An integrated buoy-satellite based coastal water quality nowcasting system: India's pioneering efforts towards addressing UN ocean decade challenges.

The Indian coastal waters are stressed due to a multitude of factors, such as the discharge of industrial effluents, urbanization (municipal sewage), agricultural runoff, and river discharge. The coastal waters along the eastern and western seaboard of India exhibit contrasting characteristics in terms of seasonality, the magnitude of river influx, circulation pattern, and degree of anthropogenic activity. Therefore, understanding these processes and forecasting their occurrence is highly necessary to secure the health of coastal waters, habitats, marine resources, and the safety of tourists. This article introduces an integrated buoy-satellite based Water Quality Nowcasting System (WQNS) to address the unique challenges of water quality monitoring in Indian coastal waters and to boost the regional blue economy. The Indian National Centre for Ocean Information Services (INCOIS) has launched a first-of-its-kind WQNS, and positioned the buoys at two important locations along the east (Visakhapatnam) and west (Kochi) coast of India, covering a range of environmental conditions and tourist-intensive zones. These buoys are equipped with different physical-biogeochemical sensors, data telemetry systems, and integration with satellite-based observations for real-time data transmission to land. The sensors onboard these buoys continuously measure 22 water quality parameters, including surface current (speed and direction), salinity, temperature, pH, dissolved oxygen, phycocyanin, phycoerythrin, Coloured Dissolved Organic Matter, chlorophyll-a, turbidity, dissolved methane, hydrocarbon (crude and refined), scattering, pCO2 (water and air), and inorganic macronutrients (nitrite, nitrate, ammonium, phosphate, silicate). This real-time data is transmitted to a central processing facility at INCOIS, and after necessary quality control, the data is disseminated through the INCOIS website. Preliminary results from the WQNS show promising outcomes, including the short-term changes in the water column oxic and hypoxic regimes within a day in coastal waters off Kochi during the monsoon period, whereas effluxing of high levels of CO2 into the atmosphere associated with the mixing of water, driven by local depression in the coastal waters off Visakhapatnam. The system has demonstrated its ability to detect changes in the water column properties due to episodic events and mesoscale processes. Additionally, it offers valuable data for research, management, and policy development related to coastal water quality.

Wave induced coastal flooding along the southwest coast of India during tropical cyclone Tauktae.

The coastal flood during the tropical cyclone Tauktae, 2021, at Chellanam coast, Kerala, India, has invited wide attention as the wave overtopping severely affected coastal properties and livelihood. We used a combination of WAVEWATCHIII and XBeach to study the coastal inundation during high waves. The effect of low-frequency waves and the rise in the coastal water level due to wave setup caused the inundation at Chellanam, even during low tide with negligible surge height. Wave setup raised the water level at the coast with steep slopes to more than 0.6 m and peaked during low tide, facilitating wave breaking at the nearshore region. The coastal regions adjacent to these steep slopes were subjected to severe inundation. The combined effect of long and short waves over wave setup formed extreme wave runups that flooded inland areas. At gently sloping beaches, the longwave component dominated and overtopped the seawalls and damaged households along the shoreline. The study emphasizes the importance of longwave and wave setup and its interaction with nearshore bathymetry during the high wave. The present study shall lead to the development of a coastal inundation prediction system for the low-lying hot spots using the combination of WAVEWATCHIII and XBeach models.

Exploring the impact of southern ocean sea ice on the Indian Ocean swells.

The present study analyzes the impact of the Southern Ocean (SO) sea ice concentration on the north Indian Ocean (NIO) wave fields through swells using 6 years (2016-2021) of WAVEWATCH III (WWIII) simulations. We did two experimental runs of WWIII, one with sea ice concentration and winds as the forcing (W3with_ice) and the second run with only wind forcing (W3no_ice). Analysis shows the impact of the SO sea ice concentration on northward swell peaks in September-November, coinciding with the maximum sea ice extent in the Antarctic region of the Indian Ocean. W3no_ice simulations are biased more by ~ 60% and ~ 37% in significant wave height and period, respectively, against W3with_ice when compared with NIO mooring data. W3no_ice simulates low-frequency swells and travels fast towards NIO, with implications for operational oceanography. We have shown that the forecasts of the timing of high swell events along NIO coasts can be erroneous by ~ 12 h if the SO sea ice concentration is not included in the model. Further, W3no_ice could potentially produce false swell alerts along southeastern Australian coasts. In summary, our study highlights the importance of the SO sea ice concentration inclusion in the wave models to accurately simulate NIO waves.

Response of coastal phytoplankton pigment composition to tropical cyclone Fani.

