bluuebunny/crossref_metadata_2025 huggingface dataset:
A mutation in the age-1 gene in Caenorhabditis elegans lengthens life and reduces hermaphrodite fertility.
Authors: Friedman D B , Johnson T E
Published: January 2021

age-1(hx546) is a recessive mutant allele in Caenorhabditis elegans that results in an increase in mean life span averaging 40% and in maximal life span averaging 60% at 20 degrees; at 25 degrees age-1(hx546) averages a 65% increase in mean life span (25.3 days vs. 15.0 days) and a 110% increase in maximum life span (46.2 days vs. 22.0 days for wild-type hermaphrodites). Mutant males also show extended life spans. age-1(hx546) is associated with a 75% decrease in hermaphrodite self-fertility as compared to the age-1+ allele at 20 degrees. Using two novel strategies for following the segregation of age-1, we present evidence that longer life results from a mutation in a single gene that increases the probability of survival at all chronological ages. The long-life and reduced-fertility phenotypes cosegregate and are tightly linked to fer-15, a locus on linkage group II. age-1(hx546) does not affect the timing of larval molts, the length of embryogenesis, food uptake, movement, or behavior in any way tested. Although age-1(hx546) lowers hermaphrodite self-fertility, it does not markedly affect the length of the reproductive period with all the increase in life expectancy due to an increase in the length of postreproductive life. In so far as we are aware, this mutant in age-1 is the only instance of a well-characterized genetic locus in which the mutant form results in lengthened fife. It is likely that the action of age-1 in lengthening life results not from eliminating a programmed aging function but rather from reduced hermaphrodite self-fertility or from some other unknown metabolic or physiologic alteration.
Escherichia coli mutations that prevent the action of the T4 unf/alc protein map in an RNA polymerase gene.
Authors: Snyder L , Jorissen L
Published: January 2021

Bacteriophage T4 has the substituted base hydroxymethylcytosine in its DNA and presumably shuts off host transcription by specifically blocking transcription of cytosine-containing DNA. When T4 incorporates cytosine into its own DNA, the shutoff mechanism is directed back at T4, blocking its late gene expression and phage production. Mutations which permit T4 multiplication with cytosine DNA should be in genes required for host shutoff. The only such mutations characterized thus far have been in the phage unf/alc gene. The product of this gene is also required for the unfolding of the host nucleoid after infection, hence its dual name unf/alc. As part of our investigation of the mechanism of action of unf/alc, we have isolated Escherichia coli mutants which propagate cytosine T4 even if the phage are genotypically alc+. These same E. coli mutants are delayed in the T4-induced unfolding of their nucleoid, lending strong support to the conclusion that blocking transcription and unfolding the host nucleoid are but different manifestations of the same activity. We have mapped two of the mutations, called paf mutations for prevent alc function. They both map at about 90 min, probably in the rpoB gene encoding a subunit of RNA polymerase. From the behavior of Paf mutants, we hypothesize that the unf/alc gene product of T4 interacts somehow with the host RNA polymerase to block transcription of cytosine DNA and unfold the host nucleoid.
Length and restriction site heteroplasmy in the mitochondrial DNA of american shad (alosa sapidissima).
Authors: Bentzen P , Leggett W C , Brown G G
Published: January 2021

Restriction endonuclease analysis was used to assess mitochondrial DNA (mtDNA) variation in American shad (Alosa sapidissima) collected from 14 rivers ranging from Florida to Quebec. Two types of heteroplasmy were observed, one involving a major length polymorphism and the other a single restriction site. Shad mtDNA occurred in two principal size classes, 18.3 and 19.8 kb. Of 244 shad examined, 30 were heteroplasmic and carried both size classes of mtDNA in varying proportions; the remainder were homoplasmic for the smaller size class of mtDNA. The large mtDNA variant occurred most frequently at the southern end of the range, and except for two individuals from Nova Scotia, was not detected among shad from rivers north of the Delaware. In contrast, ten shad heteroplasmic for a SalI restriction site originated from rivers ranging from South Carolina to Nova Scotia. DNA mapping and hybridization experiments indicated that the length polymorphism is in the D-loop-containing region and consists of a tandemly repeated 1.5-kb DNA sequence occurring in two and three copies, respectively, in the two major size classes of shad mtDNA. Continuous length variation up to approximately 40 bp occurs among copies of the repeat both within and among individuals. Restriction site data support the conclusion that both forms of heteroplasmy in shad mtDNA have originated more than once.
Packaging specific segments of the Salmonella chromosome with locked-in Mud-P22 prophages.
Authors: Youderian P , Sugiono P , Brewer K L , Higgins N P , Elliott T
Published: January 2021

Hybrid genetic elements, Mud-P and Mud-Q (collectively, Mud-P22s), have been constructed that carry two-thirds of the temperate Salmonella phage P22 genome sandwiched between the ends of transposon Mu. Insertions of these elements in the Salmonella chromosome generate locked-in P22 prophages that cannot excise. Upon induction (as a consequence of the inactivation of P22 c2 repressor), a locked-in prophage replicates its DNA in situ, resulting in the amplification of neighboring regions of the chromosome and the processive packaging of three contiguous headsful of adjacent DNA in one direction from the P22 packaging site, pac. Phage particles in an induced lysate of a Mud-P22 lysogen contain DNA molecules corresponding to several minutes of chromosomal DNA adjacent to the site of prophage insertion and transduce nearby genetic markers with high efficiencies. Mud-P22 prophages have been introduced into an F' episome by transposition; resident Mud insertions on the Salmonella chromosome may be converted to Mud-P22 insertions by homologous recombination in P22-mediated transductional crosses.
Genotypic diversity: estimation and prediction in samples.
Authors: Stoddart J A , Taylor J F
Published: January 2021

