Revealing missing human protein isoforms based on Ab initio prediction, RNA-seq and proteomics

Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.publishedVersio

Derivation of an endogenous small RNA from double-stranded Sox4 sense and natural antisense transcripts in the mouse brain

Natural antisense transcripts (NATs) are involved in cellular development and regulatory processes. Multiple NATs at the Sox4 gene locus are spatiotemporally regulated throughout murine cerebral corticogenesis. In the study, we evaluated the potential functional role of Sox4 NATs at Sox4 gene locus. We demonstrated Sox4 sense and NATs formed dsRNA aggregates in the cytoplasm of brain cells. Over expression of Sox4 NATs in NIH/3T3 cells generally did not alter the level of Sox4 mRNA expression or protein translation. Upregulation of a Sox4 NAT known as Sox4ot1 led to the production of a novel small RNA, Sox4_sir3. Its biogenesis is Dicer1-dependent and has characteristics resemble piRNA. Expression of Sox4_sir3 was observed in the marginal and germinative zones of the developing and postnatal brains suggesting a potential role in regulating neurogenesis. We proposed that Sox4 sense-NATs serve as Dicer1-dependent templates to produce a novel endo-siRNA- or piRNA-like Sox4_sir3

In depth analysis of the Sox4 gene locus that consists of sense and natural antisense transcripts

SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1] and [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense transcript known as Sox4ot1

The importance of herbicde application time for succesfull weed control in maize

The studies of different herbicide treatment effects on weeds in maize have been carried out worldwide for more than 30 years. But, there is still a lack of studies on the optimization of the herbicide application time. Herbicide efficacy is especially unpredictable when the chemical treatment is incorporated as one of measures within the cropping technology practices. The performance of pre - emergence herbicides is affected by many factors, but rainfall and soil moisture have the greatest impact. In the central part of Serbia, the weather conditions are often characterised by a small amount of precipitation during early spring, so the application of pre - emergence herbicides usually does not provide good control. This is one of the reasons why in recent times post - emergence treatments have dominated. The investigations were conducted at the MRI Zemun Polje, Belgrade during 2014-2016. The field trial was established as a RCB in a split - split plot arrangement, with four replications and with the aim to examine how time of the herbicide application - A) pre - emergence mix for grasses and broadleaf weeds of s - metolachlor + mesotrione, B) post - emergence mix of mesotrione + nicosu Ifuron and C) untreated control, affects weed infestation of maize trough the herbicide efficacy evaluation. Maize was cultivated with the application of N fertiliser in two forms (standard urea and slow release urea with urease inhibitor), and two row spacing of 50 cm and 70 cm, with density of 59.500 plants per ha and 83.333 plants per ha, respectively. Herbicides were applied with hand - held sprayer calibrated to deliver 15 I at 300 kPa ( 3 bar ) with a flat - fan nozzle (Teejet , 1.4 mm E 04-80). Three and six weeks after each herbicide application, the fresh biomass of uprooted weeds from 1 m² was measured, and coefficients of efficacy were calculated. The data were transformed from % by the formula ASIN(SQRT(V7/100))*(180/3,4159265) and statistically processed by ANOVA, and analysed by the LSD - test ( 5 % ).The meteorological conditions differed during the growing seasons of the experiment. The 2015 growing season was characterised by drought, with a higher average temperature (21.1'C) and a low amount of precipitation (285.4 mm.) Other two seasons, 2014 and 2016, were favourable and an exceptionally high amount of precipitation was recorded in 2014 (almost twice higher than in 2015 and 2016). Results showed that herbicide treatments were more efficient during the first evaluation 96.56% for pre - emergence and 97.52% for post emergence treatment, and significantly influenced by the year (P - 0.02*) and the time of application (P - 0.00**) in the second evaluation, herbicide efficacy was in average a slightly lower, 92.07% for pre emergence and 91.44% for post - emergence treatment, and significantly affected by the time of herbicide application (P - 0.00**) and some interactions - year x time of herbicide application , nitrogen form x row spacing and time of herbicide application x row spacing. The highest efficacy of herbicide treatments was obtained in the first evaluation in 2016 - 99.54% for pre - emergence and 99.60% for post - emergence treatment and with the application of standard urea and pre - emergence herbicides , in both row spacing - 99.39% and 99.02 %, respectively According to obtained results, the time of herbicide application has no significant influence on their efficacy in maiz , especially when a herbicide is incorporated as one of measures within the crop growing system

