Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract Background Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level. Results The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons. Conclusions The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.

Physiology and Biotechnology of the Hydrogen Production with the Green Microalga Chlamydomonas reinhardtii

The hydrogen production in the green microalga Chlamydomonas reinhardtii was evaluated by means of a detailed physiological and biotechnological study. First, a wide screening of the hydrogen productivity was done on 22 strains of C. reinhardtii, most of which mutated at the level of the D1 protein. The screening revealed for the first time that mutations upon the D1 protein may result on an increased hydrogen production. Indeed, productions ranged between 0 and more than 500 mL hydrogen per liter of culture (Torzillo, Scoma et al., 2007a), the highest producer (L159I-N230Y) being up to 5 times more performant than the strain cc124 widely adopted in literature (Torzillo, Scoma, et al., 2007b). Improved productivities by D1 protein mutants were generally a result of high photosynthetic capabilities counteracted by high respiration rates. Optimization of culture conditions were addressed according to the results of the physiological study of selected strains. In a first step, the photobioreactor (PBR) was provided with a multiple-impeller stirring system designed, developed and tested by us, using the strain cc124. It was found that the impeller system was effectively able to induce regular and turbulent mixing, which led to improved photosynthetic yields by means of light/dark cycles. Moreover, improved mixing regime sustained higher respiration rates, compared to what obtained with the commonly used stir bar mixing system. As far as the results of the initial screening phase are considered, both these factors are relevant to the hydrogen production. Indeed, very high energy conversion efficiencies (light to hydrogen) were obtained with the impeller device, prooving that our PBR was a good tool to both improve and study photosynthetic processes (Giannelli, Scoma et al., 2009). In the second part of the optimization, an accurate analysis of all the positive features of the high performance strain L159I-N230Y pointed out, respect to the WT, it has: (1) a larger chlorophyll optical cross-section; (2) a higher electron transfer rate by PSII; (3) a higher respiration rate; (4) a higher efficiency of utilization of the hydrogenase; (5) a higher starch synthesis capability; (6) a higher per cell D1 protein amount; (7) a higher zeaxanthin synthesis capability (Torzillo, Scoma et al., 2009). These information were gathered with those obtained with the impeller mixing device to find out the best culture conditions to optimize productivity with strain L159I-N230Y. The main aim was to sustain as long as possible the direct PSII contribution, which leads to hydrogen production without net CO2 release. Finally, an outstanding maximum rate of 11.1 ± 1.0 mL/L/h was reached and maintained for 21.8 ± 7.7 hours, when the effective photochemical efficiency of PSII (ΔF/F'm) underwent a last drop to zero. If expressed in terms of chl (24.0 ± 2.2 µmoles/mg chl/h), these rates of production are 4 times higher than what reported in literature to date (Scoma et al., 2010a submitted). DCMU addition experiments confirmed the key role played by PSII in sustaining such rates. On the other hand, experiments carried out in similar conditions with the control strain cc124 showed an improved final productivity, but no constant PSII direct contribution. These results showed that, aside from fermentation processes, if proper conditions are supplied to selected strains, hydrogen production can be substantially enhanced by means of biophotolysis. A last study on the physiology of the process was carried out with the mutant IL. Although able to express and very efficiently utilize the hydrogenase enzyme, this strain was unable to produce hydrogen when sulfur deprived. However, in a specific set of experiments this goal was finally reached, pointing out that other than (1) a state 1-2 transition of the photosynthetic apparatus, (2) starch storage and (3) anaerobiosis establishment, a timely transition to the hydrogen production is also needed in sulfur deprivation to induce the process before energy reserves are driven towards other processes necessary for the survival of the cell. This information turned out to be crucial when moving outdoor for the hydrogen production in a tubular horizontal 50-liter PBR under sunlight radiation. First attempts with laboratory grown cultures showed that no hydrogen production under sulfur starvation can be induced if a previous adaptation of the culture is not pursued outdoor. Indeed, in these conditions the hydrogen production under direct sunlight radiation with C. reinhardtii was finally achieved for the first time in literature (Scoma et al., 2010b submitted). Experiments were also made to optimize productivity in outdoor conditions, with respect to the light dilution within the culture layers. Finally, a brief study of the anaerobic metabolism of C. reinhardtii during hydrogen oxidation has been carried out. This study represents a good integration to the understanding of the complex interplay of pathways that operate concomitantly in this microalga.