We show that a commonly used statistic of genotypic diversity can be used to reflect one form of deviation from panmixia, viz. clonal reproduction, by comparing observed and predicted sample statistics. The characteristics of the statistic, in particular its relationship with population genotypic diversity, are formalised and a method of predicting the genotypic diversity of a sample drawn from a panmictic population using allelic frequencies and sample size is developed. The sensitivity of some possible tests of significance of the deviation from panmictic expectations is examined using computer simulations. Goodness-of-fit tests are robust but produce an unacceptably high level of type II error. With means and variances calculated either from Monte Carlo simulations or from distributional and series approximations, t-tests perform better than goodness-of-fit tests. Under simulation, both forms of t-test exhibit acceptable rates of type I error. Rates of type II are usually large when allele frequencies are severely skewed although the latter test performs the better in those conditions.
Zygotic expression and activity of the Drosophila Toll gene, a gene required maternally for embryonic dorsal-ventral pattern formation.
Authors: Gerttula S , Jin Y S , Anderson K V
Published: January 2021

Maternal expression of the Toll gene is required for the production and the correct spatial organization of all lateral and ventral structures of the Drosophila embryo. We show here that the Toll gene is transcribed zygotically in the embryo and that zygotic expression is important for the viability of the larva. Both genetic and molecular data indicate that the zygotic Toll product has the same biochemical activity as the maternal product. The spatial distribution of the Toll transcript in the embryo was analyzed. In contrast to the uniform distribution of the maternal RNA, the zygotic Toll RNA is present in a complex spatial and temporal pattern in the embryo. A striking feature of this pattern is the correlation of the regions of invaginating cells with sites of accumulation of zygotic Toll RNA.
Restriction map variation at the adh locus of Drosophila melanogaster in inverted and noninverted chromosomes.
Authors: Aguade M
Published: January 2021

Restriction map variation among 39 Standard and 40 In(2L)t chromosomes extracted from a Spanish natural population of Drosophila melanogaster was investigated for a 2.7-kb region encompassing the Adh locus with ten four-cutter restriction enzymes. A total of 20 polymorphisms were detected, representing 15 restriction site polymorphisms, 4 length polymorphisms and the allozyme polymorphism. Variation at the DNA level was compared among St-Adh(F), St-Adh(S) and t-Adh(S) chromosomes. t-Adh(S) chromosomes show a higher level of variation than St-Adh(F) chromosomes. This suggests that In(2L)t arose before the fast/slow allozyme divergence in the evolutionary history of D. melanogaster.
Mhc class II DNA polymorphisms within and between chromosomal species of the Spalax ehrenbergi superspecies in Israel.
Authors: Ben-Shlomo R , Figueroa F , Klein J , Nevo E
Published: January 2021

Restriction fragment length polymorphisms (RFLPs) of two major histocompatibility class II genes (P alpha 1 and Q beta) were studied in 13 populations of four chromosomal species (2n = 52, 54, 58 and 60) of the mole rat, Spalax ehrenbergi superspecies in Israel. A substantial frequency of allelic fragments was found in both genes for all populations, including a desert isolate. In the P alpha 1 gene, one allelic fragment is a result of a deletion mutation which is diagnostic of the 2n = 52 chromosomal species. All other ten allelic variants are the result of point mutations. All mutations are located in a short region flanking the 3' end of the gene. Based on Mhc polymorphisms we confirm earlier evidence that gene flow does not occur between the older chromosomal species (2n = 52, 54, 58), and that reproductive isolation decreases, progressively from the oldest to the youngest species (2n = 60).
Maternal-fetal interactions and the maintenance of HLA polymorphism.
Authors: Hedrick P W , Thomson G
Published: January 2021

There is some empirical evidence that a fetus with an HLA antigen not present in its mother has a higher survival than a fetus sharing antigens with its mother. We have developed both single locus and two-locus theoretical models to examine this mode of selection. First, this immunologically based model appears to have the potential to maintain many alleles at a single locus and to result in an excess of heterozygotes when selection is strong. Second, substantial gametic disequilibrium is maintained between alleles at two loci for this selection mode when recombination is that observed between HLA loci A, B, and DR. Overall, it appears that this mode of selection has the potential to strongly affect genetic variation in the HLA region.
Evolution of bacterial transformation: is sex with dead cells ever better than no sex at all?
Authors: Redfield R J
Published: January 2021

Computer simulations of bacterial transformation are used to show that, under a wide range of biologically reasonable assumptions, transforming populations undergoing deleterious mutation and selection have a higher mean fitness at equilibrium than asexual populations. The source of transforming DNA, the amount of DNA taken up by each transforming cell, and the relationship between number of mutations and cell viability (the fitness function) are important factors. When the DNA source is living cells, transformation resembles meiotic sex. When the DNA source is cells killed by selection against mutations, transformation increases the average number of mutations per genome but can nevertheless increase the mean fitness of the population at equilibrium. In a model of regulated transformation, in which the most fit cells of a transforming population do not transform, transforming populations are always fitter at equilibrium than asexual populations. These results show that transformation can reduce mutation load.
The use of DNA probes for taxonomic study of dictyostelium wild isolates.
Authors: Evans W B , Hughes J E , Welker D L
Published: January 2021

