Miracle-dz/UniFAR-FTUs huggingface dataset:
ISFET-Based Sensing and Electric Field Actuation of DNA for On-Chip Detection: A Review

The advent of complementary metal-oxide-semiconductor (CMOS) based lab-on-chip (LoC) technology, which combines on-chip sample handling with integrated sensing, heralds the production of revolutionary biomedical devices capable of detecting pathogenic DNA at the point-of-care (PoC) and diagnosing infectious diseases. The ion-sensitive field effect transistor’s (ISFET) inherent sensitivity to hydrogen ions makes them ideal for pairing with DNA amplification reactions to form adept LoC diagnostic devices. This paper reviews the state-of-the-art of CMOS-based LoC devices for DNA detection and discusses electric field actuation as an opportunity for enhanced sensing capabilities. Following our previous review centred on instrumentation, we provide an overview of reported architectures in recent years which have led to portable ISFET-based devices for PoC diagnostics. We then discuss the use of dielectrophoresis (DEP) for electric field manipulation of DNA using low-power, CMOS-compatible microelectrodes. The technique enables positioning of DNA close to ISFET sensing regions to localise hydrogen ion production. This provides a signal boost to the ISFETs that lowers the limit-of-detection and time-to-result of the device, as well as providing a means of on-chip sample preparation. Major challenges include electrode spoiling reactions, hindering electrokinetic effects, and the strong dependence of trapping efficiency on applied voltage. The combination of an ISFET LoC platform with a DEP actuation system is expected to represent a landmark step for the next generation of PoC diagnostics devices.
Antimicrobial and phytochemical analysis of methanolic leaf extracts of Terminalia catappa against some human pathogenic bacteria

Antibiotic resistance is one of the greatest threats of the 21st century. Scientists search for potential antimicrobial sources that can cope with antibiotic resistance. Plants of our community could be excellent source of drugs to fight off this problem. This study is focused on exploring antimicrobial properties of plants against some human pathogens. The antimicrobial potential of 20 methanolic plant extracts was screened against 8pathogenic bacteria by agar well diffusion method. The result indicated that the highest potential was observed in the methanolic extracts exhibited by leaves of Terminalia catappa against all pathogenic bacteria tested with zone of inhibition more than 20mm in all strains. The phytochemical screening of methanolic extracts of T. catappa revealed that they are positive for phyto chemicals; alkaloids, flavonoids, anthraquinones, tannins, steroids, phenols, quinones and saponins. The presence of these biologically active compounds in T. catappa, a valuable medicinal plant support that this plant is being used as medicine for curing various diseases in traditional medicinal systems and can also be employed in the treatmentof various ailements in medicine too.
Biochemistry of Polyisoprenoid Biosynthesis

CONTENTS PERSPECTIVES AND SUMMARy 113 INTRODUCTION . 114 BIOSYNTHESIS OF MEV ALONATE . liS Mevalonate Biosynthesis by a Soluble Enzyme System 116 Mevalonate Biosynthesis by a Microsomal Plus Soluble Enzyme System . 116 BIOSYNTHESIS OF PRENYL PYROPHOSPHATES 120 Biosynthesis o/Isopentenyl Pyrophosphate 120 Biosynthesis 0/ Ally/ic Pyrophosphates 123 CwSpecijic Prenyl Trans/erases 125 C}O-Specijic Prenyl Trans/erases 126 Long-Chain Prenyl Trans/erases 127 Biosynthesis 0/ Dolichols . 127 BIOSYNTHESIS OF SQUALENE 128 BIOSYNTHESIS OF CAROTENES . 132 Formation 0/ Phytoene .
Life in the cooler- starvation in the midst of plenty; and implications for microbial polar life

The physiological reasons for imposition of a lower temperature limit for growth in microorganisms has been a matter of controversy. Recent work has demonstrated that there is a consistent decrease in the affinity of microorganisms for substrates as temperature decreases, thereby reducing their ability to sequester substrates from their environment at low temperature. This applies equally to psychrotrophs, mesotrophs or thermotrophs, over the range of temperature relevant to each physiological type. Therefore, at low environmental temperature microorganisms become increasingly nutrient-limited b ecause of their reduced affinity for substrates. Addition of substrate may reverse the substrate limitation, or increase of temperature may remove the limitation by increasing affinity for substrate. The ecological implications of this are discussed with respect to uptake of both organic substrates by bacteria, and uptake of inorganic substrates by algae in polar regions. Cardinal temperatures for growth
Taxonomic relationship of black-pigmented Bacillus subtilis strains and a proposal for Bacillus atrophaeus sp. nov.

