bluuebunny/crossref_metadata_2025 huggingface dataset:
A taxonomic revision of the Australasian genera
Authors: Venter Stephanus
Published: January 2021

The genus Dracophyllum Labill. is revised, with a total of 61 species being recognised in four subgenera and two species (Dracophyllum minimum F.Muell. and D. strictum Hook.f.) are listed as incertae sedis. The genus Richea R.Br. is reduced to synonymy under Dracophyllum where it is divided into two new subgenera, namely, Dracophyllum subgenus Cystanthe (R.Br.) S.Venter and D. subgenus Richea (R.Br.) S.Venter. Replacement names published here are Dracophyllum laciniatum S.Venter, D. persistentifolium S.Venter and D. tasmanicum S.Venter, and new combinations published here are Dracophyllum alpinum (Menadue) S.Venter, D. continentis (B.L.Burtt) S.Venter, D. desgrazii (Hombr. ex Decne.) S.Venter, D. gunnii (Hook.f.) S.Venter, D. pandanifolia (Hook.f.) S.Venter, D. procerum (F.Muell.) S.Venter, D. sprengelioides (R.Br.) S.Venter and D. victorianum (Menadue) S.Venter. Nomenclature, descriptions, illustrations, photographs and distribution maps are provided for each species and lectotypes are designated where necessary. A key to the subgenera and keys to species within these are provided.
Proficiency testing for determination of pesticides residues in black tea: Comparison of three robust statistical approaches based on ISO 13528 to estimate the consensus values for small number of participants
Authors: Aryana Nurhani
Published: January 2021

In Indonesia, proficiency testing (PT) provider for determination of pesticides residues in tea is still limited. In addition, many proficiency testing schemes still use consensus value from participants’ results as the assigned value rather than reference assigned value due to some technical and economical issues. However, this mode of assigned value may lack of reliability when the number of participants are small and the test results are highly varied. In these conditions, many PT providers were not able to perform the statistical data evaluation causing the needed PT became unavailable. This study is aimed to investigate the suitable statistical approach in estimating the consensus value for small number of participants in PT for determination of pesticides residues in black tea. Three robust statistical approaches recommended by ISO 13528: variants of Algorithm A, Hampel method, and M estimator were compared to evaluate the participants’ data from the PT schemes organized by Research Center of Chemistry-LIPI in 2014 and 2015. All of the robust statistical approaches showed to be able to assess the performance of participants. The Hampel method and M estimator were the most adequate robust statistical approaches in obtaining the closest consensus values compared to the homogeneity test results, stability monitoring results, and the assigned valued in the real PT scheme, for endosulfan sulphate and bifenthrin, respectively.
Characterization of solid perfume based on Cocoa Butter with Jasmine Oil as fragrance
Authors: Septiyanti Melati , Meliana Yenny , Suryani Novia , Hendrawati
Published: January 2021

Cocoa butter can be obtained from by-product of chocolate powder processing from the result of mechanical pressing using hydraulic press. As a source of vitamin E, cocoa butter in cosmetic has some advantages which are to soften and moisturize the skin. Meanwhile, jasmine can be used as a fragrance in perfume and cosmetics. In this study, cocoa butter was used as raw material for solid perfume. Its optimal concentration in the product was determined. Solid perfume was made by melting cocoa butter and beeswax at 90°C followed by adding jasmine oil as fragrance. The formulation variation of solid perfume was done with cocoa butter concentration 10%, 20%, 30%, 40% and 50% (w/w) and addition of patchouli oil as fragrance fixative agent. The following tests were carried out on the products: functional group analysis, hardness test, homogeneity test, physical stability test, melting point test, antioxidant test, and organoleptic test. The result showed that the variation of cocoa butter concentration affected the physical characteristics of the solid perfume. The optimum product of solid perfume based on panelists’ organoleptic test was achieved with cocoa butter concentration of 30%. It had an organoleptic score of 3.63, antioxidant activity with IC50 value of 201.98µg/mL, hardness penetration 14.16 mm/second, melting point 90°C and pH value 4.
Effect of solvent concentration in sago starch fractionation
Authors: Sondari Dewi , Restu Witta Kartika , Sampora Yulianti , Devy Yenni Apriliany , Yosta Teo Duri , Muawanah Anna
Published: January 2021

The research studied the effect of solvent concentration in the fractionation process from sago starch in order to achieve the amylose fraction. The amylose is aimed to be applied as a functional material such as for edible film. The fractionation process is carried out by utilizing N-butanol as the solvent with a variety of concentration (10, 12.5 and 15%). The highest result is achieved from the concentration of butanol of 15%. It resulted in a yield of 31.19%, a 30.78% solubility, and swelling ability of 2.37%. The spectra from Fourier transform infrared showed the same specific peaks of the obtained amylose. However, each of them shows different intensity means the fractionation process affect the resulted amylose.
Antifungal of Cashew (Anacardium occidentale Linn) leaves, nutshells, and peduncle bagasse ashes extracts against sooty mould fungi (Capnodium sp)
Authors: Andayanie W R , Lukito M , Chasanatun F
Published: January 2021

