Testing a global standard for quantifying species recovery and assessing conservation impact

Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a "Green List of Species" (now the IUCN Green Status of Species). A draft Green Status framework for assessing species' progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species' viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics (conservation legacy, conservation dependence, conservation gain, and recovery potential). We tested the framework with 181 species representing diverse taxa, life histories, biomes, and IUCN Red List categories (extinction risk). Based on the observed distribution of species' recovery scores, we propose the following species recovery categories: fully recovered, slightly depleted, moderately depleted, largely depleted, critically depleted, extinct in the wild, and indeterminate. Fifty-nine percent of tested species were considered largely or critically depleted. Although there was a negative relationship between extinction risk and species recovery score, variation was considerable. Some species in lower risk categories were assessed as farther from recovery than those at higher risk. This emphasizes that species recovery is conceptually different from extinction risk and reinforces the utility of the IUCN Green Status of Species to more fully understand species conservation status. Although extinction risk did not predict conservation legacy, conservation dependence, or conservation gain, it was positively correlated with recovery potential. Only 1.7% of tested species were categorized as zero across all 4 of these conservation impact metrics, indicating that conservation has, or will, play a role in improving or maintaining species status for the vast majority of these species. Based on our results, we devised an updated assessment framework that introduces the option of using a dynamic baseline to assess future impacts of conservation over the short term to avoid misleading results which were generated in a small number of cases, and redefines short term as 10 years to better align with conservation planning. These changes are reflected in the IUCN Green Status of Species Standard.

An incentive-based mitigation strategy to encourage coexistence of large mammals and humans along the foothills of Indian Western Himalayas

Escalation of human–wildlife conflict (HWC) is a barrier to the conservation of ecological corridors across the globe. The existing mechanisms to counter HWC are either economically and socially taxing, or ineffective for long-term management. We assessed HWC in the corridor linking the Rajaji and Corbett Tiger Reserves in Uttarakhand, India, and its drivers, along with the benefits derived by local communities from the forest. We designed an innovative incentive-based mitigation mechanism to encourage coexistence of people and wildlife around the corridor. Costs incurred due to conflict and benefits derived from the forest were assessed using semi-structured questionnaire-based personal interviews (n = 757) with representatives from forest dependent households (hh). Fuelwood (1678.7 ± 131 kg hh⁻¹ year⁻¹), fodder (4772 ± 186 kg hh⁻¹ year⁻¹) and green/dry grass (3359 ± 104 kg hh⁻¹ year⁻¹) contributed 3 ± 1%, 6 ± 0.5% and 9 ± 1%, respectively, to the annual income of dependent households. 69% of the households practising agriculture reported crop damage by wild animals, 19% of the households that owned livestock reported livestock loss, and 1.58% reported attack on humans resulting in injuries. The cost incurred due to crop raiding and livestock depredation was US $ 159.83 ± 1.0 hh⁻¹ year⁻¹ and US $ 229.32 ± 34.0 hh⁻¹ year⁻¹, respectively. Crop loss was positively associated with the number of crops grown per season and cultivation of sugarcane, wheat and pulses, and negatively with distance from forest and cultivation of fodder and finger millet. Livestock depredation was negatively associated with distance from forest and positively with number of livestock owned, primarily calves. The accounting profit from cultivating a hectare of land, in the absence of crop depredation by wild animals, was estimated at US $ 3571.84 ha⁻¹ year⁻¹ and US $ 361.44 ha⁻¹ year⁻¹ for the plains and hills, respectively. This value can be used to calculate the payments to be paid to local communities to encourage them to adopt HWC resistant agricultural and pastoralism practices. The net present value of benefits from participating in the payments to encourage coexistence programme for 5 years, discounted at 12%, was US $ 12,875.7 ha⁻¹ for the plains and US $ 1302.9 ha⁻¹ for the hills.

Novel Quaternary Chalcogenide/Reduced Graphene Oxide-Based Asymmetric Supercapacitor with High Energy Density

In this work we have synthesized quaternary chalcogenide Cu₂NiSnS₄ (QC) nanoparticles grown in situ on 2D reduced graphene oxide (rGO) for application as anode material of solid-state asymmetric supercapacitors (ASCs). Thorough characterization of the synthesized composite validates the proper phase, stoichiometry, and morphology. Detailed electrochemical study of the electrode materials and ASCs has been performed. The as-fabricated device delivers an exceptionally high areal capacitance (655.1 mF cm^-2), which is much superior to that of commercial micro-supercapacitors. Furthermore, a remarkable volumetric capacitance of 16.38 F cm^-3 is obtained at a current density of 5 mA cm^-2 combined with a very high energy density of 5.68 mW h cm^-3, which is comparable to that of commercially available lithium thin film batteries. The device retains 89.2% of the initial capacitance after running for 2000 cycles, suggesting its long-term capability. Consequently, the enhanced areal and volumetric capacitances combined with decent cycle stability and impressive energy density endow the uniquely decorated QC/rGO composite material as a promising candidate in the arena of energy storage devices. Moreover, Cu₂NiSnS₄ being a narrow band gap photovoltaic material, this work offers a novel protocol for the development of self-charging supercapacitors in the days to come.

