Toward unraveling biogenesis of Dicer-independent priRNAs and siRNAs in Schizosaccharomyces pombe

RNA interference (RNAi) is a highly conserved process of gene silencing in which Argonaute family proteins are guided by small RNA molecules to complementary targets. In the fission yeast Schizosaccharomyces pombe, RNAi is required for heterochromatin formation at centromeres. Although it seems counterintuitive, pericentromeric heterochromatin in fission yeast is transcribed. The transcripts are processed by RNAi machinery, which is in turn guided back to the pericentromeric repeats by sequence complementarity of the Argonaute-bound small interfering RNA (siRNA) and the nascent transcript. This generates a positive-feedback loop of siRNA amplification that recruits factors required for the assembly of heterochromatin. Previously, it was suggested that a fission yeast class of Dicer-independent small RNAs called primal small RNAs (priRNAs) initiates the positive-feedback loop of siRNA generation and heterochromatin assembly. However, the biogenesis of priRNAs as well as of Dicer-independent small RNAs from other organisms was not well understood. The results presented here identify Triman, a novel 3’-5’ exonuclease that is involved in the final step of biogenesis of both priRNAs and siRNAs in fission yeast. It was observed that Argonaute binds longer priRNA and siRNA precursors from the total RNA fraction. This is followed by the recruitment of Triman to trim 3’ ends of Argonaute-bound small RNAs to the mature size. The final trimming of priRNAs and siRNAs is required for de novo heterochromatin formation at centromeres and the mating-type locus as well as for the maintenance of facultative heterochromatin islands. Furthermore, it was shown that in cells lacking Rrp6, a nuclease subunit of the exosome, RNAi targets various genes across the yeast genome. This demonstrated that the exosome protects the genome against aberrant RNAi. Spurious RNAi targeting in rrp6∆ cells at majority of loci occurs via accumulation of antisense transcripts that are processed into priRNAs in a Triman-dependent manner. These results suggest that Argonaute association with cellular degradation products which are processed into priRNAs might serve as a surveillance mechanism to guard the genome against invading genomic elements (Marasovic et al. 2013)

Overview and perspective of nonwoven agrotextile

Agrotextile belongs to one of the twelve sectors of technical textiles covering textile products with application in agriculture, horticulture, cattle breeding and aquaculture as well in agro engineering. The significance of agrotextiles can be stated substantial all over the world since it has been proven to be very versatile and cost effective materials. Nonwoven agrotextiles are innovative products with special structural performances designed for agricultural applications and practices such as weed control, wind protection, frost cover fabric that is used for adjustment of weather conditions from the sudden changing of temperature and seasonal changes. Furthermore, common application of nonwoven agrotextiles are for reducing the sun radiation as well as thermal protection of plants as shade cloth, furthermore for preventing insect and other pests on crops, preventing soil drainage and sediment creation. All over the world, applications of nonwoven agrotextiles products in agriculture have shown great positive impacts on growth, production and protection of various crops and vegetables. Many studies have been proving that nonwoven agrotextile covers accelerate the growth and development of seedlings as well as their nutritive values. By preventing weed growth and insect protection, the use of herbicides and pesticides are reduced. Agrotextiles made of natural fibres can be considered as a potential candidate for replacing some of today’s popular synthetic agrotextiles which are becoming ecologically less acceptable nowadays.Usage of agrotextiles is one of the growing alternatives in today’s context with respect to the increase in global population thus food quantity and food quality and in the same time growing environmental concern. Sustainable socio-economic development considers natural fibre usage in agrotextile production in all possible areas covered by agrotextile application. The main purpose of the review is to give an overview and importance of nonwoven agrotextiles with indication of nonwoven agrotextile perspective in future