Different concentrations of cashew (Anacardium occidentale Linn) leaves, nutshells, and peduncle bagasse ashes extract evaluated for growth inhibition of Capnodium sp and the antifungal activity. Results revealed that different concentration of cashew leaves, nutshells, and peduncle bagasse ashes extracts showed values difference of absorbance (DA) ranging from 0.00 to 0.42. All the concentrations of extracts showed significant inhibition in the spore germination of sooty mould. The highest levels caused maximum inhibition in the spore germination followed by lower concentrations of cashew nut shells, peduncle bagasse and leaf extracts respectively. Cashew nut shells extract had a high level of total polyphenolic, flavonoid content, pH and low values of titratable acidity, which could be attributed to its potent antifungal activity.
Anticancer activity of Lampung Robusta Coffee extract fractions
Authors: Husniati Husniati , Oktiani Devi , Suhartati Tati , Pratama Valentino Budi , Devi Anastasia Fitria , Artanti Nina
Published: January 2021

Coffee is a popular beverage that is consumed worldwide. Habitual coffee drinking is associated with cancer risk reduction including pre- and post-menopausal breast cancer. The invert correlation between coffee intake and breast cancer risk is weak, therefore coffee is potential for functional beverage. Coffee should be taken for several times per day to get its benefit. Compounds which give the cancer reduction effect are still debatable, they can be compounds with antioxidant or non-antioxidant properties. Robusta coffee from Lampung has a special meaning for Indonesian coffee lovers due to its strong aroma and flavour with affordable price. In order to observe the anticancer activity of Lampung Robusta coffee, its aqueous methanol extract was passed through a chromatography column containing polyamide with aqueous methanol as the eluent with a gradient of 10%. A total of 54 fractions were obtained and labelled as A to K fractions. Chlorogenic acid was detected in fractions A and B. Meanwhile, it was not detected in other fractions including G fraction. This G fraction, however, was the only one to show cytotoxicity against MCF-7 breast cancer cell line. This result suggests that this fraction contains potential compounds with anticancer activity.
Design of hybrid RO/NF permeate staging for the supply of clean water in Tanjung Lame Village
Authors: Prayoga Anton , Zakwan Muhammad , Bismo Setijo
Published: January 2021

The groundwater sources from community wells in Tanjung Lame village, Pandeglang district, are very salty, so they are not suitable for consumption. Reverse osmosis (RO) and nanofiltration (NF) membrane are alternative desalination technologies for treating clean water from saltwater wells. However, the pressure required on a conventional single-stage RO filtration system is very high. The purpose of this study is to design a hybrid RO/NF filtration system that can operate at low pressure. The designed hybrid RO/NF permeate staging has proven to be able to produce clean water from saltwater wells in Tanjung Lame village at low pressure. To obtain optimum results, the designed hybrid RO/NF permeate staging is operated at the first and second stage pressure of 6 and 3 bar, respectively. At that pressure, the salt rejection and TDS of permeate is 97.06% and 85 ppm, respectively. The water recovery rate and permeate flow rate is 31% and 1.55 liters/minute, respectively.
Synthesis of Nano-Composite Ag/TiO2 for Polyethylene Microplastic Degradation Applications
Authors: Maulana Didit Ardi , Ibadurrohman Muhammad , Slamet
Published: January 2021

The aim of this research is to synthesize Ag/TiO2 nano-composites to study their ability to degrade microplastics in water, followed by varying size of microplastic particles as pollutants in drinking water. The method used for synthesizing Ag/TiO2 is Photo Assisted Deposition (PAD). Characterizations done to determine the difference between TiO2 and Ag/TiO2 were SEM-EDX and UV-Vis DRS. Polyethylene microplastics were selected as samples in this study. The variation of microplastic size used is 100-125, 125-150, and 150-250 micrometers with initial concentrations of 100 ppm. Magnetic stirrers used at a rotational speed of 2000 rpm during the degradation process with a UV lamp irradiation. The addition of the Ag dopant has a good effect in microplastic degradation, where the percentage of degradation reaches 100% within 120 minutes of irradiation at an initial concentration of 100 ppm. An initial concentration of 100 ppm obtained the best percent degradation at particle size 125-150 micrometers, where 100% degradation achieved at 90 minutes irradiation.
Establishment of Traceability Chain For pH Measurement in Indonesia
Authors: Hindayani Ayu , Hamim Nuryatini , Elishian Christine , Aristiawan Yosi , Mulyana Muhammad Rizky , Handayani Eka Mardika , Pratiwi Eka , Ginanjar Gigin
Published: January 2021

As a consequence of the globalization of trade and industries, the presence of an accurate and traceable measurement has become very important for quality assurance of a product or service in the market, including pH measurement. pH measurement is a basic analysis used in a wide variety of applications, such as agriculture, wastewater treatment, industrial processes, research and development, and environmental monitoring. The reliable and comparable results of pH measurement are advantaged as one of the parameters for quality control that will affect the decision making. The Electrochemistry Laboratory under Deputy of National Measurement Standard – National Standardization Agency of Indonesia (SNSU–BSN) has a main duty to ensure the reliability, comparability, and traceability of pH measurements in Indonesia, as a commitment in building chemical metrology infrastructure. In this article, all the activities related to the establishment of traceability chain for pH measurement in Indonesia are comprehensively discussed. As of currently, the Electrochemistry Laboratory has successfully developed the secondary method for pH measurement using differential potentiometric cell, production of certified reference material (CRM) for buffer solution (oxalate, phthalate, phosphate, and borate buffer), dissemination by proficiency testing (PT) schemes for pH measurement, participation in the key comparison (KC) of APMP.QM-K91 for phthalate buffer, and claim submission for the Calibration Measurement Capabilities (CMCs) of phthalate buffer (pH 3.97-4.03) with expanded uncertainty 0.004.
Mechanical properties of edible film from Tanduk Banana (Musa corniculata Rumph) peels for food packaging
Authors: Muryeti  , Ningtyas Rina , Nugroho Herdian , Sabrina Aufi
Published: January 2021