The classification of 27 wild isolates assigned to Dictyostelium discoideum on the basis of morphological criteria was reexamined using probes specific for DNA sequences cloned from the type strain NC4. These probes included ones specific for ribosomal spacer DNA regions and for a ribosomal RNA coding sequence, as well as probes for two chromosomal gene families (actin and discoidin) and for the DIRS-1 transposable element. Four isolates (AC4, WS526, WS584 and ZA3A) which had previously been shown to have unusual mating characteristics were distinctly different from other isolates. We interpret these differences as indicating that the four atypical isolates represent species other than D. discoideum. Probes for the ribosomal spacer DNA either did not hybridize to the DNA of these four isolates or had decreased levels of hybridization to EcoRI restriction fragments of different lengths to that observed with the type strain. With the discoidin probe, all isolates had DNA fragments that hybridized but AC4, WS526, WS584 and ZA3A lacked a pair of fragments that were conserved in NC4 and other isolates. With the actin probe, AC4, WS526, WS584 and ZA3A lacked numerous fragments that the other isolates shared with NC4. The DIRS-1 probes showed strong hybridization with ZA3A and weak hybridization to the other three isolates; however, the major EcoRI fragment in WS526 and WS584 was smaller than that in NC4 while ZA3A and AC4 had fragments of similar size to that in NC4.(ABSTRACT TRUNCATED AT 250 WORDS)
The molecular analyses of an antimorphic mutation of Drosophila melanogaster, Scutoid.
Authors: McGill S , Chia W , Karp R , Ashburner M
Published: January 2021

A dominant mutation of Drosophila melanogaster, Scutoid (Sco), acts as an antimorphic allele of the no-ocelli (noc) gene. In Sco the noc region has been transposed from 35B to 35D on chromosome arm 2L and the noc gene is now adjacent to snail (sna). Induced revertants of Sco are frequently mutant for sna or are aberrations broken very close to sna. A molecular analysis of the Sco chromosome has confirmed that noc is transposed and fused to the sna region. However, only part of the noc region is included within the transposition. The breakpoints of 19 chromosomally aberrant Sco revertants have been mapped at the molecular level. Fourteen of these breakpoints map to the noc region, spread over about 80 kb of DNA. The breakpoints of the remaining five are not within the DNA of the noc region and appear to map within sequences from the sna region. This has been shown directly for three of these, those associated with T(2;3)ScoR+13, In(2L)ScoR+24 and In(2L)ScoR+26. Thus mutation of either noc or sna, genes which are apparently unrelated in their wild-type functions, can revert the antimorphic phenotype of Sco.
Suppressors of a gpa1 mutation cause sterility in Saccharomyces cerevisiae.
Authors: Miyajima I , Nakayama N , Nakafuku M , Kaziro Y , Arai K , Matsumoto K
Published: January 2021

The Saccharomyces cerevisiae GPA1 gene encodes a protein highly homologous to the alpha subunit of mammalian G proteins and is essential for haploid cell growth. We have selected 77 mutants able to suppress the lethality resulting from disruption of GPA1 (gpa1::HIS3). Two strains bearing either of two recessive mutations, sgp1 and sgp2, in combination with the disruption mutation, showed a cell type nonspecific sterile phenotype, yet expressed the major alpha-factor gene (MF alpha 1) as judged by the ability to express a MF alpha 1-lacZ fusion gene. The sgp1 mutation was closely linked to gpa1::HIS3 and probably occurred at the GPA1 locus. The sgp2 mutation was not linked to GPA1 and was different from the previously identified cell type nonspecific sterile mutations (ste4, ste5, ste7, ste11 and ste12). sgp2 GPA1 cells showed a fertile phenotype, indicating that the mating defect caused by sgp2 is associated with the loss of GPA1 function. While expression of a FUS1-lacZ fusion gene was induced in wild-type cells by the addition of alpha-factor, mutants bearing sgp1 or sgp2 as well as gpa1::HIS3 constitutively expressed FUS1-lacZ. These observations suggest that GPA1 (SGP1) and SGP2 are involved in mating factor-mediated signal transduction, which causes both cell cycle arrest in the late G1 phase and induction of genes necessary for mating such as FUS1.
Evolution of the IgA heavy chain gene in the genus Mus.
Authors: Osborne B A , Golde T E , Schwartz R L , Rudikoff S
Published: January 2021

To examine questions of immunoglobulin gene evolution, the IgA alpha heavy chain gene from Mus pahari, an evolutionarily distant relative to Mus musculus domesticus, was cloned and sequenced. The sequence, when compared to the IgA gene of BALB/c or human, demonstrated that the IgA gene is evolving in a mosaic fashion with the hinge region accumulating mutations most rapidly and the third domain at a considerably lower frequency. In spite of this pronounced accumulation of mutations, the hinge region appears to maintain the conformation of a random coil. A marked propensity to accumulate replacement over silent site changes in the coding regions was noted, as was a definite codon bias. The possibility that these two phenomena are interrelated is discussed.
A novel dominant transformer allele of the sex-determining gene her-1 of Caenorhabditis elegans.
Authors: Trent C , Wood W B , Horvitz H R
Published: January 2021

