ALBERT

Description: There are a number of clear examples in the instrumental period where positive El Niño events were coincident with a severely weakened summer monsoon over India (ISM). ENSO's influence on the Indian Monsoon has therefore remained the centerpiece of various predictive schemes of ISM rainfall for over a century. The teleconnection between the monsoon and ENSO has undergone a protracted weakening since the late 1980's suggesting the strength of ENSO's influence on the monsoon may vary considerably on multidecadal timescales. The recent weakening has specifically prompted questions as to whether this shift represents a natural mode of climate variability or a fundamental change in ENSO and/or ISM dynamics due to anthropogenic warming. The brevity of empirical observations and large systematic errors in the representation of these two systems in state-of-the-art general circulation models hamper efforts to reliably assess the low frequency nature of this dynamical coupling under varying climate forcings. Here we place the 20th century ENSO-Monsoon relationship in a millennial context by assessing the phase angle between the two systems across the time spectrum using a continuous tree-ring ENSO reconstruction from North America and a speleothem oxygen isotope (δ18O) based reconstruction of the ISM. The results suggest that in the high-frequency domain (≤ 15 yr), El Niño (La Niña) events persistently lead to a weakened (strengthened) monsoon consistent with the observed relationship between the two systems during the instrumental period. However, in the low frequency domain (≥ 60 yr), periods of strong monsoon are, in general, coincident with periods of enhanced ENSO variance. This relationship is opposite to which would be predicted dynamically and leads us to conclude that ENSO is not pacing the prominent multidecadal variability that has characterized the ISM over the last millennium.

Description: Genes, Vol. 8, Pages 210: Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree Genes doi: 10.3390/genes8090210 Authors: Kevin Gustafson Jacque Duncan Pooja Biswas Angel Soto-Hermida Hiroko Matsui David Jakubosky John Suk Amalio Telenti Kelly Frazer Radha Ayyagari Retinitis pigmentosa (RP) causes progressive photoreceptor loss resulting from mutations in over 80 genes. This study identified the genetic cause of RP in three members of a non-consanguineous pedigree. Detailed ophthalmic evaluation was performed in the three affected family members. Whole exome sequencing (WES) and whole genome sequencing (WGS) were performed in the three affected and the two unaffected family members and variants were filtered to detect rare, potentially deleterious variants segregating with disease. WES and WGS did not identify potentially pathogenic variants shared by all three affected members. However, WES identified a previously reported homozygous nonsense mutation in KIZ (c.226C>T, p.Arg76*) in two affected sisters, but not in their affected second cousin. WGS revealed a novel 1.135 kb homozygous deletion in a retina transcript of C21orf2 and a novel 30.651 kb heterozygous deletion in CACNA2D4 in the affected second cousin. The sisters with the KIZ mutation carried no copies of the C21orf2 or CACNA2D4 deletions, while the second cousin with the C21orf2 and CACNA2D4 deletions carried no copies of the KIZ mutation. This study identified two independent, homozygous mutations in genes previously reported in autosomal recessive RP in a non-consanguineous family, and demonstrated the value of WGS when WES fails to identify likely disease-causing mutations.

Description: Genes, Vol. 8, Pages 286: Correction: Gustafson et al., Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree. Genes 2017, 8, 210 Genes doi: 10.3390/genes8100286 Authors: Kevin Gustafson Jacque Duncan Pooja Biswas Angel Soto-Hermida Hiroko Matsui David Jakubosky John Suk Amalio Telenti Kelly Frazer Radha Ayyagari Following publication of our article [1], we identified discrepancies between the pedigree shown in Figure 1 and the rest of the text.[...]

Description: Genes, Vol. 9, Pages 84: Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance Genes doi: 10.3390/genes9020084 Authors: Md. Abdul Kayum Ujjal Nath Jong-In Park Manosh Biswas Eung Choi Jae-Young Song Hoy-Taek Kim Ill-Sup Nou Plant growth and development can be adversely affected by cold stress, limiting productivity. The glutathione S-transferase (GST) family comprises important detoxifying enzymes, which play major roles in biotic and abiotic stress responses by reducing the oxidative damage caused by reactive oxygen species. Pumpkins (Cucurbita maxima) are widely grown, economically important, and nutritious; however, their yield can be severely affected by cold stress. The identification of putative candidate genes responsible for cold-stress tolerance, including the GST family genes, is therefore vital. For the first time, we identified 32 C. maxima GST (CmaGST) genes using a combination of bioinformatics approaches and characterized them by expression profiling. These CmaGST genes represent seven of the 14 known classes of plant GSTs, with 18 CmaGSTs categorized into the tau class. The CmaGSTs were distributed across 13 of pumpkin’s 20 chromosomes, with the highest numbers found on chromosomes 4 and 6. The large number of CmaGST genes resulted from gene duplication; 11 and 5 pairs of CmaGST genes were segmental- and tandem-duplicated, respectively. In addition, all CmaGST genes showed organ-specific expression. The expression of the putative GST genes in pumpkin was examined under cold stress in two lines with contrasting cold tolerance: cold-tolerant CP-1 (C. maxima) and cold-susceptible EP-1 (Cucurbita moschata). Seven genes (CmaGSTU3, CmaGSTU7, CmaGSTU8, CmaGSTU9, CmaGSTU11, CmaGSTU12, and CmaGSTU14) were highly expressed in the cold-tolerant line and are putative candidates for use in breeding cold-tolerant crop varieties. These results increase our understanding of the cold-stress-related functions of the GST family, as well as potentially enhancing pumpkin breeding programs.