The widespread use of plastic has adverse environmental impacts. Therefore, it is necessary to find environmentally friendly packaging material alternatives, derived from biopolymers. This study aimed to make biodegradable films from Tanduk Banana (Musa corniculata Rumph) peels and determine the characteristics of these films. The methods used were extraction of pectin from Tanduk banana peel, making of edible film and characterization of mechanical properties of edible film. The raw materials used were variation of tapioca flour (0g; 0.6g; 1.2g and 1.8g), CMC 3%, Glycerol 0.5 ml, and 6g of banana peel pectin. Various tests were carried out to determine mechanical properties of edible film, include tensile strength, elongation, modulus Young, and thickness. Test results show the optimum value of edible film thickness is 1.025 mm and obtained at the composition of 2.4g of tapioca flour. The optimum value of tensile strength is 8.22 MPa, the elongation percentage is 40.4% and obtained at the composition of 1.2g tapioca flour. The optimum value of modulus young is 0.20347 MPa and obtained at the composition of 1.2g tapioca flour.
Protected percolation: a new universality class pertaining to heavily-doped quantum critical systems
Authors: Fayfar Sean , Bretaña Alex , Montfrooij Wouter
Published: January 2021

We present computer simulations on a class of percolative systems that forms a new universality class. We determine the universal critical exponents for this new class from simulations on lattices consisting of up to one billion sites. These new percolative systems differ from standard systems in that once a cluster breaks off the lattice spanning cluster, its sites become protected and cannot be removed. We demonstrate that despite this restriction on the evolution of isolated clusters, the scaling relationships between the critical exponents remain valid. Protected percolation closely mimics the situation in heavily-doped quantum critical systems where isolated magnetic clusters are protected from Kondo screening. We show that protected percolation in three dimensions violates the Harris criterion, explaining why universal exponents for quantum phase transitions have been elusive.
Observation of strong magneto plasmonic nonlinearity in bilayer graphene discs
Authors: Chin Matthew L , Matschy Sebastian , Stawitzki Florian , Poojali Jayaprakash , Hafez Hassan A , Turchinovich Dmitry , Winnerl Stephan , Kumar Gagan , Myers-Ward Rachael L , Dejarld Matthew T , Daniels Kevin M , Drew H Dennis , Murphy Thomas E , Mittendorff Martin
Published: January 2021

Graphene patterned into plasmonic structures like ribbons or discs strongly increases the linear and nonlinear optical interaction at resonance. The nonlinear optical response is governed by hot carriers, leading to a red-shift of the plasmon frequency. In magnetic fields, the plasmon hybridizes with the cyclotron resonance, resulting in a splitting of the plasmonic absorption into two branches. Here we present how this splitting can be exploited to tune the nonlinear optical response of graphene discs. In the absence of a magnetic field, a strong pump-induced increase in on-resonant transmission can be observed, but fields in the range of 3 T can change the characteristics completely, leading to an inverted nonlinearity. A two temperature model is provided that describes the observed behavior well.
Increased Pulse Pressure Variability Within the First 24 Hours Leads to Poor Disposition in Subarachnoid Hemorrhage Patients
Authors: Dowlati Ehsan , Triano Matthew J , Felbaum Daniel R , Mai Jeffrey C , Aulisi Edward F , Armonda Rocco A , Chang Jason J
Published: January 2021

Background

Aneurysmal subarachnoid hemorrhage (SAH) continues to be associated with significant morbidity and mortality despite treatment advancements. Although high blood pressure (BP) remains a significant risk factor in aneurysmal SAH and rerupture, the role of BP parameters and fluctuation in prognostication remains unclear. We sought to define how BP parameters and variability within 24 hours of hospitalization in acute-onset SAH affects patient discharge outcomes.

METHODS

We retrospectively analyzed a prospectively collected cohort of SAH patients. Hourly BP parameters, including systolic BP (SBP), diastolic BP, pulse pressure (PP), and their corresponding variability (delineated by SD), were collected to investigate associations with the primary endpoint of discharge disposition.

RESULTS

One hundred and seventy-four SAH patients were included in the study. On bivariate analysis, Hunt–Hess (HH) score, Fisher grade, intraventricular hemorrhage, external ventricular drain placement, and SBP and PP variability were significantly associated with a poor disposition. Poor disposition was significantly associated with age, HH score, intraventricular hemorrhage, and PP variability on multivariate analysis. PP variability remained an independent predictor for poor disposition (odds ratio 1.11, 95% confidence interval, 1.02–1.21, P = 0.02) when adjusting for potential confounders.

Conclusions

Increased BP and PP variability within the first 24 hours of admission portends a poor discharge disposition for aneurysmal SAH patients.
Interactive gene networks with KNIT
Authors: Magruder D S , Liebhoff A M , Bethune J , Bonn S
Published: January 2021

KNIT is a web application that provides a hierarchical, directed graph on how a set of genes is connected to a particular gene of interest. Its primary aim is to aid researchers in discerning direct from indirect effects that a gene might have on the expression of other genes and molecular pathways, a very common problem in omics analysis. As such, KNIT provides deep contextual information for experiments where gene or protein expression might be changed, such as gene knock-out and overexpression experiments.