Deep Learning With Sentiment Inference For Discourse-Oriented Opinion Analysis

Opinions are omnipresent in written and spoken text ranging from editorials, reviews, blogs, guides, and informal conversations to written and broadcast news. However, past research in NLP has mainly addressed explicit opinion expressions, ignoring implicit opinions. As a result, research in opinion analysis has plateaued at a somewhat superficial level, providing methods that only recognize what is explicitly said and do not understand what is implied. In this dissertation, we develop machine learning models for two tasks that presumably support propagation of sentiment in discourse, beyond one sentence. The first task we address is opinion role labeling, i.e.\ the task of detecting who expressed a given attitude toward what or who. The second task is abstract anaphora resolution, i.e.\ the task of finding a (typically) non-nominal antecedent of pronouns and noun phrases that refer to abstract objects like facts, events, actions, or situations in the preceding discourse. We propose a neural model for labeling of opinion holders and targets and circumvent the problems that arise from the limited labeled data. In particular, we extend the baseline model with different multi-task learning frameworks. We obtain clear performance improvements using semantic role labeling as the auxiliary task. We conduct a thorough analysis to demonstrate how multi-task learning helps, what has been solved for the task, and what is next. We show that future developments should improve the ability of the models to capture long-range dependencies and consider other auxiliary tasks such as dependency parsing or recognizing textual entailment. We emphasize that future improvements can be measured more reliably if opinion expressions with missing roles are curated and if the evaluation considers all mentions in opinion role coreference chains as well as discontinuous roles. To the best of our knowledge, we propose the first abstract anaphora resolution model that handles the unrestricted phenomenon in a realistic setting. We cast abstract anaphora resolution as the task of learning attributes of the relation that holds between the sentence with the abstract anaphor and its antecedent. We propose a Mention-Ranking siamese-LSTM model (MR-LSTM) for learning what characterizes the mentioned relation in a data-driven fashion. The current resources for abstract anaphora resolution are quite limited. However, we can train our models without conventional data for abstract anaphora resolution. In particular, we can train our models on many instances of antecedent-anaphoric sentence pairs. Such pairs can be automatically extracted from parsed corpora by searching for a common construction which consists of a verb with an embedded sentence (complement or adverbial), applying a simple transformation that replaces the embedded sentence with an abstract anaphor, and using the cut-off embedded sentence as the antecedent. We refer to the extracted data as silver data. We evaluate our MR-LSTM models in a realistic task setup in which models need to rank embedded sentences and verb phrases from the sentence with the anaphor as well as a few preceding sentences. We report the first benchmark results on an abstract anaphora subset of the ARRAU corpus \citep{uryupina_et_al_2016} which presents a greater challenge due to a mixture of nominal and pronominal anaphors as well as a greater range of confounders. We also use two additional evaluation datasets: a subset of the CoNLL-12 shared task dataset \citep{pradhan_et_al_2012} and a subset of the ASN corpus \citep{kolhatkar_et_al_2013_crowdsourcing}. We show that our MR-LSTM models outperform the baselines in all evaluation datasets, except for events in the CoNLL-12 dataset. We conclude that training on the small-scale gold data works well if we encounter the same type of anaphors at the evaluation time. However, the gold training data contains only six shell nouns and events and thus resolution of anaphors in the ARRAU corpus that covers a variety of anaphor types benefits from the silver data. Our MR-LSTM models for resolution of abstract anaphors outperform the prior work for shell noun resolution \citep{kolhatkar_et_al_2013} in their restricted task setup. Finally, we try to get the best out of the gold and silver training data by mixing them. Moreover, we speculate that we could improve the training on a mixture if we: (i) handle artifacts in the silver data with adversarial training and (ii) use multi-task learning to enable our models to make ranking decisions dependent on the type of anaphor. These proposals give us mixed results and hence a robust mixed training strategy remains a challenge

Contribution a la connaissance d'une Poussee extraordinaire d' algues unicellulaires (Adriatique Septentrionale)