Description: Genes, Vol. 9, Pages 97: Exploration and Exploitation of Novel SSR Markers for Candidate Transcription Factor Genes in Lilium Species Genes doi: 10.3390/genes9020097 Authors: Manosh Biswas Ujjal Nath Jewel Howlader Mita Bagchi Sathishkumar Natarajan Md Abdul Kayum Hoy-Taek Kim Jong-In Park Jong-Goo Kang Ill-Sup Nou Lilies (Lilium sp.) are commercially important horticultural crops widely cultivated for their flowers and bulbs. Here, we conducted large-scale data mining of the lily transcriptome to develop transcription factor (TF)-associated microsatellite markers (TFSSRs). Among 216,768 unigenes extracted from our sequence data, 6966 unigenes harbored simple sequence repeats (SSRs). Seventy-one SSRs were associated with TF genes, and these were used to design primers and validate their potential as markers. These 71 SSRs were accomplished with 31 transcription factor families; including bHLH, MYB, C2H2, ERF, C3H, NAC, bZIP, and so on. Fourteen highly polymorphic SSRs were selected based on Polymorphic Information Content (PIC) values and used to study genetic diversity and population structure in lily accessions. Higher genetic diversity was observed in Longiflorum compared to Oriental and Asiatic populations. Lily accessions were divided into three sub-populations based in our structure analysis, and an un-rooted neighbor-joining tree effectively separated the accessions according to Asiatic, Oriental, and Longiflorum subgroups. Finally, we showed that 46 of the SSR-associated genes were differentially expressed in response to Botrytis elliptica infection. Thus, our newly developed TFSSR markers represent a powerful tool for large-scale genotyping, high-density and comparative mapping, marker-aided backcrossing, and molecular diversity analysis of Lilium sp.

Description: Residential solid biomass cookstoves are important sources of aerosol emissions in India. Cookstove emissions rates are largely based on laboratory experiments conducted using the standard water-boiling test, but real-world emissions are often higher owing to different stove designs, fuels, and cooking methods. Constraining mass emissions factors (EFs) for prevalent cookstoves is important because they serve as inputs to bottom-up emissions inventories used to evaluate health and climate impacts. Real-world EFs were measured during winter 2015 for a traditional cookstove (chulha) burning fuel wood, agricultural residue, and dung from different regions of India. Average (±95 % confidence interval) EFs for fuel wood, agricultural residue, and dung were (1) PM2.5 mass: 10.5 (7.7–13.4) g kg−1, 11.1 (7.7–15.5) g kg−1, and 22.6 (14.9–32.9) g kg−1, respectively; (2) elemental carbon (EC): 0.9 (0.6–1.4) g kg−1, 1.6 (0.6–3.0) g kg−1, and 1.0 (0.4–2.0) g kg−1, respectively; and (3) organic carbon (OC): 4.9 (3.2–7.1) g kg−1, 7.0 (3.5–12.5) g kg−1, and 12.9 (4.2–15.01) g kg−1, respectively. The mean (±95 % confidence interval) OC ∕ EC mass ratios were 6.5 (4.5–9.1), 7.6 (4.4–12.2), and 12.7 (6.5–23.3), respectively, with OC and EC quantified by the IMPROVE_A thermal-optical reflectance protocol. These real-world EFs are higher than those from previous laboratory-based measurements. Combustion conditions have larger effects on EFs than the fuel types. We also report the carbon mass fractions of our aerosol samples determined using the thermal-optical reflectance method. The mass fraction profiles are consistent between the three fuel categories but markedly different from those reported in past literature – including the source profiles for wood stove PM2.5 emissions developed as inputs to receptor modeling studies conducted by the Central Pollution Control Board of India. Thermally stable OC (OC3 in the IMPROVE_A protocol) contributed nearly 50 % of the total carbon mass for emissions from all fuels.