Availability and implementation

KNIT is publicly available at http://knit.ims.bio. It is implemented with Django and Nuxtjs, with all major browsers supported.

Supplementary information

Supplementary data are available at Bioinformatics online.
Sleep apnoea has a dose-dependent effect on atrial remodelling in paroxysmal but not persistent atrial fibrillation: a high-density mapping study
Authors: Nalliah Chrishan Joseph , Wong Geoffrey R , Lee Geoffrey , Voskoboinik Aleksandr , Kee Kirk , Goldin Jeremy , Watts Troy , Linz Dominik , Wirth Daniel , Parameswaran Ramanathan , Sugumar Hariharan , Prabhu Sandeep , McLellan Alex , Ling Han , Joseph Stephen , Morton Joseph B , Kistler Peter , Sanders Prashanthan , Kalman Jonathan M
Published: January 2021

Aims

Obstructive sleep apnoea (OSA) associates with atrial fibrillation (AF), but the relationship of OSA severity and AF phenotype with the atrial substrate remains poorly defined. We sought to define the atrial substrate across the spectrum of OSA severity utilizing high-density mapping.

Methods and results

Sixty-six consecutive patients (male 71%, age 61 ± 9) having AF ablation (paroxysmal AF 36, persistent AF 30) were recruited. All patents underwent formal overnight polysomnography and high-density left atrial (LA) mapping (mean 2351 ± 1244 points) in paced rhythm. Apnoea–hypopnoea index (AHI) (mean 21 ± 18) associated with lower voltage (−0.34, P = 0.005), increased complex points (r = 0.43, P < 0.001), more low-voltage areas (r = 0.42, P < 0.001), and greater voltage heterogeneity (r = 0.39, P = 0.001), and persisted after multivariable adjustment. Atrial conduction heterogeneity (r = 0.24, P = 0.025) but not conduction velocity (r = −0.09, P = 0.50) associated with AHI. Patchy regions of low voltage that co-localized with slowed conduction defined the atrial substrate in paroxysmal AF, while a diffuse atrial substrate predominated in persistent AF. The association of AHI with remodelling was most apparent among paroxysmal AF [LA voltage: paroxysmal AF −0.015 (−0.025, −0.005), P = 0.004 vs. persistent AF −0.006 (−0.017, 0.005), P = 0.30]. Furthermore, in paroxysmal AF an AHI ≥ 30 defined a threshold at which atrial remodelling became most evident (nil–mild vs. moderate vs. severe: 1.92 ± 0.42 mV vs. 1.84 ± 0.28 mV vs. 1.34 ± 0.41 mV, P = 0.006). In contrast, significant remodelling was observed across all OSA categories in persistent AF (1.67 ± 0.55 mV vs. 1.50 ± 0.66 mV vs. 1.55 ± 0.67 mV, P = 0.82).

Conclusion

High-density mapping observed that OSA associates with marked atrial remodelling, predominantly among paroxysmal AF cohorts with severe OSA. This may facilitate the identification of AF patients that stand to derive the greatest benefit from OSA management.
REGULATION OF A BACTERIOPHAGE T4 LATE GENE, soc, WHICH MAPS IN AN EARLY REGION
Authors: Macdonald Paul M , Kutter Elizabeth , Mosig Gisela
Published: January 2021

We have sequenced and analyzed the expression of an early region of the bacteriophage T4 genome that surprisingly contains a late gene, soc. soc is oriented in the same direction as early genes, like the T4 lysozyme gene. Northern hybridization of early and late T4 RNA, using cloned T4 restriction fragments as probes, identified two long early transcripts and a short late transcript, all containing the soc-coding sequence. Thus, soc is transcribed both early and late. It is, however, translated only late. The inhibition of soc translation from the long early transcripts can be explained by formation of a hairpin in the RNA that sequesters the soc ribosome-binding site. The transcript initiated at the late promoter cannot form this hairpin and is, therefore, translated.
MUTAGENIC SPECIFICITY OF A NOVEL T4 DNA POLYMERASE MUTANT
Authors: Reha-Krantz Linda J , Liesner Evelyn M
Published: January 2021

The in vivo mutational specificity of a novel T4 DNA polymerase mutator mutant, tsM19, was determined. Two genetic tester systems were used to characterize the mutant. Results of our studies indicate that tsM19 promotes transition and transversion mutagenesis and, possibly, frameshift mutagenesis. Central G:C base pairs in runs of three or more consecutive G:C base pairs may be target sites for tsM19-induced transitions.
A GENETIC ANALYSIS OF TARGETED GROWTH IN MICE
Authors: Riska Bruce , Atchley William R , Rutledge J J
Published: January 2021

Effects of normal growth regulation on components of phenotypic variance and covariance of body weight were examined in a cross-fostering study of growth between 2 and 10 wk of age in ICR randombred mice. Different early growth rates caused genetic, postnatal maternal and residual environmental variances to increase, but these variances were subsequently reduced by negative autocorrelation between early and later growth. Postnatal maternal variance continued to increase for about 1 wk after weaning but then decreased substantially. Genetic variance caused by preweaning growth followed a pattern of increase and decrease very similar to that of postnatal maternal variance, but this pattern was masked by new genetic variance. Normal growth regulation affects the magnitudes of genetic variances and serial autocorrelations. The timing of these changes suggests that regulation of cell numbers reduces variance near the end of exponential growth, but this may be obscured by subsequent increase in cell size. In contrast with earlier studies, we find that targeted growth reduces both genetically and environmentally determined differences among early growth trajectories. Final size may be determined by an antagonistic balance between early growth rate and age at initiation of puberty.
MODIFICATIONS OF MEAN OVARIOLE NUMBER, FRESH WEIGHT OF ADULT FEMALES AND DEVELOPMENTAL TIME IN DROSOPHILA MELANOGASTER INDUCED BY DROSOPHILA C VIRUS
Authors: Thomas-Orillard Michele
Published: January 2021

