The shaping of modern human immune systems by multiregional admixture with archaic humans

Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.     

The mutational landscape of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.     

Mycophagous soil amoeba: Interactions with three plant pathogenic fungi

An amoeba of the order Leptomyxida was isolated from wheat take-all decline soil and was found to attack and lyse hyphae and spores of Gaeumannomyces graminis var. tritici and Phytophthora cinnamomi. The amoeba enveloped portions of hyphae of both fungi and penetrated the cell walls by means of fine holes. One-week old chlamydospores and hyphal swellings of P. cinnamomi were also attacked in this way, protoplast lysis being completed within 1 h. Hyphal fragments which could be ingested by the amoeba were lysed leaving amorphous cell debris. Three-week old chlamydospores of P. cinnamomi were enclosed within large food vacuoles and completely digested in about 20 h. Pigmented conidia of Cochliobolus sativus were transported across the substratum for up to several hours but were not perforated or lysed.     

Cotton responses to ultraviolet-B radiation: experimentation and algorithm development

The potential impact of an increase in solar ultraviolet-B (UV-B) radiation due to human activity on higher plants has been the subject of many studies. Little work has been carried out so far on cotton responses to enhanced UV-B radiation. The objective of this study was to determine whether or not the current and projected increases in UV-B levels affect cotton growth and development, and to quantify and develop UV-B radiation functional algorithms that can be used in simulation models. Two experiments were conducted during the summer of 2001 using sunlit plant growth chambers in a wide range of UV-B radiations under optimal growing conditions. Leaves exposed to UV-B radiation developed chlorotic and necrotic patches depending on the intensity and length of exposure. Along with changes in visible morphology, cotton canopy photosynthesis declined with increased UV-B radiation. The decline in canopy photosynthesis was partly due to loss of photosynthetic pigments and UV-B-induced decay of leaf-level photosynthetic efficiency (maximum photosynthesis) and capacity (quantum yield) as the leaves aged. The total leaf area was less due to smaller leaves and fewer leaves per plant. Less plant height was closely related to a shorter average internode length rather than a fewer mainstem nodes. The UV-B did not affect cotton major developmental events such as time taken to square, time to flower, and leaf addition rates on the mainstem. Lower biomass was closely related to both smaller leaf area and lower photosynthesis. The critical limit, defined as 90% of optimum or the control, for stem elongation was lower (8.7 kJ m⁻² per day UV-B) than the critical limit for leaf expansion (11.2 kJ m⁻² per day UV-B), indicating that stem elongation was more sensitive to UV-B than leaf expansion. The critical limits for canopy photosynthesis and total dry weight were 7 and 7.3 kJ m⁻² per day, respectively. The identified UV-B-specific indices for stem and leaf growth and photosynthesis parameters may be incorporated into cotton simulation models such as GOSSYM to predict yields under present and future climatic conditions.     