Prevalence of Peripheral Arterial Disease (PAD) in End Stage Renal Disease (ESRD) Patients on Hemodialysis: A Study from Central Nepal

Background Peripheral arterial disease is a common condition in the hemodialysis population with an estimated prevalence ranging from 17-48%. Many studies have been conducted to know the prevalence of peripheral vascular disease in hemodialysis population. However no such study has been conducted so far in Nepal.Objective This study was carried out with an objective to assess the prevalence of Peripheral Arterial Disease in End Stage Renal Disease Patients on Hemodialysis.Method Fifty patients with a diagnosis of End Stage Renal Disease (irrespective of the underlying cause), and those who were on hemodialytic support for more than 3 months were studied over a period of one year. Peripheral arterial disease was diagnosed on the basis of the ankle –brachial index, which was the ratio of the resting systolic blood pressure in the arteries of the ankle to that of the brachial artery, measured by using a standard mercury manometer with a cuff of appropriate size and the Doppler ultrasound. Patients with ankle –brachial index ?0.9 were considered positive for peripheral arterial disease.Result A total of 50 End Stage Renal Disease patients were analyzed. The mean age of the patient was 49.81±12.63 years. The age range was from 18- 79 years. Majority of them were males 64% (n=32). Peripheral arterial disease defined by ankle –brachial index ?0.9 was present in 30% (n=15) of patients. The three major cause of End Stage Renal Disease in the study population was Chronic Glomerulonephritis 40 % (n=20), Type 2 Diabetes Mellitus 28 % (n=14) and Hypertension 24 % (n=12). Type 2 Diabetes Mellitus was the commonest cause 53% (n=8) of End Stage Renal Disease in patients with peripheral arterial disease followed by hypertension 33% (n=5). On univariate analysis, peripheral arterial disease was found to be significantly associated with age >40 years (p value= 0.003; OR=14.8; CI=1.75-125.27), Type 2 Diabetes Mellitus (p value= 0.009; OR=5.4; CI=1.44-21.14), parasthesia of lower limbs (p value= 0.001; OR=10; CI-2.31-43.16), and intact PTH >300 ng/ml (p value =0.006; OR=5.7; CI=1.55-21.50). However on multivariate analysis only parasthesia of lower limbs and intact PTH >300 ng/ml were significantly and independently associated with peripheral arterial disease, while other variables were not significant.Conclusion Peripheral arterial disease was common occurrence in End Stage Renal Disease patients on hemodialysis. Ankle –brachial index needs to be included as a routine assessment in End Stage Renal Disease patients to detect peripheral arterial disease at its earliest.Kathmandu University Medical Journal Vol.12(3) 2014; 181-184

Genetic analysis of river, swamp and hybrid buffaloes of north-east India throw new light on phylogeography of water buffalo (Bubalus bubalis)

This study analysed buffaloes from north-east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South-East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north-east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp-type buffaloes of north-east India with Lower Assamese (significantly hybrid type) buffaloes in one plane and all the mainland river buffaloes in another plane while the upper Assamese buffaloes being distinct from both these clusters. Analysis of mtDNA D-loop region of 530-bp length was performed on 345 sequences belonging to 23 buffalo populations from various geographical regions to establish the phylogeography of Indian water buffalo. The swamp buffaloes of north-east India clustered with both the lineages of Chinese swamp buffalo. Multidimensional scaling display of pairwise FST derived from mitochondrial DNA data showed clustering of upper Assamese, Chilika and Mediterranean buffaloes distinctly from all the other Indian buffalo populations. Median-joining network analysis further confirmed the distinctness and ancestral nature of these buffaloes. The study revealed north-east region of India forming part of the wider hybrid zone of water buffalo that may probably extend from north-east India to South-East Asia.

Intradialytic Muscle Cramp and its Association with Peripheral Arterial Disease in End Stage Renal Disease Patients on Hemodialysis

INTRODUCTION

 Muscle cramp is a common intradialytic complication observed in hemodialysis patients. Similarly Peripheral arterial disease is a common condition in the hemodialysis population.