Drosophila C virus, a picornavirus that has some influence on ovarian morphogenesis, was discovered in a French strain of Drosophila melanogaster. When the strain was infected by Drosophila C virus (DCV), the mean number of ovarian tubes and weights of the adult females increased, but the developmental time from egg to imago decreased. The maternal effects observed when DCV was present disappeared when the strain was DCV free but were restored by experimental contamination.
SHORTVEIN, A NEW COMPONENT OF THE DECAPENTAPLEGIC GENE COMPLEX IN DROSOPHILA MELANOGASTER
Authors: Segal Daniel , Gelbart William M
Published: January 2021

Our laboratory has been concerned with the structure and function of the decapentaplegic gene complex (DPP-C) in Drosophila melanogaster . To define the boundaries of the complex, we have studied the genetics of mutations allelic to a previously discovered mutation shortvein (shv), known to reside near decapentaplegic. We found that shortvein resides distal to Hin-d and dpp within the same polytene chromosome doublet, 22F1-2. Lesions in shv can affect not only the formation of the wing veins but also can interfere with normal development of parts of the adult and/or be lethal. Like those of dpp mutants, the shv-associated adult abnormalities affect distal epidermal structures. Some shv lesions cause a larval lethal syndrome which is associated with an unusually long larval stage (ca. five to six times its normal duration). Lesions in shv exhibit an involved pattern of complementation with dpp mutations, indicating that both shv and dpp are parts of a single gene complex. A subset of the array of mutant phenotypes displayed by shv/dpp trans-heterozygotes appear to be dpp-specific phenotypes; we interpret these as reflecting an inactivation effect of certain shv alleles on dpp functions. The other abnormalities displayed by these trans-heterozygotes appear to be shv-specific defects; we view these as indicating an inactivation effect of certain dpp mutations on shv functions. Furthermore, embryonic lethal (EL) mutations within the DPP-C exhibit allelic interactions with all shv mutations. We conclude that the shortvein region represents a newly identified integrated portion of the DPP-C.
GENETIC ANALYSIS OF MUTANTS OF SACCHAROMYCES CEREVISIAE RESISTANT TO THE HERBICIDE SULFOMETURON METHYL
Authors: Falco S C , Dumas K S
Published: January 2021

Sulfometuron methyl (SM), a potent new sulfonylurea herbicide, inhibits growth of the yeast Saccharomyces cerevisiae on minimal media. Sixty-six spontaneous mutants resistant to SM were isolated. All of the resistance mutations segregate 2:2 in tetrads; 51 of the mutations are dominant, five are semidominant and ten are recessive. The mutations occur in three linkage groups, designated SMR1, smr2 and smr3. Several lines of evidence demonstrate that the SMR1 mutations (47 dominant and four semidominant) are alleles of ILV2 which encodes acetolactate synthase (ALS), the target of SM. First, SMR1 mutations result in the production of ALS enzyme activity with increased resistance to SM. Second, molecular cloning of the ILV2 gene permitted the isolation of mutations in the cloned gene which result in the production of SM-resistant ALS. Finally, SMR1 mutations map at the ILV2 locus. The smr2 mutations (four recessive, two dominant and one semidominant) map at the pdr1 (pleiotropic drug resistance) locus and show cross-resistance to other inhibitors, typical of mutations at this locus. The smr3 mutations (six recessive and two dominant) define a new gene which maps approximately midway between ADE2 and HIS3 on the right arm of chromosome XV.
THE GENE STRUCTURES OF SPONTANEOUS MUTATIONS AFFECTING A CAENORHABDITIS ELEGANS MYOSIN HEAVY CHAIN GENE
Authors: Eide David , Anderson Philip
Published: January 2021

We have isolated spontaneous mutations affecting the unc-54 major myosin heavy chain gene of Caenorhabditis elegans (variety Bristol). Spontaneous unc-54 mutants occur in C. elegans populations at a frequency of approximately 3 × 10-7. We have studied the gene structure of 65 independent unc-54 mutations using filter-transfer hybridization techniques. Most unc-54 mutations (50 of 65) exhibit no abnormalities detected with these techniques; these mutations are small lesions affecting less than 100 base pairs. Approximately 17% of the mutations (11 of 65) are simple deletions, ranging in size from less than 100 base pairs to greater than 17 kilobases. One isolate contains two separate deletions, each of which affects unc-54. Two mutants contain tandem genetic duplications that include a portion of unc-54 and extend 8-10 kilobases beyond the 5' terminus of the mRNA. Conspicuously absent from our collection of spontaneous unc-54 mutations are any resulting from insertion of transposable genetic elements. Such mutants, if they occur, must arise at a frequency of less than 5 × 10-9
GENE CONVERSION AT THE GRAY LOCUS OF SORDARIA FIMICOLA: FIT OF THE EXPERIMENTAL DATA TO A HYBRID DNA MODEL OF RECOMBINATION
Authors: Kalogeropoulos Angelos , Thuriaux Pierre
Published: January 2021