The taxonomic position of Bacillus subtilis strains that produce soluble black pigment is unclear. To assess the genetic relatedness between the pigmented and nonpigmented strains, deoxyribonucleic acid (DNA) reassociation was measured spectrophotometrically. Among the 40 pigmented strains examined, two distinct DNA relatedness groups were found. A total of 25 strains (group 1) showed 24 to 34% DNA relatedness and 15 strains (group 2) showed 70 to 100% relatedness to Bacillus subtilis type strain NRRL NRS-744. The intragroup DNA relatedness values for each group ranged from 85 to 100%; the intergroup relatedness values ranged from 20 to 35%. A multilocus enzyme electrophoresis analysis revealed a low level of similarity between group 1 and group 2 or the nonpigmented group. The group 2 strains and the nonpigmented strains clustered in a common group, indicating the close genetic relationship of these organisms. My results strongly suggest that group 2 is a pigmented variant of B. subtilis, but group 1 is a new species, for which the name Bacillus atrophaeus is proposed. The type strain of the new species is strain NRRL NRS-213.
Elevated anthocyanins protect young Eucalyptus leaves from high irradiance but also indicate foliar nutritional quality to visually attuned psyllids

1. Foliar colour changes with age and, as a consequence, reflects the internal physiology of leaves. Anthocyanins are ‘red’ pigments known for their photoprotective role in young leaves and have been suggested to influence the host‐finding behaviour of insect herbivores. The existence of colour vision in some species of Eucalyptus‐feeding psyllid provides evidence for the possibility of them being able to locate and select leaves based on their age.
Accomplishments and new challenges in dairy genetic evaluations

This review presents the evolution of dairy genetic methods to estimate breeding values. For centuries, human action has shaped animal populations by choosing progenitors of the next generation. Since the twentieth century, applied concepts were integrated into a new discipline, quantitative genetics. The past quarter-century in genetic evaluation of dairy cattle has been marked by evolution in methodology and computer capacity, expansion in the array of evaluated traits, and globalization. Selection index was replaced by mixed model procedures and animal models replaced sire and sire-maternal grandsire models. Recently, application of Bayesian theory to breeding values prediction and variance components estimation has become standard. Individual test-day observations have been used more effectively in the estimation of lactation yield as direct input to evaluation models. Computer speed and storage are less limiting in choosing procedures. National evaluations combined internationally provide evaluations for bulls from all participating countries on each of the national scales, facilitating choices from among many more bulls. Selection within countries has increased inbreeding and the use of similar genetics across countries reduces the previously available genetic diversity. Finally, considerable progress in genomics has created a new tool, genomic selection. The collection and analysis of several types of phenotypic data to evaluate genetic merit will continue to be the most important tool for genetic progress in the foreseeable future. Information will increasingly be obtained from smaller reference populations and the extrapolation from these data will require careful validation.
UNDERSTANDING THE SUCCESS AND FAILURE OF OYSTER POPULATIONS: CLIMATIC CYCLES AND PERKINSUS MARINUS

Abstract Perkinsus (= Dermocystidium) marinus is a major cause of mortality in eastern oysters, Crassostrea virginica. Because initiation of infection and progression of disease are favored by high temperature and high salinity, we hypothesized that climatic cycles influence cycles of disease. Analyses of a 10-y time series of disease prevalence and intensity, chlorophyll a, suspended sediments, water temperature and salinity from a Louisiana site, using a wavelet technique, show a teleconnection between the El Niño-Southern Oscillation (ENSO) and oyster disease in the northern Gulf of Mexico. Salinity increases precede increased disease prevalence by several months. The changes in salinity that trigger changes in disease prevalence and intensity are strongly driven by ENSO events. Interannual variation is important in the initiation and intensification of disease, and salinity is the primary driving factor. The patterns in the environmental and disease time series suggest that epizootics can be initiated within 6 mo of a La Niña event, which produces increased water temperature and salinity. This relationship suggests an approach for predicting epizootics of P. marinus from climate models, which in turn can inform the management of oyster populations.
Construction of a Linkage Map and Identification of Resistance Gene Analog Markers for Root-knot Nematodes in Wild Peach, Prunus kansuensis

