Multi-input multi-output control of a continuous fermenter using nonlinear model based controllers

Internal Model Control (IMC) and Model Predictive Control (MPC), the two most important members of model based controllers, are favourable alternatives for control of nonlinear processes. However, the performance of these controllers deteriorates drastically in the presence of substantial process-model mismatch. Hu and Rangaiah (1998) proposed feedback augmentation for nonlinear IMC (hence named Augmented IMC, AuIMC) for improving control in the presence of modelling errors, and demonstrated its success on a neutralization process. In the present study, IMC, MPC and AuIMC strategies are tested in a more difficult case of multi-input multi-output (MIMO) operation of a highly nonlinear continuous fermenter. A new control configuration is introduced as the conventional configuration is not applicable. Simulation results for different modelling errors show that IMC is better than MPC for fermenter control. The advantage of augmentation as in AuIMC manifests in the significantly improved regulatory control of the fermenter.     

Efficient algorithms for polyploid haplotype phasing

Background

Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of identity by descent and imputation. Haplotype phasing based on sequencing reads has attracted lots of attentions. Diploid haplotype phasing where the two haplotypes are complimentary have been studied extensively. In this work, we focused on Polyploid haplotype phasing where we aim to phase more than two haplotypes at the same time from sequencing data. The problem is much more complicated as the search space becomes much larger and the haplotypes do not need to be complimentary any more.

Results

We proposed two algorithms, (1) Poly-Harsh, a Gibbs Sampling based algorithm which alternatively samples haplotypes and the read assignments to minimize the mismatches between the reads and the phased haplotypes, (2) An efficient algorithm to concatenate haplotype blocks into contiguous haplotypes.

Conclusions

Our experiments showed that our method is able to improve the quality of the phased haplotypes over the state-of-the-art methods. To our knowledge, our algorithm for haplotype blocks concatenation is the first algorithm that leverages the shared information across multiple individuals to construct contiguous haplotypes. Our experiments showed that it is both efficient and effective.

     

A Route to Direct Fitness: Natural and Experimentally Induced Queen Succession in the Tropical Primitively Eusocial Wasp <Emphasis Type="Italic">Ropalidia marginata</Emphasis>

Insect societies are hallmarks of cooperation because one or a few queens monopolize reproduction and several non-reproductive workers cooperatively raise brood. However, the loss of the queen exposes a colony to potential reproductive conflict, which is resolved only after a new queen takes over. We studied queen succession in natural and experimental colonies of the primitively eusocial wasp Ropalidia marginata to understand the proximate behavioral strategies involved in the resolution of this conflict. Previous work has shown that in this species, experimental queen removal always results in only one worker becoming hyper-aggressive and taking over the colony as its next queen, without ever being challenged. Here we show that even during natural queen turnover, one and only one worker becomes hyper-aggressive and takes over as the next queen, without being challenged. During natural queen turn-over, aggression of the successor may sometimes begin before the loss of the old queen and may sometimes decline more rapidly, unlike in the case of experimental queen removal. The successor begins to lay eggs sooner after a natural queen turn-over as compared to experimental queen removal. This is expected because workers might detect the gradual decline of the queen preceding her disappearance. Because queen succession is expected to be more prevalent in tropical perennial species, we expect natural selection to have favored such an orderly queen succession so that a route to direct fitness is available without significant reduction in cooperation.     

Modulation of physiological responses with TiO<Subscript>2</Subscript> nano-particle in <Emphasis Type="Italic">Azolla pinnata</Emphasis> R.Br. under 2,4-D toxicity

The present work is emphasised with the herbicidal tolerance of Azolla pinnata R.Br. and its modulation with TiO₂ nano-particle. Both carbohydrate and nitrogen metabolism were effected with 2,4-D as herbicide and in few cases TiO₂-NP had recovered few detrimental effects. From the nutrient status in Azolla it recorded the recovery of nitrogen as well as potassium by TiO₂-NP but not in case of phosphorus. However, a conversion of nitrate to ammonium was more induced by TiO₂-NP under herbicidal toxicity. Similar results were obtained for inter-conversion of amino acid–nitrate pool, but no changes with glutamine synthase activity with TiO₂-NP. Initially, the effects of 2,4-D was monitored with changes of chlorophyll content but had not been recovered with nanoparticle. Photosynthetic reserves expressed as both total and reducing sugar were insensitive to TiO₂-NP interference but activity of soluble and wall bound invertase was in reverse trend as compared to control. The 2,4-D mediated changes of redox and its oxidative stress was ameliorated in plants with over expressed ADH activity. As a whole the Azolla bio system with TiO₂ supplementation may be useful in sustenance against 2,4-D toxicity through recovery of nitrogen metabolism. Thus, Azolla-TiO₂-NP bio system would be realised to monitor the herbicidal toxicity in soil and its possible bioremediation.     