A hybrid DNA (hDNA) model of recombination has been algebraically formulated, which allows the prediction of frequencies of postmeiotic segregation and conversion of a given allele and their probability of being associated with a crossing over. The model considered is essentially the "Aviemore model." In contrast to some other interpretations of recombination, it states that gene conversion can only result from the repair of heteroduplex hDNA, with postmeiotic segregation resulting from unrepaired heteroduplexes. The model also postulates that crossing over always occurs distally to the initiation site of the hDNA. Eleven types of conversion and postmeiotic segregation with or without associated crossover were considered. Their theoretical frequencies are given by 11 linear equations with ten variables, four describing heteroduplex repair, four giving the probability of hDNA formation and its topological properties and two giving the probability that crossing over occurs at the left or right of the converting allele.—Using the experimental data of Kitani and coworkers on conversion at the six best studied gray alleles of Sordaria fimicola, we found that the model considered fit the data at a P level above or very close (allele h4) to the 5% level of sampling error provided that the hDNA is partly asymmetric. The best fitting solutions are such that the hDNA has an equal probability of being formed on either chromatid or, alternatively, that both DNA strands have the same probability of acting as the invading strand during hDNA formation. The two mismatches corresponding to a given allele are repaired with different efficiencies. Optimal solutions are found if one allows for repair to be more efficient on the asymmetric hDNA than on the symmetric one. In the case of allele g1, our data imply that the direction of repair is nonrandom with respect to the strand on which it occurs.
SPONTANEOUS IR DUPLICATIONS GENERATED AT MITOSIS IN ASPERGILLUS NIDULANS: FURTHER EVIDENCE OF A PREFERENTIAL SITE OF TRANSPOSED ATTACHMENT
Authors: Daud F , Ortori G S , Roper J A
Published: January 2021

A radiation-induced translocation, T(IIR → IIIL), has been shown to be nonreciprocal and to have most of IIR, including its terminus, attached uninverted to the terminus of IIIL.—Progeny with the IIR segment in duplicate, obtained from crosses of T(IIR → IIIL) to strains with a standard genome, were unstable at mitosis; like earlier duplication strains, they suffered deletions from either duplicate segment. Frequent mitotic crossing over occurred between the duplicate IIR segments so that, following deletions, more than two classes of stable, balanced products arose from each heterozygous duplication strain.— Spontaneous, mitotically arising duplications of the IR segment, bearing the rate-limiting adE20 allele, can be selected on adenine-free medium on which they emerge as vigorous sectors from the stunted adE20 colony. It was shown previously that most such duplications, when selected from a strain with standard genome, had the terminal IR segment attached to the end of IIR. Selection has now been made from an adE20 strain carrying T(IIR → IIIL), and seven of the 13 independent IR duplications were linked to the III-IIR translocation complex. In three strains analyzed further, the duplicate IR segments, which included the IR terminus, were attached uninverted to the terminus of IIR; the segments of IR were of approximately equal genetic length.—This supports earlier suggestions that there is a preferential site for the initiation of IR duplications and a preferential site, the IIR terminus, for their attachment.
POPULATION BOTTLENECKS AND NONEQUILIBRIUM MODELS IN POPULATION GENETICS. II. NUMBER OF ALLELES IN A SMALL POPULATION THAT WAS FORMED BY A RECENT BOTTLENECK
Authors: Maruyama Takeo , Fuerst Paul A
Published: January 2021

A model is presented in which a large population in mutation/drift equilibrium undergoes a severe restriction in size and subsequently remains at the small size. The rate of loss of genetic variability has been studied. Allelic loss occurs more rapidly than loss of genic heterozygosity. Rare alleles are lost especially rapidly. The result is a transient deficiency in the total number of alleles observed in samples taken from the reduced population when compared with the number expected in a sample from a steady-state population having the same observed heterozygosity. Alternatively, the population can be considered to posses excess gene diversity if the number of alleles is used as the statistical estimator of mutation rate. The deficit in allele number arises principally from a lack of those alleles that are expected to appear only once or twice in the sample. The magnitude of the allelic deficiency is less, however, than the excess that an earlier study predicted to follow a rapid population expansion. This suggests that populations that have undergone a single bottleneck event, followed by rapid population growth, should have an apparent excess number of alleles, given the observed level of genic heterozygosity and provided that the bottleneck has not occurred very recently. Conversely, such populations will be deficient for observed heterozygosity if allele number is used as the sufficient statistic for the estimation of 4Nev. Populations that have undergone very recent restrictions in size should show the opposite tendencies.
LETHAL MUTATIONS FLANKING THE 68C GLUE GENE CLUSTER ON CHROMOSOME 3 OF DROSOPHILA MELANOGASTER
Authors: Crosby Madeline A , Meyerowitz Elliot M
Published: January 2021