We have characterized a novel dominant allele of the sex-determining gene her-1 of Caenorhabditis elegans. This allele, called n695, results in the incomplete transformation of XX animals into phenotypic males. Previously characterized recessive her-1 alleles transform XO animals into phenotypic hermaphrodites. We have identified five new recessive her-1 mutations as intragenic suppressors of n695. Three of these suppressors are weak, temperature-sensitive alleles. We show that the recessive her-1 mutations are loss-of-function alleles, and that the her-1(n695) mutation results in a gain-of-function at the her-1 locus. The existence of dominant and recessive alleles that cause opposite phenotypic transformations demonstrates that the her-1 gene acts to control sexual identity in C. elegans.
Characterization of the two maize embryo-lethal defective kernel mutants rgh*-1210 and fl*-1253b: effects on embryo and gametophyte development.
Authors: Clark J K , Sheridan W F
Published: January 2021

We have examined the effects on embryonic and gametophytic development of two nonallelic defective-kernel mutants of maize. Earlier studies indicated that both mutants are abnormal in embryonic morphogenesis as well as in the formation of their endosperm. Mutant rgh*-1210 embryos depart from the normal embryogenic pathway at the proembryo and transition stage, by developing meristematic lobes and losing bilateral symmetry. They continue growth as irregular cell masses that enlarge and become necrotic. Somatic embryos arising in rgh*-1210 callus cultures display the rgh*-1210 mutant phenotype. Mutant fl*-1253B embryos are variably blocked from the coleoptilar stage through stage 2. Following formation of the shoot apex in the mutant embryos the leaf primordia and tissues surrounding the embryonic axis continue growth and cell division, while the scutellum ceases development and becomes hypertrophied. Mutant fl*-1253B embryos are unable to germinate, either in mutant kernels or as immature embryos in culture, and the mutant scutellar tissue does not produce regenerable callus. Expression of the fl*-1253B locus during male gametophytic development is revealed by a marked reduction in pollen transmission as a result of mutant expression during the interval between meiosis and the initiation of pollen tube growth. In both mutants, there is considerable proliferation of the aleurone cells of the endosperm. Mutant expression of rgh*-1210 in the female gametophyte is revealed by the abnormal antipodal cells of the embryo sac. These results show that these two gene loci play unique and crucial roles in normal morphogenesis of the embryo. In addition, it is evident that both mutants are pleiotropic in affecting the development of the endosperm and gametophyte as well as the embryo. These pleiotropisms suggest some commonality in the gene regulation of development in these three tissues.
Mammal hyaluronidase activity on chondroitin sulfate and dermatan sulfate: Mass spectrometry analysis of oligosaccharide products
Authors: Bilong Mélanie , Bayat Parisa , Bourderioux Matthieu , Jérôme Murielle , Giuliani Alexandre , Daniel Régis
Published: January 2021

Mammalian hyaluronidases are endo-N-acetyl-D-hexosaminidases involved in the catabolism of hyaluronic acid (HA) but their role in the catabolism of chondroitin sulfate (CS) is also examined. HA and CS are glycosaminoglycans implicated in several physiological and pathological processes, and understanding their metabolism is of significant importance. Data have been previously reported on the degradation of CS under the action of hyaluronidase, yet a detailed structural investigation of CS depolymerization products remains necessary to improve our knowledge of the CS depolymerizing activity of hyaluronidase. For that purpose, the fine structural characterization of CS oligosaccharides formed upon the enzymatic depolymerization of various CS subtypes by hyaluronidase has been carried out by high-resolution Orbitrap mass spectrometry (MS) and extreme UV (XUV) photodissociation tandem MS. The exact mass measurements show the formation of wide size range of even oligosaccharides upon digestion of CS-A and CS-C comprising hexa- and octa-saccharides among the main digestion products, as well as formation of small quantities of odd-numbered oligosaccharides, while no hyaluronidase activity was detected on CS-B. In addition, slight differences have been observed in the distribution of oligosaccharides in the digestion mixture of CS-A and CS-C, the contribution of longer oligosaccharides being significantly higher for CS-C. The sequence of CS oligosaccharide products determined XUV photodissociation experiments verifies the selective β(1 → 4) glycosidic bond cleavage catalyzed by mammal hyaluronidase. The ability of the mammal hyaluronidase to produce hexa- and higher oligosaccharides supports its role in the catabolism of CS anchored to membrane proteoglycans and in extra-cellular matrix.
Evolutionary history of sickle-cell mutation: implications for global genetic medicine
Authors: Esoh Kevin , Wonkam Ambroise
Published: January 2021