The root-knot nematode (RKN) Meloidogyne incognita can cause severe crop loss in economically important Prunusspecieslikepeach(P.persica),almond(P.communis),plum(P.salicina),and apricot(P. armeniaca). Somepeach rootstock, including Nemaguard (P. persica), Nemared (P. persica), and Myrobalan plum (P. cerasifera), display significant resistance to RKN. We present a genetic linkage map constructed by using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) for a peach backcross population (190 individuals) of RKN- resistant 'Honggengansutao' (P. kansuensis) and susceptible 'Bailey' (P. persica). Degenerate primers designed from conserved motifs of known plant resistance gene (R) products were used to amplify genomic DNA sequences. Twenty- two resistance gene analog (RGA) sequences were selected from 48 RGAs with open-reading frames to design sequence-tagged site markers. The linkage map of 'Honggengansutao' is composed of 138 loci (30 SSRs, 102 SRAPs, five RGAs, and one morphological marker for RKN resistance) assigned to eight linkage groups. The map covers 616 cM ofthe peach genomewith anaverage markerspacing of 4.9 cM.ThefiveRGAswere mappedto Groups 2, 7,and 8. One gene (designated PkMi) involved in resistance to RKN was mapped to Group 2 (which also includes the known RKN-resistance RMia gene). BLASTN analysis mapped all RGAs to the peach genome sequence. The map constructed in the study will aid future rootstock breeding with marker-assisted selection to identify additional candidate RGA sequences.
Antidiarrhoeic activity of Sclerocarya birrea bark extract and its active tannin constituent in rats

The antidiarrhoeic activity of the bark of Sclerocarya birrea was investigated. The lyophilized decoction demonstrated antidiarrhoeic activity in experimental models of diarrhoea induced by magnesium sulphate and sodium picosulphate. This antidiarrhoeic activity was related to an inhibition of intestinal transit rather than to inhibition of net secretion of fluid and electrolytes provoked by the laxative agents. A condensed tannin was isolated from the crude drug which produced inhibition in intestinal motility, and the monomer of which was identified as procyanidin.
Research article EVALUATION OF RAPD AND SSR MOLECULAR MARKERS IN BREAD WHEAT GENOTYPES

In this study was evaluated the molecular analysis of 10 bread wheat genotypes using RAPD and SSR markers. In RAPD with 6 primers and in SSR with 5 primers were detected 33 and 17 polymorphism allels for genotypes. The most Polymorphic Information Content (PIC) value and polymorphism percentage was detected by UBC 350 and UBC 109 markers with values 0.53 and 0.50 respectively in RAPDs. In SSRs, Xgwm 469-6D marker detected 14 bands with 5 polymorphic alleles but Xgwm120-2B had the most PIC with 57%. For both markers UPGMA was the best method of clustering. Although markers could show genotypes in 2 clusters but that was very different in molecular analysis. In final results RAPDs could detect more polymorphism alleles than SSRs. Key word: Wheat, Molecular marker, RAPD, SSR, Cluster
Analysis Of DNA Motifs In The Human Genome

DNA motifs include repeat elements, promoter elements and gene regulator elements, and play a critical role in the human genome. This thesis describes a genome-wide computational study on two groups of motifs: tandem repeats and core promoter elements. Tandem repeats in DNA sequences are extremely relevant in biological phenomena and diagnostic tools. Computational programs that discover tandem repeats generate a huge volume of data, which can be difficult to decipher without further organization. A new method is presented here to organize and rank detected tandem repeats through clustering and classification. Our work presents multiple ways of expressing tandem repeats using the n-gram model with different clustering distance measures. Analysis of the clusters for the tandem repeats in the human genome shows that the method yields a well-defined grouping in which similarity among repeats is apparent. Our new, alignment-free method facilitates the analysis of the myriad of tandem repeats replete in the human genome. We believe that this work will lead to new discoveries on the roles, origins, and significance of tandem repeats. As with tandem repeats, promoter sequences of genes contain binding sites for proteins that play critical roles in mediating expression levels. Promoter region binding proteins and their co-factors influence timing and context of transcription. Despite the critical regulatory role of these non-coding sequences, computational methods to identify and predict DNA binding sites are extremely limited. The work reported here analyzes the relative occurrence of core promoter elements (CPEs) in and around transcription start sites. We found that out of all the data sets 49%-63% upstream regions have either TATA box or DPE elements. Our results suggest the possibility of predicting transcription start sites through combining CPEs signals with other promoter signals such as CpG islands and clusters of specific transcription binding sites.
The Role of MicroRNA in Tumor Invasion and Metastasis

