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.     

Evaluating effect of arbuscular mycorrhizal fungal consortia and Azotobacter chroococcum in improving biomass yield of Jatropha curcas

This study was conducted to study the long-term impact of bioinoculants, Azotobacter chroococcum and arbuscular mycorrhizal fungi (AMF) on growth and biomass yield of Jatropha curcas grown in nursery and in field conditions. The experiment was set up in a randomized block design, and the following treatments was designed (T₁ = control, T₂ = Azotobacter, T₃ = inoculation with AMF, and T₄ = inoculation with Azotobacter + AMF). Data on various growth attributes (shoot height and shoot diameter) and biochemical parameters [leaf relative water content (LRWC), sugars, protein, and photosynthetic pigments] were recorded up to 6 months in the nursery and in the field (18 months). Results pertaining to morpho-physiological traits showed Azotobacter and AMF consortia increase shoot height, shoot diameter, LRWC, sugars, proteins, and photosynthetic pigments over control under nursery conditions. Besides enhancing the plant growth, these bioinoculants helped in better establishment of Jatropha plants under field conditions. A significant improvement in the shoot height, shoot diameter, fruit yield/plant, and seed yield (g)/plant was evident in 18-month-old Jatropha plants under field conditions when Azotobacter and AMF were co-inoculated. This work supports the application of bioinoculants for establishment of Jatropha curcas in semi-arid regions.     

LiGAPS-Beef,a mechanistic model to explore potential and feed-limited beef production 1: model description and illustration

The expected increase in the global demand for livestock products calls for insight in the scope to increase actual production levels across the world. This insight can be obtained by using theoretical concepts of production ecology. These concepts distinguish three production levels for livestock: potential (i.e. theoretical maximum) production, which is defined by genotype and climate only; feed-limited production, which is limited by feed quantity and quality; and actual production. The difference between the potential or limited production and the actual production is the yield gap. The objective of this paper, the first in a series of three, is to present a mechanistic, dynamic model simulating potential and feed-limited production for beef cattle, which can be used to assess yield gaps. A novelty of this model, named LiGAPS-Beef (Livestock simulator for Generic analysis of Animal Production Systems – Beef cattle), is the identification of the defining factors (genotype and climate) and limiting factors (feed quality and available feed quantity) for cattle growth by integrating sub-models on thermoregulation, feed intake and digestion, and energy and protein utilisation. Growth of beef cattle is simulated at the animal and herd level. The model is designed to be applicable to different beef production systems across the world. Main model inputs are breed-specific parameters, daily weather data, information about housing, and data on feed quality and quantity. Main model outputs are live weight gain, feed intake and feed efficiency (FE) at the animal and herd level. Here, the model is presented, and its use is illustrated for Charolais and Brahman × Shorthorn cattle in France and Australia. Potential and feed-limited production were assessed successfully, and we show that FE of herds is highest for breeds most adapted to the local climate conditions. LiGAPS-Beef also identified the factors that define and limit growth and production of cattle. Hence, we argue the model has scope to be used as a tool for the assessment and analysis of yield gaps in beef production systems.     

Variation of Pleurotus ostreatus (Jacq. Ex Fr.) P. Kumm. (1871) performance subjected to differentdoses and timings of nano-urea

Supplementation of the growing substrate by nitrogenous additives has been known to improve the production of oyster mushroom (Pleurotus ostreatus (Jacq. ex Fr.) P. Kumm. (1871)). However, the application of nano-additives has not been reported in such cultivation yet. The study investigated the effect of nano-urea added in two different doses (3 g and 5 g per kg substrate), once (at spawning or after first flush) or twice (at spawning and after first flush) to the growing substrate consisting of wheat straw and spent oyster substrate (1:1, w/w). Results showed that the application of nano-urea once has induced the highest number of mushroom flushes (four flushes) despite the dose applied. Contrarily to early findings, where high doses of nitrogen have caused inhibition of mushroom growth and production, nano-urea application has had better effects when applied twice. With 5 g/kg, it induced the shortest period between the first and the third flush (15 days). With 3 g/kg, it resulted in the highest biological and economic yields at the third flush (332.7 g/bag and 283.1 g/bag respectively), in total (973.4 g/bag and 854.0 g/bag respectively), the highest biological efficiency (109.6%), and pileus diameter/stipe length ratio (2.8). Experimental findings of the current study may be potentially applied at commercial scale.     