METHODS

 Fifty patients with a diagnosis of End Stage Renal Disease who were on hemodialysis were studied over a period of one year. Muscle cramp was defined clinically as contractions of a large muscle group and Peripheral arterial disease was diagnosed on the basis of the ankle -brachial index (ABI).

RESULTS

 A total of 50 End Stage Renal Disease patients were analyzed. The major causes of End Stage Renal Disease in the study population was Chronic Glomerulonephritis 40 % (n=20). Muscle cramps were present in 26% (n=13) cases. Peripheral arterial disease was present in 30% (n=15) of patients. However there was no statistically significant association between the presence of Intradialytic Muscle cramps and peripheral arterial disease (p value =0.18) CONCLUSIONS: Intradialytic Muscle cramps and peripheral arterial disease were common occurrence in end stage renal disease patients on hemodialysis patients, however there was no association between the presence of intradialytic Muscle cramps and peripheral arterial disease.

Acute renal failure in falciparum malaria: clinical characteristics, demonstration of oxidative stress, and prognostication

In this prospective study, we aimed to assess the clinical characteristics of acute renal failure (ARF), determine oxidative stress, as well as to predict the outcome in patients with severe falciparum malaria (FM). The study included a total of 75 subjects; there were 25 adult patients with acute severe FM and ARF, 25 adult patients with uncomplicated FM without ARF, and 25 age- and sex-matched healthy subjects who served as controls. In patients with severe FM and ARF (n = 25), renal failure was non-oliguric in 28% and oliguric in 72%. The average duration of renal failure was 10.53 ± 4.0 days. Sixty percent recovered and 40% died. All patients with non-oliguric presentation recovered. The mean serum malondialdehyde (MDA) levels were 0.82 ± 0.43 μmol/L, 2.97 ± 1.11 μmol/L, and 6.86 ± 2.62 μmol/L, respectively, in healthy controls, in patients with uncomplicated FM, and in those with severe FM with ARF. The Acute Physiology Age and Chronic Health Evaluation II (APACHE II) score, Sequential Organ Failure Assessment (SOFA) score, and the Acute Tubular Necrosis-Individual Severity Index (ATN-ISI) score were all significantly higher in the expired group (19 ± 5.49) when compared to the survivor group (14.4 ± 3.15) (P = 0.014). Kaplan-Meier survival analysis showed that survival was low in patients with delayed hospitalization and longer duration of symptoms. Also, we observed a high occurrence of acute respiratory distress syndrome and central nervous system involvement among the patients who expired.

Carotid intima-media thickness in patients with end-stage renal disease

Accelerated atherosclerosis and cardiovascular disease are major causes of morbidity and mortality in patients of end-stage renal disease. Carotid intima media thickness is taken as a useful surrogate marker of atherosclerosis. Thirty end-stage renal disease (ESRD) patients were subjected to ultrasonography to study CIMT before the initiation of dialysis. CIMT was found to be higher in ESRD patients than in controls. Levels of a serum marker of oxidative stress were also found to be higher in patients than in the controls. CIMT is an easy, noninvasive, reproducible, and cost-effective investigation in patients with chronic renal failure.

Lattice resistance to dislocation motion at the nanoscale

In this Letter, we propose a model that demonstrates the effect of a free surface on the lattice resistance experienced by a moving dislocation in nanodimensional systems. This effect manifests in an enhanced velocity of dislocation due to the proximity of the dislocation line to the surface. To verify this finding, molecular dynamics simulations for an edge dislocation in bcc molybdenum are performed, and the results are found to be in agreement with the numerical implementations of this model. The reduction in this effect at higher stresses and temperatures, as revealed by the simulations, confirms the role of lattice resistance behind the observed change in the dislocation velocity.

A giant vesical calculus

Massive or giant vesical calculus is a rare entity in the recent urological practice. Males are affected more than the females. Vesical calculi are usually secondary to bladder outlet obstruction. These patients present with recurrent urinary tract infection, haematuria or with retention of urine. We report a young male patient who presented with defaecatory problems along with other urinary symptoms. The patient having an average built, non diabetic but hypertensive. The stone could be palpated by physical examination. His urea levels were within normal limits but urine examination shows infection. USG reveals bilateral hydronephrosis with multiple stones in both kidneys along with a giant vesical calculus. After controlling urinary infection and hypertention he underwent an open cystolithotomy. During operation digital rectal help was needed to remove the stone as it was adherent with bladder mucosa. Post operative period was uneventful. His urinary output was quite normal and had no defaecatory problems. Patient left the hospital 10 days after operation.