Resistance afforded by the sickle-cell trait against severe malaria has led to high frequencies of the sickle-cell mutation [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)] in most parts of Africa. High-coverage sequencing and genotype data have now confirmed the single African origin of the sickle-cell gene variant [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)]. Nevertheless, the classical HBB-like genes cluster haplotypes remain a rich source of HBB-βS evolutionary information. The overlapping distribution of HBB-βS and other disease-associated variants means that their evolutionary genetics must be investigated concurrently. In this review: (1) we explore the evolutionary history of HBB-βS and its implications in understanding human migration within and out of Africa: e.g. HBB haplotypes and recent migration paths of the Bantu expansion, occurrence of ~7% of the Senegal haplotype in Angola reflecting changes in population/SCD dynamics, and existence of all five classical HBB haplotype in Cameroon and Egypt suggesting a much longer presence of HBB-βS in these regions; (2) we discuss the time estimates of the emergence of HBB-βS in Africa and finally, (3) we discuss implications for genetic medicine in understanding complex epistatic interactions between HBB-βS and other gene variants selected under environmental pressure in Africa e.g. variants in HBB, HBA, G6PD, APOL1, APOE, OSBPL10 and RXRA.
Experimental comparison analysis of two heat transfer enhancement methods on a thermochemical reactor
Authors: Han Xiaojing , Liu Shuli , Zeng Cheng , Shen Yongliang , Yang Liu
Published: January 2021

This paper experimentally investigates the performance of a thermochemical reactor for space heating using two heat enhancement methods, copper fins and copper plates. It is evaluated under laboratory conditions with the varying inlet air relative humidity and inlet air flow rate. The evaluated parameters are the reactor air pressure drop, outlet air temperature and outlet water temperature. While improving the reactor performance, the study presents comparative reactor performance of the two methods. The study shows that the copper plate reactor achieves a better desorption performance than the copper fin reactor. In charging, the copper plate reactor can reach the maximum outlet air temperature lifts at 95.1°C in 0.35 h, which is 12.3°C higher than copper fin reactor under the same conditions. In discharging, the peak reactor outlet air temperatures for the two reactors are found under different inlet air flow rate for the different internal air flow characteristics resulted from the copper fins and plates. Also, the copper fin reactor presents higher pressure drop than the copper plate reactor. Additionally, the copper fin reactor presents a slightly higher outlet water temperature in discharging than the plate reactor for the relatively larger thermal contact area between the copper fins and water pipe. Further research should be conducted in improving the reactor performance including reducing the heat loss, reactor optimisation and identifying suitable operating conditions.
Antagonistic Effects of Delia antiqua (Diptera: Anthomyiidae)-Associated Bacteria Against Four Phytopathogens
Authors: Liu Mei , Zhao Xiaoyan , Li Xianxian , Wu Xiaoqing , Zhou Hongzi , Gao Yunxiao , Zhang Xinjian , Zhou Fangyuan
Published: January 2021

Recent studies have revealed multiple roles of insect-associated microbes such as lignin degradation, entomopathogen inhibition, and antibiotic production. These functions improve insect host fitness, and provide a novel source of discovering beneficial microbes for industrial and agricultural production. Previously published research found that in the symbiosis formed by the dipteran pest Delia antiqua (Meigen) (Diptera: Anthomyiidae) and its associated bacteria, the bacteria showed effective inhibition of one fungal entomopathogen, Beauveria bassiana. The antifungal activity of those associated bacteria indicates their potential to be used as biocontrol agents for fungal phytopathogens. In this study, we first isolated and identified bacteria associated with D. antiqua using a culture-dependent method. Second, we tested the antifungal activity of these bacteria against four phytopathogens including Fusarium moniliforme, Botryosphaeria dothidea, and two Fusarium oxysporum strains using the dual-culture method. In total, 74 species belonging to 30 genera, 23 families, eight classes, and four phyla were isolated and identified. Among those bacteria, Ochrobactrum anthropi, Morganella morganii, Arthrobacter sp. 3, and Acinetobacter guillouiae showed significant volatile inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum, respectively. Moreover, bacteria including Rhodococcus equi, Leucobacter aridicollis, Paenibacillus sp. 3, and Lampropedia sp. showed significant contact inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum. Our work provides a new source for discovering biocontrol agents against phytopathogens.
Life History and Damage by Systena frontalis F. (Coleoptera: Chrysomelidae) on Vaccinium macrocarpon Ait.
Authors: Jaffe Benjamin D , Rink Stephanie , Guédot Christelle
Published: January 2021

Pest management of emerging pests can be challenging because very little fundamental knowledge is available to inform management strategies. One such pest, the red-headed flea beetle Systena frontalis (Fabricius) (Coleoptera: Chrysomelidae), is increasingly being identified as a pest of concern in cranberries Vaccinium macrocarpon Aiton (Ericales: Ericaceae). To improve our understanding of this pest and to develop more targeted management programs, we conducted field and laboratory studies to characterize the development, seasonal emergence patterns, and density-dependent plant injury. We found that significantly more flea beetle eggs hatched when exposed to sustained cold treatment between 0 and 5°C for 15 wk than at warmer temperatures, and for shorter and longer cold-period durations. The adults emerged sporadically over the summer, were patchily distributed, fed on both fruit and foliage, and preferentially fed on new plant growth. Using soil cores, we found eggs and larvae located relatively deep (>30 cm) in the soil. These patterns indicate that S. frontalis likely overwinters as eggs, and that targeting the larval stage may be the most effective management approach. Despite the cryptic nature of the larvae, continuing to improve our understanding of this life stage will be critical to optimizing control strategies.
A method for characterizing Cas9 variants via a one-million target sequence library of self-targeting sgRNAs
Authors: Tálas András , Huszár Krisztina , Kulcsár Péter István , Varga Julia K , Varga Éva , Tóth Eszter , Welker Zsombor , Erdős Gergely , Pach Péter Ferenc , Welker Ágnes , Györgypál Zoltán , Tusnády Gábor E , Welker Ervin
Published: January 2021

