Precision breeding for RNAi suppression of a major 4-coumarate:coenzyme A ligase gene improves cell wall saccharification from field grown sugarcane

Sugarcane (Saccharum spp. hybrids) is a major feedstock for commercial bioethanol production. The recent integration of conversion technologies that utilize lignocellulosic sugarcane residues as well as sucrose from stem internodes has elevated bioethanol yields. RNAi suppression of lignin biosynthetic enzymes is a successful strategy to improve the saccharification of lignocellulosic biomass. 4-coumarate:coenzyme A ligase (4CL) is a key enzyme in the biosynthesis of phenylpropanoid metabolites, such as lignin and flavonoids. Identifying a major 4CL involved in lignin biosynthesis among multiple isoforms with functional divergence is key to manipulate lignin biosynthesis. In this study, two full length 4CL genes (Sh4CL1 and Sh4CL2) were isolated and characterized in sugarcane. Phylogenetic, expression and RNA interference (RNAi) analysis confirmed that Sh4CL1 is a major lignin biosynthetic gene. An intragenic precision breeding strategy may facilitate the regulatory approval of the genetically improved events and was used for RNAi suppression of Sh4CL1. Both, the RNAi inducing cassette and the expression cassette for the mutated ALS selection marker consisted entirely of DNA sequences from sugarcane or the sexually compatible species Sorghum bicolor. Field grown sugarcane with intragenic RNAi suppression of Sh4CL1 resulted in reduction of the total lignin content by up to 16.5?% along with altered monolignol ratios without reduction in biomass yield. Mature, field grown, intragenic sugarcane events displayed 52–76?% improved saccharification efficiency of lignocellulosic biomass compared to wild type (WT) controls. This demonstrates for the first time that an intragenic approach can add significant value to lignocellulosic feedstocks for biofuel and biochemical production.     

Length–weight and length–length relationships for 23 fish species of Porto Primavera reservoir,Upper Paraná River,Brazil

The study presents length–weight relationships (LWR) and length–length relationships (LLR) for 23 fish species captured in the Porto Primavera Reservoir, Upper Paraná River. Seventeen of the LWRs and 20 of the LLRs are reported for the first time. New maximum standard lengths are presented for 17 species as well as weights for three species and new total weight records for 19 species.     

Reproductive biology of Syzygiella rubricaulis (Nees) Steph. (Adelanthaceae,Marchantiophyta), a liverwort disjunctly distributed in high‐altitude Neotropical mountains

Syzygiella rubricaulis is a dioecious leafy liverwort disjunctly distributed and restricted to high‐altitude mountains in the Neotropics and the Azores. This study is part of a larger project examining the phylogeography of S. rubricaulis in the Neotropics, and our main goals were to understand its reproductive biology, where sex expression occurs, if vegetative propagules are frequently found, how the sexes are distributed in populations, how frequently sporophytes are formed and what environmental conditions influence sexual expression. S. rubricaulis patches are mostly female, but all patches also contain non sex‐expressing shoots. Out of 42 patches examined, 29 (69%) were sex‐expressing: 25 were unisexual (21 female and four male) and four of mixed sex (two male‐biased and two unbiased). At shoot level, out of 4200 shoots 18% were female and 7% male; among sex‐expressing shoots, 73% were female, representing a sex ratio of 0.8 (female‐biased). We encountered a total of 33 sporophytes in six patches (in Brazil, Venezuela and Ecuador). Leaf regenerants were found in one patch in Mexico. Low rates of sporophytes were likely related to low frequencies of male shoots and large distances between the sexes. As 25% of S. rubricaulis shoots expressed sex (occasionally producing sporophytes), we suggest that short‐distance (and rarely long‐distance) spore dispersal events occur in mountainous areas on a short‐term basis. On a long‐term basis, however, these events likely contribute to dynamic exchanges among populations in the Neotropics.     

Absence of Tau triggers age‐dependent sciatic nerve morphofunctional deficits and motor impairment

Dementia is the cardinal feature of Alzheimer's disease (AD), yet the clinical symptoms of this disorder also include a marked loss of motor function. Tau abnormal hyperphosphorylation and malfunction are well‐established key events in AD neuropathology but the impact of the loss of normal Tau function in neuronal degeneration and subsequent behavioral deficits is still debated. While Tau reduction has been increasingly suggested as therapeutic strategy against neurodegeneration, particularly in AD, there is controversial evidence about whether loss of Tau progressively impacts on motor function arguing about damage of CNS motor components. Using a variety of motor‐related tests, we herein provide evidence of an age‐dependent motor impairment in Tau?/? animals that is accompanied by ultrastructural and functional impairments of the efferent fibers that convey motor‐related information. Specifically, we show that the sciatic nerve of old (17–22‐months) Tau?/? mice displays increased degenerating myelinated fibers and diminished conduction properties, as compared to age‐matched wild‐type (Tau+/+) littermates and younger (4–6 months) Tau?/? and Tau+/+ mice. In addition, the sciatic nerves of Tau?/? mice exhibit a progressive hypomyelination (assessed by g‐ratio) specifically affecting large‐diameter, motor‐related axons in old animals. These findings suggest that loss of Tau protein may progressively impact on peripheral motor system.     