Phytoplankton pigment composition was evaluated during the pre-cyclone phase (PRCP) and post-cyclone phase (POCP) of tropical cyclone Fani in the coastal waters of the northwestern Bay of Bengal. The chromatographic analysis revealed higher pigment diversity and an increase in individual pigment concentration during POCP. Chlorophyll-a (chl-a) was the dominant pigment during PRCP and POCP, followed by fucoxanthin. However, chl-a and fucoxanthin concentrations increased 18- and 14-folds, respectively, during the POCP, signifying Bacillariophyta bloom. Complementing microscopy confirmed the dominance of the toxic Bacillariophyta species Pseudo-nitzschia pungens (reaching 5.47 × 104 cells l-1) during the POCP. The cyclone-induced nutrient recharge of the ambient medium could have promoted phytoplankton growth, causing the reappearance of diatom bloom during the later phase of the pre-southwest monsoon. Small-sized Prymnesiophyta and Cryptophyta were not detected microscopically; however, they were identified by chromatographic analysis through pigment markers during POCP.

Physicochemical controls on the initiation of phytoplankton bloom during the winter monsoon in the Arabian Sea.

Occurrence of phytoplankton bloom in the northern Arabian Sea (NAS) during the winter monsoon is perplexing. The convective mixing leads to a deeper and well-oxygenated (> 95% saturation) mixed layer. We encountered low chlorophyll conditions though the nutrient conditions were favorable for a bloom. The mean ratio of silicate (Si) to DIN (Dissolved Inorganic Nitrogen: nitrate + nitrite + ammonium) in the euphotic zone was 0.52 indicating a "silicate-stressed" condition for the proliferation of diatoms. Also, the euphotic depth was much shallower (~ 49 m) than the mixed layer (~ 110 m) suggesting the Sverdrup critical depth limitation in the NAS. We show that the bloom in this region initiates only when the mixed layer shoals towards the euphotic zone. Our observations further suggest that two primary factors, the stoichiometric ratio of nutrients, especially the Si/DIN ratio, in the mixed layer and re-stratification of the upper water column, govern the phytoplankton blooming in NAS during the later winter monsoon. The important finding of the present study is that the Sverdrup's critical depth limitation gives rise to the observed low chl-a concentration in the NAS, despite having enough nutrients.

Unravelling tidal effect on zooplankton community structure in a tropical estuary.

The variability in zooplankton density and species composition in response to tidal oscillations were investigated in the lesser saline upper reaches (E1) and higher saline lower reaches (E2) of the Mahanadi Estuary, located at the mouth of the third largest river in Indian Peninsula. This is the first of its kind high frequency observation over the tidal cycle ranging from highest high tide to lowest low tide in this estuary revealing dynamic variability of zooplankton assemblages. Zooplankton abundance was higher during high tide in comparison to low tide, irrespective of salinity regimes. On the diurnal scale, it was higher at night in comparison to the day at both E1 and E2. The higher abundance of zooplankton groups such as Copepoda, Cladocera, and planktonic larvae during the night at E1 as well as E2 indicating an upward migration. Many of the zooplankton taxa (e.g., Pseudodiaptomus serricaudatus, Pseudodiaptomus sp., Acartia danae, Acrocalanus longicornis, Oithona sp., Corycaeus andrewsi) migrated towards E1 due to tidal effect during high tide and maintained their position even during low tide. In contrast, the prevalence of limnetic taxa (e.g., Brachionus rubens, Polyarthra vulgaris, Bosminopsis deitersi, Moina micrura, Heliodiaptomus sp.) at E2 during low tide indicated a predominant riverine source. The tidal variability of Brachyura (zoea and megalopa) revealed different emergence times that indicated dispersal of zoeas to the adjacent Bay of Bengal and the return of magalopa to the Mahanadi Estuary. Species diversity index was higher during high tide, and prominent at E2. At E1, marine, fresh, marine-brackish, and marine-brackish-fresh zooplankton species dominated during high tide, while brackish-fresh taxa dominated during low tide. Differently, E2 was enriched with marine, marine-brackish, and marine-brackish-fresh taxa during high tide, whereas fresh, brackish-fresh, and marine-fresh dominated during low tide. Salinity and suspended matter influenced the dominant zooplankton taxa at E2 and E1, respectively. Zooplankton assemblages exhibited a pattern of prominent diurnal-spatial variation in comparison to the tidal scale in the Mahanadi Estuary. Overall, this study documented a very high zooplankton diversity (92 taxa belonging to 13 groups) and significant variations in species abundance which highlighted the importance of carrying out sampling over the tidal cycle at contrasting salinity regimes.

Effect of Tidal Cycle on Escherichia coli Variability in a Tropical Estuary.