Detailed target-selectivity information and experiment-based efficacy prediction tools are primarily available for Streptococcus pyogenes Cas9 (SpCas9). One obstacle to develop such tools is the rarity of accurate data. Here, we report a method termed ‘Self-targeting sgRNA Library Screen’ (SLS) for assaying the activity of Cas9 nucleases in bacteria using random target/sgRNA libraries of self-targeting sgRNAs. Exploiting more than a million different sequences, we demonstrate the use of the method with the SpCas9-HF1 variant to analyse its activity and reveal motifs that influence its target-selectivity. We have also developed an algorithm for predicting the activity of SpCas9-HF1 with an accuracy matching those of existing tools. SLS is a facile alternative to the much more expensive and laborious approaches used currently and has the capability of delivering sufficient amount of data for most of the orthologs and variants of SpCas9.
Are declines in insects and insectivorous birds related?
Authors: Tallamy Douglas W , Shriver W Gregory
Published: January 2021

A flurry of recently published studies indicates that both insects and birds have experienced wide-scale population declines in the last several decades. Curiously, whether insect and bird declines are causally linked has received little empirical attention. Here, we hypothesize that insect declines are an important factor contributing to the decline of insectivorous birds. We further suggest that insect populations essential to insectivorous birds decline whenever non-native lumber, ornamental, or invasive plant species replace native plant communities. We support our hypothesis by reviewing studies that show (1) due to host plant specialization, insect herbivores typically do poorly on non-native plants; (2) birds are often food limited; (3) populations of insectivorous bird species fluctuate with the supply of essential insect prey; (4) not all arthropod prey support bird reproduction equally well; and (5) terrestrial birds for which insects are an essential source of food have declined by 2.9 billion individuals over the last 50 years, while terrestrial birds that do not depend on insects during their life history have gained by 26.2 million individuals, a 111-fold difference. Understanding the consequences of insect declines, particularly as they affect charismatic animals like birds, may motivate land managers, homeowners, and restoration ecologists to take actions that reverse these declines by favoring the native plant species that support insect herbivores most productively.
Sucrose promotes stem branching through cytokinin
Authors: Salam Bolaji Babajide , Barbier Francois , Danieli Raz , Teper-Bamnolker Paula , Ziv Carmit , Spíchal Lukáš , Aruchamy Kalaivani , Shnaider Yula , Leibman Diana , Shaya Felix , Carmeli-Weissberg Mira , Gal-On Amit , Jiang Jiming , Ori Naomi , Beveridge Christine , Eshel Dani
Published: January 2021

Shoot branching is an important aspect of plant architecture because it substantially affects plant biology and agricultural performance. Sugars play an important role in the induction of shoot branching in several species, including potato (Solanum tuberosum L.). However, the mechanism by which sugars affect shoot branching remains mostly unknown. In the present study, we addressed this question using sugar-mediated induction of bud outgrowth in potato stems under etiolated conditions. Our results indicate that sucrose feeding to detached stems promotes the accumulation of cytokinin (CK), as well as the expression of vacuolar invertase (VInv), an enzyme that contributes to sugar sink strength. These effects of sucrose were suppressed by CK synthesis and perception inhibitors, while CK supplied to detached stems induced bud outgrowth and VInv activity in the absence of sucrose. CK-induced bud outgrowth was suppressed in vinv mutants, which we generated by genome editing. Altogether, our results identify a branching-promoting module, and suggest that sugar-induced lateral bud outgrowth is in part promoted by the induction of CK-mediated VInv activity.
Psychometric Assessment of the Connor-Davidson Resilience Scale for People With Lower-Limb Amputation
Authors: Miller Matthew J , Mealer Meredith L , Cook Paul F , Kittelson Andrew J , Christiansen Cory L
Published: January 2021

Objective

The purpose of this study was to (1) determine the psychometric properties of the 25- and 10-item Connor-Davidson Resilience Scales (CD-RISC25, CD-RISC10) for people with lower-limb amputation (LLA) in middle age or later, and (2) describe relationships of the CD-RISC with biopsychosocial, sociodemographic, and health variables.

Methods

Participants were included if their most recent LLA was 1 or more years prior, if they were independently walking with a prosthesis, and if they were between 45 and 88 years of age (N = 122; mean = 62.5 years of age [SD = 8]; 59.5 [mean = 58] months since LLA; 88.5% male; 82.0% with dysvascular etiology; 68.0% with unilateral transtibial LLA). Psychometric analyses included assessment of skewness, floor and ceiling effects, internal consistency, and agreement between versions. Correlation analyses were used to determine associations between the CD-RISC with disability, perceived functional capacity, falls efficacy, life-space, anxiety, depression, self-efficacy, social support, sociodemographic, and health variables. Additionally, quartiles of participants were identified using CD-RISC25 and CD-RISC10 scores and compared using ANOVA and post-hoc comparisons for disability, perceived functional capacity, falls efficacy, and life-space.