E-cadherin roles in animal biology: A perspective on thyroid hormone-influence

The establishment, remodeling and maintenance of tissular architecture during animal development, and even across juvenile to adult life, are deeply regulated by a delicate interplay of extracellular signals, cell membrane receptors and intracellular signal messengers. It is well known that cell adhesion molecules (cell-cell and cell-extracellular matrix) play a critical role in these processes. Particularly, adherens junctions (AJs) mediated by E-cadherin and catenins determine cell-cell contact survival and epithelia function. Consequently, this review seeks to encompass the complex and prolific knowledge about E-cadherin roles during physiological and pathological states, particularly focusing on the influence exerted by the thyroid hormone (TH).     

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome Proceeds Via High Specificity

Comprehensive analysis of the complex nature of the Human Leukocyte Antigen (HLA) class II ligandome is of utmost importance to understand the basis for CD4⁺ T cell mediated immunity and tolerance. Here, we implemented important improvements in the analysis of the repertoire of HLA-DR-presented peptides, using hybrid mass spectrometry-based peptide fragmentation techniques on a ligandome sample isolated from matured human monocyte-derived dendritic cells (DC). The reported data set constitutes nearly 14 thousand unique high-confident peptides, i.e. the largest single inventory of human DC derived HLA-DR ligands to date. From a technical viewpoint the most prominent finding is that no single peptide fragmentation technique could elucidate the majority of HLA-DR ligands, because of the wide range of physical chemical properties displayed by the HLA-DR ligandome. Our in-depth profiling allowed us to reveal a strikingly poor correlation between the source proteins identified in the HLA class II ligandome and the DC cellular proteome. Important selective sieving from the sampled proteome to the ligandome was evidenced by specificity in the sequences of the core regions both at their N- and C- termini, hence not only reflecting binding motifs but also dominant protease activity associated to the endolysosomal compartments. Moreover, we demonstrate that the HLA-DR ligandome reflects a surface representation of cell-compartments specific for biological events linked to the maturation of monocytes into antigen presenting cells. Our results present new perspectives into the complex nature of the HLA class II system and will aid future immunological studies in characterizing the full breadth of potential CD4⁺ T cell epitopes relevant in health and disease.Human Leukocyte Antigen (HLA)¹ class II molecules on professional antigen presenting cells such as dendritic cells (DC) expose peptide fragments derived from exogenous and endogenous proteins to be screened by CD4⁺ T cells (1, 2). The activation and recruitment of CD4⁺ T cells recognizing disease-related peptide antigens is critical for the development of efficient antipathogen or antitumor immunity. Furthermore, the presentation of self-peptides and their interaction with CD4⁺ T cells is essential to maintain immunological tolerance and homeostasis (3). Knowledge of the nature of HLA class II-presented peptides on DC is of great importance to understand the rules of antigen processing and peptide binding motifs (4), whereas the identity of disease-related antigens may provide new knowledge on immunogenicity and leads for the development of vaccines and immunotherapy (5, 6).Mass spectrometry (MS) has proven effective for the analysis HLA class II-presented peptides (4, 7, 8). MS-based ligandome studies have demonstrated that HLA class II molecules predominantly present peptides derived from exogenous proteins that entered the cells by endocytosis and endogenous proteins that are associated with the endo-lysosomal compartments (4). Yet proteins residing in the cytosol, nucleus or mitochondria can also be presented by HLA class II molecules, primarily through autophagy (9–11). Multiple studies have mapped the HLA class II ligandome of antigen presenting cells in the context of infectious pathogens (12), autoimmune diseases (13–17) or cancer (14, 18, 19), or those that are essential for self-tolerance in the human thymus (3, 20). Notwithstanding these efforts, and certainly not in line with the extensive knowledge on the HLA class I ligandome (21), the nature of the HLA class II-presented peptide repertoire and particular its relationship to the cellular source proteome remains poorly understood.To advance our knowledge on the HLA-DR ligandome on activated DC without having to deal with limitations in cell yield from peripheral human blood (12, 21, 22) or tissue isolates (3), we explored the use of MUTZ-3 cells. This cell line has been used as a model of human monocyte-derived DCs. MUTZ-3 cells can be matured to act as antigen presenting cells and express then high levels of HLA class II molecules, and can be propagated in vitro to large cell densities (23–25). We also evaluated the performance of complementary and hybrid MS fragmentation techniques electron-transfer dissociation (ETD), electron-transfer/higher-energy collision dissociation (EThcD) (26), and higher-energy collision dissociation (HCD) to sequence and identify the HLA class II ligandome. Together this workflow allowed for the identification of an unprecedented large set of about 14 thousand unique peptide sequences presented by DC derived HLA-DR molecules, providing an in-depth view of the complexity of the HLA class II ligandome, revealing underlying features of antigen processing and surface-presentation to CD4⁺ T cells.     