We have conducted a genetic analysis of the region flanking the 68C glue gene cluster in Drosophila melanogaster by isolating lethal and semilethal mutations uncovered by deficiencies which span this region. Three different mutagens were used: ethyl methanesulfonate (EMS), ethyl nitrosourea (ENU) and diepoxybutane (DEB). In the region from 68A3 to 68C11, 64 lethal, semilethal, and visible mutations were recovered. These include alleles of 13 new lethal complementation groups, as well as new alleles of rotated, low xanthine dehydrogenase, lethal(3)517 and lethal(3)B76. Six new visible mutations from within this region were recovered on the basis of their reduced viability; all proved to be semiviable alleles of lethal complementation groups. No significant differences were observed in the distributions of lethals recovered using the three different mutagens. Each lethal was mapped on the basis of complementation with overlapping deficiencies; mutations that mapped within the same interval were tested for complementation, and the relative order of the lethal groups within each interval was determined by recombination. The cytological distribution of genes within the 68A3-68C11 region is not uniform: the region from 68A2,3 to 68B1,3 (seven to ten polytene chromosome bands) contains at least 13 lethal complementation groups and the mutation low xanthine dehydrogenase; the adjoining region from 68B1,3 to 68C5,6 (six to nine bands) includes the 68C glue gene cluster, but no known lethal or visible complementation groups; and the interval from 68C5,6 to 68C10,11 (three to five bands) contains at least three lethal complementation groups and the visible mutation rotated. The developmental stage at which lethality is observed was determined for a representative allele from each lethal complementation group.
LIMITS TO THE RELATIONSHIP AMONG RECOMBINATION, DISEQUILIBRIUM AND EPISTASIS IN TWO-LOCUS MODELS
Authors: Hastings Alan
Published: January 2021

I determine limits to the equilibrium relationship among epistasis, recombination and disequilibrium in two-locus, two-allele models using linear programming techniques. I show that when allele frequencies are one-half at each locus, the symmetric model is the fitness pattern that generates the most disequilibrium for the smallest level of epistasis. When allele frequencies deviate from one-half, much larger levels of epistasis are required to generate similar levels of disequilibrium. I determine the level of epistasis required to generate observed significant levels of disequilibrium in natural populations. The overall implication is that disequilibrium will be large at equilibrium only between strongly interacting, closely linked loci.
ESTERASE GENES IN PARALLEL COMPOSITE CROSS BARLEY POPULATIONS
Authors: Luckett D J , Edwards K J R
Published: January 2021

The California population of Composite Cross V of barley was used as the source of three subpopulations that were started from generations 10, 20 and 30, respectively, and were grown in parallel environmental conditions in Cambridge for eight generations. Outcrossing rates (0.2%) were even lower than in the California material, and heterozygotes were correspondingly rare, so that the populations were essentially mixtures of homozygous lines. Four esterase loci that were polymorphic in the base Composite Cross V remained so in all the derived populations, but showed considerable changes in allelic frequency over time, particularly at two of the genes. Multilocus analysis showed that strong directional changes occurred in all three populations, but they were not consistent. One particular genotype became predominant in the population derived from generation 10, whereas in the other two populations it was a genotype with different alleles at the Est1 and Est3 loci that rose to frequencies of more than 50%. Strong directional selection undoubtedly occurred in these populations, but did not cause parallel changes in esterase gene frequencies. These data do not facilitate a discrimination between the alternative explanations of hitchhiking or multilocus selection at these loci.
MODIFICATIONS IN ESTIMATING THE NUMBER OF GENES FOR A QUANTITATIVE CHARACTER
Authors: Cockerham C Clark
Published: January 2021

In estimating the minimum number of genes contributing to a quantitative character, it is suggested that the squared difference between the means of the two parents be corrected for experimental variance and that the genetic variance stemming from differences in gene frequencies of the parents be estimated by least squares utilizing information on all entries.
FRAMESHIFT SUPPRESSION BY thyA MUTANTS OF ESCHERICHIA COLI K-12
Authors: Herrington Muriel B , Kohli Anjali , Faraci Maria
Published: January 2021

We have extended our previous study on the suppression of frameshift mutants by Escherichia coli thyA mutants by assaying suppression of 15 rIIB frameshift mutants of bacteriophage T4 on one of our suppressing thyA mutant strains. The majority of insertion mutants were suppressible, whereas none of the deletion mutants tested was suppressible. Frameshift suppression could be inhibited by adding thymidine to the assay medium, but was not affected by the presence of a restrictive rpsL mutation in the host strain. We suggest that the frameshift suppression event occurs at a nonsense codon generated by the frameshift mutation.
WHAT CAN BE LEARNT ABOUT SELECTION FROM GENE FREQUENCY DISTRIBUTION?
Authors: Mani G S , Cook L M , Marvdashti R
Published: January 2021

Polymorphism has been studied at the Esterase 6 locus in the Yellow Fever mosquito Aedes aegypti (L.) in laboratory stocks. At least 12 alleles are present, with up to four coexisting in a stock. The allele frequency distribution is quite sharply peaked at a mode of about 0.25. The experimental data are compared with the results of simulation based on two models, one in which the initial global distribution is taken to be the stationary distribution obtained from the neutral model assuming M = 4μ Ne = 1 and the other in which the initial global distribution is generated from the experimental populations studied. The results suggest that the patterns observed are not likely to arise through random fluctuation of frequencies in neutral alleles, but that some kind of selection maintains polymorphism, either in the wild or in the laboratory, or both.
VERY SHORT PATCH MISMATCH REPAIR IN PHAGE LAMBDA: REPAIR SITES AND LENGTH OF REPAIR TRACTS
Authors: Lieb M , Allen E , Read D
Published: January 2021

