ZmNF-YC13 regulates plant architecture in maize

Leaf angle (LA) and leaf orientation value (LOV) are critical agronomic traits for maize plant architecture. Many genes related to plant architecture have been identified in maize, but the functions of NF-Y members in regulating plant architecture have not been reported before. Here, we identified a regulator of maize plant architecture, ZmNF-YC13. ZmNF-YC13 was highly expressed in the leaf base zone of maize plants. ZmNF-YC13 overexpression plants showed upright leaves with narrow LA and larger LOV, while ZmNF-YC13 knockout plants had larger LA and smaller LOV, compared with wild-type plants. The changes in plant architecture were due to the changes of the expression levels of cytochrome P450 family members. ZmNF-YC13 can interact with two ZmNF-YBs (ZmNF-YB9 and ZmNF-YB10) of the LEC1 subfamily, and further recruit ZmNF-YA3 to form two NF-Y complexes. The two complexes can both activate the promoters of the transcriptional repressors (ZmWRKY76 and ZmBT2) and the promoters of PLA cluster gene can be repressed by ZmWRKY76 and ZmBT2 in maize protoplasts. We propose that ZmNF-YC13 functions as a transcriptional regulator and, together with ZmNF-YBs and ZmNF-YA3, affects plant architecture by regulating the expression of ZmWRKY76 and ZmBT2, which repress the expression of PLA clustered cytochrome P450 family members.

Visualizing the organization and differentiation of the male-specific nervous system of C. elegans

Sex differences in the brain are prevalent throughout the animal kingdom and particularly well appreciated in the nematode C. elegans. While 294 neurons are shared between the two sexes, the nervous system of the male contains an additional 93 male-specific neurons, most of which have received very little attention so far. To make these neurons amenable for future study, we describe here how a multicolor, multipromoter reporter transgene, NeuroPAL, is capable of visualizing the distinct identities of all male specific neurons. We used this tool to visualize and characterize a number of features of the male-specific nervous system. We provide several proofs of concept for using NeuroPAL to identify the sites of expression of gfp-tagged reporter genes. We demonstrate the usage of NeuroPAL for cellular fate analysis by analyzing the effect of removal of developmental patterning genes, including a HOX cluster gene (egl-5), a miRNA (lin-4) and a proneural gene (lin-32/Ato), on neuronal identity acquisition within the male-specific nervous system. We use NeuroPAL and its intrinsic cohort of more than 40 distinct differentiation markers to show that, even though male-specific neurons are generated throughout all four larval stages, they execute their terminal differentiation program in a coordinated manner in the fourth larval stage that is concomitant with male tale retraction. This wave of differentiation couples neuronal maturation programs with the appearance of sexual organs. We call this wave 'just-in-time' differentiation by its analogy to the mechanism of 'just-in-time' transcription of metabolic pathway genes.

Development of monospecific polyclonal antibodies against hypervirulent Klebsiella pneumoniae

Darniati, Setiyaningsih S, Agungpriyono DR, Handharyani E. 2021. Development of monospecific polyclonal antibodies against hypervirulent Klebsiella pneumoniae. Biodiversitas 22: 99-105. The aim of the research was to produce monospecific antibodies against Klebsiella pneumoniae serotype K1 and K2. Klebsiella pneumonia isolates were recovered from pneumonic lungs of Aceh cattle. The bacteria were identified by rpoB (RNA polymerase β subunit) PCR amplification specific for K. pneumoniae. The presence of capsule cluster gene magA and k2A was used to characterize capsular serotype K1 and K2, respectively. Antisera were produced using serial immunization of New Zealand White rabbits with K. pneumoniae serotypes K1 and K2. The presence of antibodies was determined by using immunodiffusion test and purification was performed by immunoaffinity purification method. K. pneumoniae antibodies began to appear on the 14th day after the first injection and progressively intensified after the 1st and 2nd booster. The cross-reactivity between the antigen was eliminated by absorbing the antisera with the opposite antigen and several serotypes of non-K1/K2. After purification, serum protein concentrations were substantially decreased from 58.48 µg/µL and 53.99 µg/µL to 2.38 µg / µL and 3.72 µg / µL for K1 and K2, respectively). The SDS-PAGE analysis showed two bands with molecular weight at 54 kDa and 25 kDa representing the heavy and light chains of immunoglobulin G, respectively. Purified polyclonal antiseras against K. pneumoniae serotypes K1 and K2 showed high affinity and specificity for homologous antigens in immunodiffusion and direct agglutination tests, and immunohistochemical staining.

MicroRNA retrocopies generated via L1-mediated retrotransposition in placental mammals help to reveal how their parental genes were transcribed

In mammalian genomes, most retrocopies emerged via the L1 retrotransposition machinery. The hallmarks of an L1-mediated retrocopy, i.e., the intronlessness, the presence of a 3′ poly-A tail, and the TSDs at both ends, were frequently used to identify retrotransposition events. However, most previous studies only focused on protein-coding genes as their possible parental sources and thus only a few retrocopies derived from non-coding genes were reported. Remarkably, none of them was from microRNAs. Here in this study, we found several retrocopies generated from the mir-302–367 cluster gene (MIR302CHG), and identified a novel alternatively spliced exon encoding mir-302a. The other recognized microRNA retrotransposition events are primate-specific with mir-373 and mir-498 as their parental genes. The 3′ poly-A tracts of these two retrocopy groups were directly attached to the end of the microRNA precursor homologous regions, which suggests that their parental transcripts might alternatively terminate at the end of mir-373 and mir-498. All the three parental microRNAs are highly expressed in specific tissues with elevated retrotransposon activity, such as the embryonic stem cells and the placenta. This might be the reason that our first microRNA retrocopy findings were derived from these three microRNA genes.