The phenomenon known as "sea-water bloom" ("mare sporco", "Meeresbliite") was observed in the northern Adriatic in summer 1983. It appears as a gelatinous, dense mass floating at the sea surface. Samples from Crikvenica (July) and Lopar, Rab Island (August) were analysed. A total of 58 diatoms, of which 32 benthic species, 25 dinoflagellates and 10 coccolithophorids were identified by microscopy. A recently described genus, Spatulodinium Cachon & Cachon, represented by the type species S. pseudonoctiluca (Pouchet) Cachon & Cachon, was also found. With respect to the known ecology of individual algal groups it may be concluded that benthic diatoms had reproduced intensively at the sea bottom a long while before the phenomenon became visible at the sea surface. Reproduction is also the period of the most intensive secretion of mucus. Release of the gelatinous mass from the sea bottom at summer temperatures which are unfavourable for diatoms, is actually the end of the bloom. A gelatinous mass full of gases released by bacterial degradation begins to ascend and on its way towards the sea surface, it embeds plankton organisms. In the final stage torn mucus descends to the bottom where it is gradually completely degraded.peer-reviewe

Toward unraveling biogenesis of Dicer-independent priRNAs and siRNAs in Schizosaccharomyces pombe

RNA interference (RNAi) is a highly conserved process of gene silencing in which Argonaute family proteins are guided by small RNA molecules to complementary targets. In the fission yeast Schizosaccharomyces pombe, RNAi is required for heterochromatin formation at centromeres. Although it seems counterintuitive, pericentromeric heterochromatin in fission yeast is transcribed. The transcripts are processed by RNAi machinery, which is in turn guided back to the pericentromeric repeats by sequence complementarity of the Argonaute-bound small interfering RNA (siRNA) and the nascent transcript. This generates a positive-feedback loop of siRNA amplification that recruits factors required for the assembly of heterochromatin. Previously, it was suggested that a fission yeast class of Dicer-independent small RNAs called primal small RNAs (priRNAs) initiates the positive-feedback loop of siRNA generation and heterochromatin assembly. However, the biogenesis of priRNAs as well as of Dicer-independent small RNAs from other organisms was not well understood. The results presented here identify Triman, a novel 3’-5’ exonuclease that is involved in the final step of biogenesis of both priRNAs and siRNAs in fission yeast. It was observed that Argonaute binds longer priRNA and siRNA precursors from the total RNA fraction. This is followed by the recruitment of Triman to trim 3’ ends of Argonaute-bound small RNAs to the mature size. The final trimming of priRNAs and siRNAs is required for de novo heterochromatin formation at centromeres and the mating-type locus as well as for the maintenance of facultative heterochromatin islands. Furthermore, it was shown that in cells lacking Rrp6, a nuclease subunit of the exosome, RNAi targets various genes across the yeast genome. This demonstrated that the exosome protects the genome against aberrant RNAi. Spurious RNAi targeting in rrp6∆ cells at majority of loci occurs via accumulation of antisense transcripts that are processed into priRNAs in a Triman-dependent manner. These results suggest that Argonaute association with cellular degradation products which are processed into priRNAs might serve as a surveillance mechanism to guard the genome against invading genomic elements (Marasovic et al. 2013)

Towards water literacy: an interdisciplinary analysis of standards for teaching and learning about humans and Water

Water is critical to sustain human existence. Water literacy involves understanding the interactions within and between natural and human dimensions of water systems to support informed decision-making, an important outcome for learners of all ages. It is therefore critical to foster water literacy in today’s global citizens, particularly through formal education. The purpose of this study, in tandem with a parallel study focusing on natural dimensions of water systems (Mostacedo-Marasovic et al., in press), is to examine water-related K-12 standards for teaching and learning about human dimensions of water systems to develop a comprehensive and transdisciplinary perspective on water education. Our overarching question is, “What do disciplinary standards specify as outcomes for students’ learning about water and humans?”. Our research questions are: i) “To what extent do these water-related standards address recognized domains of learning?” and ii) “What thematic outcomes for students’ learning are apparent across grades in these water-related standards?”. We use chi-square statistics and a conventional qualitative content analysis method complemented by processes from grounded theory to analyze water-related education standards (N = 341) from 12 education-oriented, governmental and non-governmental organizations based in the United States. Our results indicate that first, water-related standards emphasize the cognitive domain, including declarative and procedural knowledge. The affective domain and its social and emotional components are much less prevalent. Second, the water-related standards illustrate five categories which encompass human dimensions of water spanning K-12 grade bands, including human settlements; the nexus between water, food, and energy; public health; impacts of human activities on water quality and quantity; and water resources management. Overall, the study contributes to a more holistic and comprehensive perspective of water and human systems that can help inform teaching and learning to cultivate water literacy, including curriculum development and classroom pedagogy