Prinos suve mase kukuruza u različitim sistemima gajenja useva

Proučavanja sistema proizvodnje kukuruza su uglavnom bila usmerena na računavanje gubitaka prinosa kao posledice delovanja mnogih faktora , uključujući i konkurenciju korova ( Simiâ i sar , 2012 ) . Savremeni pristupi poljoprivrednoj proizvodnji podrazumevaju integrisanu primenu različitih mera gajenja u okviru ekološki zasnovane tehnologije ( Hendrickson et al . , 2008 ). Cil istraživanja bio je da se ispita i uporedi razvoj i proizvodnja biomase hibrida kukuruza novije generacije gajenog na standardnom ( 70 ) cm i užem međurednom rastojanju ( 50 cm ) sa hemijskim suzbijanjem korova pre i posle nicanja Ogled je izveden u Institutu za kukuruz Beograd , u periodu 2014-2016 . godine . Novostvoreni hibrid kukuruza 311 388 gajen je na međurednom rastojanju od 50 cm i 70 cm ( 39.500 i 83.333 biljaka ha ' ) . Primena herbicida podrazumevala je : tretiranje pre nicanja kombinacijom S - metodahlora + mezotriona ( 960 g ha +120 g ha am ) . Tretiranje posle nicana kombinacijom nikosulfuron + me triona ( 40 g ha-1 + 120 g ha-1 am ) i kontrolu . Šest nedelja posle primene heribicida , suva masa cele biljke kukuruza je merena i preračunata po m² . Za analizu podataka korišćena je ANOVA. Suva masa kukuruza bila je , u proseku , značajno viša u 2015. ( 154,69 g m² ) i 2016 godini ( 153,54 g m-2 ) nego u 2014. ( 110,92 g m -2 ) . Kukuruz je imao veću suvu masu biljaka u tretmanu posle nicanja ( + 28,19 % na 50 cm i + 39,45 % na 70 cm ) u odnosu na tretman pre nicanja kukuruza i kontrolu . Gajenje kukuruza u međurednom rastojanju od 50 cm doprinelo je proizvodnji veće prosečne cu suve mase u svim godinama ispitivanja u odnosu na konvencionalno gajenje kukuruza u međurednom rastojanju od 70 cm , što je i za očekivati s obzorom na veću gustinu useva u ovom tretmanu . Statistička analiza je pokazala da je interakcija svih faktora - godina , primena heribicida i međuredno rastojanje - značajno uticala na proizvodnju suve mase bilke u prvom delu vegetacionog perioda kukuruza . Tehnologiju gajenja kukuruza treba da čine pažljivo odabrane i pravilno kombinovane mere . Novostvoreni hibridi mogu uspevati i u manjem međurednom rastojanju(veći broj biljaka po jedinici površine) sa primenom herbicida posle nicanja kukuruza

Maize response to weed interference under changed production technology

Weeds interfere with the utilization of resources and thus adversely affect https://www. sciencedirect.com/topics/agricultural-and-biological-sciences/crop-production. Intensity of their interference is especially important during stages when yield is being determined. Weed species differently response to herbicides and this may reflect differences in selection pressure caused by a cropping system. Under changed row space of maize and plant density, weed abundance and biomass production are also different. Fertilizer application and soil fertility have a definite influence on weed diversity and growth, and maize leaf area index, harvest index and yield. The investigations were conducted in the MRI Zemun Polje, Belgrade, Serbia during 2014-2016. Nitrogen fertilizer was applied in two forms: standard urea and slow realize urea with ureaze inhibitor, applied at maize stage BBCH 05. Herbicides mix for grasses and broadleaf weeds were applied pre-emergence (s-metolachlor + mesotrione) and post-emergence (nicosulfuron + mesotrione). Maize was sown with row space of 50 cm and 70 cm - 59.500 and 83.333 plants per ha, respectively. Three weeks after herbicide application, dry matter was measured from uprooted weeds from 1 m2 randomly selected in each elementary plot. Maize parameters – LAI, HI and grain yield were evaluated when plants fully matured. The data were processed by ANOVA. Weed dry matter was highly dependent on the year and time of herbicide application, as well as of some interactions: year x urea form, year x herbicide application and year x urea form x herbicide application. Differences in average weed dry matter between urea forms and maize row space were not noticeable. The lowest weed dry matter was obtained after post-emergence herbicide application (5.01 g m-2). Based on the correlation analysis, weeds very significantly and negatively influences leaf area index (R2 = - 0.524), harvest index (R2 = - 0.598) and grain yield of maize (R2 = - 0.688

Acute poisonings by household bleaching agents

ISEE/ISEA 2006 Conference, 2006, Paris, Franc