Description: Controlled bench scale pulverized coal combustion studies were performed, demonstrating that inorganic particles play a critical role as carriers of organic species. Two commonly-used aerosol mass spectrometry techniques were applied to characterize fine particle formation during coal combustion. It was found that the organic species in coal combustion aerosols have mass spectra similar to those generated by biomass combustion. Ambient measurements in Shanghai, China confirm the presence of these species in approximately 29–38% of the sampled particles. With the absence of major biomass sources in the Shanghai area, it is suggested that coal combustion may be the main source of these particles. This work indicates there is a significant potential for incorrect apportionment of coal combustion particles to biomass burning sources using widely adopted mass spectrometry techniques.

Description: Spatiotemporal behavior of soil water is essential to understand the science of hydrodynamics. Data intensive measurement of surface soil water using remote sensing has established that the spatial variability of soil water can be described using the principle of self-similarity (scaling properties) or fractal theory. This information can be used in determining land management practices provided the surface scaling properties are kept at deep layers. The current study examined the scaling properties of sub-surface soil water and their relationship to surface soil water, thereby serving as supporting information for plant root and vadose zone models. Soil water storage (SWS) down to 1.4 m depth at seven equal intervals was measured along a transect of 576 m for 5 years in Saskatchewan. The surface SWS showed multifractal nature only during the wet period (from snowmelt until mid- to late June) indicating the need for multiple scaling indices in transferring soil water variability information over multiple scales. However, with increasing depth, the SWS became monofractal in nature indicating the need for a single scaling index to upscale/downscale soil water variability information. In contrast, all soil layers during the dry period (from late June to the end of the growing season in early November) were monofractal in nature, probably resulting from the high evapotranspirative demand of the growing vegetation that surpassed other effects. This strong similarity between the scaling properties at the surface layer and deep layers provides the possibility of inferring about the whole profile soil water dynamics using the scaling properties of the easy-to-measure surface SWS data.

Description: Knowledge about the scaling properties of soil water storage is crucial in transferring locally measured fluctuations to larger scales and vice-versa. Studies based on remotely sensed data have shown that the variability in surface soil water has clear scaling properties (i.e., statistically self similar) over a wider range of spatial scales. However, the scaling property of soil water storage to a certain depth at a field scale is not well understood. The major challenges in scaling analysis for soil water are the presence of localized trends and nonstationarities in the spatial series. The objective of this study was to characterize scaling properties of soil water storage variability through multifractal detrended fluctuation analysis (MFDFA). A field experiment was conducted in a sub-humid climate at Alvena, Saskatchewan, Canada. A north-south transect of 624-m long was established on a rolling landscape. Soil water storage was monitored weekly between 2002 and 2005 at 104 locations along the transect. The spatial scaling property of the surface 0 to 40 cm depth was characterized using the MFDFA technique for six of the soil water content series (all gravimetrically determined) representing soil water storage after snowmelt, rainfall, and evapotranspiration. For the studied transect, scaling properties of soil water storage are different between drier periods and wet periods. It also appears that local controls such as site topography and texture (that dominantly control the pattern during wet states) results in multiscaling property. The nonlocal controls such as evapotranspiration results in the reduction of the degree of multiscaling and improvement in the simple scaling. Therefore, the scaling property of soil water storage is a function of both soil moisture status and the spatial extent considered.

Description: Understanding of the nitrogen (N) cycle and its spatial variability is important for managing ecosystems. Soil δ15N, as an important indicator of different soil nitrogen cycling processes, may provide critical information about the spatial variability in soil N cycling. The objective of this study was to examine the dominant landscape scale variability of δ15N, the location of the variability and its spatial relationship with elevation. Soil δ15N and elevation were measured along two transects (Davidson and Elstow, Saskatchewan, Canada). Each transect had 128 points with 3 m sampling intervals. Higher δ15N values typically occurred in topographic depressions as compared to knolls. The coefficient of determination revealed a significant linear relationship between δ15N and elevation (r2=0.27) at Davidson whereas no relationship (r2=0.00) was detected for the Elstow transect. However, wavelet spectra, cross wavelet, and squared wavelet coherency analysis revealed spatial relationships between δ15N and elevation at both sites. A strong coherency between δ15N and elevation at large scales (96 m or more) was detected for both transects. The Davidson transect showed an out of phase coherency at a topographically elevated area at the beginning and the end of the transect. The Elstow transect had a strong out of phase correlation (negative relationship) at the middle of the transect (corresponding to a depressions) indicating a location dependent relationship between δ15N and elevation. The relationship between δ15N and elevation reflects the effects of hydrology and soil water content over the landscape on N cycling processes.