Taxol-induced cell cycle arrest and apoptosis: dose-response relationship in lung cancer cells of different wild-type p53 status and under isogenic condition

The effective dose, schedule, molecular basis of the cytotoxicity of taxol and their dependence on the genetic background in tumor cells are still not well understood. Here, we examined how the dose-response relationship for taxol varies in lung cancer cells with different p53 status and under isogenic conditions. DNA content analyses in A 549 (p53, +/+) and H 1299 (p53, -/-) cells, showed that taxol progressively induced G2/M arrest in both cell lines in a concentration-dependent manner, which was accompanied by a parallel decrease in the G1 population. G2/M arrest, however, occurred at a lower concentration in A 549 cell lines than in H 1299 cells. The S-phase population in A 549 cells was not significantly changed up to 0.025 microM, but dropped by six-fold at 1.0 microM taxol, in contrast to that in H 1299 cells. A sub-G1 apoptotic population was present at 24 h, even at 0.002 microM taxol, when G2/M arrest was not appreciably detected. In both cell lines, the maximum apoptosis of about 28% was achieved at 0.025 microM taxol, implicating that wild-type p53 does not modulate the level of taxol-induced apoptosis. When we examined the role of the wild-type p53 in isogenic cell lines developed in a H 1299 background, the maximum level of apoptosis was in the range of 28-34% at a drug concentration around 0.03 microM, not significantly different from that observed in parental H 1299 cells. We conclude that taxol is effective in inducing apoptosis at very low doses (0.020-0.035 microM), and that the presence or absence of the wild-type p53 does not make a statistically significant difference in the level of apoptotic cell death in these lung cancer cell lines, but the maximum is attained at a lower drug concentration in the presence of p53.

The A enhancer of polyomavirus: protein-protein interactions for the differential early and late promoter function under nonreplicating conditions

The A enhancer of the polyomavirus early promoter is a 110-bp domain located in the late region and it contains the major late RNA initiation site. The 'core' of this enhancer binds several cellular proteins, including proteins PEA1, PEA2 and PEA3. Another element, NF-D/YY1, is also located in this enhancer. The A enhancer is known to stimulate the early promoter, contains auxiliary elements for replication and serves as the initiator for late transcription. It may also be involved in early-to-late switch. We were interested in investigating how the A-core- and NF-D-binding proteins regulate early and late promoter activity under nonreplicating conditions and how the protein-protein interactions affect the function of the individual elements. By point mutational analysis, we show that, except for PEA1, all other proteins activate the early and late promoters differentially under nonreplicating conditions. All three core-binding proteins, and the protein bound to the NF-D site, are activators and have a combinatorial effect on early promoter activity. On late transcription, only PEA1 acts positively and inactivation of the NF-D site is without any effect. In contrast, PEA2 and PEA3 have a repressor-like activity under nonreplicating conditions, indicating that these two proteins might be involved in repressing late transcription, probably early in infection. By increasing the spacing between two consecutive elements, we further show that protein-protein interaction is important for enhancer function. Transactivation of the early promoter was affected by mutations in all four protein-binding sites. Responsiveness of these factors in regard to the late promoter was parallel to their intrinsic promoter strength. The effects of middle and large T antigens are parallel for both the early and the late promoter, suggesting that the pathway(s) for transactivation function of these oncoproteins may overlap downstream. This study with cloned viral promoter will be reflective of situations in vivo, at least partially, under nonreplicating conditions.

Activation of the insulin-like growth factor II transcription by aflatoxin B1 induced p53 mutant 249 is caused by activation of transcription complexes; implications for a gain-of-function during the formation of hepatocellular carcinoma

Aflatoxin B1 (AFB1) induced mutation of the p53 gene at codon 249 (p53mt249) is critical during the formation of hepatocellular carcinoma (HCC) following hepatitis B virus (HBV) infection. p53mt249 markedly increases insulin-like growth factor II (IGF-II) transcription largely from promoter 4, accumulating the fetal form of IGF-II. Modulation of the transcription factor binding to IGF-II P4 by wild-type p53 and p53mt249 was identified. Wild-type p53 inhibited binding of transcription factors Sp1 and TBP on the P4 promoter, while p53mt249 enhanced the formation of transcriptional complexes through enhanced DNA-protein (Sp1 or TBP) and protein-protein (Sp1 and TBP) interactions. p53mt249 stimulates transcription factor Sp1 phosphorylation which might be a cause of increased transcription factor binding on the P4 promoter while wild-type p53 does not. Transfection of hepatocytes with p53mt249 impaired induction of apoptosis by the HBV-X protein and TNF-alpha. Therefore, the blocking of apoptosis through enhanced production of IGF-II should provide a favorable opportunity for the selection of transformed hepatocytes. These results explain the molecular basis for the genesis of HCC by p53mt249 which was found to be induced by a potent mutagen, AFB1.