Invasion and metastasis are the hallmarks of malignant tumors differing from benign diseases. Most of cancer deaths are mainly due to the development of tumor metastasis rather than primary lesions. Therefore, understanding the molecular mechanisms of invasion and metastasis that take place in malignant cells will provide insight into the development of new therapeutic approaches. However, the complex processes of tumor invasion and metastasis pose a great difficulty in studying their molecular bases. Recent studies have shown that a class of endogenous small nonprotein coding RNAs, termed microRNAs (miRNAs), play an important role in invasion and metastasis of several malignancies, such as breast, liver, prostate and colorectal cancers. In this review, we will summarize the recent studies on the miRNAs in tumor invasion and metastasis, and accentuate the role of miRNAs in elucidating molecular mechanisms of these important processes.
Association between water-use efficiency components and total chlorophyll content (SPAD) in wheat (Triticum aestivum L.) under well-watered and drought stress conditions

This study was conducted to determine the effect of total chlorophyll content (SPAD) on water-use efficiency (WUE) and its components in wheat (Triticum aestivum L.) and to explore a new and cheap method of indirect selection for improving WUE in wheat. Seven bread wheat cultivars were grown in pots under different watering levels. The pattern of variation for WUE and its components was different for cultivars in well-watered and drought stress conditions. The cultivars with high transpiration efficiency (TE) had also high chlorophyll content in wellwatered and drought stress conditions, and there was a positive correlation (0.56) between SPAD and TE in drought stress. TE being relatively tedious to measure in large populations, the SPAD could be used as less expensive surrogates of measuring TE in the early stages of a breeding program.
Fractionation ofThylakoid Membranes withtheNonionic Detergent Octyl-,f.-D-gluc

Thedetergent octyl--gucopyranoside (30mh rin2mHsnolar Tris-maleate, pH7.0) preferentiafly extracts complexes containing protein andchiorophylbs aplus b(CP)fromspinach, leaving aresidue hbly enriched inCPI(P700-chlorophyll aprotein). Useofthedetergent results inarelatively gentle extraction since little free chlorophyll isformed and since sodium dodecyl sulfate-gel electrophoresis (on10%acrylamide) of theextract also reveals thepresence oftwominor chlorophyll acomplexes (apparent molecular weight, 47,000 and43,000) instead oftheusual single complex. Themajor complex preserved isCP64, achlorophyll a/bcomplex (apparent molecular wegh 64,000) which isanoligomer ofanother chlorophyl a/bcomplex, CP27,theNght-harvesting complex (apparent molecular weight, 27,000). Dissociation ofeachcomplex reveals twopolypeptides (molecular weight, 32,000 and28,000) andlimited proteolysis confirms that those ofCP64havethesamestructure asthose ofCP27. Anadditional chlorophyl a/bcomplex (apparent molecular weight, 29,000) isclearly separable fromCP27, anddiffers fromitandCP64inhaving a higher chlorophyll a/bratio andasingle polypeptide (molecular weight, 29,000) which differs structurally fromthose oftheother complexes.
MERCURY AND STABLE ISOTOPES IN FEATHERS OF AUDOUIN'S GULLS AS INDICATORS OF FEEDING HABITS AND MIGRATORY CONNECTIVITY