El rol de los ciliados en la red trófica microbiana de la zona eutrófica de la bahía de Kaštela (Adriático central)

Interactions among phytoplankton, bacterioplankton, heterotrophic nanoflagellates (HNF), ciliated protozoa and copepod nauplii were studied in the eutrophicated part of Kas?tela Bay from May 1998 to November 1999. Special emphasis was placed on relationships between size categories of nonloricate ciliates (NLC) and other microbial food web components. Biomasses of phytoplankton and bacteria were primarily influenced by abiotic parameters. Temperature indirectly controlled variation in HNF biomass through the changes in biomass of bacteria and the smaller phytoplankton fraction. Besides HNF, bacterial biomass was affected by the NLCLas interacciones entre fitoplancton, bacterioplancton, nanoflagelados heterótrofos (HNF), ciliados y nauplios de copepodos fueron estudiadas en una zona eutrófica de la bahía de Kas?tela desde Mayo de 1998 hasta Noviembre de 1999. Se dedicó una atención especial a la relación entre distintas clases de tamaños de ciliados no loricados (NLC) y otros componentes de las redes tróficas microbianas. Las biomasas de fitoplancton y bacterioplancton estaban principalmente influenciadas por parámentros abióticos. La temperatura de forma indirecta controlaba la variación de la biomasa de HNF, a través de cambios en la biomasa bacteriana y de la fracción de menor tamaño de fitoplancton. Aparte de los nanoflagelados heterótrofos, la biomasa bacteriana estaba afectada por los NL

Vineyard protection with rain-shelter: relationships between radiometric properties of plastic covers and table grape quality

The rise of unpredictable, heavy rainfalls increases incidence of diseases, berry rot, berry cracking, and enhance the need for rain shelters. The influence of the type of rain shelter on microclimate and grape quality is still little explored. The aim of this trial was to investigate the radiometric properties of a new type of cover, its effect on vineyard microclimate and on table grape quality, as compared with a reference cover, during a vintage with unusually abundant precipitation for Southern Italy. The new cover was characterized by lower transmissivity to IRshort radiation, and by a very higher transmissivity to UV radiation. It showed a tendency to decrease air temperature by 1 °C, increase RH by 2–3%, reduce VPD, and improve vine water status with respect to the reference. At harvest, grapes covered with the new sheet had higher TSS concentration, TSS / TA ratio, total skin polyphenol and flavonoids content, and berry skin resistance to rupture. Those berries, moreover, increased the level of volatile compounds such as linalool, typical of ‘Italia’ muscat aroma, and terpineol

Sexual reproduction and two different encystment strategies of Lingulodinium polyedrum (Dinophyceae) in culture

Unreported aspects in the sexual cycle of the marine dinoflagellate Lingulodinium polyedrum (Stein) Dodge were described. Our observations included the description of two types of hypnozygote formation, because culture planozygotes were observed to encyst in two different ways: an ecdysal sexual stage or a spiny resting cyst. Phosphate deficiency was the main nutritional condition required for fusing gamete pairs to form resting cysts, whereas replete conditions prevented their appearance and favored the formation of ecdysal sexual forms. Mating experiments revealed the existence of two sexual types (+/−), which were enough to explain resting cyst appearance (simple heterothallism). Morphological aspects and timing of gamete mating, fusion, and the efficiency of encystment under different external levels of nitrate and phosphate were analyzed after isolating and monitoring individual pairs of fusing gametes. The staining of sexual stages showed that nuclear fusion was completed at the same time as the cytoplasmic fusion. After 1 to 2 h, the planozygotes presented one quadrolobulated nucleus. Germination of ecdysal sexual stages occurred after <24–72 h, whereas excystment of resting cysts was dependent on the studied parental cross and took place after 2–4 months. Newly germinated cells from both types of cysts had a similar, big, U-shaped nucleus. Twenty-four to 48 h after excystment, the germlings divided by desmoschisis, a process before which enlargement of the nucleus was observed.Postprin