Interaction of human polyomavirus BK with the tumor-suppressor protein p53

We have been studying the interaction of the oncogenic human polyomavirus BK (BKV) with the tumor-suppressor protein p53 to understand the biology of this virus as well as to understand the basic mechanisms of p53 transactivation. We here demonstrate that p53 binds specifically to the viral promoter at two different sites, S-I (np 361-383) and S-II (np 314-336) in the late region. Site S-I is a 23 bp domain comprising an unique combination of a 10 bp consensus monomer binding site (Pu Pu Pu C (A/T) (T/A) G Py Py Py) which is contiguous with a GC-rich Sp-1 motif that binds p53 in the SV40 promoter. Site S-II also spans a 23 bp sequence containing two tandem consensus binding sites with three base pair mismatches in each and a one base pair deletion. A dimer of a 100 bp region spanning both the binding sites or the site S-I alone induced p53 responsiveness to a basal promoter when cloned upstream from the TATA box, but a similar construct using S-II did not. One tumor-derived mutant protein, p53-175 H, which is defective in DNA binding, also failed to transactivate the reporter gene. We further show that p53 binding-dependent transactivation is abrogated by BKV large T antigen, thereby suggesting an interaction between these two proteins in vivo. In contrast to the isolated p53 binding site, viral early promoter is repressed by p53 in H 1299 cells and the mutants are defective in this function to varying extent. This is suggestive of an involvement of cellular factors in modulating p53's function in the context of the whole promoter. p53 binding sites in BKV are flanked by the binding sites for transcription factors Sp-1 and NF-1 and we show that these transcription factors are present in the immunocomplex with purified p53, implicating modification of p53's transactivation function by protein-protein interaction. Thus, oncoprotein synthesis in this virus might be modulated by p53 in vivo by a complex mechanism other than simple DNA binding and sequestration of the TATA binding protein. Together with SV40 and polyomavirus, which also harbor p53 binding sites, this viral system will serve as a model to understand the role of p53 in viral infection.

Cell-specific modulation of the papovavirus promoters by tumor-suppressor protein p53 in the absence of large T-antigen

The oncoproteins from several DNA tumor viruses form a complex with p53 and inactivate its function. Wild-type p53 is a transcription factor and can regulate eukaryotic promoters both positively and negatively. To elucidate the basis of the opposing functions and to understand whether and how oncoprotein synthesis in papovaviruses is regulated by p53, we studied modulation of the early promoters of SV40, polyomavirus and BK virus in the absence of the interfering effect of viral large T antigens. We here show that murine p53 can regulate the viral promoters either positively or negatively depending on the cell type. A temperature-sensitive mutant p53, 135 Val, at 37 degrees C also showed a cell-specific effect. These results suggest that promoter activation by p53 is not solely determined by p53 binding site, but host factors modulate p53's transactivation function. A TATA-less polyomavirus late promoter was also repressed in HeLa cells and the level of repression was much less in the presence of active early promoter. As p53 and 135 Val were overexpressed to similar extent in different transfected cell lines, variation in transactivation function is not due to the difference in the level of expressed protein. Our observations thus suggest that p53 interactions with cellular factors in addition to the TATA binding protein (TBP) are important for activator and repressor functions of p53. Well-defined viral promoters could thus provide us with an important tool for the identification and characterization of cellular factors that modulate p53-binding dependent gene regulation in animal cells.

Acute renal failure associated with freshwater fish toxin

Clinical observations on toxicity after ingestion of gall bladder of Labeo rohita, a freshwater fish found commonly in India, were recorded from 22 patients between 1985 to 1990. The gall bladder in raw, cooked or desiccated form was swallowed as a traditional method of treatment for various chronic diseases. Patients generally presented with gastrointestinal symptoms such as cramping pain, nausea and vomiting within 12 hours (mean 4.6 +/- 3.7 hours) after ingestion. Subsequently renal failure was observed in all and hepatic dysfunction in some (36.3%) patients. The outcome in general is good. From the clinical course the role of toxic substance(s) is presumed as the causative factor(s), which needs further evaluation.