A faecal indicator bacteria, Escherichia coli (E. coli), is widely used in monitoring health of estuaries, where tidal amplitude plays a critical role in its variability. Mahanadi estuary, formed at the mouth of a major tropical river Mahanadi, has large socio-economic importance. This anthropogenically stressed estuary remains understudied with respect to E. coli. Hence, this study addressed E. coli variability in Mahanadi estuary with novel sampling strategy that can be implemented at other tropical estuaries. The sampling strategy includes simultaneous measurements, at lesser-saline upper-estuary and higher-saline lower-estuary, over a tidal cycle. Although no significant variability of E. coli was observed between upper and lower-estuary, overall average count was higher during low tide and lower during high tide attributed to salinity fluctuations. Intermittent surpass of E. coli counts above recommended limits in Mahanadi estuary, indicated potential health risk, thus demands for frequent water quality monitoring and management strategies.

The influence of boreal summer intra-seasonal oscillations on Indo-western Pacific Ocean surface waves.

The present study examines the influence of Boreal Summer Intra-Seasonal Oscillation (BSISO) on Tropical Indian Ocean surface waves using the latest version of ECMWF reanalysis (ERA5) during summer monsoon months June through August (JJA). BSISO is a distinct mode of ISO during JJA having a northward and eastward movement from the equatorial Indian Ocean to the western Pacific Ocean. Composite analysis of anomalies of significant wave heights (SWH), wind sea, swell, and mean wave period for 8 phases of BSISO has been carried out to understand its influence. SWH anomalies in response to BSISO's are phase-dependent. Negative SWH anomalies are noticed with strong northward and weak eastward propagation during the phases 1-3 in response to the easterly wind anomalies over the north Indian Ocean (NIO). During phases 5-7, high positive SWH anomalies (~ 0.5 m) in response to the westerly wind anomalies with northward and weak eastward propagation over NIO. Phases 4 and 8 behave like transition phases. In addition, enhanced (suppressed) SWH anomalies (~ 0.5 m) are seen during the active (break) spells of BSISO over NIO. Over the southern tip of India, negative (positive) SWH anomalies prevail during the active (break) conditions. This study clearly suggests that the wave forecast advisories during intra-seasonal time scales would be more useful for offshore and coastal activities during the summer monsoon.

A database designed to computationally aid an experimental approach to alternative splicing.

A unique microarray approach has been developed to profile alternative splicing in the cell. To support the development of this approach, we have developed the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is a unique alternative splicing information resource designed specifically with experimentalists in mind. MAASE is an online resource for the convenient access, identification, and annotation of alternative splicing events (ASEs). MAASE consists of two components: an annotation system and a curated database. The annotation system is a web-based workspace that combines manual and computational approaches to identifying and annotating ASEs, a combination that is vital if a comprehensive collection is to be obtained. The annotation system is publicly available and provides a scalable solution to acquiring as well as contributing to annotated ASEs. MAASE annotated ASEs are deposited into the database component, which can either be queried one entry at a time or multiple entries at a time with convenient access to alternatively spliced junctional and surrounding sequences to facilitate the design of microarray experiments.

Web alert. Proteins catalysis and regulation.

A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology.

Surface plasmon resonance kinetic studies of the HIV TAR RNA kissing hairpin complex and its stabilization by 2-thiouridine modification.

Surface plasmon resonance (BIACORE) was used to determine the kinetic values for formation of the HIV TAR-TAR* ('kissing hairpin') RNA complex. The TAR component was also synthesized with the modified nucleoside 2-thiouridine at position 7 in the loop and the kinetics and equilibrium dissociation constants compared with the unmodified TAR hairpin. The BIACORE data show an equilibrium dissociation constant of 1.58 nM for the complex containing the s(2)U modified TAR hairpin, which is 8-fold lower than for the parent hairpin (12.5 nM). This is a result of a 2-fold faster k(a) (4.14x10(5) M(-1) s(-1) versus 2.1x10(5) M(-1) s(-1)) and a 4-fold slower k(d) (6.55x10(-4) s(-1) versus 2.63x10(-3) s(-1)). (1)H NMR imino spectra show that the secondary structure interactions involved in complex formation are retained in the s(2)U-modified complex. Magnesium has been reported to significantly stabilize the TAR-TAR* complex and we found that Mn(2+) and Ca(2+) are also strongly stabilizing, while Mg(2+) exhibited the greatest effect on the complex kinetics. The stabilizing effects of 2-thiouridine indicate that this base modification may be generally useful as an antisense RNA modification for oligonucleotide therapeutics which target RNA loops.

External hydrocephalus in primary hypomagnesaemia: a new finding.