Enzyme activities and microbial biomass in coastal soils of India

Soil salinity is a serious problem for agriculture in coastal regions, wherein salinity is temporal in nature. We studied the effect of salinity, in summer, monsoon and winter seasons, on microbial biomass carbon (MBC) and enzyme activities (EAs) of the salt-affected soils of the coastal region of the Bay of Bengal, Sundarbans, India. The average pH of soils collected from different sites, during different seasons varied from 4.8 to 7.8. The average organic C (OC) and total N (TN) content of the soils ranged between 5.2-14.1 and 0.6-1.4 g kg⁻¹, respectively. The electrical conductivity of the saturation extract (ECe) of soils, averaged over season, varied from 2.2 to 16.3 dSm⁻¹. The ECe of the soils increased five fold during the summer season (13.8 dSm⁻¹) than the monsoon season (2.7 dSm⁻¹). The major cation and anion detected were Na⁺ and Cl⁻, respectively. Seasonality exerted considerable effects on MBC and soil EAs, with the lowest values recorded during the summer season. The activities of β-glucosidase, urease, acid phosphatase and alkaline phosphatase were similar during the winter and monsoon season. The dehydrogenase activity of soils was higher in monsoon than in winter. Average MBC, dehydrogenase, β-glucosidase, urease, acid phosphatase and alkaline phosphatase activities of the saline soils ranged from 125 to 346 mg kg⁻¹ oven dry soil, 6-9.9 mg triphenyl formazan (TPF) kg⁻¹ oven dry soil h⁻¹, 18-53 mg p-nitro phenol (PNP) kg⁻¹ oven dry soil h⁻¹, 38-86 mg urea hydrolyzed kg⁻¹ oven dry soil h⁻¹, 213-584 mg PNP kg⁻¹ oven dry soil h⁻¹ and 176-362 mg PNP g⁻¹ oven dry soil h⁻¹, respectively. The same for the non-saline soils were 274-446 mg kg⁻¹ oven dry soil, 8.8-14.4 mg TPF kg⁻¹ oven dry soil h⁻¹, 41-80 mg PNP kg⁻¹ oven dry soil h⁻¹, 89-134 mg urea hydrolyzed kg⁻¹ oven dry soil h⁻¹, 219-287 mg PNP kg⁻¹ oven dry soil h⁻¹ and 407-417 mg PNP kg⁻¹ oven dry soil h⁻¹, respectively. About 48%, 82%, 48%, 63%, 40% and 48% variation in MBC, dehydrogenase activity, β-glucosidase activity, urease activity, acid phosphatase activity and alkaline phosphatase activity, respectively, could be explained by the variation in ECe of saline soils. Suppression of EAs of the coastal soils during summer due to salinity rise is of immense agronomic significance and needs suitable interventions for sustainable crop production.     

Genotype and hormonal effects on callus formation and regeneration in mulberry

Summary Twenty-five mulberry genotypes were studied for callus induction, to evaluate the effectiveness of hormones in promoting callus growth and to identify genotypes capable of regenerating plants. Fifteen genotypes showed callus initiation. Genotypic variation was also noted for longevity and rate of growth of callus cultures. Calli of different genotypes were maintained for more than one year. Frequency of callus initiation was high on Murashige & Skoog's modified medium incorporated with 2.0 mg/l 2,4-D, 100 mg/l casein acid hydrolysate and 150 ml/l coconut water. Regeneration through organogenesis was achieved in six genotypes indicating genotypic specificity.     

Anti-viral activity of methyl 1-chloro-7-methyl-2-propyl-1h-benzo[d] imidazole-5-carboxylate against white spot syndrome virus in freshwater crab (Paratelphusa hydrodromous)

Shrimp farming industries are subjected to severe economic loss due to a disease called white spot syndrome, a viral disease caused by white spot syndrome virus (WSSV) in penaeid shrimp. Numerous active compounds in the market possess anti-viral activity against the white spot syndrome virus, yet the issue remains unsolved. The present study was carried out to determine the anti-viral activity of methyl 1-chloro-7-methyl-2-propyl-1h-benzo[d] imidazole-5-carboxylate (C₁₃H₁₅N₂O₂Cl) against WSSV. The anti-viral activity of the synthetic compound was determined in freshwater crabs. Crabs were divided into three different experimental groups: healthy control groups (N.C.) received NTE buffer, positive control group (P.C.) crabs received WSSV, and treatment group crabs received WSSV along with synthetic weight compound. Experimental groups were observed for 30 days post-infection. Three different organs (gills, muscles, and head soft tissue (HST)) were dissected from all three groups and analyzed using molecular-based techniques, including polymerase chain reaction (PCR), Western blot, and histopathology. Clinical signs of WSSV were observed in the positive and N.C. groups; however, the treatment group showed a 100% survival rate. Confirmation was done using PCR, Western blot, and histopathology. These results demonstrated that the given synthetic compound has significant anti-viral activity against WSSV.