Results

Skewness, floor, and ceiling effects of both CD-RISC versions were acceptable. Both versions of the CD-RISC were internally consistent (CD-RISC25: α = .92; CD-RISC10: α = .89). The CD-RISC25 and CD-RISC10 were highly correlated with disability, perceived functional capacity, falls efficacy, anxiety, depression, and self-efficacy (r = 0.52–0.67). CD-RISC25 and CD-RISC10 quartile differences, especially the lowest quartile, were identified for disability, perceived functional capacity, falls efficacy, and life-space.

Conclusion

The CD-RISC25 and CD-RISC10 have acceptable psychometric properties for use with people who have LLA. CD-RISC scores are associated with clinically relevant biopsychosocial measures targeted by physical therapist intervention following LLA.

Impact

The CD-RISC may be an appropriate tool to measure resilience following LLA.
Fungicide Sensitivity in Strawberry Powdery Mildew Caused by Podosphaera aphanis in California
Authors: Palmer Michael G. , Holmes Gerald J.
Published: January 2021

Field observations suggest that reduced fungicide sensitivity exists in field populations of Podosphaera aphanis, the causal agent of strawberry powdery mildew (SPM). SPM is one of the most common diseases in strawberry production and is controlled with foliar fungicide applications. This study characterizes the sensitivity of 19 P. aphanis isolates to the most common fungicides used against SPM in California. Isolates were collected from commercial fruit production fields in Oxnard, Ventura, Santa Maria, Salinas, and Watsonville and from a plant nursery in Balico, California. Healthy, unfurled strawberry leaves (cultivar Monterey) free of visual disease symptoms were removed from actively growing plants and treated with one of six commercially formulated fungicides at the minimum labeled rate and inoculated with conidia of P. aphanis. Inoculated leaves were incubated at 20°C under 16/8 h of day/night lighting and assessed for disease incidence after 14 days. Pathogen growth on the treated leaflets constituted a measure of insensitivity to the fungicide. The six fungicide treatments and their average disease incidence on treated leaves for the 19 isolates are penthiopyrad (51.4%), quinoxyfen (41.5%), myclobutanil (39.8%), trifloxystrobin (19.8%), cyflufenamid (19.3%), and fluopyram + trifloxystrobin (3.5%). The average disease incidence for the trifloxystrobin treatment was raised significantly by two isolates considered to be resistant to the product (disease incidence >66.6%). Two isolates collected from organic production systems were sensitive to all fungicides. We document compromised fungicide efficacy due to resistance to most of the fungicides currently used for control of SPM in California. This is the first report of resistance in P. aphanis to any fungicide in California and the first report of resistance in P. aphanis to penthiopyrad and quinoxyfen worldwide.
Management of Central Venous Access in Children With Intestinal Failure
Authors: Wendel Danielle , Mezoff Ethan A. , Raghu Vikram K. , Kinberg Sivan , Soden Jason , Avitzur Yaron , Rudolph Jeffrey A. , Gniadek Michelle , Cohran Valeria C. , Venick Robert S. , Cole Conrad R.
Published: January 2021

Intestinal failure requires the placement and maintenance of a long‐term central venous catheter for the provision of fluids and/or nutrients. Complications associated with this access contribute to significant morbidity and mortality, while the loss of access is an increasingly common reason for intestinal transplant referral. As more emphasis has been placed on the prevention of central line‐associated bloodstream infections and new technologies have developed, care for central lines has improved; however, because care has evolved independently in local centers, care of central venous access varies significantly in this vulnerable population. The present position paper from the Intestinal Failure Special Interest Group of the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) reviews current evidence and provides recommendations for central line management in children with intestinal failure.
Global DNA methylation in suicidal ideation and suicide attempt in schizophrenia
Authors: Bani-Fatemi Ali , Raymond Roger , Adanty Christopher , Dai Nasia , Gerretsen Philip , Graff Ariel , Nobrega Jose N. , De Luca Vincenzo
Published: January 2021

Suicidal behavior is influenced by many risk factors such as childhood trauma, stressful life events, genetic factors, and severe mental illnesses. Suicidal ideation is present in 50% of schizophrenia patients and is associated with an elevated risk of suicide attempt. Studies have shown that epigenetic mechanisms are associated with suicidal behavior in schizophrenia. Although several studies have suggested the importance of epigenetic factors in suicidal ideation and behavior, no studies have investigated global methylation in association with these two phenotypes. This study investigated global methylation level/change in association with current and emergent suicidal ideation and also with suicide attempt. Forty-seven schizophrenia patients were assessed for the association between global methylation and suicide attempt, and a subsample of these patients (n = 27) was assessed for current suicidal ideation. Afterwards, we performed a longitudinal analysis in which global methylation changes during a 3-month follow-up were compared between patients with and without emergent suicidal ideation. This methylation analysis did not find evidence for a significant association between global methylation and suicidal ideation or suicide attempt. To date, there are no robust biomarkers predicting suicidal ideation or behavior in psychotic patients. This study is the first to investigate global methylation in predicting suicidal ideation and behavior. Although we did not find evidence for an association between global methylation and these phenotypes, our findings may offer novel insights into the molecular mechanisms linked to suicide. Future investigation may measure global methylation in association with suicidal ideation or behavior in larger samples.
Early prediction of renal graft function: Analysis of a multi-centre, multi-level data set
Authors: Blazquez-Navarro Arturo , Bauer Chris , Wittenbrink Nicole , Wolk Kerstin , Sabat Robert , Dang-Heine Chantip , Neumann Sindy , Roch Toralf , Wehler Patrizia , Blazquez-Navarro Rodrigo , Olek Sven , Thomusch Oliver , Seitz Harald , Reinke Petra , Hugo Christian , Sawitzki Birgit , Babel Nina , Or-Guil Michal
Published: January 2021

Introduction

Long-term graft survival rates after renal transplantation are still moderate. We aimed to build an early predictor of an established long-term outcomes marker, the glomerular filtration rate (eGFR) one year post-transplant (eGFR-1y).