Biochemical and mutational analysis of the polyomavirus core promoter: involvement of nuclear factor-1 in early promoter function

The polyomavirus enhancer is separated from the early RNA initiation sites by a 120 bp promoter region. To identify the core promoter elements, we introduced base-substitution mutations within the potential elements in the vicinity of the RNA initiation site. Three of these mutants, two with mutations within a putative nuclear factor-1 (NF-1) binding site and the other within the TATA box, exhibited reduced promoter activity by about threefold in the mouse NIH 3T3 cell line. The activity of the other three mutants was either little affected or remained unchanged. Mobility shift assays using specific competitors and antibodies against NF-1 demonstrated the binding of a protein of the NF-1 family at a site adjacent to the TATA box, suggesting a role for NF-1 binding in early promoter function. The effect of these mutations was also evaluated in undifferentiated mouse embryonal carcinoma (F9) cells in the presence of an additional mutation (F441) at nucleotide position 5233. This additional mutation creates a strong binding site for a transcription factor, TEF-1, and helps the virus to grow in this cell line. While the TATA box and the GC box mutants behaved qualitatively in a similar fashion, the NF-1 motif now played a minor role in F9 cells. Western blot experiments demonstrated low levels of NF-1 protein in this cell line. The NF-1 motif partially overlaps a T-antigen binding motif and this motif is not involved in T-antigen-mediated regulation of the early promoter. Our results suggest that a protein of the NF-1 family binds to the core promoter and is important for early transcription in vivo. We further demonstrate that undifferentiated F9 cells contain a very low level of NF-1 and the F441 mutant possibly follows a different mechanism for promoter function in these cells.

Identification of proteins binding to the F441 locus of polyomavirus B enhancer that are required for its activity in embryonic carcinoma cells

A point mutation at nucleotide 5233 of the polyomavirus (A2 strain) enables it to overcome growth restriction in undifferentiated embryonal carcinoma cells. We analysed the binding of nuclear proteins from F9 cells to a 38 bp region that spans this site of mutation and encompasses two copies of the bovine papillomavirus core sequence, CCACCC, and characterized this domain by mutational analysis. Our results showed that the F441 mutation creates a sequence motif which binds TEF-1 or a TEF-1-like protein from F9 cells more strongly than its wild-type counterpart and increases its activity by about 10-fold. Another protein identified as CP1 binds with increased affinity in the presence of the F441 mutation to the CAT box-like sequences which is contiguous with the downstream CCACCC box. Point mutations within these two motifs that abolished binding in vitro also impaired the activity of the F441 locus in vivo. As neither the wild-type sequence without the F441 mutation, nor the F441 template without the CAT box has appreciable activity in vivo, interaction between these two elements is required for function. At a higher level of organization, this interaction is probably extended to factors bound to other domains in the A and B enhancer.

Proteins of the nuclear factor-1 family act as an activator of the late promoter in human polyomavirus BK in vitro

The cis-acting elements for the early and late promoters, as well as the enhancer in the prototype strains of human polyomavirus BK (BKV) are located within a 500 bp intergenic region. We previously studied the specificity of protein binding in this region in vitro and showed that the interaction of proteins of the nuclear factor-1 (NF-1) family is crucial for early promoter activity. We have now extended our study to the BKV late promoter. We show that the late promoter activity in HeLa cell extracts is poor compared to the activity of the early promoter. Using a high template to protein ratio, multiple start sites were detected by primer extension analysis. DNase I protection experiments revealed the presence of three NF-1 binding sites in the late side, in addition to those identified previously in the 68 bp repeats and C element. Competition transcription assays using binding sites for NF-1, AP-1, Sp-1 and a complete 68 bp repeat indicated that only the 68 bp repeat and the NF-1 binding site competed significantly with the late promoter activity. A point mutation in the NF-1 binding site, which destroys the ability of the oligonucleotide to bind NF-1, also impaired its capacity to compete with the late promoter. The ability of NF-1 to activate both the early and late promoters suggests that the proteins of this family act as a bidirectional transcriptional activator in this virus.

Purification and biochemical characterization of hepatocyte nuclear factor 2 involved in liver-specific transcription of the human alpha 1-antitrypsin gene

The upstream region of the human alpha 1-antitrypsin gene binds liver-specific proteins. Two of these proteins, hepatocyte nuclear factors 1 and 2, are essential for liver-specific transcription of this gene. We report for the first time the purification of hepatocyte nuclear factor 2 from rat liver nuclei. This protein, purified to apparent homogeneity by DNA sequence-specific affinity chromatography, appeared on sodium dodecyl sulfate-polyacrylamide gels as a single polypeptide band of molecular mass of 68 kDa. The polypeptide after extraction from the gel matrix and subsequent renaturation bound specifically to the recognition sequences (-88 to -125) and protected the same region of the promoter against DNase I digestion.