Use of Biotechnology to increase the content of bioactive compounds in fermented foods of plant origin

The objectives of this PhD research were: i) to evaluate the use of bread making process to increase the content of β-glucans, resistant starch, fructans, dietary fibers and phenolic compounds of kamut khorasan and wheat breads made with flours obtained from kernels at different maturation stage (at milky stage and fully ripe) and ii) to study the impact of whole grains consumption in the human gut. The fermentation and the stages of kernel development or maturation had a great impact on the amount of resistant starch, fructans and β-glucans as well as their interactions resulted highly statistically significant. The amount of fructans was high in kamut bread (2.1g/100g) at the fully ripe stage compared to wheat during industrial fermentation (baker’s yeast). The sourdough increases the content of polyphenols more than industrial fermentation especially in bread made by flour at milky stage. From the analysis of volatile compounds it resulted that the sensors of electronic nose perceived more aromatic compound in kamut products, as well as the SPME-GC-MS, thus we can assume that kamut is more aromatic than wheat, so using it in sourdough process can be a successful approach to improve the bread taste and flavor. The determination of whole grain biormakers such as alkylresorcinols and others using FIE-MS AND GC-tof-MS is a valuable alternative for further metabolic investigations. The decrease of N-acetyl-glucosamine and 3-methyl-hexanedioic acid in kamut faecal samples suggests that kamut can have a role in modulating mucus production/degradation or even gut inflammation. This work gives a new approach to the innovation strategies in bakery functional foods, that can help to choose the right or best combination between stages of kernel maturation-fermentation process and baking temperature.

By-products of the dairy farming as raw material for the biotechnology production of polyhydroxyalkanoates

I Poliidrossialcanoati (PHA) sono poliesteri completamente biodegradabili, prodotti da microrganismi come fonte di energia e di carbonio per la sintesi di nuovo materiale cellulare, utilizzando come substrato materie prime rinnovabili. Questi poliesteri sono considerati potenziali candidati per la sostituzione delle materie plastiche convenzionali. Tuttavia, i più alti costi di produzione dei PHA in confronto a quelli delle materie plastiche derivanti dal petrolio, rappresentano il principale ostacolo per la parziale sostituzione di questi ultimi con i biopolimeri. Gli alti costi sono principalmente dovuti all'utilizzo di colture microbiche pure (in cui sia presente un solo ceppo batterico) e substrati puri e costosi. Nell'ultimo decennio è stato sviluppato un processo di produzione a tre stadi alternativo e potenzialmente a minor costo, basato sull'utilizzo di colture microbiche miste (Mixed Microbials Culture, MMC) e una varietà di substrati organici a costo contenuto o nullo, quali alcuni rifiuti dell’industria agro-alimentare. Il presente studio si è concentrato sulla prima fase del processo di produzione dei PHA da colture miste, la fermentazione acidogenica, utilizzando siero di latte come fonte di carbonio per produrre acidi organici. In particolare questo lavoro ha avuto come obiettivo quello di studiare come diverse condizioni operative utilizzate nella fase di fermentazione acidogenica possono influenzare la concentrazione e il profilo degli acidi organici prodotti. Sono stati valutati anche gli effetti dei diversi profili degli acidi organici sulla fase di selezione della coltura microbica, in termini di capacità di stoccaggio di PHA e composizione polimerica.

