Influence of Agronomic Practices on Crop Production

The ultimate goal of any farmer is to get maximum yield per unit area. To obtain high yield, effective crop management practices, appeared to be of paramount value. Crop production in Nigeria is faced with many challenges among which are: untimely planting, incorrect plant spacing, wrong method of planting, poor sowing depth, delayed weeding

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Abstract Background In Drosophila embryos, many biochemically and functionally unrelated transcription factors bind quantitatively to highly overlapping sets of genomic regions, with much of the lowest levels of binding being incidental, non-functional interactions on DNA. The primary biochemical mechanisms that drive these genome-wide occupancy patterns have yet to be established. Results Here we use data resulting from the DNaseI digestion of isolated embryo nuclei to provide a biophysical measure of the degree to which proteins can access different regions of the genome. We show that the in vivo binding patterns of 21 developmental regulators are quantitatively correlated with DNA accessibility in chromatin. Furthermore, we find that levels of factor occupancy in vivo correlate much more with the degree of chromatin accessibility than with occupancy predicted from in vitro affinity measurements using purified protein and naked DNA. Within accessible regions, however, the intrinsic affinity of the factor for DNA does play a role in determining net occupancy, with even weak affinity recognition sites contributing. Finally, we show that programmed changes in chromatin accessibility between different developmental stages correlate with quantitative alterations in factor binding. Conclusions Based on these and other results, we propose a general mechanism to explain the widespread, overlapping DNA binding by animal transcription factors. In this view, transcription factors are expressed at sufficiently high concentrations in cells such that they can occupy their recognition sequences in highly accessible chromatin without the aid of physical cooperative interactions with other proteins, leading to highly overlapping, graded binding of unrelated factors

Watershed-scale changes in terrestrial nitrogen cycling during a period of decreased atmospheric nitrate and sulfur deposition

AbstractRecent reports suggest that decreases in atmospheric nitrogen (N) deposition throughout Europe and North America may have resulted in declining nitrate export in surface waters in recent decades, yet it is unknown if and how terrestrial N cycling was affected. During a period of decreased atmospheric N deposition, we assessed changes in forest N cycling by evaluating trends in tree-ring δ15N values (between 1980 and 2010; n = 20 trees per watershed), stream nitrate yields (between 2000 and 2011), and retention of atmospherically-deposited N (between 2000 and 2011) in the North and South Tributaries (North and South, respectively) of Buck Creek in the Adirondack Mountains, USA. We hypothesized that tree-ring δ15N values would decline following decreases in atmospheric N deposition (after approximately 1995), and that trends in stream nitrate export and retention of atmospherically deposited N would mirror changes in tree-ring δ15N values. Three of the six sampled tree species and the majority of individual trees showed declining linear trends in δ15N for the period 1980–2010; only two individual trees showed increasing trends in δ15N values. From 1980 to 2010, trees in the watersheds of both tributaries displayed long-term declines in tree-ring δ15N values at the watershed scale (R = −0.35 and p = 0.001 in the North and R = −0.37 and p <0.001 in the South). The decreasing δ15N trend in the North was associated with declining stream nitrate concentrations (−0.009 mg N L−1 yr−1, p = 0.02), but no change in the retention of atmospherically deposited N was observed. In contrast, nitrate yields in the South did not exhibit a trend, and the watershed became less retentive of atmospherically deposited N (−7.3% yr−1, p < 0.001). Our δ15N results indicate a change in terrestrial N availability in both watersheds prior to decreases in atmospheric N deposition, suggesting that decreased atmospheric N deposition was not the sole driver of tree-ring δ15N values at these sites. Other factors, such as decreased sulfur deposition, disturbance, long-term successional trends, and/or increasing atmospheric CO2 concentrations, may also influence trends in tree-ring δ15N values. Furthermore, declines in terrestrial N availability inferred from tree-ring δ15N values do not always correspond with decreased stream nitrate export or increased retention of atmospherically deposited N

Small non-coding RNA profiling in plasma extracellular vesicles of bladder cancer patients by next-generation sequencing: Expression levels of miR-126-3p and piR-5936 increase with higher histologic grades

Bladder cancer (BC) is the tenth most frequent cancer worldwide. Due to the need for recurrent cystoscopies and the lack of non-invasive biomarkers, BC is associated with a high management burden. In this respect, small non-coding RNAs (sncRNAs) have been investigated in urine as possible biomarkers for BC, but in plasma their potential has not yet been defined. The expression levels of sncRNAs contained in plasma extracellular vesicles (EVs) from 47 men with BC and 46 healthy controls were assessed by next-generation sequencing. The sncRNA profiles were compared with urinary profiles from the same subjects. miR-4508 resulted downregulated in plasma EVs of muscle-invasive BC patients, compared to controls (adj-p = 0.04). In World Health Organization (WHO) grade 3 (G3) BC, miR-126-3p was upregulated both in plasma EVs and urine, when compared to controls (for both, adj-p &lt; 0.05). Interestingly, two sncRNAs were associated with the risk class: miR-4508 with a downward trend going from controls to high risk BC, and piR-hsa-5936 with an upward trend (adj-p = 0.04 and adj-p = 0.05, respectively). Additionally, BC cases with low expression of miR-185-5p and miR-106a-5p or high expression of miR-10b-5p showed shorter survival (adj-p = 0.0013, adj-p = 0.039 and adj-p = 0.047, respectively). SncRNAs from plasma EVs could be diagnostic biomarkers for BC, especially in advanced grade

Change in chirality of semiconducting single-walled carbon nanotubes can overcome anionic surfactant stabilisation: a systematic study of aggregation kinetics

Single-walled carbon nanotubes’ (SWNT) effectiveness in applications is enhanced by debundling or stabilisation. Anionic surfactants are known to effectively stabilise SWNTs. However, the role of specific chirality on surfactant-stabilised SWNT aggregation has not been studied to date. The aggregation behaviour of chirally enriched (6,5) and (7,6) semiconducting SWNTs, functionalised with three anionic surfactants – sodium dodecyl sulfate, sodium dodecyl benzene sulfonate and sodium deoxycholate – was evaluated with time-resolved dynamic light scattering. A wide range of mono- (NaCl) and divalent (CaCl2) electrolytes as well as a 2.5 mg total organic carbon (TOC) L–1 Suwannee River humic acid were used as background chemistry. Overall, sodium dodecyl benzene sulfonate showed the most effectiveness in stabilising SWNTs, followed by sodium deoxycholate and sodium dodecyl sulfate. However, the larger diameter (7,6) chirality tubes (compared to (6,5) diameter), compromised the surfactant stability due to enhanced van der Waals interaction. The presence of divalent electrolytes overshadowed the chirality effects and resulted in similar aggregation behaviour for both the SWNT samples. Molecular modelling results elucidated key differences in surfactant conformation on SWNT surfaces and identified interaction energy changes between the two chiralities to delineate aggregation mechanisms. The stability of SWNTs increased in the presence of Suwannee River humic acid under 10 mM monovalent and mixed-electrolyte conditions. The results suggest that change in chirality can overcome surfactant stabilisation of semiconducting SWNTs. SWNT stability can also be strongly influenced by the anionic surfactant structure

Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement

Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species