Characteristics of the Solitary Waves in Multicomponent Plasmas

We have investigated ion-acoustic solitary waves in a multicomponent plasma. The study shows an interaction of the negatively charged particles with the solitary waves, due to which interesting physical behaviour of the solitary waves is observed. Moreover, the isothermality and the non-isothermality of the plasma exhibit different soliton-type solutions and a transition of the soliton's behaviour can be shown through the changes of the non-isothermality in the plasma.

Soliton Characteristics at the Critical Density of Negative Ions in Ion-beam Plasmas

By using the reductive perturbation technique, ion-acoustic waves are studied in a generalised multicomponent plasma. The multiple ions modify drastically the characteristics of the solitary waves. In particular, the negative ions have a critical density at which the nonlinearity of the Korteweg-deVries (K-dV) equation vanishes and the ion-acoustic solitary wave is seen to be described by a modified K-dV (mK-dV) equation. Using higher order nonlinearities, the non-uniform transition of the K-dV equation to the mK-dV equation along with the conservation of the Sagdeev potential is described. Theoretical observations on the existence of the solitary waves, as expected, could be of interest in laboratory plasmas

Identification of HeLa cell nuclear factors that bind to and activate the early promoter of human polyomavirus BK in vitro

Human polyomavirus BK (BKV), an oncogenic DNA virus, differs from other papovaviruses in the organization of the regulatory region and in tissue tropism for kidney cells. The noncoding regulatory region of the viral genome in prototype strains includes three 68-base-pair (bp) repeats, each containing a number of potential regulatory elements. Some of these signals are unique to human papovaviruses, and others are homologous to those identified in many viral and cellular genes. We evaluated the contribution of individual 68-bp repeats to the initiation of transcription from the early promoter in a HeLa cell extract and identified cis-acting elements to which human cellular factors bind to activate transcription. The early promoter with only one copy of the 68-bp repeat could accurately initiate transcription in vitro, but additional copies were required for its stimulation. DNA-binding assays and DNase I protection experiments identified six domains in the regulatory region protected by human cellular factors. Two of these footprints were located within the proximal and distal 68-bp repeats, and one was located at the late side of the repeats. These footprints were centered over a TGGA(N)5-6GCCA core and were produced by a protein of the nuclear factor 1 (NF-1) family. This protein is either identical or similar to that which binds to the high-affinity site at the origin of adenovirus DNA replication. Three other domains, two at the junctions of the 68-bp repeats and one in the late side of the repeats, were partially protected by proteins with AP-1- and Sp-1-like activities. Transcription initiation from the early promoter was drastically reduced when a complete 68-bp repeat or the NF-1 binding site was used as a competitor in the in vitro assay. However, a point mutation within the NF-1 binding site, which reduced NF-1 binding in vitro to a level comparable to that of nonspecific DNA, also eliminated its ability to compete with early transcription. The murine homolog of the AP-1 binding site had a modest effect on in vitro transcription. Our results suggest that, among the multiple HeLa cell nuclear factors, NF-1 acts as a major activator of the early promoter in vitro.

Promoter activity of the two chicken delta-crystallin genes in a Hela cell extract

The in vitro transcriptional activity of the two delta-crystallin genes (5'-delta 1-delta 2-3') of the chicken was studied in a whole Hela cell extract. Both the delta 1 and delta 2 promoters were recognized by RNA polymerase II in this heterologous system. The major RNA initiation site from the delta 1 promoter was the same in vitro as that which occurs in vivo, as judged by mapping with S1-nuclease, although other minor initiation sites upstream and downstream of the major initiation site were noted. A primer extension experiment showed that the longest RNA synthesized in vitro from a delta 2 template initiated near the beginning of the first exon. The delta 1 promoter was several-fold stronger than that of delta 2 under the present in vitro conditions. Transcription from the delta 1 promoter was abolished by a competitor fragment (c'-II; includes -328 to -63) purified from the delta 2 promoter, indicating that one or more common transcription factors binding upstream from the TATA box are required for in vitro function of the two delta-crystallin promoters. Thus, in the Hela cell extract both delta-crystallin genes contain a functional promoter. We consider the possibility that the single 5'CCAAT3' sequence present in the delta 1 promoter (but lacking in the delta 2 promoter) may contribute to its greater core activity under our conditions. The greater promoter activity of the delta 1-crystallin gene in the Hela cell extract was not sufficient to account for the large ratio of delta 1 to delta 2 mRNA (approximately 50 to 100) in the embryonic chicken lens.