Evaluation of the photosynthetic efficiency of sweet sorghum under drought and cold conditions

Sweet sorghum, a C4 crop of tropical origin, is gaining momentum as a multipurpose feedstock to tackle the growing environmental, food and energy security demands. Under temperate climates sweet sorghum is considered as a potential bioethanol feedstock, however, being a relatively new crop in such areas its physiological and metabolic adaptability has to be evaluated; especially to the more frequent and severe drought spells occurring throughout the growing season and to the cold temperatures during the establishment period of the crop. The objective of this thesis was to evaluate some adaptive photosynthetic traits of sweet sorghum to drought and cold stress, both under field and controlled conditions. To meet such goal, a series of experiments were carried out. A new cold-tolerant sweet sorghum genotype was sown in rhizotrons of 1 m3 in order to evaluate its tolerance to progressive drought until plant death at young and mature stages. Young plants were able to retain high photosynthetic rate for 10 days longer than mature plants. Such response was associated to the efficient PSII down-regulation capacity mediated by light energy dissipation, closure of reaction centers (JIP-test parameters), and accumulation of glucose and sucrose. On the other hand, when sweet sorghum plants went into blooming stage, neither energy dissipation nor sugar accumulation counteracted the negative effect of drought. Two hybrids with contrastable cold tolerance, selected from an early sowing field trial were subjected to chilling temperatures under controlled growth conditions to evaluate in deep their physiological and metabolic cold adaptation mechanisms. The hybrid which poorly performed under field conditions (ICSSH31), showed earlier metabolic changes (Chl a + b, xanthophyll cycle) and greater inhibition of enzymatic activity (Rubisco and PEPcase activity) than the cold tolerant hybrid (Bulldozer). Important insights on the potential adaptability of sweet sorghum to temperate climates are given.

The Legal Protection of Fundamental Human Values in Central and Eastern Europe and Modern Biotechnology: Towards European Harmonization

The protection of the fundamental human values (life, bodily integrity, human dignity, privacy) becomes imperative with the rapid progress in modern biotechnology, which can result in major alterations in the genetic make-up of organisms. It has become possible to insert human genes into pigs so that their internal organs coated in human proteins are more suitable for transplantation into humans (xenotransplantation), and micro-organisms that cam make insulin have been created, thus changing the genetic make-up of humans. At the end of the 1980s, the Central and Eastern European (CEE) countries either initiated new legislation or started to amend existing laws in this area (clinical testing of drugs, experiments on man, prenatal genetic diagnosis, legal protection of the embryo/foetus, etc.). The analysis here indicates that the CEE countries have not sufficiently adjusted their regulations to the findings of modern biotechnology, either because of the relatively short period they have had to do so, or because there are no definite answers to the questions which modern biotechnology has raised (ethical aspects of xenotransplantation, or of the use of live-aborted embryonic or foetal tissue in neuro-transplantation, etc.). In order to harmonise the existing regulations in CEE countries with respect to the EU and supranational contexts, two critical issues should be taken into consideration. The first is the necessity for CEE countries to recognise the place of humans within the achievements of modern biotechnology (a broader affirmation of the principle of autonomy, an explicit ban on the violation of the genetic identity of either born or unborn life, etc.). The second concerns the definition of the status of different biotechnological procedures and their permissibility (gene therapy, therapeutic genomes, xenotransplantation, etc.). The road towards such answers may be more easily identified once all CEE countries become members of the Council of Europe and express their wish to join the EU, which in turn presupposes taking over the entire body of EU legislation.

Colloidal Nano-apatite Particles with Active Luminescent and Magentic Properties for Biotechnology Applications

Colloidal Nano-apatite Particles with Active Luminescent and Magentic Properties for Biotechnology Applications. The synthesis of functional nano-materials is a burgeoning field that has produced remarkable and consistent breakthroughs over the last two decades. Individual particles have become smaller and shown potential for well defined functionality. However, there are still unresolved problems, a primary one being the loss of functionality and novelty due to uncontrolled aggregation driven by surface energy considerations. As such the first design criteria to harness the true potential of nanoparticles is to prevent unwanted agglomeration by: (1) improving, and, if possible, (2) controlling aggregation behavior. This requires specific knowledge of the chemistry of the immediate locale of the intended application; especially for biologically relevant applications. The latter criterion is also application driven but should be considered, generally, to diversify the range of functional properties that can be achieved. We have now reason to believe that such a novel system with multifunctional capabilities can be synthesized rather conveniently and have far reaching impact in biotechnology and other applications in the near future. We are presently experimenting with the syntheses of spheroidal, metal-doped, colloidal apatite nano-particles (~10 nm) for several potential biomedical applications.