Length‐weight and length‐length relationships of three small indigenous fishes from the Payra River,southern Bangladesh

Length‐weight relationships (LWRs) and length‐length relationships (LLRs) for three small indigenous fishes (Esomus danrica, Pachypterus atherinoides and Salmostoma bacaila) were reported from the Payra River, southern Bangladesh. Samples were collected using traditional fishing gear including cast net (mesh size ranges from 1.0 to 2.0 cm), seine net (mesh size ranges from 1.5 to 2.5 cm) and square lift net (mesh size ~ 1.0 cm) in August to September 2017. Allometric coefficient (b) values were 2.66 for E. danrica, 3.08 for P. atherinoides and 3.06 for S. bacaila. The LLRs were also highly significant with r² ≥ .956.     

Reproductive biology of Apocryptes bato (Gobiidae) in the Payra River,southern Bangladesh

The gobioid fish Apocryptes bato (Hamilton, 1822) is a species of mudskipper found in Bangladesh, India, and Myanmar. The reproductive biology of A. bato including sex ratio, size at sexual maturity, breeding season, fecundity, and condition factor was studied in the Payra River, southern Bangladesh during May 2016 to April 2017. A total of 1,028 specimens (303 males and 725 females) were collected. The overall sex ratio was significantly different from the expected value of 1:1 (male: female = 1:2.39, χ² = 173.23, p < 0.05). Size at sexual maturity was estimated as 4.9 cm standard length. Monthly variations in gonadosomatic index indicate that the main breeding season is from May to December. There was a significant positive correlation of body length and body weight with fecundity. Fulton's condition factor varied in both sexes and was attributed to variations in GSI with maturity. Breeding season was significantly associated with rainfall, but not air temperature. Our findings should improve management and conservation of this fish in the Payra River and surrounding ecosystems.     

Woody vegetation composition and diversity in woodlands inside and outside a Forest Reserve in Jos,Nigeria

Protected areas such as forest reserves are often assumed to be best ways to conserve biodiversity and maintain intact ecosystems. We examined woody plant composition and diversity in the gallery forest and savannah woodland habitats of Amurum Forest Reserve and areas immediately surrounding it in Jos, Nigeria. A total of 100 10 × 10 m sample plots were established inside and outside the reserve. All woody plants ≥1 cm diameter at breast height (dbh) were identified and measured. A total of 7,564 individual plants categorized as 134 species from 44 families were recorded. Overall species diversity was significantly higher in the Forest Reserve than outside the reserve, although more species were encountered outside the reserve. Our findings suggest that, protected areas and the areas surrounding them are important for the conservation of biodiversity as the areas outside protected areas also contain species of conservation value. The continuous degrading areas outside protected areas isolates them and poses a serious threat to the long‐term viability of wildlife populations, so it is important that biodiversity in protected areas and their surrounding areas be conserved.     

Spike‐dip transformation of Setaria viridis

Traditional method of Agrobacterium‐mediated transformation through the generation of tissue culture had limited success for Setaria viridis, an emerging C4 monocot model. Here we present an efficient in planta method for Agrobacterium‐mediated genetic transformation of S. viridis using spike dip. Pre‐anthesis developing spikes were dipped into a solution of Agrobacterium tumefaciens strain AGL1 harboring the β‐glucuronidase (GUS) reporter gene driven by the cauliflower mosaic virus 35S (CaMV35S) promoter to standardize and optimize conditions for transient as well as stable transformations. A transformation efficiency of 0.8 ± 0.1% was obtained after dipping of 5‐day‐old S3 spikes for 20 min in Agrobacterium cultures containing S. viridis spike‐dip medium supplemented with 0.025% Silwet L‐77 and 200 μm acetosyringone. Reproducibility of this method was demonstrated by generating stable transgenic lines expressing β‐glucuronidase plus (GUSplus), green fluorescent protein (GFP) and Discosoma sp. red fluorescent protein (DsRed) reporter genes driven by either CaMV35S or intron‐interrupted maize ubiquitin (Ubi) promoters from three S. viridis genotypes. Expression of these reporter genes in transient assays as well as in T1 stable transformed plants was monitored using histochemical, fluorometric GUS activity and fluorescence microscopy. Molecular analysis of transgenic lines revealed stable integration of transgenes into the genome, and inherited transgenes expressed in the subsequent generations. This approach provides opportunities for the high‐throughput transformation and potentially facilitates translational research in a monocot model plant.     

Genetic and Genomic Resources of Small Millets

Small millets are very promising agricultural entity to ensure global food security. They gained remarkable importance in agriculture due to their resilience to climatic changes and increasing demand for nutritious food and feed. The genetic variability in the core and mini-core germplasm of small millets was characterized for nutritional composition and capacity to tolerate abiotic stresses that can be infused in breeding programs. Other than the foxtail millet, availability of genomic information in small millets is far below the mark for use in marker-assisted breeding and other genetic improvement programs. The genome sequence of foxtail millet has recently triggered a plethora of post-genomic analysis and envisaged foxtail millet as a model organism for the C₄ grasses and bioenergy research. Recent developments in the next-generation sequencing technologies enabled us, with the simultaneous discovery of high-throughput markers and multiplexed genotyping of germplasm, to speedup marker-assisted breeding. In this context, an in-depth analysis of the wealth of diverse germplasm resources and future perspectives of integrating genomics in genome-wide marker-trait association and breeding in small millets is worthy.