It is better to be ignorant of our moral enhancement: A reply to Zambrano

In a recent issue of Bioethics, I argued that compulsory moral bioenhancement should be administered covertly. Alexander Zambrano has criticized this argument on two fronts. First, contrary to my claim, Zambrano claims that the prevention of ultimate harm by covert moral bioenhancement fails to meet conditions for permissible liberty-restricting public health interventions. Second, contrary to my claim, Zambrano claims that covert moral bioenhancement undermines autonomy to a greater degree than does overt moral bioenhancement. In this paper, I rebut both of these arguments, then finish by noting important avenues of research that Zambrano’s arguments motivate.     

EFFECTS OF ARSENATE ON GROWTH OF NITROGEN-AND PHOSPHORUS-LIMITED CHLORELLA VULGARIS (CHLOROPHYCEAE) ISOLATES1

The effects of arsenate on the growth characteristics of five isolates of the freshwater alga, Chlorella vulgaris Beij., were examined. Two field isolates originated from arsenic-contaminated sites in Yukon, Canada and Kyushi, Japan; two reference isolates were obtained from the University of Texas Culture Collection. One isolate was selected for arsenic-tolerance in the laboratory. All five strains survived in culture solutions containing high arsenate concentrations. Arsenate (1–25 mM As) reduced photosynthesis and cell growth, as reflected by induced lag periods, slower growth rates, and lower stationary cell yields. Field isolates had shorter lag periods, higher growth rates, and enhanced cell yields compared to lab isolates when exposed to the same arsenic concentrations. Growth of the phosphorus-limited field strains was stimulated by the addition of arsenic. The cell yield of phosphorus-limited C. vulgaris Yukon, when treated with arsenic, was two times that of the phosphorus-limited control. This pattern was not evident when photosynthesis was used as a measure of cell response.     

Instrumental test to estimate a model of forecast yield: a non-parametric application to the pollen index in South Italy

A statistical test is described to verify the characteristics of the biological information contained in the dynamics of the flowering process. The test focuses on interactions between the pollen index and climatic variables to investigate if the biological indicator can synthesise the information of the pre-flowering phases. The multiple-regression model is built upon two pre-flowering climate macro-indicators extracted by Principal Component Analysis (PCA) and the optimised pollen index is obtained by non-parametric estimation. The empirical analysis is applied to 15 stations located in southern Italy in regions that have a longstanding tradition of olive production. Using the variance explained, we find that an optimised pollen index is fairly well predicted by the pre-flowering climatic data. We conclude that the optimised pollen index makes more parsimonious the modelling for predicting olive production.     

Empirical relationships to estimate asymptotic length, length at first maturity and length at maximum yield per recruit in fishes, with a simple method to evaluate length frequency data

Empirical relationships are presented to estimate in fishes, asymptotic length (L∞) from maximum observed length (L_max), length at first maturity (L_m) from L_∞, life span (t_max) from age at first maturity (t_m), and length at maximum possible yield per recruit (L_opt) from L_∞ and from L_m, respectively. The age at L_opt is found to be a good indicator of generation time in fishes. A spreadsheet containing the various equations can be downloaded from the Internet at http://www.fishbase.org/download as popdynJFB.zip. A simple method is presented for evaluation of length–frequency data in their relationship to L_∞, L_m and L_opt. This can be used to evaluate the quality of the length–frequency sample and the status of the population. Three examples demonstrate the usefulness of this method. 2000 The Fisheries Society of the British Isles