Difference in sequences of the Streptomyces globisporus 1912 and 2 its mutants

Aim. The wild-type strain Streptomyces globisporus 1912 was isolated in 1967 from a sample of farmland (Armenia). Two mutants with different phenotypic characteristics were obtained (1912-2 and 1912-4Crt). The nucleotide sequences of 19 genes of the original strain and up to 90% of the genome sequence of its 2 mutants were determined. The aim of the study was to identify differences in the identified sequences of genomic DNA contigs of 2 mutants and individual genes of the original strain. Methods. BLASTN programs were used when comparing the DNA sequences. Results. BLAST analyzes of the sequences of 2 mutants S. globisporus (1912-2 and 1912-4Crt) revealed that they were identical (99.99%). Query cover of homologous sequences of mutants 1912-4Crt and 1912-4Crt was 95%. It was found that a number of mutant contigs (both 1912-2 and 1912-4Crt) were unique - their sequences were completely dissimilar to the sequences contigs of another variant. Conclusions. The determined sequences of genomes of 3 cultures will be useful in the construction of the genetic map of S. globisporus 1912. In addition, the comparative analysis of sequences of mutants can reveal the genetic basis of phenotypic changes. Keywords: BLAST analysis, sequences, genome, cluster, gene, identity, overlap.

Foliar Spraying with Compound Amino Acid-Iron Fertilizer Increases Leaf Fresh Weight, Photosynthesis, and Fe-S Cluster Gene Expression in Peach (Prunus persica (L.) Batsch)

As one of the most important micronutrients, iron (Fe) plays a critical role in various metabolic processes during plant growth and development. However, the molecular mechanisms towards Fe metabolism and nutrition in fruit trees are largely unknown. In this study, we examined the effects of amino acid-Fe compound fertilizer spraying on leaf development in peach (Prunus persica (L.) Batsch) at different developmental stages. Foliar spraying with amino acid-Fe compound fertilizer did not cause any significant changes in leaf morphology but remarkably increased leaf fresh weights. Fe concentration, photosynthetic parameter, and Fe-S protein analyses revealed that Fe accumulation, total chlorophyll content, net photosynthetic rate (PN), and stomatal conductance (gs), as well as nitrite reductase (NIR) and succinate dehydrogenase (SDH) activities, were significantly higher in the leaves sprayed with amino acid-Fe compound fertilizer than in the control leaves sprayed with distilled water. Further quantitative real-time PCR (qRT-PCR) analyses demonstrated that Fe-S cluster biosynthesis genes were differentially expressed in the leaves at different developmental stages. Foliar spraying with amino acid-Fe compound fertilizer significantly increased the expression of the most tested Fe-S cluster biosynthesis genes. Our findings provide new insights into the understanding of effects of Fe fertilization application on leaf development in perennial woody fruit trees.

The prevalence of ESBL and AmpC β-lactamases in uropathogenic isolates of Escherichia coli in a tertiary care hospital in Southwest Iran

Objectives: The spread of extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases (AmpC) in Escherichia coli ( E. coli) is an important public health concern and ESBL-producing bacteria are commonly reported in uropathogenic Escherichia coli (UPEC). The aim of this study is to determine the molecular detection of AmpC and ESBLs, among clinical E. coli isolated from inpatients who presented with symptomatic urinary tract infection (UTI) in Shiraz, the southwest of Iran. Results: Among total 177 urinary isolates, the analysis showed that 46.3% of the isolates were ESBLs positive and that fifteen strains revealed the AmpC cluster genes. Among all ESBL-positive E. coli isolates, the CTX-M was the most prevalent ESBL type (68.2%), and in AmpC-positive isolates, fifteen isolates (88.2%) were positive for CITM cluster gene and two (11.7%) were positive for DHAM cluster gene. ACCM, FOXM , EBCM and MOXM cluster genes were not found in this study. Our findings revealed that the prevalence of AmpC β-lactamases is rising in Iran, leading to failure in treatment. Therefore, the current study recommended that accurate and precise methods and guidelines should be designed for detection of antibiotic-resistant mechanisms because it is very important for the treatment and prevention of such isolates.

Genome-Wide Analysis of the Zn(II)2Cys6 Zinc Cluster-Encoding Gene Family in Tolypocladium guangdongense and Its Light-Induced Expression

The Zn(II)2Cys6 zinc cluster gene family is a subclass of zinc-finger proteins, which are transcriptional regulators involved in a wide variety of biological processes in fungi. We performed genome-wide identification and characterization of Zn(II)2Cys6 zinc-cluster gene (C6 zinc gene) family in Tolypocladium guangdongense, Cordyceps militaris and Ophiocordyceps sinensis. Based on the structures of the C6 zinc domains, these proteins were observed to be evolutionarily conserved in ascomycete fungi. We focused on T. guangdongense, a medicinal fungus, and identified 139 C6 zinc genes which could be divided into three groups. Among them, 49.6% belonged to the fungal specific transcriptional factors, and 16% had a DUF3468 domain. Homologous and phylogenetic analysis indicated that 29 C6 zinc genes were possibly involved in the metabolic process, while five C6 zinc genes were supposed to be involved in asexual or sexual development. Gene expression analysis revealed that 54 C6 zinc genes were differentially expressed under light, including two genes that possibly influenced the development, and seven genes that possibly influenced the metabolic processes. This indicated that light may affect the development and metabolic processes, at least partially, through the regulation of C6 zinc genes in T. guangdongense. Our results provide comprehensive data for further analyzing the functions of the C6 zinc genes.