Abstract To better understand migratory connectivity between breeding and nonbreeding populations, we analyzed mercury (Hg) and stable isotope signatures of nitrogen (δ15N), carbon (δ13C), and sulfur (δ34S) in Audouin's Gulls (Larus audouinii) breeding in two different colonies, the Ebro Delta (northeastern Spain) and the Chafarinas Islands (southwestern Mediterranean). Although abundant information is available on the biology and trophic ecology of this gull's breeding populations, little is known about migration patterns, distribution in winter, or conditions faced during the nonbreeding period. Analyses were carried out on first primary feathers, grown during the summer while gulls are on the breeding grounds, and mantle feathers, grown during the winter. Different isotopic signatures (δ15N, δ13C, and δ34S) in summer (primary) feathers from each area agree with the observed differences in diet between the two colonies. In winter (mantle) feathers, isotopic signatures did not differ, consistent with a common wintering ground and common diet, although the lack of isotopic basemaps in marine systems precludes assignment to a geographical area of reference. Future research is needed to relate isotopic signatures and Hg values in mantle feathers to trophic ecology in wintering areas. Results for Hg indicate that the excretory role played by primary feathers precludes their use as indicators of trophic ecology.
MOLECULAR APPROACHES TO THE STUDY OF PARENTAGE, RELATEDNESS, AND FITNESS: PRACTICAL APPLICATIONS FOR WILD ANIMALS

Abstract Historically, novel molecular techniques have been developed by the human genetics community, adapted for nonhuman organisms by evolutionary biologists, and gradually adopted by the wildlife and fisheries communities. Today, evolutionary biologists routinely rely on molecules to assess mate choice, dispersal, parentage, sex ratios, and other population parameters. All in all, the use of molecular genetic markers has revolutionized population biology—human and otherwise. Prescient wildlife and fisheries biologists have recognized the importance of this revolution and are now using molecular genetic tools to evaluate captive or supplemental breeding programs, population dynamics, stocking strategies, and taxonomic issues. Herein, I explore the use of molecular genetic markers to address questions in wildlife biology and management. Specifically, I review how—among other topics—cannibalism, sex-ratios, dispersal, enumeration, genotoxicology, hybridization, and genetically modified organisms can be e.
Reassessing the Conservation Status of an Island Endemic Frog

Abstract Amphibians are among the most endangered organisms on Earth; however, few monitoring studies have been conducted in the tropics despite high amphibian diversity in these regions. To help fill this gap, we completed fieldwork to reassess the status of the Bloody Bay Poison Frog (Mannophryne olmonae, an endemic from the island of Tobago), classified as “Critically Endangered” by the original IUCN Global Amphibian Assessment, though recently downgraded to “Vulnerable. ” To assess occupancy patterns and population stability, we used occupancy modeling with three years of listening survey data (2011–2013) from 35 sites. To examine patterns of relative abundance and recruitment, we gathered frog encounter rate and body size data from 18 stream-side transects. To assess current distributional limits, we conducted listening surveys at and beyond the known range limits. Together, these data suggest that M. olmonae is more widely distributed than previously reported (we found 23 extralimital populations), is present at a high percentage of sites surveyed (>70%), and is successfully reproducing along all of the stream-side transects on which they were found. Also, we found M. olmonae in a variety of forest types including both degraded secondary forest and abandoned cacao plantations. These field data were instrumental in downgrading this species and emphasize that species of conservation concern need to be monitored on the ground after listing, and these efforts must be continued to detect ongoing change. Our study suggests that even brief surveys in limited areas can quickly provide useful conservation data.
A Comprehensive Curated Reaction Map of Leptin Signaling Pathway

Leptin, a peptide hormone, regulates endocrine function and maintains body weight homeostasis by regulating food intake and energy expenditure via hypothalamus-mediated effects. Impairment in leptin signaling induces obesity, a major health problem worldwide. Leptin signaling regulates other physiological processes such as angiogenesis, hematopoiesis and also has effects on the reproductive, cardiovascular and immune systems. Despite its biomedical importance, a comprehensive catalog of the signaling events activated by leptin is not available as a public resource. Therefore, we initiated cataloging of the molecular reactions in this pathway to develop a detailed reaction map of leptin signaling. For the benefit of scientific community, we provided the leptin signaling pathway through NetPath (http://www.netpath.org), a freely accessible pathway resource previously developed by our group. We anticipate that leptin/leptin receptor signaling map and the data comprising these signaling events will enable future biomedical investigations.