The chicken delta 1-crystallin gene promoter: binding of transcription factor(s) to the upstream G+C-rich region is necessary for promoter function in vitro

There are two linked delta-crystallin genes in the chicken (5' delta 1-delta 2 3'). Only the delta 1 gene has been shown definitively to be active in the lens. Transcription of deletion mutants, reported here, shows that the sequences necessary for the functioning of the delta 1 promoter in a HeLa cell extract are located upstream from the RNA initiation site, between nucleotide positions -121 and -38. This region includes a number of G+C-rich motifs, including one hexanucleotide sequence, CCGCCC, that is repeated six times in the simian virus 40 (SV40) promoter. Competition experiments with purified fragments from the delta 1-crystallin gene promoter showed that binding of transcription factor(s) from the HeLa cell extract to this G+C-rich region is required for promoter activity in vitro. Further, competition experiments using three different fragments from the SV40 promoter suggest that the transcription factor(s) is similar to Sp1, which stimulates transcription by binding to the G+C-rich 21-base-pair repeats of the SV40 promoter, and differs from that which interacts with the SV40 enhancer region.

Ethidium bromide binding to core particle: comparison with native chromatin

Ethidium bromide intercalation into DNA of nuclease digested erythrocyte chromatin and core particle, was followed at low ionic strength by fluorescence measurements, equilibrium dialysis using 14C labelled dye, circular dichroism and electron microscopy. High affinity binding sites in the chromatin are no more present in the core particle, i.e. when the linker is removed. In the case of core particle, a cooperative process occurs, accompanied by a partial stripping of the DNA from the core histone. Finally two populations of core particles can be detected by electron microscopy as far as their binding properties are concerned.

Superstructure and CD spectrum as probes of chromatin integrity

Two types of chromatin were extracted from the same stock of rat liver nuclei by a short exposure to micrococcal nuclease and by shearing respectively. These two materials which are identical in their protein/DNA content and by the presence of the five histones, were compared by means of circular dichroism and electron microscopy. Under the electron microscope and in absence of any divalent cation a superstructure of the unfixed chromatin fiber can be viewed only with native material but is no more present in sheared one. The increase of CD signal at 280 nm (from 2000 to about 4000 cm2 deg.dmole-1) in the case of sheared chromatin is not related to the loss of superstructure but to the structural changes of DNA inside the nucleosomal core which are always produced by shearing. These two correlated observations offer new sensitive probes of the integrity of any native or reconstituted chromatin.

Studies on the melting of DNA

The thermal denaturation of the native DNA in solvents of varying salt concentrations was studied by viscometric and spectrophotometric methods. It was observed that within the molarity range of 0.02 ᴍ to 0.3 ᴍ, the melting temperatures obtained by the two independent methods agreed well, but that at lower ionic strength the agreement was not satisfactory. Both the visco­metric and the spectrophotometric measurements showed an increase of the melting temperature with increasing counterion concentration and a levelling off effect in the neighbourhood of 0.3 ᴍ.

Viscometric studies on the stability of DNA-proflavine complex-II

The binding of proflavine to native DNA increased its stability against thermal denaturation as measured by viscometric method. Up to a moderate ionic strength of 0.058 ᴍ, the melting temperature of the complex increased almost linearly with the increase of dye concentrations and a saturation was reached when one proflavine molecule was added per four to five DNA-Phosphates (D/P≅0.2). The extent of stabilization (ΔTm) produced by dye binding decreased gradually with the increase of ionic strength and no stabilization effect was observed at an ionic strength of about 0.3 ᴍ. The maximum melting temperature attained by Proflavine binding was almost independent of the ionic strength of the medium. The same maximum value was reached as obtained simply by increasing the sodium ion concentration.

Viscometric studies on the stability of DNA-proflavine complex

Viscometric technique has been used to estimate the relative contributions of strong and weak binding modes towards thermal stabilization of the Proflavine-DNA complex. Variation of the ratio of the specific viscosity of the dye-bound DNA to that of the DNA solution (η′sp/η sp) with different dye to DNA-phosphate ratios (D/P) shows that the saturation is attained at D/P value of about 0.2. This effect is more pronounced at lower ionic strengths. Heat-induced helix-coil transition curves at different D/P values at a fixed ionic strength of the buffer reveal a gradual shift towards higher temperature with the increase of D/P and levelling off at D/P of about 0.22. It is suggested that only the strong binding mode causes thermal stabilization of the DNA double helix and the double helix having all the possible intercalating sites saturated by the dye molecules attains the most stable configuration.