This paper reports a new finding in two siblings with primary hypomagnesaemia as a result of renal magnesium wasting, namely, rapidly increasing head size. External hydrocephalus and brain shrinkage in primary hypomagnesaemia seen on computed tomography of the brain with reversibility after magnesium treatment has not been reported previously.

Evidence for intrinsic DNA bends within the human cdc2 promoter.

Cyclin-dependent protein kinases (Cdks) are key regulatory proteins of the eukaryotic cell cycle. The product of the cdc2 gene, p34cdc2 (cdk1), is the catalytic subunit of a serine/ threonine protein kinase that is expressed in S phase and functions in the G2 to M phase transition. Previous studies indicate that the human cdc2 gene expression is dependent on cell growth, and is transcriptionally regulated in a complex manner involving multiple transcription factors binding to specific sites in the promoter. One possible mechanism by which these transcription factors regulate transcription is that by binding to their cognate sites they induce bends in the DNA helix, thereby allowing their interaction with the basal transcription machinery through protein-protein contacts. Such protein-induced DNA bending is also influenced by intrinsic bends in the regulatory region. Using both theoretical and experimental approaches, the study reports that the human cdc2 promoter has an intrinsic DNA bend with a broad locus of curvature.

Calliper randomization: an artificial neural network based analysis of E. coli ribosome binding sites.

An artificial neural network based approach has been used in analyzing the translation initiation region of E. coli. The approach is based on using a trained network capable of recognizing a particular region and presenting the network with randomized calliper inputs of the true sequence. The network responds with an error when the regions which have been the main source of knowledge are randomized. Analysis of the E. coli ribosome binding sites using this approach reveal that the initiation codon and the Shine/Dalgarno sequence which are known to be important for translation initiation are also important in imparting knowledge to the network. Further, selectively changing the usually occurring initiation codon AUG, to GUG, UUG and AUU, which occur less frequently, decreases the network performance in accordance with the frequency of their occurrence. This approach can be used as a general method to derive consensus.

Theoretical permutation gel electrophoretic analysis of a curved DNA fragment located in circular permutation.

Using the theoretical model for DNA curvature, we analyzed a set of fragments with a curved insert located in circular permutation. The theoretical permutation analysis of each of the cyclically located fragments reveals the presence of a shifting molecular bend locus. The delineation of the molecular bend locus associated with the fragments obtained by a second permutation helps in providing an explanation for the differential mobility behavior of the fragments.

Analysis of transcription control signals using artificial neural networks.

The role of the upstream region in controlling the transcription efficiency of a gene is well established. However, the question of predicting the extent of gene expressed given the upstream region has so far remained unresolved. Using an artificial neural network (ANN) to capture the internal representation associated with the transcription control signal, the present work predicts the rate of mRNA synthesis based on the pattern contained in the upstream region. Further, the model has been used to predict the transcription efficiency for all possible single base mutations associated with the beta-globin promoter. The simulation results reveal that apart from the experimental observation that alpha-79G-A and -78G-A mutation increases the efficiency of transcription, mutation in these regions by C or T also causes an increase in transcription. Furthermore the simulation results verify that mutations in the conserved region, in general, decrease the transcriptional efficiency. However, the results also show that certain sequence elements, when mutated, either cause a marginal increase in the level of transcription or have no effect on transcription levels. The simulation results can be used as a guide in designing mutation experiments since an a priori estimate of the possible outcome of a mutation can be obtained.

Differential binding of RNA polymerase to the wild type Mu mom promoter and its C independent mutant: a theoretical analysis.

Using the theoretical model for DNA bending we have analyzed the Mu mom promoter wild type and its mutant tin7 which showed differential binding to the RNA polymerase. We have demonstrated here the structural change as a result of the point mutation which may be responsible for the altered binding of RNA polymerase. Analysis using both sets of parameters essentially gives the same result.

On the mobility behavior of a curved DNA fragment located in circular permutation.

Experimental and theoretical investigations on the mobility behavior of a set of permuted fragments with a K-DNA insert is reported. The fragments with the permuted flanking sequences have the K-DNA insert located differentially with respect to the fragment ends. The fragment wherein the insert is located in the center showed maximum retardation as compared to fragments where the insert was at the end. The experimental analysis is also in accord with the theoretical investigation.

Application of artificial neural networks for prokaryotic transcription terminator prediction.

Artificial neural networks (ANN) to predict terminator sequences, based on a feed-forward architecture and trained using the error back propagation technique, have been developed. The network uses two different methods for coding nucleotide sequences. In one the nucleotide bases are coded in binary while the other uses the electron-ion interaction potential values (EIIP) of the nucleotide bases. The latter strategy is new, property based and substantially reduces the network size. The prediction capacity of the artificial neural network using both coding strategies is more than 95%.