Five amber mutations in the repressor (cl) gene of bacteriophage λ recombine anomalously with nearby cl mutations. When any of these markers is used in four-factor crosses, cl  + recombinants that are expected to require three crossovers occur at high frequencies. These recombinants are attributable to very-short-patch (VSP) repair of specific mismatches in DNA heteroduplexes formed during recombination between the markers flanking cl. The sites of the repairprone mutations and the lengths of repair tracts have now been determined. Amber mutations subject to VSP repair are C to T transitions in (see PDF), the sequence methylated by the product of gene dcm, and also in the related 5′CAGG or 5′CCAG sequences. Ambers arising in CAG sequences found in other contexts, or in codons other than CAG, were not subject to VSP repair. Repair tracts rarely, if ever, exceed ten nucleotides in length, and can be as short as two nucleotides. A repair-prone mutation does not stimulate recombination between flanking cl markers.
A RECESSIVE CIRCADIAN CLOCK MUTATION AT THE frq LOCUS OF NEUROSPORA CRASSA
Authors: Loros Jennifer J , Richman Adam , Feldman Jerry F
Published: January 2021

A circadian clock mutant of Neurospora crassa, the most distinctive characteristic of which is the complete loss of temperature compensation of its period length, maps to the frq locus where seven other clock mutants have previously been mapped. This mutant, designated frq-9, is recessive to the wild-type allele and to each of the other frq mutants; thus, it differs from the other mutants, which show incomplete dominance to wild type and to each other. Complementation analysis suggests either that the frq locus is a single gene or that frq-9 is a deletion that overlaps adjacent genes. Preliminary efforts at fine structure mapping have indicated that recombination between certain pairs of frq mutations is less than 0.005%, a distance consistent with the locus being a single gene. The recessive nature of frq-9, coupled with complete loss of temperature compensation, suggests that this mutant may represent the null phenotype of the locus and that the frq gene is involved in the temperature compensation mechanism of the clock.—Genetic mapping studies have placed the frq locus on linkage group VIIR, midway between oli (oligomycin resistance) and for (formate auxotrophy), about 2 map units from each, and clearly indicate that frq and oli are separate genes.
The Responding Site of the Rex Locus of Drosophila melanogaster
Authors: Swanson Ellen E
Published: January 2021

Rex is a dominant, maternal-effect locus in the heterochromatin of the X chromosome Drosophila melanogaster. It causes an early mitotic exchange-like event between heterochromatic elements of an attached- XY in X/attached-XY embryos of Rex mothers. Evidence is presented here that the site of Rex action is the ribosomal RNA gene cluster (the bb locus) only; no other heterochromatin is affected. The Rex locus may be useful in studying regulation of rRNA-gene copy number, mitotic chromosome behavior and heterochromatic function.
Regulation of NADP-Malic Enzyme in the Eye-Antennal Disc of D. melanogaster/D. simulans Hybrids: Evidence for cis- and trans-Regulation
Authors: Kuhn David T , Sprey Th E
Published: January 2021

Pattern regulation of malic enzyme (ME) distribution in D. melanogaster/D. simulans (mel/sim) hybrid eye-antennal discs was investigated. Both cis- and trans-regulation of the spatial distribution pattern was observed within the eye portion of the disc complex. D. simulans possesses gene(s) that operate in trans in the hybrids to suppress ME staining along the morphogenetic furrow, a region that always stains in D. melanogaster. ME structural genes of both species were expressed in cis within the ommatidial preclusters and clusters of the hybrids. Malic enzyme was not expressed elsewhere in the eye disc of either species. Restoration of the D. melanogaster furrow pattern element occurred in partial hybrids that were homozygous for the D. melanogaster 3R where the structural gene resides. Therefore, a dominant gene(s) in the D. simulans 3R suppresses the D. melanogaster furrow pattern, while a recessive gene(s) in the D. melanogaster 3R restores the pattern when the trans-suppressor is removed. These conclusions agree with those found for regulation of aldehyde oxidase distribution in D. melanogaster/D. simulans hybrid wing discs.
Molecular Analysis of Diepoxybutane-Induced Mutations at the rosy Locus of Drosophila melanogaster
Authors: Reardon J T , Liljestrand-Golden C A , Dusenbery R L , Smith P D
Published: January 2021

We have analyzed at the molecular level diepoxybutane-induced mutants determined to have lesions affecting expression of the ry locus. Of the 21 mutants analyzed here, genetic analysis suggested that five were putative deficiencies involving ry and adjacent lethal loci. However, molecular analysis confirmed that only two of these five putative deficiencies were in fact deletions detectable by the methods used in the analysis. The remaining 16 mutants were viable as homozygotes, suggesting that their lesions were confined to the ry locus. Seven of these 16 intragenic mutants were determined to be deletions of genetic material as evidenced by altered restriction patterns relative to the wild type patterns. Thus, nine of 21 (43%) diepoxybutane-induced mutants are due to deletions ranging in size from approximately 50 base pairs to more than 8 kilobase pairs. Most of the deletions (seven of nine or 78%) are intragenic and less than 250 base pairs in size; it seems that most, if not all, affect coding rather than regulatory sequences.
Isolation and Characterization of a Photorepair-Deficient Mutant in Drosophila melanogaster
Authors: Boyd James B , Harris Paul V
Published: January 2021

A mutation abolishing photorepair has been localized to map position 56.8 centimorgans on the second chromosome of Drosophila melanogaster. Strains homozygous for the phr allele are totally devoid of photorepair and partially deficient in excision repair. Both defects map to the chromosomal region between pr and c. Since a homozygous phr stock exhibits reduced photoreactivation, the corresponding wild-type allele plays a significant role in UV resistance.