Evaluation of Stockpiled Berseem Clover and Brown Midrib Sorghum x Sudangrass as Supplements for Grazed Cornstalks in Beef Cow Wintering Systems

Berseem clover and oats were incorporated into a corncorn- oat/berseem clover rotation in 1994 and 1995. Two cuttings of oat-berseem clover hay were harvested during the summer before forage was allowed to stockpile for winter grazing. In 1995, a brown midrib sorghum x sudangrass hybrid was seeded into a field adjacent to a corn field. After corn grain harvest in 1994 and 1995, Charolais x Angus x Simmental cows in midgestation were allotted to replicated fields containing corn crop residues with no complementary forages at 2.5 acres/cow, or corn crop residues and stockpiled berseem clover (2:1) at 2.5 acres/cow to simultaneously graze, or to a drylot. In 1995, cows were allotted to fields containing corn crop residues and brown midrib sorghum x sudangrass (7:3) at 2.5 acres/cow. Berseem clover had greater concentrations of digestible organic matter and crude protein than corn crop residues at the initiation of grazing, but had a more rapid decrease in digestible organic matter concentration than corn crop residues. Brown midrib sorghum x sudangrass forage also had a higher initial concentration of digestible organic matter, but an equal rate of decrease in digestible organic matter concentration to corn crop residues in ungrazed areas of the field. Cows grazing berseem clover with corn crop residues had greater body condition score increases during the first half of the grazing season than cows grazing corn crop residues without complementary forages. Cows grazing corn crop residues without complementary forages required 2,786 and 1,412 less lb hay per cow than cows maintained in a drylot in 1994 and 1995. In 1994, simultaneous grazing of berseem clover with corn crop residues did not reduce hay feeding more than feeding corn crop residues alone. However, in 1995, grazing berseem clover or brown midrib sorghum x sudangrass with corn crop residues reduced the amount of hay required to maintain cows by 358 and 376 lb hay per cow compared with grazing corn crop residues without complementary forage.

Evaluation of Stockpiled Berseem Clover and Brown Midrib Sorghum x Sudangrass as Supplements for Grazed Cornstalks in Beef Cow Wintering Systems

Berseem clover and oats were incorporated into a corn-oat/berseem clover rotation in 1994-1996. Two cuttings of oat-berseem clover hay were harvested during the summer before forage was stockpiled for winter grazing. In 1995, brown midrib sorghum x sudangrass hybrid was seeded into a field adjacent to a corn field. This was repeated in 1996 with a standard sorghum x sudangrass hybrid. After corn harvest in 1994–1996, Charolais x Angus x Simmental cows and heifers in midgestation were allotted to corn crop residue, corn crop residue-berseem clover, and corn crop residue-sorghum x sudangrass fields at 2.5 acres/cow, or to a drylot. Berseem clover had greater concentration of digestible organic matter and crude protein than corn crop residues. Corn crop residue digestible organic matter concentration was lower than berseem clover and the brown midrib sorghum x sudangrass, but was higher than that of the standard sorghum x sudangrass hybrid in 1996. Cows grazing corn crop residues without complementary forages required an average of 2,374 less lb. hay per cow than cows maintained in a drylot in 1994-1996. In 1994 and 1996, simultaneous grazing of berseem clover with corn crop residues did not reduce hay feeding more than feeding corn crop residues alone, yet did significantly reduce the amount of hay needed in 1995 to maintain cows by 358 and 376 lb. hay per cow compared with grazing corn crop residues without complementary forage.