Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed.     

Monitoring Brain Tumor Vascular Heamodynamic following Anti-Angiogenic Therapy with Advanced Magnetic Resonance Imaging in Mice

Advanced MR imaging methods have an essential role in classification, grading, follow-up and therapeutic management in patients with brain tumors. With the introduction of new therapeutic options, the challenge for better tissue characterization and diagnosis increase, calling for new reliable non-invasive imaging methods. In the current study we evaluated the added value of a combined protocol of blood oxygen level dependent (BOLD) imaging during hyperoxic challenge (termed hemodynamic response imaging (HRI)) in an orthotopic mouse model for glioblastoma under anti-angiogenic treatment with B20-4.1.1, an anti-VEGF antibody. In glioblastoma tumors, the elevated HRI indicated progressive angiogenesis as further confirmed by histology. In the current glioblastoma model, B20-treatment caused delayed tumor progression with no significant changes in HRI yet with slightly reduced tumor vascularity as indicated by histology. Furthermore, fewer apoptotic cells and higher proliferation index were detected in the B20-treated tumors compared to control-treated tumors. In conclusion, HRI provides an easy, safe and contrast agent free method for the assessment of the brain hemodynamic function, an additionally important clinical information.     

Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design

Designed retroaldolases have utilized a nucleophilic lysine to promote carbon–carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest k_cat (> 10^− 3 s^− 1) and k_cat/K_M (11–25 M^− 1 s^− 1) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the > 10⁵-fold rate accelerations that were achieved are within 1–3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (k_cat/k_uncat = 10⁶ to 10⁸) and an extensively evolved computational design (k_cat/k_uncat > 10⁷). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches.     

Nitrogen fertilization raises CO2 efflux from inorganic carbon: A global assessment

Nitrogen (N) fertilization is an indispensable agricultural practice worldwide, serving the survival of half of the global population. Nitrogen transformation (e.g., nitrification) in soil as well as plant N uptake releases protons and increases soil acidification. Neutralizing this acidity in carbonate‐containing soils (7.49 × 10⁹ ha; ca. 54% of the global land surface area) leads to a CO₂ release corresponding to 0.21 kg C per kg of applied N. We here for the first time raise this problem of acidification of carbonate‐containing soils and assess the global CO₂ release from pedogenic and geogenic carbonates in the upper 1 m soil depth. Based on a global N‐fertilization map and the distribution of soils containing CaCO₃, we calculated the CO₂ amount released annually from the acidification of such soils to be 7.48 × 10¹² g C/year. This level of continuous CO₂ release will remain constant at least until soils are fertilized by N. Moreover, we estimated that about 273 × 10¹² g CO₂‐C are released annually in the same process of CaCO₃ neutralization but involving liming of acid soils. These two CO₂ sources correspond to 3% of global CO₂ emissions by fossil fuel combustion or 30% of CO₂ by land‐use changes. Importantly, the duration of CO₂ release after land‐use changes usually lasts only 1–3 decades before a new C equilibrium is reached in soil. In contrast, the CO₂ released by CaCO₃ acidification cannot reach equilibrium, as long as N fertilizer is applied until it becomes completely neutralized. As the CaCO₃ amounts in soils, if present, are nearly unlimited, their complete dissolution and CO₂ release will take centuries or even millennia. This emphasizes the necessity of preventing soil acidification in N‐fertilized soils as an effective strategy to inhibit millennia of CO₂ efflux to the atmosphere. Hence, N fertilization should be strictly calculated based on plant‐demand, and overfertilization should be avoided not only because N is a source of local and regional eutrophication, but also because of the continuous CO₂ release by global acidification.     

Carbon input by roots into the soil: Quantification of rhizodeposition from root to ecosystem scale

Despite its fundamental role for carbon (C) and nutrient cycling, rhizodeposition remains ‘the hidden half of the hidden half’: it is highly dynamic and rhizodeposits are rapidly incorporated into microorganisms, soil organic matter, and decomposed to CO₂. Therefore, rhizodeposition is rarely quantified and remains the most uncertain part of the soil C cycle and of C fluxes in terrestrial ecosystems. This review synthesizes and generalizes the literature on C inputs by rhizodeposition under crops and grasslands (281 data sets). The allocation dynamics of assimilated C (after ¹³C‐CO₂ or ¹⁴C‐CO₂ labeling of plants) were quantified within shoots, shoot respiration, roots, net rhizodeposition (i.e., C remaining in soil for longer periods), root‐derived CO₂, and microorganisms. Partitioning of C pools and fluxes were used to extrapolate belowground C inputs via rhizodeposition to ecosystem level. Allocation from shoots to roots reaches a maximum within the first day after C assimilation. Annual crops retained more C (45% of assimilated ¹³C or ¹⁴C) in shoots than grasses (34%), mainly perennials, and allocated 1.5 times less C belowground. For crops, belowground C allocation was maximal during the first 1–2 months of growth and decreased very fast thereafter. For grasses, it peaked after 2–4 months and remained very high within the second year causing much longer allocation periods. Despite higher belowground C allocation by grasses (33%) than crops (21%), its distribution between various belowground pools remains very similar. Hence, the total C allocated belowground depends on the plant species, but its further fate is species independent. This review demonstrates that C partitioning can be used in various approaches, e.g., root sampling, CO₂ flux measurements, to assess rhizodeposits’ pools and fluxes at pot, plot, field and ecosystem scale and so, to close the most uncertain gap of the terrestrial C cycle.     