Fecundity of fishes inhabiting coastal and estuarine environments in the southwest Atlantic Ocean

The aim of this study was to estimate the fecundity of six marine fish species from the southwest Atlantic off the coast of São Paulo State, Brazil. In particular, the number of oocytes in the most advanced vitellogenic stage (NDO), batch fecundity and the number of batches that will be produced were estimated. Specimens of longfinger anchovy Anchoa filifera, atlantic anchoveta Cetengraulis edentulus, bay whiff Citharichthys spilopterus, Stellifer brasiliensis, rake stardrum S. rastrifer and southern kingcroaker Menticirrhus americanus were captured bimonthly, from June (2012) to May (2013). The mature ovaries were removed, weighed, fixed in formalin solution and histologically analysed. All histological sections were photographed and the images analysed using advanced image processing techniques. The estimated number of batches that will be recruited to the germinal vesicle migration/hydrated stock ranged from one to four batches. NDO is positively related to ovarian and female size. Small females with low ovary weight produce low NDO. The NDO in A. filifera, C. edentulus and M. americanus may represent the final number of oocytes to be spawned in the next spawning event, which could be used for batch fecundity estimation. This study contributes to a better understanding of the reproduction of species inhabiting shrimp fishery grounds which are caught as by-catch in tropical and subtropical ecosystems. Information on the maturity and fecundity of these populations is an important element in assessing stock status and the degree of fishing pressure these populations are experiencing.     

Stress responses of the sea cucumber Holothuria forskali during aquaculture handling and transportation

Animal welfare during handling and transportation to aquaculture facilities or public aquaria is commonly estimated by addressing injury and mortality levels. Although these procedures have been optimized for different species, data on individual species’ cellular capabilities to tolerate stress are still scarce. In the present study, several biomarkers related with oxidative stress and energy metabolism were assessed in Holothuria forskali during animal acclimation, pre-transport, transport and quarantine. Combined analyses confirmed that sea cucumbers experienced high oxidative stress during transport, but had the capability to deal with it using a complex of cellular defence mechanisms, which enabled recovery from oxidative stress without permanent damage. Through a better understanding of individual species and the development of optimal parameters, this approach has the potential to improve animal wellbeing during and after acclimation, transportation and recovery processes.     

Beauty before age: landscape factors influence bird functional diversity in naturally regenerating fragments,but regeneration age does not

Effective ecological restoration actions should be able to recover ecosystem processes that influence community development in the long term. However, there is scarce information on how landscape factors promote or accelerate fauna recovery. We used a landscape framework to evaluate how functional groups respond to natural regeneration in a highly fragmented region of Atlantic Forest. Using bird functional groups sampled in 15 regenerating forest fragments, we built and ranked models using a model selection approach to test the relative effect of landscape variables on each group. Our results showed that bird community recovery is not determined by the duration of the regeneration process (i.e. forest age), but by how the species responds to the landscape context. Functional diversity and the abundance of the functional groups were mainly related to composition metrics, whereas the functional metric affected only specific groups. Our findings highlight the importance of considering the landscape level to ensure both the colonization of fauna and the restoration of ecological functions.     

Multiparametric magnetic resonance imaging-guided salvage radiotherapy in prostate cancer

AimTo analyse the efficacy and toxicity of postprostatectomy SRT in patients with a BCR evaluated with mpMRI.BackgroundMultiparametric magnetic resonance imaging (mpMRI) has the ability to detect the site of pelvic recurrence in patients with biochemical recurrence (BCR) after radical prostatectomy (RP). However, we do not know the oncological outcomes of mpMRI-guided savage radiotherapy (SRT).ResultsLocal, lymph node, and pelvic bone recurrence was observed in 13, 4 and 2 patients, respectively. PSA levels were significantly lower in patients with negative mpMRI (0.4 ng/mL [0.4]) vs. positive mpMRI (2.2 ng/mL [4.1], p = 0.003). Median planning target volume doses in patients with visible vs. non-visible recurrences were 76 Gy vs. 70 Gy. Overall, mean follow-up was 41 months (6–81). Biochemical relapse-free survival (bRFS) at 3 years was 82.3% and 82.5%, respectively, for the negative and positive mpMRI groups (p = 0.800). Three-year rates of late grade ≥2 urinary and rectal toxicity were 14.8% and 1.9%, respectively; all but one patient recovered without sequelae.ConclusionSRT to the macroscopic recurrence identified by mpMRI is a feasible and well-tolerated option. In this study, there were no differences in bRFS between MRI-positive and MRI-negative patients, indicating effective targeting of MRI-positive lesions.