Analysis of cell cycle in root meristems

We have analyzed the cell proliferation in a meristem assuming a single file model for root architecture. The meristem file appears to be built up by two clearly separated zones: the first going from the initial cell to the middle of the meristem and the second from the middle to the meristem boundary. The first half of the meristem shows an exponential age distribution for the cell population. In contrast, in the second half of the meristem, the cell kinetics of cycling cells strongly disagree with exponential kinetics and due to the compensation between the observed deviations in both halves, cell supply in the file meristem is in line with linear kinetics. However, we proposed that exponential kinetic equations offer a suitable approach to problems of cell cycle compartments and population age distributions in real meristems, where non-cycling cells cannot be identified inside the meristem, whether we consider the meristem as a whole or study a “window” inside it. Nevertheless, for more exact kinetic analysis, when estimating the proliferative fraction, the width of the “window” and its location along the axis must carefully be taken into account.     

Is diversionary feeding a useful tool to avoid human-ungulate conflicts? A case study with the aoudad

Diversionary feeding (i.e. supplementary feeding used to mitigate damage to human activities) is a management tool widely employed to avoid human-wildlife conflicts, which could alter the spatial behaviour of target species and can also affect other species present in the area, among other effects. We evaluated the effect of diversionary feeding in the spatial behaviour of the aoudad (Ammotragus lervia), an exotic ungulate associated with crop damage in the area, and we assessed the use of diversionary feeding stations (DFS) by non-target species. Nine aoudads were tracked with GPS/GSM collars. We compared their core home ranges and number of GPS locations in the DFS before and meanwhile food was available on them. Eight DFS were monitored with cameras to identify which species used the feeding sites. The home ranges changed for some individuals, but this variation was not related to supplementary feeding. Just five out of the nine tracked aoudads used DFS, and the number of GPS locations in the DFS by aoudad increased when food was available. DFS were used by fifteen non-target species of birds and mammals, and especially by the wild boar. Aoudads and wild boars segregated temporally but not spatially in their use of the DFS. Our study suggests that diversionary feeding had a limited effect on the spatial behaviour of the aoudad, suggesting that its effectiveness to reduce crop damage may be restricted.     

Daily Activity Patterns and Thermal Tolerance of Three Sympatric Dung Beetle Species (Scarabaeidae: Scarabaeinae: Eucraniini) from the Monte Desert,Argentina

Tolerance to extreme temperatures, thermal limits, and the mechanisms of thermoregulation are related to internal functions of insects and partly define their ecological niche. We study the association between daily activity of dung beetles from the Monte Desert in Argentina and their tolerance to high temperatures. Results indicate that for all three sympatric species studied, Eucranium belenae Ocampo, Anomiopsoides cavifrons (Burmeister), and Anomiopsoides fedemariai Ocampo, daily activity is associated to ground temperature. Eucranium belenae is active when ground temperature is relatively low and it is less tolerant to long periods of activity at high temperatures in the lab, while A. cavifrons and A. fedemariai are active when ground temperatures are higher, and they tolerate high temperatures for longer periods of time than E. belenae in the lab. These species coexist and use similar food sources, and this eco-physiological study may help to explain how they differentiate under the same environmental conditions. The Monte Desert is considered an extreme environment, and studies on thermal tolerance offer testable predictions to understand how species would respond to climate change.     

Gonad characterization and reproductive seasonality in Siphonaria lessonii (Gastropoda: Heterobranchia) from the southwestern Atlantic Ocean

Histological characterization of the hermaphroditic gonad (HG) and seasonality of gametogenesis were investigated in a population of Siphonaria lessonii from the coast of Buenos Aires Province (37°16′S, 56°58′W). Monthly analysis of the frequency of gametogenic stages, as well as the number and mean size of oocytes, were used to determine reproductive events over a 2‐year period (June 2012–May 2014). Female and male gametes were observed simultaneously within acini of adult individuals and continuously throughout the period studied. Oogenesis commenced in the beginning of austral autumn, with gonads characterized mainly by proliferation of female cells. From this moment, oocytes gradually increased in number and area until spring, when a large number of individuals were found in the evacuation stage. The same trend was observed from early gonad maturation to advanced stages, indicating that gonad development was closely related to the frequency of oocyte stages and to the area (size) of oocytes. Spermatogenesis was also observed as a continuous process throughout the year, although spent acini were more frequent from November until February. Reproductive seasonality and gametogenesis were associated with changes in temperature and day length.     

Relationship between land uses and diversity of dung beetles (Coleoptera: Scarabaeinae) in the southern Atlantic forest of Argentina: which are the key factors?

The loss of natural habitats is one of the main drivers of biodiversity decline. Anthropogenic land uses preserving biotic and abiotic conditions of the native ecosystem are more suitable to preserve the native biodiversity. In this study, we explored changes in species richness and composition in different land uses of the southern Atlantic forest, considering three independent factors: (1) canopy (presence–absence), (2) type of vegetation (native–exotic) and (3) livestock (presence–absence). We expected a gradient of response in the richness and composition of the native forest dung beetle community, from land uses preserving canopy and native vegetation to open land uses with exotic vegetation. Dung beetles were sampled in protected native forests and four land uses, using two potential food resources: human dung and carrion. The species richness and composition of each habitat, as well as differences in composition and the influence of factors over diversity, were then analyzed. As expected, our results showed that land uses preserving canopy and native vegetation maintain the dung beetle diversity of the native forest. Moreover, while the three factors analyzed influenced dung beetle diversity, canopy cover was the main driver of dung beetle diversity loss. The main conclusion of this study is that the conservation of canopy (either native or exotic) is determinant to preserve highly diverse dung beetle communities and subsequently, the ecological functions performed by this taxon. However, the ecophysiological mechanism behind the response of dung beetles to habitat disturbance is poorly understood.     