Regeneration of Lycium barbarum L. plants from leaf tissue,callus culture and callus protoplasts

The possibility of plant regeneration from leaf tissue, callus and callus protoplasts of Lycium barbarum L. has been studied. Leaf segments were cultured on B5 medium (Gamborg et al. 1968) containing 1.5 mg/1 6-benzylaminopurine and 0.5 mg/1 -naphthaleneacetic acid. Regeneration of shoots was initiated after 30 days of cultivation. Callus was obtained from leaf and internode tissues on MS medium (Murashige and Skoog 1962) containing 0.4 mg/1 of 2,4dichlorophenoxyacetic acid. Subsequently, callus was successfully subcultured on the same medium with 1 mg/l of 2,4-dichlorophenoxyacetic acid and 0.2 mg/l -naphthaleneacetic acid. Organogenesis in callus culture was obtained in the course of 40 days after transferring to TM-4 (Shahin 1984). Protoplasts were isolated from callus tissue grown in vitro using an enzymatic method. Cell colonies, minicallus formation and organogenesis were obtained. Shoots were rooted on Murashige and Skoog medium containing 0..1 mg/l -naphthaleneacetic acid. Regenerated plants were transferred to soil and were grown to maturity. Regenerated plants carried normal morphological traits.Abbreviations BA 6-benzylaminopurine - 2,4-D 2,4-dichlorophenoxyacetic acid - NAA -naphthaleneacetic acid - Zea zeatin - GA₃ gibberellic acid - MS Murashige and Skoog medium - B5 Gamborg medium     

Zinc in taste function

Zinc has been associated with taste function in humans at several levels of organization—the taste bud, the nerves transmitting taste information, and the brain. Zinc plays specific yet varied roles at each organizational level, although many of these roles have not been clearly identified. They include participation in the structural architecture of the cell, maintenance of cell membrane integrity, and control of activity of several cytoplasmic and membrane enzymes. Early investigators noted that some patients given drugs that altered zinc metabolism or who experienced disease processes associated with abnormalities of zinc metabolism exhibited taste dysfunction. Because of these findings zinc was given to a variety of patients as treatment for taste dysfunction. Initial treatment success was observed, but was quickly tempered by more extensive studies that yielded widely variable results leading to confusion about the role of zinc in both taste function and taste treatment. Further studies revealed that taste disorders were diverse and complex with multiple underlying pathophysiologies that were little understood. Subsequent work by several investigators revealed that patients with zinc deficiency, of any etiology, exhibited taste dysfunction and that treatment of these patients with zinc usually produced improvement of clinical symptoms. These results raised the question of how to define zinc deficiency, for zinc treatment in patients without zinc deficiency was unsuccessful and these patients represent more than three-quarters of all patients with taste dysfunction. New clinical techniques for the definition of human zinc deficiency have been achieved through the use of binding and displacement of⁶⁵Zn on specific sites on erythrocyte membranes; these results offer a guide to the identification of patients (i.e., those with zinc deficiency) who may benefit from zinc treatment.     

Response of root respiration and root exudation to alterations in root C supply and demand in wheat

Rising atmospheric CO₂ concentrations have highlighted the importance of being able to understand and predict C fluxes in plant-soil systems. We investigated the responses of the two fluxes contributing to below-ground efflux of plant root-dependent CO₂, root respiration and rhizomicrobial respiration of root exudates. Wheat (Triticum aestivum L., var. Consort) plants were grown in hydroponics at 20°C, pulse-labelled with ¹⁴CO₂ and subjected to two regimes of temperature and light (12 h photoperiod or darkness at either 15°C or 25°C), to alter plant C supply and demand. Root respiration was increased by temperature with a Q ₁₀ of 1.6. Root exudation was, in itself, unaltered by temperature, however, it was reduced when C supply to the roots was reduced and demand for C for respiration was increased by elevated temperature. The rate of exudation responded much more rapidly to the restriction of C input than did respiration and was approximately four times more sensitive to the decline in C supply than respiration. Although temporal responses of exudation and respiration were treatment dependent, at the end of the experimental period (2 days) the relative proportion of C lost by the two processes was conserved despite differences in the magnitude of total root C loss. Approximately 77% of total C and 67% of ¹⁴C lost from roots was accounted for by root respiration. The ratio of exudate specific activity to CO₂ specific activity converged to a common value for all treatments of 2, suggesting that exudates and respired CO₂were not composed of C of the same age. The results suggest that the contributions of root and rhizomicrobial respiration to root-dependent below-ground respiration are conserved and highlight the dangers in estimating short-term respiration and exudation only from measurements of labelled C. The differences in responses over time and in the age of C lost may ultimately prove useful in improving estimates of root and rhizomicrobial respiration.