, residues in a closed active site in the post-rigor motor domain undergo subtle structural variations that lead to consistently higher calculated ATP hydrolysis barriers than in the pre-powerstroke state. In other words, starting from the post-rigor state, turning on the ATPase activity requires not only displacement of Switch II to close the active site but also structural transitions in the N-terminus of the relay helix and the “wedge loop,” which have been proposed previously to be ultimately coupled to the rotation of the converter subdomain 40 Å away.     

Extracellular amino acids and lipid peroxidation products in periventricular white matter during and after cerebral ischemia in preterm fetal sheep

It is widely hypothesized that accumulation of excitatory amino acids, and oxygen free radicals during or after exposure to hypoxia–ischemia play a pivotal role in preterm periventricular white matter injury; however, there is limited evidence in the intact brain. In preterm fetal sheep (0.65 gestation; term 147 days) we found no significant increase in extracellular levels of excitatory amino acids measured by microdialysis in the periventricular white matter during cerebral ischemia induced by bilateral carotid occlusion. There was no significant change in 8-isoprostane or malondialdehyde levels in the early phase of recovery after occlusion. In contrast, there was a significant delayed increase in most amino acids and in malondialdehyde (but not 8-isoprostane) that was maximal approximately 2–3 days after occlusion. The increase in glutamate was significantly correlated with a secondary increase in cortical impedance, an index of cytotoxic edema, and with white matter damage 3 days post-insult. In conclusion, no significant accumulation of cytotoxins was found within immature white matter during cerebral ischemia. Although a minority of fetuses showed a delayed increase in some cytotoxins, this occurred many days after ischemia, in association with secondary cytotoxic edema, strongly suggesting that these changes are mainly a consequence of evolving cell death.     

The effects of locomotion on the structural characteristics of avian limb bones

Despite the wide range of locomotor adaptations in birds, little detailed attention has been given to the relationships between the quantitative structural characteristics of avian limb bones and bird behaviour. Possible differences in forelimb relative to hindlimb strength across species have been especially neglected. We generated cross‐sectional, geometric data from peripheral quantitative computed tomography scans of the humerus and femur of 127 avian skeletons, representing 15 species of extant birds in 13 families. The sample includes terrestrial runners, arboreal perchers, hindlimb‐propelled divers, forelimb‐propelled divers and dynamic soarers. The hindlimb‐propelled diving class includes a recently flightless island form. Our results demonstrate that locomotor dynamics can be differentiated in most cases based on cross‐sectional properties, and that structural proportions are often more informative than bone length proportions for determining behaviour and locomotion. Recently flightless forms, for example, are more easily distinguished using structural ratios than using length ratios. A proper phylogenetic context is important for correctly interpreting structural characteristics, especially for recently flightless forms. Some of the most extreme adaptations to mechanical loading are seen in aquatic forms. Penguins have forelimbs adapted to very high loads. Aquatic species differ from non‐aquatic species on the basis of relative cortical thickness. The combination of bone structural strength and relative cortical area of the humerus successfully differentiates all of our locomotor groups. The methods used in this study are highly applicable to fossil taxa, for which morphology is known but behaviour is not. The use of bone structural characteristics is particularly useful in palaeontology not only because it generates strong signals for many locomotor guilds, but also because analysing such traits does not require knowledge of body mass, which can be difficult to estimate reliably for fossil taxa. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 601–624.     

Knowledge and Use Value of Plant Species in a Rarámuri Community: A Gender Perspective for Conservation

We used a quantitative ethnobotanical approach to analyze factors influencing the use value of plant species among men and women of the Rarámuri people in Cuiteco, Chihuahua, Mexico. We constructed a use value index (UV) combining the use frequency (U) and the quality perception (Q) of useful plant species by local people. We identified all plant species used by the Rarámuri and classified them into 14 general use categories. We interviewed 34 households in the village to compare men and women’s knowledge on the five main general use categories (and on their respective subcategories and specific uses), to document how they practice gathering activities and to calculate scores of plants UV. A total of 226 useful plant species were identified, but only 12% of them had high UV scores for the 42 specific uses defined. When the overall knowledge of plant species was examined, no significant differences were detected between men and women, but significant differences were identified in general use categories such as medicinal plants, plants for construction and domestic goods, but not in plants used as food and firewood. We identified a division of labor in gathering activities associated with gender, with women mainly gathering medicinal and edible plants and being involved in preparing medicines and food, whereas men were primarily gathering and using plants for manufacturing domestic goods, firewood, and building materials. Plant species UV associated to gender were significantly different between men and women at the level of specific uses in the general category of domestic goods and building. Frequency of use is highly associated with plant species quality perception.     

糖基化终末产物（AGEs）诱导下SOCS基因在肾小管上皮细胞中的表达及意义

目的观察SOCS-1、SOCS-3在肾小管上皮细胞（HKC）中的基础表达及在糖基化终末产物（AGEs）诱导下的表达及意义。方法体外培养HKC细胞,随机分为正常对照组、AGEs组,倒置显微镜观察细胞形态学改变,采用流式细胞术,免疫细胞化学和检测SOCS-1、SOCS-3蛋白表达,RT-PCR法检测HKCSOCS-1、SOCS-3 mRNA表达。结果与正常组比较,AGES诱导的肾小管上皮细胞发生形态学改变;免疫细胞化学、流式细胞学发现SOCS-1、SOCS-3表达以胞浆为主,散在胞核表达;12、24、48hSOCS-1、SOCS-3蛋白表达AGEs组均高于正常对照组,差异有统计学意义,其中SOCS-1以12h表达量最大,SOCS-3以24h表达最高,RT-PCR检测SOCS-3 mRNA表达量,AGEs组高于正常组,差异有统计学意义。结论SOCS-1、SOCS-3在正常肾小管上皮细胞中有基础表达,AGEs可诱导肾小管上皮细胞SOCS-1、SOCS-3表达上调,为我们进一步研究SOCS基因与糖尿病肾病的关系提供了理论依据。