     

Micronutrients (Fe,Mn, Zn and Cu) balance under long-term application of fertilizer and manure in a tropical rice-rice system

Purpose

The balance of micronutrients in soils is important in nutrient use efficiency, environmental protection and the sustainability of agro-ecological systems. The deficiency or excess of micronutrients in the plough layer may decrease crop yield and/or quality. Therefore, it is essential to maintain appropriate levels of micronutrients in soil, not only for satisfying plant needs in order to sustain agricultural production but also for preventing any potential build-up of certain nutrients.

Materials and methods

A long-term fertilizer experiment started in 1969 at Central Rice Research Institute, Cuttack, Odisha, India. Using this experiment, a study was conducted to analyze the balance of micronutrients and their interrelationship. The experiment was composed of ten nutrient management treatments viz. control; nitrogen (N); N + phosphorus (NP); N + potassium (NK); nitrogen, phosphorus and potassium (NPK); farmyard manure (FYM); N + FYM; NP + FYM; NK + FYM; and NPK + FYM with three replications. Micronutrients in soil (total and available), added fertilizers and organic manures and in rice plant were analyzed. Besides, atmospheric deposition of the micronutrients to the experimental site was also calculated. A micronutrient balance sheet was prepared by the difference between output and input of total micronutrients.

Results and discussion

Application of FYM alone or in combination with chemical fertilizer increased the diethylenetriamine pentaacetate (DTPA)-extractable Fe, Mn and Zn over the control treatment. The treatment with NPK + FYM had the highest soil DTPA-extractable Fe, Mn, Zn and Cu after 41 years of cropping and fertilization. Application of chemical fertilizers without P decreased the DTPA-extractable Zn over the control while the inclusion of P in the fertilizer treatments maintained it on a par with the control. The application of P fertilizer and FYM either alone or in combination significantly increased the contents of total Fe, Mn, Zn and Cu in soil mainly due to their micronutrient content and atmospheric depositions. A negative balance of Zn was observed in the N, NP, NK and NPK treatments, while a positive balance observed in the remaining treatments. The balance of Mn was negative in all the treatments, due to higher uptake by the rice crop than its addition.

Conclusions

Long-term application of chemical fertilizers together with FYM maintained the availability of micronutrients in soil and, thus, their uptake by rice crop.

     

Amoebae from a take-all suppressive soil which feed on Gaeumannomyces graminis tritici and other soil fungi

Amoebae were isolated from soil of the Waite Institute permanent pasture plot which is suppressive to take-all of wheat. Nine species of amoebae belonging to eight genera were tested for their mycophagy against Gaeumannomyces graminis var. tritici, Cochliobolus sativus and Phytophthora cinnamomi. Members of the genera, Gephyramoeba, Mayorella, Saccamoeba, Thecamoeba and an unidentified species of the order Leptomyxida, were mycophagous. Feeding of mycophagous amoebae and their ability to perforate and lyse melanized propagules of fungi are discussed.     

Sequence analysis of Toll-like receptor genes 1-10 of goat (Capra hircus)

This study involved cloning and sequencing of the coding regions of all 10 Toll-like receptor (TLR) genes of goat. Goat TLR 1-10 gene sequences revealed a high degree of nucleotide identity with sheep and cattle sequences (>90%) and 75-85% with pig, mouse and human sequences. At the amino acid level, 85-99% similarity was observed with sheep and cattle and 60-85% with pig, mouse and human. TLR9c DNA of goat showed the highest amino acid identity to that of sheep (99%) while TLR8 cDNA showed the lowest identity of 88.7% to that of sheep. Variations were seen in the number of leucine rich repeats (LRRs) of goat TLRs as compared to other ruminant species with maximum differences in the TLR3 gene. Phylogenetic analysis through molecular evolution and genetic analysis (MEGA) software and multi dimensional scaling revealed a high degree of conservation of goat TLRs with those from other species. However when the TIR domain of all the TLRs were compared, goat TLR7 TIR alone showed a high divergence of 19.3 as compared to sheep sequences. This is the first report of the full-length cDNA sequences of all the 10 TLR genes of goats which would be a useful tool for the study of evolutionary lineages and for phylogenetic analysis.