Materials and Methods

A large cohort of 376 patients was characterized for a multi-level bio-marker panel including gene expression, cytokines, metabolomics and antibody reactivity profiles. Almost one thousand samples from the pre-transplant and early post-transplant period were analysed. Machine learning-based predictors were built employing stacked generalization.

Results

Pre-transplant data led to a prediction achieving a Pearson’s correlation coefficient of r=0.39 between measured and predicted eGFR-1y. Two weeks post-transplant, the correlation was improved to r=0.63, and at the third month, to r=0.76. eGFR values were remarkably stable throughout the first year post-transplant and were the best estimators of eGFR-1y already two weeks post-transplant. Several markers were associated with eGFR: The cytokine stem cell factor demonstrated a strong negative correlation; and a subset of 19 NMR bins of the urine metabolome data was shown to have potential applications in non-invasive eGFR monitoring. Importantly, we identified the expression of the genes TMEM176B and HMMR as potential prognostic markers for changes in the eGFR.

Discussion

Our multi-centre, multi-level data set represents a milestone in the efforts to predict transplant outcome. While an acceptable predictive capacity was achieved, we are still very far from predicting changes in the eGFR precisely. Further studies employing further marker panels are needed in order to establish predictors of eGFR-1y for clinical application; herein, gene expression markers seem to hold the most promise.
swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution
Authors: Chen Lulu , Wu Chiung-Ting , Lin Chia-Hsiang , Dai Rujia , Liu Chunyu , Clarke Robert , Yu Guoqiang , Van Eyk Jennifer E. , Herrington David M. , Wang Yue
Published: January 2021

Motivation

Complex biological tissues are often a heterogeneous mixture of several molecularly distinct cell or tissue subtypes. Both subtype compositions and expressions in individual samples can vary across different biological states or conditions. Computational deconvolution aims to dissect patterns of bulk gene expression data into subtype compositions and subtype-specific expressions. Typically, existing deconvolution methods can only estimate averaged subtype-specific expressions in a population, while detecting differential expressions or co-expression networks in particular subtypes requires unique subtype expression estimates in individual samples. Different from population-level deconvolution, however, individual-level deconvolution is mathematically an underdetermined problem because there are more variables than observations.

Results

We report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and subtype-specific expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm andℓ2,1-norm regularized matrix factorization problem. We determine hyperparameter values using a cross-validation scheme with random entry exclusion and obtain a swCAM solution using an efficient alternating direction method of multipliers. The swCAM is implemented in open-source R scripts. Experimental results on realistic simulation data show that swCAM can accurately estimate subtype-specific expressions in individual samples and successfully extract co-expression networks in particular subtypes that are otherwise unobtainable using bulk expression data. Application of swCAM to bulk-tissue data of 320 samples from bipolar disorder patients and controls identified changes in cell proportions, expression and coexpression modules in patient neurons. Mitochondria related genes showed significant changes suggesting an important role of energy dysregulation in bipolar disorder.

Availability and implementation

The R Scripts of swCAM is freely available athttps://github.com/Lululuella/swCAM. A user’s guide and a vignette are provided.

Contact

yuewang@vt.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Molecular Mechanism of the N501Y Mutation for Enhanced Binding between SARS-CoV-2’s Spike Protein and Human ACE2 Receptor
Authors: Luan Binquan , Wang Haoran , Huynh Tien
Published: January 2021

Coronavirus disease 2019 (COVID-19) has been an ongoing global pandemic for over a year. Recently, an emergent SARS-CoV-2 variant (B.1.1.7) with an unusually large number of mutations had become highly contagious and wide-spreading in United Kingdom. From genome analysis, the N501Y mutation within the receptor binding domain (RBD) of the SARS-CoV-2’s spike protein might have enhanced the viral protein’s binding with the human angiotensin converting enzyme 2 (hACE2). The latter is the prelude for the virus’ entry into host cells. So far, the molecular mechanism of this enhanced binding is still elusive, which prevents us from assessing its effects on existing therapeutic antibodies. Using all atom molecular dynamics simulations, we demonstrated that Y501 in mutated RBD can be well coordinated by Y41 and K353 in hACE2 through hydrophobic interactions, increasing the overall binding affinity between RBD and hACE2 by about 0.81 kcal/mol. We further explored how the N501Y mutation might affect the binding between a neutralizing antibody (CB6) and RBD. We expect that our work can help researchers design proper measures responding to this urgent virus mutation, such as adding a modified/new neutralizing antibody specifically targeting at this variant in the therapeutic antibody cocktail.

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