Low‐gluten,nontransgenic wheat engineered with CRISPR/Cas9

Coeliac disease is an autoimmune disorder triggered in genetically predisposed individuals by the ingestion of gluten proteins from wheat, barley and rye. The α‐gliadin gene family of wheat contains four highly stimulatory peptides, of which the 33‐mer is the main immunodominant peptide in patients with coeliac. We designed two sgRNAs to target a conserved region adjacent to the coding sequence for the 33‐mer in the α‐gliadin genes. Twenty‐one mutant lines were generated, all showing strong reduction in α‐gliadins. Up to 35 different genes were mutated in one of the lines of the 45 different genes identified in the wild type, while immunoreactivity was reduced by 85%. Transgene‐free lines were identified, and no off‐target mutations have been detected in any of the potential targets. The low‐gluten, transgene‐free wheat lines described here could be used to produce low‐gluten foodstuff and serve as source material to introgress this trait into elite wheat varieties.     

Analysis of significant protein abundance from multiple reaction-monitoring data

Background

Discovering reliable protein biomarkers is one of the most important issues in biomedical research. The ELISA is a traditional technique for accurate quantitation of well-known proteins. Recently, the multiple reaction-monitoring (MRM) mass spectrometry has been proposed for quantifying newly discovered protein and has become a popular alternative to ELISA. For the MRM data analysis, linear mixed modeling (LMM) has been used to analyze MRM data. MSstats is one of the most widely used tools for MRM data analysis that is based on the LMMs. However, LMMs often provide various significance results, depending on model specification. Sometimes it would be difficult to specify a correct LMM method for the analysis of MRM data. Here, we propose a new logistic regression-based method for Significance Analysis of Multiple Reaction Monitoring (LR-SAM).

Results

Through simulation studies, we demonstrate that LMM methods may not preserve type I error, thus yielding high false- positive errors, depending on how random effects are specified. Our simulation study also shows that the LR-SAM approach performs similarly well as LMM approaches, in most cases. However, LR-SAM performs better than the LMMs, particularly when the effects sizes of peptides from the same protein are heterogeneous. Our proposed method was applied to MRM data for identification of proteins associated with clinical responses of treatment of 115 hepatocellular carcinoma (HCC) patients with the tyrosine kinase inhibitor sorafenib. Of 124 candidate proteins, LMM approaches provided 6 results varying in significance, while LR-SAM, by contrast, yielded 18 significant results that were quite reproducibly consistent.

Conclusion

As exemplified by an application to HCC data set, LR-SAM more effectively identified proteins associated with clinical responses of treatment than LMM did.

     

Extensive analysis of 40 infertile patients with congenital absence of the vas deferens: in 50% of cases only one CFTR allele could be detected

Mutations in the cystic fibrosis (CF) conductance transmembrane regulator (CFTR) gene have been detected in patients with CF and in males with infertility attributable to congenital bilateral absence of the vas deferens (CBAVD). Thirty individuals with CBAVD and 10 with congenital unilateral absence of the vas deferens (CUAVD) were analyzed by single-strand conformation analysis and denaturing gradient gel electrophoresis for mutations in most of the CFTR gene. All 40 individuals were pancreatic sufficient, but twenty patients had recurrent or sporadic respiratory infections, asthma/asthmatic bronchitis, and/or rhino-sinusitis. Agenesia or displasia of one or both seminal vesicles was detected in 30 men and other urogenital malformations were present in six subjects. Among the 40 samples, we identified 13 different CFTR mutations, two of which were previously unknown. One new mutation in exon 4 was the deletion of glutamic acid at codon 115 (E115). A second new mutation was found in exon 17b, viz., an AC substitution at position 3311, changing lysine to threonine at codon 1060 (K1060T). CFTR mutations were detected in 22 out of 30 (73.3%) CBAVD patients and in one out of 10 (10%) CUAVD individuals, showing a significantly lower incidence of CFTR mutations in CBAVD/CUAVD patients (P 0.0001), compared with that found in the CF patient population. Only three CBAVD patients were found with more than one CFTR mutation (F508/L206W, F508/R74W+D1270N, Rl 17H/712-1GT), highlighting L206W, R74W/ D1270N, and R117H as benign CF mutations. Sweat electrolyte values were increased in 76.6% of CBAVD patients, but three individuals without CFTR mutations had normal sweat electrolyte levels (10% of the total CBAVD patients), suggesting that factors other than CFTR mutations are involved in CBAVD. The failure to identify a second mutation in exons and their flanking regions of the CFTR gene suggests that these mutations could be located in introns or in the promoter region of CFTR. Such mutations could result in CFTR levels below the minimum 6%–10% necessary for normal protein function.