Abnormal hermaphroditic skipjack, Katsuwonus pelamis (Linnaeus, 1758) from Agatti coast, Lakshadweep, India

A hermaphroditic specimen of skipjack tuna, Katsuwonus pelamis of forklength (FL) – 56 cm and total weight (TW) – 3.20 kg was caught by pole and line on 21st November 2005 from the Agatti coast, Lakshadweep. Histological studies revealed that both the ovarian and testicular portions had developed a complete series of gametogenic cell lines

Response of varieties of elephant foot yam (Amorphophallus paeoniifolius) to organic management

Consumer awareness regarding the impacts of high-input chemical intensive conventional agriculture on the soil, environment and human health has spurred the growth of organic agriculture systems. Organic agriculture ensures sustainable production, safe food and environmental conservation. It is estimated that more than 95% of organic production is based on crop varieties that were bred for the conventional high-input sector. Such varieties lack important traits required under organic and low-input production conditions. There is dearth of information on the response of varieties to organic management. Field experiments were conducted for two years during 2010 and 2011 at the Central Tuber Crops Research Institute, Thiruvananthapuram, to compare the growth, yield and quality performance of five elephant foot yam [Amorphallus paeoniifolius (Dennst.) Nicolson] varieties (Peerumade local, Gajendra, Sree Padma, Vegetable and Fruit Promotion Council Keralam (VFPCK) local and Sree Athira) and soil physicochemical and biological properties under organic vs conventional systems in split plot design. Varieties × production systems interaction was not significant for most of the variables. The elite as well as the local varieties responded equally well to both the systems with average corm yields of 27.72 tonnes/ha under organic and 28.55 tonnes/ha under conventional practice. The var. Gajendra responded well to organic management producing higher yield (+10%). The other varieties had lower yield losses (-2.5-15.0%) under the organic system. The corms of the varieties had slightly higher dry matter, sugar, P, K and Fe contents under organic system. The varieties also exerted similar effects on soil physicochemical and biological properties, when tested under organic and conventional management. However, Gajendra and Sree Padma effected significantly higher organic C status under organic management due to greater biomass addition on account of their innate robust plant type. In general, there was significant improvement in soil pH and bacterial count, slight lowering of bulk density and particle density, improvement in water holding capacity, secondary and micronutrient status, N fixers and dehydrogenase enzyme activity in the organic system

Development and annotation of perennial Triticeae ESTs and SSR markers.

Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus x L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database (http://titan.biotec.uiuc.edu/triticeae/)

Mechanisms of reactivation of latent tuberculosis infection due to SIV coinfection

HIV is a major driver of tuberculosis (TB) reactivation. Depletion of CD4+ T cells is assumed to be the basis behind TB reactivation in individuals with latent tuberculosis infection (LTBI) coinfected with HIV. Nonhuman primates (NHPs) coinfected with a mutant simian immunodeficiency virus (SIVΔGY) that does not cause depletion of tissue CD4+ T cells during infection failed to reactivate TB. To investigate the contribution of CD4+ T cell depletion relative to other mechanisms of SIV-induced reactivation of LTBI, we used CD4R1 antibody to deplete CD4+ T cells in animals with LTBI without lentiviral infection. The mere depletion of CD4+ T cells during LTBI was insufficient in generating reactivation of LTBI. Instead, direct cytopathic effects of SIV resulting in chronic immune activation, along with the altered effector T cell phenotypes and dysregulated T cell homeostasis, were likely mediators of reactivation of LTBI. These results revealed important implications for TB control in HIV-coinfected individuals

INCOIS-Real time Automatic Weather Station(IRAWS) dataset - Quality control and significance of height correction

The INCOIS-Real time Automatic Weather Station(IRAWS) program was started in the year 2009 and was first installed onboard ORV Sagar Nidhi. Currently, there are 36 ships carrying IRAWS setup. Apart from storing one minute observations in the log onboard the ship, hourly averaged observations are reported through INSAT satellite communication. This report briefs about the hourly dataset of IRAWS and its quality control. In this report, QC results of SST and all meteorological parameters except radiation parameters is discussed. Specific quality check was applied to wind speed (WS) and sea surface temperature (SST) observations. The WS observations measured onboard few ships had a dimensional correction and SST was observed only on few ships. As SST observations are required to compute meteorological variables like DBT, RH, WS to standard height of 10 m, level-3 dataset of AVHRR SST was utilized in place of IRAWS SST wherever the data is found to be faulty. On similar terms bias correction could not be applied to IRAWS SST with the help of AVHRR SST as the error in SST observations are due to the failure of sensor. However all those IRAWS SST observations that passed the QC check were observed to be of high quality and have a correlation coefficient of 0.5 with AVHRR SST and is significant at 95% significant level. Apart from SST and radiation observations, all other parameters observations are found out to be of good quality with 70 to 90 QC pass percentage . Apart from the details of QC check, significance of representing climate variable at a homogeneous standard height is also shown in this repor

Hydrophobic and metallophobic surfaces: Highly stable non-wetting inorganic surfaces based on lanthanum phosphate nanorods

Metal oxides, in general, are known to exhibit significant wettability towards water molecules because of the high feasibility of synergetic hydrogen-bonding interactions possible at the solid-water interface. Here we show that the nano sized phosphates of rare earth materials (Rare Earth Phosphates, REPs), LaPO 4 in particular, exhibit without any chemical modification, unique combination of intrinsic properties including remarkable hydrophobicity that could be retained even after exposure to extreme temperatures and harsh hydrothermal conditions. Transparent nanocoatings of LaPO 4 as well as mixture of other REPs on glass surfaces are shown to display notable hydrophobicity with water contact angle (WCA) value of 120° while sintered and polished monoliths manifested WCA greater than 105°. Significantly, these materials in the form of coatings and monoliths also exhibit complete non-wettability and inertness towards molten metals like Ag, Zn, and Al well above their melting points. These properties, coupled with their excellent chemical and thermal stability, ease of processing, machinability and their versatile photo-physical and emission properties, render LaPO 4 and other REP ceramics utility in diverse applications

Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform

BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method) is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1), after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming) but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies

Perspectives on tracking data reuse across biodata resources

c The Author(s) 2024. Published by Oxford University Press.Motivation: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge. Results: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use. Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources